Merge remote-tracking branch 'origin/master' into bf-2847

* origin/master: (63 commits)
  Update nipype/interfaces/dipy/tracks.py
  Update nipype/interfaces/dipy/reconstruction.py
  MNT: Install numpy!=1.16.0 from conda in Docker
  Add FSL auto test
  remake specs
  Update nipype/interfaces/io.py
  Remove return type named tuple
  Update nipype/info.py
  STY: Whitespace, line length
  Remove out_ prefix from EddyQuad outputs
  Apply minor edits from code review
  Use os.path.basename for the fallback output_dir in EddyQuad._list_outputs()
  Add output_dir check to EddyQuad._list_outputs()
  Remove redundant out_avg_b_png lines
  Add glob stuff back in
  Edit in response to @effigies comments on PR #2825
  Fix tests for EddyQuad in interfaces/fsl/epi.py
  Add name to .zenodo.json
  Add doctest for EddyQuad
  fix: made the outputdir be mandatory and use the default val
  ...

Author: yarikoptic

.mailmap

@@ -93,7 +93,7 @@ Josh Warner <silvertrumpet999+github@gmail.com> JDWarner <warner.joshua@mayo.edu
 Josh Warner <silvertrumpet999+github@gmail.com> Josh Warner (Mac) <warner.joshua@mayo.edu>
 Kai Schlamp <schlamp@gmx.de> medihack <schlamp@gmx.de>Jessica Forbes <jessica-forbes@uiowa.edu> jessicaforbes <jessica-forbes@uiowa.edu>
 Katie Bottenhorn <kbott006@fiu.edu> 62442katieb <kbott006@fiu.edu>
-Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> 
+Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshi.jordan@gmail.com>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshijordan@D-108-179-130-38.dhcp4.washington.edu>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshijordan@D-69-91-152-99.dhcp4.washington.edu>

.travis.yml

@@ -60,6 +60,9 @@ matrix:
           NIPYPE_EXTRAS="doc,tests,nipy,profiler"
           EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
           CI_SKIP_TEST=1
+  allow_failures:
+    - python: 2.7
+      env: INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,nipy,profiler" EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS" CI_SKIP_TEST=1
 
 addons:
   apt:
@@ -86,14 +89,15 @@ before_install:
   fi;
 
 - travis_retry pip install -r requirements.txt
-- travis_retry pip install grabbit==0.1.2
-- travis_retry git clone -b 0.6.5 https://github.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids
+- travis_retry pip install grabbit==0.2.6
+- travis_retry pip install -e git+https://github.com/bids-standard/pybids.git@0.7.0#egg=pybids
 
 install:
 - travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install pytest-xdist
 
 script:
-- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype
+- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
 
 after_script:
 - codecov --file cov.xml --flags unittests -e TRAVIS_JOB_NUMBER

.zenodo.json

@@ -589,6 +589,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University of Washington",
+      "name": "Richie-Halford, Adam",
+      "orcid": "0000-0001-9276-9084"
     }
   ],
   "keywords": [

README.rst

@@ -91,7 +91,7 @@ To participate in the Nipype development related discussions please use the foll
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
-You can even hangout with the Nipype developers in their 
+You can even hangout with the Nipype developers in their
 `Gitter <https://gitter.im/nipy/nipype>`_ channel or in the BrainHack `Slack <https://brainhack.slack.com/messages/C1FR76RAL>`_ channel. (Click `here <https://brainhack-slack-invite.herokuapp.com>`_ to join the Slack workspace.)
 
 

doc/devel/interface_specs.rst

@@ -12,8 +12,8 @@ In case of trouble, we encourage you to post on `NeuroStars <https://neurostars.
 NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
 You can also post on the nipype developers mailing list: http://mail.python.org/mailman/listinfo/neuroimaging.
 As we are sharing a mailing list with the nipy community, please add ``[nipype]`` to the message title.
-Alternatively, you're welcome to chat with us in the Nipype 
-`Gitter <https://gitter.im/nipy/nipype>`_ channel or in the 
+Alternatively, you're welcome to chat with us in the Nipype
+`Gitter <https://gitter.im/nipy/nipype>`_ channel or in the
 BrainHack `Slack <https://brainhack.slack.com/messages/C1FR76RAL>`_ channel.
 (Click `here <https://brainhack-slack-invite.herokuapp.com>`_ to join the Slack workspace.)
 

doc/index.rst

@@ -16,7 +16,7 @@
         these packages within a single workflow. Nipype provides an environment
         that encourages interactive exploration of algorithms from different
         packages (e.g., ANTS_, SPM_, FSL_, FreeSurfer_, Camino_, MRtrix_, MNE_, AFNI_,
-        Slicer_), eases the design of workflows within and between packages, and
+        Slicer_, DIPY_), eases the design of workflows within and between packages, and
         reduces the learning curve necessary to use different packages. Nipype is
         creating a collaborative platform for neuroimaging software development
         in a high-level language and addressing limitations of existing pipeline

doc/links_names.txt

@@ -97,6 +97,7 @@
 .. _MRtrix3: http://www.mrtrix.org/
 .. _MNE: https://martinos.org/mne/index.html
 .. _ANTS: http://stnava.github.io/ANTs/
+.. _DIPY: http://dipy.org
 
 .. General software
 .. _gcc: http://gcc.gnu.org

docker/files/run_pytests.sh

@@ -29,6 +29,7 @@ export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}
 py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml \
     --cov nipype --cov-config /src/nipype/.coveragerc \
     --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml \
+    -n auto \
     -c ${TESTPATH}/pytest.ini ${TESTPATH}
 exit_code=$?
 

docker/generate_dockerfiles.sh

@@ -90,9 +90,9 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                               icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
+                               icu=58.1 libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
                                pandas psutil scikit-learn scipy traits=4.6.0' \
-                pip_install="grabbit==0.1.2 https://github.com/INCF/pybids/tarball/0.6.5" \
+                pip_install="pytest-xdist" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
            docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
@@ -107,7 +107,7 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda use_env=neuro \
                 pip_opts="-e" \
-                pip_install="/src/nipype[all]" \
+                pip_install="/src/nipype[all] https://github.com/bids-standard/pybids/tarball/0.7.0" \
     --workdir /work \
     --label org.label-schema.build-date='$BUILD_DATE' \
             org.label-schema.name="NIPYPE" \

nipype/__init__.py

@@ -25,17 +25,22 @@
 
 
 class NipypeTester(object):
-    def __call__(self, doctests=True, parallel=True):
+    def __call__(self, doctests=True, parallel=False):
         try:
             import pytest
-        except:
+        except ImportError:
             raise RuntimeError(
                 'py.test not installed, run: pip install pytest')
         args = []
         if not doctests:
             args.extend(['-p', 'no:doctest'])
-        if not parallel:
-            args.append('-n0')
+        if parallel:
+            try:
+                import xdist
+            except ImportError:
+                raise RuntimeError(
+                    "pytest-xdist required for parallel run")
+            args.append('-n auto')
         args.append(os.path.dirname(__file__))
         pytest.main(args=args)