Merge branch 'master' of git://github.com/nipy/nipype into fix/lgtm

Author: mgxd

.travis.yml

@@ -12,7 +12,7 @@ python:
 env:
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
 
 addons:
@@ -40,7 +40,7 @@ before_install:
   fi;
 
 # handle python operations separately to reduce timeouts
-- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-4.3.31-Linux-x86_64.sh
+- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
     -O /home/travis/.cache/conda.sh
 - bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
 - export PATH=${HOME}/conda/bin:$PATH

CONTRIBUTING.md

@@ -35,6 +35,14 @@ The current list of issue labels are [here][link_labels] and include:
     Please try to make sure that your requested enhancement is distinct from any others that have already been requested or implemented.
     If you find one that's similar but there are subtle differences, please reference the other request in your issue.
 
+* [![Orphaned](https://img.shields.io/badge/-orphaned-9baddd.svg)][link_orphaned] *These pull requests have been closed for inactivity.*
+
+    Before proposing a new pull request, browse through the "orphaned" pull requests.
+    You may find that someone has already made significant progress toward your goal, and you can re-use their
+    unfinished work.
+    An adopted PR should be updated to merge or rebase the current master, and a new PR should be created (see
+    below) that references the original PR.
+
 ## Making a change
 
 We appreciate all contributions to Nipype, but those accepted fastest will follow a workflow similar to the following:
@@ -57,8 +65,9 @@ Make sure to [keep your fork up to date][link_updateupstreamwiki] with the maste
 If you're adding a new tool from an existing neuroimaging toolkit (e.g., 3dDeconvolve from AFNI), check out the [guide for adding new interfaces to Nipype][link_new_interfaces].
 
 To confirm that your changes worked as intended, [clone your fork][link_cloning] to create a local directory.
-In this local directory, run `python setup.py develop`.
-This will add your version of nipype to your local python environment.
+In this local directory, run `pip install -e .[dev]`.
+This will add your version of nipype to your local python environment and
+install dependencies needed for development.
 
 Then, in this local nipype directory, run `make check-before-commit`. If you get no errors, you're ready to submit your changes!
 
@@ -131,6 +140,7 @@ You're awesome. :wave::smiley:
 [link_helpwanted]: https://github.com/nipy/nipype/labels/help-wanted
 [link_good_first_issue]: https://github.com/nipy/nipype/issues?q=is%3Aopen+is%3Aissue+label%3Agood-first-issue
 [link_enhancement]: https://github.com/nipy/nipype/labels/enhancement
+[link_orphaned]: https://github.com/nipy/nipype/pulls?q=is%3Apr+label%3Aorphaned+is%3Aclosed
 
 [link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/
 [link_fork]: https://help.github.com/articles/fork-a-repo/

docker/generate_dockerfiles.sh

@@ -54,7 +54,7 @@ done
 
 
 # neurodocker version 0.3.1-22-gb0ee069
-NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:c670ec2e0666a63d4e017a73780f66554283e294f3b12250928ee74b8a48bc59"
+NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:f15ca90803f4b89acfca55cd1c7269bf2ec2dfd95b3de1118b08afa34b87d9d1"
 
 # neurodebian:stretch-non-free pulled on November 3, 2017
 BASE_IMAGE="neurodebian@sha256:7590552afd0e7a481a33314724ae27f76ccedd05ffd7ac06ec38638872427b9b"
@@ -88,7 +88,6 @@ function generate_main_dockerfile() {
   --user neuro \
   --miniconda env_name=neuro \
               activate=true \
-              miniconda_version=4.3.31 \
   --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
          docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
   --copy . /src/nipype \
@@ -103,7 +102,7 @@ function generate_main_dockerfile() {
   --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
   --miniconda env_name=neuro \
               conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                             icu=58.1 libxml2 libxslt matplotlib mkl numpy
+                             icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
                              pandas psutil scikit-learn scipy traits=4.6.0' \
               pip_opts="-e" \
               pip_install="/src/nipype[all]" \

nipype/__init__.py

@@ -25,19 +25,19 @@
 
 
 class NipypeTester(object):
-    def __call__(self, doctests=True):
+    def __call__(self, doctests=True, parallel=True):
         try:
             import pytest
         except:
             raise RuntimeError(
                 'py.test not installed, run: pip install pytest')
-        params = {'args': []}
-        if doctests:
-            params['args'].append('--doctest-modules')
-        nipype_path = os.path.dirname(__file__)
-        params['args'].extend(
-            ['-x', '--ignore={}/external'.format(nipype_path), nipype_path])
-        pytest.main(**params)
+        args = []
+        if not doctests:
+            args.extend(['-p', 'no:doctest'])
+        if not parallel:
+            args.append('-n0')
+        args.append(os.path.dirname(__file__))
+        pytest.main(args=args)
 
 
 test = NipypeTester()

nipype/algorithms/confounds.py

@@ -3,13 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 '''
 Algorithms to compute confounds in :abbr:`fMRI (functional MRI)`
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname(os.path.realpath(__file__))
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/mesh.py

@@ -3,14 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
 Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
-
-  .. testsetup::
-    # Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname(os.path.realpath( __file__ ))
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-    >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/metrics.py

@@ -4,13 +4,6 @@
 '''
 Image assessment algorithms. Typical overlap and error computation
 measures to evaluate results from other processing units.
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/misc.py

@@ -3,13 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 '''
 Miscellaneous algorithms
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname(os.path.realpath(__file__))
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/modelgen.py

@@ -10,13 +10,6 @@
 These functions include:
 
   * SpecifyModel: allows specification of sparse and non-sparse models
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-   >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/rapidart.py

@@ -11,12 +11,6 @@
 
   * StimulusCorrelation: determines correlation between stimuli
     schedule and movement/intensity parameters
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/caching/memory.py

@@ -2,12 +2,6 @@
 """
 Using nipype with persistence and lazy recomputation but without explicit
 name-steps pipeline: getting back scope in command-line based programming.
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/conftest.py

@@ -2,12 +2,20 @@
 import numpy
 import os
 
+DATADIR = os.path.realpath(
+    os.path.join(os.path.dirname(__file__), 'testing/data'))
+
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
     doctest_namespace['np'] = numpy
     doctest_namespace['os'] = os
 
-    filepath = os.path.dirname(os.path.realpath(__file__))
-    datadir = os.path.realpath(os.path.join(filepath, 'testing/data'))
-    doctest_namespace["datadir"] = datadir
+    doctest_namespace["datadir"] = DATADIR
+
+
+@pytest.fixture(autouse=True)
+def in_testing(request):
+    # This seems to be a reliable way to distinguish tests from doctests
+    if request.function is None:
+        os.chdir(DATADIR)

nipype/info.py

@@ -152,7 +152,7 @@ def get_nipype_gitversion():
 if sys.version_info <= (3, 4):
     REQUIRES.append('configparser')
 
-TESTS_REQUIRES = ['pytest-cov', 'codecov']
+TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-xdist', 'pytest-env']
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
@@ -162,11 +162,20 @@ def get_nipype_gitversion():
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
-    'pybids': ['pybids']
+    'pybids': ['pybids'],
+    'ssh': ['paramiko'],
     # 'mesh': ['mayavi']  # Enable when it works
 }
 
+
+def _list_union(iterable):
+    return list(set(sum(iterable, [])))
+
+
 # Enable a handle to install all extra dependencies at once
-EXTRA_REQUIRES['all'] = [val for _, val in list(EXTRA_REQUIRES.items())]
+EXTRA_REQUIRES['all'] = _list_union(EXTRA_REQUIRES.values())
+# dev = doc + tests + specs
+EXTRA_REQUIRES['dev'] = _list_union(val for key, val in EXTRA_REQUIRES.items()
+                                    if key in ('doc', 'tests', 'specs'))
 
 STATUS = 'stable'

nipype/interfaces/afni/model.py

@@ -6,11 +6,6 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
-  .. testsetup::
-    # Change directory to provide relative paths for doctests
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/preprocess.py

@@ -2,12 +2,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """AFNI preprocessing interfaces
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/svm.py

@@ -2,12 +2,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft = python sts = 4 ts = 4 sw = 4 et:
 """Afni svm interfaces
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/utils.py

@@ -6,11 +6,6 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
-  .. testsetup::
-    # Change directory to provide relative paths for doctests
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/legacy.py

@@ -4,12 +4,6 @@
 #        of the antsApplyTransform program.  This implementation is here
 #        for backwards compatibility.
 """ANTS Apply Transforms interface
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 
 from builtins import range

nipype/interfaces/ants/registration.py

@@ -1,12 +1,6 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants
    functions.
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/resampling.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """ANTS Apply Transforms interface
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/segmentation.py

@@ -1,12 +1,5 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants functions.
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/utils.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """ANTS Apply Transforms interface
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/visualization.py

@@ -1,10 +1,5 @@
 # -*- coding: utf-8 -*-
 """The ants visualisation module provides basic functions based on ITK.
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/bru2nii.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """The bru2nii module provides basic functions for dicom conversion
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)