Merge remote-tracking branch 'upstream/master' into enh/antsRegistrationMinorAdd

Author: oesteban

.circle/tests.sh

@@ -17,8 +17,8 @@ fi
 # 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 -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -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 CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -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
@@ -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 -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)

.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
+-
+-

.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

@@ -8,9 +8,10 @@ python:
 - 3.5
 - 3.6
 env:
-- 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"
+- 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" PIP_FLAGS="--pre" CI_SKIP_TEST=1
 before_install:
 - function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
@@ -36,12 +37,17 @@ before_install:
   conda install python=${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*; }
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
+  pushd $HOME;
+  git clone https://github.com/INCF/pybids.git;
+  cd pybids;
+  pip install -e .;
+  popd; }
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
 - travis_retry apt_inst
 - travis_retry conda_inst
 install:
-- travis_retry pip install -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
 script:
 - py.test -v --doctest-modules nipype
 deploy: