Merge branch 'master' into mc_ref_mod

Author: oliver-contier

.circle/tests.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+#
+# Balance nipype testing workflows across CircleCI build nodes
+#
+
+# Setting      # $ help set
+set -e         # Exit immediately if a command exits with a non-zero status.
+set -u         # Treat unset variables as an error when substituting.
+set -x         # Print command traces before executing command.
+
+if [ "${CIRCLE_NODE_TOTAL:-}" != "4" ]; then
+  echo "These tests were designed to be run at 4x parallelism."
+  exit 1
+fi
+
+# These tests are manually balanced based on previous build timings. 
+# They may need to be rebalanced in the future.
+case ${CIRCLE_NODE_INDEX} in
+  0)
+    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc --entrypoint=/usr/bin/run_builddocs.sh nipype/nipype:py36 /usr/bin/run_builddocs.sh && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
+    exitcode=$?
+    ;;
+  1)
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
+    exitcode=$?
+    ;;
+  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 $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
+    exitcode=$?
+    ;;
+  3)
+    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 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
+    exitcode=$?
+    ;;
+esac
+
+cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
+
+# Exit with error if any of the tests failed
+if [ "$exitcode" != "0" ]; then exit 1; fi
+codecov -f "coverage*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F unittests -e CIRCLE_NODE_INDEX
+codecov -f "smoketest*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F smoketests -e CIRCLE_NODE_INDEX
+

.coveragerc

@@ -1,9 +1,2 @@
 [run]
 branch = True
-source = nipype
-include = */nipype/*
-omit =
-    */nipype/external/*
-    */nipype/workflows/*
-    */nipype/fixes/*
-    */setup.py

.dockerignore

@@ -0,0 +1,37 @@
+# python cache
+__pycache__
+**/__pycache__
+**/*.pyc
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+nipype.egg-info/**/*
+nipype.egg-info
+.eggs/**/*
+.eggs
+src/**/*
+src/
+
+# git
+.gitignore
+.git/**/*
+.git
+
+# other
+docs/**/*
+docs/
+.cache/
+.circle/**/*
+.circle/
+circle.yml
+rtd_requirements.txt
+Vagrantfile
+.travis.yml
+.mailmap
+
+# Previous coverage results
+.coverage

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,22 @@
+### Summary
+
+### Actual behavior
+
+### Expected behavior
+
+### How to replicate the behavior
+
+### Script/Workflow details
+
+Please put URL to code or code here (if not too long).
+
+### Platform details:
+
+Please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`
+
+### Execution environment
+
+Choose one
+- Container [Tag: ???]
+- My python environment inside container [Base Tag: ???]
+- My python environment outside container

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,15 @@
+Pull-request guidelines (Remove this section after reading):
+
+1. If you would like to list yourself as a Nipype contributor and your name is not mentioned please modify .zenodo.json file.
+2. By submitting this request you acknowledge that your contributions are available under the Apache 2 license.
+3. Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
+4. The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
+5. Run `make check-before-commit` before submitting the PR.
+
+----- REMOVE TILL HERE -----
+
+Fixes # .
+
+Changes proposed in this pull request
+-
+-

.gitignore

@@ -5,15 +5,25 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
 *.so
 .project
 .settings
 .pydevproject
+.eggs
 .idea/
 /documentation.zip
 .DS_Store
 nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
+crash*.pklz
+.coverage
+htmlcov/
+__pycache__/
+*~
+.*.swp
+.ipynb_checkpoints/
+.ruby-version

.mailmap

@@ -1,11 +1,106 @@
+Aimi Watanabe <[email protected]> stymy <[email protected]>
+Aimi Watanabe <[email protected]> stymy <[email protected]>
+Alexander Schaefer <[email protected]> Alexander Schaefer <[email protected]>
+Alexander Schaefer <[email protected]> alexschaefer83 <[email protected]>
+Alexander Schaefer <[email protected]> aschaefer <aschaefer@aschaefer-U36SD.(none)>
+Alexandre M. Savio <[email protected]> Alexandre M. S <[email protected]>
+Alexandre M. Savio <[email protected]> Alexandre M. S <[email protected]>
+Alexandre M. Savio <[email protected]> Alexandre Manhaes Savio <[email protected]>
+Anisha Keshavan <[email protected]> Anisha Keshavan <[email protected]>
+Anisha Keshavan <[email protected]> akeshavan <[email protected]>
 Ariel Rokem <[email protected]> arokem <[email protected]>
-Cindee Madison <[email protected]> cindeem <>
-Cindee Madison <[email protected]> cindeem
-Chris Filo Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
+Ariel Rokem <[email protected]> arokem <[email protected]>
+Arman Eshaghi <[email protected]> armaneshaghi <[email protected]>
+Ashely Gillman <[email protected]> Ashley Gillman <[email protected]>
+Ashely Gillman <[email protected]> ashgillman <[email protected]>
+Basille Pinsard <[email protected]> bpinsard <[email protected]>
+Basille Pinsard <[email protected]> bpinsard <[email protected]>
+Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Benjamin Yvernault <[email protected]> Benjamin Yvernault <[email protected]>
+Benjamin Yvernault <[email protected]> byvernault <[email protected]>
+Blake Dewey <[email protected]> Blake Dewey <[email protected]>
+Blake Dewey <[email protected]> blakedewey <[email protected]>
+Blake Dewey <[email protected]> blakedewey <[email protected]>
+Brendan Moloney <[email protected]> moloney <[email protected]>
+Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <filo@filo-Precision-M6500.(none)>
+Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
+Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
+Chris Filo Gorgolewski <[email protected]> Chris Gorgolewski <[email protected]>
 Chris Filo Gorgolewski <[email protected]> Krzysztof Gorgolewski <[email protected]>
-Erik Ziegler <[email protected]> erikz <[email protected]>
-Michael Waskom <[email protected]> mwaskom <[email protected]> Michael Waskom <[email protected]> mwaskom <[email protected]>
+Chris Filo Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
+Chris Filo Gorgolewski <[email protected]> filo <filo@filo-dtc-laptop>
+Chris Filo Gorgolewski <[email protected]> filo <filo@filolaptop>
+Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Christopher J. Johnson <[email protected]>
+Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Cindee Madison <[email protected]> cindeem
+Cindee Madison <[email protected]> cindeem <>
+Colin Buchanan <[email protected]> Colin Buchanan <cbuchanan@cray4.(none)>
+Colin Buchanan <[email protected]> colinbuchanan <[email protected]>
+Daniel Clark <[email protected]> dclark87 <[email protected]>
+Daniel Ginsburg <[email protected]> danginsburg <[email protected]>
+Daniel McNamee <[email protected]> danmc <[email protected]>
+David Ellis <[email protected]> David Ellis <[email protected]>
+David Ellis <[email protected]> David Ellis <[email protected]>
+David Welch <[email protected]> David Welch <[email protected]>
+Dmytro <[email protected]> belevtsoff <[email protected]>
+Erik Ziegler <[email protected]> Erik <[email protected]>
+Erik Ziegler <[email protected]> Erik Ziegler <[email protected]>
+Erik Ziegler <[email protected]> erik <erik@erik-ubuntu.(none)>
+Erik Ziegler <[email protected]> erikz <[email protected]>
+Erik Ziegler <[email protected]> swederik <[email protected]>
+Fernando Pérez-García <[email protected]> Fernando <[email protected]>
+Franz Liem <[email protected]> fliem <[email protected]>
+Franz Liem <[email protected]> fliem <franz.liem>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
-Daniel Ginsburg <[email protected]> danginsburg <[email protected]>
-Colin Buchanan <[email protected]> colinbuchanan <[email protected]>
+Gavin Cooper <[email protected]> gjcooper <[email protected]>
+Hans Johnson <[email protected]> Hans Johnson <[email protected]>
+Hans Johnson <[email protected]> hjmjohnson <[email protected]>
+Horea Christian <[email protected]> Horea Christian <[email protected]>
+Isaac Schwabacher <[email protected]> ischwabacher <[email protected]>
+James Kent <[email protected]> jdkent <[email protected]>
+Jason Wong <[email protected]> Jason <[email protected]>
+Jason Wong <[email protected]> jason <[email protected]>
+Jason Wong <[email protected]> Jason W <[email protected]>
+Jason Wong <[email protected]> Jason W <[email protected]>
+Jason Wong <[email protected]> jason-wg <[email protected]>
+Jens Kleesiek <[email protected]> JensNRAD <[email protected]>
+Joerg Stadler <[email protected]> Joerg Stadler <[email protected]>
+Joerg Stadler <[email protected]> Jörg Stadler <[email protected]>
+Joke Durnez <[email protected]> jokedurnez <[email protected]>
+Josh Warner <[email protected]> Josh Warner (Mac) <[email protected]>
+Kai Schlamp <[email protected]> medihack <[email protected]>Jessica Forbes <[email protected]> jessicaforbes <[email protected]>
+Leonie Lampe <[email protected]> Leonie Lmape <[email protected]>
+Mathias Goncalves <[email protected]> mathiasg <[email protected]>
+Michael Dayan <[email protected]> Michael <[email protected]>
+Michael Dayan <[email protected]> Michael <[email protected]>
+Michael Dayan <[email protected]> mick-d <mid2021@CHUCK.(none)>
+Michael Clark <[email protected]> Clark <[email protected]>
+Michael Notter <[email protected]> miykael <[email protected]>
+Michael Waskom <[email protected]> Michael Waskom <[email protected]>
+Michael Waskom <[email protected]> Michael Waskom <[email protected]>
+Michael Waskom <[email protected]> mwaskom <[email protected]>
+Michael Waskom <[email protected]> mwaskom <[email protected]>
+Michael Waskom <[email protected]> mwaskom <[email protected]>
+Oscar Esteban <[email protected]> Oscar Esteban <code@oscaresteban>
+Oscar Esteban <[email protected]> oesteban <[email protected]>
+Russell Poldrack <[email protected]> Russ Poldrack <[email protected]>
+Russell Poldrack <[email protected]> poldrack <[email protected]>
+Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
+Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
+Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
+Shoshana Berleant <[email protected]> Shoshana Berleant <nope>
+Shoshana Berleant <[email protected]> Shoshana Berleant <[email protected]>
+Simon R <[email protected]> Simon Rothmeier <[email protected]>
+Siqi Liu <[email protected]> siqi liu <[email protected]>
+Siqi Liu <[email protected]> sql <[email protected]>
+Steven Giavasis <[email protected]> Steven Giavasis <[email protected]>
+Steven Giavasis <[email protected]> sgiavasis <[email protected]>
+Steven Giavasis <[email protected]> sgiavasis <[email protected]>
+Tristan Glatard <[email protected]> Tristan Glatard <[email protected]>
+Victor Saase <[email protected]> vsaase <[email protected]>
+William Triplett <[email protected]> William Triplett <[email protected]>
+Yaroslav Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>
+pipolose <[email protected]> pipolose <[email protected]>

.travis.yml

@@ -1,43 +1,49 @@
 cache:
-- apt
+  apt: true
+
 language: python
 python:
 - 2.7
+- 3.4
+- 3.5
+- 3.6
 env:
-- INSTALL_DEB_DEPENDECIES=true
-- INSTALL_DEB_DEPENDECIES=false
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
 before_install:
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh
-  -O miniconda.sh; fi
-- chmod +x miniconda.sh
-- "./miniconda.sh -b"
-- export PATH=/home/travis/miniconda/bin:$PATH
-- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
-- if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
-- if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
-  fi
-- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends
-  fsl afni elastix; fi
-- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases;
-  fi
-- if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
+- function apt_inst {
+  if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
+  if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
+  bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
+  sudo apt-get -y update &&
+  sudo apt-get -y install xvfb fusefat graphviz &&
+  if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
+  fsl afni elastix fsl-atlases; fi &&
+  if $INSTALL_DEB_DEPENDECIES; then
+    source /etc/fsl/fsl.sh;
+    source /etc/afni/afni.sh;
+    export FSLOUTPUTTYPE=NIFTI_GZ; fi }
+- function conda_inst {
+  export CONDA_HOME=$HOME/conda &&
+  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/travis/.cache/conda.sh -b -p ${CONDA_HOME} &&
+  export PATH=${CONDA_HOME}/bin:$PATH &&
+  hash -r &&
+  conda config --set always_yes yes --set changeps1 no &&
+  conda update -q conda &&
+  conda install python=${TRAVIS_PYTHON_VERSION} &&
+  conda config --add channels conda-forge &&
+  conda install -y nipype icu &&
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
+- travis_retry apt_inst
+- travis_retry conda_inst
 install:
-- conda update --yes conda
-- conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
-- source activate testenv
-- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-- conda install --yes numpy scipy nose traits networkx dateutil
-- pip install nibabel
-- pip install python-coveralls
-- pip install nose-cov
-- pip install https://github.com/RDFLib/rdflib/archive/master.zip
-- pip install https://github.com/trungdong/prov/archive/rdf.zip
-- python setup.py install
+- travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
-- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
-after_success:
-- coveralls --config_file .coveragerc
+- py.test -v --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra
@@ -47,4 +53,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist bdist_wheel"
+  distributions: "sdist"