From da6681fe216418a45b76437cd2912ae09d571832 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 21 Sep 2017 16:47:16 -0700 Subject: [PATCH 01/40] [WIP,ENH] Revision to the resource profiler This PR revises the resource profiler with the following objectives: - Increase robustness (and making sure it does not crash nipype) - Extend profiling to all interfaces (including pure python) The increase of robustness will be expected from: 1. Trying to reduce (or remove at all if possible) the logger callback to register the estimations of memory and cpus. This could be achieved by making interfaces responsible or keeping track of their resources to then collect all results after execution of the node. 2. Centralize profiler imports, like the config or logger object so that the applicability of the profiler is checked only once. This first commit just creates one new module nipype.utils.profiler, and moves the related functions in there. --- doc/users/config_file.rst | 7 +- docker/files/run_examples.sh | 2 +- nipype/interfaces/base.py | 163 +------------------------ nipype/interfaces/utility/wrappers.py | 17 +-- nipype/pipeline/engine/nodes.py | 4 +- nipype/utils/config.py | 2 +- nipype/utils/filemanip.py | 2 +- nipype/utils/logger.py | 12 +- nipype/utils/profiler.py | 164 ++++++++++++++++++++++++++ 9 files changed, 187 insertions(+), 186 deletions(-) create mode 100644 nipype/utils/profiler.py diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index 7d55cc522d..1a1a550311 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -16,9 +16,10 @@ Logging *workflow_level* How detailed the logs regarding workflow should be (possible values: ``INFO`` and ``DEBUG``; default value: ``INFO``) -*filemanip_level* - How detailed the logs regarding file operations (for example overwriting - warning) should be (possible values: ``INFO`` and ``DEBUG``; default value: +*utils_level* + How detailed the logs regarding nipype utils like file operations + (for example overwriting warning) or the resource profiler should be + (possible values: ``INFO`` and ``DEBUG``; default value: ``INFO``) *interface_level* How detailed the logs regarding interface execution should be (possible diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh index a23c27e76b..f23bc6f44c 100644 --- a/docker/files/run_examples.sh +++ b/docker/files/run_examples.sh @@ -12,7 +12,7 @@ mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests echo "[logging]" > ${HOME}/.nipype/nipype.cfg echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg -echo "filemanip_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg +echo "utils_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 19cf9ccaa6..c626328fde 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -44,22 +44,12 @@ File, Directory, DictStrStr, has_metadata, ImageFile) from ..external.due import due -runtime_profile = str2bool(config.get('execution', 'profile_runtime')) nipype_version = Version(__version__) iflogger = logging.getLogger('interface') FLOAT_FORMAT = '{:.10f}'.format PY35 = sys.version_info >= (3, 5) PY3 = sys.version_info[0] > 2 - -if runtime_profile: - try: - import psutil - except ImportError as exc: - iflogger.info('Unable to import packages needed for runtime profiling. '\ - 'Turning off runtime profiler. Reason: %s' % exc) - runtime_profile = False - __docformat__ = 'restructuredtext' @@ -1270,118 +1260,6 @@ def _read(self, drain): self._lastidx = len(self._rows) -# Get number of threads for process -def _get_num_threads(proc): - """Function to get the number of threads a process is using - NOTE: If - - Parameters - ---------- - proc : psutil.Process instance - the process to evaluate thead usage of - - Returns - ------- - num_threads : int - the number of threads that the process is using - """ - - # Import packages - import psutil - - # If process is running - if proc.status() == psutil.STATUS_RUNNING: - num_threads = proc.num_threads() - elif proc.num_threads() > 1: - tprocs = [psutil.Process(thr.id) for thr in proc.threads()] - alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] - num_threads = len(alive_tprocs) - else: - num_threads = 1 - - # Try-block for errors - try: - child_threads = 0 - # Iterate through child processes and get number of their threads - for child in proc.children(recursive=True): - # Leaf process - if len(child.children()) == 0: - # If process is running, get its number of threads - if child.status() == psutil.STATUS_RUNNING: - child_thr = child.num_threads() - # If its not necessarily running, but still multi-threaded - elif child.num_threads() > 1: - # Cast each thread as a process and check for only running - tprocs = [psutil.Process(thr.id) for thr in child.threads()] - alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] - child_thr = len(alive_tprocs) - # Otherwise, no threads are running - else: - child_thr = 0 - # Increment child threads - child_threads += child_thr - # Catch any NoSuchProcess errors - except psutil.NoSuchProcess: - pass - - # Number of threads is max between found active children and parent - num_threads = max(child_threads, num_threads) - - # Return number of threads found - return num_threads - - -# Get ram usage of process -def _get_ram_mb(pid, pyfunc=False): - """Function to get the RAM usage of a process and its children - - Parameters - ---------- - pid : integer - the PID of the process to get RAM usage of - pyfunc : boolean (optional); default=False - a flag to indicate if the process is a python function; - when Pythons are multithreaded via multiprocess or threading, - children functions include their own memory + parents. if this - is set, the parent memory will removed from children memories - - Reference: http://ftp.dev411.com/t/python/python-list/095thexx8g/multiprocessing-forking-memory-usage - - Returns - ------- - mem_mb : float - the memory RAM in MB utilized by the process PID - """ - - # Import packages - import psutil - - # Init variables - _MB = 1024.0**2 - - # Try block to protect against any dying processes in the interim - try: - # Init parent - parent = psutil.Process(pid) - # Get memory of parent - parent_mem = parent.memory_info().rss - mem_mb = parent_mem/_MB - - # Iterate through child processes - for child in parent.children(recursive=True): - child_mem = child.memory_info().rss - if pyfunc: - child_mem -= parent_mem - mem_mb += child_mem/_MB - - # Catch if process dies, return gracefully - except psutil.NoSuchProcess: - pass - - # Return memory - return mem_mb - - def _canonicalize_env(env): """Windows requires that environment be dicts with bytes as keys and values This function converts any unicode entries for Windows only, returning the @@ -1411,54 +1289,19 @@ def _canonicalize_env(env): return out_env -# Get max resources used for process -def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): - """Function to get the RAM and threads usage of a process - - Parameters - ---------- - pid : integer - the process ID of process to profile - mem_mb : float - the high memory watermark so far during process execution (in MB) - num_threads: int - the high thread watermark so far during process execution - - Returns - ------- - mem_mb : float - the new high memory watermark of process (MB) - num_threads : float - the new high thread watermark of process - """ - - # Import packages - import psutil - - try: - mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) - num_threads = max(num_threads, _get_num_threads(psutil.Process(pid))) - except Exception as exc: - iflogger.info('Could not get resources used by process. Error: %s'\ - % exc) - - # Return resources - return mem_mb, num_threads - - def run_command(runtime, output=None, timeout=0.01, redirect_x=False): """Run a command, read stdout and stderr, prefix with timestamp. The returned runtime contains a merged stdout+stderr log with timestamps """ - - # Init logger - logger = logging.getLogger('workflow') + # Check profiling + from ..utils.profiler import get_max_resources_used, runtime_profile # Init variables PIPE = subprocess.PIPE cmdline = runtime.cmdline + if redirect_x: exist_xvfb, _ = _exists_in_path('xvfb-run', runtime.environ) if not exist_xvfb: diff --git a/nipype/interfaces/utility/wrappers.py b/nipype/interfaces/utility/wrappers.py index 4de11d7ea8..87332c633b 100644 --- a/nipype/interfaces/utility/wrappers.py +++ b/nipype/interfaces/utility/wrappers.py @@ -20,21 +20,13 @@ from builtins import str, bytes from ... import logging -from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile, - BaseInterfaceInputSpec, get_max_resources_used) +from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, + BaseInterfaceInputSpec) from ..io import IOBase, add_traits from ...utils.filemanip import filename_to_list from ...utils.misc import getsource, create_function_from_source logger = logging.getLogger('interface') -if runtime_profile: - try: - import psutil - except ImportError as exc: - logger.info('Unable to import packages needed for runtime profiling. '\ - 'Turning off runtime profiler. Reason: %s' % exc) - runtime_profile = False - class FunctionInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec): function_str = traits.Str(mandatory=True, desc='code for function') @@ -137,8 +129,8 @@ def _add_output_traits(self, base): return base def _run_interface(self, runtime): - # Get workflow logger for runtime profile error reporting - logger = logging.getLogger('workflow') + # Check profiling + from ..utils.profiler import runtime_profile # Create function handle function_handle = create_function_from_source(self.inputs.function_str, @@ -163,6 +155,7 @@ def _function_handle_wrapper(queue, **kwargs): # Profile resources if set if runtime_profile: import multiprocessing + from ..utils.profiler import get_max_resources_used # Init communication queue and proc objs queue = multiprocessing.Queue() proc = multiprocessing.Process(target=_function_handle_wrapper, diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 622003f8a2..65f69093ef 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -46,8 +46,7 @@ from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined, TraitedSpec, DynamicTraitedSpec, Bunch, InterfaceResult, md5, Interface, - TraitDictObject, TraitListObject, isdefined, - runtime_profile) + TraitDictObject, TraitListObject, isdefined) from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, clean_working_directory, format_dot, topological_sort, @@ -690,6 +689,7 @@ def update(self, **opts): self.inputs.update(**opts) def write_report(self, report_type=None, cwd=None): + from ...utils.profiler import runtime_profile if not str2bool(self.config['execution']['create_report']): return report_dir = op.join(cwd, '_report') diff --git a/nipype/utils/config.py b/nipype/utils/config.py index ebea9e5816..c749a5480f 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -34,7 +34,7 @@ default_cfg = """ [logging] workflow_level = INFO -filemanip_level = INFO +utils_level = INFO interface_level = INFO log_to_file = false log_directory = %s diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 59b269e943..e321a597a6 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -27,7 +27,7 @@ from .misc import is_container from ..interfaces.traits_extension import isdefined -fmlogger = logging.getLogger("filemanip") +fmlogger = logging.getLogger('utils') related_filetype_sets = [ diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index b30b50bc72..73088a2fcf 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -33,11 +33,11 @@ def __init__(self, config): stream=sys.stdout) # logging.basicConfig(stream=sys.stdout) self._logger = logging.getLogger('workflow') - self._fmlogger = logging.getLogger('filemanip') + self._utlogger = logging.getLogger('utils') self._iflogger = logging.getLogger('interface') self.loggers = {'workflow': self._logger, - 'filemanip': self._fmlogger, + 'utils': self._utlogger, 'interface': self._iflogger} self._hdlr = None self.update_logging(self._config) @@ -53,14 +53,14 @@ def enable_file_logging(self): formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt) hdlr.setFormatter(formatter) self._logger.addHandler(hdlr) - self._fmlogger.addHandler(hdlr) + self._utlogger.addHandler(hdlr) self._iflogger.addHandler(hdlr) self._hdlr = hdlr def disable_file_logging(self): if self._hdlr: self._logger.removeHandler(self._hdlr) - self._fmlogger.removeHandler(self._hdlr) + self._utlogger.removeHandler(self._hdlr) self._iflogger.removeHandler(self._hdlr) self._hdlr = None @@ -69,8 +69,8 @@ def update_logging(self, config): self.disable_file_logging() self._logger.setLevel(logging.getLevelName(config.get('logging', 'workflow_level'))) - self._fmlogger.setLevel(logging.getLevelName(config.get('logging', - 'filemanip_level'))) + self._utlogger.setLevel(logging.getLevelName(config.get('logging', + 'utils_level'))) self._iflogger.setLevel(logging.getLevelName(config.get('logging', 'interface_level'))) if str2bool(config.get('logging', 'log_to_file')): diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py new file mode 100644 index 0000000000..bf6f3d2daa --- /dev/null +++ b/nipype/utils/profiler.py @@ -0,0 +1,164 @@ +# -*- coding: utf-8 -*- +# @Author: oesteban +# @Date: 2017-09-21 15:50:37 +# @Last Modified by: oesteban +# @Last Modified time: 2017-09-21 16:43:42 + +try: + import psutil +except ImportError as exc: + psutil = None + +from .. import config, logging +from .misc import str2bool + +proflogger = logging.getLogger('utils') + +runtime_profile = str2bool(config.get('execution', 'profile_runtime')) +if runtime_profile and psutil is None: + proflogger.warn('Switching "profile_runtime" off: the option was on, but the ' + 'necessary package "psutil" could not be imported.') + runtime_profile = False + + +# Get max resources used for process +def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): + """ + Function to get the RAM and threads utilized by a given process + + Parameters + ---------- + pid : integer + the process ID of process to profile + mem_mb : float + the high memory watermark so far during process execution (in MB) + num_threads: int + the high thread watermark so far during process execution + + Returns + ------- + mem_mb : float + the new high memory watermark of process (MB) + num_threads : float + the new high thread watermark of process + """ + + try: + mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) + num_threads = max(num_threads, _get_num_threads(psutil.Process(pid))) + except Exception as exc: + proflogger = logging.getLogger('profiler') + proflogger.info('Could not get resources used by process. Error: %s', exc) + + return mem_mb, num_threads + + +# Get number of threads for process +def _get_num_threads(proc): + """ + Function to get the number of threads a process is using + + Parameters + ---------- + proc : psutil.Process instance + the process to evaluate thead usage of + + Returns + ------- + num_threads : int + the number of threads that the process is using + + """ + + # If process is running + if proc.status() == psutil.STATUS_RUNNING: + num_threads = proc.num_threads() + elif proc.num_threads() > 1: + tprocs = [psutil.Process(thr.id) for thr in proc.threads()] + alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] + num_threads = len(alive_tprocs) + else: + num_threads = 1 + + # Try-block for errors + try: + child_threads = 0 + # Iterate through child processes and get number of their threads + for child in proc.children(recursive=True): + # Leaf process + if len(child.children()) == 0: + # If process is running, get its number of threads + if child.status() == psutil.STATUS_RUNNING: + child_thr = child.num_threads() + # If its not necessarily running, but still multi-threaded + elif child.num_threads() > 1: + # Cast each thread as a process and check for only running + tprocs = [psutil.Process(thr.id) for thr in child.threads()] + alive_tprocs = [tproc for tproc in tprocs + if tproc.status() == psutil.STATUS_RUNNING] + child_thr = len(alive_tprocs) + # Otherwise, no threads are running + else: + child_thr = 0 + # Increment child threads + child_threads += child_thr + # Catch any NoSuchProcess errors + except psutil.NoSuchProcess: + pass + + # Number of threads is max between found active children and parent + num_threads = max(child_threads, num_threads) + + # Return number of threads found + return num_threads + + +# Get ram usage of process +def _get_ram_mb(pid, pyfunc=False): + """ + Function to get the RAM usage of a process and its children + Reference: http://ftp.dev411.com/t/python/python-list/095thexx8g/\ +multiprocessing-forking-memory-usage + + Parameters + ---------- + pid : integer + the PID of the process to get RAM usage of + pyfunc : boolean (optional); default=False + a flag to indicate if the process is a python function; + when Pythons are multithreaded via multiprocess or threading, + children functions include their own memory + parents. if this + is set, the parent memory will removed from children memories + + + Returns + ------- + mem_mb : float + the memory RAM in MB utilized by the process PID + + """ + + # Init variables + _MB = 1024.0**2 + + # Try block to protect against any dying processes in the interim + try: + # Init parent + parent = psutil.Process(pid) + # Get memory of parent + parent_mem = parent.memory_info().rss + mem_mb = parent_mem / _MB + + # Iterate through child processes + for child in parent.children(recursive=True): + child_mem = child.memory_info().rss + if pyfunc: + child_mem -= parent_mem + mem_mb += child_mem / _MB + + # Catch if process dies, return gracefully + except psutil.NoSuchProcess: + pass + + # Return memory + return mem_mb From 32c2f39e86431331c54780455d0b09d139b45d32 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 21 Sep 2017 17:27:55 -0700 Subject: [PATCH 02/40] fix tests --- nipype/interfaces/tests/test_runtime_profiler.py | 9 +++------ nipype/interfaces/utility/wrappers.py | 2 +- nipype/utils/profiler.py | 6 +++++- 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/nipype/interfaces/tests/test_runtime_profiler.py b/nipype/interfaces/tests/test_runtime_profiler.py index 400b2728ae..1e86d6a653 100644 --- a/nipype/interfaces/tests/test_runtime_profiler.py +++ b/nipype/interfaces/tests/test_runtime_profiler.py @@ -11,12 +11,9 @@ from builtins import open, str # Import packages -from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec, - runtime_profile) import pytest -import sys - -run_profile = runtime_profile +from nipype.utils.profiler import runtime_profile as run_profile +from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec) if run_profile: try: @@ -39,7 +36,7 @@ class UseResourcesInputSpec(CommandLineInputSpec): num_gb = traits.Float(desc='Number of GB of RAM to use', argstr='-g %f') num_threads = traits.Int(desc='Number of threads to use', - argstr='-p %d') + argstr='-p %d') # UseResources interface diff --git a/nipype/interfaces/utility/wrappers.py b/nipype/interfaces/utility/wrappers.py index 87332c633b..94f69e5bba 100644 --- a/nipype/interfaces/utility/wrappers.py +++ b/nipype/interfaces/utility/wrappers.py @@ -130,7 +130,7 @@ def _add_output_traits(self, base): def _run_interface(self, runtime): # Check profiling - from ..utils.profiler import runtime_profile + from ...utils.profiler import runtime_profile # Create function handle function_handle = create_function_from_source(self.inputs.function_str, diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index bf6f3d2daa..4bc3a1de22 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-21 16:43:42 +# @Last Modified time: 2017-09-21 17:18:40 try: import psutil @@ -43,6 +43,10 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): the new high thread watermark of process """ + if not runtime_profile: + raise RuntimeError('Attempted to measure resources with ' + '"profile_runtime" set off.') + try: mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) num_threads = max(num_threads, _get_num_threads(psutil.Process(pid))) From 0e2c5812f8630c2c3a99077796d1d1092e25b5b0 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 21 Sep 2017 17:35:56 -0700 Subject: [PATCH 03/40] Python 2 compatibility --- nipype/utils/profiler.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 4bc3a1de22..0973fc1bf8 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,11 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-21 17:18:40 +# @Last Modified time: 2017-09-21 17:33:39 +""" +Utilities to keep track of performance +""" +from __future__ import print_function, division, unicode_literals, absolute_import try: import psutil From 5a8e7fe7230d9b5cfac68451643a9556f69331d9 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 21 Sep 2017 18:11:03 -0700 Subject: [PATCH 04/40] add nipype_mprof --- nipype/utils/profiler.py | 38 +++++++++++++++++++++++++++++++++----- setup.py | 1 + 2 files changed, 34 insertions(+), 5 deletions(-) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 0973fc1bf8..b1842a9c83 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-21 17:33:39 +# @Last Modified time: 2017-09-21 18:03:32 """ Utilities to keep track of performance """ @@ -53,7 +53,7 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): try: mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) - num_threads = max(num_threads, _get_num_threads(psutil.Process(pid))) + num_threads = max(num_threads, _get_num_threads(pid)) except Exception as exc: proflogger = logging.getLogger('profiler') proflogger.info('Could not get resources used by process. Error: %s', exc) @@ -62,14 +62,14 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): # Get number of threads for process -def _get_num_threads(proc): +def _get_num_threads(pid): """ Function to get the number of threads a process is using Parameters ---------- - proc : psutil.Process instance - the process to evaluate thead usage of + pid : integer + the process ID of process to profile Returns ------- @@ -78,6 +78,7 @@ def _get_num_threads(proc): """ + proc = psutil.Process(pid) # If process is running if proc.status() == psutil.STATUS_RUNNING: num_threads = proc.num_threads() @@ -170,3 +171,30 @@ def _get_ram_mb(pid, pyfunc=False): # Return memory return mem_mb + + +def main(): + """ + A minimal entry point to measure any process using psutil + """ + import sys + wait = None + if len(sys.argv) > 2: + wait = float(sys.argv[2]) + + _probe_loop(int(sys.argv[1]), wait=wait) + + +def _probe_loop(pid, wait=None): + from time import sleep + + if wait is None: + wait = 5 + + while True: + print('mem=%f cpus=%d' % (_get_ram_mb(pid), _get_num_threads(pid))) + sleep(wait) + + +if __name__ == "__main__": + main() diff --git a/setup.py b/setup.py index 331fa5905b..3453901b3e 100755 --- a/setup.py +++ b/setup.py @@ -148,6 +148,7 @@ def main(): entry_points=''' [console_scripts] nipypecli=nipype.scripts.cli:cli + nipype_mprof=nipype.utils.profiler:main ''' ) From 7d953cc74020767d2e8f155d9d1f1b3746cb6486 Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 22 Sep 2017 09:33:10 -0700 Subject: [PATCH 05/40] implement monitor in a parallel process --- nipype/interfaces/base.py | 222 ++++++++++++-------------- nipype/interfaces/utility/wrappers.py | 46 +----- nipype/utils/config.py | 6 +- nipype/utils/profiler.py | 115 ++++++------- nipype/utils/provenance.py | 23 ++- 5 files changed, 184 insertions(+), 228 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index c626328fde..2816a8e6de 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -24,7 +24,7 @@ import platform from string import Template import select -import subprocess +import subprocess as sp import sys import time from textwrap import wrap @@ -52,6 +52,9 @@ PY3 = sys.version_info[0] > 2 __docformat__ = 'restructuredtext' +if sys.version_info < (3, 3): + setattr(sp, 'DEVNULL', os.devnull) + class Str(traits.Unicode): pass @@ -1053,6 +1056,13 @@ def run(self, **inputs): results : an InterfaceResult object containing a copy of the instance that was executed, provenance information and, if successful, results """ + from ..utils.profiler import runtime_profile + + force_raise = not ( + hasattr(self.inputs, 'ignore_exception') and + isdefined(self.inputs.ignore_exception) and + self.inputs.ignore_exception + ) self.inputs.trait_set(**inputs) self._check_mandatory_inputs() self._check_version_requirements(self.inputs) @@ -1070,66 +1080,59 @@ def run(self, **inputs): platform=platform.platform(), hostname=platform.node(), version=self.version) + + proc_prof = None + if runtime_profile: + ifpid = '%d' % os.getpid() + fname = os.path.abspath('.prof-%s_freq-%0.3f' % (ifpid, 1)) + proc_prof = sp.Popen( + ['nipype_mprof', ifpid, '-o', fname, '-f', '1'], + cwd=os.getcwd(), + stdout=sp.DEVNULL, + stderr=sp.DEVNULL, + preexec_fn=os.setsid + ) + iflogger.debug('Started runtime profiler monitor (PID=%d) to file "%s"', + proc_prof.pid, fname) + + # Grab inputs now, as they should not change during execution + inputs = self.inputs.get_traitsfree() + outputs = None try: runtime = self._run_wrapper(runtime) outputs = self.aggregate_outputs(runtime) - runtime.endTime = dt.isoformat(dt.utcnow()) - timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 100000.) - results = InterfaceResult(interface, runtime, - inputs=self.inputs.get_traitsfree(), - outputs=outputs) - prov_record = None - if str2bool(config.get('execution', 'write_provenance')): - prov_record = write_provenance(results) - results.provenance = prov_record except Exception as e: - runtime.endTime = dt.isoformat(dt.utcnow()) - timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 100000.) - if len(e.args) == 0: - e.args = ("") - - message = "\nInterface %s failed to run." % self.__class__.__name__ - - if config.has_option('logging', 'interface_level') and \ - config.get('logging', 'interface_level').lower() == 'debug': - inputs_str = "\nInputs:" + str(self.inputs) + "\n" - else: - inputs_str = '' - - if len(e.args) == 1 and isinstance(e.args[0], (str, bytes)): - e.args = (e.args[0] + " ".join([message, inputs_str]),) - else: - e.args += (message, ) - if inputs_str != '': - e.args += (inputs_str, ) - - # exception raising inhibition for special cases import traceback - runtime.traceback = traceback.format_exc() - runtime.traceback_args = e.args - inputs = None - try: - inputs = self.inputs.get_traitsfree() - except Exception as e: - pass - results = InterfaceResult(interface, runtime, inputs=inputs) - prov_record = None - if str2bool(config.get('execution', 'write_provenance')): - try: - prov_record = write_provenance(results) - except Exception: - prov_record = None - results.provenance = prov_record - if hasattr(self.inputs, 'ignore_exception') and \ - isdefined(self.inputs.ignore_exception) and \ - self.inputs.ignore_exception: - pass - else: - raise + # Retrieve the maximum info fast + setattr(runtime, 'traceback', traceback.format_exc()) + # Gather up the exception arguments and append nipype info. + exc_args = e.args if getattr(e, 'args') else tuple() + exc_args += ('An exception of type %s occurred while running interface %s.' % + (type(e).__name__, self.__class__.__name__), ) + if config.get('logging', 'interface_level', 'info').lower() == 'debug': + exc_args += ('Inputs: %s' % str(self.inputs),) + + setattr(runtime, 'traceback_args', ('\n'.join(exc_args),)) + + # Fill in runtime times + runtime = _tearup_runtime(runtime) + results = InterfaceResult(interface, runtime, inputs=inputs, outputs=outputs) + + # Add provenance (if required) + results.provenance = None + if str2bool(config.get('execution', 'write_provenance', 'false')): + # Provenance will throw a warning if something went wrong + results.provenance = write_provenance(results) + + # Make sure runtime profiler is shut down + if runtime_profile: + import signal + os.killpg(os.getpgid(proc_prof.pid), signal.SIGINT) + iflogger.debug('Killing runtime profiler monitor (PID=%d)', proc_prof.pid) + + if force_raise and getattr(runtime, 'traceback', None): + raise NipypeInterfaceError('Fatal error:\n%s\n\n%s' % + (runtime.traceback, runtime.traceback_args)) return results def _list_outputs(self): @@ -1294,14 +1297,11 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False): The returned runtime contains a merged stdout+stderr log with timestamps """ - # Check profiling - from ..utils.profiler import get_max_resources_used, runtime_profile # Init variables - PIPE = subprocess.PIPE + PIPE = sp.PIPE cmdline = runtime.cmdline - if redirect_x: exist_xvfb, _ = _exists_in_path('xvfb-run', runtime.environ) if not exist_xvfb: @@ -1319,28 +1319,23 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False): stderr = open(errfile, 'wb') # t=='text'===default stdout = open(outfile, 'wb') - proc = subprocess.Popen(cmdline, - stdout=stdout, - stderr=stderr, - shell=True, - cwd=runtime.cwd, - env=env) + proc = sp.Popen(cmdline, + stdout=stdout, + stderr=stderr, + shell=True, + cwd=runtime.cwd, + env=env) else: - proc = subprocess.Popen(cmdline, - stdout=PIPE, - stderr=PIPE, - shell=True, - cwd=runtime.cwd, - env=env) + proc = sp.Popen(cmdline, + stdout=PIPE, + stderr=PIPE, + shell=True, + cwd=runtime.cwd, + env=env) result = {} errfile = os.path.join(runtime.cwd, 'stderr.nipype') outfile = os.path.join(runtime.cwd, 'stdout.nipype') - # Init variables for memory profiling - mem_mb = 0 - num_threads = 1 - interval = .5 - if output == 'stream': streams = [Stream('stdout', proc.stdout), Stream('stderr', proc.stderr)] @@ -1356,13 +1351,11 @@ def _process(drain=0): else: for stream in res[0]: stream.read(drain) + while proc.returncode is None: - if runtime_profile: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) proc.poll() _process() - time.sleep(interval) + _process(drain=1) # collect results, merge and return @@ -1376,12 +1369,6 @@ def _process(drain=0): result['merged'] = [r[1] for r in temp] if output == 'allatonce': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) stdout, stderr = proc.communicate() stdout = stdout.decode(default_encoding) stderr = stderr.decode(default_encoding) @@ -1389,32 +1376,20 @@ def _process(drain=0): result['stderr'] = stderr.split('\n') result['merged'] = '' if output == 'file': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) ret_code = proc.wait() stderr.flush() stdout.flush() - result['stdout'] = [line.decode(default_encoding).strip() for line in open(outfile, 'rb').readlines()] - result['stderr'] = [line.decode(default_encoding).strip() for line in open(errfile, 'rb').readlines()] + result['stdout'] = [line.decode(default_encoding).strip() + for line in open(outfile, 'rb').readlines()] + result['stderr'] = [line.decode(default_encoding).strip() + for line in open(errfile, 'rb').readlines()] result['merged'] = '' if output == 'none': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) proc.communicate() result['stdout'] = [] result['stderr'] = [] result['merged'] = '' - setattr(runtime, 'runtime_memory_gb', mem_mb/1024.0) - setattr(runtime, 'runtime_threads', num_threads) runtime.stderr = '\n'.join(result['stderr']) runtime.stdout = '\n'.join(result['stdout']) runtime.merged = result['merged'] @@ -1428,19 +1403,19 @@ def get_dependencies(name, environ): Uses otool on darwin, ldd on linux. Currently doesn't support windows. """ - PIPE = subprocess.PIPE + PIPE = sp.PIPE if sys.platform == 'darwin': - proc = subprocess.Popen('otool -L `which %s`' % name, - stdout=PIPE, - stderr=PIPE, - shell=True, - env=environ) + proc = sp.Popen('otool -L `which %s`' % name, + stdout=PIPE, + stderr=PIPE, + shell=True, + env=environ) elif 'linux' in sys.platform: - proc = subprocess.Popen('ldd `which %s`' % name, - stdout=PIPE, - stderr=PIPE, - shell=True, - env=environ) + proc = sp.Popen('ldd `which %s`' % name, + stdout=PIPE, + stderr=PIPE, + shell=True, + env=environ) else: return 'Platform %s not supported' % sys.platform o, e = proc.communicate() @@ -1588,12 +1563,12 @@ def version_from_command(self, flag='-v'): if _exists_in_path(cmdname, env): out_environ = self._get_environ() env.update(out_environ) - proc = subprocess.Popen(' '.join((cmdname, flag)), - shell=True, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - ) + proc = sp.Popen(' '.join((cmdname, flag)), + shell=True, + env=env, + stdout=sp.PIPE, + stderr=sp.PIPE, + ) o, e = proc.communicate() return o @@ -2009,3 +1984,10 @@ class InputMultiPath(MultiPath): """ pass + +def _tearup_runtime(runtime): + runtime.endTime = dt.isoformat(dt.utcnow()) + timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) + runtime.duration = (timediff.days * 86400 + timediff.seconds + + timediff.microseconds / 1e6) + return runtime diff --git a/nipype/interfaces/utility/wrappers.py b/nipype/interfaces/utility/wrappers.py index 94f69e5bba..4fa10205d2 100644 --- a/nipype/interfaces/utility/wrappers.py +++ b/nipype/interfaces/utility/wrappers.py @@ -129,22 +129,9 @@ def _add_output_traits(self, base): return base def _run_interface(self, runtime): - # Check profiling - from ...utils.profiler import runtime_profile - # Create function handle function_handle = create_function_from_source(self.inputs.function_str, self.imports) - - # Wrapper for running function handle in multiprocessing.Process - # Can catch exceptions and report output via multiprocessing.Queue - def _function_handle_wrapper(queue, **kwargs): - try: - out = function_handle(**kwargs) - queue.put(out) - except Exception as exc: - queue.put(exc) - # Get function args args = {} for name in self._input_names: @@ -152,38 +139,7 @@ def _function_handle_wrapper(queue, **kwargs): if isdefined(value): args[name] = value - # Profile resources if set - if runtime_profile: - import multiprocessing - from ..utils.profiler import get_max_resources_used - # Init communication queue and proc objs - queue = multiprocessing.Queue() - proc = multiprocessing.Process(target=_function_handle_wrapper, - args=(queue,), kwargs=args) - - # Init memory and threads before profiling - mem_mb = 0 - num_threads = 0 - - # Start process and profile while it's alive - proc.start() - while proc.is_alive(): - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads, - pyfunc=True) - - # Get result from process queue - out = queue.get() - # If it is an exception, raise it - if isinstance(out, Exception): - raise out - - # Function ran successfully, populate runtime stats - setattr(runtime, 'runtime_memory_gb', mem_mb / 1024.0) - setattr(runtime, 'runtime_threads', num_threads) - else: - out = function_handle(**args) - + out = function_handle(**args) if len(self._output_names) == 1: self._out[self._output_names[0]] = out else: diff --git a/nipype/utils/config.py b/nipype/utils/config.py index c749a5480f..6baada07e3 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -114,8 +114,10 @@ def set_log_dir(self, log_dir): """ self._config.set('logging', 'log_directory', log_dir) - def get(self, section, option): - return self._config.get(section, option) + def get(self, section, option, default=None): + if self._config.has_option(section, option): + return self._config.get(section, option) + return default def set(self, section, option, value): if isinstance(value, bool): diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index b1842a9c83..8087dbd361 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-21 18:03:32 +# @Last Modified time: 2017-09-22 09:28:21 """ Utilities to keep track of performance """ @@ -24,6 +24,8 @@ 'necessary package "psutil" could not be imported.') runtime_profile = False +from builtins import open + # Get max resources used for process def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): @@ -89,31 +91,26 @@ def _get_num_threads(pid): else: num_threads = 1 - # Try-block for errors - try: - child_threads = 0 - # Iterate through child processes and get number of their threads - for child in proc.children(recursive=True): - # Leaf process - if len(child.children()) == 0: - # If process is running, get its number of threads - if child.status() == psutil.STATUS_RUNNING: - child_thr = child.num_threads() - # If its not necessarily running, but still multi-threaded - elif child.num_threads() > 1: - # Cast each thread as a process and check for only running - tprocs = [psutil.Process(thr.id) for thr in child.threads()] - alive_tprocs = [tproc for tproc in tprocs - if tproc.status() == psutil.STATUS_RUNNING] - child_thr = len(alive_tprocs) - # Otherwise, no threads are running - else: - child_thr = 0 - # Increment child threads - child_threads += child_thr - # Catch any NoSuchProcess errors - except psutil.NoSuchProcess: - pass + child_threads = 0 + # Iterate through child processes and get number of their threads + for child in proc.children(recursive=True): + # Leaf process + if len(child.children()) == 0: + # If process is running, get its number of threads + if child.status() == psutil.STATUS_RUNNING: + child_thr = child.num_threads() + # If its not necessarily running, but still multi-threaded + elif child.num_threads() > 1: + # Cast each thread as a process and check for only running + tprocs = [psutil.Process(thr.id) for thr in child.threads()] + alive_tprocs = [tproc for tproc in tprocs + if tproc.status() == psutil.STATUS_RUNNING] + child_thr = len(alive_tprocs) + # Otherwise, no threads are running + else: + child_thr = 0 + # Increment child threads + child_threads += child_thr # Number of threads is max between found active children and parent num_threads = max(child_threads, num_threads) @@ -150,24 +147,17 @@ def _get_ram_mb(pid, pyfunc=False): # Init variables _MB = 1024.0**2 - # Try block to protect against any dying processes in the interim - try: - # Init parent - parent = psutil.Process(pid) - # Get memory of parent - parent_mem = parent.memory_info().rss - mem_mb = parent_mem / _MB - - # Iterate through child processes - for child in parent.children(recursive=True): - child_mem = child.memory_info().rss - if pyfunc: - child_mem -= parent_mem - mem_mb += child_mem / _MB - - # Catch if process dies, return gracefully - except psutil.NoSuchProcess: - pass + # Init parent + parent = psutil.Process(pid) + # Get memory of parent + parent_mem = parent.memory_info().rss + mem_mb = parent_mem / _MB + # Iterate through child processes + for child in parent.children(recursive=True): + child_mem = child.memory_info().rss + if pyfunc: + child_mem -= parent_mem + mem_mb += child_mem / _MB # Return memory return mem_mb @@ -177,23 +167,38 @@ def main(): """ A minimal entry point to measure any process using psutil """ - import sys - wait = None - if len(sys.argv) > 2: - wait = float(sys.argv[2]) - - _probe_loop(int(sys.argv[1]), wait=wait) - - -def _probe_loop(pid, wait=None): + from argparse import ArgumentParser + from argparse import RawTextHelpFormatter + + parser = ArgumentParser(description='A minimal process monitor', + formatter_class=RawTextHelpFormatter) + parser.add_argument('pid', action='store', type=int, + help='process PID to monitor') + parser.add_argument('-o', '--out-file', action='store', default='.prof', + help='file where monitor will be writting') + parser.add_argument('-f', '--freq', action='store', type=float, default=5.0, + help='sampling frequency') + opts = parser.parse_args() + _probe_loop(opts.pid, opts.out_file, wait=opts.freq) + + +def _probe_loop(pid, fname, wait=None): from time import sleep + print('Start monitoring') if wait is None: wait = 5 + proffh = open(fname, 'w') while True: - print('mem=%f cpus=%d' % (_get_ram_mb(pid), _get_num_threads(pid))) - sleep(wait) + try: + proffh.write('%f,%d\n' % (_get_ram_mb(pid), _get_num_threads(pid))) + proffh.flush() + sleep(wait) + except (Exception, KeyboardInterrupt): + proffh.close() + print('\nFinished.') + return if __name__ == "__main__": diff --git a/nipype/utils/provenance.py b/nipype/utils/provenance.py index 066cbb9a57..c316f67272 100644 --- a/nipype/utils/provenance.py +++ b/nipype/utils/provenance.py @@ -21,7 +21,7 @@ from .. import get_info, logging, __version__ from .filemanip import (md5, hashlib, hash_infile) -iflogger = logging.getLogger('interface') +logger = logging.getLogger('utils') foaf = pm.Namespace("foaf", "http://xmlns.com/foaf/0.1/") dcterms = pm.Namespace("dcterms", "http://purl.org/dc/terms/") nipype_ns = pm.Namespace("nipype", "http://nipy.org/nipype/terms/") @@ -173,7 +173,7 @@ def safe_encode(x, as_literal=True): jsonstr = json.dumps(outdict) except UnicodeDecodeError as excp: jsonstr = "Could not encode dictionary. {}".format(excp) - iflogger.warn('Prov: %s', jsonstr) + logger.warning('Prov: %s', jsonstr) if not as_literal: return jsonstr @@ -203,7 +203,7 @@ def safe_encode(x, as_literal=True): jsonstr = json.dumps(x) except UnicodeDecodeError as excp: jsonstr = "Could not encode list/tuple. {}".format(excp) - iflogger.warn('Prov: %s', jsonstr) + logger.warning('Prov: %s', jsonstr) if not as_literal: return jsonstr @@ -285,9 +285,20 @@ def prov_encode(graph, value, create_container=True): def write_provenance(results, filename='provenance', format='all'): - ps = ProvStore() - ps.add_results(results) - return ps.write_provenance(filename=filename, format=format) + prov = None + try: + ps = ProvStore() + ps.add_results(results) + prov = ps.write_provenance(filename=filename, format=format) + except Exception as e: + import traceback + err_msg = traceback.format_exc() + if getattr(e, 'args'): + err_msg += '\n\nException arguments:\n' + ', '.join(['"%s"' % arg for arg in e.args]) + logger.warning('Writing provenance failed - Exception details:\n%s', err_msg) + + return prov + class ProvStore(object): From 306c4ec6158ea57e0026e65844217deedd72f046 Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 22 Sep 2017 13:16:13 -0700 Subject: [PATCH 06/40] set profiling outputs to runtime object, read it from node execution --- nipype/interfaces/base.py | 25 ++++++++++++++++++------- nipype/pipeline/engine/nodes.py | 12 +++++------- 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 2816a8e6de..483eeea207 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1081,19 +1081,19 @@ def run(self, **inputs): hostname=platform.node(), version=self.version) - proc_prof = None + mon_sp = None if runtime_profile: ifpid = '%d' % os.getpid() - fname = os.path.abspath('.prof-%s_freq-%0.3f' % (ifpid, 1)) - proc_prof = sp.Popen( - ['nipype_mprof', ifpid, '-o', fname, '-f', '1'], + mon_fname = os.path.abspath('.prof-%s_freq-%0.3f' % (ifpid, 1)) + mon_sp = sp.Popen( + ['nipype_mprof', ifpid, '-o', mon_fname, '-f', '1'], cwd=os.getcwd(), stdout=sp.DEVNULL, stderr=sp.DEVNULL, preexec_fn=os.setsid ) iflogger.debug('Started runtime profiler monitor (PID=%d) to file "%s"', - proc_prof.pid, fname) + mon_sp.pid, mon_fname) # Grab inputs now, as they should not change during execution inputs = self.inputs.get_traitsfree() @@ -1127,8 +1127,19 @@ def run(self, **inputs): # Make sure runtime profiler is shut down if runtime_profile: import signal - os.killpg(os.getpgid(proc_prof.pid), signal.SIGINT) - iflogger.debug('Killing runtime profiler monitor (PID=%d)', proc_prof.pid) + import numpy as np + os.killpg(os.getpgid(mon_sp.pid), signal.SIGINT) + iflogger.debug('Killing runtime profiler monitor (PID=%d)', mon_sp.pid) + + # Read .prof file in and set runtime values + mem_peak_gb = None + nthreads_max = None + vals = np.loadtxt(mon_fname, delimiter=',') + if vals: + mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() + + setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) + setattr(runtime, 'nthreads_max', int(nthreads_max)) if force_raise and getattr(runtime, 'traceback', None): raise NipypeInterfaceError('Fatal error:\n%s\n\n%s' % diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 65f69093ef..2f748f2085 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -724,15 +724,13 @@ def write_report(self, report_type=None, cwd=None): return fp.writelines(write_rst_header('Runtime info', level=1)) # Init rst dictionary of runtime stats - rst_dict = {'hostname' : self.result.runtime.hostname, - 'duration' : self.result.runtime.duration} + rst_dict = {'hostname': self.result.runtime.hostname, + 'duration': self.result.runtime.duration} # Try and insert memory/threads usage if available if runtime_profile: - try: - rst_dict['runtime_memory_gb'] = self.result.runtime.runtime_memory_gb - rst_dict['runtime_threads'] = self.result.runtime.runtime_threads - except AttributeError: - logger.info('Runtime memory and threads stats unavailable') + rst_dict['runtime_memory_gb'] = getattr(self.result.runtime, 'mem_peak_gb') + rst_dict['runtime_threads'] = getattr(self.result.runtime, 'nthreads_max') + if hasattr(self.result.runtime, 'cmdline'): rst_dict['command'] = self.result.runtime.cmdline fp.writelines(write_rst_dict(rst_dict)) From 8a903f0923c0badb187cc2d8d4fdfa818b73e3f6 Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 22 Sep 2017 13:47:31 -0700 Subject: [PATCH 07/40] revise profiler callback --- nipype/interfaces/base.py | 12 +++---- nipype/pipeline/plugins/base.py | 10 +++--- nipype/pipeline/plugins/callback_log.py | 46 +++++++++---------------- nipype/pipeline/plugins/multiproc.py | 7 ++-- 4 files changed, 29 insertions(+), 46 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 483eeea207..358892f450 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1115,7 +1115,10 @@ def run(self, **inputs): setattr(runtime, 'traceback_args', ('\n'.join(exc_args),)) # Fill in runtime times - runtime = _tearup_runtime(runtime) + runtime.endTime = dt.isoformat(dt.utcnow()) + timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) + runtime.duration = (timediff.days * 86400 + timediff.seconds + + timediff.microseconds / 1e6) results = InterfaceResult(interface, runtime, inputs=inputs, outputs=outputs) # Add provenance (if required) @@ -1995,10 +1998,3 @@ class InputMultiPath(MultiPath): """ pass - -def _tearup_runtime(runtime): - runtime.endTime = dt.isoformat(dt.utcnow()) - timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 1e6) - return runtime diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 7334e00c52..2f40748774 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -188,10 +188,8 @@ class PluginBase(object): """Base class for plugins""" def __init__(self, plugin_args=None): - if plugin_args and 'status_callback' in plugin_args: - self._status_callback = plugin_args['status_callback'] - else: - self._status_callback = None + if plugin_args: + self._status_callback = plugin_args.get('status_callback') return def run(self, graph, config, updatehash=False): @@ -601,8 +599,8 @@ class GraphPluginBase(PluginBase): """ def __init__(self, plugin_args=None): - if plugin_args and 'status_callback' in plugin_args: - warn('status_callback not supported for Graph submission plugins') + if plugin_args and plugin_args.get('status_callback'): + logger.warning('status_callback not supported for Graph submission plugins') super(GraphPluginBase, self).__init__(plugin_args=plugin_args) def run(self, graph, config, updatehash=False): diff --git a/nipype/pipeline/plugins/callback_log.py b/nipype/pipeline/plugins/callback_log.py index 5ddc9eedd5..4e9d7a3b50 100644 --- a/nipype/pipeline/plugins/callback_log.py +++ b/nipype/pipeline/plugins/callback_log.py @@ -26,41 +26,29 @@ def log_nodes_cb(node, status): status info to the callback logger """ + if status != 'end': + return + # Import packages - import datetime import logging import json - # Check runtime profile stats - if node.result is not None: - try: - runtime = node.result.runtime - runtime_memory_gb = runtime.runtime_memory_gb - runtime_threads = runtime.runtime_threads - except AttributeError: - runtime_memory_gb = runtime_threads = 'Unknown' - else: - runtime_memory_gb = runtime_threads = 'N/A' - # Init variables logger = logging.getLogger('callback') - status_dict = {'name' : node.name, - 'id' : node._id, - 'estimated_memory_gb' : node._interface.estimated_memory_gb, - 'num_threads' : node._interface.num_threads} - - # Check status and write to log - # Start - if status == 'start': - status_dict['start'] = str(datetime.datetime.now()) - # End - elif status == 'end': - status_dict['finish'] = str(datetime.datetime.now()) - status_dict['runtime_threads'] = runtime_threads - status_dict['runtime_memory_gb'] = runtime_memory_gb - # Other - else: - status_dict['finish'] = str(datetime.datetime.now()) + status_dict = { + 'name': node.name, + 'id': node._id, + 'start': getattr(node.result.runtime, 'startTime'), + 'finish': getattr(node.result.runtime, 'endTime'), + 'runtime_threads': getattr( + node.result.runtime, 'nthreads_max', 'N/A'), + 'runtime_memory_gb': getattr( + node.result.runtime, 'mem_peak_gb', 'N/A'), + 'estimated_memory_gb': node._interface.estimated_memory_gb, + 'num_threads': node._interface.num_threads, + } + + if status_dict['start'] is None or status_dict['end'] is None: status_dict['error'] = True # Dump string to log diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 3994f2e1cd..46a81d12b8 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -242,7 +242,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): free_processors = self.processors - busy_processors # Check all jobs without dependency not run - jobids = np.flatnonzero((self.proc_done == False) & \ + jobids = np.flatnonzero((self.proc_done is False) & (self.depidx.sum(axis=0) == 0).__array__()) # Sort jobs ready to run first by memory and then by number of threads @@ -251,14 +251,15 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): key=lambda item: (self.procs[item]._interface.estimated_memory_gb, self.procs[item]._interface.num_threads)) - if str2bool(config.get('execution', 'profile_runtime')): + profile_runtime = str2bool(config.get('execution', 'profile_runtime', 'false')) + if profile_runtime: logger.debug('Free memory (GB): %d, Free processors: %d', free_memory_gb, free_processors) # While have enough memory and processors for first job # Submit first job on the list for jobid in jobids: - if str2bool(config.get('execution', 'profile_runtime')): + if profile_runtime: logger.debug('Next Job: %d, memory (GB): %d, threads: %d' \ % (jobid, self.procs[jobid]._interface.estimated_memory_gb, From e3982d758f2d138a483b8c08872971557b987569 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Sun, 24 Sep 2017 20:31:31 -0700 Subject: [PATCH 08/40] robuster constructor --- nipype/pipeline/plugins/base.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 2f40748774..3ddb433f6c 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -188,8 +188,10 @@ class PluginBase(object): """Base class for plugins""" def __init__(self, plugin_args=None): - if plugin_args: - self._status_callback = plugin_args.get('status_callback') + if plugin_args is None: + plugin_args = {} + + self._status_callback = plugin_args.get('status_callback') return def run(self, graph, config, updatehash=False): From 48f87af77161a54b41ce8157010de6e8ea123a3a Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Sun, 24 Sep 2017 20:40:53 -0700 Subject: [PATCH 09/40] remove unused import --- nipype/pipeline/plugins/base.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 3ddb433f6c..e199d5b041 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -16,7 +16,6 @@ import uuid from time import strftime, sleep, time from traceback import format_exception, format_exc -from warnings import warn import numpy as np import scipy.sparse as ssp From 46dde3228d6b0c18c56714b7f7613da2a6944548 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 14:31:29 -0700 Subject: [PATCH 10/40] various fixes --- nipype/interfaces/afni/base.py | 2 +- nipype/interfaces/base.py | 74 ++++++++------- nipype/interfaces/spm/base.py | 30 +++--- nipype/pipeline/engine/tests/test_engine.py | 33 ++++--- nipype/pipeline/plugins/base.py | 8 +- nipype/pipeline/plugins/callback_log.py | 3 +- nipype/pipeline/plugins/multiproc.py | 95 ++++++------------- .../pipeline/plugins/tests/test_multiproc.py | 25 ++--- nipype/utils/draw_gantt_chart.py | 61 ++---------- nipype/utils/profiler.py | 31 +++++- 10 files changed, 160 insertions(+), 202 deletions(-) diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index 3ab5756f03..35751d4e5c 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -105,7 +105,7 @@ def standard_image(img_name): '''Grab an image from the standard location. Could be made more fancy to allow for more relocatability''' - clout = CommandLine('which afni', + clout = CommandLine('which afni', ignore_exception=True, terminal_output='allatonce').run() if clout.runtime.returncode is not 0: return None diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 358892f450..ba16c8767b 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1070,6 +1070,8 @@ def run(self, **inputs): self._duecredit_cite() # initialize provenance tracking + store_provenance = str2bool(config.get( + 'execution', 'write_provenance', 'false')) env = deepcopy(dict(os.environ)) runtime = Bunch(cwd=os.getcwd(), returncode=None, @@ -1112,41 +1114,45 @@ def run(self, **inputs): if config.get('logging', 'interface_level', 'info').lower() == 'debug': exc_args += ('Inputs: %s' % str(self.inputs),) - setattr(runtime, 'traceback_args', ('\n'.join(exc_args),)) + setattr(runtime, 'traceback_args', + ('\n'.join(['%s' % arg for arg in exc_args]),)) - # Fill in runtime times - runtime.endTime = dt.isoformat(dt.utcnow()) - timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 1e6) - results = InterfaceResult(interface, runtime, inputs=inputs, outputs=outputs) - - # Add provenance (if required) - results.provenance = None - if str2bool(config.get('execution', 'write_provenance', 'false')): - # Provenance will throw a warning if something went wrong - results.provenance = write_provenance(results) - - # Make sure runtime profiler is shut down - if runtime_profile: - import signal - import numpy as np - os.killpg(os.getpgid(mon_sp.pid), signal.SIGINT) - iflogger.debug('Killing runtime profiler monitor (PID=%d)', mon_sp.pid) - - # Read .prof file in and set runtime values - mem_peak_gb = None - nthreads_max = None - vals = np.loadtxt(mon_fname, delimiter=',') - if vals: - mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() - - setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) - setattr(runtime, 'nthreads_max', int(nthreads_max)) - - if force_raise and getattr(runtime, 'traceback', None): - raise NipypeInterfaceError('Fatal error:\n%s\n\n%s' % - (runtime.traceback, runtime.traceback_args)) + if force_raise: + raise + finally: + # This needs to be done always + runtime.endTime = dt.isoformat(dt.utcnow()) + timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) + runtime.duration = (timediff.days * 86400 + timediff.seconds + + timediff.microseconds / 1e6) + results = InterfaceResult(interface, runtime, inputs=inputs, outputs=outputs, + provenance=None) + + # Add provenance (if required) + if store_provenance: + # Provenance will only throw a warning if something went wrong + results.provenance = write_provenance(results) + + # Make sure runtime profiler is shut down + if runtime_profile: + import signal + import numpy as np + os.killpg(os.getpgid(mon_sp.pid), signal.SIGINT) + iflogger.debug('Killing runtime profiler monitor (PID=%d)', mon_sp.pid) + + # Read .prof file in and set runtime values + mem_peak_gb = None + nthreads_max = None + vals = np.loadtxt(mon_fname, delimiter=',') + if vals: + mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() + + setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) + setattr(runtime, 'nthreads_max', int(nthreads_max)) + + # if force_raise and getattr(runtime, 'traceback', None): + # raise NipypeInterfaceError('Fatal error:\n%s\n\n%s' % + # (runtime.traceback, runtime.traceback_args)) return results def _list_outputs(self): diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index 6c3fbab32e..33c540f457 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -29,7 +29,7 @@ # Local imports from ... import logging from ...utils import spm_docs as sd, NUMPY_MMAP -from ..base import (BaseInterface, traits, isdefined, InputMultiPath, +from ..base import (BaseInterface, CommandLine, traits, isdefined, InputMultiPath, BaseInterfaceInputSpec, Directory, Undefined, ImageFile) from ..matlab import MatlabCommand from ...external.due import due, Doi, BibTeX @@ -151,18 +151,18 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): returns None of path not found """ - if use_mcr or 'FORCE_SPMMCR' in os.environ: - use_mcr = True - if matlab_cmd is None: - try: - matlab_cmd = os.environ['SPMMCRCMD'] - except KeyError: - pass - if matlab_cmd is None: - try: - matlab_cmd = os.environ['MATLABCMD'] - except KeyError: - matlab_cmd = 'matlab -nodesktop -nosplash' + + # Test if matlab is installed, exit quickly if not. + clout = CommandLine('which matlab', ignore_exception=True, + terminal_output='allatonce').run() + if clout.runtime.returncode is not 0: + return None + + use_mcr = use_mcr or 'FORCE_SPMMCR' in os.environ + matlab_cmd = (os.getenv('SPMMCRCMD') or + os.getenv('MATLABCMD') or + 'matlab -nodesktop -nosplash') + mlab = MatlabCommand(matlab_cmd=matlab_cmd) mlab.inputs.mfile = False if paths: @@ -187,7 +187,7 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): except (IOError, RuntimeError) as e: # if no Matlab at all -- exception could be raised # No Matlab -- no spm - logger.debug(str(e)) + logger.debug('%s', e) return None else: out = sd._strip_header(out.runtime.stdout) @@ -276,7 +276,7 @@ def _find_mlab_cmd_defaults(self): def _matlab_cmd_update(self): # MatlabCommand has to be created here, - # because matlab_cmb is not a proper input + # because matlab_cmd is not a proper input # and can be set only during init self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd, mfile=self.inputs.mfile, diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py index 90d566ddf9..56c4f78e84 100644 --- a/nipype/pipeline/engine/tests/test_engine.py +++ b/nipype/pipeline/engine/tests/test_engine.py @@ -475,7 +475,7 @@ def double_func(x): def test_mapnode_nested(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() from nipype import MapNode, Function def func1(in1): @@ -505,7 +505,7 @@ def func1(in1): def test_mapnode_expansion(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() from nipype import MapNode, Function def func1(in1): @@ -527,9 +527,8 @@ def func1(in1): def test_node_hash(tmpdir): - wd = str(tmpdir) - os.chdir(wd) from nipype.interfaces.utility import Function + tmpdir.chdir() def func1(): return 1 @@ -548,13 +547,13 @@ def func2(a): modify = lambda x: x + 1 n1.inputs.a = 1 w1.connect(n1, ('a', modify), n2, 'a') - w1.base_dir = wd + w1.base_dir = os.getcwd() # generate outputs w1.run(plugin='Linear') # ensure plugin is being called w1.config['execution'] = {'stop_on_first_crash': 'true', 'local_hash_check': 'false', - 'crashdump_dir': wd} + 'crashdump_dir': os.getcwd()} # create dummy distributed plugin class from nipype.pipeline.plugins.base import DistributedPluginBase @@ -576,14 +575,14 @@ def _submit_job(self, node, updatehash=False): # set local check w1.config['execution'] = {'stop_on_first_crash': 'true', 'local_hash_check': 'true', - 'crashdump_dir': wd} + 'crashdump_dir': os.getcwd()} w1.run(plugin=RaiseError()) def test_old_config(tmpdir): - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype.interfaces.utility import Function def func1(): @@ -614,8 +613,8 @@ def func2(a): def test_mapnode_json(tmpdir): """Tests that mapnodes don't generate excess jsons """ - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype import MapNode, Function, Workflow def func1(in1): @@ -671,8 +670,8 @@ def test_parameterize_dirs_false(tmpdir): def test_serial_input(tmpdir): - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype import MapNode, Function, Workflow def func1(in1): @@ -697,9 +696,9 @@ def func1(in1): assert n1.num_subnodes() == len(n1.inputs.in1) # test running the workflow on default conditions - w1.run(plugin='MultiProc') + # w1.run(plugin='MultiProc') - # test output of num_subnodes method when serial is True + # # test output of num_subnodes method when serial is True n1._serial = True assert n1.num_subnodes() == 1 @@ -708,7 +707,7 @@ def func1(in1): def test_write_graph_runs(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): @@ -736,7 +735,7 @@ def test_write_graph_runs(tmpdir): def test_deep_nested_write_graph_runs(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index e199d5b041..93b33aba90 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -239,12 +239,12 @@ def run(self, graph, config, updatehash=False): self.mapnodesubids = {} # setup polling - TODO: change to threaded model notrun = [] - while np.any(self.proc_done == False) | \ - np.any(self.proc_pending == True): + while not np.all(self.proc_done) or np.any(self.proc_pending): toappend = [] # trigger callbacks for any pending results while self.pending_tasks: + logger.info('Processing %d pending tasks.', len(self.pending_tasks)) taskid, jobid = self.pending_tasks.pop() try: result = self._get_result(taskid) @@ -263,6 +263,8 @@ def run(self, graph, config, updatehash=False): 'traceback': format_exc()} notrun.append(self._clean_queue(jobid, graph, result=result)) + + logger.debug('Appending %d new tasks.' % len(toappend)) if toappend: self.pending_tasks.extend(toappend) num_jobs = len(self.pending_tasks) @@ -348,7 +350,7 @@ def _submit_mapnode(self, jobid): def _send_procs_to_workers(self, updatehash=False, graph=None): """ Sends jobs to workers """ - while np.any(self.proc_done == False): + while not np.all(self.proc_done): num_jobs = len(self.pending_tasks) if np.isinf(self.max_jobs): slots = None diff --git a/nipype/pipeline/plugins/callback_log.py b/nipype/pipeline/plugins/callback_log.py index 4e9d7a3b50..fb3cddd4aa 100644 --- a/nipype/pipeline/plugins/callback_log.py +++ b/nipype/pipeline/plugins/callback_log.py @@ -40,6 +40,7 @@ def log_nodes_cb(node, status): 'id': node._id, 'start': getattr(node.result.runtime, 'startTime'), 'finish': getattr(node.result.runtime, 'endTime'), + 'duration': getattr(node.result.runtime, 'duration'), 'runtime_threads': getattr( node.result.runtime, 'nthreads_max', 'N/A'), 'runtime_memory_gb': getattr( @@ -48,7 +49,7 @@ def log_nodes_cb(node, status): 'num_threads': node._interface.num_threads, } - if status_dict['start'] is None or status_dict['end'] is None: + if status_dict['start'] is None or status_dict['finish'] is None: status_dict['error'] = True # Dump string to log diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 46a81d12b8..8f087d8d62 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -20,12 +20,14 @@ from ... import logging, config from ...utils.misc import str2bool +from ...utils.profiler import get_system_total_memory_gb from ..engine import MapNode from .base import (DistributedPluginBase, report_crash) # Init logger logger = logging.getLogger('workflow') + # Run node def run_node(node, updatehash, taskid): """Function to execute node.run(), catch and log any errors and @@ -44,6 +46,10 @@ def run_node(node, updatehash, taskid): dictionary containing the node runtime results and stats """ + from nipype import logging + logger = logging.getLogger('workflow') + + logger.debug('run_node called on %s', node.name) # Init variables result = dict(result=None, traceback=None, taskid=taskid) @@ -77,34 +83,6 @@ class NonDaemonPool(pool.Pool): Process = NonDaemonProcess -# Get total system RAM -def get_system_total_memory_gb(): - """Function to get the total RAM of the running system in GB - """ - - # Import packages - import os - import sys - - # Get memory - if 'linux' in sys.platform: - with open('/proc/meminfo', 'r') as f_in: - meminfo_lines = f_in.readlines() - mem_total_line = [line for line in meminfo_lines \ - if 'MemTotal' in line][0] - mem_total = float(mem_total_line.split()[1]) - memory_gb = mem_total/(1024.0**2) - elif 'darwin' in sys.platform: - mem_str = os.popen('sysctl hw.memsize').read().strip().split(' ')[-1] - memory_gb = float(mem_str)/(1024.0**3) - else: - err_msg = 'System platform: %s is not supported' - raise Exception(err_msg) - - # Return memory - return memory_gb - - class MultiProcPlugin(DistributedPluginBase): """Execute workflow with multiprocessing, not sending more jobs at once than the system can support. @@ -131,36 +109,29 @@ class MultiProcPlugin(DistributedPluginBase): def __init__(self, plugin_args=None): # Init variables and instance attributes super(MultiProcPlugin, self).__init__(plugin_args=plugin_args) + + if plugin_args is None: + plugin_args = {} + self.plugin_args = plugin_args + self._taskresult = {} self._task_obj = {} self._taskid = 0 - non_daemon = True - self.plugin_args = plugin_args - self.processors = cpu_count() - self.memory_gb = get_system_total_memory_gb()*0.9 # 90% of system memory - - self._timeout=2.0 + self._timeout = 2.0 self._event = threading.Event() - - - # Check plugin args - if self.plugin_args: - if 'non_daemon' in self.plugin_args: - non_daemon = plugin_args['non_daemon'] - if 'n_procs' in self.plugin_args: - self.processors = self.plugin_args['n_procs'] - if 'memory_gb' in self.plugin_args: - self.memory_gb = self.plugin_args['memory_gb'] - - logger.debug("MultiProcPlugin starting %d threads in pool"%(self.processors)) + # Read in options or set defaults. + non_daemon = self.plugin_args.get('non_daemon', True) + self.processors = self.plugin_args.get('n_procs', cpu_count()) + self.memory_gb = self.plugin_args.get('memory_gb', # Allocate 90% of system memory + get_system_total_memory_gb() * 0.9) # Instantiate different thread pools for non-daemon processes - if non_daemon: - # run the execution using the non-daemon pool subclass - self.pool = NonDaemonPool(processes=self.processors) - else: - self.pool = Pool(processes=self.processors) + logger.debug('MultiProcPlugin starting in "%sdaemon" mode (n_procs=%d, mem_gb=%0.2f)', + 'non' if non_daemon else '', self.processors, self.memory_gb) + self.pool = (NonDaemonPool(processes=self.processors) + if non_daemon else Pool(processes=self.processors)) + def _wait(self): if len(self.pending_tasks) > 0: @@ -172,15 +143,11 @@ def _wait(self): self._event.clear() def _async_callback(self, args): - self._taskresult[args['taskid']]=args + self._taskresult[args['taskid']] = args self._event.set() def _get_result(self, taskid): - if taskid not in self._taskresult: - result=None - else: - result=self._taskresult[taskid] - return result + return self._taskresult.get(taskid) def _report_crash(self, node, result=None): if result and result['traceback']: @@ -217,16 +184,15 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): executing_now = [] # Check to see if a job is available - currently_running_jobids = np.flatnonzero((self.proc_pending == True) & \ - (self.depidx.sum(axis=0) == 0).__array__()) + currently_running_jobids = np.flatnonzero( + self.proc_pending & (self.depidx.sum(axis=0) == 0).__array__()) # Check available system resources by summing all threads and memory used busy_memory_gb = 0 busy_processors = 0 for jobid in currently_running_jobids: if self.procs[jobid]._interface.estimated_memory_gb <= self.memory_gb and \ - self.procs[jobid]._interface.num_threads <= self.processors: - + self.procs[jobid]._interface.num_threads <= self.processors: busy_memory_gb += self.procs[jobid]._interface.estimated_memory_gb busy_processors += self.procs[jobid]._interface.num_threads @@ -242,7 +208,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): free_processors = self.processors - busy_processors # Check all jobs without dependency not run - jobids = np.flatnonzero((self.proc_done is False) & + jobids = np.flatnonzero((self.proc_done == False) & (self.depidx.sum(axis=0) == 0).__array__()) # Sort jobs ready to run first by memory and then by number of threads @@ -301,9 +267,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): hash_exists, _, _, _ = self.procs[ jobid].hash_exists() logger.debug('Hash exists %s' % str(hash_exists)) - if (hash_exists and (self.procs[jobid].overwrite == False or - (self.procs[jobid].overwrite == None and - not self.procs[jobid]._interface.always_run))): + if hash_exists and not self.procs[jobid].overwrite and \ + not self.procs[jobid]._interface.always_run: self._task_finished_cb(jobid) self._remove_node_dirs() continue diff --git a/nipype/pipeline/plugins/tests/test_multiproc.py b/nipype/pipeline/plugins/tests/test_multiproc.py index 6dab555a11..b99a9135d5 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc.py +++ b/nipype/pipeline/plugins/tests/test_multiproc.py @@ -1,15 +1,15 @@ # -*- coding: utf-8 -*- import logging -import os, sys +import os from multiprocessing import cpu_count import nipype.interfaces.base as nib from nipype.utils import draw_gantt_chart -import pytest import nipype.pipeline.engine as pe from nipype.pipeline.plugins.callback_log import log_nodes_cb from nipype.pipeline.plugins.multiproc import get_system_total_memory_gb + class InputSpec(nib.TraitedSpec): input1 = nib.traits.Int(desc='a random int') input2 = nib.traits.Int(desc='a random int') @@ -32,6 +32,7 @@ def _list_outputs(self): outputs['output1'] = [1, self.inputs.input1] return outputs + def test_run_multiproc(tmpdir): os.chdir(str(tmpdir)) @@ -82,8 +83,8 @@ def find_metrics(nodes, last_node): from dateutil.parser import parse import datetime - start = nodes[0]['start'] - total_duration = int((last_node['finish'] - start).total_seconds()) + start = parse(nodes[0]['start']) + total_duration = max(int((parse(last_node['finish']) - start).total_seconds()), 1) total_memory = [] total_threads = [] @@ -100,8 +101,8 @@ def find_metrics(nodes, last_node): x = now for j in range(start_index, len(nodes)): - node_start = nodes[j]['start'] - node_finish = nodes[j]['finish'] + node_start = parse(nodes[j]['start']) + node_finish = parse(nodes[j]['finish']) if node_start < x and node_finish > x: total_memory[i] += float(nodes[j]['estimated_memory_gb']) @@ -115,8 +116,10 @@ def find_metrics(nodes, last_node): return total_memory, total_threads -def test_no_more_memory_than_specified(): - LOG_FILENAME = 'callback.log' + +def test_no_more_memory_than_specified(tmpdir): + tmpdir.chdir() + LOG_FILENAME = tmpdir.join('callback.log').strpath my_logger = logging.getLogger('callback') my_logger.setLevel(logging.DEBUG) @@ -146,10 +149,9 @@ def test_no_more_memory_than_specified(): plugin_args={'memory_gb': max_memory, 'status_callback': log_nodes_cb}) - nodes = draw_gantt_chart.log_to_dict(LOG_FILENAME) last_node = nodes[-1] - #usage in every second + # usage in every second memory, threads = find_metrics(nodes, last_node) result = True @@ -173,6 +175,7 @@ def test_no_more_memory_than_specified(): os.remove(LOG_FILENAME) + def test_no_more_threads_than_specified(): LOG_FILENAME = 'callback.log' my_logger = logging.getLogger('callback') @@ -205,7 +208,7 @@ def test_no_more_threads_than_specified(): nodes = draw_gantt_chart.log_to_dict(LOG_FILENAME) last_node = nodes[-1] - #usage in every second + # usage in every second memory, threads = find_metrics(nodes, last_node) result = True diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py index 4c18a66f8f..74705ebe38 100644 --- a/nipype/utils/draw_gantt_chart.py +++ b/nipype/utils/draw_gantt_chart.py @@ -102,61 +102,14 @@ def log_to_dict(logfile): ''' # Init variables - #keep track of important vars - nodes_list = [] #all the parsed nodes - unifinished_nodes = [] #all start nodes that dont have a finish yet - with open(logfile, 'r') as content: - #read file separating each line - content = content.read() - lines = content.split('\n') - - for l in lines: - #try to parse each line and transform in a json dict. - #if the line has a bad format, just skip - node = None - try: - node = json.loads(l) - except ValueError: - pass - - if not node: - continue - - #if it is a start node, add to unifinished nodes - if 'start' in node: - node['start'] = parser.parse(node['start']) - unifinished_nodes.append(node) - - #if it is end node, look in uninished nodes for matching start - #remove from unifinished list and add to node list - elif 'finish' in node: - node['finish'] = parser.parse(node['finish']) - #because most nodes are small, we look backwards in the unfinished list - for s in range(len(unifinished_nodes)): - aux = unifinished_nodes[s] - #found the end for node start, copy over info - if aux['id'] == node['id'] and aux['name'] == node['name'] \ - and aux['start'] < node['finish']: - node['start'] = aux['start'] - node['duration'] = \ - (node['finish'] - node['start']).total_seconds() - - unifinished_nodes.remove(aux) - nodes_list.append(node) - break - - #finished parsing - #assume nodes without finish didn't finish running. - #set their finish to last node run - last_node = nodes_list[-1] - for n in unifinished_nodes: - n['finish'] = last_node['finish'] - n['duration'] = (n['finish'] - n['start']).total_seconds() - nodes_list.append(n) - - # Return list of nodes - return nodes_list + # read file separating each line + lines = content.readlines() + + nodes_list = [json.loads(l) for l in lines] + + # Return list of nodes + return nodes_list def calculate_resource_timeseries(events, resource): diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 8087dbd361..8dee35ba01 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-22 09:28:21 +# @Last Modified time: 2017-09-25 10:06:54 """ Utilities to keep track of performance """ @@ -27,6 +27,35 @@ from builtins import open +# Get total system RAM +def get_system_total_memory_gb(): + """ + Function to get the total RAM of the running system in GB + """ + + # Import packages + import os + import sys + + # Get memory + if 'linux' in sys.platform: + with open('/proc/meminfo', 'r') as f_in: + meminfo_lines = f_in.readlines() + mem_total_line = [line for line in meminfo_lines + if 'MemTotal' in line][0] + mem_total = float(mem_total_line.split()[1]) + memory_gb = mem_total / (1024.0**2) + elif 'darwin' in sys.platform: + mem_str = os.popen('sysctl hw.memsize').read().strip().split(' ')[-1] + memory_gb = float(mem_str) / (1024.0**3) + else: + err_msg = 'System platform: %s is not supported' + raise Exception(err_msg) + + # Return memory + return memory_gb + + # Get max resources used for process def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): """ From 9d70a2f3319713b20675afe8f0d4b4bf17b958a2 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 15:24:03 -0700 Subject: [PATCH 11/40] cleaning up code --- doc/users/resource_sched_profiler.rst | 4 +- nipype/pipeline/plugins/__init__.py | 2 +- nipype/pipeline/plugins/base.py | 14 ++--- nipype/pipeline/plugins/callback_log.py | 56 ------------------- nipype/pipeline/plugins/multiproc.py | 6 -- .../pipeline/plugins/tests/test_multiproc.py | 3 +- nipype/utils/draw_gantt_chart.py | 2 +- nipype/utils/profiler.py | 51 ++++++++++++++++- .../tests/test_profiler.py} | 4 +- 9 files changed, 63 insertions(+), 79 deletions(-) delete mode 100644 nipype/pipeline/plugins/callback_log.py rename nipype/{interfaces/tests/test_runtime_profiler.py => utils/tests/test_profiler.py} (99%) diff --git a/doc/users/resource_sched_profiler.rst b/doc/users/resource_sched_profiler.rst index 37404b27da..7fa0819c19 100644 --- a/doc/users/resource_sched_profiler.rst +++ b/doc/users/resource_sched_profiler.rst @@ -82,7 +82,7 @@ by setting the ``status_callback`` parameter to point to this function in the :: - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb} To set the filepath for the callback log the ``'callback'`` logger must be @@ -141,7 +141,7 @@ The pandas_ Python package is required to use this feature. :: - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb} workflow.run(plugin='MultiProc', plugin_args=args_dict) diff --git a/nipype/pipeline/plugins/__init__.py b/nipype/pipeline/plugins/__init__.py index cb2c193004..34d3abdebc 100644 --- a/nipype/pipeline/plugins/__init__.py +++ b/nipype/pipeline/plugins/__init__.py @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import print_function, division, unicode_literals, absolute_import from .debug import DebugPlugin from .linear import LinearPlugin @@ -19,5 +20,4 @@ from .slurm import SLURMPlugin from .slurmgraph import SLURMGraphPlugin -from .callback_log import log_nodes_cb from . import semaphore_singleton diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 93b33aba90..dab48b15f0 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -58,9 +58,9 @@ def report_crash(node, traceback=None, hostname=None): timeofcrash = strftime('%Y%m%d-%H%M%S') login_name = getpass.getuser() crashfile = 'crash-%s-%s-%s-%s' % (timeofcrash, - login_name, - name, - str(uuid.uuid4())) + login_name, + name, + str(uuid.uuid4())) crashdir = node.config['execution']['crashdump_dir'] if crashdir is None: crashdir = os.getcwd() @@ -142,7 +142,8 @@ def create_pyscript(node, updatehash=False, store_exception=True): from collections import OrderedDict config_dict=%s config.update_config(config_dict) - ## Only configure matplotlib if it was successfully imported, matplotlib is an optional component to nipype + ## Only configure matplotlib if it was successfully imported, + ## matplotlib is an optional component to nipype if can_import_matplotlib: config.update_matplotlib() logging.update_logging(config) @@ -189,6 +190,7 @@ class PluginBase(object): def __init__(self, plugin_args=None): if plugin_args is None: plugin_args = {} + self.plugin_args = plugin_args self._status_callback = plugin_args.get('status_callback') return @@ -222,9 +224,7 @@ def __init__(self, plugin_args=None): self.mapnodesubids = None self.proc_done = None self.proc_pending = None - self.max_jobs = np.inf - if plugin_args and 'max_jobs' in plugin_args: - self.max_jobs = plugin_args['max_jobs'] + self.max_jobs = self.plugin_args.get('max_jobs', np.inf) def run(self, graph, config, updatehash=False): """Executes a pre-defined pipeline using distributed approaches diff --git a/nipype/pipeline/plugins/callback_log.py b/nipype/pipeline/plugins/callback_log.py deleted file mode 100644 index fb3cddd4aa..0000000000 --- a/nipype/pipeline/plugins/callback_log.py +++ /dev/null @@ -1,56 +0,0 @@ -# -*- coding: utf-8 -*- -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: -"""Callback logger for recording workflow and node run stats -""" -from __future__ import print_function, division, unicode_literals, absolute_import - - -# Log node stats function -def log_nodes_cb(node, status): - """Function to record node run statistics to a log file as json - dictionaries - - Parameters - ---------- - node : nipype.pipeline.engine.Node - the node being logged - status : string - acceptable values are 'start', 'end'; otherwise it is - considered and error - - Returns - ------- - None - this function does not return any values, it logs the node - status info to the callback logger - """ - - if status != 'end': - return - - # Import packages - import logging - import json - - # Init variables - logger = logging.getLogger('callback') - status_dict = { - 'name': node.name, - 'id': node._id, - 'start': getattr(node.result.runtime, 'startTime'), - 'finish': getattr(node.result.runtime, 'endTime'), - 'duration': getattr(node.result.runtime, 'duration'), - 'runtime_threads': getattr( - node.result.runtime, 'nthreads_max', 'N/A'), - 'runtime_memory_gb': getattr( - node.result.runtime, 'mem_peak_gb', 'N/A'), - 'estimated_memory_gb': node._interface.estimated_memory_gb, - 'num_threads': node._interface.num_threads, - } - - if status_dict['start'] is None or status_dict['finish'] is None: - status_dict['error'] = True - - # Dump string to log - logger.debug(json.dumps(status_dict)) diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 8f087d8d62..ce6b76d203 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -7,7 +7,6 @@ http://stackoverflow.com/a/8963618/1183453 """ from __future__ import print_function, division, unicode_literals, absolute_import -from builtins import open # Import packages from multiprocessing import Process, Pool, cpu_count, pool @@ -109,11 +108,6 @@ class MultiProcPlugin(DistributedPluginBase): def __init__(self, plugin_args=None): # Init variables and instance attributes super(MultiProcPlugin, self).__init__(plugin_args=plugin_args) - - if plugin_args is None: - plugin_args = {} - self.plugin_args = plugin_args - self._taskresult = {} self._task_obj = {} self._taskid = 0 diff --git a/nipype/pipeline/plugins/tests/test_multiproc.py b/nipype/pipeline/plugins/tests/test_multiproc.py index b99a9135d5..20718feda6 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc.py +++ b/nipype/pipeline/plugins/tests/test_multiproc.py @@ -6,8 +6,7 @@ import nipype.interfaces.base as nib from nipype.utils import draw_gantt_chart import nipype.pipeline.engine as pe -from nipype.pipeline.plugins.callback_log import log_nodes_cb -from nipype.pipeline.plugins.multiproc import get_system_total_memory_gb +from nipype.utils.profiler import log_nodes_cb, get_system_total_memory_gb class InputSpec(nib.TraitedSpec): diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py index 74705ebe38..e21965480f 100644 --- a/nipype/utils/draw_gantt_chart.py +++ b/nipype/utils/draw_gantt_chart.py @@ -406,7 +406,7 @@ def generate_gantt_chart(logfile, cores, minute_scale=10, ----- # import logging # import logging.handlers - # from nipype.pipeline.plugins.callback_log import log_nodes_cb + # from nipype.utils.profiler import log_nodes_cb # log_filename = 'callback.log' # logger = logging.getLogger('callback') diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 8dee35ba01..f730c7e175 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-25 10:06:54 +# @Last Modified time: 2017-09-25 15:06:56 """ Utilities to keep track of performance """ @@ -15,6 +15,7 @@ from .. import config, logging from .misc import str2bool +from builtins import open proflogger = logging.getLogger('utils') @@ -24,7 +25,53 @@ 'necessary package "psutil" could not be imported.') runtime_profile = False -from builtins import open + +# Log node stats function +def log_nodes_cb(node, status): + """Function to record node run statistics to a log file as json + dictionaries + + Parameters + ---------- + node : nipype.pipeline.engine.Node + the node being logged + status : string + acceptable values are 'start', 'end'; otherwise it is + considered and error + + Returns + ------- + None + this function does not return any values, it logs the node + status info to the callback logger + """ + + if status != 'end': + return + + # Import packages + import logging + import json + + status_dict = { + 'name': node.name, + 'id': node._id, + 'start': getattr(node.result.runtime, 'startTime'), + 'finish': getattr(node.result.runtime, 'endTime'), + 'duration': getattr(node.result.runtime, 'duration'), + 'runtime_threads': getattr( + node.result.runtime, 'nthreads_max', 'N/A'), + 'runtime_memory_gb': getattr( + node.result.runtime, 'mem_peak_gb', 'N/A'), + 'estimated_memory_gb': node._interface.estimated_memory_gb, + 'num_threads': node._interface.num_threads, + } + + if status_dict['start'] is None or status_dict['finish'] is None: + status_dict['error'] = True + + # Dump string to log + logging.getLogger('callback').debug(json.dumps(status_dict)) # Get total system RAM diff --git a/nipype/interfaces/tests/test_runtime_profiler.py b/nipype/utils/tests/test_profiler.py similarity index 99% rename from nipype/interfaces/tests/test_runtime_profiler.py rename to nipype/utils/tests/test_profiler.py index 1e86d6a653..f979300f6e 100644 --- a/nipype/interfaces/tests/test_runtime_profiler.py +++ b/nipype/utils/tests/test_profiler.py @@ -230,7 +230,7 @@ def _run_cmdline_workflow(self, num_gb, num_threads): import nipype.pipeline.engine as pe import nipype.interfaces.utility as util - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb # Init variables base_dir = tempfile.mkdtemp() @@ -305,7 +305,7 @@ def _run_function_workflow(self, num_gb, num_threads): import nipype.pipeline.engine as pe import nipype.interfaces.utility as util - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb # Init variables base_dir = tempfile.mkdtemp() From 1fabd25aec8fa01f9c561face8f358d21cf57361 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 15:26:13 -0700 Subject: [PATCH 12/40] remove comment --- nipype/interfaces/base.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index ba16c8767b..268aeedb64 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1150,9 +1150,6 @@ def run(self, **inputs): setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) setattr(runtime, 'nthreads_max', int(nthreads_max)) - # if force_raise and getattr(runtime, 'traceback', None): - # raise NipypeInterfaceError('Fatal error:\n%s\n\n%s' % - # (runtime.traceback, runtime.traceback_args)) return results def _list_outputs(self): From ecedfcf0587ec91439b19926e14db776a75900f7 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 15:32:25 -0700 Subject: [PATCH 13/40] interface.base cleanup --- nipype/interfaces/base.py | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 268aeedb64..9ec20f4c6c 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -59,8 +59,10 @@ class Str(traits.Unicode): pass + traits.Str = Str + class NipypeInterfaceError(Exception): def __init__(self, value): self.value = value @@ -68,6 +70,7 @@ def __init__(self, value): def __str__(self): return '{}'.format(self.value) + def _exists_in_path(cmd, environ): """ Based on a code snippet from @@ -137,7 +140,6 @@ class Bunch(object): """ - def __init__(self, *args, **kwargs): self.__dict__.update(*args, **kwargs) @@ -574,7 +576,6 @@ def get_hashval(self, hash_method=None): hash_files=hash_files))) return dict_withhash, md5(to_str(dict_nofilename).encode()).hexdigest() - def _get_sorteddict(self, objekt, dictwithhash=False, hash_method=None, hash_files=True): if isinstance(objekt, dict): @@ -775,7 +776,6 @@ def __init__(self, from_file=None, **inputs): for name, value in list(inputs.items()): setattr(self.inputs, name, value) - @classmethod def help(cls, returnhelp=False): """ Prints class help @@ -896,7 +896,7 @@ def _outputs_help(cls): """ helpstr = ['Outputs::', ''] if cls.output_spec: - outputs = cls.output_spec() #pylint: disable=E1102 + outputs = cls.output_spec() # pylint: disable=E1102 for name, spec in sorted(outputs.traits(transient=None).items()): helpstr += cls._get_trait_desc(outputs, name, spec) if len(helpstr) == 2: @@ -908,7 +908,7 @@ def _outputs(self): """ outputs = None if self.output_spec: - outputs = self.output_spec() #pylint: disable=E1102 + outputs = self.output_spec() # pylint: disable=E1102 return outputs @@ -1004,7 +1004,6 @@ def _check_version_requirements(self, trait_object, raise_exception=True): return unavailable_traits def _run_wrapper(self, runtime): - sysdisplay = os.getenv('DISPLAY') if self._redirect_x: try: from xvfbwrapper import Xvfb @@ -1180,7 +1179,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None): self.__class__.__name__)) try: setattr(outputs, key, val) - _ = getattr(outputs, key) + getattr(outputs, key) except TraitError as error: if hasattr(error, 'info') and \ error.info.startswith("an existing"): @@ -1393,7 +1392,7 @@ def _process(drain=0): result['stderr'] = stderr.split('\n') result['merged'] = '' if output == 'file': - ret_code = proc.wait() + proc.wait() stderr.flush() stdout.flush() result['stdout'] = [line.decode(default_encoding).strip() @@ -1442,7 +1441,7 @@ def get_dependencies(name, environ): class CommandLineInputSpec(BaseInterfaceInputSpec): args = Str(argstr='%s', desc='Additional parameters to the command') environ = DictStrStr(desc='Environment variables', usedefault=True, - nohash=True) + nohash=True) # This input does not have a "usedefault=True" so the set_default_terminal_output() # method would work terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none', @@ -1585,7 +1584,7 @@ def version_from_command(self, flag='-v'): env=env, stdout=sp.PIPE, stderr=sp.PIPE, - ) + ) o, e = proc.communicate() return o @@ -1740,7 +1739,7 @@ def _list_outputs(self): metadata = dict(name_source=lambda t: t is not None) traits = self.inputs.traits(**metadata) if traits: - outputs = self.output_spec().get() #pylint: disable=E1102 + outputs = self.output_spec().get() # pylint: disable=E1102 for name, trait_spec in list(traits.items()): out_name = name if trait_spec.output_name is not None: @@ -1788,8 +1787,8 @@ def _parse_inputs(self, skip=None): final_args[pos] = arg else: all_args.append(arg) - first_args = [arg for pos, arg in sorted(initial_args.items())] - last_args = [arg for pos, arg in sorted(final_args.items())] + first_args = [el for _, el in sorted(initial_args.items())] + last_args = [el for _, el in sorted(final_args.items())] return first_args + all_args + last_args @@ -1860,7 +1859,7 @@ class SEMLikeCommandLine(CommandLine): """ def _list_outputs(self): - outputs = self.output_spec().get() #pylint: disable=E1102 + outputs = self.output_spec().get() # pylint: disable=E1102 return self._outputs_from_inputs(outputs) def _outputs_from_inputs(self, outputs): @@ -1897,7 +1896,7 @@ def validate(self, object, name, value): # want to treat range and other sequences (except str) as list if not isinstance(value, (str, bytes)) and isinstance(value, collections.Sequence): - value = list(value) + value = list(value) if not isdefined(value) or \ (isinstance(value, list) and len(value) == 0): From 2d359598d8a23cd86ec9d42c57a403537e27f7cf Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 16:35:41 -0700 Subject: [PATCH 14/40] update new config settings --- doc/users/config_file.rst | 7 ++++++ docker/files/run_pytests.sh | 6 ++--- nipype/interfaces/base.py | 32 ++++++++++--------------- nipype/pipeline/plugins/multiproc.py | 8 +++---- nipype/utils/config.py | 2 +- nipype/utils/profiler.py | 36 ++++++++++++++++++++++++---- 6 files changed, 59 insertions(+), 32 deletions(-) diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index 1a1a550311..b32e5602bc 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -147,6 +147,13 @@ Execution crashfiles allow portability across machines and shorter load time. (possible values: ``pklz`` and ``txt``; default value: ``pklz``) +*resource_monitor* + Enables monitoring the resources occupation. + +*resource_monitor_frequency* + Sampling period (in seconds) between measurements of resources (memory, cpus) + being used by an interface. Requires ``resource_monitor`` to be ``true``. + Example ~~~~~~~ diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh index f76734ad45..ad13ef75f6 100644 --- a/docker/files/run_pytests.sh +++ b/docker/files/run_pytests.sh @@ -17,10 +17,10 @@ echo '[logging]' > ${HOME}/.nipype/nipype.cfg echo 'log_to_file = true' >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> ${HOME}/.nipype/nipype.cfg -# Enable profile_runtime tests only for python 2.7 +# Enable resource_monitor tests only for python 2.7 if [[ "${PYTHON_VERSION}" -lt "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg - echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg fi # Run tests using pytest @@ -31,7 +31,7 @@ exit_code=$? # Workaround: run here the profiler tests in python 3 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg - echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py exit_code=$(( $exit_code + $? )) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 9ec20f4c6c..9e37fe32ca 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1055,7 +1055,7 @@ def run(self, **inputs): results : an InterfaceResult object containing a copy of the instance that was executed, provenance information and, if successful, results """ - from ..utils.profiler import runtime_profile + from ..utils.profiler import runtime_profile, ResourceMonitor force_raise = not ( hasattr(self.inputs, 'ignore_exception') and @@ -1084,17 +1084,11 @@ def run(self, **inputs): mon_sp = None if runtime_profile: - ifpid = '%d' % os.getpid() - mon_fname = os.path.abspath('.prof-%s_freq-%0.3f' % (ifpid, 1)) - mon_sp = sp.Popen( - ['nipype_mprof', ifpid, '-o', mon_fname, '-f', '1'], - cwd=os.getcwd(), - stdout=sp.DEVNULL, - stderr=sp.DEVNULL, - preexec_fn=os.setsid - ) - iflogger.debug('Started runtime profiler monitor (PID=%d) to file "%s"', - mon_sp.pid, mon_fname) + mon_freq = config.get('execution', 'resource_monitor_frequency', 1) + proc_pid = os.getpid() + mon_fname = os.path.abspath('.prof-%d_freq-%0.3f' % (proc_pid, mon_freq)) + mon_sp = ResourceMonitor(proc_pid, freq=mon_freq, fname=mon_fname) + mon_sp.start() # Grab inputs now, as they should not change during execution inputs = self.inputs.get_traitsfree() @@ -1134,20 +1128,18 @@ def run(self, **inputs): # Make sure runtime profiler is shut down if runtime_profile: - import signal import numpy as np - os.killpg(os.getpgid(mon_sp.pid), signal.SIGINT) - iflogger.debug('Killing runtime profiler monitor (PID=%d)', mon_sp.pid) + mon_sp.stop() + + setattr(runtime, 'mem_peak_gb', None) + setattr(runtime, 'nthreads_max', None) # Read .prof file in and set runtime values - mem_peak_gb = None - nthreads_max = None vals = np.loadtxt(mon_fname, delimiter=',') if vals: mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() - - setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) - setattr(runtime, 'nthreads_max', int(nthreads_max)) + setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) + setattr(runtime, 'nthreads_max', int(nthreads)) return results diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index ce6b76d203..50543825ec 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -131,7 +131,7 @@ def _wait(self): if len(self.pending_tasks) > 0: if self._config['execution']['poll_sleep_duration']: self._timeout = float(self._config['execution']['poll_sleep_duration']) - sig_received=self._event.wait(self._timeout) + sig_received = self._event.wait(self._timeout) if not sig_received: logger.debug('MultiProcPlugin timeout before signal received. Deadlock averted??') self._event.clear() @@ -211,15 +211,15 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): key=lambda item: (self.procs[item]._interface.estimated_memory_gb, self.procs[item]._interface.num_threads)) - profile_runtime = str2bool(config.get('execution', 'profile_runtime', 'false')) - if profile_runtime: + resource_monitor = str2bool(config.get('execution', 'resource_monitor', 'false')) + if resource_monitor: logger.debug('Free memory (GB): %d, Free processors: %d', free_memory_gb, free_processors) # While have enough memory and processors for first job # Submit first job on the list for jobid in jobids: - if profile_runtime: + if resource_monitor: logger.debug('Next Job: %d, memory (GB): %d, threads: %d' \ % (jobid, self.procs[jobid]._interface.estimated_memory_gb, diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 6baada07e3..6aaf3bf2d3 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -64,7 +64,7 @@ parameterize_dirs = true poll_sleep_duration = 2 xvfb_max_wait = 10 -profile_runtime = false +resource_monitor = false [check] interval = 1209600 diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index f730c7e175..789ae9fb85 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,12 +2,13 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-25 15:06:56 +# @Last Modified time: 2017-09-25 16:34:23 """ Utilities to keep track of performance """ from __future__ import print_function, division, unicode_literals, absolute_import +import threading try: import psutil except ImportError as exc: @@ -19,13 +20,40 @@ proflogger = logging.getLogger('utils') -runtime_profile = str2bool(config.get('execution', 'profile_runtime')) +runtime_profile = str2bool(config.get('execution', 'resource_monitor')) if runtime_profile and psutil is None: - proflogger.warn('Switching "profile_runtime" off: the option was on, but the ' + proflogger.warn('Switching "resource_monitor" off: the option was on, but the ' 'necessary package "psutil" could not be imported.') runtime_profile = False +class ResourceMonitor(threading.Thread): + def __init__(self, pid, freq=5, fname=None): + if freq <= 0: + raise RuntimeError('Frequency (%0.2fs) cannot be lower than zero' % freq) + + if fname is None: + fname = '.nipype.prof' + + self._pid = pid + self._log = open(fname, 'w') + self._freq = freq + threading.Thread.__init__(self) + self._event = threading.Event() + + def stop(self): + self._event.set() + self._log.close() + self.join() + + def run(self): + while not self._event.is_set(): + self._log.write('%f,%d\n' % (_get_ram_mb(self._pid), + _get_num_threads(self._pid))) + self._log.flush() + self._event.wait(self._freq) + + # Log node stats function def log_nodes_cb(node, status): """Function to record node run statistics to a log file as json @@ -127,7 +155,7 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): if not runtime_profile: raise RuntimeError('Attempted to measure resources with ' - '"profile_runtime" set off.') + '"resource_monitor" set off.') try: mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) From 3f34711e33129415a108b0d3e93c8e9b2e8ac66e Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 16:41:26 -0700 Subject: [PATCH 15/40] make naming consistent across tests --- docker/files/run_pytests.sh | 2 +- nipype/interfaces/base.py | 6 +++--- nipype/pipeline/engine/nodes.py | 4 ++-- nipype/utils/profiler.py | 10 +++++----- nipype/utils/tests/test_profiler.py | 6 +++--- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh index ad13ef75f6..2bb2d64f22 100644 --- a/docker/files/run_pytests.sh +++ b/docker/files/run_pytests.sh @@ -33,7 +33,7 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra - py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py + py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_monitor.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py exit_code=$(( $exit_code + $? )) fi diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 9e37fe32ca..a261195c6f 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1055,7 +1055,7 @@ def run(self, **inputs): results : an InterfaceResult object containing a copy of the instance that was executed, provenance information and, if successful, results """ - from ..utils.profiler import runtime_profile, ResourceMonitor + from ..utils.profiler import resource_monitor, ResourceMonitor force_raise = not ( hasattr(self.inputs, 'ignore_exception') and @@ -1083,7 +1083,7 @@ def run(self, **inputs): version=self.version) mon_sp = None - if runtime_profile: + if resource_monitor: mon_freq = config.get('execution', 'resource_monitor_frequency', 1) proc_pid = os.getpid() mon_fname = os.path.abspath('.prof-%d_freq-%0.3f' % (proc_pid, mon_freq)) @@ -1127,7 +1127,7 @@ def run(self, **inputs): results.provenance = write_provenance(results) # Make sure runtime profiler is shut down - if runtime_profile: + if resource_monitor: import numpy as np mon_sp.stop() diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 2f748f2085..c5ee3f28f3 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -689,7 +689,7 @@ def update(self, **opts): self.inputs.update(**opts) def write_report(self, report_type=None, cwd=None): - from ...utils.profiler import runtime_profile + from ...utils.profiler import resource_monitor if not str2bool(self.config['execution']['create_report']): return report_dir = op.join(cwd, '_report') @@ -727,7 +727,7 @@ def write_report(self, report_type=None, cwd=None): rst_dict = {'hostname': self.result.runtime.hostname, 'duration': self.result.runtime.duration} # Try and insert memory/threads usage if available - if runtime_profile: + if resource_monitor: rst_dict['runtime_memory_gb'] = getattr(self.result.runtime, 'mem_peak_gb') rst_dict['runtime_threads'] = getattr(self.result.runtime, 'nthreads_max') diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 789ae9fb85..2bfc9746c5 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-25 16:34:23 +# @Last Modified time: 2017-09-25 16:37:02 """ Utilities to keep track of performance """ @@ -20,11 +20,11 @@ proflogger = logging.getLogger('utils') -runtime_profile = str2bool(config.get('execution', 'resource_monitor')) -if runtime_profile and psutil is None: +resource_monitor = str2bool(config.get('execution', 'resource_monitor')) +if resource_monitor and psutil is None: proflogger.warn('Switching "resource_monitor" off: the option was on, but the ' 'necessary package "psutil" could not be imported.') - runtime_profile = False + resource_monitor = False class ResourceMonitor(threading.Thread): @@ -153,7 +153,7 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): the new high thread watermark of process """ - if not runtime_profile: + if not resource_monitor: raise RuntimeError('Attempted to measure resources with ' '"resource_monitor" set off.') diff --git a/nipype/utils/tests/test_profiler.py b/nipype/utils/tests/test_profiler.py index f979300f6e..f27ac3dc3a 100644 --- a/nipype/utils/tests/test_profiler.py +++ b/nipype/utils/tests/test_profiler.py @@ -1,10 +1,10 @@ # -*- coding: utf-8 -*- -# test_runtime_profiler.py +# test_profiler.py # # Author: Daniel Clark, 2016 """ -Module to unit test the runtime_profiler in nipype +Module to unit test the resource_monitor in nipype """ from __future__ import print_function, division, unicode_literals, absolute_import @@ -12,7 +12,7 @@ # Import packages import pytest -from nipype.utils.profiler import runtime_profile as run_profile +from nipype.utils.profiler import resource_monitor as run_profile from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec) if run_profile: From 99ded42cd94afb898b92b24549f7f098a5e8bc6e Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 17:22:57 -0700 Subject: [PATCH 16/40] implement raise_insufficient --- doc/users/plugins.rst | 7 ++++ nipype/pipeline/plugins/multiproc.py | 59 ++++++++++++++++------------ 2 files changed, 40 insertions(+), 26 deletions(-) diff --git a/doc/users/plugins.rst b/doc/users/plugins.rst index 6c825aa8f8..2a3620b838 100644 --- a/doc/users/plugins.rst +++ b/doc/users/plugins.rst @@ -74,6 +74,13 @@ Optional arguments:: n_procs : Number of processes to launch in parallel, if not set number of processors/threads will be automatically detected + memory_gb : Total memory available to be shared by all simultaneous tasks + currently running, if not set it will be automatically estimated. + + raise_insufficient : Raise exception when the estimated resources of a node + exceed the total amount of resources available (memory and threads), when + ``False`` (default), only a warning will be issued. + To distribute processing on a multicore machine, simply call:: workflow.run(plugin='MultiProc') diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 50543825ec..713bdb85e2 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -112,13 +112,14 @@ def __init__(self, plugin_args=None): self._task_obj = {} self._taskid = 0 self._timeout = 2.0 - self._event = threading.Event() + # self._event = threading.Event() # Read in options or set defaults. non_daemon = self.plugin_args.get('non_daemon', True) self.processors = self.plugin_args.get('n_procs', cpu_count()) self.memory_gb = self.plugin_args.get('memory_gb', # Allocate 90% of system memory get_system_total_memory_gb() * 0.9) + self.raise_insufficient = self.plugin_args.get('raise_insufficient', True) # Instantiate different thread pools for non-daemon processes logger.debug('MultiProcPlugin starting in "%sdaemon" mode (n_procs=%d, mem_gb=%0.2f)', @@ -126,19 +127,18 @@ def __init__(self, plugin_args=None): self.pool = (NonDaemonPool(processes=self.processors) if non_daemon else Pool(processes=self.processors)) - - def _wait(self): - if len(self.pending_tasks) > 0: - if self._config['execution']['poll_sleep_duration']: - self._timeout = float(self._config['execution']['poll_sleep_duration']) - sig_received = self._event.wait(self._timeout) - if not sig_received: - logger.debug('MultiProcPlugin timeout before signal received. Deadlock averted??') - self._event.clear() + # def _wait(self): + # if len(self.pending_tasks) > 0: + # if self._config['execution']['poll_sleep_duration']: + # self._timeout = float(self._config['execution']['poll_sleep_duration']) + # sig_received = self._event.wait(self._timeout) + # if not sig_received: + # logger.debug('MultiProcPlugin timeout before signal received. Deadlock averted??') + # self._event.clear() def _async_callback(self, args): self._taskresult[args['taskid']] = args - self._event.set() + # self._event.set() def _get_result(self, taskid): return self._taskresult.get(taskid) @@ -185,18 +185,25 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): busy_memory_gb = 0 busy_processors = 0 for jobid in currently_running_jobids: - if self.procs[jobid]._interface.estimated_memory_gb <= self.memory_gb and \ - self.procs[jobid]._interface.num_threads <= self.processors: - busy_memory_gb += self.procs[jobid]._interface.estimated_memory_gb - busy_processors += self.procs[jobid]._interface.num_threads - - else: - raise ValueError( - "Resources required by jobid {0} ({3}GB, {4} threads) exceed what is " - "available on the system ({1}GB, {2} threads)".format( - jobid, self.memory_gb, self.processors, - self.procs[jobid]._interface.estimated_memory_gb, - self.procs[jobid]._interface.num_threads)) + est_mem_gb = self.procs[jobid]._interface.estimated_memory_gb + est_num_th = self.procs[jobid]._interface.num_threads + + if est_mem_gb > self.memory_gb: + logger.warning( + 'Job %s - Estimated memory (%0.2fGB) exceeds the total amount' + ' available (%0.2fGB).', self.procs[jobid].name, est_mem_gb, self.memory_gb) + if self.raise_insufficient: + raise RuntimeError('Insufficient resources available for job') + + if est_num_th > self.processors: + logger.warning( + 'Job %s - Requested %d threads, but only %d are available.', + self.procs[jobid].name, est_num_th, self.processors) + if self.raise_insufficient: + raise RuntimeError('Insufficient resources available for job') + + busy_memory_gb += min(est_mem_gb, self.memory_gb) + busy_processors += min(est_num_th, self.processors) free_memory_gb = self.memory_gb - busy_memory_gb free_processors = self.processors - busy_processors @@ -276,8 +283,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): logger.debug('Finished checking hash') if self.procs[jobid].run_without_submitting: - logger.debug('Running node %s on master thread' \ - % self.procs[jobid]) + logger.debug('Running node %s on master thread', + self.procs[jobid]) try: self.procs[jobid].run() except Exception: @@ -288,7 +295,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): self._remove_node_dirs() else: - logger.debug('MultiProcPlugin submitting %s' % str(jobid)) + logger.debug('MultiProcPlugin submitting %s', str(jobid)) tid = self._submit_job(deepcopy(self.procs[jobid]), updatehash=updatehash) if tid is None: From b0d25bde97d7599b7a923002c581258772ec432a Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 22:42:10 -0700 Subject: [PATCH 17/40] fix test --- docker/files/run_pytests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh index 2bb2d64f22..e994b0ca41 100644 --- a/docker/files/run_pytests.sh +++ b/docker/files/run_pytests.sh @@ -33,7 +33,7 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra - py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_monitor.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py + py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/utils/tests/test_runtime_monitor.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py exit_code=$(( $exit_code + $? )) fi From 2a37693e0ac0ff5ec23a95c8382c8e92d41f2cf7 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 25 Sep 2017 23:34:23 -0700 Subject: [PATCH 18/40] fix test (amend previous commit) --- docker/files/run_pytests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh index e994b0ca41..622772d3ae 100644 --- a/docker/files/run_pytests.sh +++ b/docker/files/run_pytests.sh @@ -33,7 +33,7 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra - py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/utils/tests/test_runtime_monitor.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py + py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/utils/tests/test_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py exit_code=$(( $exit_code + $? )) fi From 10d0f39e9728236ee35069d732d13b8243dd5a2c Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 00:46:23 -0700 Subject: [PATCH 19/40] address review comments --- doc/users/config_file.rst | 9 +++-- doc/users/plugins.rst | 3 +- nipype/interfaces/base.py | 10 +---- nipype/interfaces/spm/base.py | 2 +- nipype/pipeline/engine/tests/test_engine.py | 4 +- nipype/pipeline/plugins/multiproc.py | 25 ++++++------ nipype/utils/config.py | 25 ++++++++++-- nipype/utils/draw_gantt_chart.py | 1 - nipype/utils/profiler.py | 42 --------------------- setup.py | 1 - 10 files changed, 47 insertions(+), 75 deletions(-) diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index b32e5602bc..bca5f0eb00 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -17,8 +17,8 @@ Logging How detailed the logs regarding workflow should be (possible values: ``INFO`` and ``DEBUG``; default value: ``INFO``) *utils_level* - How detailed the logs regarding nipype utils like file operations - (for example overwriting warning) or the resource profiler should be + How detailed the logs regarding nipype utils, like file operations + (for example overwriting warning) or the resource profiler, should be (possible values: ``INFO`` and ``DEBUG``; default value: ``INFO``) *interface_level* @@ -148,10 +148,11 @@ Execution (possible values: ``pklz`` and ``txt``; default value: ``pklz``) *resource_monitor* - Enables monitoring the resources occupation. + Enables monitoring the resources occupation (possible values: ``true`` and + ``false``; default value: ``false``) *resource_monitor_frequency* - Sampling period (in seconds) between measurements of resources (memory, cpus) + Sampling period (in seconds) between measurements of resources (memory, cpus) being used by an interface. Requires ``resource_monitor`` to be ``true``. Example diff --git a/doc/users/plugins.rst b/doc/users/plugins.rst index 2a3620b838..4c0960c554 100644 --- a/doc/users/plugins.rst +++ b/doc/users/plugins.rst @@ -75,7 +75,8 @@ Optional arguments:: processors/threads will be automatically detected memory_gb : Total memory available to be shared by all simultaneous tasks - currently running, if not set it will be automatically estimated. + currently running, if not set it will be automatically set to 90\% of + system RAM. raise_insufficient : Raise exception when the estimated resources of a node exceed the total amount of resources available (memory and threads), when diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index a261195c6f..e2a3ebf29c 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -52,9 +52,6 @@ PY3 = sys.version_info[0] > 2 __docformat__ = 'restructuredtext' -if sys.version_info < (3, 3): - setattr(sp, 'DEVNULL', os.devnull) - class Str(traits.Unicode): pass @@ -1057,11 +1054,7 @@ def run(self, **inputs): """ from ..utils.profiler import resource_monitor, ResourceMonitor - force_raise = not ( - hasattr(self.inputs, 'ignore_exception') and - isdefined(self.inputs.ignore_exception) and - self.inputs.ignore_exception - ) + force_raise = not getattr(self.inputs, 'ignore_exception', False) self.inputs.trait_set(**inputs) self._check_mandatory_inputs() self._check_version_requirements(self.inputs) @@ -1363,6 +1356,7 @@ def _process(drain=0): while proc.returncode is None: proc.poll() _process() + time.sleep(interval) _process(drain=1) diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index 33c540f457..b4659a6a5c 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -159,7 +159,7 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): return None use_mcr = use_mcr or 'FORCE_SPMMCR' in os.environ - matlab_cmd = (os.getenv('SPMMCRCMD') or + matlab_cmd = ((use_mcr and os.getenv('SPMMCRCMD')) or os.getenv('MATLABCMD') or 'matlab -nodesktop -nosplash') diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py index 56c4f78e84..adaf506122 100644 --- a/nipype/pipeline/engine/tests/test_engine.py +++ b/nipype/pipeline/engine/tests/test_engine.py @@ -696,9 +696,9 @@ def func1(in1): assert n1.num_subnodes() == len(n1.inputs.in1) # test running the workflow on default conditions - # w1.run(plugin='MultiProc') + w1.run(plugin='MultiProc') - # # test output of num_subnodes method when serial is True + # test output of num_subnodes method when serial is True n1._serial = True assert n1.num_subnodes() == 1 diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 713bdb85e2..4f25a3f286 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -124,8 +124,7 @@ def __init__(self, plugin_args=None): # Instantiate different thread pools for non-daemon processes logger.debug('MultiProcPlugin starting in "%sdaemon" mode (n_procs=%d, mem_gb=%0.2f)', 'non' if non_daemon else '', self.processors, self.memory_gb) - self.pool = (NonDaemonPool(processes=self.processors) - if non_daemon else Pool(processes=self.processors)) + self.pool = (NonDaemonPool if non_daemon else Pool)(processes=self.processors) # def _wait(self): # if len(self.pending_tasks) > 0: @@ -234,7 +233,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): if self.procs[jobid]._interface.estimated_memory_gb <= free_memory_gb and \ self.procs[jobid]._interface.num_threads <= free_processors: - logger.info('Executing: %s ID: %d' %(self.procs[jobid]._id, jobid)) + logger.info('Executing: %s ID: %d' % (self.procs[jobid]._id, jobid)) executing_now.append(self.procs[jobid]) if isinstance(self.procs[jobid], MapNode): @@ -265,11 +264,13 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): if str2bool(self.procs[jobid].config['execution']['local_hash_check']): logger.debug('checking hash locally') try: - hash_exists, _, _, _ = self.procs[ - jobid].hash_exists() - logger.debug('Hash exists %s' % str(hash_exists)) - if hash_exists and not self.procs[jobid].overwrite and \ - not self.procs[jobid]._interface.always_run: + hash_exists, _, _, _ = self.procs[jobid].hash_exists() + overwrite = self.procs[jobid].overwrite + always_run = self.procs[jobid]._interface.always_run + if (hash_exists and (overwrite is False or + (overwrite is None and not always_run))): + logger.debug('Skipping cached node %s with ID %s.', + self.procs[jobid]._id, jobid) self._task_finished_cb(jobid) self._remove_node_dirs() continue @@ -280,7 +281,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): self._clean_queue(jobid, graph) self.proc_pending[jobid] = False continue - logger.debug('Finished checking hash') + finally: + logger.debug('Finished checking hash') if self.procs[jobid].run_without_submitting: logger.debug('Running node %s on master thread', @@ -291,8 +293,9 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): etype, eval, etr = sys.exc_info() traceback = format_exception(etype, eval, etr) report_crash(self.procs[jobid], traceback=traceback) - self._task_finished_cb(jobid) - self._remove_node_dirs() + finally: + self._task_finished_cb(jobid) + self._remove_node_dirs() else: logger.debug('MultiProcPlugin submitting %s', str(jobid)) diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 6aaf3bf2d3..86bc0738a0 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -11,21 +11,24 @@ ''' from __future__ import print_function, division, unicode_literals, absolute_import import os -import shutil import errno from warnings import warn from io import StringIO from distutils.version import LooseVersion -from simplejson import load, dump +import configparser import numpy as np from builtins import str, object, open + +from simplejson import load, dump +from ..external import portalocker from future import standard_library standard_library.install_aliases() -import configparser -from ..external import portalocker +CONFIG_DEPRECATIONS = { + 'profile_runtime': ('resource_monitor', '1.13.2'), +} NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0') @@ -115,6 +118,13 @@ def set_log_dir(self, log_dir): self._config.set('logging', 'log_directory', log_dir) def get(self, section, option, default=None): + if option in CONFIG_DEPRECATIONS: + msg = ('Config option "%s" has been deprecated as of nipype %s. Please use ' + '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1], + CONFIG_DEPRECATIONS[option][0]) + warn(msg) + option = CONFIG_DEPRECATIONS[option][0] + if self._config.has_option(section, option): return self._config.get(section, option) return default @@ -123,6 +133,13 @@ def set(self, section, option, value): if isinstance(value, bool): value = str(value) + if option in CONFIG_DEPRECATIONS: + msg = ('Config option "%s" has been deprecated as of nipype %s. Please use ' + '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1], + CONFIG_DEPRECATIONS[option][0]) + warn(msg) + option = CONFIG_DEPRECATIONS[option][0] + return self._config.set(section, option, value) def getboolean(self, section, option): diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py index e21965480f..c91acf662c 100644 --- a/nipype/utils/draw_gantt_chart.py +++ b/nipype/utils/draw_gantt_chart.py @@ -11,7 +11,6 @@ import random import datetime import simplejson as json -from dateutil import parser from builtins import str, range, open # Py2 compat: http://python-future.org/compatible_idioms.html#collections-counter-and-ordereddict from future import standard_library diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 2bfc9746c5..07a7a51035 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -265,45 +265,3 @@ def _get_ram_mb(pid, pyfunc=False): # Return memory return mem_mb - - -def main(): - """ - A minimal entry point to measure any process using psutil - """ - from argparse import ArgumentParser - from argparse import RawTextHelpFormatter - - parser = ArgumentParser(description='A minimal process monitor', - formatter_class=RawTextHelpFormatter) - parser.add_argument('pid', action='store', type=int, - help='process PID to monitor') - parser.add_argument('-o', '--out-file', action='store', default='.prof', - help='file where monitor will be writting') - parser.add_argument('-f', '--freq', action='store', type=float, default=5.0, - help='sampling frequency') - opts = parser.parse_args() - _probe_loop(opts.pid, opts.out_file, wait=opts.freq) - - -def _probe_loop(pid, fname, wait=None): - from time import sleep - - print('Start monitoring') - if wait is None: - wait = 5 - - proffh = open(fname, 'w') - while True: - try: - proffh.write('%f,%d\n' % (_get_ram_mb(pid), _get_num_threads(pid))) - proffh.flush() - sleep(wait) - except (Exception, KeyboardInterrupt): - proffh.close() - print('\nFinished.') - return - - -if __name__ == "__main__": - main() diff --git a/setup.py b/setup.py index 3453901b3e..331fa5905b 100755 --- a/setup.py +++ b/setup.py @@ -148,7 +148,6 @@ def main(): entry_points=''' [console_scripts] nipypecli=nipype.scripts.cli:cli - nipype_mprof=nipype.utils.profiler:main ''' ) From 62a65938fdec7bf333f1b74ce9c7e6ecd5bf4f08 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 00:50:14 -0700 Subject: [PATCH 20/40] fix typo --- nipype/interfaces/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index e2a3ebf29c..56677c466c 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1356,7 +1356,7 @@ def _process(drain=0): while proc.returncode is None: proc.poll() _process() - time.sleep(interval) + time.sleep(0) _process(drain=1) From d6401f3c6eee244178e9496d10637ded424d977a Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 09:06:47 -0700 Subject: [PATCH 21/40] fixes to the tear-up section of interfaces --- nipype/interfaces/base.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 56677c466c..bff625b329 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1124,15 +1124,15 @@ def run(self, **inputs): import numpy as np mon_sp.stop() - setattr(runtime, 'mem_peak_gb', None) - setattr(runtime, 'nthreads_max', None) + runtime.mem_peak_gb = None + runtime.nthreads_max = None # Read .prof file in and set runtime values vals = np.loadtxt(mon_fname, delimiter=',') - if vals: + if vals.tolist(): mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() - setattr(runtime, 'mem_peak_gb', mem_peak_gb / 1024) - setattr(runtime, 'nthreads_max', int(nthreads)) + runtime.mem_peak_gb = mem_peak_gb / 1024 + runtime.nthreads_max = int(nthreads) return results From ce3f08a46ab77d5ae949f14e5d1ddce8f1ade38b Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 09:13:46 -0700 Subject: [PATCH 22/40] fix NoSuchProcess exception --- nipype/utils/profiler.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 07a7a51035..89e1457306 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-25 16:37:02 +# @Last Modified time: 2017-09-26 09:12:36 """ Utilities to keep track of performance """ @@ -42,14 +42,20 @@ def __init__(self, pid, freq=5, fname=None): self._event = threading.Event() def stop(self): - self._event.set() - self._log.close() - self.join() + if not self._event.is_set(): + self._event.set() + self._log.close() + self.join() def run(self): while not self._event.is_set(): - self._log.write('%f,%d\n' % (_get_ram_mb(self._pid), - _get_num_threads(self._pid))) + try: + ram = _get_ram_mb(self._pid) + cpus = _get_num_threads(self._pid) + except psutil.NoSuchProcess: + self.stop() + + self._log.write('%f,%d\n' % (ram, cpus)) self._log.flush() self._event.wait(self._freq) From ffb750986c71c79634533fabd264eb381d83bdff Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 11:05:51 -0700 Subject: [PATCH 23/40] making monitor robuster --- nipype/interfaces/base.py | 7 +-- nipype/utils/profiler.py | 114 +++++++++++++++++++++----------------- 2 files changed, 66 insertions(+), 55 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index bff625b329..898caed50a 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1092,7 +1092,7 @@ def run(self, **inputs): except Exception as e: import traceback # Retrieve the maximum info fast - setattr(runtime, 'traceback', traceback.format_exc()) + runtime.traceback = traceback.format_exc() # Gather up the exception arguments and append nipype info. exc_args = e.args if getattr(e, 'args') else tuple() exc_args += ('An exception of type %s occurred while running interface %s.' % @@ -1100,8 +1100,7 @@ def run(self, **inputs): if config.get('logging', 'interface_level', 'info').lower() == 'debug': exc_args += ('Inputs: %s' % str(self.inputs),) - setattr(runtime, 'traceback_args', - ('\n'.join(['%s' % arg for arg in exc_args]),)) + runtime.traceback_args = ('\n'.join(['%s' % arg for arg in exc_args]),) if force_raise: raise @@ -1130,7 +1129,7 @@ def run(self, **inputs): # Read .prof file in and set runtime values vals = np.loadtxt(mon_fname, delimiter=',') if vals.tolist(): - mem_peak_gb, nthreads = vals.max(0).astype(float).tolist() + mem_peak_gb, nthreads = np.atleast_2d(vals).max(0).astype(float).tolist() runtime.mem_peak_gb = mem_peak_gb / 1024 runtime.nthreads_max = int(nthreads) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 89e1457306..68b55d48c0 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,13 +2,14 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-26 09:12:36 +# @Last Modified time: 2017-09-26 10:56:03 """ Utilities to keep track of performance """ from __future__ import print_function, division, unicode_literals, absolute_import import threading +from time import time try: import psutil except ImportError as exc: @@ -26,6 +27,9 @@ 'necessary package "psutil" could not be imported.') resource_monitor = False +# Init variables +_MB = 1024.0**2 + class ResourceMonitor(threading.Thread): def __init__(self, pid, freq=5, fname=None): @@ -37,6 +41,8 @@ def __init__(self, pid, freq=5, fname=None): self._pid = pid self._log = open(fname, 'w') + self._log.write('%s,0.0,0\n' % time()) + self._log.flush() self._freq = freq threading.Thread.__init__(self) self._event = threading.Event() @@ -52,11 +58,15 @@ def run(self): try: ram = _get_ram_mb(self._pid) cpus = _get_num_threads(self._pid) - except psutil.NoSuchProcess: - self.stop() + if all(ram is not None, cpus is not None): + self._log.write('%s,%f,%d\n' % (time(), ram, cpus)) + self._log.flush() + except ValueError as e: + if e.args == ('I/O operation on closed file.',): + pass + except Exception: + pass - self._log.write('%f,%d\n' % (ram, cpus)) - self._log.flush() self._event.wait(self._freq) @@ -190,37 +200,40 @@ def _get_num_threads(pid): """ - proc = psutil.Process(pid) - # If process is running - if proc.status() == psutil.STATUS_RUNNING: - num_threads = proc.num_threads() - elif proc.num_threads() > 1: - tprocs = [psutil.Process(thr.id) for thr in proc.threads()] - alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] - num_threads = len(alive_tprocs) - else: - num_threads = 1 - - child_threads = 0 - # Iterate through child processes and get number of their threads - for child in proc.children(recursive=True): - # Leaf process - if len(child.children()) == 0: - # If process is running, get its number of threads - if child.status() == psutil.STATUS_RUNNING: - child_thr = child.num_threads() - # If its not necessarily running, but still multi-threaded - elif child.num_threads() > 1: - # Cast each thread as a process and check for only running - tprocs = [psutil.Process(thr.id) for thr in child.threads()] - alive_tprocs = [tproc for tproc in tprocs - if tproc.status() == psutil.STATUS_RUNNING] - child_thr = len(alive_tprocs) - # Otherwise, no threads are running - else: - child_thr = 0 - # Increment child threads - child_threads += child_thr + try: + proc = psutil.Process(pid) + # If process is running + if proc.status() == psutil.STATUS_RUNNING: + num_threads = proc.num_threads() + elif proc.num_threads() > 1: + tprocs = [psutil.Process(thr.id) for thr in proc.threads()] + alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] + num_threads = len(alive_tprocs) + else: + num_threads = 1 + + child_threads = 0 + # Iterate through child processes and get number of their threads + for child in proc.children(recursive=True): + # Leaf process + if len(child.children()) == 0: + # If process is running, get its number of threads + if child.status() == psutil.STATUS_RUNNING: + child_thr = child.num_threads() + # If its not necessarily running, but still multi-threaded + elif child.num_threads() > 1: + # Cast each thread as a process and check for only running + tprocs = [psutil.Process(thr.id) for thr in child.threads()] + alive_tprocs = [tproc for tproc in tprocs + if tproc.status() == psutil.STATUS_RUNNING] + child_thr = len(alive_tprocs) + # Otherwise, no threads are running + else: + child_thr = 0 + # Increment child threads + child_threads += child_thr + except psutil.NoSuchProcess: + return None # Number of threads is max between found active children and parent num_threads = max(child_threads, num_threads) @@ -253,21 +266,20 @@ def _get_ram_mb(pid, pyfunc=False): the memory RAM in MB utilized by the process PID """ - - # Init variables - _MB = 1024.0**2 - - # Init parent - parent = psutil.Process(pid) - # Get memory of parent - parent_mem = parent.memory_info().rss - mem_mb = parent_mem / _MB - # Iterate through child processes - for child in parent.children(recursive=True): - child_mem = child.memory_info().rss - if pyfunc: - child_mem -= parent_mem - mem_mb += child_mem / _MB + try: + # Init parent + parent = psutil.Process(pid) + # Get memory of parent + parent_mem = parent.memory_info().rss + mem_mb = parent_mem / _MB + # Iterate through child processes + for child in parent.children(recursive=True): + child_mem = child.memory_info().rss + if pyfunc: + child_mem -= parent_mem + mem_mb += child_mem / _MB + except psutil.NoSuchProcess: + return None # Return memory return mem_mb From c9b474b014fad7802d8f612e57cab09a07efa645 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 16:40:12 -0700 Subject: [PATCH 24/40] first functional prototype --- nipype/interfaces/afni/base.py | 7 ++++-- nipype/interfaces/base.py | 18 ++++++++++------ nipype/interfaces/dynamic_slicer.py | 3 ++- nipype/interfaces/matlab.py | 1 + nipype/interfaces/spm/base.py | 14 +++++------- nipype/pipeline/engine/utils.py | 8 ++++--- nipype/pipeline/plugins/condor.py | 2 ++ nipype/pipeline/plugins/dagman.py | 1 + nipype/pipeline/plugins/lsf.py | 2 ++ nipype/pipeline/plugins/oar.py | 1 + nipype/pipeline/plugins/pbs.py | 2 ++ nipype/pipeline/plugins/pbsgraph.py | 1 + nipype/pipeline/plugins/sge.py | 1 + nipype/pipeline/plugins/sgegraph.py | 1 + nipype/pipeline/plugins/slurm.py | 2 ++ nipype/pipeline/plugins/slurmgraph.py | 1 + nipype/utils/docparse.py | 2 ++ nipype/utils/profiler.py | 31 ++++++++++++--------------- nipype/utils/spm_docs.py | 2 +- 19 files changed, 61 insertions(+), 39 deletions(-) diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index 35751d4e5c..b834b34163 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -45,6 +45,7 @@ def version(): """ try: clout = CommandLine(command='afni --version', + resource_monitor=False, terminal_output='allatonce').run() except IOError: # If afni_vcheck is not present, return None @@ -105,7 +106,9 @@ def standard_image(img_name): '''Grab an image from the standard location. Could be made more fancy to allow for more relocatability''' - clout = CommandLine('which afni', ignore_exception=True, + clout = CommandLine('which afni', + ignore_exception=True, + resource_monitor=False, terminal_output='allatonce').run() if clout.runtime.returncode is not 0: return None @@ -295,4 +298,4 @@ def cmd(self): @property def cmdline(self): - return "{} {}".format(self.inputs.py27_path, super(AFNIPythonCommand, self).cmdline) \ No newline at end of file + return "{} {}".format(self.inputs.py27_path, super(AFNIPythonCommand, self).cmdline) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 898caed50a..a200eb900f 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -729,9 +729,12 @@ def _get_filecopy_info(self): class BaseInterfaceInputSpec(TraitedSpec): - ignore_exception = traits.Bool(False, desc="Print an error message instead \ -of throwing an exception in case the interface fails to run", usedefault=True, - nohash=True) + ignore_exception = traits.Bool(False, usedefault=True, nohash=True, + desc='Print an error message instead of throwing an exception ' + 'in case the interface fails to run') + resource_monitor = traits.Bool(True, usedefault=True, nohash=True, + desc='Disable the resource monitor for this interface ' + '(overloads the default nipype config).') class BaseInterface(Interface): @@ -1054,6 +1057,7 @@ def run(self, **inputs): """ from ..utils.profiler import resource_monitor, ResourceMonitor + enable_rm = resource_monitor and self.inputs.resource_monitor force_raise = not getattr(self.inputs, 'ignore_exception', False) self.inputs.trait_set(**inputs) self._check_mandatory_inputs() @@ -1076,10 +1080,12 @@ def run(self, **inputs): version=self.version) mon_sp = None - if resource_monitor: + if enable_rm: mon_freq = config.get('execution', 'resource_monitor_frequency', 1) proc_pid = os.getpid() mon_fname = os.path.abspath('.prof-%d_freq-%0.3f' % (proc_pid, mon_freq)) + iflogger.debug('Creating a ResourceMonitor on a %s interface: %s', + self.__class__.__name__, mon_fname) mon_sp = ResourceMonitor(proc_pid, freq=mon_freq, fname=mon_fname) mon_sp.start() @@ -1119,7 +1125,7 @@ def run(self, **inputs): results.provenance = write_provenance(results) # Make sure runtime profiler is shut down - if resource_monitor: + if enable_rm: import numpy as np mon_sp.stop() @@ -1129,7 +1135,7 @@ def run(self, **inputs): # Read .prof file in and set runtime values vals = np.loadtxt(mon_fname, delimiter=',') if vals.tolist(): - mem_peak_gb, nthreads = np.atleast_2d(vals).max(0).astype(float).tolist() + _, mem_peak_gb, nthreads = np.atleast_2d(vals).max(0).astype(float).tolist() runtime.mem_peak_gb = mem_peak_gb / 1024 runtime.nthreads_max = int(nthreads) diff --git a/nipype/interfaces/dynamic_slicer.py b/nipype/interfaces/dynamic_slicer.py index d38f4171f3..4d1df1e136 100644 --- a/nipype/interfaces/dynamic_slicer.py +++ b/nipype/interfaces/dynamic_slicer.py @@ -25,7 +25,8 @@ class SlicerCommandLine(CommandLine): output_spec = DynamicTraitedSpec def _grab_xml(self, module): - cmd = CommandLine(command="Slicer3", args="--launch %s --xml" % module) + cmd = CommandLine(command="Slicer3", resource_monitor=False, + args="--launch %s --xml" % module) ret = cmd.run() if ret.runtime.returncode == 0: return xml.dom.minidom.parseString(ret.runtime.stdout) diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py index d3f6f26993..b56ef3ce17 100644 --- a/nipype/interfaces/matlab.py +++ b/nipype/interfaces/matlab.py @@ -22,6 +22,7 @@ def get_matlab_command(): try: res = CommandLine(command='which', args=matlab_cmd, + resource_monitor=False, terminal_output='allatonce').run() matlab_path = res.runtime.stdout.strip() except Exception as e: diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index b4659a6a5c..391528e83b 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -29,7 +29,7 @@ # Local imports from ... import logging from ...utils import spm_docs as sd, NUMPY_MMAP -from ..base import (BaseInterface, CommandLine, traits, isdefined, InputMultiPath, +from ..base import (BaseInterface, traits, isdefined, InputMultiPath, BaseInterfaceInputSpec, Directory, Undefined, ImageFile) from ..matlab import MatlabCommand from ...external.due import due, Doi, BibTeX @@ -152,18 +152,13 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): returns None of path not found """ - # Test if matlab is installed, exit quickly if not. - clout = CommandLine('which matlab', ignore_exception=True, - terminal_output='allatonce').run() - if clout.runtime.returncode is not 0: - return None - use_mcr = use_mcr or 'FORCE_SPMMCR' in os.environ matlab_cmd = ((use_mcr and os.getenv('SPMMCRCMD')) or os.getenv('MATLABCMD') or 'matlab -nodesktop -nosplash') - mlab = MatlabCommand(matlab_cmd=matlab_cmd) + mlab = MatlabCommand(matlab_cmd=matlab_cmd, + resource_monitor=False) mlab.inputs.mfile = False if paths: mlab.inputs.paths = paths @@ -280,7 +275,8 @@ def _matlab_cmd_update(self): # and can be set only during init self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd, mfile=self.inputs.mfile, - paths=self.inputs.paths) + paths=self.inputs.paths, + resource_monitor=False) self.mlab.inputs.script_file = 'pyscript_%s.m' % \ self.__class__.__name__.split('.')[-1].lower() if isdefined(self.inputs.use_mcr) and self.inputs.use_mcr: diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py index f677d6c253..48e3f6ed49 100644 --- a/nipype/pipeline/engine/utils.py +++ b/nipype/pipeline/engine/utils.py @@ -1022,7 +1022,8 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, _write_detailed_dot(graph, outfname) if format != 'dot': cmd = 'dot -T%s -O %s' % (format, outfname) - res = CommandLine(cmd, terminal_output='allatonce').run() + res = CommandLine(cmd, terminal_output='allatonce', + resource_monitor=False).run() if res.runtime.returncode: logger.warn('dot2png: %s', res.runtime.stderr) pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form) @@ -1033,7 +1034,8 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, nx.drawing.nx_pydot.write_dot(pklgraph, simplefname) if format != 'dot': cmd = 'dot -T%s -O %s' % (format, simplefname) - res = CommandLine(cmd, terminal_output='allatonce').run() + res = CommandLine(cmd, terminal_output='allatonce', + resource_monitor=False).run() if res.runtime.returncode: logger.warn('dot2png: %s', res.runtime.stderr) if show: @@ -1053,7 +1055,7 @@ def format_dot(dotfilename, format='png'): if format != 'dot': cmd = 'dot -T%s -O \'%s\'' % (format, dotfilename) try: - CommandLine(cmd).run() + CommandLine(cmd, resource_monitor=False).run() except IOError as ioe: if "could not be found" in str(ioe): raise IOError("Cannot draw directed graph; executable 'dot' is unavailable") diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py index 9b8b5c218d..de4265e3f3 100644 --- a/nipype/pipeline/plugins/condor.py +++ b/nipype/pipeline/plugins/condor.py @@ -46,6 +46,7 @@ def __init__(self, **kwargs): def _is_pending(self, taskid): cmd = CommandLine('condor_q', + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%d' % taskid # check condor cluster @@ -59,6 +60,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('condor_qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py index 1001ab5dac..61aa44229e 100644 --- a/nipype/pipeline/plugins/dagman.py +++ b/nipype/pipeline/plugins/dagman.py @@ -154,6 +154,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): child)) # hand over DAG to condor_dagman cmd = CommandLine('condor_submit_dag', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') # needs -update_submit or re-running a workflow will fail cmd.inputs.args = '%s -update_submit %s' % (self._dagman_args, diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py index 6e27b3ab95..d065b521d8 100644 --- a/nipype/pipeline/plugins/lsf.py +++ b/nipype/pipeline/plugins/lsf.py @@ -45,6 +45,7 @@ def _is_pending(self, taskid): finished and is ready to be checked for completeness. So return True if status is either 'PEND' or 'RUN'""" cmd = CommandLine('bjobs', + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%d' % taskid # check lsf task @@ -60,6 +61,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('bsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) bsubargs = '' diff --git a/nipype/pipeline/plugins/oar.py b/nipype/pipeline/plugins/oar.py index ca77fade1e..d3a9c6f360 100644 --- a/nipype/pipeline/plugins/oar.py +++ b/nipype/pipeline/plugins/oar.py @@ -68,6 +68,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('oarsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) oarsubargs = '' diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py index 5288bb36cb..62b35fa99a 100644 --- a/nipype/pipeline/plugins/pbs.py +++ b/nipype/pipeline/plugins/pbs.py @@ -48,6 +48,7 @@ def _is_pending(self, taskid): result = CommandLine('qstat {}'.format(taskid), environ=dict(os.environ), terminal_output='allatonce', + resource_monitor=False, ignore_exception=True).run() stderr = result.runtime.stderr errmsg = 'Unknown Job Id' # %s' % taskid @@ -59,6 +60,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py index 1aafd24e37..719b82578c 100644 --- a/nipype/pipeline/plugins/pbsgraph.py +++ b/nipype/pipeline/plugins/pbsgraph.py @@ -55,6 +55,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): qsub_args, batchscriptfile)) cmd = CommandLine('sh', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index 268fecf2a9..d337ebb961 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -364,6 +364,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py index dd4b8076e8..882c455450 100644 --- a/nipype/pipeline/plugins/sgegraph.py +++ b/nipype/pipeline/plugins/sgegraph.py @@ -147,6 +147,7 @@ def make_job_name(jobnumber, nodeslist): batchscript=batchscriptfile) fp.writelines(full_line) cmd = CommandLine('bash', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index 3f83772f6a..083f804a75 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -62,6 +62,7 @@ def _is_pending(self, taskid): # subprocess.Popen requires taskid to be a string res = CommandLine('squeue', args=' '.join(['-j', '%s' % taskid]), + resource_monitor=False, terminal_output='allatonce').run() return res.runtime.stdout.find(str(taskid)) > -1 @@ -72,6 +73,7 @@ def _submit_batchtask(self, scriptfile, node): formatting/processing """ cmd = CommandLine('sbatch', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py index 794a35bc84..ed571ecffe 100644 --- a/nipype/pipeline/plugins/slurmgraph.py +++ b/nipype/pipeline/plugins/slurmgraph.py @@ -146,6 +146,7 @@ def make_job_name(jobnumber, nodeslist): batchscript=batchscriptfile) fp.writelines(full_line) cmd = CommandLine('bash', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index ebf52d06d3..0d6bce7d45 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -254,6 +254,7 @@ def get_doc(cmd, opt_map, help_flag=None, trap_error=True): """ res = CommandLine('which %s' % cmd.split(' ')[0], + resource_monitor=False, terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': @@ -330,6 +331,7 @@ def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True): """ res = CommandLine('which %s' % cmd.split(' ')[0], + resource_monitor=False, terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 68b55d48c0..4ace5ef6d7 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-26 10:56:03 +# @Last Modified time: 2017-09-26 15:05:24 """ Utilities to keep track of performance """ @@ -40,33 +40,30 @@ def __init__(self, pid, freq=5, fname=None): fname = '.nipype.prof' self._pid = pid - self._log = open(fname, 'w') - self._log.write('%s,0.0,0\n' % time()) - self._log.flush() + self._fname = fname self._freq = freq + + self._log = open(self._fname, 'w') + print('%s,0.0,0' % time(), file=self._log) + self._log.flush() threading.Thread.__init__(self) self._event = threading.Event() def stop(self): if not self._event.is_set(): self._event.set() - self._log.close() self.join() + self._log.flush() + self._log.close() def run(self): while not self._event.is_set(): - try: - ram = _get_ram_mb(self._pid) - cpus = _get_num_threads(self._pid) - if all(ram is not None, cpus is not None): - self._log.write('%s,%f,%d\n' % (time(), ram, cpus)) - self._log.flush() - except ValueError as e: - if e.args == ('I/O operation on closed file.',): - pass - except Exception: - pass - + ram = _get_ram_mb(self._pid) + cpus = _get_num_threads(self._pid) + if ram is not None and cpus is not None: + print('%s,%f,%d' % (time(), ram, cpus), + file=self._log) + self._log.flush() self._event.wait(self._freq) diff --git a/nipype/utils/spm_docs.py b/nipype/utils/spm_docs.py index 1b7a1a1dc4..89869c1e87 100644 --- a/nipype/utils/spm_docs.py +++ b/nipype/utils/spm_docs.py @@ -27,7 +27,7 @@ def grab_doc(task_name): """ - cmd = matlab.MatlabCommandLine() + cmd = matlab.MatlabCommandLine(resource_monitor=False) # We need to tell Matlab where to find our spm_get_doc.m file. cwd = os.path.dirname(__file__) # Build matlab command From cf1f15bc26d30ef3714d38851086eecafc7566d6 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 17:55:55 -0700 Subject: [PATCH 25/40] add warning to old filemanip logger --- nipype/utils/logger.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index 73088a2fcf..59230210b3 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -6,6 +6,7 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: import logging +from warnings import warn import os import sys from .misc import str2bool @@ -15,7 +16,6 @@ RFHandler except ImportError: # Next 2 lines are optional: issue a warning to the user - from warnings import warn warn("ConcurrentLogHandler not installed. Using builtin log handler") from logging.handlers import RotatingFileHandler as RFHandler @@ -34,10 +34,12 @@ def __init__(self, config): # logging.basicConfig(stream=sys.stdout) self._logger = logging.getLogger('workflow') self._utlogger = logging.getLogger('utils') + self._fmlogger = logging.getLogger('filemanip') self._iflogger = logging.getLogger('interface') self.loggers = {'workflow': self._logger, 'utils': self._utlogger, + 'filemanip': self._fmlogger, 'interface': self._iflogger} self._hdlr = None self.update_logging(self._config) @@ -55,6 +57,7 @@ def enable_file_logging(self): self._logger.addHandler(hdlr) self._utlogger.addHandler(hdlr) self._iflogger.addHandler(hdlr) + self._fmlogger.addHandler(hdlr) self._hdlr = hdlr def disable_file_logging(self): @@ -62,6 +65,7 @@ def disable_file_logging(self): self._logger.removeHandler(self._hdlr) self._utlogger.removeHandler(self._hdlr) self._iflogger.removeHandler(self._hdlr) + self._fmlogger.removeHandler(self._hdlr) self._hdlr = None def update_logging(self, config): @@ -73,10 +77,15 @@ def update_logging(self, config): 'utils_level'))) self._iflogger.setLevel(logging.getLevelName(config.get('logging', 'interface_level'))) + self._fmlogger.setLevel(logging.getLevelName(config.get('logging', + 'filemanip_level'))) if str2bool(config.get('logging', 'log_to_file')): self.enable_file_logging() def getLogger(self, name): + if name == 'filemanip': + warn('The "filemanip" logger has been deprecated and replaced by ' + 'the "utils" logger as of nipype 1.13.2') if name in self.loggers: return self.loggers[name] return None From 4b7ab934ae00fa3b213f85a87c9dd6472099a29c Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 21:24:52 -0700 Subject: [PATCH 26/40] do not search for filemanip_level in config --- nipype/utils/logger.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index 59230210b3..f07d2f8cd0 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -77,8 +77,6 @@ def update_logging(self, config): 'utils_level'))) self._iflogger.setLevel(logging.getLevelName(config.get('logging', 'interface_level'))) - self._fmlogger.setLevel(logging.getLevelName(config.get('logging', - 'filemanip_level'))) if str2bool(config.get('logging', 'log_to_file')): self.enable_file_logging() From c7a1992a2943e65ba1d130d11b51d16c24312bee Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 21:25:15 -0700 Subject: [PATCH 27/40] fix CommandLine interface doctest --- nipype/interfaces/base.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index a200eb900f..8c61878f56 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1472,6 +1472,7 @@ class must be instantiated with a command argument {'args': '-al', 'environ': {'DISPLAY': ':1'}, 'ignore_exception': False, + 'resource_monitor': True, 'terminal_output': 'stream'} >>> cli.inputs.get_hashval()[0][0] # doctest: +ALLOW_UNICODE From 8d02397c34b2937d50c11ea1a1f65d003535a4b0 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 21:26:58 -0700 Subject: [PATCH 28/40] update specs --- nipype/algorithms/tests/test_auto_ACompCor.py | 3 ++ .../algorithms/tests/test_auto_AddCSVRow.py | 3 ++ .../tests/test_auto_ArtifactDetect.py | 3 ++ .../tests/test_auto_CalculateMedian.py | 3 ++ .../tests/test_auto_ComputeDVARS.py | 3 ++ .../tests/test_auto_ComputeMeshWarp.py | 3 ++ .../algorithms/tests/test_auto_CreateNifti.py | 3 ++ nipype/algorithms/tests/test_auto_Distance.py | 3 ++ .../tests/test_auto_FramewiseDisplacement.py | 3 ++ .../tests/test_auto_FuzzyOverlap.py | 3 ++ nipype/algorithms/tests/test_auto_Gunzip.py | 3 ++ nipype/algorithms/tests/test_auto_ICC.py | 3 ++ .../tests/test_auto_MeshWarpMaths.py | 3 ++ .../tests/test_auto_ModifyAffine.py | 3 ++ .../tests/test_auto_NonSteadyStateDetector.py | 3 ++ .../algorithms/tests/test_auto_P2PDistance.py | 3 ++ .../algorithms/tests/test_auto_PickAtlas.py | 3 ++ .../algorithms/tests/test_auto_Similarity.py | 3 ++ .../tests/test_auto_SimpleThreshold.py | 3 ++ .../tests/test_auto_SpecifyModel.py | 3 ++ .../tests/test_auto_SpecifySPMModel.py | 3 ++ .../tests/test_auto_SpecifySparseModel.py | 3 ++ .../tests/test_auto_StimulusCorrelation.py | 3 ++ nipype/algorithms/tests/test_auto_TCompCor.py | 3 ++ .../tests/test_auto_TVTKBaseInterface.py | 3 ++ .../algorithms/tests/test_auto_WarpPoints.py | 3 ++ .../afni/tests/test_auto_ABoverlap.py | 3 ++ .../afni/tests/test_auto_AFNICommand.py | 3 ++ .../afni/tests/test_auto_AFNICommandBase.py | 3 ++ .../afni/tests/test_auto_AFNIPythonCommand.py | 3 ++ .../afni/tests/test_auto_AFNItoNIFTI.py | 3 ++ .../afni/tests/test_auto_AlignEpiAnatPy.py | 3 ++ .../afni/tests/test_auto_Allineate.py | 3 ++ .../afni/tests/test_auto_AutoTLRC.py | 3 ++ .../afni/tests/test_auto_AutoTcorrelate.py | 3 ++ .../afni/tests/test_auto_Autobox.py | 3 ++ .../afni/tests/test_auto_Automask.py | 3 ++ .../afni/tests/test_auto_Axialize.py | 3 ++ .../afni/tests/test_auto_Bandpass.py | 3 ++ .../afni/tests/test_auto_BlurInMask.py | 3 ++ .../afni/tests/test_auto_BlurToFWHM.py | 3 ++ .../afni/tests/test_auto_BrickStat.py | 3 ++ .../interfaces/afni/tests/test_auto_Bucket.py | 3 ++ .../interfaces/afni/tests/test_auto_Calc.py | 3 ++ nipype/interfaces/afni/tests/test_auto_Cat.py | 3 ++ .../afni/tests/test_auto_CatMatvec.py | 3 ++ .../afni/tests/test_auto_ClipLevel.py | 3 ++ .../interfaces/afni/tests/test_auto_Copy.py | 3 ++ .../afni/tests/test_auto_Deconvolve.py | 3 ++ .../afni/tests/test_auto_DegreeCentrality.py | 3 ++ .../afni/tests/test_auto_Despike.py | 3 ++ .../afni/tests/test_auto_Detrend.py | 3 ++ nipype/interfaces/afni/tests/test_auto_Dot.py | 3 ++ nipype/interfaces/afni/tests/test_auto_ECM.py | 3 ++ .../interfaces/afni/tests/test_auto_Edge3.py | 3 ++ .../interfaces/afni/tests/test_auto_Eval.py | 3 ++ .../interfaces/afni/tests/test_auto_FWHMx.py | 3 ++ nipype/interfaces/afni/tests/test_auto_Fim.py | 3 ++ .../afni/tests/test_auto_Fourier.py | 3 ++ .../interfaces/afni/tests/test_auto_GCOR.py | 3 ++ .../interfaces/afni/tests/test_auto_Hist.py | 3 ++ .../interfaces/afni/tests/test_auto_LFCD.py | 3 ++ .../afni/tests/test_auto_MaskTool.py | 3 ++ .../afni/tests/test_auto_Maskave.py | 3 ++ .../interfaces/afni/tests/test_auto_Means.py | 3 ++ .../interfaces/afni/tests/test_auto_Merge.py | 3 ++ .../interfaces/afni/tests/test_auto_Notes.py | 3 ++ .../afni/tests/test_auto_NwarpApply.py | 3 ++ .../afni/tests/test_auto_OneDToolPy.py | 3 ++ .../afni/tests/test_auto_OutlierCount.py | 3 ++ .../afni/tests/test_auto_QualityIndex.py | 3 ++ .../interfaces/afni/tests/test_auto_Qwarp.py | 3 ++ .../afni/tests/test_auto_QwarpPlusMinus.py | 3 ++ .../afni/tests/test_auto_ROIStats.py | 3 ++ .../interfaces/afni/tests/test_auto_Refit.py | 3 ++ .../afni/tests/test_auto_Remlfit.py | 3 ++ .../afni/tests/test_auto_Resample.py | 3 ++ .../afni/tests/test_auto_Retroicor.py | 3 ++ .../afni/tests/test_auto_SVMTest.py | 3 ++ .../afni/tests/test_auto_SVMTrain.py | 3 ++ nipype/interfaces/afni/tests/test_auto_Seg.py | 3 ++ .../afni/tests/test_auto_SkullStrip.py | 3 ++ .../interfaces/afni/tests/test_auto_TCat.py | 3 ++ .../afni/tests/test_auto_TCorr1D.py | 3 ++ .../afni/tests/test_auto_TCorrMap.py | 3 ++ .../afni/tests/test_auto_TCorrelate.py | 3 ++ .../interfaces/afni/tests/test_auto_TNorm.py | 3 ++ .../interfaces/afni/tests/test_auto_TShift.py | 3 ++ .../interfaces/afni/tests/test_auto_TStat.py | 3 ++ .../interfaces/afni/tests/test_auto_To3D.py | 3 ++ .../interfaces/afni/tests/test_auto_Undump.py | 3 ++ .../afni/tests/test_auto_Unifize.py | 3 ++ .../interfaces/afni/tests/test_auto_Volreg.py | 3 ++ .../interfaces/afni/tests/test_auto_Warp.py | 3 ++ .../interfaces/afni/tests/test_auto_ZCutUp.py | 3 ++ .../interfaces/afni/tests/test_auto_Zcat.py | 3 ++ .../afni/tests/test_auto_Zeropad.py | 3 ++ .../interfaces/ants/tests/test_auto_ANTS.py | 3 ++ .../ants/tests/test_auto_ANTSCommand.py | 3 ++ .../ants/tests/test_auto_AffineInitializer.py | 3 ++ .../ants/tests/test_auto_AntsJointFusion.py | 3 ++ .../ants/tests/test_auto_ApplyTransforms.py | 3 ++ .../test_auto_ApplyTransformsToPoints.py | 3 ++ .../ants/tests/test_auto_Atropos.py | 3 ++ .../tests/test_auto_AverageAffineTransform.py | 3 ++ .../ants/tests/test_auto_AverageImages.py | 3 ++ .../ants/tests/test_auto_BrainExtraction.py | 3 ++ .../test_auto_ConvertScalarImageToRGB.py | 3 ++ .../ants/tests/test_auto_CorticalThickness.py | 3 ++ ...est_auto_CreateJacobianDeterminantImage.py | 3 ++ .../ants/tests/test_auto_CreateTiledMosaic.py | 3 ++ .../ants/tests/test_auto_DenoiseImage.py | 3 ++ .../ants/tests/test_auto_GenWarpFields.py | 3 ++ .../ants/tests/test_auto_JointFusion.py | 3 ++ .../ants/tests/test_auto_KellyKapowski.py | 3 ++ .../tests/test_auto_LaplacianThickness.py | 3 ++ .../tests/test_auto_MeasureImageSimilarity.py | 3 ++ .../ants/tests/test_auto_MultiplyImages.py | 3 ++ .../tests/test_auto_N4BiasFieldCorrection.py | 3 ++ .../ants/tests/test_auto_Registration.py | 3 ++ .../test_auto_WarpImageMultiTransform.py | 3 ++ ..._auto_WarpTimeSeriesImageMultiTransform.py | 3 ++ .../tests/test_auto_antsBrainExtraction.py | 3 ++ .../tests/test_auto_antsCorticalThickness.py | 3 ++ .../ants/tests/test_auto_antsIntroduction.py | 3 ++ .../tests/test_auto_buildtemplateparallel.py | 3 ++ .../brainsuite/tests/test_auto_BDP.py | 3 ++ .../brainsuite/tests/test_auto_Bfc.py | 3 ++ .../brainsuite/tests/test_auto_Bse.py | 3 ++ .../brainsuite/tests/test_auto_Cerebro.py | 3 ++ .../brainsuite/tests/test_auto_Cortex.py | 3 ++ .../brainsuite/tests/test_auto_Dewisp.py | 3 ++ .../brainsuite/tests/test_auto_Dfs.py | 3 ++ .../brainsuite/tests/test_auto_Hemisplit.py | 3 ++ .../brainsuite/tests/test_auto_Pialmesh.py | 3 ++ .../brainsuite/tests/test_auto_Pvc.py | 3 ++ .../brainsuite/tests/test_auto_SVReg.py | 3 ++ .../brainsuite/tests/test_auto_Scrubmask.py | 3 ++ .../brainsuite/tests/test_auto_Skullfinder.py | 3 ++ .../brainsuite/tests/test_auto_Tca.py | 3 ++ .../tests/test_auto_ThicknessPVC.py | 3 ++ .../camino/tests/test_auto_AnalyzeHeader.py | 3 ++ .../tests/test_auto_ComputeEigensystem.py | 3 ++ .../test_auto_ComputeFractionalAnisotropy.py | 3 ++ .../tests/test_auto_ComputeMeanDiffusivity.py | 3 ++ .../tests/test_auto_ComputeTensorTrace.py | 3 ++ .../camino/tests/test_auto_Conmat.py | 3 ++ .../camino/tests/test_auto_DT2NIfTI.py | 3 ++ .../camino/tests/test_auto_DTIFit.py | 3 ++ .../camino/tests/test_auto_DTLUTGen.py | 3 ++ .../camino/tests/test_auto_DTMetric.py | 3 ++ .../camino/tests/test_auto_FSL2Scheme.py | 3 ++ .../camino/tests/test_auto_Image2Voxel.py | 3 ++ .../camino/tests/test_auto_ImageStats.py | 3 ++ .../camino/tests/test_auto_LinRecon.py | 3 ++ .../interfaces/camino/tests/test_auto_MESD.py | 3 ++ .../camino/tests/test_auto_ModelFit.py | 3 ++ .../camino/tests/test_auto_NIfTIDT2Camino.py | 3 ++ .../camino/tests/test_auto_PicoPDFs.py | 3 ++ .../camino/tests/test_auto_ProcStreamlines.py | 3 ++ .../camino/tests/test_auto_QBallMX.py | 3 ++ .../camino/tests/test_auto_SFLUTGen.py | 3 ++ .../camino/tests/test_auto_SFPICOCalibData.py | 3 ++ .../camino/tests/test_auto_SFPeaks.py | 3 ++ .../camino/tests/test_auto_Shredder.py | 3 ++ .../camino/tests/test_auto_Track.py | 3 ++ .../camino/tests/test_auto_TrackBallStick.py | 3 ++ .../camino/tests/test_auto_TrackBayesDirac.py | 3 ++ .../tests/test_auto_TrackBedpostxDeter.py | 3 ++ .../tests/test_auto_TrackBedpostxProba.py | 3 ++ .../camino/tests/test_auto_TrackBootstrap.py | 3 ++ .../camino/tests/test_auto_TrackDT.py | 3 ++ .../camino/tests/test_auto_TrackPICo.py | 3 ++ .../camino/tests/test_auto_TractShredder.py | 3 ++ .../camino/tests/test_auto_VtkStreamlines.py | 3 ++ .../tests/test_auto_Camino2Trackvis.py | 3 ++ 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.../tests/test_auto_gtractConcatDwi.py | 3 ++ .../test_auto_gtractCopyImageOrientation.py | 3 ++ .../tests/test_auto_gtractCoregBvalues.py | 3 ++ .../tests/test_auto_gtractCostFastMarching.py | 3 ++ .../tests/test_auto_gtractCreateGuideFiber.py | 3 ++ .../test_auto_gtractFastMarchingTracking.py | 3 ++ .../tests/test_auto_gtractFiberTracking.py | 3 ++ .../tests/test_auto_gtractImageConformity.py | 3 ++ .../test_auto_gtractInvertBSplineTransform.py | 3 ++ ...test_auto_gtractInvertDisplacementField.py | 3 ++ .../test_auto_gtractInvertRigidTransform.py | 3 ++ .../test_auto_gtractResampleAnisotropy.py | 3 ++ .../tests/test_auto_gtractResampleB0.py | 3 ++ .../test_auto_gtractResampleCodeImage.py | 3 ++ .../test_auto_gtractResampleDWIInPlace.py | 3 ++ .../tests/test_auto_gtractResampleFibers.py | 3 ++ .../diffusion/tests/test_auto_gtractTensor.py | 3 ++ ...auto_gtractTransformToDisplacementField.py | 3 ++ .../diffusion/tests/test_auto_maxcurvature.py | 3 ++ .../tests/test_auto_UKFTractography.py | 3 ++ .../tests/test_auto_fiberprocess.py | 3 ++ .../tests/test_auto_fiberstats.py | 3 ++ .../tests/test_auto_fibertrack.py | 3 ++ .../filtering/tests/test_auto_CannyEdge.py | 3 ++ ...to_CannySegmentationLevelSetImageFilter.py | 3 ++ .../filtering/tests/test_auto_DilateImage.py | 3 ++ .../filtering/tests/test_auto_DilateMask.py | 3 ++ .../filtering/tests/test_auto_DistanceMaps.py | 3 ++ .../test_auto_DumpBinaryTrainingVectors.py | 3 ++ .../filtering/tests/test_auto_ErodeImage.py | 3 ++ .../tests/test_auto_FlippedDifference.py | 3 ++ .../test_auto_GenerateBrainClippedImage.py | 3 ++ .../test_auto_GenerateSummedGradientImage.py | 3 ++ .../tests/test_auto_GenerateTestImage.py | 3 ++ ...GradientAnisotropicDiffusionImageFilter.py | 3 ++ .../tests/test_auto_HammerAttributeCreator.py | 3 ++ .../tests/test_auto_NeighborhoodMean.py | 3 ++ .../tests/test_auto_NeighborhoodMedian.py | 3 ++ .../tests/test_auto_STAPLEAnalysis.py | 3 ++ .../test_auto_TextureFromNoiseImageFilter.py | 3 ++ .../tests/test_auto_TextureMeasureFilter.py | 3 ++ .../tests/test_auto_UnbiasedNonLocalMeans.py | 3 ++ .../legacy/tests/test_auto_scalartransform.py | 3 ++ .../tests/test_auto_BRAINSDemonWarp.py | 3 ++ .../registration/tests/test_auto_BRAINSFit.py | 3 ++ .../tests/test_auto_BRAINSResample.py | 3 ++ .../tests/test_auto_BRAINSResize.py | 3 ++ .../test_auto_BRAINSTransformFromFiducials.py | 3 ++ .../tests/test_auto_VBRAINSDemonWarp.py | 3 ++ .../segmentation/tests/test_auto_BRAINSABC.py | 3 ++ .../test_auto_BRAINSConstellationDetector.py | 3 ++ ...BRAINSCreateLabelMapFromProbabilityMaps.py | 3 ++ .../segmentation/tests/test_auto_BRAINSCut.py | 3 ++ .../tests/test_auto_BRAINSMultiSTAPLE.py | 3 ++ .../tests/test_auto_BRAINSROIAuto.py | 3 ++ ...t_auto_BinaryMaskEditorBasedOnLandmarks.py | 3 ++ .../segmentation/tests/test_auto_ESLR.py | 3 ++ .../semtools/tests/test_auto_DWICompare.py | 3 ++ .../tests/test_auto_DWISimpleCompare.py | 3 ++ ...o_GenerateCsfClippedFromClassifiedImage.py | 3 ++ .../tests/test_auto_BRAINSAlignMSP.py | 3 ++ .../tests/test_auto_BRAINSClipInferior.py | 3 ++ .../test_auto_BRAINSConstellationModeler.py | 3 ++ .../tests/test_auto_BRAINSEyeDetector.py | 3 ++ ...est_auto_BRAINSInitializedControlPoints.py | 3 ++ .../test_auto_BRAINSLandmarkInitializer.py | 3 ++ .../test_auto_BRAINSLinearModelerEPCA.py | 3 ++ .../tests/test_auto_BRAINSLmkTransform.py | 3 ++ .../utilities/tests/test_auto_BRAINSMush.py | 3 ++ .../tests/test_auto_BRAINSSnapShotWriter.py | 3 ++ .../tests/test_auto_BRAINSTransformConvert.py | 3 ++ ...st_auto_BRAINSTrimForegroundInDirection.py | 3 ++ .../tests/test_auto_CleanUpOverlapLabels.py | 3 ++ .../tests/test_auto_FindCenterOfBrain.py | 3 ++ ...auto_GenerateLabelMapFromProbabilityMap.py | 3 ++ .../tests/test_auto_ImageRegionPlotter.py | 3 ++ .../tests/test_auto_JointHistogram.py | 3 ++ .../tests/test_auto_ShuffleVectorsModule.py | 3 ++ .../utilities/tests/test_auto_fcsv_to_hdf5.py | 3 ++ .../tests/test_auto_insertMidACPCpoint.py | 3 ++ ...test_auto_landmarksConstellationAligner.py | 3 ++ ...test_auto_landmarksConstellationWeights.py | 3 ++ .../diffusion/tests/test_auto_DTIexport.py | 3 ++ .../diffusion/tests/test_auto_DTIimport.py | 3 ++ .../test_auto_DWIJointRicianLMMSEFilter.py | 3 ++ .../tests/test_auto_DWIRicianLMMSEFilter.py | 3 ++ .../tests/test_auto_DWIToDTIEstimation.py | 3 ++ ..._auto_DiffusionTensorScalarMeasurements.py | 3 ++ ...est_auto_DiffusionWeightedVolumeMasking.py | 3 ++ .../tests/test_auto_ResampleDTIVolume.py | 3 ++ .../test_auto_TractographyLabelMapSeeding.py | 3 ++ .../tests/test_auto_AddScalarVolumes.py | 3 ++ .../tests/test_auto_CastScalarVolume.py | 3 ++ .../tests/test_auto_CheckerBoardFilter.py | 3 ++ ...test_auto_CurvatureAnisotropicDiffusion.py | 3 ++ .../tests/test_auto_ExtractSkeleton.py | 3 ++ .../test_auto_GaussianBlurImageFilter.py | 3 ++ .../test_auto_GradientAnisotropicDiffusion.py | 3 ++ .../test_auto_GrayscaleFillHoleImageFilter.py | 3 ++ ...test_auto_GrayscaleGrindPeakImageFilter.py | 3 ++ .../tests/test_auto_HistogramMatching.py | 3 ++ .../tests/test_auto_ImageLabelCombine.py | 3 ++ .../tests/test_auto_MaskScalarVolume.py | 3 ++ .../tests/test_auto_MedianImageFilter.py | 3 ++ .../tests/test_auto_MultiplyScalarVolumes.py | 3 ++ .../test_auto_N4ITKBiasFieldCorrection.py | 3 ++ ...test_auto_ResampleScalarVectorDWIVolume.py | 3 ++ .../tests/test_auto_SubtractScalarVolumes.py | 3 ++ .../tests/test_auto_ThresholdScalarVolume.py | 3 ++ ...auto_VotingBinaryHoleFillingImageFilter.py | 3 ++ ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 3 ++ .../tests/test_auto_AffineRegistration.py | 3 ++ ...test_auto_BSplineDeformableRegistration.py | 3 ++ .../test_auto_BSplineToDeformationField.py | 3 ++ .../test_auto_ExpertAutomatedRegistration.py | 3 ++ .../tests/test_auto_LinearRegistration.py | 3 ++ ..._auto_MultiResolutionAffineRegistration.py | 3 ++ .../test_auto_OtsuThresholdImageFilter.py | 3 ++ .../test_auto_OtsuThresholdSegmentation.py | 3 ++ .../tests/test_auto_ResampleScalarVolume.py | 3 ++ .../tests/test_auto_RigidRegistration.py | 3 ++ .../test_auto_IntensityDifferenceMetric.py | 3 ++ ..._auto_PETStandardUptakeValueComputation.py | 3 ++ .../tests/test_auto_ACPCTransform.py | 3 ++ .../tests/test_auto_BRAINSDemonWarp.py | 3 ++ .../registration/tests/test_auto_BRAINSFit.py | 3 ++ .../tests/test_auto_BRAINSResample.py | 3 ++ .../tests/test_auto_FiducialRegistration.py | 3 ++ .../tests/test_auto_VBRAINSDemonWarp.py | 3 ++ .../tests/test_auto_BRAINSROIAuto.py | 3 ++ .../tests/test_auto_EMSegmentCommandLine.py | 3 ++ .../test_auto_RobustStatisticsSegmenter.py | 3 ++ ...st_auto_SimpleRegionGrowingSegmentation.py | 3 ++ .../tests/test_auto_DicomToNrrdConverter.py | 3 ++ ...test_auto_EMSegmentTransformToNewFormat.py | 3 ++ .../tests/test_auto_GrayscaleModelMaker.py | 3 ++ .../tests/test_auto_LabelMapSmoothing.py | 3 ++ .../slicer/tests/test_auto_MergeModels.py | 3 ++ .../slicer/tests/test_auto_ModelMaker.py | 3 ++ .../slicer/tests/test_auto_ModelToLabelMap.py | 3 ++ .../tests/test_auto_OrientScalarVolume.py | 3 ++ .../tests/test_auto_ProbeVolumeWithModel.py | 3 ++ .../tests/test_auto_SlicerCommandLine.py | 3 ++ .../spm/tests/test_auto_Analyze2nii.py | 6 ++++ .../spm/tests/test_auto_ApplyDeformations.py | 3 ++ .../test_auto_ApplyInverseDeformation.py | 3 ++ .../spm/tests/test_auto_ApplyTransform.py | 3 ++ .../spm/tests/test_auto_CalcCoregAffine.py | 3 ++ .../spm/tests/test_auto_Coregister.py | 3 ++ .../spm/tests/test_auto_CreateWarped.py | 3 ++ .../interfaces/spm/tests/test_auto_DARTEL.py | 3 ++ .../spm/tests/test_auto_DARTELNorm2MNI.py | 3 ++ .../spm/tests/test_auto_DicomImport.py | 3 ++ .../spm/tests/test_auto_EstimateContrast.py | 3 ++ .../spm/tests/test_auto_EstimateModel.py | 3 ++ .../spm/tests/test_auto_FactorialDesign.py | 3 ++ .../spm/tests/test_auto_Level1Design.py | 3 ++ .../test_auto_MultipleRegressionDesign.py | 3 ++ .../spm/tests/test_auto_NewSegment.py | 3 ++ .../spm/tests/test_auto_Normalize.py | 3 ++ .../spm/tests/test_auto_Normalize12.py | 3 ++ .../tests/test_auto_OneSampleTTestDesign.py | 3 ++ .../spm/tests/test_auto_PairedTTestDesign.py | 3 ++ .../interfaces/spm/tests/test_auto_Realign.py | 3 ++ .../interfaces/spm/tests/test_auto_Reslice.py | 3 ++ .../spm/tests/test_auto_ResliceToReference.py | 3 ++ .../spm/tests/test_auto_SPMCommand.py | 3 ++ .../interfaces/spm/tests/test_auto_Segment.py | 3 ++ .../spm/tests/test_auto_SliceTiming.py | 3 ++ .../interfaces/spm/tests/test_auto_Smooth.py | 3 ++ .../spm/tests/test_auto_Threshold.py | 3 ++ .../tests/test_auto_ThresholdStatistics.py | 3 ++ .../tests/test_auto_TwoSampleTTestDesign.py | 3 ++ .../spm/tests/test_auto_VBMSegment.py | 3 ++ .../tests/test_auto_BIDSDataGrabber.py | 28 +++++++++++++++++++ .../tests/test_auto_BaseInterface.py | 3 ++ nipype/interfaces/tests/test_auto_Bru2.py | 3 ++ .../tests/test_auto_C3dAffineTool.py | 3 ++ .../interfaces/tests/test_auto_CommandLine.py | 3 ++ .../interfaces/tests/test_auto_DataFinder.py | 3 ++ .../interfaces/tests/test_auto_DataGrabber.py | 3 ++ nipype/interfaces/tests/test_auto_DataSink.py | 3 ++ nipype/interfaces/tests/test_auto_Dcm2nii.py | 3 ++ nipype/interfaces/tests/test_auto_Dcm2niix.py | 3 ++ .../tests/test_auto_FreeSurferSource.py | 3 ++ nipype/interfaces/tests/test_auto_IOBase.py | 3 ++ .../tests/test_auto_JSONFileGrabber.py | 3 ++ .../tests/test_auto_JSONFileSink.py | 3 ++ .../tests/test_auto_MatlabCommand.py | 3 ++ nipype/interfaces/tests/test_auto_MeshFix.py | 3 ++ .../tests/test_auto_MpiCommandLine.py | 3 ++ .../interfaces/tests/test_auto_MySQLSink.py | 3 ++ .../tests/test_auto_NiftiGeneratorBase.py | 3 ++ nipype/interfaces/tests/test_auto_PETPVC.py | 3 ++ .../interfaces/tests/test_auto_Quickshear.py | 3 ++ .../tests/test_auto_S3DataGrabber.py | 3 ++ .../tests/test_auto_SEMLikeCommandLine.py | 3 ++ .../interfaces/tests/test_auto_SQLiteSink.py | 3 ++ .../tests/test_auto_SSHDataGrabber.py | 3 ++ .../interfaces/tests/test_auto_SelectFiles.py | 3 ++ .../tests/test_auto_SignalExtraction.py | 3 ++ .../tests/test_auto_SlicerCommandLine.py | 3 ++ .../tests/test_auto_StdOutCommandLine.py | 3 ++ nipype/interfaces/tests/test_auto_XNATSink.py | 3 ++ .../interfaces/tests/test_auto_XNATSource.py | 3 ++ .../utility/tests/test_auto_AssertEqual.py | 3 ++ .../utility/tests/test_auto_Function.py | 3 ++ .../utility/tests/test_auto_Merge.py | 3 ++ .../utility/tests/test_auto_Select.py | 3 ++ .../utility/tests/test_auto_Split.py | 3 ++ .../vista/tests/test_auto_Vnifti2Image.py | 3 ++ .../vista/tests/test_auto_VtoMat.py | 3 ++ 748 files changed, 2272 insertions(+) create mode 100644 nipype/interfaces/tests/test_auto_BIDSDataGrabber.py diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index 5c44844cf9..0e04841ad7 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -30,6 +30,9 @@ def test_ACompCor_inputs(): regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_pre_filter=dict(), use_regress_poly=dict(deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index f38319040b..e9ed0f5ba8 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -11,6 +11,9 @@ def test_AddCSVRow_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = AddCSVRow.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 054bc1da99..6468176307 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -27,6 +27,9 @@ def test_ArtifactDetect_inputs(): ), realignment_parameters=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_threshold=dict(mandatory=True, xor=['norm_threshold'], ), diff --git a/nipype/algorithms/tests/test_auto_CalculateMedian.py b/nipype/algorithms/tests/test_auto_CalculateMedian.py index 88888d5bbe..21ed0d19ae 100644 --- a/nipype/algorithms/tests/test_auto_CalculateMedian.py +++ b/nipype/algorithms/tests/test_auto_CalculateMedian.py @@ -11,6 +11,9 @@ def test_CalculateMedian_inputs(): median_file=dict(), median_per_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CalculateMedian.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index 7c59f851d1..729f9a1f40 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -21,6 +21,9 @@ def test_ComputeDVARS_inputs(): ), remove_zerovariance=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_all=dict(usedefault=True, ), save_nstd=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 61f64de033..5e30acf0ad 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -13,6 +13,9 @@ def test_ComputeMeshWarp_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface1=dict(mandatory=True, ), surface2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index 3e365b8894..e8a7139526 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -12,6 +12,9 @@ def test_CreateNifti_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CreateNifti.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 5cf8c425c8..3f9398a777 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -10,6 +10,9 @@ def test_Distance_inputs(): mask_volume=dict(), method=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index e230992eec..b4f8f0ddeb 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -23,6 +23,9 @@ def test_FramewiseDisplacement_inputs(): ), radius=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_plot=dict(usedefault=True, ), series_tr=dict(), diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index 764d821bc6..dd57ef5c4f 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -13,6 +13,9 @@ def test_FuzzyOverlap_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), weighting=dict(usedefault=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index 6b06654f1d..9d84480279 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -9,6 +9,9 @@ def test_Gunzip_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Gunzip.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index da3110fd76..4e629376b3 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -9,6 +9,9 @@ def test_ICC_inputs(): ), mask=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_sessions=dict(mandatory=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index 3c6077922b..65ae52f5f9 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -18,6 +18,9 @@ def test_MeshWarpMaths_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MeshWarpMaths.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index c7b4b25d0c..fa0daec97c 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -7,6 +7,9 @@ def test_ModifyAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), transformation_matrix=dict(usedefault=True, ), volumes=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 7b12363ee8..1380ea134e 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -9,6 +9,9 @@ def test_NonSteadyStateDetector_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = NonSteadyStateDetector.input_spec() diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 59c749da30..bf0c3cb1b8 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -13,6 +13,9 @@ def test_P2PDistance_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface1=dict(mandatory=True, ), surface2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 990b71e289..e8c7a77258 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -16,6 +16,9 @@ def test_PickAtlas_inputs(): labels=dict(mandatory=True, ), output_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = PickAtlas.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index 4dce363864..61184a3330 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -11,6 +11,9 @@ def test_Similarity_inputs(): mask2=dict(), metric=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index 0031f4bb7f..746759cef8 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -7,6 +7,9 @@ def test_SimpleThreshold_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), threshold=dict(mandatory=True, ), volumes=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index 33d5435b5f..512b3cbb65 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -23,6 +23,9 @@ def test_SpecifyModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_info=dict(mandatory=True, xor=['subject_info', 'event_files'], ), diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index 7a33ac63c4..3337a9ee49 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -27,6 +27,9 @@ def test_SpecifySPMModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_info=dict(mandatory=True, xor=['subject_info', 'event_files'], ), diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index 4caf1c1033..43508b7ff3 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -24,6 +24,9 @@ def test_SpecifySparseModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_plot=dict(), scale_regressors=dict(usedefault=True, ), diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 95581bb111..d988df85af 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -13,6 +13,9 @@ def test_StimulusCorrelation_inputs(): ), realignment_parameters=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(mandatory=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index b39c946d9d..4eb731b766 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -32,6 +32,9 @@ def test_TCompCor_inputs(): regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_pre_filter=dict(), use_regress_poly=dict(deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py index d6e38722fe..36548065de 100644 --- a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py +++ b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py @@ -7,6 +7,9 @@ def test_TVTKBaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TVTKBaseInterface.input_spec() diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index ab59d22cff..fd65a3c7b8 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -17,6 +17,9 @@ def test_WarpPoints_inputs(): ), points=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), warp=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 93219fe3dc..72a0d77eea 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -30,6 +30,9 @@ def test_ABoverlap_inputs(): outputtype=dict(), quiet=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index aef42ee585..1e22ac7cbf 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -17,6 +17,9 @@ def test_AFNICommand_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py index 37efbcee2d..5a8376af07 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py @@ -12,6 +12,9 @@ def test_AFNICommandBase_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py index e8efb62f5d..337ef9de50 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py @@ -17,6 +17,9 @@ def test_AFNIPythonCommand_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 5fe66e9df7..587eeb4b8c 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -33,6 +33,9 @@ def test_AFNItoNIFTI_inputs(): outputtype=dict(), pure=dict(argstr='-pure', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index 8193270c5d..0a0f080922 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -32,6 +32,9 @@ def test_AlignEpiAnatPy_inputs(): outputtype=dict(), py27_path=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_skullstrip=dict(argstr='-save_skullstrip', ), suffix=dict(argstr='-suffix %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index d1a8ae2187..c8df1643ae 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -97,6 +97,9 @@ def test_Allineate_inputs(): ), replacemeth=dict(argstr='-replacemeth %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_automask=dict(argstr='-source_automask+%d', ), source_mask=dict(argstr='-source_mask %s', diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index 3c95374697..18e87a49a7 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -22,6 +22,9 @@ def test_AutoTLRC_inputs(): no_ss=dict(argstr='-no_ss', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index f7a3d89278..f77cfe17cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -34,6 +34,9 @@ def test_AutoTcorrelate_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 91479c241d..c5a0a88577 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -25,6 +25,9 @@ def test_Autobox_inputs(): outputtype=dict(), padding=dict(argstr='-npad %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index f0a76037c2..3e1571624b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -32,6 +32,9 @@ def test_Automask_inputs(): name_template='%s_mask', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 6d04decdaa..f70c3771a3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -30,6 +30,9 @@ def test_Axialize_inputs(): name_template='%s_axialize', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal=dict(argstr='-sagittal', xor=['coronal', 'axial'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index 5310eaa256..c8ee04bde6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -55,6 +55,9 @@ def test_Bandpass_inputs(): position=1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tr=dict(argstr='-dt %f', diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index eb4a571079..7224a8fb66 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -39,6 +39,9 @@ def test_BlurInMask_inputs(): outputtype=dict(), preserve=dict(argstr='-preserve', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index bf4d2a194c..ef54b9b30a 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -30,6 +30,9 @@ def test_BlurToFWHM_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index f15a8d972d..937d5c4e4f 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -28,6 +28,9 @@ def test_BrickStat_inputs(): ), percentile=dict(argstr='-percentile %.3f %.3f %.3f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slow=dict(argstr='-slow', ), sum=dict(argstr='-sum', diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index 1cf812fd73..f50c3e742b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -20,6 +20,9 @@ def test_Bucket_inputs(): name_template='buck', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index aa9d1222b7..d6f9488624 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -35,6 +35,9 @@ def test_Calc_inputs(): outputtype=dict(), overwrite=dict(argstr='-overwrite', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_idx=dict(), start_idx=dict(requires=['stop_idx'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index c35c3e86b9..a4ebbd3620 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -42,6 +42,9 @@ def test_Cat_inputs(): xor=['out_format', 'out_int', 'out_double', 'out_fint', 'out_cint'], ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sel=dict(argstr='-sel %s', ), stack=dict(argstr='-stack', diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index d3d94569be..9ddfd91b85 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -35,6 +35,9 @@ def test_CatMatvec_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 8bd4cd346a..8a11bce555 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -27,6 +27,9 @@ def test_ClipLevel_inputs(): mfrac=dict(argstr='-mfrac %s', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 80338ccc57..05e56803a0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -23,6 +23,9 @@ def test_Copy_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index 0dfbec8deb..10073109a2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -81,6 +81,9 @@ def test_Deconvolve_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rmsmin=dict(argstr='-rmsmin %f', ), rout=dict(argstr='-rout', diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index cd4146a7b9..c60bfcf508 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -32,6 +32,9 @@ def test_DegreeCentrality_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sparsity=dict(argstr='-sparsity %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index aedb50b684..972942cabd 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -22,6 +22,9 @@ def test_Despike_inputs(): name_template='%s_despike', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 3fb771cbfc..77474e4fe2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -22,6 +22,9 @@ def test_Detrend_inputs(): name_template='%s_detrend', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index 21cebb28fe..08ee9592d7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -39,6 +39,9 @@ def test_Dot_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_labels=dict(argstr='-show_labels', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 39bdefe0ba..64ce4c45e7 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -40,6 +40,9 @@ def test_ECM_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-scale %f', ), shift=dict(argstr='-shift %f', diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 51a4dc865d..cd7a1d47c6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -32,6 +32,9 @@ def test_Edge3_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale_floats=dict(argstr='-scale_floats %f', xor=['fscale', 'gscale', 'nscale'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 490b09e486..2e10a1702e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -35,6 +35,9 @@ def test_Eval_inputs(): name_template='%s_calc', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_idx=dict(), start_idx=dict(requires=['stop_idx'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 527c7fdb22..10084c1736 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -56,6 +56,9 @@ def test_FWHMx_inputs(): name_source='in_file', name_template='%s_subbricks.out', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), unif=dict(argstr='-unif', diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index e80adb6801..7080d0b483 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -32,6 +32,9 @@ def test_Fim_inputs(): name_template='%s_fim', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 0573252de4..fd22a63b59 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -28,6 +28,9 @@ def test_Fourier_inputs(): name_template='%s_fourier', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), retrend=dict(argstr='-retrend', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 5cc9bf390c..bbf7eecd8e 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -24,6 +24,9 @@ def test_GCOR_inputs(): ), no_demean=dict(argstr='-no_demean', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index 91f4238834..cf300d45ad 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -38,6 +38,9 @@ def test_Hist_inputs(): name_template='%s_hist.out', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), showhist=dict(argstr='-showhist', usedefault=True, ), diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index c3690b8fd5..195269bfd8 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -30,6 +30,9 @@ def test_LFCD_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='-thresh %f', diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 0121d68d7d..b4234c0536 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -40,6 +40,9 @@ def test_MaskTool_inputs(): name_template='%s_mask', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), union=dict(argstr='-union', diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 9c58ea432b..b6844372b0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -30,6 +30,9 @@ def test_Maskave_inputs(): quiet=dict(argstr='-quiet', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 03bab07dcc..524ae33d0a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -34,6 +34,9 @@ def test_Means_inputs(): name_template='%s_mean', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-%sscale', ), sqr=dict(argstr='-sqr', diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index f943128da9..2a2a6cd82e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -27,6 +27,9 @@ def test_Merge_inputs(): name_template='%s_merge', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index ca08111696..ae7e3876d8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -30,6 +30,9 @@ def test_Notes_inputs(): rep_history=dict(argstr='-HH "%s"', xor=['add_history'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ses=dict(argstr='-ses', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index 273d0fed47..8b79cfadf7 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -30,6 +30,9 @@ def test_NwarpApply_inputs(): quiet=dict(argstr='-quiet', xor=['verb'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), short=dict(argstr='-short', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index fd6aed4b12..85f2875473 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -29,6 +29,9 @@ def test_OneDToolPy_inputs(): outputtype=dict(), py27_path=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), set_nruns=dict(argstr='-set_nruns %d', ), show_censor_count=dict(argstr='-show_censor_count', diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index 23f768f3dd..3d842f7ab6 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -52,6 +52,9 @@ def test_OutlierCount_inputs(): ), qthr=dict(argstr='-qthr %.5f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_outliers=dict(usedefault=True, ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index 2659fc8d91..a55370728e 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -41,6 +41,9 @@ def test_QualityIndex_inputs(): quadrant=dict(argstr='-quadrant', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spearman=dict(argstr='-spearman', usedefault=True, ), diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index 2848fe97f8..d973f4b18f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -122,6 +122,9 @@ def test_Qwarp_inputs(): ), resample=dict(argstr='-resample', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index 04f12426de..5b8a5008db 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -26,6 +26,9 @@ def test_QwarpPlusMinus_inputs(): ), pblur=dict(argstr='-pblur %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='-source %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 1e5de5806f..32f780c2a6 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -25,6 +25,9 @@ def test_ROIStats_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(mandatory=True, nohash=True, usedefault=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index b6c167198c..522b521979 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -31,6 +31,9 @@ def test_Refit_inputs(): ), nosaveatr=dict(argstr='-nosaveatr', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveatr=dict(argstr='-saveatr', ), space=dict(argstr='-space %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index a061a01449..36fbf91ca3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -79,6 +79,9 @@ def test_Remlfit_inputs(): ), rbeta_file=dict(argstr='-Rbeta %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rout=dict(argstr='-rout', ), slibase=dict(argstr='-slibase %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 4fabc2749c..c769ddee4b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -28,6 +28,9 @@ def test_Resample_inputs(): outputtype=dict(), resample_mode=dict(argstr='-rmode %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_size=dict(argstr='-dxyz %f %f %f', diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 6822425f00..49214e8de8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -33,6 +33,9 @@ def test_Retroicor_inputs(): position=1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resp=dict(argstr='-resp %s', position=-3, ), diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 496f947a28..5a907560fe 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -32,6 +32,9 @@ def test_SVMTest_inputs(): name_template='%s_predictions', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), testlabels=dict(argstr='-testlabels %s', diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index 25973372e6..517aafcd46 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -46,6 +46,9 @@ def test_SVMTrain_inputs(): suffix='_bucket', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trainlabels=dict(argstr='-trainlabels %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index e8114e5838..9dcf8a0217 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -39,6 +39,9 @@ def test_Seg_inputs(): ), prefix=dict(argstr='-prefix %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 37b24cfb76..3265f955dd 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -22,6 +22,9 @@ def test_SkullStrip_inputs(): name_template='%s_skullstrip', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 9c72dcd545..aa7619909e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -22,6 +22,9 @@ def test_TCat_inputs(): name_template='%s_tcat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlt=dict(argstr='-rlt%s', position=1, ), diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index e42ac2b7d5..19cd65e053 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -30,6 +30,9 @@ def test_TCorr1D_inputs(): position=1, xor=['pearson', 'spearman', 'ktaub'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spearman=dict(argstr=' -spearman', position=1, xor=['pearson', 'quadrant', 'ktaub'], diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 8c80f15080..75c00044aa 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -72,6 +72,9 @@ def test_TCorrMap_inputs(): ), regress_out_timeseries=dict(argstr='-ort %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seeds=dict(argstr='-seed %s', xor='seeds_width', ), diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index e2e100cdb7..e16a089fd2 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -21,6 +21,9 @@ def test_TCorrelate_inputs(): ), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xset=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index 3b9fac4b98..55a16754f3 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -34,6 +34,9 @@ def test_TNorm_inputs(): outputtype=dict(), polort=dict(argstr='-polort %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index e167205995..63976b11cd 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -26,6 +26,9 @@ def test_TShift_inputs(): name_template='%s_tshift', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlt=dict(argstr='-rlt', ), rltplus=dict(argstr='-rlt+', diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index f09fb5b4af..5945a0858c 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -26,6 +26,9 @@ def test_TStat_inputs(): name_template='%s_tstat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 0df075d87f..3ea2e120e4 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -29,6 +29,9 @@ def test_To3D_inputs(): name_template='%s', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skipoutliers=dict(argstr='-skip_outliers', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index 808de86daf..3b30bd9111 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -33,6 +33,9 @@ def test_Undump_inputs(): name_source='in_file', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), srad=dict(argstr='-srad -%f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index 2c37e13fb1..10ed9ff677 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -29,6 +29,9 @@ def test_Unifize_inputs(): name_source='in_file', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale_file=dict(argstr='-ssave %s', ), t2=dict(argstr='-T2', diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 314ac04743..9085e9f8ee 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -45,6 +45,9 @@ def test_Volreg_inputs(): name_template='%s_volreg', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeshift=dict(argstr='-tshift 0', diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index e370d32058..88cf4bd503 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -34,6 +34,9 @@ def test_Warp_inputs(): name_template='%s_warp', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tta2mni=dict(argstr='-tta2mni', diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 8019b1dcf8..27c7b86bab 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -24,6 +24,9 @@ def test_ZCutUp_inputs(): name_template='%s_zcutup', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 48f742df5e..c99ec2b141 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -29,6 +29,9 @@ def test_Zcat_inputs(): name_template='zcat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index 551498e1ab..dc33e3a80c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -54,6 +54,9 @@ def test_Zeropad_inputs(): name_template='zeropad', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), z=dict(argstr='-z %i', diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index e7fbe117ae..907a93d0e5 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -57,6 +57,9 @@ def test_ANTS_inputs(): ), regularization_gradient_field_sigma=dict(requires=['regularization'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smoothing_sigmas=dict(argstr='--gaussian-smoothing-sigmas %s', sep='x', ), diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 4f6920645b..ecc4288a14 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -15,6 +15,9 @@ def test_ANTSCommand_inputs(): num_threads=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index 319798e13f..00533675ad 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -43,6 +43,9 @@ def test_AffineInitializer_inputs(): position=5, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_factor=dict(argstr='%f', position=4, usedefault=True, diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index dcd115429f..6ad79d70b5 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -55,6 +55,9 @@ def test_AntsJointFusion_inputs(): maxlen=3, minlen=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), retain_atlas_voting_images=dict(argstr='-f', usedefault=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index 4b27963757..42cdf28e9e 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -43,6 +43,9 @@ def test_ApplyTransforms_inputs(): reference_image=dict(argstr='--reference-image %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 5a20ac0f43..d727b9eb46 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -26,6 +26,9 @@ def test_ApplyTransformsToPoints_inputs(): name_source=['input_file'], name_template='%s_transformed.csv', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 50fd85477d..41e58651d4 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -56,6 +56,9 @@ def test_Atropos_inputs(): prior_probability_threshold=dict(requires=['prior_weighting'], ), prior_weighting=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_posteriors=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 25a7f0b892..e087800c50 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -24,6 +24,9 @@ def test_AverageAffineTransform_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 47accd6758..8bb58062d1 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -32,6 +32,9 @@ def test_AverageImages_inputs(): position=1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index 86f652cbbe..d34a899530 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -40,6 +40,9 @@ def test_BrainExtraction_inputs(): out_prefix=dict(argstr='-o %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_floatingpoint_precision=dict(argstr='-q %d', diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 42d049990b..17a8d35ab9 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -57,6 +57,9 @@ def test_ConvertScalarImageToRGB_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index 5fe224b494..44a1452a1f 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -53,6 +53,9 @@ def test_CorticalThickness_inputs(): ), quick_registration=dict(argstr='-q 1', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_iterations=dict(argstr='-n %d', ), segmentation_priors=dict(argstr='-p %s', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index f7aafb27be..398be1d292 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -31,6 +31,9 @@ def test_CreateJacobianDeterminantImage_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), useGeometric=dict(argstr='%d', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 09340f631f..bc2eee5ca0 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -33,6 +33,9 @@ def test_CreateTiledMosaic_inputs(): ), permute_axes=dict(argstr='-g', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgb_image=dict(argstr='-r %s', mandatory=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 6c28016de6..9786afbc08 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -35,6 +35,9 @@ def test_DenoiseImage_inputs(): name_source=['input_image'], name_template='%s_noise_corrected', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_noise=dict(mandatory=True, usedefault=True, xor=['noise_image'], diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index f5d79bd851..fc10358d49 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -41,6 +41,9 @@ def test_GenWarpFields_inputs(): copyfile=True, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), similarity_metric=dict(argstr='-s %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index cddfb487be..c0c330e161 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -49,6 +49,9 @@ def test_JointFusion_inputs(): maxlen=3, minlen=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_radius=dict(argstr='-rs %s', maxlen=3, minlen=3, diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 046d31d158..46089b0584 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -38,6 +38,9 @@ def test_KellyKapowski_inputs(): ), number_integration_points=dict(argstr='--number-of-integration-points %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_image=dict(argstr='--segmentation-image "%s"', mandatory=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 71b0483f92..5120e689a0 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -39,6 +39,9 @@ def test_LaplacianThickness_inputs(): prior_thickness=dict(argstr='priorthickval=%d', position=5, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_param=dict(argstr='smoothparam=%d', position=4, ), diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 3dba65d8bb..6eede97bcc 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -35,6 +35,9 @@ def test_MeasureImageSimilarity_inputs(): radius_or_number_of_bins=dict(mandatory=True, requires=['metric'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_percentage=dict(mandatory=True, requires=['metric'], ), diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 2175db201d..11b9b56616 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -28,6 +28,9 @@ def test_MultiplyImages_inputs(): mandatory=True, position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), second_input=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index b863f888d9..b2b85441d8 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -40,6 +40,9 @@ def test_N4BiasFieldCorrection_inputs(): genfile=True, hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_bias=dict(mandatory=True, usedefault=True, xor=['bias_image'], diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index d437e437f3..7a70014b85 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -87,6 +87,9 @@ def test_Registration_inputs(): radius_or_number_of_bins=dict(requires=['metric_weight'], usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), restore_state=dict(argstr='--restore-state %s', ), restrict_deformation=dict(), diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index e016aac163..60a78ed4db 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -39,6 +39,9 @@ def test_WarpImageMultiTransform_inputs(): ), reslice_by_header=dict(argstr='--reslice-by-header', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tightest_box=dict(argstr='--tightest-bounding-box', diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 79fbf89302..0e956145aa 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -32,6 +32,9 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ), reslice_by_header=dict(argstr='--reslice-by-header', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tightest_box=dict(argstr='--tightest-bounding-box', diff --git a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py index 230176c856..1c6d3304d3 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py @@ -40,6 +40,9 @@ def test_antsBrainExtraction_inputs(): out_prefix=dict(argstr='-o %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_floatingpoint_precision=dict(argstr='-q %d', diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index 02f2d46c59..80be6a63a0 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -53,6 +53,9 @@ def test_antsCorticalThickness_inputs(): ), quick_registration=dict(argstr='-q 1', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_iterations=dict(argstr='-n %d', ), segmentation_priors=dict(argstr='-p %s', diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index 0a9646ae2c..7334aeda39 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -41,6 +41,9 @@ def test_antsIntroduction_inputs(): copyfile=True, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), similarity_metric=dict(argstr='-s %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 9232bb32b1..f4854948a3 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -42,6 +42,9 @@ def test_buildtemplateparallel_inputs(): parallelization=dict(argstr='-c %d', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid_body_registration=dict(argstr='-r 1', ), similarity_metric=dict(argstr='-s %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index a2cbc2a440..875ed96064 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -94,6 +94,9 @@ def test_BDP_inputs(): ), phaseEncodingDirection=dict(argstr='--dir=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigidRegMeasure=dict(argstr='--rigid-reg-measure %s', ), skipDistortionCorr=dict(argstr='--no-distortion-correction', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index f24900c6a4..8644ea5785 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -60,6 +60,9 @@ def test_Bfc_inputs(): outputMaskedBiasField=dict(argstr='--maskedbias %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splineLambda=dict(argstr='-w %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index a253bdcafc..129a07ee06 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -52,6 +52,9 @@ def test_Bse_inputs(): radius=dict(argstr='-r %f', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index f219aa82af..387e366b53 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -42,6 +42,9 @@ def test_Cerebro_inputs(): outputWarpTransformFile=dict(argstr='--warp %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tempDirectory=dict(argstr='--tempdir %s', ), tempDirectoryBase=dict(argstr='--tempdirbase %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 6e0fe3851c..bef8d4f0af 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -29,6 +29,9 @@ def test_Cortex_inputs(): outputCerebrumMask=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index be334c7096..96ad0ca409 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -20,6 +20,9 @@ def test_Dewisp_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sizeThreshold=dict(argstr='-t %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index 42887e8883..ab6552088a 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -30,6 +30,9 @@ def test_Dfs_inputs(): ), postSmoothFlag=dict(argstr='--postsmooth', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalingPercentile=dict(argstr='-f %f', ), smoothingConstant=dict(argstr='-a %f', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 5bdfa45f0e..f6c55ccc03 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -32,6 +32,9 @@ def test_Hemisplit_inputs(): ), pialSurfaceFile=dict(argstr='-p %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index d4511fee33..3185157fe7 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -43,6 +43,9 @@ def test_Pialmesh_inputs(): ), recomputeNormals=dict(argstr='--norm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), searchRadius=dict(argstr='-r %f', usedefault=True, ), diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index 08c7f3b894..9ab6f77511 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -23,6 +23,9 @@ def test_Pvc_inputs(): outputTissueFractionFile=dict(argstr='-f %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialPrior=dict(argstr='-l %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py index 305fd26bf8..e898a2f3bd 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py @@ -31,6 +31,9 @@ def test_SVReg_inputs(): ), refineOutputs=dict(argstr="'-r'", ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shortMessages=dict(argstr="'-gui'", ), skipToIntensityReg=dict(argstr="'-p'", diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index 5a2b0931f8..bce9e758a6 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -26,6 +26,9 @@ def test_Scrubmask_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index e96363e4f7..0588aca6ae 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -29,6 +29,9 @@ def test_Skullfinder_inputs(): ), performFinalOpening=dict(argstr='--finalOpening', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalpLabelValue=dict(argstr='--scalplabel %d', ), skullLabelValue=dict(argstr='--skulllabel %d', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index 498dd56e05..4c432fbcd1 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -26,6 +26,9 @@ def test_Tca_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py index 8bd388c36c..0138cc0f83 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py @@ -12,6 +12,9 @@ def test_ThicknessPVC_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjectFilePrefix=dict(argstr='%s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 39700f5304..e9b99a94ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -65,6 +65,9 @@ def test_AnalyzeHeader_inputs(): readheader=dict(argstr='-readheader %s', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleinter=dict(argstr='-scaleinter %d', units='NA', ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 7016825269..8b8c568795 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -30,6 +30,9 @@ def test_ComputeEigensystem_inputs(): outputdatatype=dict(argstr='-outputdatatype %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 6bf41d7b95..a7be61e132 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -26,6 +26,9 @@ def test_ComputeFractionalAnisotropy_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 16b3e6f163..fa66b9c213 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -26,6 +26,9 @@ def test_ComputeMeanDiffusivity_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 3adc971f7b..3164e2c98b 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -26,6 +26,9 @@ def test_ComputeTensorTrace_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 715db443da..8f33d6a936 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -18,6 +18,9 @@ def test_Conmat_inputs(): output_root=dict(argstr='-outputroot %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalar_file=dict(argstr='-scalarfile %s', requires=['tract_stat'], ), diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index f0f1c789c4..10c98bc483 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -24,6 +24,9 @@ def test_DT2NIfTI_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index e4a0115dc3..86c64c8fd3 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -25,6 +25,9 @@ def test_DTIFit_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 285891f0cf..eeb488cafb 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -31,6 +31,9 @@ def test_DTLUTGen_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samples=dict(argstr='-samples %d', units='NA', ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index ebde9241a1..c0b9038a61 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -29,6 +29,9 @@ def test_DTMetric_inputs(): outputfile=dict(argstr='-outputfile %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index efbaa1e95f..d96cc5c7ef 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -41,6 +41,9 @@ def test_FSL2Scheme_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), usegradmod=dict(argstr='-usegradmod', diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 2a17d57bc8..c6d214360c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -24,6 +24,9 @@ def test_Image2Voxel_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index cd0aa1380e..014d66291e 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -22,6 +22,9 @@ def test_ImageStats_inputs(): output_root=dict(argstr='-outputroot %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stat=dict(argstr='-stat %s', mandatory=True, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index a8f03034d3..69f31ea9b8 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -30,6 +30,9 @@ def test_LinRecon_inputs(): mandatory=True, position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index c9ac46d3d1..87356a90a8 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -39,6 +39,9 @@ def test_MESD_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index c3555de524..9267e72df3 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -42,6 +42,9 @@ def test_ModelFit_inputs(): ), residualmap=dict(argstr='-residualmap %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 999db17138..75db7a39cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -24,6 +24,9 @@ def test_NIfTIDT2Camino_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s0_file=dict(argstr='-s0 %s', ), scaleinter=dict(argstr='-scaleinter %s', diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 1a64aa285c..58d9bd7103 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -39,6 +39,9 @@ def test_PicoPDFs_inputs(): position=4, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index da68661ea7..39a23b1b6c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -78,6 +78,9 @@ def test_ProcStreamlines_inputs(): resamplestepsize=dict(argstr='-resamplestepsize %d', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedfile=dict(argstr='-seedfile %s', ), seedpointmm=dict(argstr='-seedpointmm %s', diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index d55474e837..a9a3238401 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -28,6 +28,9 @@ def test_QBallMX_inputs(): rbfsigma=dict(argstr='-rbfsigma %f', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index ca5044349d..212d5bf11c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -39,6 +39,9 @@ def test_SFLUTGen_inputs(): pdf=dict(argstr='-pdf %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index ba9993d7bb..fa6fd83132 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -27,6 +27,9 @@ def test_SFPICOCalibData_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index f95f139256..7d0dc31929 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -45,6 +45,9 @@ def test_SFPeaks_inputs(): rbfpointset=dict(argstr='-rbfpointset %d', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', ), searchradius=dict(argstr='-searchradius %f', diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index f74dee86b3..af3ce192cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -28,6 +28,9 @@ def test_Shredder_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space=dict(argstr='%d', position=3, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index 4903bbf163..02c69ae012 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -53,6 +53,9 @@ def test_Track_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 94b2abedaf..8d8a6f369d 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -53,6 +53,9 @@ def test_TrackBallStick_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 3855f8ecc1..75b8813817 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -70,6 +70,9 @@ def test_TrackBayesDirac_inputs(): ), pointset=dict(argstr='-pointset %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index e3572430b7..da710533b9 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -59,6 +59,9 @@ def test_TrackBedpostxDeter_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index bb4c0ed898..293384fb9c 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -62,6 +62,9 @@ def test_TrackBedpostxProba_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 30d87816b8..c0ded6c2ec 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -63,6 +63,9 @@ def test_TrackBootstrap_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 1edd055921..a2b1fcf0e0 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -53,6 +53,9 @@ def test_TrackDT_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index b62e25cd93..2409f7af48 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -58,6 +58,9 @@ def test_TrackPICo_inputs(): ), pdf=dict(argstr='-pdf %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index 5f991d4090..13d7c31a7b 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -28,6 +28,9 @@ def test_TractShredder_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space=dict(argstr='%d', position=3, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 775f3eedd9..aa9a488e78 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -29,6 +29,9 @@ def test_VtkStreamlines_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalar_file=dict(argstr='-scalarfile %s', position=3, ), diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 258286bd9d..a0fb4c433a 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -32,6 +32,9 @@ def test_Camino2Trackvis_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_dims=dict(argstr='-x %s', diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 9ebd53f272..c0c0bec9fd 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -23,6 +23,9 @@ def test_Trackvis2Camino_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index 6252ee9218..21408aa2d8 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -14,6 +14,9 @@ def test_AverageNetworks_inputs(): out_gexf_groupavg=dict(), out_gpickled_groupavg=dict(), resolution_network_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = AverageNetworks.input_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index ea97eaecd8..3f52c3dd10 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -23,6 +23,9 @@ def test_CFFConverter_inputs(): publisher=dict(), references=dict(), relation=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rights=dict(), script_files=dict(), species=dict(usedefault=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 3126066243..72d4bf0800 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -11,6 +11,9 @@ def test_CreateNodes_inputs(): ), resolution_network_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_file=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index 18dd6c1ec6..11b86bedc3 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -11,6 +11,9 @@ def test_MergeCNetworks_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MergeCNetworks.input_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index e031b8cae2..0567c9a0ed 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -18,6 +18,9 @@ def test_NetworkBasedStatistic_inputs(): ), out_nbs_network=dict(), out_nbs_pval_network=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), t_tail=dict(usedefault=True, ), threshold=dict(usedefault=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index 46c077af1b..7f3e803832 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -25,6 +25,9 @@ def test_NetworkXMetrics_inputs(): ), out_pickled_extra_measures=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), treat_as_weighted_graph=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index f62f98b51e..6f9d01889c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -14,6 +14,9 @@ def test_Parcellate_inputs(): ), parcellation_name=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(mandatory=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index 41f99aa5bf..cfc645f105 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -17,6 +17,9 @@ def test_ROIGen_inputs(): ), out_roi_file=dict(genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_freesurfer_LUT=dict(xor=['LUT_file'], ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 333578742e..4af5c8253c 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -36,6 +36,9 @@ def test_DTIRecon_inputs(): output_type=dict(argstr='-ot %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index ea20252ae3..728fa94aab 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -49,6 +49,9 @@ def test_DTITracker_inputs(): ), random_seed=dict(argstr='-rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 699c5c920d..966479bce8 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -34,6 +34,9 @@ def test_HARDIMat_inputs(): ), reference_file=dict(argstr='-ref %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 8fa38aab42..1dd2897d9c 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -47,6 +47,9 @@ def test_ODFRecon_inputs(): output_type=dict(argstr='-ot %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sharpness=dict(argstr='-s %f', ), subtract_background=dict(argstr='-bg', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 647cb3767e..d775595ea0 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -56,6 +56,9 @@ def test_ODFTracker_inputs(): ), random_seed=dict(argstr='-rseed %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), runge_kutta2=dict(argstr='-rk2', ), slice_order=dict(argstr='-sorder %d', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 0ce7d67281..7dd679c810 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -16,6 +16,9 @@ def test_SplineFilter_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step_length=dict(argstr='%f', mandatory=True, position=1, diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 296c311663..926804ffcf 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -16,6 +16,9 @@ def test_TrackMerge_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), track_files=dict(argstr='%s...', diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index 934bc3efff..673c825dbd 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -17,6 +17,9 @@ def test_APMQball_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = APMQball.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index 658294df02..a724fa94e3 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -18,6 +18,9 @@ def test_CSD_inputs(): in_mask=dict(), out_fods=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(), save_fods=dict(usedefault=True, ), diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index fddaeb3bcb..cd4e7ebb96 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -17,6 +17,9 @@ def test_DTI_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DTI.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py index 5b98c1353d..a4b4e636ff 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py @@ -7,6 +7,9 @@ def test_DipyBaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DipyBaseInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index 6bee2dde83..27106b1c08 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -16,6 +16,9 @@ def test_DipyDiffusionInterface_inputs(): in_file=dict(mandatory=True, ), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DipyDiffusionInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index d03508c8ce..26566c314c 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -27,6 +27,9 @@ def test_EstimateResponseSH_inputs(): out_prefix=dict(), recursive=dict(xor=['auto'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(usedefault=True, ), roi_radius=dict(usedefault=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index 5458d5bb98..1dc8d9d407 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -18,6 +18,9 @@ def test_RESTORE_inputs(): in_mask=dict(), noise_mask=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = RESTORE.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index a3d708fb71..03c07bd158 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -37,6 +37,9 @@ def test_SimulateMultiTensor_inputs(): ), out_mask=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), snr=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 80ef4ecab4..2b9ad2cdc2 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -27,6 +27,9 @@ def test_StreamlineTractography_inputs(): peak_threshold=dict(mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_seeds=dict(mandatory=True, usedefault=True, ), diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 02000714a1..957f78da57 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -17,6 +17,9 @@ def test_TensorMode_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TensorMode.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 8308be79e8..ec71c7ddee 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -15,6 +15,9 @@ def test_TrackDensityMap_inputs(): points_space=dict(usedefault=True, ), reference=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index 1be5007b28..8898ddfff1 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -19,6 +19,9 @@ def test_AnalyzeWarp_inputs(): mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index eb88b4c7e5..4901a73053 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -22,6 +22,9 @@ def test_ApplyWarp_inputs(): mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index cd995b8aa2..25e78b48d6 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -16,6 +16,9 @@ def test_EditTransform_inputs(): output_type=dict(argstr='ResultImagePixelType', ), reference_image=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), transform_file=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index 713f912ef7..2ea6803da2 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -22,6 +22,9 @@ def test_PointsWarp_inputs(): points_file=dict(argstr='-def %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index b14af447c8..b9c261981c 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -34,6 +34,9 @@ def test_Registration_inputs(): parameters=dict(argstr='-p %s...', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index 5961ef84cc..86400f7812 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -22,6 +22,9 @@ def test_AddXFormToHeader_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index bcab8391db..c85f3dd3a3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -35,6 +35,9 @@ def test_Aparc2Aseg_inputs(): out_file=dict(argstr='--o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_annotation=dict(mandatory=True, ), rh_pial=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 802ebbc1d3..b5b7b0a02c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -18,6 +18,9 @@ def test_Apas2Aseg_inputs(): out_file=dict(argstr='--o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 2910fbdc62..37065c3621 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -33,6 +33,9 @@ def test_ApplyMask_inputs(): name_template='%s_masked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index e4f93a1ce2..a507947805 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -55,6 +55,9 @@ def test_ApplyVolTransform_inputs(): mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--mov %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 4550cb071b..857132d39b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -55,6 +55,9 @@ def test_Binarize_inputs(): ), out_type=dict(argstr='', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rmax=dict(argstr='--rmax %f', ), rmin=dict(argstr='--rmin %f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 17028f990d..188654ecbe 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -37,6 +37,9 @@ def test_CALabel_inputs(): ), relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index ab6912accf..7932397f8e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -33,6 +33,9 @@ def test_CANormalize_inputs(): name_template='%s_norm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index e76437e24d..5bc8fa3217 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -36,6 +36,9 @@ def test_CARegister_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 19b38b0273..e3992d793c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -17,6 +17,9 @@ def test_CheckTalairachAlignment_inputs(): position=-1, xor=['subject'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject=dict(argstr='-subj %s', mandatory=True, position=-1, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 8f702078ea..7c17ea8787 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -40,6 +40,9 @@ def test_Concatenate_inputs(): ), paired_stats=dict(argstr='--paired-%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sign=dict(argstr='--%s', ), sort=dict(argstr='--sort', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index b15dfee307..a3662b584b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -27,6 +27,9 @@ def test_ConcatenateLTA_inputs(): name_template='%s-long', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 57d56b9726..e4bf7756d1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -24,6 +24,9 @@ def test_Contrast_inputs(): ), rawavg=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index 03474551d6..8c892bd5bf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -24,6 +24,9 @@ def test_Curvature_inputs(): ), n=dict(argstr='-n', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save=dict(argstr='-w', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index 9bb6f9fc50..7737fe66d0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -32,6 +32,9 @@ def test_CurvatureStats_inputs(): name_source=['hemisphere'], name_template='%s.curv.stats', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-4, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index a0e7b0fbdb..da2f91336e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -22,6 +22,9 @@ def test_DICOMConvert_inputs(): ), out_type=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seq_list=dict(requires=['dicom_info'], ), subject_dir_template=dict(usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index 97e5910c17..af82ac8f2c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -28,6 +28,9 @@ def test_EMRegister_inputs(): name_template='%s_transform.lta', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skull=dict(argstr='-skull', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index 081856a5fa..72b4627a6e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -26,6 +26,9 @@ def test_EditWMwithAseg_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg_file=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index d2eba7ed16..b6dbb51e3d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -16,6 +16,9 @@ def test_EulerNumber_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index eb85cba81b..49b6c9a2f9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -21,6 +21,9 @@ def test_ExtractMainComponent_inputs(): name_template='%s.maincmp', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index e718c1c4cb..4137399e28 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -12,6 +12,9 @@ def test_FSCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index 072161bd52..323b39a53a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -13,6 +13,9 @@ def test_FSCommandOpenMP_inputs(): usedefault=True, ), num_threads=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index b685a4d82a..789999d08e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -12,6 +12,9 @@ def test_FSScriptCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 8496ca2ae5..519290bc7f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -21,6 +21,9 @@ def test_FitMSParams_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), te_list=dict(), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index ec064372eb..3fe86e03ff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -30,6 +30,9 @@ def test_FixTopology_inputs(): ), mgz=dict(argstr='-mgz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), sphere=dict(argstr='-sphere %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 24c8214fba..f93292317d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -24,6 +24,9 @@ def test_FuseSegmentations_inputs(): out_file=dict(mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', position=-3, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index e99a1de407..f26aadb064 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -88,6 +88,9 @@ def test_GLMFit_inputs(): prune_thresh=dict(argstr='--prune_thr %f', xor=['noprune'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resynth_test=dict(argstr='--resynthtest %d', ), save_cond=dict(argstr='--save-cond', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index c479c7727a..9f9dee34db 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -15,6 +15,9 @@ def test_ImageInfo_inputs(): in_file=dict(argstr='%s', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 4f986f6a93..e69ce01446 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -27,6 +27,9 @@ def test_Jacobian_inputs(): name_template='%s.jacobian', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index a7e4a121af..4f4cf94c7f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -51,6 +51,9 @@ def test_LTAConvert_inputs(): ), out_reg=dict(argstr='--outreg %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--src %s', ), target_conform=dict(argstr='--trgconform', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index bba05d8690..0b4bd7a406 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -28,6 +28,9 @@ def test_Label2Annot_inputs(): out_annot=dict(argstr='--a %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index ab1a98f286..3353b02aff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -25,6 +25,9 @@ def test_Label2Label_inputs(): registration_method=dict(argstr='--regmethod %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_label=dict(argstr='--srclabel %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index c58fd71532..20327f2aa7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -53,6 +53,9 @@ def test_Label2Vol_inputs(): reg_header=dict(argstr='--regheader %s', xor=('reg_file', 'reg_header', 'identity'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg_file=dict(argstr='--seg %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index acf272a603..aee3cc1636 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -31,6 +31,9 @@ def test_MNIBiasCorrection_inputs(): ), protocol_iterations=dict(argstr='--proto-iters %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shrink=dict(argstr='--shrink %d', ), stop=dict(argstr='--stop %f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index b0b1b39a36..2af45858a0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -18,6 +18,9 @@ def test_MPRtoMNI305_inputs(): reference_dir=dict(mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 9a1f011d77..223456e780 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -144,6 +144,9 @@ def test_MRIConvert_inputs(): ), reslice_like=dict(argstr='--reslice_like %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sdcm_list=dict(argstr='--sdcmlist %s', ), skip_n=dict(argstr='--nskip %d', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index 5ba95570c8..c48de3868b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -65,6 +65,9 @@ def test_MRICoreg_inputs(): reference_mask=dict(argstr='--ref-mask %s', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saturation_threshold=dict(argstr='--sat %g', ), sep=dict(argstr='--sep %s...', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 1302f7a2dd..f1429e60a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -22,6 +22,9 @@ def test_MRIFill_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation=dict(argstr='-segmentation %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index 13c70086df..d66ae62824 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -28,6 +28,9 @@ def test_MRIMarchingCubes_inputs(): genfile=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 85db09eb46..4db4d5ab0c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -35,6 +35,9 @@ def test_MRIPretess_inputs(): name_template='%s_pretesswm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index a35c091e04..9c9d1c759f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -35,6 +35,9 @@ def test_MRISPreproc_inputs(): ), proj_frac=dict(argstr='--projfrac %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index e3a266d61a..94fe364872 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -38,6 +38,9 @@ def test_MRISPreprocReconAll_inputs(): ), proj_frac=dict(argstr='--projfrac %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_surfreg_target=dict(requires=['surfreg_files'], ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 58979a75a7..945b35d11b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -24,6 +24,9 @@ def test_MRITessellate_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 50897b18a7..79f87e3cdb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -39,6 +39,9 @@ def test_MRIsCALabel_inputs(): name_template='%s.aparc.annot', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), smoothwm=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index ad45ba32ed..c15c91db95 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -35,6 +35,9 @@ def test_MRIsCalc_inputs(): out_file=dict(argstr='-o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index 2eae71deea..fbc627ff11 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -21,6 +21,9 @@ def test_MRIsCombine_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 6d4501c8ca..0e27b2956d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -45,6 +45,9 @@ def test_MRIsConvert_inputs(): ), rescale=dict(argstr='-r', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalarcurv_file=dict(argstr='-c %s', ), scale=dict(argstr='-s %.3f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index c74f31bd59..99ff1791a1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -32,6 +32,9 @@ def test_MRIsExpand_inputs(): pial=dict(argstr='-pial %s', copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_averages=dict(argstr='-A %d', ), sphere=dict(copyfile=False, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index a2ea82a4f0..62cb3386ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -29,6 +29,9 @@ def test_MRIsInflate_inputs(): ), out_sulc=dict(xor=['no_save_sulc'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index cf4f27522e..367a2fff60 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -27,6 +27,9 @@ def test_MS_LDA_inputs(): ), mask_file=dict(argstr='-mask %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shift=dict(argstr='-shift %d', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index a230fac5f4..f68334c203 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -15,6 +15,9 @@ def test_MakeAverageSubject_inputs(): out_name=dict(argstr='--out %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), subjects_ids=dict(argstr='--subjects %s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index ff49e627ba..ed9b9e450b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -49,6 +49,9 @@ def test_MakeSurfaces_inputs(): ), orig_white=dict(argstr='-orig_white %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index c081e76912..068e0053e3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -28,6 +28,9 @@ def test_Normalize_inputs(): name_template='%s_norm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation=dict(argstr='-aseg %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index e5d7c18980..5e42735f03 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -88,6 +88,9 @@ def test_OneSampleTTest_inputs(): prune_thresh=dict(argstr='--prune_thr %f', xor=['noprune'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resynth_test=dict(argstr='--resynthtest %d', ), save_cond=dict(argstr='--save-cond', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index 3713464c7c..730b4ccf6a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -25,6 +25,9 @@ def test_Paint_inputs(): name_template='%s.avg_curv', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 28de43ee39..c1c57f31a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -44,6 +44,9 @@ def test_ParcellationStats_inputs(): genfile=True, requires=['tabular_output'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_pial=dict(mandatory=True, ), rh_white=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 54bf4467e5..1c81ac4e0b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -18,6 +18,9 @@ def test_ParseDICOMDir_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sortbyrun=dict(argstr='--sortbyrun', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 9a84bf9f28..942322631f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -96,6 +96,9 @@ def test_ReconAll_inputs(): ), parallel=dict(argstr='-parallel', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='-subjid %s', usedefault=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index 33c6e0c941..7090037d5c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -29,6 +29,9 @@ def test_Register_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index c10b12911c..2196294c63 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -20,6 +20,9 @@ def test_RegisterAVItoTalairach_inputs(): position=3, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 4e46bbc03d..aea7cc51b8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -26,6 +26,9 @@ def test_RelabelHypointensities_inputs(): name_template='%s.hypos.mgz', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_white=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index 14a9cd8edb..439888c525 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -24,6 +24,9 @@ def test_RemoveIntersection_inputs(): name_template='%s', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 023bf6552a..9a5a01e32c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -25,6 +25,9 @@ def test_RemoveNeck_inputs(): ), radius=dict(argstr='-radius %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 811fb85cde..02593f33ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -20,6 +20,9 @@ def test_Resample_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index c8b7080c26..aac06d6347 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -63,6 +63,9 @@ def test_RobustRegister_inputs(): ), registered_file=dict(argstr='--warp %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--mov %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index d2b89e3235..4e0c742a57 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -42,6 +42,9 @@ def test_RobustTemplate_inputs(): mandatory=True, xor=['auto_detect_sensitivity'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaled_intensity_outputs=dict(argstr='--iscaleout %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index a257fd7e2e..013a87d58c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -74,6 +74,9 @@ def test_SampleToSurface_inputs(): ), reshape_slices=dict(argstr='--rf %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_method=dict(argstr='%s', mandatory=True, requires=['sampling_range', 'sampling_units'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 04e9f830d1..f3383237ed 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -76,6 +76,9 @@ def test_SegStats_inputs(): ), partial_volume_file=dict(argstr='--pv %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict(argstr='--seg %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index eecc3aa4e5..4e2f3875ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -85,6 +85,9 @@ def test_SegStatsReconAll_inputs(): partial_volume_file=dict(argstr='--pv %s', ), presurf_seg=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_orig_nofix=dict(mandatory=True, ), rh_pial=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index f54484b5b7..101356461d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -27,6 +27,9 @@ def test_SegmentCC_inputs(): out_rotation=dict(argstr='-lta %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-1, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index 450ad4f95b..cff075eef3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -20,6 +20,9 @@ def test_SegmentWM_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 5720c12975..141c6e3e0d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -28,6 +28,9 @@ def test_Smooth_inputs(): reg_file=dict(argstr='--reg %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smoothed_file=dict(argstr='--o %s', genfile=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 2419164f5f..5ac3782ce9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -35,6 +35,9 @@ def test_SmoothTessellation_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), smoothing_iterations=dict(argstr='-n %d', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 8afabb96e6..af2a0a40ff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -28,6 +28,9 @@ def test_Sphere_inputs(): name_template='%s.sphere', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index 928a2a5127..777c51961c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -36,6 +36,9 @@ def test_SphericalAverage_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='-o %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 2590827648..4aec7985b0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -24,6 +24,9 @@ def test_Surface2VolTransform_inputs(): mandatory=True, xor=['subject_id'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--surfval %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 835d4bc601..977d2e62c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -29,6 +29,9 @@ def test_SurfaceSmooth_inputs(): ), reshape=dict(argstr='--reshape', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_iters=dict(argstr='--smooth %d', xor=['fwhm'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 2043603124..637be86cc0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -58,6 +58,9 @@ def test_SurfaceSnapshots_inputs(): ), patch_file=dict(argstr='-patch %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), reverse_overlay=dict(argstr='-revphaseflag 1', ), screenshot_stem=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 99c54a8f78..52a0ca1a53 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -22,6 +22,9 @@ def test_SurfaceTransform_inputs(): ), reshape_factor=dict(argstr='--reshape-factor', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_annot_file=dict(argstr='--sval-annot %s', mandatory=True, xor=['source_file'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index bc5fb23eb7..23c3abddae 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -26,6 +26,9 @@ def test_SynthesizeFLASH_inputs(): mandatory=True, position=6, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), t1_image=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index f301168b01..7c168986ab 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -20,6 +20,9 @@ def test_TalairachAVI_inputs(): out_file=dict(argstr='--xfm %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index a6ae75b3ff..4f8d39e993 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -16,6 +16,9 @@ def test_TalairachQC_inputs(): mandatory=True, position=0, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index c5e3d65274..b8917c826a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -36,6 +36,9 @@ def test_Tkregister2_inputs(): ), reg_header=dict(argstr='--regheader', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 8a1aecaa22..5bc42a466e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -26,6 +26,9 @@ def test_UnpackSDICOMDir_inputs(): ), output_dir=dict(argstr='-targ %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), run_info=dict(argstr='-run %d %s %s %s', mandatory=True, xor=('run_info', 'config', 'seq_config'), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index b1bcaa4e40..3ebb182f5f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -28,6 +28,9 @@ def test_VolumeMask_inputs(): ), lh_white=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_pial=dict(mandatory=True, ), rh_white=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index 53ff443424..e76ade04ba 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -24,6 +24,9 @@ def test_WatershedSkullStrip_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), t1=dict(argstr='-T1', ), diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index 2c3eda86cb..9de2144826 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -35,6 +35,9 @@ def test_AR1Image_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index 1e4fb9406c..ab3e679421 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -21,6 +21,9 @@ def test_AccuracyTester_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trained_wts_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 0a74d811c3..f6c96c596f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -35,6 +35,9 @@ def test_ApplyMask_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 7b08c18c28..5f7bee70e6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -40,6 +40,9 @@ def test_ApplyTOPUP_inputs(): name_template='%s_corrected', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index bcdcc670ac..d2f784f5fc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -46,6 +46,9 @@ def test_ApplyWarp_inputs(): position=-1, xor=['abswarp'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), superlevel=dict(argstr='--superlevel=%s', ), supersample=dict(argstr='--super', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index 438f4ce486..52d5a32dc1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -109,6 +109,9 @@ def test_ApplyXFM_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid2D=dict(argstr='-2D', ), save_log=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index e19577b71f..f33bd9ee75 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -20,6 +20,9 @@ def test_AvScale_inputs(): ref_file=dict(argstr='%s', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index ee6b749d7e..c29318f3c0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -33,6 +33,9 @@ def test_B0Calc_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), x_b0=dict(argstr='--b0x=%0.2f', diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 782c1a9317..38b147d924 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -69,6 +69,9 @@ def test_BEDPOSTX5_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='-s %d', diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index 98af74707d..fa0e2a2ecc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -50,6 +50,9 @@ def test_BET_inputs(): remove_eyes=dict(argstr='-S', xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), robust=dict(argstr='-R', xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index aae4a436dd..0dde4928d0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -45,6 +45,9 @@ def test_BinaryMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index 6d2952c073..ecc5270c90 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -32,6 +32,9 @@ def test_ChangeDataType_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index 713666b754..6acae3c3c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -17,6 +17,9 @@ def test_Classifier_inputs(): copyfile=False, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index 76487d6adc..7680f29830 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -35,6 +35,9 @@ def test_Cleaner_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 886ef8885b..c44784bbe0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -65,6 +65,9 @@ def test_Cluster_inputs(): pthreshold=dict(argstr='--pthresh=%.10f', requires=['dlh', 'volume'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), std_space_file=dict(argstr='--stdvol=%s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index c0544c799d..a1cabb7248 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -83,6 +83,9 @@ def test_Complex_inputs(): position=1, xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), start_vol=dict(argstr='%d', position=-2, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index 5fa6e7828c..d4964186b9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -28,6 +28,9 @@ def test_ContrastMgr_inputs(): copyfile=False, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigmasquareds=dict(argstr='', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 97c0a06315..5f9bb4c208 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -47,6 +47,9 @@ def test_ConvertWarp_inputs(): relwarp=dict(argstr='--rel', xor=['abswarp'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shift_direction=dict(argstr='--shiftdir=%s', requires=['shift_in_file'], ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index 5146d1f718..0ea43bd196 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -39,6 +39,9 @@ def test_ConvertXFM_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 70922a9da9..49e79b0287 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -28,6 +28,9 @@ def test_CopyGeom_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 4badbfb2dc..b440a17341 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -51,6 +51,9 @@ def test_DTIFit_inputs(): min_z=dict(argstr='-z %d', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_tensor=dict(argstr='--save_tensor', ), sse=dict(argstr='--sse', diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 40da7affbe..774289c011 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -46,6 +46,9 @@ def test_DilateImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 87cde59644..73e4f8ffcb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -27,6 +27,9 @@ def test_DistanceMap_inputs(): mask_file=dict(argstr='--mask=%s', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 02c68ebc24..546b68ec43 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -44,6 +44,9 @@ def test_DualRegression_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 5f49d5a89e..7632e44a93 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -38,6 +38,9 @@ def test_EPIDeWarp_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %s', usedefault=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index c5f521045f..30cb1abf43 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -70,6 +70,9 @@ def test_Eddy_inputs(): output_type=dict(), repol=dict(argstr='--repol', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session=dict(argstr='--session=%s', ), slm=dict(argstr='--slm=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index c7606a2cea..e7eb3dca4d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -28,6 +28,9 @@ def test_EddyCorrect_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index c34014dd57..c15960b141 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -36,6 +36,9 @@ def test_EpiReg_inputs(): output_type=dict(), pedir=dict(argstr='--pedir=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), t1_brain=dict(argstr='--t1brain=%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index a64c6f5d9e..2202a1b2e1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -46,6 +46,9 @@ def test_ErodeImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 77be2edb95..176a4f62ab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -21,6 +21,9 @@ def test_ExtractROI_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_file=dict(argstr='%s', genfile=True, hash_files=False, diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 11e6cec5de..d47d4afda5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -53,6 +53,9 @@ def test_FAST_inputs(): output_type=dict(), probability_maps=dict(argstr='-p', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segment_iters=dict(argstr='-W %d', ), segments=dict(argstr='-g', diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index f2c5e46e7e..50fbe55433 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -17,6 +17,9 @@ def test_FEAT_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index e0956ee674..e402831f41 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -23,6 +23,9 @@ def test_FEATModel_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index a0f5e09177..4a021bcab7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -13,6 +13,9 @@ def test_FEATRegister_inputs(): ), reg_image=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = FEATRegister.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 7b98ac128c..a441709d8d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -45,6 +45,9 @@ def test_FIRST_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-v', diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index ed8093853d..ed7c29e3a6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -44,6 +44,9 @@ def test_FLAMEO_inputs(): outlier_iter=dict(argstr='--ioni=%d', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), run_mode=dict(argstr='--runmode=%s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index fabfa4054c..ffd85d95a4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -108,6 +108,9 @@ def test_FLIRT_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid2D=dict(argstr='-2D', ), save_log=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 8e4cf47fc3..e273a5dfb5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -94,6 +94,9 @@ def test_FNIRT_inputs(): ), regularization_model=dict(argstr='--regmod=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skip_implicit_in_masking=dict(argstr='--impinm=0', ), skip_implicit_ref_masking=dict(argstr='--imprefm=0', diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index 2ade472bfa..617f3ad140 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -13,6 +13,9 @@ def test_FSLCommand_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index 280cf3a588..819f31e453 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -66,6 +66,9 @@ def test_FSLXCommand_inputs(): xor=('no_spat', 'non_linear', 'cnlinear'), ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='--sampleevery=%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 93b41ea6de..01e221d454 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -57,6 +57,9 @@ def test_FUGUE_inputs(): ), poly_order=dict(argstr='--poly=%d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_fmap=dict(xor=['save_unmasked_fmap'], ), save_shift=dict(xor=['save_unmasked_shift'], diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index c0e763640c..59582898ad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -16,6 +16,9 @@ def test_FeatureExtractor_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index ac62586ec5..c52b6dadbc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -40,6 +40,9 @@ def test_FilterRegressor_inputs(): out_vnscales=dict(argstr='--out_vnscales', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), var_norm=dict(argstr='--vn', diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index ef7e14fcbf..e2aa619d60 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -22,6 +22,9 @@ def test_FindTheBiggest_inputs(): position=2, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index d9ab6bc168..de64bc16b8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -61,6 +61,9 @@ def test_GLM_inputs(): out_z_name=dict(argstr='--out_z=%s', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), var_norm=dict(argstr='--vn', diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index 9102d667b3..884b2f30c0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -46,6 +46,9 @@ def test_ICA_AROMA_inputs(): out_dir=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 8c1aef8b5c..5e500a2947 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -31,6 +31,9 @@ def test_ImageMaths_inputs(): position=4, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), suffix=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 73deecb7e5..38ba476069 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -30,6 +30,9 @@ def test_ImageMeants_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_all=dict(argstr='--showall', ), spatial_coord=dict(argstr='-c %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 1a4739a320..5fcb8cf070 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -23,6 +23,9 @@ def test_ImageStats_inputs(): position=3, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), split_4d=dict(argstr='-t', position=1, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 02624a6d2c..55e2aef927 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -37,6 +37,9 @@ def test_InvWarp_inputs(): relative=dict(argstr='--rel', xor=['absolute'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp=dict(argstr='--warp=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 0d33d852a2..c324d7b250 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -36,6 +36,9 @@ def test_IsotropicSmooth_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='-s %.5f', mandatory=True, position=4, diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 81f74cc923..fd1de91739 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -9,6 +9,9 @@ def test_L2Model_inputs(): ), num_copes=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = L2Model.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index f5fcfe4093..da42942fab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -15,6 +15,9 @@ def test_Level1Design_inputs(): model_serial_correlations=dict(mandatory=True, ), orthogonalization=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session_info=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 300f829bfa..ddfaf2d411 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -37,6 +37,9 @@ def test_MCFLIRT_inputs(): ), ref_vol=dict(argstr='-refvol %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation=dict(argstr='-rotation %d', ), save_mats=dict(argstr='-mats', diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index 1c14c441d9..a873dfaf6d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -93,6 +93,9 @@ def test_MELODIC_inputs(): ), report_maps=dict(argstr='--report_maps=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s_con=dict(argstr='--Scon=%s', ), s_des=dict(argstr='--Sdes=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index ed921d092a..48cb0c2a10 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -28,6 +28,9 @@ def test_MakeDyadicVectors_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), theta_vol=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 1962cd5ad9..dfe53cbf87 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -31,6 +31,9 @@ def test_MathsCommand_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 22ba2f24ad..fd0e5a6e48 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -35,6 +35,9 @@ def test_MaxImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index 12444f2e3b..c621aa2bf6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -35,6 +35,9 @@ def test_MaxnImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 86b23eb8b9..fd448b1684 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -35,6 +35,9 @@ def test_MeanImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index c4be8d6687..70fce4a5d3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -35,6 +35,9 @@ def test_MedianImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 32c966edaf..5a2b008edc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -27,6 +27,9 @@ def test_Merge_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tr=dict(argstr='%.2f', diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index 973bc9a369..9ac450018e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -35,6 +35,9 @@ def test_MinImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index a4268fd930..5fe4695d07 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -42,6 +42,9 @@ def test_MotionOutliers_inputs(): name_template='%s_metrics.txt', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--thresh=%g', diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 964605e726..6b6edab63d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -37,6 +37,9 @@ def test_MultiImageMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 69ef20f16c..1ae400cfcd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -12,6 +12,9 @@ def test_MultipleRegressDesign_inputs(): ), regressors=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MultipleRegressDesign.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 84885f6c10..6b93e456e7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -41,6 +41,9 @@ def test_Overlay_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_negative_stats=dict(argstr='%s', position=8, xor=['stat_image2'], diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 38d8f7bdf3..97c6826220 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -47,6 +47,9 @@ def test_PRELUDE_inputs(): ), removeramps=dict(argstr='--removeramps', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), savemask_file=dict(argstr='--savemask=%s', hash_files=False, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index 49f1ed3538..9ff68fb02c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -39,6 +39,9 @@ def test_PercentileImage_inputs(): position=5, usedefault=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 9dc7a30fd0..3d4aca5d15 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -28,6 +28,9 @@ def test_PlotMotionParams_inputs(): plot_type=dict(argstr='%s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 03467e1dcf..ea24858481 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -36,6 +36,9 @@ def test_PlotTimeSeries_inputs(): plot_start=dict(argstr='--start=%d', xor=('plot_range',), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sci_notation=dict(argstr='--sci', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 114feac427..eced97b4c5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -22,6 +22,9 @@ def test_PowerSpectrum_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 8400c376e6..5c34ea2f3d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -33,6 +33,9 @@ def test_PrepareFieldmap_inputs(): position=4, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scanner=dict(argstr='%s', position=1, usedefault=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index d88ab0b0b9..2e39bc2e58 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -65,6 +65,9 @@ def test_ProbTrackX_inputs(): ), random_seed=dict(argstr='--rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2tastext=dict(argstr='--s2tastext', ), sample_random_points=dict(argstr='--sampvox', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index 770eafe3cb..0256789574 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -82,6 +82,9 @@ def test_ProbTrackX2_inputs(): ), random_seed=dict(argstr='--rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2tastext=dict(argstr='--s2tastext', ), sample_random_points=dict(argstr='--sampvox', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index 318e67c9d9..470da8bfb8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -17,6 +17,9 @@ def test_ProjThresh_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 53e999893c..8f75d74b5c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -48,6 +48,9 @@ def test_Randomise_inputs(): ), raw_stats_imgs=dict(argstr='-R', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed=%d', ), show_info_parallel_mode=dict(argstr='-Q', diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index fd37a51ecb..069bba1691 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -20,6 +20,9 @@ def test_Reorient2Std_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 26d3c45c6f..58491ab7f1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -29,6 +29,9 @@ def test_RobustFOV_inputs(): name_template='%s_to_ROI', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 301a5fdd47..a9dd76b9a5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -21,6 +21,9 @@ def test_SMM_inputs(): position=2, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatial_data_file=dict(argstr='--sdf="%s"', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index bdaba2cad6..d576fed82c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -34,6 +34,9 @@ def test_SUSAN_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), usans=dict(argstr='', diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index c2b645b540..8d5f85eec3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -23,6 +23,9 @@ def test_SigLoss_inputs(): genfile=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_direction=dict(argstr='-d %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 681e9157b2..894692e63f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -31,6 +31,9 @@ def test_SliceTimer_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_direction=dict(argstr='--direction=%d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index d00aeafbaf..b2ec44662f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -53,6 +53,9 @@ def test_Slicer_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sample_axial=dict(argstr='-S %d', position=10, requires=['image_width'], diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index af09615294..0e7fc4c864 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -22,6 +22,9 @@ def test_Smooth_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='-kernel gauss %.03f -fmean', mandatory=True, position=1, diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index 066af89a60..fbbe43909b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -23,6 +23,9 @@ def test_SmoothEstimate_inputs(): residual_fit_file=dict(argstr='--res=%s', requires=['dof'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), zstat_file=dict(argstr='--zstat=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 949254bdcc..d53d58d85c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -46,6 +46,9 @@ def test_SpatialFilter_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index 7eb80a9f12..761506bb0c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -24,6 +24,9 @@ def test_Split_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 5fd80d2dc0..fc7fd50eca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -35,6 +35,9 @@ def test_StdImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 1fe20d3351..3eb2ff9da4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -24,6 +24,9 @@ def test_SwapDimensions_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 8223b5dac4..d1206866f3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -83,6 +83,9 @@ def test_TOPUP_inputs(): ), regrid=dict(argstr='--regrid=%d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='--scale=%d', ), splineorder=dict(argstr='--splineorder=%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index f5a4f5835a..6b20f6b3ba 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -39,6 +39,9 @@ def test_TemporalFilter_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index bd56d6270b..778d6ede61 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -33,6 +33,9 @@ def test_Threshold_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 360a5b9b57..cdeb8c39e7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -26,6 +26,9 @@ def test_TractSkeleton_inputs(): requires=['threshold', 'distance_map', 'data_file'], ), projected_data=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_mask_file=dict(xor=['use_cingulum_mask'], ), skeleton_file=dict(argstr='-o %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index c5b1f12874..3b712ab176 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -19,6 +19,9 @@ def test_Training_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trained_wts_filestem=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py index abe2237832..6099379f55 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py +++ b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py @@ -11,6 +11,9 @@ def test_TrainingSetCreator_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TrainingSetCreator.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 9ac8a42d7f..659c4db2ef 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -35,6 +35,9 @@ def test_UnaryMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 9ea57c1677..2a96f49641 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -31,6 +31,9 @@ def test_VecReg_inputs(): ref_vol=dict(argstr='-r %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_mat=dict(argstr='--rotmat=%s', ), rotation_warp=dict(argstr='--rotwarp=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 3c5e999c51..861eeebbfe 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -29,6 +29,9 @@ def test_WarpPoints_inputs(): name_template='%s_warped', output_name='out_file', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), src_file=dict(argstr='-src %s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index aa9d63ceca..5ab79eeb6c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -31,6 +31,9 @@ def test_WarpPointsToStd_inputs(): ), premat_file=dict(argstr='-premat %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), std_file=dict(argstr='-std %s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index a32d067588..3c69784764 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -30,6 +30,9 @@ def test_WarpUtils_inputs(): reference=dict(argstr='--ref=%s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f', diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 6a3022ed2d..90c64b56f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -68,6 +68,9 @@ def test_XFibres5_inputs(): xor=('no_spat', 'non_linear', 'cnlinear'), ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='--sampleevery=%d', diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 5b9f60d0d3..efdacbe423 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -92,6 +92,9 @@ def test_Average_inputs(): quiet=dict(argstr='-quiet', xor=('verbose', 'quiet'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sdfile=dict(argstr='-sdfile %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index 3ef4392a2c..cd98a54dc8 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -35,6 +35,9 @@ def test_BBox_inputs(): name_template='%s_bbox.txt', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='-threshold', diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 10a804e98f..006b4003f3 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -52,6 +52,9 @@ def test_Beast_inputs(): ), probability_map=dict(argstr='-probability', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), same_resolution=dict(argstr='-same_resolution', ), search_area=dict(argstr='-search_area %s', diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index 0bec968390..6104e85eb6 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -31,6 +31,9 @@ def test_BestLinReg_inputs(): name_template='%s_bestlinreg.xfm', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(argstr='%s', mandatory=True, position=-4, diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index 1fc965370c..787a8757e0 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -29,6 +29,9 @@ def test_BigAverage_inputs(): ), output_float=dict(argstr='--float', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), robust=dict(argstr='-robust', ), sd_file=dict(argstr='--sdfile %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index 0f87d37bb2..b698723ed4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -27,6 +27,9 @@ def test_Blob_inputs(): name_template='%s_blob.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trace=dict(argstr='-trace', diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index 77342e4f9d..7908162c3b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -44,6 +44,9 @@ def test_Blur_inputs(): rect=dict(argstr='-rect', xor=('gaussian', 'rect'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), standard_dev=dict(argstr='-standarddev %s', mandatory=True, xor=('fwhm', 'fwhm3d', 'standard_dev'), diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 6ac13c47b1..e79ddf0f56 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -103,6 +103,9 @@ def test_Calc_inputs(): quiet=dict(argstr='-quiet', xor=('verbose', 'quiet'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), two=dict(argstr='-2', diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index 10bbdad6a6..c927d2aec6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -31,6 +31,9 @@ def test_Convert_inputs(): name_template='%s_convert_output.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template=dict(argstr='-template', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index 62fa8b7470..52f6c31790 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -29,6 +29,9 @@ def test_Copy_inputs(): real_values=dict(argstr='-real_values', xor=('pixel_values', 'real_values'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index 07e183e009..a50c6cf9ca 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -45,6 +45,9 @@ def test_Dump_inputs(): ), precision=dict(argstr='%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), variables=dict(argstr='-v %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index f4fb2c6e2b..8530d6eb52 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -77,6 +77,9 @@ def test_Extract_inputs(): name_template='%s.raw', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), start=dict(argstr='-start %s', sep=',', ), diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index 77ffe4d114..89e921ed51 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -26,6 +26,9 @@ def test_Gennlxfm_inputs(): name_template='%s_gennlxfm.xfm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step=dict(argstr='-step %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index b12e3cd60a..c09318f7e2 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -126,6 +126,9 @@ def test_Math_inputs(): ), propagate_nan=dict(argstr='-propagate_nan', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-scale -const2 %s %s', ), segment=dict(argstr='-segment -const2 %s %s', diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index a30e856276..e48268b2c8 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -26,6 +26,9 @@ def test_NlpFit_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(argstr='%s', mandatory=True, position=-3, diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 410309a364..99c8dc9d3d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -44,6 +44,9 @@ def test_Norm_inputs(): name_source=['input_file'], name_template='%s_norm_threshold_mask.mnc', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='-threshold', diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index b3f5e6cf78..100ff9aaa1 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -48,6 +48,9 @@ def test_Pik_inputs(): ), png=dict(xor=('jpg', 'png'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal_offset=dict(argstr='--sagittal_offset %s', ), sagittal_offset_perc=dict(argstr='--sagittal_offset_perc %d', diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index dd3e788557..d7e8805a03 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -92,6 +92,9 @@ def test_Resample_inputs(): ), output_range=dict(argstr='-range %s %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal_slices=dict(argstr='-sagittal', xor=('transverse', 'sagittal', 'coronal'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 11ee473e78..8192222731 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -26,6 +26,9 @@ def test_Reshape_inputs(): name_template='%s_reshape.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index dea6132cdf..0bd0ff72e2 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -38,6 +38,9 @@ def test_ToEcat_inputs(): name_template='%s_to_ecat.v', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxels_as_integers=dict(argstr='-label', diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index d92ee7322b..2622ad80f3 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -32,6 +32,9 @@ def test_ToRaw_inputs(): name_template='%s.raw', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), write_byte=dict(argstr='-byte', diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index cf0550b1b1..6b4986c1ce 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -35,6 +35,9 @@ def test_VolSymm_inputs(): name_template='%s_vol_symm.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trans_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index 89bd7bda04..33d19c9731 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -30,6 +30,9 @@ def test_Volcentre_inputs(): name_template='%s_volcentre.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 74efb575c1..c997f851b6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -32,6 +32,9 @@ def test_Voliso_inputs(): name_template='%s_voliso.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 063db70230..aec28a9749 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -32,6 +32,9 @@ def test_Volpad_inputs(): name_template='%s_volpad.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth=dict(argstr='-smooth', ), smooth_distance=dict(argstr='-smooth_distance %s', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index e90331196f..d48443c650 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -33,6 +33,9 @@ def test_XfmAvg_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index 1e7702b92e..f8e81b1ace 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -28,6 +28,9 @@ def test_XfmConcat_inputs(): name_template='%s_xfmconcat.xfm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index 2ee570e7fe..dd93bc55ad 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -23,6 +23,9 @@ def test_XfmInvert_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index 7aa5289887..99cf618f98 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -58,6 +58,9 @@ def test_JistBrainMgdmSegmentation_inputs(): outSegmented=dict(argstr='--outSegmented %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index dae7e339d7..f2659ec465 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -25,6 +25,9 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): outDura=dict(argstr='--outDura %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index 077ec1f574..d60ed9b2f0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -36,6 +36,9 @@ def test_JistBrainMp2rageSkullStripping_inputs(): outMasked3=dict(argstr='--outMasked3 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 10e55ce20e..1c9f51377b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -23,6 +23,9 @@ def test_JistBrainPartialVolumeFilter_inputs(): outPartial=dict(argstr='--outPartial %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index 1fef3cc678..3a6658f2a3 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -34,6 +34,9 @@ def test_JistCortexSurfaceMeshInflation_inputs(): outOriginal=dict(argstr='--outOriginal %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 0fd3ed52e4..98cbf1c090 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -38,6 +38,9 @@ def test_JistIntensityMp2rageMasking_inputs(): outSignal2=dict(argstr='--outSignal_Mask %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 54c3909e85..7dbd011ea5 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -23,6 +23,9 @@ def test_JistLaminarProfileCalculator_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index 34b8b80569..2c3acecbab 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -27,6 +27,9 @@ def test_JistLaminarProfileGeometry_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index cc2b743f3e..f2adb4344f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -26,6 +26,9 @@ def test_JistLaminarProfileSampling_inputs(): outProfilemapped=dict(argstr='--outProfilemapped %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index e51df02dc1..99153da4ca 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -25,6 +25,9 @@ def test_JistLaminarROIAveraging_inputs(): outROI3=dict(argstr='--outROI3 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 562e5846d0..c06bf175d6 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -45,6 +45,9 @@ def test_JistLaminarVolumetricLayering_inputs(): outLayer=dict(argstr='--outLayer %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 8254b959fd..f4b4b9d060 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -23,6 +23,9 @@ def test_MedicAlgorithmImageCalculator_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 328072d54d..1d111f73d9 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -83,6 +83,9 @@ def test_MedicAlgorithmLesionToads_inputs(): outWM=dict(argstr='--outWM %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index 9422fda7ac..b6c23dfc26 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -36,6 +36,9 @@ def test_MedicAlgorithmMipavReorient_inputs(): outReoriented=dict(argstr='--outReoriented %s', sep=';', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index cbe6f4e2d5..d5f2057a86 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -38,6 +38,9 @@ def test_MedicAlgorithmN3_inputs(): outInhomogeneity2=dict(argstr='--outInhomogeneity2 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index c273c2f223..f1ec227970 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -109,6 +109,9 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): outd0=dict(argstr='--outd0 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index 9b98541542..0cf3dabbfe 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -26,6 +26,9 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): outBinary=dict(argstr='--outBinary %s', sep=';', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index 19ea1c4c89..35b3302f07 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -35,6 +35,9 @@ def test_RandomVol_inputs(): outRand1=dict(argstr='--outRand1 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 8f5f876b73..6cd546b026 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -17,6 +17,9 @@ def test_WatershedBEM_inputs(): overwrite=dict(argstr='--overwrite', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--subject %s', mandatory=True, ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 400f79676c..733f33d978 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -43,6 +43,9 @@ def test_ConstrainedSphericalDeconvolution_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response_file=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 4593e247bb..791c9b29cd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -29,6 +29,9 @@ def test_DWI2SphericalHarmonicsImage_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index c7d5675bc1..73ec54052f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -39,6 +39,9 @@ def test_DWI2Tensor_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 1a3dcc9edb..18ae66cd00 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -83,6 +83,9 @@ def test_DiffusionTensorStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index 4a88fd9cb3..da5392481a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -36,6 +36,9 @@ def test_Directions2Amplitude_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 7580cfd40c..6a1e876e09 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -31,6 +31,9 @@ def test_Erode_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index b0ee191fe1..8ab5587837 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -36,6 +36,9 @@ def test_EstimateResponseForSH_inputs(): ), quiet=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 7b9dd09517..dfdaf207bc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -53,6 +53,9 @@ def test_FilterTracks_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 5f14e69f35..798479dd67 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -42,6 +42,9 @@ def test_FindShPeaks_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index ab805c35cb..83ab7ac124 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -32,6 +32,9 @@ def test_GenerateDirections_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 2aa1a3cffa..eff3328fe1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -30,6 +30,9 @@ def test_GenerateWhiteMatterMask_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 7f970f0dc4..98b34adf82 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -50,6 +50,9 @@ def test_MRConvert_inputs(): position=3, units='mm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_dims=dict(argstr='-vox %s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 9074271d16..a295728da4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -26,6 +26,9 @@ def test_MRMultiply_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 28985f43b2..71f1c906aa 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -38,6 +38,9 @@ def test_MRTransform_inputs(): replace_transform=dict(argstr='-replace', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_image=dict(argstr='-template %s', position=1, ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 09ffc2a900..cf72940b0b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -16,6 +16,9 @@ def test_MRTrixInfo_inputs(): mandatory=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index a6fe757114..526e99ad7b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -22,6 +22,9 @@ def test_MRTrixViewer_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 796c607791..2b8148ebea 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -26,6 +26,9 @@ def test_MedianFilter3D_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 64605ad510..f4bdd96511 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -81,6 +81,9 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index fd23f4479d..7c9e4a7609 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -79,6 +79,9 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 3e466057b0..1dec4525fd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -79,6 +79,9 @@ def test_StreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 8ffdad429f..1af2a6295d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -26,6 +26,9 @@ def test_Tensor2ApparentDiffusion_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index e234065864..329f508e0f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -26,6 +26,9 @@ def test_Tensor2FractionalAnisotropy_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 08f0837540..11842c914f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -26,6 +26,9 @@ def test_Tensor2Vector_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 4ff6fa9759..51314b4fc6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -36,6 +36,9 @@ def test_Threshold_inputs(): replace_zeros_with_NaN=dict(argstr='-nan', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index 079273f9e2..240837a242 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -33,6 +33,9 @@ def test_Tracks2Prob_inputs(): position=3, units='mm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_file=dict(argstr='-template %s', position=1, ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 91af4ef87e..a3e3682fc3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -21,6 +21,9 @@ def test_ACTPrepareFSL_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 33de89ccbb..aaaeaa8c00 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -33,6 +33,9 @@ def test_BrainMask_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 9e44d4134a..2d2309df43 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -35,6 +35,9 @@ def test_BuildConnectome_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_forward=dict(argstr='-assignment_forward_search %f', ), search_radius=dict(argstr='-assignment_radial_search %f', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 18c6868538..9ebf19c72f 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -43,6 +43,9 @@ def test_ComputeTDI_inputs(): ), reference=dict(argstr='-template %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stat_tck=dict(argstr='-stat_tck %s', ), stat_vox=dict(argstr='-stat_vox %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index daaddaceca..5fac437c07 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -43,6 +43,9 @@ def test_EstimateFOD_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index fa7126432b..8ef82fd44b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -39,6 +39,9 @@ def test_FitTensor_inputs(): ), reg_term=dict(argstr='-regularisation %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 6ad81cc00c..70b2f79ecb 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -24,6 +24,9 @@ def test_Generate5tt_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 564a986116..1e29d9d880 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -35,6 +35,9 @@ def test_LabelConfig_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spine=dict(argstr='-spine %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index 63de8538d0..52d2f3e85d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -12,6 +12,9 @@ def test_MRTrix3Base_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 1e3c6983ed..a46e3d0a88 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -27,6 +27,9 @@ def test_Mesh2PVE_inputs(): mandatory=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index ddefa4361e..a1522c7a78 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -28,6 +28,9 @@ def test_ReplaceFSwithFIRST_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 216e905c11..38765e7fa6 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -47,6 +47,9 @@ def test_ResponseSD_inputs(): ), out_sf=dict(argstr='-sf %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shell=dict(argstr='-shell %s', sep=',', ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 558a90df40..aac61137f5 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -25,6 +25,9 @@ def test_TCK2VTK_inputs(): ), reference=dict(argstr='-image %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel=dict(argstr='-image %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 2719e25ea6..abf1f929c3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -31,6 +31,9 @@ def test_TensorMetrics_inputs(): ), out_fa=dict(argstr='-fa %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index dcbc5a0489..f5194de88b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -72,6 +72,9 @@ def test_Tractography_inputs(): ), power=dict(argstr='-power %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_excl=dict(argstr='-exclude %s', ), roi_incl=dict(argstr='-include %s', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py index 8d5d0e2b14..a20a9c76e6 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py @@ -77,6 +77,9 @@ def test_DwiTool_inputs(): position=6, xor=['mono_flag', 'ivim_flag', 'dti_flag', 'dti_flag2', 'ball_flag', 'ballv_flag', 'nod_flag'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgbmap_file=dict(argstr='-rgbmap %s', name_source=['source_file'], name_template='%s_rgbmap.nii.gz', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py index aa67c92149..7c12d60c76 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py @@ -67,6 +67,9 @@ def test_FitAsl_inputs(): ), pv_threshold=dict(argstr='-pvthreshold', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg=dict(argstr='-seg %s', ), segstyle=dict(argstr='-segstyle', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py index e03d999463..c2bc5ee025 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py @@ -106,6 +106,9 @@ def test_FitDwi_inputs(): name_source=['source_file'], name_template='%s_resmap.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgbmap_file=dict(argstr='-rgbmap %s', name_source=['source_file'], name_template='%s_rgbmap.nii.gz', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 86c15efaa5..292b84860a 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -68,6 +68,9 @@ def test_FitQt1_inputs(): name_source=['source_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_no=dict(argstr='-slice %d', position=9, ), diff --git a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py index a89cdf40ce..9055062ee8 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py @@ -12,6 +12,9 @@ def test_NiftyFitCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py index e18211fee7..2b5a2dc1d4 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py @@ -15,6 +15,9 @@ def test_NiftyRegCommand_inputs(): omp_core_val=dict(argstr='-omp %i', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index b4910d1a1e..5f383b0bf9 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -61,6 +61,9 @@ def test_RegAladin_inputs(): name_source=['flo_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rig_only_flag=dict(argstr='-rigOnly', ), rmask_file=dict(argstr='-rmask %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index 119b6c5e82..4626a8ec28 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -49,6 +49,9 @@ def test_RegAverage_inputs(): genfile=True, position=0, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp_files=dict(argstr='%s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index 660532fb15..bf053d7c32 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -95,6 +95,9 @@ def test_RegF3D_inputs(): name_source=['flo_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlwth2_thr_val=dict(argstr='-rLwTh %d %f', ), rlwth_thr_val=dict(argstr='--rLwTh %f', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index b5eb132c39..ba91924f57 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -22,6 +22,9 @@ def test_RegJacobian_inputs(): ), ref_file=dict(argstr='-ref %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trans_file=dict(argstr='-trans %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index f0504cb3dc..9359b86092 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -28,6 +28,9 @@ def test_RegMeasure_inputs(): ref_file=dict(argstr='-ref %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index e1ca405567..5d5f3459ea 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -34,6 +34,9 @@ def test_RegResample_inputs(): ref_file=dict(argstr='-ref %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tensor_flag=dict(argstr='-tensor ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 495e0854d7..8162c95308 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -40,6 +40,9 @@ def test_RegTools_inputs(): name_source=['in_file'], name_template='%s_tools.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rms_val=dict(argstr='-rms %s', ), smo_g_val=dict(argstr='-smoG %f %f %f', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index 00c017d1d3..b1553b28ef 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -70,6 +70,9 @@ def test_RegTransform_inputs(): position=1, requires=['ref1_file'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upd_s_form_input=dict(argstr='-updSform %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index 714e201fc3..e465b176df 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -43,6 +43,9 @@ def test_BinaryMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index 484f2ac3b4..223c536ffb 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -32,6 +32,9 @@ def test_BinaryMathsInteger_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index 14ea5463b0..3fb7cb25d9 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -36,6 +36,9 @@ def test_BinaryStats_inputs(): mandatory=True, position=4, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index a54501c730..f3bae45fb8 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -26,6 +26,9 @@ def test_CalcTopNCC_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), top_templates=dict(argstr='-n %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index c42acf6a70..5950c76423 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -58,6 +58,9 @@ def test_EM_inputs(): ), relax_priors=dict(argstr='-rf %s %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index aae126636a..eea089b911 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -39,6 +39,9 @@ def test_FillLesions_inputs(): name_template='%s_lesions_filled.nii.gz', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search=dict(argstr='-search %f', ), size=dict(argstr='-size %d', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index b572ac940c..2e98bf6723 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -42,6 +42,9 @@ def test_LabelFusion_inputs(): ), proportion=dict(argstr='-prop %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), set_pq=dict(argstr='-setPQ %f %f', ), sm_ranking=dict(argstr='-%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index 640c7088bf..ee121879ea 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -24,6 +24,9 @@ def test_MathsCommand_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index 3980bc9ac3..4b7eba953c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -30,6 +30,9 @@ def test_Merge_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py index 55dc5d9d1d..45021be8ff 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py @@ -12,6 +12,9 @@ def test_NiftySegCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index f535133dee..528c733789 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -22,6 +22,9 @@ def test_StatsCommand_inputs(): mask_file=dict(argstr='-m %s', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 9bd5ca771d..99e8237713 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -48,6 +48,9 @@ def test_TupleMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index ed98de196f..792a310115 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -28,6 +28,9 @@ def test_UnaryMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index 17252084c6..41266c950c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -26,6 +26,9 @@ def test_UnaryStats_inputs(): mandatory=True, position=4, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 915f2c85d2..4e1e1e300e 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -13,6 +13,9 @@ def test_ComputeMask_inputs(): mean_volume=dict(mandatory=True, ), reference_volume=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = ComputeMask.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 7d44248cbc..77d9fe79ee 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -22,6 +22,9 @@ def test_EstimateContrast_inputs(): ), reg_names=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 5c3f881179..959e7e0ee6 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -22,6 +22,9 @@ def test_FitGLM_inputs(): ), plot_design_matrix=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_residuals=dict(usedefault=True, ), session_info=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 80902a7d0c..4a5444736c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -13,6 +13,9 @@ def test_FmriRealign4d_inputs(): ), loops=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_order=dict(requires=['time_interp'], ), speedup=dict(usedefault=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index f9c815fedb..fd6474c09d 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -11,6 +11,9 @@ def test_Similarity_inputs(): mask2=dict(), metric=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index b4e495a434..3325ffa67c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -10,6 +10,9 @@ def test_SpaceTimeRealigner_inputs(): in_file=dict(mandatory=True, min_ver='0.4.0.dev', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_info=dict(requires=['slice_times'], ), slice_times=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index c1bc16e103..e052b9cec3 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -14,6 +14,9 @@ def test_Trim_inputs(): in_file=dict(mandatory=True, ), out_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), suffix=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 4d970500d2..72d36fb8e3 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -21,6 +21,9 @@ def test_CoherenceAnalyzer_inputs(): ), output_csv_file=dict(), output_figure_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CoherenceAnalyzer.input_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 9c3d3928e5..867e937dc3 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -29,6 +29,9 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 273d140224..29444a14a5 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -40,6 +40,9 @@ def test_BRAINSTalairach_inputs(): outputGrid=dict(argstr='--outputGrid %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index daee0ded09..50f11b8c5f 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -21,6 +21,9 @@ def test_BRAINSTalairachMask_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), talairachBox=dict(argstr='--talairachBox %s', ), talairachParameters=dict(argstr='--talairachParameters %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index f5275319a6..7a86062f31 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -30,6 +30,9 @@ def test_GenerateEdgeMapImage_inputs(): outputMaximumGradientImage=dict(argstr='--outputMaximumGradientImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperPercentileMatching=dict(argstr='--upperPercentileMatching %f', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index 262ef2c485..3481277f7f 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -20,6 +20,9 @@ def test_GeneratePurePlugMask_inputs(): outputMaskFile=dict(argstr='--outputMaskFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold %f', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index c2d76581be..64783a16fb 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -29,6 +29,9 @@ def test_HistogramMatchingFilter_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index c7bac4f4f6..0e74ef5eb9 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -18,6 +18,9 @@ def test_SimilarityIndex_inputs(): ), outputCSVFilename=dict(argstr='--outputCSVFilename %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdInterval=dict(argstr='--thresholdInterval %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index b355239d30..28950f2130 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -43,6 +43,9 @@ def test_DWIConvert_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index 209c267fdc..a4d357c8b2 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -18,6 +18,9 @@ def test_compareTractInclusion_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), standardFiber=dict(argstr='--standardFiber %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index c3bff362a2..b2dab2104b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -16,6 +16,9 @@ def test_dtiaverage_inputs(): ), inputs=dict(argstr='--inputs %s...', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tensor_output=dict(argstr='--tensor_output %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 74c63221dc..14b596d206 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -36,6 +36,9 @@ def test_dtiestim_inputs(): ), method=dict(argstr='--method %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shiftNeg=dict(argstr='--shiftNeg ', ), shiftNegCoeff=dict(argstr='--shiftNegCoeff %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index f6822c5558..e6caee54b4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -76,6 +76,9 @@ def test_dtiprocess_inputs(): ), reorientation=dict(argstr='--reorientation %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rot_output=dict(argstr='--rot_output %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index b6a904d649..5eeb234494 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -19,6 +19,9 @@ def test_extractNrrdVectorIndex_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), setImageOrientation=dict(argstr='--setImageOrientation %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index c9a1a591cc..741ee46e1b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -21,6 +21,9 @@ def test_gtractAnisotropyMap_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 318ad5fea4..5e77d4f61a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -23,6 +23,9 @@ def test_gtractAverageBvalues_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index 0b3f2ec979..489243f9be 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -23,6 +23,9 @@ def test_gtractClipAnisotropy_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 9453af96ea..a5ff744bdf 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -46,6 +46,9 @@ def test_gtractCoRegAnatomy_inputs(): ), relaxationFactor=dict(argstr='--relaxationFactor %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), spatialScale=dict(argstr='--spatialScale %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 68d85d66b6..2af2f82f90 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -21,6 +21,9 @@ def test_gtractConcatDwi_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index 13fa034804..a2f60ebb74 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -21,6 +21,9 @@ def test_gtractCopyImageOrientation_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index fa7444c2a2..6d7ce9d9d8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -42,6 +42,9 @@ def test_gtractCoregBvalues_inputs(): ), relaxationFactor=dict(argstr='--relaxationFactor %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), spatialScale=dict(argstr='--spatialScale %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 6cdb0ca6b8..fc77653036 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -28,6 +28,9 @@ def test_gtractCostFastMarching_inputs(): outputSpeedVolume=dict(argstr='--outputSpeedVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index 1d2da52d72..4c82e1cef4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -21,6 +21,9 @@ def test_gtractCreateGuideFiber_inputs(): outputFiber=dict(argstr='--outputFiber %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 9b30f161c6..1c3eee20dd 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -33,6 +33,9 @@ def test_gtractFastMarchingTracking_inputs(): outputTract=dict(argstr='--outputTract %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index e3db9ee6d2..7b6bcf5ced 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -47,6 +47,9 @@ def test_gtractFiberTracking_inputs(): ), randomSeed=dict(argstr='--randomSeed %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index a78b5bb9f9..62f9c07799 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -21,6 +21,9 @@ def test_gtractImageConformity_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index de662d068b..74d6b44fe3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -24,6 +24,9 @@ def test_gtractInvertBSplineTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index 10b14f9def..fb2e08674b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -21,6 +21,9 @@ def test_gtractInvertDisplacementField_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subsamplingFactor=dict(argstr='--subsamplingFactor %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index a995a4e4cd..b41fa4153e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -19,6 +19,9 @@ def test_gtractInvertRigidTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index e9b668a716..7d9a96fe5a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -23,6 +23,9 @@ def test_gtractResampleAnisotropy_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index edc706cf4e..cb59797fa3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -23,6 +23,9 @@ def test_gtractResampleB0_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index 860e96fd09..fe9bde4fdc 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -23,6 +23,9 @@ def test_gtractResampleCodeImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index 3ecd5742e5..58f5567780 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -31,6 +31,9 @@ def test_gtractResampleDWIInPlace_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpDWITransform=dict(argstr='--warpDWITransform %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index 34997e8799..efa141c3de 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -23,6 +23,9 @@ def test_gtractResampleFibers_inputs(): outputTract=dict(argstr='--outputTract %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 0cd3f101db..b3c9d0b682 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -37,6 +37,9 @@ def test_gtractTensor_inputs(): ), resampleIsotropic=dict(argstr='--resampleIsotropic ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), size=dict(argstr='--size %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 7feeabae6f..921f56142c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -21,6 +21,9 @@ def test_gtractTransformToDisplacementField_inputs(): outputDeformationFieldVolume=dict(argstr='--outputDeformationFieldVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 7ded2e168c..e94813ed60 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -17,6 +17,9 @@ def test_maxcurvature_inputs(): output=dict(argstr='--output %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 0927be112c..63ca97942c 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -61,6 +61,9 @@ def test_UKFTractography_inputs(): ), recordTrace=dict(argstr='--recordTrace ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedFALimit=dict(argstr='--seedFALimit %f', ), seedsFile=dict(argstr='--seedsFile %s', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index 11c67161dc..af0e2dd827 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -29,6 +29,9 @@ def test_fiberprocess_inputs(): ), no_warp=dict(argstr='--no_warp ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveProperties=dict(argstr='--saveProperties ', ), tensor_volume=dict(argstr='--tensor_volume %s', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index 613664bb15..f0aa1d7f2f 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -14,6 +14,9 @@ def test_fiberstats_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index 3dda03843f..28b10d1c79 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -29,6 +29,9 @@ def test_fibertrack_inputs(): ), really_verbose=dict(argstr='--really_verbose ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_label=dict(argstr='--source_label %d', ), step_size=dict(argstr='--step_size %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index 446f520077..4c5621231f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -19,6 +19,9 @@ def test_CannyEdge_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperThreshold=dict(argstr='--upperThreshold %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 6014c01238..355b623ff5 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -32,6 +32,9 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 6690a83005..31b9ed1f46 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -21,6 +21,9 @@ def test_DilateImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 80c7fe1636..9a9d28cc28 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -21,6 +21,9 @@ def test_DilateMask_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sizeStructuralElement=dict(argstr='--sizeStructuralElement %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index ad886bd5c5..1ee1484880 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -21,6 +21,9 @@ def test_DistanceMaps_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index 017f27c3af..1d4589a1e6 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -16,6 +16,9 @@ def test_DumpBinaryTrainingVectors_inputs(): ), inputVectorFilename=dict(argstr='--inputVectorFilename %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index c5cbd6fc35..1b77316f68 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -21,6 +21,9 @@ def test_ErodeImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 6e73eb584a..7633350f63 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -19,6 +19,9 @@ def test_FlippedDifference_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 5a3bcbd888..2c1220677b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -21,6 +21,9 @@ def test_GenerateBrainClippedImage_inputs(): outputFileName=dict(argstr='--outputFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index ddca6453e8..ba15282815 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -23,6 +23,9 @@ def test_GenerateSummedGradientImage_inputs(): outputFileName=dict(argstr='--outputFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index 09915d813c..6edb1d58ec 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -21,6 +21,9 @@ def test_GenerateTestImage_inputs(): ), outputVolumeSize=dict(argstr='--outputVolumeSize %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperBoundOfOutputVolume=dict(argstr='--upperBoundOfOutputVolume %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 625a0fe338..f0d1c5bfea 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -21,6 +21,9 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 128d3d62d1..bd72549a2e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -24,6 +24,9 @@ def test_HammerAttributeCreator_inputs(): ), outputVolumeBase=dict(argstr='--outputVolumeBase %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index c029f33409..565e0b8dd4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -21,6 +21,9 @@ def test_NeighborhoodMean_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 4a80af0377..f6ea39bf50 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -21,6 +21,9 @@ def test_NeighborhoodMedian_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 03ffe65d04..b2cf49922b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -19,6 +19,9 @@ def test_STAPLEAnalysis_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index de0816897c..8e78238b32 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -19,6 +19,9 @@ def test_TextureFromNoiseImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index de8a74c45e..01b616fe5e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -23,6 +23,9 @@ def test_TextureMeasureFilter_inputs(): outputFilename=dict(argstr='--outputFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index f20b6b5ca7..f591f04dc9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -26,6 +26,9 @@ def test_UnbiasedNonLocalMeans_inputs(): rc=dict(argstr='--rc %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rs=dict(argstr='--rs %s', sep=',', ), diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 83aaec5ea3..fd4b5da5c6 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -25,6 +25,9 @@ def test_scalartransform_inputs(): output_image=dict(argstr='--output_image %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformation=dict(argstr='--transformation %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index 9aee3d80d1..1ec3021f74 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_BRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 7447f574af..3758413206 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -118,6 +118,9 @@ def test_BRAINSFit_inputs(): ), reproportionScale=dict(argstr='--reproportionScale %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), scaleOutputValues=dict(argstr='--scaleOutputValues ', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 6e10f86ca0..f20909a41b 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -34,6 +34,9 @@ def test_BRAINSResample_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpTransform=dict(argstr='--warpTransform %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 4c90eaf915..2b176c5ddc 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -19,6 +19,9 @@ def test_BRAINSResize_inputs(): ), pixelType=dict(argstr='--pixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleFactor=dict(argstr='--scaleFactor %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index bc0ead4e53..bbaa6cf436 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -22,6 +22,9 @@ def test_BRAINSTransformFromFiducials_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveTransform=dict(argstr='--saveTransform %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index 96e28abafa..bda28deeee 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_VBRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 110cfcef77..68060131d6 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -77,6 +77,9 @@ def test_BRAINSABC_inputs(): ), purePlugsThreshold=dict(argstr='--purePlugsThreshold %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), restoreState=dict(argstr='--restoreState %s', ), saveState=dict(argstr='--saveState %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 30ffbaa945..dc9cf1a974 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -91,6 +91,9 @@ def test_BRAINSConstellationDetector_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 5a8f506310..51da71bbec 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -30,6 +30,9 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): priorLabelCodes=dict(argstr='--priorLabelCodes %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 6e7652979e..806c4a6d55 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -38,6 +38,9 @@ def test_BRAINSCut_inputs(): ), randomTreeDepth=dict(argstr='--randomTreeDepth %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trainModel=dict(argstr='--trainModel ', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 1cd57a8267..0a7d620e0b 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -28,6 +28,9 @@ def test_BRAINSMultiSTAPLE_inputs(): ), resampledVolumePrefix=dict(argstr='--resampledVolumePrefix %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skipResampling=dict(argstr='--skipResampling ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index fe1ce50a3d..e25820b7e8 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -34,6 +34,9 @@ def test_BRAINSROIAuto_inputs(): ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdCorrectionFactor=dict(argstr='--thresholdCorrectionFactor %f', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 2e754dd1b1..7b620aac56 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -25,6 +25,9 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): outputBinaryVolume=dict(argstr='--outputBinaryVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), setCutDirectionForLandmark=dict(argstr='--setCutDirectionForLandmark %s', sep=',', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 4ebd23e30f..317cbd994c 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -29,6 +29,9 @@ def test_ESLR_inputs(): ), preserveOutside=dict(argstr='--preserveOutside ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), safetySize=dict(argstr='--safetySize %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 2d50880990..7662bfffe6 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -16,6 +16,9 @@ def test_DWICompare_inputs(): ), inputVolume2=dict(argstr='--inputVolume2 %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 437d2d9087..adacb240a3 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -18,6 +18,9 @@ def test_DWISimpleCompare_inputs(): ), inputVolume2=dict(argstr='--inputVolume2 %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 0ae702b805..f5a43a29af 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -17,6 +17,9 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 9636e284f7..7a72ae3256 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -30,6 +30,9 @@ def test_BRAINSAlignMSP_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index d08f270b5e..9304d97b9b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -23,6 +23,9 @@ def test_BRAINSClipInferior_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index ff5447109c..246a1f9420 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -30,6 +30,9 @@ def test_BRAINSConstellationModeler_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index b9286e8835..d4af5fb35d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -21,6 +21,9 @@ def test_BRAINSEyeDetector_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index d8288ff86f..c2ff4f215e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -24,6 +24,9 @@ def test_BRAINSInitializedControlPoints_inputs(): permuteOrder=dict(argstr='--permuteOrder %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splineGridSize=dict(argstr='--splineGridSize %s', sep=',', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 332534edf8..8cf8b49dfa 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -21,6 +21,9 @@ def test_BRAINSLandmarkInitializer_inputs(): outputTransformFilename=dict(argstr='--outputTransformFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index 9bcf5409c7..ec44e1a7ac 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -16,6 +16,9 @@ def test_BRAINSLinearModelerEPCA_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 048b66b32b..cd71b5c734 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -28,6 +28,9 @@ def test_BRAINSLmkTransform_inputs(): outputResampledVolume=dict(argstr='--outputResampledVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 31548abd1c..528775dfe7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -43,6 +43,9 @@ def test_BRAINSMush_inputs(): outputWeightsFile=dict(argstr='--outputWeightsFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed %s', sep=',', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index a4fd3abf5d..882e44fa20 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -31,6 +31,9 @@ def test_BRAINSSnapShotWriter_inputs(): outputFilename=dict(argstr='--outputFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index 5c168fbb6a..901daed765 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -26,6 +26,9 @@ def test_BRAINSTransformConvert_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index 364747314a..507da98cca 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -29,6 +29,9 @@ def test_BRAINSTrimForegroundInDirection_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index bf91238a1d..ed022450cd 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -17,6 +17,9 @@ def test_CleanUpOverlapLabels_inputs(): outputBinaryVolumes=dict(argstr='--outputBinaryVolumes %s...', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index d15f647808..2e60991a5b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -50,6 +50,9 @@ def test_FindCenterOfBrain_inputs(): ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index cda3720812..928b90c2f3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -19,6 +19,9 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): outputLabelVolume=dict(argstr='--outputLabelVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 6823172b50..c07cae9efe 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -24,6 +24,9 @@ def test_ImageRegionPlotter_inputs(): ), outputJointHistogramData=dict(argstr='--outputJointHistogramData %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), useIntensityForHistogram=dict(argstr='--useIntensityForHistogram ', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index 9b8df83880..68e8759fea 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -22,6 +22,9 @@ def test_JointHistogram_inputs(): ), outputJointHistogramImage=dict(argstr='--outputJointHistogramImage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 1cf264afcc..22a851a5ed 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -19,6 +19,9 @@ def test_ShuffleVectorsModule_inputs(): ), resampleProportion=dict(argstr='--resampleProportion %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 927a33fd04..985296aa5d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -24,6 +24,9 @@ def test_fcsv_to_hdf5_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), versionID=dict(argstr='--versionID %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index abb847e478..4c57c439a4 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -17,6 +17,9 @@ def test_insertMidACPCpoint_inputs(): outputLandmarkFile=dict(argstr='--outputLandmarkFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index 3122d627ed..8bc07fb12d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -17,6 +17,9 @@ def test_landmarksConstellationAligner_inputs(): outputLandmarksPaired=dict(argstr='--outputLandmarksPaired %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 49772ca873..2dedbf2f06 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -21,6 +21,9 @@ def test_landmarksConstellationWeights_inputs(): outputWeightsList=dict(argstr='--outputWeightsList %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 649b1db802..9016a579c4 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -19,6 +19,9 @@ def test_DTIexport_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 05f18b318e..3c3b575046 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -19,6 +19,9 @@ def test_DTIimport_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), testingmode=dict(argstr='--testingmode ', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index 9cf7cc1008..346c5b826b 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -26,6 +26,9 @@ def test_DWIJointRicianLMMSEFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rf=dict(argstr='--rf %s', sep=',', ), diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 97c015d7f4..29f3adc716 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -36,6 +36,9 @@ def test_DWIRicianLMMSEFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rf=dict(argstr='--rf %s', sep=',', ), diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index ba807a5052..7a6f93dc76 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -27,6 +27,9 @@ def test_DWIToDTIEstimation_inputs(): hash_files=False, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shiftNeg=dict(argstr='--shiftNeg ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 0b997a9c40..8ec3d8f77e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -21,6 +21,9 @@ def test_DiffusionTensorScalarMeasurements_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 0deaf6543e..c098d4ce9f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -23,6 +23,9 @@ def test_DiffusionWeightedVolumeMasking_inputs(): ), removeislands=dict(argstr='--removeislands ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdMask=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index d54f99f55d..ae7d3a1646 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -46,6 +46,9 @@ def test_ResampleDTIVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_point=dict(argstr='--rotation_point %s', ), size=dict(argstr='--size %s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 55f127a6c9..64fe0e391f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -38,6 +38,9 @@ def test_TractographyLabelMapSeeding_inputs(): ), randomgrid=dict(argstr='--randomgrid ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedspacing=dict(argstr='--seedspacing %f', ), stoppingcurvature=dict(argstr='--stoppingcurvature %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 7914b71736..fbc6addebe 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -24,6 +24,9 @@ def test_AddScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index eed01c2996..64174e81d6 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -19,6 +19,9 @@ def test_CastScalarVolume_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), type=dict(argstr='--type %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index be6ae4ba84..d8a1193d1e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -25,6 +25,9 @@ def test_CheckerBoardFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 01c28d842f..3f0c3f837e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -23,6 +23,9 @@ def test_CurvatureAnisotropicDiffusion_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 8ec1aa362c..b05e6e0240 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -25,6 +25,9 @@ def test_ExtractSkeleton_inputs(): ), pointsFile=dict(argstr='--pointsFile %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), type=dict(argstr='--type %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index c5aa979bc6..8f5b51f783 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -19,6 +19,9 @@ def test_GaussianBlurImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index ce307bde81..20e5753aa8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -23,6 +23,9 @@ def test_GradientAnisotropicDiffusion_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 115c25ceab..39500d65aa 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -19,6 +19,9 @@ def test_GrayscaleFillHoleImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 12c4c5402f..78c431092e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -19,6 +19,9 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 00ef1b26dc..cc60f4b6fd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -26,6 +26,9 @@ def test_HistogramMatching_inputs(): referenceVolume=dict(argstr='%s', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold ', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 9640cf5457..358a04dcc4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -24,6 +24,9 @@ def test_ImageLabelCombine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index c9f6c1bd8a..29482142ea 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -26,6 +26,9 @@ def test_MaskScalarVolume_inputs(): ), replace=dict(argstr='--replace %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 07f11bddae..8f1cef1c0e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -22,6 +22,9 @@ def test_MedianImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index f53fe36ef0..560bf28903 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -24,6 +24,9 @@ def test_MultiplyScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index a9cf9f449d..9a6f012822 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -35,6 +35,9 @@ def test_N4ITKBiasFieldCorrection_inputs(): outputimage=dict(argstr='--outputimage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), splinedistance=dict(argstr='--splinedistance %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index d317e139f8..388daafe55 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -44,6 +44,9 @@ def test_ResampleScalarVectorDWIVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_point=dict(argstr='--rotation_point %s', ), size=dict(argstr='--size %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 78fd010e43..de96efb3aa 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -24,6 +24,9 @@ def test_SubtractScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 840f527211..22ebe5aa1d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -23,6 +23,9 @@ def test_ThresholdScalarVolume_inputs(): ), outsidevalue=dict(argstr='--outsidevalue %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold %d', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 9d8a717dac..986592cc9e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -28,6 +28,9 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): radius=dict(argstr='--radius %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index de89d21763..a712864f18 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -29,6 +29,9 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rs=dict(argstr='--rs %s', sep=',', ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 1095a2169b..71532612fa 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -34,6 +34,9 @@ def test_AffineRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 2965724b45..e7fb49ea0b 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -41,6 +41,9 @@ def test_BSplineDeformableRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 9b0c0cb41e..117468b129 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -17,6 +17,9 @@ def test_BSplineToDeformationField_inputs(): ), refImage=dict(argstr='--refImage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tfm=dict(argstr='--tfm %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 5c6ca38748..bde2730d11 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -61,6 +61,9 @@ def test_ExpertAutomatedRegistration_inputs(): resampledImage=dict(argstr='--resampledImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigidMaxIterations=dict(argstr='--rigidMaxIterations %d', ), rigidSamplingRatio=dict(argstr='--rigidSamplingRatio %f', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index e62a728d7d..659b4944c3 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -38,6 +38,9 @@ def test_LinearRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index cea84022e4..70b1f13b01 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -31,6 +31,9 @@ def test_MultiResolutionAffineRegistration_inputs(): resampledImage=dict(argstr='--resampledImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveTransform=dict(argstr='--saveTransform %s', hash_files=False, ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index a598be2eee..298b6bf46c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -25,6 +25,9 @@ def test_OtsuThresholdImageFilter_inputs(): ), outsideValue=dict(argstr='--outsideValue %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index ee088157b2..4bba73c371 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -27,6 +27,9 @@ def test_OtsuThresholdSegmentation_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 6084ba5d83..c89ce07e4b 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -21,6 +21,9 @@ def test_ResampleScalarVolume_inputs(): ), interpolation=dict(argstr='--interpolation %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spacing=dict(argstr='--spacing %s', sep=',', ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index ef5b7f2168..725711ec20 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -38,6 +38,9 @@ def test_RigidRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index fc174efcfa..678c64dc30 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -30,6 +30,9 @@ def test_IntensityDifferenceMetric_inputs(): reportFileName=dict(argstr='--reportFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sensitivityThreshold=dict(argstr='--sensitivityThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 0b66af94f3..58c58ca846 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -33,6 +33,9 @@ def test_PETStandardUptakeValueComputation_inputs(): ), petVolume=dict(argstr='--petVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 35e08a6db1..3624fb5cd5 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -21,6 +21,9 @@ def test_ACPCTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index 9aee3d80d1..1ec3021f74 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_BRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index f7521f7551..38e482a47a 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -114,6 +114,9 @@ def test_BRAINSFit_inputs(): ), reproportionScale=dict(argstr='--reproportionScale %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleOutputValues=dict(argstr='--scaleOutputValues ', ), skewScale=dict(argstr='--skewScale %f', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 6e10f86ca0..f20909a41b 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -34,6 +34,9 @@ def test_BRAINSResample_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpTransform=dict(argstr='--warpTransform %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index ee3db65e07..142c4703c8 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -18,6 +18,9 @@ def test_FiducialRegistration_inputs(): ), outputMessage=dict(argstr='--outputMessage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rms=dict(argstr='--rms %f', ), saveTransform=dict(argstr='--saveTransform %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 96e28abafa..bda28deeee 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_VBRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 8792856f51..66ccf7f87d 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -30,6 +30,9 @@ def test_BRAINSROIAuto_inputs(): ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdCorrectionFactor=dict(argstr='--thresholdCorrectionFactor %f', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 3e51e217f2..e89c2bcc17 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -43,6 +43,9 @@ def test_EMSegmentCommandLine_inputs(): ), registrationPackage=dict(argstr='--registrationPackage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultMRMLSceneFileName=dict(argstr='--resultMRMLSceneFileName %s', hash_files=False, ), diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 844bf8a0e0..6ed3a6e4e2 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -28,6 +28,9 @@ def test_RobustStatisticsSegmenter_inputs(): originalImageFileName=dict(argstr='%s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentedImageFileName=dict(argstr='%s', hash_files=False, position=-1, diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 9600134d40..5ae3f611e0 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -27,6 +27,9 @@ def test_SimpleRegionGrowingSegmentation_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed %s...', ), smoothingIterations=dict(argstr='--smoothingIterations %d', diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index b533e70237..5892977f6b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -19,6 +19,9 @@ def test_DicomToNrrdConverter_inputs(): ), outputVolume=dict(argstr='--outputVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index fd8a401276..9ecf032b4d 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -17,6 +17,9 @@ def test_EMSegmentTransformToNewFormat_inputs(): outputMRMLFileName=dict(argstr='--outputMRMLFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), templateFlag=dict(argstr='--templateFlag ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 7c9d4b027d..4f5e38f6b5 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -25,6 +25,9 @@ def test_GrayscaleModelMaker_inputs(): ), pointnormals=dict(argstr='--pointnormals ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth=dict(argstr='--smooth %d', ), splitnormals=dict(argstr='--splitnormals ', diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index b066a5081f..1ebdca13d1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -27,6 +27,9 @@ def test_LabelMapSmoothing_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 2102c77cdf..89ce57b851 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -22,6 +22,9 @@ def test_MergeModels_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 4e84c252a9..6a37b524b1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -41,6 +41,9 @@ def test_ModelMaker_inputs(): ), pointnormals=dict(argstr='--pointnormals ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveIntermediateModels=dict(argstr='--saveIntermediateModels ', ), skipUnNamed=dict(argstr='--skipUnNamed ', diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 1b7dcd8076..1595d99ae6 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -21,6 +21,9 @@ def test_ModelToLabelMap_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface=dict(argstr='%s', position=-2, ), diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index a75c12d463..7d1338a038 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -21,6 +21,9 @@ def test_OrientScalarVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index d5e50cf6c9..ff04f1fd72 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -22,6 +22,9 @@ def test_ProbeVolumeWithModel_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index 1a24d5901e..6a81f1bc19 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -12,6 +12,9 @@ def test_SlicerCommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index c5064f2f59..2ebb74f4a7 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -13,6 +13,9 @@ def test_Analyze2nii_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, @@ -34,6 +37,9 @@ def test_Analyze2nii_outputs(): ), nifti_file=dict(), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index 5847ad98fe..b9b5bf2acd 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -22,6 +22,9 @@ def test_ApplyDeformations_inputs(): reference_volume=dict(field='comp{2}.id.space', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 849c5580db..e08957db57 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -24,6 +24,9 @@ def test_ApplyInverseDeformation_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(field='comp{1}.inv.space', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 8100981604..0d22e8bc70 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -18,6 +18,9 @@ def test_ApplyTransform_inputs(): out_file=dict(genfile=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 04bae31f0d..dbb2ef21d0 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -16,6 +16,9 @@ def test_CalcCoregAffine_inputs(): mandatory=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(mandatory=True, ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 468ad7e3e3..c9680d6438 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -23,6 +23,9 @@ def test_Coregister_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), separation=dict(field='eoptions.sep', ), source=dict(copyfile=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index c1a8d34725..251df4707c 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -25,6 +25,9 @@ def test_CreateWarped_inputs(): modulate=dict(field='crt_warped.jactransf', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index c7197a586f..1dc974bc81 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -21,6 +21,9 @@ def test_DARTEL_inputs(): paths=dict(), regularization_form=dict(field='warp.settings.rform', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_prefix=dict(field='warp.settings.template', usedefault=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index d3e7815756..d7be1bcbd5 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -24,6 +24,9 @@ def test_DARTELNorm2MNI_inputs(): modulate=dict(field='mni_norm.preserve', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_file=dict(copyfile=False, field='mni_norm.template', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index dff4b04d06..3c65bcb9dd 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -26,6 +26,9 @@ def test_DicomImport_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 76d4a25bf5..3c5b040cc8 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -21,6 +21,9 @@ def test_EstimateContrast_inputs(): residual_image=dict(copyfile=False, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, field='spmmat', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 703c97c6fc..6e143e19bc 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -15,6 +15,9 @@ def test_EstimateModel_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, field='spmmat', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index eaa4272d8d..21b4421273 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -28,6 +28,9 @@ def test_FactorialDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 908672beb7..28bb7b196c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -31,6 +31,9 @@ def test_Level1Design_inputs(): model_serial_correlations=dict(field='cvi', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session_info=dict(field='sess', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 54ec275450..4d3b20d1a2 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -34,6 +34,9 @@ def test_MultipleRegressionDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 4c77c5d203..b2d839daec 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -19,6 +19,9 @@ def test_NewSegment_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='warp.samp', ), tissues=dict(field='tissue', diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index f6cb425d6a..4436ad5c26 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -32,6 +32,9 @@ def test_Normalize_inputs(): xor=['source', 'template'], ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(copyfile=True, field='subj.source', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index 9d537e34b1..a37d596871 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -35,6 +35,9 @@ def test_Normalize12_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='eoptions.samp', ), smoothness=dict(field='eoptions.fwhm', diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 1148cbf9fa..19eb4562cf 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -31,6 +31,9 @@ def test_OneSampleTTestDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index f9cce92a37..f1562df787 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -35,6 +35,9 @@ def test_PairedTTestDesign_inputs(): mandatory=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 6c54c4a945..5fe77d6977 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -28,6 +28,9 @@ def test_Realign_inputs(): ), register_to_mean=dict(field='eoptions.rtm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), separation=dict(field='eoptions.sep', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 4a433e5b3d..d64785469b 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -16,6 +16,9 @@ def test_Reslice_inputs(): ), out_file=dict(), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space_defining=dict(mandatory=True, ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 06e8f2e607..5ea5d2af27 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -18,6 +18,9 @@ def test_ResliceToReference_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(field='comp{1}.id.space', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index ed841142dd..874aeda7db 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -11,6 +11,9 @@ def test_SPMCommand_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index 739a4e1ca9..e4c9a274c1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -31,6 +31,9 @@ def test_Segment_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='opts.samp', ), save_bias_corrected=dict(field='output.biascor', diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index 739d0157a1..9f0373978c 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -24,6 +24,9 @@ def test_SliceTiming_inputs(): ref_slice=dict(field='refslice', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_order=dict(field='so', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index 378f504328..e5fb9e1fbb 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -24,6 +24,9 @@ def test_Smooth_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index e30b163857..1927ba29a0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -23,6 +23,9 @@ def test_Threshold_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index d73cd4f98f..82d0d81ac5 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -17,6 +17,9 @@ def test_ThresholdStatistics_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index cb19a35f62..2dbcd8304d 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -36,6 +36,9 @@ def test_TwoSampleTTestDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index f02579b66c..52f98a2586 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -82,6 +82,9 @@ def test_VBMSegment_inputs(): pve_label_normalized=dict(field='estwrite.output.label.warped', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='estwrite.opts.samp', usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py new file mode 100644 index 0000000000..36d02d5fe9 --- /dev/null +++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py @@ -0,0 +1,28 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..bids_utils import BIDSDataGrabber + + +def test_BIDSDataGrabber_inputs(): + input_map = dict(base_dir=dict(mandatory=True, + ), + output_query=dict(), + raise_on_empty=dict(usedefault=True, + ), + return_type=dict(usedefault=True, + ), + ) + inputs = BIDSDataGrabber.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value + + +def test_BIDSDataGrabber_outputs(): + output_map = dict() + outputs = BIDSDataGrabber.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index 9c1f2cfaa6..670ea84cc7 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -7,6 +7,9 @@ def test_BaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = BaseInterface.input_spec() diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index b67b83bf5f..30c361226e 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -25,6 +25,9 @@ def test_Bru2_inputs(): output_filename=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 2acfbfbaab..847c88bcac 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -22,6 +22,9 @@ def test_C3dAffineTool_inputs(): reference_file=dict(argstr='-ref %s', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='-src %s', position=2, ), diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index 01f7c8f6fb..e42d5984a9 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -12,6 +12,9 @@ def test_CommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index f402bdc53d..a9621efbad 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -12,6 +12,9 @@ def test_DataFinder_inputs(): ), max_depth=dict(), min_depth=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), root_paths=dict(mandatory=True, ), unpack_single=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 5795ce969d..72f0378392 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -10,6 +10,9 @@ def test_DataGrabber_inputs(): ), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), template=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 0ea2b71a6d..98c69b7065 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -20,6 +20,9 @@ def test_DataSink_inputs(): regexp_substitutions=dict(), remove_dest_dir=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), strip_dir=dict(), substitutions=dict(), ) diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index eb155ff975..775fde2497 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -50,6 +50,9 @@ def test_Dcm2nii_inputs(): reorient_and_crop=dict(argstr='-x', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_dir=dict(argstr='%s', mandatory=True, position=-1, diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index a396853b70..5e6b5118de 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -33,6 +33,9 @@ def test_Dcm2niix_inputs(): output_dir=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_file=dict(argstr='-s', usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 1af0874410..30bfa03a45 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -9,6 +9,9 @@ def test_FreeSurferSource_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(mandatory=True, ), subjects_dir=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index 02e45692a9..a6ac687661 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -7,6 +7,9 @@ def test_IOBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = IOBase.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 3a93359459..a5be775470 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -9,6 +9,9 @@ def test_JSONFileGrabber_inputs(): usedefault=True, ), in_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = JSONFileGrabber.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 32b51c9dc5..6d22a770f4 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -12,6 +12,9 @@ def test_JSONFileSink_inputs(): in_dict=dict(usedefault=True, ), out_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = JSONFileSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 6801f40353..fdbc90b304 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -29,6 +29,9 @@ def test_MatlabCommand_inputs(): ), prescript=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), script=dict(argstr='-r "%s;exit"', mandatory=True, position=-1, diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 7abd5878a0..acc5f6e0fb 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -67,6 +67,9 @@ def test_MeshFix_inputs(): ), remove_handles=dict(argstr='--remove-handles', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_as_freesurfer_mesh=dict(argstr='--fsmesh', xor=['save_as_vrml', 'save_as_stl'], ), diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index f1bc2486b2..12d3f98117 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -13,6 +13,9 @@ def test_MpiCommandLine_inputs(): usedefault=True, ), n_procs=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_mpi=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 1218d8fac0..0405d6d5ea 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -18,6 +18,9 @@ def test_MySQLSink_inputs(): usedefault=True, ), password=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), table_name=dict(mandatory=True, ), username=dict(), diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 773e7e24a3..6841df94ad 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -7,6 +7,9 @@ def test_NiftiGeneratorBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = NiftiGeneratorBase.input_spec() diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index 9c62a83a23..2c31794e11 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -43,6 +43,9 @@ def test_PETPVC_inputs(): pvc=dict(argstr='-p %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stop_crit=dict(argstr='-a %.4f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index 7debd4dd84..df68cfd506 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -29,6 +29,9 @@ def test_Quickshear_inputs(): name_template='%s_defaced', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index a3c918c465..d3953457dc 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -18,6 +18,9 @@ def test_S3DataGrabber_inputs(): ), region=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), template=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index c7aee569d5..31a7144c85 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -12,6 +12,9 @@ def test_SEMLikeCommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 74c9caaa46..ba3835e2f3 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -9,6 +9,9 @@ def test_SQLiteSink_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), table_name=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index 99e71d1ffe..73f1ac8b6e 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -16,6 +16,9 @@ def test_SSHDataGrabber_inputs(): password=dict(), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), ssh_log_to_file=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index da119bfcf6..25593366fa 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -12,6 +12,9 @@ def test_SelectFiles_inputs(): ), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index 4f101450b0..fc60690d30 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -21,6 +21,9 @@ def test_SignalExtraction_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = SignalExtraction.input_spec() diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 891eff2394..4bec246b86 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -13,6 +13,9 @@ def test_SlicerCommandLine_inputs(): usedefault=True, ), module=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index 46a0974b34..27b8618241 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -16,6 +16,9 @@ def test_StdOutCommandLine_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 286c8b2ca9..39b698a955 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -22,6 +22,9 @@ def test_XNATSink_inputs(): pwd=dict(), reconstruction_id=dict(xor=['assessor_id'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), server=dict(mandatory=True, requires=['user', 'pwd'], xor=['config'], diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index b399d143aa..514d21ac45 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -16,6 +16,9 @@ def test_XNATSource_inputs(): ), query_template_args=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), server=dict(mandatory=True, requires=['user', 'pwd'], xor=['config'], diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 739725a417..b1403216c6 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -7,6 +7,9 @@ def test_AssertEqual_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/interfaces/utility/tests/test_auto_Function.py b/nipype/interfaces/utility/tests/test_auto_Function.py index 649d626a5f..27ca7ed1b3 100644 --- a/nipype/interfaces/utility/tests/test_auto_Function.py +++ b/nipype/interfaces/utility/tests/test_auto_Function.py @@ -9,6 +9,9 @@ def test_Function_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Function.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Merge.py b/nipype/interfaces/utility/tests/test_auto_Merge.py index f98e70892b..dd9247ebc6 100644 --- a/nipype/interfaces/utility/tests/test_auto_Merge.py +++ b/nipype/interfaces/utility/tests/test_auto_Merge.py @@ -13,6 +13,9 @@ def test_Merge_inputs(): ), ravel_inputs=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Merge.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Select.py b/nipype/interfaces/utility/tests/test_auto_Select.py index 3c67785702..b3041ecfce 100644 --- a/nipype/interfaces/utility/tests/test_auto_Select.py +++ b/nipype/interfaces/utility/tests/test_auto_Select.py @@ -11,6 +11,9 @@ def test_Select_inputs(): ), inlist=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Select.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Split.py b/nipype/interfaces/utility/tests/test_auto_Split.py index 663ff65b13..33ae28bda4 100644 --- a/nipype/interfaces/utility/tests/test_auto_Split.py +++ b/nipype/interfaces/utility/tests/test_auto_Split.py @@ -9,6 +9,9 @@ def test_Split_inputs(): ), inlist=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splits=dict(mandatory=True, ), squeeze=dict(usedefault=True, diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 460c1eac79..2603a5b567 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -26,6 +26,9 @@ def test_Vnifti2Image_inputs(): name_template='%s.v', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 055e665abc..af7b5d1f27 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -23,6 +23,9 @@ def test_VtoMat_inputs(): name_template='%s.mat', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) From c789b17c5432f834995d43357402f5c21f09dffe Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 21:44:27 -0700 Subject: [PATCH 29/40] fix tests --- nipype/interfaces/fsl/tests/test_preprocess.py | 3 ++- nipype/utils/tests/test_cmd.py | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py index 7d3d6a9dce..32f0266ddb 100644 --- a/nipype/interfaces/fsl/tests/test_preprocess.py +++ b/nipype/interfaces/fsl/tests/test_preprocess.py @@ -258,7 +258,8 @@ def test_flirt(setup_flirt): if key in ('trait_added', 'trait_modified', 'in_file', 'reference', 'environ', 'output_type', 'out_file', 'out_matrix_file', 'in_matrix_file', 'apply_xfm', 'ignore_exception', - 'terminal_output', 'out_log', 'save_log'): + 'resource_monitor', 'terminal_output', 'out_log', + 'save_log'): continue param = None value = None diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py index 315d55441f..b590ecb351 100644 --- a/nipype/utils/tests/test_cmd.py +++ b/nipype/utils/tests/test_cmd.py @@ -104,6 +104,7 @@ def test_run_4d_realign_without_arguments(self): [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]] [--ignore_exception] [--loops [LOOPS [LOOPS ...]]] + [--resource_monitor] [--slice_order SLICE_ORDER] [--speedup [SPEEDUP [SPEEDUP ...]]] [--start START] From a9824f1d1d4efb21c71f69eaf1fa2d7426ed9a45 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 23:30:07 -0700 Subject: [PATCH 30/40] fix location of use_resources --- nipype/{interfaces => utils}/tests/use_resources | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename nipype/{interfaces => utils}/tests/use_resources (100%) diff --git a/nipype/interfaces/tests/use_resources b/nipype/utils/tests/use_resources similarity index 100% rename from nipype/interfaces/tests/use_resources rename to nipype/utils/tests/use_resources From 30d79e9a5db334e267389e0d1a2b251a4f1a2113 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 23:32:13 -0700 Subject: [PATCH 31/40] fix attribute error when input spec is not standard --- nipype/interfaces/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 8c61878f56..ee8cb998e1 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1057,7 +1057,7 @@ def run(self, **inputs): """ from ..utils.profiler import resource_monitor, ResourceMonitor - enable_rm = resource_monitor and self.inputs.resource_monitor + enable_rm = resource_monitor and getattr(self.inputs, 'resource_monitor', True) force_raise = not getattr(self.inputs, 'ignore_exception', False) self.inputs.trait_set(**inputs) self._check_mandatory_inputs() From 49d484396861b74a4769aaaf50250306c3a0bc71 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 26 Sep 2017 23:46:43 -0700 Subject: [PATCH 32/40] re-include filemanip logger into config documentation --- doc/users/config_file.rst | 131 +++++++++++++++++++------------------- 1 file changed, 67 insertions(+), 64 deletions(-) diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index bca5f0eb00..8fccf7e42a 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -14,49 +14,52 @@ Logging ~~~~~~~ *workflow_level* - How detailed the logs regarding workflow should be (possible values: - ``INFO`` and ``DEBUG``; default value: ``INFO``) + How detailed the logs regarding workflow should be (possible values: + ``INFO`` and ``DEBUG``; default value: ``INFO``) *utils_level* - How detailed the logs regarding nipype utils, like file operations - (for example overwriting warning) or the resource profiler, should be - (possible values: ``INFO`` and ``DEBUG``; default value: - ``INFO``) + How detailed the logs regarding nipype utils, like file operations + (for example overwriting warning) or the resource profiler, should be + (possible values: ``INFO`` and ``DEBUG``; default value: + ``INFO``) *interface_level* - How detailed the logs regarding interface execution should be (possible - values: ``INFO`` and ``DEBUG``; default value: ``INFO``) + How detailed the logs regarding interface execution should be (possible + values: ``INFO`` and ``DEBUG``; default value: ``INFO``) +*filemanip_level* (deprecated as of 0.13.2) + How detailed the logs regarding file operations (for example overwriting + warning) should be (possible values: ``INFO`` and ``DEBUG``) *log_to_file* Indicates whether logging should also send the output to a file (possible values: ``true`` and ``false``; default value: ``false``) *log_directory* - Where to store logs. (string, default value: home directory) + Where to store logs. (string, default value: home directory) *log_size* - Size of a single log file. (integer, default value: 254000) + Size of a single log file. (integer, default value: 254000) *log_rotate* - How many rotation should the log file make. (integer, default value: 4) + How many rotation should the log file make. (integer, default value: 4) Execution ~~~~~~~~~ *plugin* - This defines which execution plugin to use. (possible values: ``Linear``, - ``MultiProc``, ``SGE``, ``IPython``; default value: ``Linear``) + This defines which execution plugin to use. (possible values: ``Linear``, + ``MultiProc``, ``SGE``, ``IPython``; default value: ``Linear``) *stop_on_first_crash* - Should the workflow stop upon first node crashing or try to execute as many - nodes as possible? (possible values: ``true`` and ``false``; default value: - ``false``) + Should the workflow stop upon first node crashing or try to execute as many + nodes as possible? (possible values: ``true`` and ``false``; default value: + ``false``) *stop_on_first_rerun* - Should the workflow stop upon first node trying to recompute (by that we - mean rerunning a node that has been run before - this can happen due changed - inputs and/or hash_method since the last run). (possible values: ``true`` - and ``false``; default value: ``false``) + Should the workflow stop upon first node trying to recompute (by that we + mean rerunning a node that has been run before - this can happen due changed + inputs and/or hash_method since the last run). (possible values: ``true`` + and ``false``; default value: ``false``) *hash_method* - Should the input files be checked for changes using their content (slow, but - 100% accurate) or just their size and modification date (fast, but - potentially prone to errors)? (possible values: ``content`` and - ``timestamp``; default value: ``timestamp``) + Should the input files be checked for changes using their content (slow, but + 100% accurate) or just their size and modification date (fast, but + potentially prone to errors)? (possible values: ``content`` and + ``timestamp``; default value: ``timestamp``) *keep_inputs* Ensures that all inputs that are created in the nodes working directory are @@ -64,44 +67,44 @@ Execution value: ``false``) *single_thread_matlab* - Should all of the Matlab interfaces (including SPM) use only one thread? - This is useful if you are parallelizing your workflow using MultiProc or - IPython on a single multicore machine. (possible values: ``true`` and - ``false``; default value: ``true``) + Should all of the Matlab interfaces (including SPM) use only one thread? + This is useful if you are parallelizing your workflow using MultiProc or + IPython on a single multicore machine. (possible values: ``true`` and + ``false``; default value: ``true``) *display_variable* - What ``DISPLAY`` variable should all command line interfaces be - run with. This is useful if you are using `xnest - `_ - or `Xvfb `_ - and you would like to redirect all spawned windows to - it. (possible values: any X server address; default value: not - set) + What ``DISPLAY`` variable should all command line interfaces be + run with. This is useful if you are using `xnest + `_ + or `Xvfb `_ + and you would like to redirect all spawned windows to + it. (possible values: any X server address; default value: not + set) *remove_unnecessary_outputs* - This will remove any interface outputs not needed by the workflow. If the - required outputs from a node changes, rerunning the workflow will rerun the - node. Outputs of leaf nodes (nodes whose outputs are not connected to any - other nodes) will never be deleted independent of this parameter. (possible - values: ``true`` and ``false``; default value: ``true``) + This will remove any interface outputs not needed by the workflow. If the + required outputs from a node changes, rerunning the workflow will rerun the + node. Outputs of leaf nodes (nodes whose outputs are not connected to any + other nodes) will never be deleted independent of this parameter. (possible + values: ``true`` and ``false``; default value: ``true``) *try_hard_link_datasink* - When the DataSink is used to produce an orginized output file outside - of nipypes internal cache structure, a file system hard link will be - attempted first. A hard link allow multiple file paths to point to the - same physical storage location on disk if the conditions allow. By - refering to the same physical file on disk (instead of copying files - byte-by-byte) we can avoid unnecessary data duplication. If hard links - are not supported for the source or destination paths specified, then - a standard byte-by-byte copy is used. (possible values: ``true`` and - ``false``; default value: ``true``) + When the DataSink is used to produce an orginized output file outside + of nipypes internal cache structure, a file system hard link will be + attempted first. A hard link allow multiple file paths to point to the + same physical storage location on disk if the conditions allow. By + refering to the same physical file on disk (instead of copying files + byte-by-byte) we can avoid unnecessary data duplication. If hard links + are not supported for the source or destination paths specified, then + a standard byte-by-byte copy is used. (possible values: ``true`` and + ``false``; default value: ``true``) *use_relative_paths* - Should the paths stored in results (and used to look for inputs) - be relative or absolute. Relative paths allow moving the whole - working directory around but may cause problems with - symlinks. (possible values: ``true`` and ``false``; default - value: ``false``) + Should the paths stored in results (and used to look for inputs) + be relative or absolute. Relative paths allow moving the whole + working directory around but may cause problems with + symlinks. (possible values: ``true`` and ``false``; default + value: ``false``) *local_hash_check* Perform the hash check on the job submission machine. This option minimizes @@ -116,10 +119,10 @@ Execution done after a job finish is detected. (float in seconds; default value: 5) *remove_node_directories (EXPERIMENTAL)* - Removes directories whose outputs have already been used - up. Doesn't work with IdentiInterface or any node that patches - data through (without copying) (possible values: ``true`` and - ``false``; default value: ``false``) + Removes directories whose outputs have already been used + up. Doesn't work with IdentiInterface or any node that patches + data through (without copying) (possible values: ``true`` and + ``false``; default value: ``false``) *stop_on_unknown_version* If this is set to True, an underlying interface will raise an error, when no @@ -160,13 +163,13 @@ Example :: - [logging] - workflow_level = DEBUG + [logging] + workflow_level = DEBUG - [execution] - stop_on_first_crash = true - hash_method = timestamp - display_variable = :1 + [execution] + stop_on_first_crash = true + hash_method = timestamp + display_variable = :1 Workflow.config property has a form of a nested dictionary reflecting the structure of the .cfg file. From ff94a4bd67dedd17ef65411ec3206ae4c9df4f7f Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 00:53:46 -0700 Subject: [PATCH 33/40] minor additions to resource_monitor option --- nipype/utils/config.py | 4 +++- nipype/utils/profiler.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 86bc0738a0..241f2de8ee 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -67,7 +67,6 @@ parameterize_dirs = true poll_sleep_duration = 2 xvfb_max_wait = 10 -resource_monitor = false [check] interval = 1209600 @@ -191,3 +190,6 @@ def update_matplotlib(self): def enable_provenance(self): self._config.set('execution', 'write_provenance', 'true') self._config.set('execution', 'hash_method', 'content') + + def enable_resource_monitor(self): + self._config.set('execution', 'resource_monitor', 'true') diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 4ace5ef6d7..7e784fad32 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -21,7 +21,7 @@ proflogger = logging.getLogger('utils') -resource_monitor = str2bool(config.get('execution', 'resource_monitor')) +resource_monitor = str2bool(config.get('execution', 'resource_monitor', 'false')) if resource_monitor and psutil is None: proflogger.warn('Switching "resource_monitor" off: the option was on, but the ' 'necessary package "psutil" could not be imported.') From 55acde04c4402b29f29f27800c6c3e675089742f Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 00:54:26 -0700 Subject: [PATCH 34/40] fix resource_monitor tests --- nipype/utils/tests/test_profiler.py | 49 +++++++++++------------------ 1 file changed, 18 insertions(+), 31 deletions(-) diff --git a/nipype/utils/tests/test_profiler.py b/nipype/utils/tests/test_profiler.py index f27ac3dc3a..7c08330d13 100644 --- a/nipype/utils/tests/test_profiler.py +++ b/nipype/utils/tests/test_profiler.py @@ -15,16 +15,6 @@ from nipype.utils.profiler import resource_monitor as run_profile from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec) -if run_profile: - try: - import psutil - skip_profile_msg = 'Run profiler tests' - except ImportError as exc: - skip_profile_msg = 'Missing python packages for runtime profiling, skipping...\n'\ - 'Error: %s' % exc - run_profile = False -else: - skip_profile_msg = 'Not running profiler' # UseResources inputspec class UseResourcesInputSpec(CommandLineInputSpec): @@ -160,17 +150,17 @@ def _collect_range_runtime_stats(self, num_threads): # Iterate through all combos for num_gb in np.arange(0.25, ram_gb_range+ram_gb_step, ram_gb_step): # Cmd-level - cmd_start_str, cmd_fin_str = self._run_cmdline_workflow(num_gb, num_threads) - cmd_start_ts = json.loads(cmd_start_str)['start'] - cmd_node_stats = json.loads(cmd_fin_str) + cmd_node_str = self._run_cmdline_workflow(num_gb, num_threads) + cmd_node_stats = json.loads(cmd_node_str) + cmd_start_ts = cmd_node_stats['start'] cmd_runtime_threads = int(cmd_node_stats['runtime_threads']) cmd_runtime_gb = float(cmd_node_stats['runtime_memory_gb']) cmd_finish_ts = cmd_node_stats['finish'] # Func-level - func_start_str, func_fin_str = self._run_function_workflow(num_gb, num_threads) - func_start_ts = json.loads(func_start_str)['start'] - func_node_stats = json.loads(func_fin_str) + func_node_str = self._run_function_workflow(num_gb, num_threads) + func_node_stats = json.loads(func_node_str) + func_start_ts = func_node_stats['start'] func_runtime_threads = int(func_node_stats['runtime_threads']) func_runtime_gb = float(func_node_stats['runtime_memory_gb']) func_finish_ts = func_node_stats['finish'] @@ -238,6 +228,7 @@ def _run_cmdline_workflow(self, num_gb, num_threads): # Init logger logger = logging.getLogger('callback') + logger.propagate = False logger.setLevel(logging.DEBUG) handler = logging.FileHandler(log_file) logger.addHandler(handler) @@ -271,14 +262,14 @@ def _run_cmdline_workflow(self, num_gb, num_threads): # Get runtime stats from log file with open(log_file, 'r') as log_handle: lines = log_handle.readlines() - start_str = lines[0].rstrip('\n') - finish_str = lines[1].rstrip('\n') + + node_str = lines[0].rstrip('\n') # Delete wf base dir shutil.rmtree(base_dir) # Return runtime stats - return start_str, finish_str + return node_str # Test node def _run_function_workflow(self, num_gb, num_threads): @@ -350,17 +341,15 @@ def _run_function_workflow(self, num_gb, num_threads): # Get runtime stats from log file with open(log_file, 'r') as log_handle: lines = log_handle.readlines() - start_str = lines[0].rstrip('\n') - finish_str = lines[1].rstrip('\n') # Delete wf base dir shutil.rmtree(base_dir) # Return runtime stats - return start_str, finish_str + return lines[0].rstrip('\n') # Test resources were used as expected in cmdline interface - @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) + @pytest.mark.skipif(run_profile is False, reason='resources monitor is disabled') def test_cmdline_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -376,9 +365,9 @@ def test_cmdline_profiling(self): num_threads = self.num_threads # Run workflow and get stats - start_str, finish_str = self._run_cmdline_workflow(num_gb, num_threads) + node_str = self._run_cmdline_workflow(num_gb, num_threads) # Get runtime stats as dictionary - node_stats = json.loads(finish_str) + node_stats = json.loads(node_str) # Read out runtime stats runtime_gb = float(node_stats['runtime_memory_gb']) @@ -401,8 +390,8 @@ def test_cmdline_profiling(self): assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err # Test resources were used as expected - @pytest.mark.skipif(True, reason="https://github.com/nipy/nipype/issues/1663") - @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) + # @pytest.mark.skipif(True, reason="https://github.com/nipy/nipype/issues/1663") + @pytest.mark.skipif(run_profile is False, reason='resources monitor is disabled') def test_function_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -418,9 +407,9 @@ def test_function_profiling(self): num_threads = self.num_threads # Run workflow and get stats - start_str, finish_str = self._run_function_workflow(num_gb, num_threads) + node_str = self._run_function_workflow(num_gb, num_threads) # Get runtime stats as dictionary - node_stats = json.loads(finish_str) + node_stats = json.loads(node_str) # Read out runtime stats runtime_gb = float(node_stats['runtime_memory_gb']) @@ -441,5 +430,3 @@ def test_function_profiling(self): # Assert runtime stats are what was input assert runtime_gb_err <= allowed_gb_err, mem_err assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err - - From 7cd02eeee26fac648d8871419103b09416e619e3 Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 09:48:14 -0700 Subject: [PATCH 35/40] run build 2 (the shortest) with the resource monitor on --- .circle/tests.sh | 4 ++-- docker/files/run_examples.sh | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.circle/tests.sh b/.circle/tests.sh index 202f9c5918..7267873ab1 100644 --- a/.circle/tests.sh +++ b/.circle/tests.sh @@ -30,8 +30,8 @@ case ${CIRCLE_NODE_INDEX} in exitcode=$? ;; 2) - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline exitcode=$? ;; 3) diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh index f23bc6f44c..67364b0b0f 100644 --- a/docker/files/run_examples.sh +++ b/docker/files/run_examples.sh @@ -16,6 +16,11 @@ echo "utils_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg +if [[ "${NIPYPE_RESOURCE_MONITOR}" == "1" ]]; then + echo '[execution]' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg +fi + # Set up coverage export COVERAGE_FILE=${WORKDIR}/tests/.coverage.${example_id} if [ "$2" == "MultiProc" ]; then From a42ef6079fbf68d22d67243acb059a3a63775d2a Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 11:47:21 -0700 Subject: [PATCH 36/40] fix unbound variable --- docker/files/run_examples.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh index 67364b0b0f..de5a45306e 100644 --- a/docker/files/run_examples.sh +++ b/docker/files/run_examples.sh @@ -16,7 +16,7 @@ echo "utils_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg -if [[ "${NIPYPE_RESOURCE_MONITOR}" == "1" ]]; then +if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg fi From 10865f13d60f3930d70323cc22ac13c01854a9b2 Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 12:51:38 -0700 Subject: [PATCH 37/40] collect resource_monitor info after run --- nipype/interfaces/base.py | 11 +++++-- nipype/pipeline/engine/utils.py | 45 +++++++++++++++++++++++++++++ nipype/pipeline/engine/workflows.py | 4 +++ 3 files changed, 58 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index ee8cb998e1..4cb929ba7f 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1135,10 +1135,17 @@ def run(self, **inputs): # Read .prof file in and set runtime values vals = np.loadtxt(mon_fname, delimiter=',') if vals.tolist(): - _, mem_peak_gb, nthreads = np.atleast_2d(vals).max(0).astype(float).tolist() - runtime.mem_peak_gb = mem_peak_gb / 1024 + vals = np.atleast_2d(vals) + _, mem_peak_mb, nthreads = vals.max(0).astype(float).tolist() + runtime.mem_peak_gb = mem_peak_mb / 1024 runtime.nthreads_max = int(nthreads) + runtime.prof_dict = { + 'time': vals[:, 0].tolist(), + 'mem_gb': (vals[:, 1] / 1024).tolist(), + 'cpus': vals[:, 2].astype(int).tolist(), + } + return results def _list_outputs(self): diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py index 48e3f6ed49..bedd3c0c63 100644 --- a/nipype/pipeline/engine/utils.py +++ b/nipype/pipeline/engine/utils.py @@ -1296,6 +1296,51 @@ def write_workflow_prov(graph, filename=None, format='all'): return ps.g +def write_workflow_resources(graph, filename=None): + import simplejson as json + if not filename: + filename = os.path.join(os.getcwd(), 'resource_monitor.json') + + big_dict = { + 'time': [], + 'name': [], + 'interface': [], + 'mem_gb': [], + 'cpus': [], + 'mapnode': [], + 'params': [], + } + + for idx, node in enumerate(graph.nodes()): + nodename = node.fullname + classname = node._interface.__class__.__name__ + + params = '' + if node.parameterization: + params = '_'.join(['{}'.format(p) + for p in node.parameterization]) + + rt_list = node.result.runtime + if not isinstance(rt_list, list): + rt_list = [rt_list] + + for subidx, runtime in enumerate(rt_list): + nsamples = len(runtime.prof_dict['time']) + + for key in ['time', 'mem_gb', 'cpus']: + big_dict[key] += runtime.prof_dict[key] + + big_dict['interface'] += [classname] * nsamples + big_dict['name'] += [nodename] * nsamples + big_dict['mapnode'] += [subidx] * nsamples + big_dict['params'] += [params] * nsamples + + with open(filename, 'w') as rsf: + json.dump(big_dict, rsf) + + return filename + + def topological_sort(graph, depth_first=False): """Returns a depth first sorted order if depth_first is True """ diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index 17d49b046a..936881dd0f 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -51,6 +51,7 @@ write_rst_list, to_str) from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, + write_workflow_resources, clean_working_directory, format_dot, topological_sort, get_print_name, merge_dict, evaluate_connect_function, _write_inputs, format_node) @@ -593,6 +594,9 @@ def run(self, plugin=None, plugin_args=None, updatehash=False): 'workflow_provenance_%s' % datestr) logger.info('Provenance file prefix: %s' % prov_base) write_workflow_prov(execgraph, prov_base, format='all') + + if str2bool(self.config['execution'].get('resource_monitor', 'false')): + write_workflow_resources(execgraph) return execgraph # PRIVATE API AND FUNCTIONS From e0e341b4afa59225761ac1206940c0b1d8b37d30 Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 12:54:57 -0700 Subject: [PATCH 38/40] reduce resource_monitor_frequency on tests (and we test it works) --- docker/files/run_examples.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh index de5a45306e..f71ac60dde 100644 --- a/docker/files/run_examples.sh +++ b/docker/files/run_examples.sh @@ -19,6 +19,7 @@ echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/ if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor_frequency = 3' >> ${HOME}/.nipype/nipype.cfg fi # Set up coverage From 06c9f20010b9fca579e545c276d54bfae84d178b Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 12:58:48 -0700 Subject: [PATCH 39/40] store a new trace before exit --- nipype/utils/profiler.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 7e784fad32..75bb19a611 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -2,7 +2,7 @@ # @Author: oesteban # @Date: 2017-09-21 15:50:37 # @Last Modified by: oesteban -# @Last Modified time: 2017-09-26 15:05:24 +# @Last Modified time: 2017-09-27 12:57:50 """ Utilities to keep track of performance """ @@ -53,6 +53,10 @@ def stop(self): if not self._event.is_set(): self._event.set() self.join() + ram = _get_ram_mb(self._pid) or 0 + cpus = _get_num_threads(self._pid) or 0 + print('%s,%f,%d' % (time(), ram, cpus), + file=self._log) self._log.flush() self._log.close() From 03c8d2e16a1c019859e9a8b2745f6496788cdcbf Mon Sep 17 00:00:00 2001 From: oesteban Date: Wed, 27 Sep 2017 13:03:29 -0700 Subject: [PATCH 40/40] run resource_monitor only for level2 of fmri_spm_nested, switch python versions --- .circle/tests.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circle/tests.sh b/.circle/tests.sh index 7267873ab1..e6e9861ab7 100644 --- a/.circle/tests.sh +++ b/.circle/tests.sh @@ -30,8 +30,8 @@ case ${CIRCLE_NODE_INDEX} in exitcode=$? ;; 2) - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline exitcode=$? ;; 3)