Merge branch 'master' into fix/2300

Author: mgxd

CHANGES

@@ -8,6 +8,8 @@ Upcoming release
 ###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
 
 * FIX: MultiProc mishandling crashes (https://github.com/nipy/nipype/pull/2301)
+* MAINT: Revise use of `subprocess.Popen` (https://github.com/nipy/nipype/pull/2289)
+* ENH: Memorize version checks (https://github.com/nipy/nipype/pull/2274, https://github.com/nipy/nipype/pull/2295)
 
 
 0.14.0rc1 (November 21, 2017)

nipype/interfaces/afni/tests/test_auto_Unifize.py

@@ -32,6 +32,8 @@ def test_Unifize_inputs():
     name_source='in_file',
     ),
     outputtype=dict(),
+    rbt=dict(argstr='-rbt %f %f %f',
+    ),
     scale_file=dict(argstr='-ssave %s',
     ),
     t2=dict(argstr='-T2',

nipype/interfaces/afni/utils.py

@@ -2329,6 +2329,14 @@ class UnifizeInputSpec(AFNICommandInputSpec):
         argstr='-EPI',
         requires=['no_duplo', 't2'],
         xor=['gm'])
+    rbt = traits.Tuple(
+        traits.Float(), traits.Float(), traits.Float(),
+        desc='Option for AFNI experts only.'
+             'Specify the 3 parameters for the algorithm:\n'
+             'R = radius; same as given by option \'-Urad\', [default=18.3]\n'
+             'b = bottom percentile of normalizing data range, [default=70.0]\n'
+             'r = top percentile of normalizing data range, [default=80.0]\n',
+        argstr='-rbt %f %f %f')
 
 
 class UnifizeOutputSpec(TraitedSpec):

nipype/interfaces/base.py

@@ -9,11 +9,10 @@
 Requires Packages to be installed
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from future import standard_library
-standard_library.install_aliases()
+import gc
+
 from builtins import range, object, open, str, bytes
 
-from configparser import NoOptionError
 from copy import deepcopy
 import datetime
 from datetime import datetime as dt
@@ -26,7 +25,6 @@
 import select
 import subprocess as sp
 import sys
-import time
 from textwrap import wrap
 from warnings import warn
 import simplejson as json
@@ -43,6 +41,8 @@
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
     File, Directory, DictStrStr, has_metadata, ImageFile)
 from ..external.due import due
+from future import standard_library
+standard_library.install_aliases()
 
 nipype_version = Version(__version__)
 iflogger = logging.getLogger('interface')
@@ -58,6 +58,7 @@
 class Str(traits.Unicode):
     """Replacement for the default traits.Str based in bytes"""
 
+
 traits.Str = Str
 
 
@@ -1260,6 +1261,7 @@ class SimpleInterface(BaseInterface):
     >>> os.chdir(old.strpath)
 
     """
+
     def __init__(self, from_file=None, resource_monitor=None, **inputs):
         super(SimpleInterface, self).__init__(
             from_file=from_file, resource_monitor=resource_monitor, **inputs)
@@ -1387,8 +1389,7 @@ def run_command(runtime, output=None, timeout=0.01):
                     shell=True,
                     cwd=runtime.cwd,
                     env=env,
-                    close_fds=True,
-    )
+                    close_fds=True)
     result = {
         'stdout': [],
         'stderr': [],
@@ -1427,37 +1428,50 @@ def _process(drain=0):
         temp.sort()
         result['merged'] = [r[1] for r in temp]
 
-    if output == 'allatonce':
-        stdout, stderr = proc.communicate()
-        result['stdout'] = read_stream(stdout, logger=iflogger)
-        result['stderr'] = read_stream(stderr, logger=iflogger)
-
-    elif output.startswith('file'):
+    if output.startswith('file'):
         proc.wait()
         if outfile is not None:
             stdout.flush()
             stdout.close()
             with open(outfile, 'rb') as ofh:
                 stdoutstr = ofh.read()
             result['stdout'] = read_stream(stdoutstr, logger=iflogger)
+            del stdoutstr
 
         if errfile is not None:
             stderr.flush()
             stderr.close()
             with open(errfile, 'rb') as efh:
                 stderrstr = efh.read()
             result['stderr'] = read_stream(stderrstr, logger=iflogger)
+            del stderrstr
 
         if output == 'file':
             result['merged'] = result['stdout']
             result['stdout'] = []
     else:
-        proc.communicate()  # Discard stdout and stderr
+        stdout, stderr = proc.communicate()
+        if output == 'allatonce':  # Discard stdout and stderr otherwise
+            result['stdout'] = read_stream(stdout, logger=iflogger)
+            result['stderr'] = read_stream(stderr, logger=iflogger)
+
+    runtime.returncode = proc.returncode
+    try:
+        proc.terminate()  # Ensure we are done
+    except OSError as error:
+        # Python 2 raises when the process is already gone
+        if error.errno != errno.ESRCH:
+            raise
+
+    # Dereference & force GC for a cleanup
+    del proc
+    del stdout
+    del stderr
+    gc.collect()
 
     runtime.stderr = '\n'.join(result['stderr'])
     runtime.stdout = '\n'.join(result['stdout'])
     runtime.merged = '\n'.join(result['merged'])
-    runtime.returncode = proc.returncode
     return runtime
 
 
@@ -1467,21 +1481,26 @@ def get_dependencies(name, environ):
     Uses otool on darwin, ldd on linux. Currently doesn't support windows.
 
     """
+    cmd = None
     if sys.platform == 'darwin':
-        proc = sp.Popen('otool -L `which %s`' % name,
-                        stdout=sp.PIPE,
-                        stderr=sp.PIPE,
-                        shell=True,
-                        env=environ)
+        cmd = 'otool -L `which {}`'.format
     elif 'linux' in sys.platform:
-        proc = sp.Popen('ldd `which %s`' % name,
-                        stdout=sp.PIPE,
-                        stderr=sp.PIPE,
-                        shell=True,
-                        env=environ)
-    else:
+        cmd = 'ldd -L `which {}`'.format
+
+    if cmd is None:
         return 'Platform %s not supported' % sys.platform
-    o, e = proc.communicate()
+
+    try:
+        proc = sp.Popen(
+            cmd(name), stdout=sp.PIPE, stderr=sp.PIPE, shell=True,
+            env=environ, close_fds=True)
+        o, _ = proc.communicate()
+        proc.terminate()
+        gc.collect()
+    except:
+        iflogger.warning(
+            'Could not get linked libraries for "%s".', name)
+        return 'Failed collecting dependencies'
     return o.rstrip()
 
 
@@ -1572,6 +1591,9 @@ def __init__(self, command=None, terminal_output=None, **inputs):
         # Set command. Input argument takes precedence
         self._cmd = command or getattr(self, '_cmd', None)
 
+        # Store dependencies in runtime object
+        self._ldd = str2bool(config.get('execution', 'get_linked_libs', 'true'))
+
         if self._cmd is None:
             raise Exception("Missing command")
 
@@ -1620,6 +1642,8 @@ def _get_environ(self):
         return getattr(self.inputs, 'environ', {})
 
     def version_from_command(self, flag='-v'):
+        iflogger.warning('version_from_command member of CommandLine was '
+                         'Deprecated in nipype-1.0.0 and deleted in 1.1.0')
         cmdname = self.cmd.split()[0]
         env = dict(os.environ)
         if _exists_in_path(cmdname, env):
@@ -1664,7 +1688,8 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
                           (self.cmd.split()[0], runtime.hostname))
 
         runtime.command_path = cmd_path
-        runtime.dependencies = get_dependencies(executable_name, runtime.environ)
+        runtime.dependencies = (get_dependencies(executable_name, runtime.environ)
+                                if self._ldd else '<skipped>')
         runtime = run_command(runtime, output=self.terminal_output)
         if runtime.returncode is None or \
                 runtime.returncode not in correct_return_codes:

nipype/interfaces/fsl/base.py

@@ -26,56 +26,47 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open, object
 
 from glob import glob
 import os
 
 from ... import logging
 from ...utils.filemanip import fname_presuffix
-from ..base import traits, isdefined, CommandLine, CommandLineInputSpec
+from ..base import traits, isdefined, CommandLine, CommandLineInputSpec, PackageInfo
 from ...external.due import BibTeX
 
 IFLOGGER = logging.getLogger('interface')
 
 
-class Info(object):
-    """Handle fsl output type and version information.
-
-    version refers to the version of fsl on the system
+class Info(PackageInfo):
+    """
+    Handle FSL ``output_type`` and version information.
 
     output type refers to the type of file fsl defaults to writing
     eg, NIFTI, NIFTI_GZ
 
+    Examples
+    --------
+
+    >>> from nipype.interfaces.fsl import Info
+    >>> Info.version()  # doctest: +SKIP
+    >>> Info.output_type()  # doctest: +SKIP
+
+
     """
 
     ftypes = {'NIFTI': '.nii',
               'NIFTI_PAIR': '.img',
               'NIFTI_GZ': '.nii.gz',
               'NIFTI_PAIR_GZ': '.img.gz'}
 
-    @staticmethod
-    def version():
-        """Check for fsl version on system
-
-        Parameters
-        ----------
-        None
-
-        Returns
-        -------
-        version : str
-           Version number as string or None if FSL not found
+    if os.getenv('FSLDIR'):
+        version_file = os.path.join(
+            os.getenv('FSLDIR'), 'etc', 'fslversion')
 
-        """
-        # find which fsl being used....and get version from
-        # /path/to/fsl/etc/fslversion
-        try:
-            basedir = os.environ['FSLDIR']
-        except KeyError:
-            return None
-        out = open('%s/etc/fslversion' % (basedir)).read()
-        return out.strip('\n')
+    @staticmethod
+    def parse_version(raw_info):
+        return raw_info.splitlines()[0]
 
     @classmethod
     def output_type_to_ext(cls, output_type):

nipype/pipeline/engine/workflows.py

@@ -62,6 +62,7 @@
 
 logger = logging.getLogger('workflow')
 
+
 class Workflow(EngineBase):
     """Controls the setup and execution of a pipeline of processes."""
 
@@ -196,7 +197,7 @@ def connect(self, *args, **kwargs):
                 # determine their inputs/outputs depending on
                 # connection settings.  Skip these modules in the check
                 if dest in connected_ports[destnode]:
-                    raise Exception("""
+                    raise Exception("""\
 Trying to connect %s:%s to %s:%s but input '%s' of node '%s' is already
 connected.
 """ % (srcnode, source, destnode, dest, dest, destnode))
@@ -297,7 +298,7 @@ def disconnect(self, *args):
             remove = []
             for edge in conn:
                 if edge in ed_conns:
-                    idx = ed_conns.index(edge)
+                    # idx = ed_conns.index(edge)
                     remove.append((edge[0], edge[1]))
 
             logger.debug('disconnect(): remove list %s', to_str(remove))
@@ -426,7 +427,7 @@ def write_graph(self, dotfilename='graph.dot', graph2use='hierarchical',
                 base_dir = os.getcwd()
         base_dir = make_output_dir(base_dir)
         if graph2use in ['hierarchical', 'colored']:
-            if self.name[:1].isdigit(): # these graphs break if int
+            if self.name[:1].isdigit():  # these graphs break if int
                 raise ValueError('{} graph failed, workflow name cannot begin '
                                  'with a number'.format(graph2use))
             dotfilename = op.join(base_dir, dotfilename)
@@ -646,7 +647,7 @@ def _write_report_info(self, workingdir, name, graph):
         # Avoid RuntimeWarning: divide by zero encountered in log10
         num_nodes = len(nodes)
         if num_nodes > 0:
-           index_name = np.ceil(np.log10(num_nodes)).astype(int)
+            index_name = np.ceil(np.log10(num_nodes)).astype(int)
         else:
             index_name = 0
         template = '%%0%dd_' % index_name
@@ -794,10 +795,10 @@ def _get_outputs(self):
                 setattr(outputdict, node.name, outputs)
         return outputdict
 
-    def _set_input(self, object, name, newvalue):
+    def _set_input(self, objekt, name, newvalue):
         """Trait callback function to update a node input
         """
-        object.traits()[name].node.set_input(name, newvalue)
+        objekt.traits()[name].node.set_input(name, newvalue)
 
     def _set_node_input(self, node, param, source, sourceinfo):
         """Set inputs of a node given the edge connection"""

nipype/pipeline/plugins/multiproc.py

@@ -127,7 +127,7 @@ 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)
+                     'non' * int(non_daemon), self.processors, self.memory_gb)
 
         NipypePool = NonDaemonPool if non_daemon else Pool
         try: