Skip to content

Commit d7dc606

Browse files
oestebanoesteban
committed
Merge remote-tracking branch 'upstream/master' into enh/antsRegistrationMinorAdd
2 parents 031e0c3 + 56b7c81 commit d7dc606

File tree

855 files changed

+18271
-4485
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

855 files changed

+18271
-4485
lines changed

‎.circle/tests.sh‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -17,8 +17,8 @@ fi
1717
# They may need to be rebalanced in the future.
1818
case ${CIRCLE_NODE_INDEX} in
1919
0)
20-
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 && \
21-
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 && \
20+
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 && \
21+
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 && \
2222
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 && \
2323
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 && \
2424
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 ${CIRCLE_NODE_INDEX} in
3030
exitcode=$?
3131
;;
3232
2)
33-
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 && \
34-
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
33+
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 && \
34+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
3535
exitcode=$?
3636
;;
3737
3)

‎.github/PULL_REQUEST_TEMPLATE.md‎

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
Pull-request guidelines (Remove this section after reading):
2+
3+
1. If you would like to list yourself as a Nipype contributor and your name is not mentioned please modify .zenodo.json file.
4+
2. By submitting this request you acknowledge that your contributions are available under the Apache 2 license.
5+
3. Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
6+
4. The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
7+
5. Run `make check-before-commit` before submitting the PR.
8+
9+
----- REMOVE TILL HERE -----
10+
11+
Fixes # .
12+
13+
Changes proposed in this pull request
14+
-
15+
-

‎.mailmap‎

Lines changed: 102 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,106 @@
1+
Aimi Watanabe <watanabe.aimi@gmail.com> stymy <rschadmin@cmi-rsch-li002.childmind.org>
2+
Aimi Watanabe <watanabe.aimi@gmail.com> stymy <watanabe.aimi@gmail.com>
3+
Alexander Schaefer <alexschaefer83@gmail.com> Alexander Schaefer <aschaefer@melisse.cbs.mpg.de>
4+
Alexander Schaefer <alexschaefer83@gmail.com> alexschaefer83 <alexschaefer83@gmail.com>
5+
Alexander Schaefer <alexschaefer83@gmail.com> aschaefer <aschaefer@aschaefer-U36SD.(none)>
6+
Alexandre M. Savio <alexsavio@gmail.com> Alexandre M. S <alexsavio@gmail.com>
7+
Alexandre M. Savio <alexsavio@gmail.com> Alexandre M. S <alexsavio@users.noreply.github.com>
8+
Alexandre M. Savio <alexsavio@gmail.com> Alexandre Manhaes Savio <alexsavio@gmail.com>
9+
Anisha Keshavan <akeshavan@gmail.com> Anisha Keshavan <akeshavan@ucla.edu>
10+
Anisha Keshavan <akeshavan@gmail.com> akeshavan <keshavan@berkeley.edu>
111
Ariel Rokem <arokem@berkeley.edu> arokem <arokem@berkeley.edu>
2-
Cindee Madison <cindee@berkeley.edu> cindeem <>
3-
Cindee Madison <cindee@berkeley.edu> cindeem
4-
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filo-Precision-M6500>
12+
Ariel Rokem <arokem@berkeley.edu> arokem <arokem@gmail.com>
13+
Arman Eshaghi <arman.eshaghi@gmail.com> armaneshaghi <arman.eshaghi@gmail.com>
14+
Ashely Gillman <gillmanash@gmail.com> Ashley Gillman <ashley.gillman@csiro.au>
15+
Ashely Gillman <gillmanash@gmail.com> ashgillman <ashley.gillman@csiro.au>
16+
Basille Pinsard <basile.pinsard@umontreal.ca> bpinsard <basile.pinsard@umontreal.ca>
17+
Basille Pinsard <basile.pinsard@umontreal.ca> bpinsard <bpinsard@imed.jussieu.fr>
18+
Ben Cipollini <bcipollini@classy.org> Ben Cipollini <bcipolli@ucsd.edu>
19+
Benjamin Yvernault <byvernault@gmail.com> Benjamin Yvernault <mathieusaboye@MBP-de-Mathieu.fritz.box>
20+
Benjamin Yvernault <byvernault@gmail.com> byvernault <byvernault@gmail.com>
21+
Blake Dewey <blake.dewey@jhu.edu> Blake Dewey <blake.dewey@nih.gov>
22+
Blake Dewey <blake.dewey@jhu.edu> blakedewey <deweybe@ndsl-nib-bdewey.local>
23+
Blake Dewey <blake.dewey@jhu.edu> blakedewey <deweybe@ndsl-nib-bdewey.ninds.nih.gov>
24+
Brendan Moloney <moloney.brendan@gmail.com> moloney <moloney.brendan@gmail.com>
25+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Chris Filo Gorgolewski <filo@filo-Precision-M6500.(none)>
26+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Chris Filo Gorgolewski <krzysztof.gorgolewski+fake@gmail.com>
27+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Chris Filo Gorgolewski <krzysztof.gorgolewski@gmail.com>
28+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
529
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Krzysztof Gorgolewski <krzysztof.gorgolewski@gmail.com>
6-
Erik Ziegler <erik.ziegler@ulg.ac.be> erikz <erik.ziegler@ulg.ac.be>
7-
Michael Waskom <mwaskom@stanford.edu> mwaskom <mwaskom@stanford.edu> Michael Waskom <mwaskom@mit.edu> mwaskom <mwaskom@mit.edu>
30+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filo-Precision-M6500>
31+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filo-dtc-laptop>
32+
Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filolaptop>
33+
Christopher J. Markiewicz <effigies@gmail.com> Chris Markiewicz <effigies@gmail.com>
34+
Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Johnson <effigies@gmail.com>
35+
Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
36+
Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <markiewicz@stanford.edu>
37+
Cindee Madison <cindee@berkeley.edu> cindeem
38+
Cindee Madison <cindee@berkeley.edu> cindeem <>
39+
Colin Buchanan <colinrbuchanan@gmail.com> Colin Buchanan <cbuchanan@cray4.(none)>
40+
Colin Buchanan <colinrbuchanan@gmail.com> colinbuchanan <colinrbuchanan@gmail.com>
41+
Daniel Clark <danieljclark87@gmail.com> dclark87 <danieljclark87@gmail.com>
42+
Daniel Ginsburg <daniel.ginsburg@childrens.harvard.edu> danginsburg <daniel.ginsburg@childrens.harvard.edu>
43+
Daniel McNamee <dmcx88@gmail.com> danmc <dmcx88@gmail.com>
44+
David Ellis <dgellis90@gmail.com> David Ellis <david-ellis@uiowa.edu>
45+
David Ellis <dgellis90@gmail.com> David Ellis <david.ellis@unmc.edu>
46+
David Welch <david.m.welch@gmail.com> David Welch <dmwelch@users.noreply.github.com>
47+
Dmytro <belevtsoff@gmail.com> belevtsoff <belevtsoff@gmail.com>
48+
Erik Ziegler <erik.sweed@gmail.com> Erik <erik.ziegler@ulg.ac.be>
49+
Erik Ziegler <erik.sweed@gmail.com> Erik Ziegler <erik.ziegler@ulg.ac.be>
50+
Erik Ziegler <erik.sweed@gmail.com> erik <erik@erik-ubuntu.(none)>
51+
Erik Ziegler <erik.sweed@gmail.com> erikz <erik.ziegler@ulg.ac.be>
52+
Erik Ziegler <erik.sweed@gmail.com> swederik <erik.sweed@gmail.com>
53+
Fernando Pérez-García <fepegar@gmail.com> Fernando <fepegar@gmail.com>
54+
Franz Liem <franz.liem@gmail.com> fliem <franz.liem@gmail.com>
55+
Franz Liem <franz.liem@gmail.com> fliem <franz.liem>
856
Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux
957
Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux <gael.varoquaux@noramlesup.org>
10-
Daniel Ginsburg <daniel.ginsburg@childrens.harvard.edu> danginsburg <daniel.ginsburg@childrens.harvard.edu>
11-
Colin Buchanan <colinrbuchanan@gmail.com> colinbuchanan <colinrbuchanan@gmail.com>
58+
Gavin Cooper <Gavin.Cooper@newcastle.edu.au> gjcooper <gjcooper@gmail.com>
59+
Hans Johnson <hans-johnson@uiowa.edu> Hans Johnson <hans.j.johnson@gmail.com>
60+
Hans Johnson <hans-johnson@uiowa.edu> hjmjohnson <hans.j.johnson@gmail.com>
61+
Horea Christian <horea.christ@yandex.com> Horea Christian <h.chr@mail.ru>
62+
Isaac Schwabacher <ischwabacher@wisc.edu> ischwabacher <ischwabacher@wisc.edu>
63+
James Kent <james-kent@uiowa.edu> jdkent <james-kent@uiowa.edu>
64+
Jason Wong <jf126dolphin@gmail.com> Jason <jf126dolphin@gmail.com>
65+
Jason Wong <jf126dolphin@gmail.com> jason <jf126dolphin@gmail.com>
66+
Jason Wong <jf126dolphin@gmail.com> Jason W <jf126dolphin@gmail.com>
67+
Jason Wong <jf126dolphin@gmail.com> Jason W <jasonwong73@ucla.edu>
68+
Jason Wong <jf126dolphin@gmail.com> jason-wg <jf126dolphin@gmail.com>
69+
Jens Kleesiek <kleesiek@uni-heidelberg.de> JensNRAD <kleesiek@uni-heidelberg.de>
70+
Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Joerg Stadler <joerg.stadler@lin-magdeburg.de>
71+
Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Jörg Stadler <Stadler@lin-magdeburg.de>
72+
Joke Durnez <joke.durnez@gmail.com> jokedurnez <joke.durnez@gmail.com>
73+
Josh Warner <silvertrumpet999+github@gmail.com> Josh Warner (Mac) <warner.joshua@mayo.edu>
74+
Kai Schlamp <schlamp@gmx.de> medihack <schlamp@gmx.de>Jessica Forbes <jessica-forbes@uiowa.edu> jessicaforbes <jessica-forbes@uiowa.edu>
75+
Leonie Lampe <leonie.lampe@gmail.com> Leonie Lmape <leonie.lampe@gmail.com>
76+
Mathias Goncalves <goncalves.mathias@gmail.com> mathiasg <mathiasg@mit.edu>
77+
Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.research@gmail.com>
78+
Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.comp@gmail.com>
79+
Michael Dayan <mdayan.research@gmail.com> mick-d <mid2021@CHUCK.(none)>
80+
Michael Clark <michael.clark195@gmail.com> Clark <clarkmg@nih.gov>
81+
Michael Notter <michaelnotter@hotmail.com> miykael <michaelnotter@hotmail.com>
82+
Michael Waskom <michael.l.waskom@gmail.com> Michael Waskom <mwaskom@mit.edu>
83+
Michael Waskom <michael.l.waskom@gmail.com> Michael Waskom <mwaskom@stanford.edu>
84+
Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@mit.edu>
85+
Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@stanford.edu>
86+
Michael Waskom <michael.l.waskom@gmail.com> mwaskom <mwaskom@nyu.edu>
87+
Oscar Esteban <code@oscaresteban.es> Oscar Esteban <code@oscaresteban>
88+
Oscar Esteban <code@oscaresteban.es> oesteban <code@oscaresteban.es>
89+
Russell Poldrack <poldrack@gmail.com> Russ Poldrack <poldrack@gmail.com>
90+
Russell Poldrack <poldrack@gmail.com> poldrack <poldrack@gmail.com>
91+
Satrajit Ghosh <satrajit.ghosh@gmail.com> Satrajit Ghosh <satra@mit.edu>
92+
Shariq Iqbal <shariqiqbal2810@gmail.com> shariqiqbal2810 <shariqiqbal2810@gmail.com>
93+
Shariq Iqbal <shariqiqbal2810@gmail.com> shariqiqbal2810 <shariqiqbal2810@users.noreply.github.com>
94+
Shoshana Berleant <berleant@stanford.edu> Shoshana Berleant <nope>
95+
Shoshana Berleant <berleant@stanford.edu> Shoshana Berleant <shoshber@users.noreply.github.com>
96+
Simon R <srothmei@mailbox.tu-berlin.de> Simon Rothmeier <srothmei@users.noreply.github.com>
97+
Siqi Liu <lsqshr@gmail.com> siqi liu <lsqshr@gmail.com>
98+
Siqi Liu <lsqshr@gmail.com> sql <lsqshr@gmail.com>
99+
Steven Giavasis <sgiava77@gmail.com> Steven Giavasis <steven.giavasis@cmi-rsch-li001.childmind.org>
100+
Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiava77@gmail.com>
101+
Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiavasis@ieee.org>
102+
Tristan Glatard <tristan.glatard@mcgill.ca> Tristan Glatard <tristan.glatard@creatis.insa-lyon.fr>
103+
Victor Saase <victor@saase.net> vsaase <victor@saase.net>
104+
William Triplett <wtriplett@gmail.com> William Triplett <wtriplett@ufl.edu>
105+
Yaroslav Halchenko <debian@onerussian.com> Yaroslav Halchenko <yoh@dartmouth.edu>
106+
pipolose <pipolose@pipoloses-air.watson.ibm.com> pipolose <pipolose@pipoloses-MacBook-Air.local>

‎.travis.yml‎

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -8,9 +8,10 @@ python:
88
- 3.5
99
- 3.6
1010
env:
11-
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
12-
- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
13-
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
11+
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
12+
- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
13+
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit" CI_SKIP_TEST=1
14+
- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
1415
before_install:
1516
- function apt_inst {
1617
if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
@@ -36,12 +37,17 @@ before_install:
3637
conda install python=${TRAVIS_PYTHON_VERSION} &&
3738
conda config --add channels conda-forge &&
3839
conda install -y nipype icu &&
39-
rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
40+
rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
41+
pushd $HOME;
42+
git clone https://github.com/INCF/pybids.git;
43+
cd pybids;
44+
pip install -e .;
45+
popd; }
4046
# Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
4147
- travis_retry apt_inst
4248
- travis_retry conda_inst
4349
install:
44-
- travis_retry pip install -e .[$NIPYPE_EXTRAS]
50+
- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
4551
script:
4652
- py.test -v --doctest-modules nipype
4753
deploy:

0 commit comments

Comments
 (0)