From ab11581078ee846badf2c8147b24522597db44b0 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 12 May 2017 14:24:00 -0400 Subject: [PATCH 01/20] fix: for conda build, restrict configparser requirement to py34 or earlier --- nipype/info.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 00323450d0..12d746b84b 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -4,6 +4,7 @@ """ from __future__ import print_function, division, unicode_literals, absolute_import +import sys # nipype version information. An empty version_extra corresponds to a # full release. '.dev' as a version_extra string means this is a development @@ -138,12 +139,14 @@ def get_nipype_gitversion(): 'prov>=%s' % PROV_MIN_VERSION, 'click>=%s' % CLICK_MIN_VERSION, 'funcsigs', - 'configparser', 'pytest>=%s' % PYTEST_MIN_VERSION, 'mock', 'pydotplus' ] +if sys.version_info <= (3, 4): + REQUIRES.append('configparser') + TESTS_REQUIRES = [ 'pytest-cov', 'codecov' From 408854cc7f9296dd232d2d73c5293654c91c5773 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 13 May 2017 12:53:42 -0400 Subject: [PATCH 02/20] fix: setuptools to be more precise --- setup.py | 6 ++++-- setup_egg.py | 23 ----------------------- 2 files changed, 4 insertions(+), 25 deletions(-) delete mode 100755 setup_egg.py diff --git a/setup.py b/setup.py index ef207ca9b7..e3ab87e2a1 100755 --- a/setup.py +++ b/setup.py @@ -119,6 +119,9 @@ def main(): with open(ver_file) as infofile: exec(infofile.read(), globals(), ldict) + SETUP_REQUIRES = ['future'] + if sys.version_info <= (3, 4): + SETUP_REQUIRES.append('configparser') setup( name=ldict['NAME'], maintainer=ldict['MAINTAINER'], @@ -134,14 +137,13 @@ def main(): platforms=ldict['PLATFORMS'], version=ldict['VERSION'], install_requires=ldict['REQUIRES'], - setup_requires=['future', 'configparser'], + setup_requires=SETUP_REQUIRES, provides=ldict['PROVIDES'], packages=find_packages(), package_data={'nipype': testdatafiles}, scripts=glob('bin/*'), cmdclass={'build_py': BuildWithCommitInfoCommand}, tests_require=ldict['TESTS_REQUIRES'], - test_suite='nose.collector', zip_safe=False, extras_require=ldict['EXTRA_REQUIRES'], entry_points=''' diff --git a/setup_egg.py b/setup_egg.py deleted file mode 100755 index 2fe767fe3c..0000000000 --- a/setup_egg.py +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env python -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: -"""Wrapper to run setup.py using setuptools.""" -from __future__ import print_function, division, unicode_literals, absolute_import -from io import open -import os.path - -################################################################################ -# Call the setup.py script, injecting the setuptools-specific arguments. - -extra_setuptools_args = dict(tests_require=['nose'], - test_suite='nose.collector', - zip_safe=False, - ) - - -if __name__ == '__main__': - setup_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'setup.py') - with open(setup_file) as f: - code = compile(f.read(), setup_file, 'exec') - exec(code, dict(__name__='__main__', - extra_setuptools_args=extra_setuptools_args)) From 9d775a07e2a0a338f73102b4a635b95ba9d6b3ce Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 13 May 2017 14:37:11 -0400 Subject: [PATCH 03/20] fix: update mailmap to fix contributor aliases --- .mailmap | 100 +++++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 93 insertions(+), 7 deletions(-) diff --git a/.mailmap b/.mailmap index 42816b7524..34ff4ed674 100644 --- a/.mailmap +++ b/.mailmap @@ -1,11 +1,97 @@ +Aimi Watanabe stymy +Aimi Watanabe stymy +Alexander Schaefer Alexander Schaefer +Alexander Schaefer alexschaefer83 +Alexander Schaefer aschaefer +Alexandre M. Savio Alexandre M. S +Alexandre M. Savio Alexandre M. S +Alexandre M. Savio Alexandre Manhaes Savio +Anisha Keshavan Anisha Keshavan +Anisha Keshavan akeshavan Ariel Rokem arokem -Cindee Madison cindeem <> -Cindee Madison cindeem -Chris Filo Gorgolewski filo +Ariel Rokem arokem +Arman Eshaghi armaneshaghi +Ashely Gillman Ashley Gillman +Ashely Gillman ashgillman +Basille Pinsard bpinsard +Basille Pinsard bpinsard +Ben Cipollini Ben Cipollini +Benjamin Yvernault Benjamin Yvernault +Benjamin Yvernault byvernault +Blake Dewey Blake Dewey +Blake Dewey blakedewey +Blake Dewey blakedewey +Brendan Moloney moloney +Chris Filo Gorgolewski Chris Filo Gorgolewski +Chris Filo Gorgolewski Chris Filo Gorgolewski +Chris Filo Gorgolewski Chris Filo Gorgolewski +Chris Filo Gorgolewski Chris Gorgolewski Chris Filo Gorgolewski Krzysztof Gorgolewski -Erik Ziegler erikz -Michael Waskom mwaskom Michael Waskom mwaskom +Chris Filo Gorgolewski filo +Chris Filo Gorgolewski filo +Chris Filo Gorgolewski filo +Christopher J. Markiewicz Chris Markiewicz +Christopher J. Markiewicz Christopher J. Johnson +Christopher J. Markiewicz Christopher J. Markiewicz +Christopher J. Markiewicz Christopher J. Markiewicz +Cindee Madison cindeem +Cindee Madison cindeem <> +Colin Buchanan Colin Buchanan +Colin Buchanan colinbuchanan +Daniel Clark dclark87 +Daniel Ginsburg danginsburg +David Ellis David Ellis +David Ellis David Ellis +David Welch David Welch +Dmytro belevtsoff +Erik Ziegler Erik +Erik Ziegler Erik Ziegler +Erik Ziegler erik +Erik Ziegler erikz +Erik Ziegler swederik Gael Varoquaux GaelVaroquaux Gael Varoquaux GaelVaroquaux -Daniel Ginsburg danginsburg -Colin Buchanan colinbuchanan +Gavin Cooper gjcooper +Hans Johnson Hans Johnson +Hans Johnson hjmjohnson +Horea Christian Horea Christian +James Kent jdkent +Jason jason +Jason W Jason +Jason W Jason W +Jason W jason-wg +Jessica Forbes jessicaforbes +Joerg Stadler Joerg Stadler +Joerg Stadler Jörg Stadler +Joke Durnez jokedurnez +Josh Warner Josh Warner (Mac) +Leonie Lampe Leonie Lmape +Mathias Goncalves mathiasg +Michael Michael +Michael mick-d +Michael Clark Clark +Michael Notter miykael +Michael Waskom Michael Waskom +Michael Waskom Michael Waskom +Michael Waskom mwaskom +Michael Waskom mwaskom +Oscar Esteban Oscar Esteban +Oscar Esteban oesteban +Russell Poldrack Russ Poldrack +Russell Poldrack poldrack +Satrajit Ghosh Satrajit Ghosh +Shoshana Berleant Shoshana Berleant +Shoshana Berleant Shoshana Berleant +Simon R Simon Rothmeier +Siqi Liu siqi liu +Siqi Liu sql +Steven Giavasis Steven Giavasis +Steven Giavasis sgiavasis +Steven Giavasis sgiavasis +Tristan Glatard Tristan Glatard +Victor Saase vsaase +William Triplett William Triplett +Yaroslav Halchenko Yaroslav Halchenko +fliem fliem +pipolose pipolose +shariqiqbal2810 shariqiqbal2810 \ No newline at end of file From e0f3f7703a1a5d5e80e60e95b2aad752b835ad7a Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 13 May 2017 14:38:00 -0400 Subject: [PATCH 04/20] fix: revert to 0.13.1 release and address setup issues for conda-forge --- doc/conf.py | 2 +- nipype/info.py | 4 ++-- setup.py | 1 - 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index b3ef6e4e61..65ee4c1e6a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -82,7 +82,7 @@ # The short X.Y version. version = nipype.__version__ # The full version, including alpha/beta/rc tags. -release = "0.13.0" +release = "0.13.1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/nipype/info.py b/nipype/info.py index 12d746b84b..e688fc9c75 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -10,7 +10,7 @@ # full release. '.dev' as a version_extra string means this is a development # version # Remove -dev for release -__version__ = '1.0.0-dev' +__version__ = '0.13.1' def get_nipype_gitversion(): @@ -19,7 +19,7 @@ def get_nipype_gitversion(): Returns ------- None or str - Version of NiPype according to git. + Version of Nipype according to git. """ import os import subprocess diff --git a/setup.py b/setup.py index e3ab87e2a1..331fa5905b 100755 --- a/setup.py +++ b/setup.py @@ -141,7 +141,6 @@ def main(): provides=ldict['PROVIDES'], packages=find_packages(), package_data={'nipype': testdatafiles}, - scripts=glob('bin/*'), cmdclass={'build_py': BuildWithCommitInfoCommand}, tests_require=ldict['TESTS_REQUIRES'], zip_safe=False, From a01ccd996108d00018b1fbee3bde00082aac48de Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 13 May 2017 14:38:20 -0400 Subject: [PATCH 05/20] enh: add current names from google doc --- .zenodo.json | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 58 insertions(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index f5ec9ab0ea..6a5deeceec 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -112,7 +112,7 @@ "orcid": "0000-0002-6652-3512" }, { - "affiliation": "Boston University", + "affiliation": "Stanford University", "name": "Markiewicz, Christopher J.", "orcid": "0000-0002-6533-164X" }, @@ -313,6 +313,63 @@ "name": "Durnez, Joke", "orcid": "0000-0001-9030-2202" }, + { + "affiliation": "Molecular Imaging Research Center, CEA, France", + "name": "Bougacha, Salma" + }, + { + "affiliation": "National Institutes of Health", + "name": "Clark, Michael G. " + }, + { + "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", + "name": "Horea, Christian", + "orcid": "0000-0001-7037-2449" + }, + { + "affiliation": "University of Pennsylvania", + "name": "Kahn, Ari E.", + "orcid": "0000-0002-2127-0507" + }, + + { + "affiliation": "California Institute of Technology", + "name": "PAULI, WOLFGANG M.", + "orcid": "0000-0002-0966-0254" + }, + { + "affiliation": "Stereotaxy Core, Brain & Spine Institute", + "name": "Pérez-García, Fernando", + "orcid": "0000-0001-9090-3024" + }, + { + "affiliation": "MIT", + "name": "Jarecka, Dorota", + "orcid": "0000-0003-1857-8129" + }, + { + "affiliation": "University College London", + "name": "Malone, Ian B.", + "orcid": "0000-0001-7512-7856" + }, + { + "name": "McDermottroe, Conor" + }, + { + "affiliation": "Florida International University", + "name": "Salo, Taylor", + "orcid": "0000-0001-9813-3167" + }, + { + "affiliation": "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", + "name": "Pannetier, Nicolas", + "orcid": "0000-0002-0744-5155" + }, + { + "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", + "name": "Gillman, Ashley", + "orcid": "0000-0001-9130-1092" + }, { "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", From c1e85520caf52d12fea0c9a3927b2c42655a892e Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 13 May 2017 22:27:19 -0400 Subject: [PATCH 06/20] enh: update to jessie versions for some packages --- nipype/info.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nipype/info.py b/nipype/info.py index e688fc9c75..9f6b9a0082 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -97,11 +97,11 @@ def get_nipype_gitversion(): # versions NIBABEL_MIN_VERSION = '2.1.0' -NETWORKX_MIN_VERSION = '1.7' -NUMPY_MIN_VERSION = '1.6.2' -SCIPY_MIN_VERSION = '0.11' +NETWORKX_MIN_VERSION = '1.9' +NUMPY_MIN_VERSION = '1.8.2' +SCIPY_MIN_VERSION = '0.14' TRAITS_MIN_VERSION = '4.6' -DATEUTIL_MIN_VERSION = '1.5' +DATEUTIL_MIN_VERSION = '2.2' PYTEST_MIN_VERSION = '3.0' FUTURE_MIN_VERSION = '0.16.0' SIMPLEJSON_MIN_VERSION = '3.8.0' From 3def5cb074cf39b7f598d1d2739f5f185a3de094 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sun, 14 May 2017 00:54:34 -0400 Subject: [PATCH 07/20] enh: updated internal ordering based on lines --- .mailmap | 26 +- .zenodo.json | 912 +++++++++++++++++++++++++++++---------------------- 2 files changed, 544 insertions(+), 394 deletions(-) diff --git a/.mailmap b/.mailmap index 34ff4ed674..af5a39bd66 100644 --- a/.mailmap +++ b/.mailmap @@ -40,6 +40,7 @@ Colin Buchanan Colin Buchanan colinbuchanan Daniel Clark dclark87 Daniel Ginsburg danginsburg +Daniel McNamee danmc David Ellis David Ellis David Ellis David Ellis David Welch David Welch @@ -49,26 +50,33 @@ Erik Ziegler Erik Ziegler Erik Ziegler erik Erik Ziegler erikz Erik Ziegler swederik +Fernando Pérez-García Fernando +Franz Liem fliem +Franz Liem fliem Gael Varoquaux GaelVaroquaux Gael Varoquaux GaelVaroquaux Gavin Cooper gjcooper Hans Johnson Hans Johnson Hans Johnson hjmjohnson Horea Christian Horea Christian +Isaac Schwabacher ischwabacher James Kent jdkent -Jason jason -Jason W Jason -Jason W Jason W -Jason W jason-wg -Jessica Forbes jessicaforbes +Jason Wong Jason +Jason Wong jason +Jason Wong Jason W +Jason Wong Jason W +Jason Wong jason-wg +Jens Kleesiek JensNRAD Joerg Stadler Joerg Stadler Joerg Stadler Jörg Stadler Joke Durnez jokedurnez Josh Warner Josh Warner (Mac) +Kai Schlamp medihack Jessica Forbes jessicaforbes Leonie Lampe Leonie Lmape Mathias Goncalves mathiasg -Michael Michael -Michael mick-d +Michael Dayan Michael +Michael Dayan Michael +Michael Dayan mick-d Michael Clark Clark Michael Notter miykael Michael Waskom Michael Waskom @@ -80,6 +88,8 @@ Oscar Esteban oesteban Russell Poldrack Russ Poldrack Russell Poldrack poldrack Satrajit Ghosh Satrajit Ghosh +Shariq Iqbal shariqiqbal2810 +Shariq Iqbal shariqiqbal2810 Shoshana Berleant Shoshana Berleant Shoshana Berleant Shoshana Berleant Simon R Simon Rothmeier @@ -92,6 +102,4 @@ Tristan Glatard Tristan Glatard vsaase William Triplett William Triplett Yaroslav Halchenko Yaroslav Halchenko -fliem fliem pipolose pipolose -shariqiqbal2810 shariqiqbal2810 \ No newline at end of file diff --git a/.zenodo.json b/.zenodo.json index 6a5deeceec..802d0f41c7 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,386 +1,528 @@ { - "creators": [ - { - "affiliation": "Department of Psychology, Stanford University", - "name": "Gorgolewski, Krzysztof J.", - "orcid": "0000-0003-3321-7583" - }, - { - "affiliation": "Department of Psychology, Stanford University", - "name": "Esteban, Oscar", - "orcid": "0000-0001-8435-6191" - }, - { - "name": "Burns, Christopher" - }, - { - "affiliation": "Independent", - "name": "Ziegler, Erik", - "orcid": "0000-0003-1857-8129" - }, - { - "name": "Pinsard, Basile" - }, - { - "name": "Madison, Cindee" - }, - { - "affiliation": "Department of Psychology, Stanford University", - "name": "Waskom, Michael" - }, - { - "affiliation": "The University of Iowa", - "name": "Ellis, David Gage", - "orcid": "0000-0002-3718-6836" - }, - { - "affiliation": "UC Berkeley", - "name": "Clark, Dav", - "orcid": "0000-0002-3982-4416" - }, - { - "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", - "name": "Wong, Jason" - }, - { - "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA", - "name": "Dayan, Michael", - "orcid": "0000-0002-2666-0969" - }, - { - "affiliation": "Klinikum rechts der Isar, TUM. ACPySS", - "name": "Manh\u00e3es-Savio, Alexandre", - "orcid": "0000-0002-6608-6885" - }, - { - "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", - "name": "Notter, Michael Philipp", - "orcid": "0000-0002-5866-047X" - }, - { - "affiliation": "University of Iowa", - "name": "Johnson, Hans", - "orcid": "0000-0001-9513-2660" - }, - { - "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", - "name": "Dewey, Blake E", - "orcid": "0000-0003-4554-5058" - }, - { - "affiliation": "Dartmouth College: Hanover, NH, United States", - "name": "Halchenko, Yaroslav O.", - "orcid": "0000-0003-3456-2493" - }, - { - "name": "Hamalainen, Carlo", - "orcid": "0000-0001-7655-3830" - }, - { - "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", - "name": "Keshavan, Anisha", - "orcid": "0000-0003-3554-043X" - }, - { - "affiliation": "Developer", - "name": "Clark, Daniel", - "orcid": "0000-0002-8121-8954" - }, - { - "affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", - "name": "Huntenburg, Julia M.", - "orcid": "0000-0003-0579-9811" - }, - { - "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", - "name": "Hanke, Michael", - "orcid": "0000-0001-6398-6370" - }, - { - "affiliation": "SRI International", - "name": "Nichols, B. Nolan", - "orcid": "0000-0003-1099-3328" - }, - { - "affiliation": "Athena EPI, Inria Sophia-Antipolis", - "name": "Wassermann , Demian", - "orcid": "0000-0001-5194-6056" - }, - { - "affiliation": "University College London", - "name": "Eshaghi, Arman", - "orcid": "0000-0002-6652-3512" - }, - { - "affiliation": "Stanford University", - "name": "Markiewicz, Christopher J.", - "orcid": "0000-0002-6533-164X" - }, - { - "affiliation": "INRIA", - "name": "Varoquaux, Gael", - "orcid": "0000-0003-1076-5122" - }, - { - "affiliation": "Washington University in St Louis", - "name": "Acland, Benjamin", - "orcid": "0000-0001-6392-6634" - }, - { - "name": "Forbes, Jessica" - }, - { - "affiliation": "The University of Washington eScience Institute", - "name": "Rokem, Ariel", - "orcid": "0000-0003-0679-1985" - }, - { - "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands", - "name": "Kong, Xiang-Zhen", - "orcid": "0000-0002-0805-1350" - }, - { - "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay", - "name": "Gramfort, Alexandre", - "orcid": "0000-0001-9791-4404" - }, - { - "affiliation": "UniversityHospital Heidelberg, Germany", - "name": "Kleesiek, Jens" - }, - { - "affiliation": "National University Singapore", - "name": "Schaefer, Alexander", - "orcid": "0000-0001-6488-4739" - }, - { - "affiliation": "Nathan s Kline institute for psychiatric research", - "name": "Sikka, Sharad" - }, - { - "affiliation": "Neurospin/Unicog/Inserm/CEA", - "name": "Perez-Guevara, Martin Felipe", - "orcid": "0000-0003-4497-861X" - }, - { - "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.", - "name": "Glatard, Tristan", - "orcid": "0000-0003-2620-5883" - }, - { - "affiliation": "Duke University", - "name": "Iqbal, Shariq", - "orcid": "0000-0003-2766-8425" - }, - { - "affiliation": "The University of Sydney", - "name": "Liu, Siqi" - }, - { - "affiliation": "University of Iowa", - "name": "Welch, David" - }, - { - "affiliation": "University of illinois urbana champaign", - "name": "Sharp, Paul" - }, - { - "affiliation": "Mayo Clinic", - "name": "Warner, Joshua", - "orcid": "0000-0003-3579-4835" - }, - { - "affiliation": "Harvard University - Psychology", - "name": "Kastman, Erik", - "orcid": "0000-0001-7221-9042" - }, - { - "affiliation": "MPI CBS Leipzig, Germany", - "name": "Lampe, Leonie" - }, - { - "affiliation": "Boston University", - "name": "Perkins, L. Nathan" - }, - { - "affiliation": "Child Mind Institite", - "name": "Craddock, R. Cameron", - "orcid": "0000-0002-4950-1303" - }, - { - "name": "K\u00fcttner, Ren\u00e9" - }, - { - "name": "Bielievtsov, Dmytro", - "orcid": "0000-0003-3846-7696" - }, - { - "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", - "name": "Geisler, Daniel", - "orcid": "0000-0003-2076-5329" - }, - { - "affiliation": "Institute of Neuroinformatics, ETH/University of Zurich", - "name": "Gerhard, Stephan", - "orcid": "0000-0003-4454-6171" - }, - { - "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", - "name": "Liem, Franziskus", - "orcid": "0000-0003-0646-4810" - }, - { - "affiliation": "German Institute for International Educational Research", - "name": "Linkersd\u00f6rfer, Janosch", - "orcid": "0000-0002-1577-1233" - }, - { - "affiliation": "Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", - "name": "Margulies, Daniel S.", - "orcid": "0000-0002-8880-9204" - }, - { - "affiliation": "University of Helsinki", - "name": "Andberg, Sami Kristian", - "orcid": "0000-0002-5650-3964" - }, - { - "affiliation": "Leibniz Institute for Neurobiology", - "name": "Stadler, J\u00f6rg", - "orcid": "0000-0003-4313-129X" - }, - { - "affiliation": "MPI-CBS; McGill University", - "name": "Steele, Christopher John", - "orcid": "0000-0003-1656-7928" - }, - { - "affiliation": "Duke University", - "name": "Broderick, William", - "orcid": "0000-0002-8999-9003" - }, - { - "affiliation": "UC San Diego", - "name": "Cipollini, Ben", - "orcid": "0000-0002-7782-0790" - }, - { - "affiliation": "University of Newcastle, Australia", - "name": "Cooper, Gavin", - "orcid": "0000-0002-7186-5293" - }, - { - "affiliation": "The University of Texas at Austin", - "name": "Floren, Andrew", - "orcid": "0000-0003-3618-2056" - }, - { - "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China", - "name": "Huang, Lijie", - "orcid": "0000-0002-9910-5069" - }, - { - "affiliation": "Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA", - "name": "Gonzalez, Ivan", - "orcid": "0000-0002-6451-6909" - }, - { - "affiliation": "University of Cambridge", - "name": "McNamee, Daniel", - "orcid": "0000-0001-9928-4960" - }, - { - "affiliation": "CEA", - "name": "Papadopoulos Orfanos, Dimitri", - "orcid": "0000-0002-1242-8990" - }, - { - "affiliation": "Child Mind Institute / Nathan Kline Institute", - "name": "Pellman, John", - "orcid": "0000-0001-6810-4461" - }, - { - "affiliation": "Department of Psychology, Stanford University", - "name": "Triplett, William", - "orcid": "0000-0002-9546-1306" - }, - { - "affiliation": "MIT", - "name": "Goncalves, Mathias" - }, - { - "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", - "name": "Durnez, Joke", - "orcid": "0000-0001-9030-2202" - }, - { - "affiliation": "Molecular Imaging Research Center, CEA, France", - "name": "Bougacha, Salma" - }, - { - "affiliation": "National Institutes of Health", - "name": "Clark, Michael G. " - }, - { - "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", - "name": "Horea, Christian", - "orcid": "0000-0001-7037-2449" - }, - { - "affiliation": "University of Pennsylvania", - "name": "Kahn, Ari E.", - "orcid": "0000-0002-2127-0507" - }, - - { - "affiliation": "California Institute of Technology", - "name": "PAULI, WOLFGANG M.", - "orcid": "0000-0002-0966-0254" - }, - { - "affiliation": "Stereotaxy Core, Brain & Spine Institute", - "name": "Pérez-García, Fernando", - "orcid": "0000-0001-9090-3024" - }, - { - "affiliation": "MIT", - "name": "Jarecka, Dorota", - "orcid": "0000-0003-1857-8129" - }, - { - "affiliation": "University College London", - "name": "Malone, Ian B.", - "orcid": "0000-0001-7512-7856" - }, - { - "name": "McDermottroe, Conor" - }, - { - "affiliation": "Florida International University", - "name": "Salo, Taylor", - "orcid": "0000-0001-9813-3167" - }, - { - "affiliation": "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", - "name": "Pannetier, Nicolas", - "orcid": "0000-0002-0744-5155" - }, - { - "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", - "name": "Gillman, Ashley", - "orcid": "0000-0001-9130-1092" - }, - { - "affiliation": "MIT, HMS", - "name": "Ghosh, Satrajit", - "orcid": "0000-0002-5312-6729" - } - ], - "keywords": [ - "neuroimaging", - "workflow", - "pipeline" - ], - "license": "Apache-2.0", - "upload_type": "software" - } + "creators": [ + { + "affiliation": "Department of Psychology, Stanford University", + "name": "Gorgolewski, Krzysztof J.", + "orcid": "0000-0003-3321-7583" + }, + { + "affiliation": "Department of Psychology, Stanford University", + "name": "Esteban, Oscar", + "orcid": "0000-0001-8435-6191" + }, + { + "affiliation": "The University of Iowa", + "name": "Ellis, David Gage", + "orcid": "0000-0002-3718-6836" + }, + { + "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", + "name": "Notter, Michael Philipp", + "orcid": "0000-0002-5866-047X" + }, + { + "affiliation": "Independent", + "name": "Ziegler, Erik", + "orcid": "0000-0003-1857-8129" + }, + { + "affiliation": "University of Iowa", + "name": "Johnson, Hans", + "orcid": "0000-0001-9513-2660" + }, + { + "name": "Hamalainen, Carlo", + "orcid": "0000-0001-7655-3830" + }, + { + "name": "Yvernault, Benjamin" + }, + { + "name": "Burns, Christopher" + }, + { + "affiliation": "Klinikum rechts der Isar, TUM. ACPySS", + "name": "Manh\u00e3es-Savio, Alexandre", + "orcid": "0000-0002-6608-6885" + }, + { + "affiliation": "MIT", + "name": "Jarecka, Dorota", + "orcid": "0000-0003-1857-8129" + }, + { + "affiliation": "Stanford University", + "name": "Markiewicz, Christopher J.", + "orcid": "0000-0002-6533-164X" + }, + { + "affiliation": "Florida International University", + "name": "Salo, Taylor", + "orcid": "0000-0001-9813-3167" + }, + { + "affiliation": "Developer", + "name": "Clark, Daniel", + "orcid": "0000-0002-8121-8954" + }, + { + "affiliation": "Department of Psychology, Stanford University", + "name": "Waskom, Michael" + }, + { + "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", + "name": "Wong, Jason" + }, + { + "name": "Modat, Marc" + }, + { + "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", + "name": "Dewey, Blake E", + "orcid": "0000-0003-4554-5058" + }, + { + "affiliation": "National Institutes of Health", + "name": "Clark, Michael G. " + }, + { + "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA", + "name": "Dayan, Michael", + "orcid": "0000-0002-2666-0969" + }, + { + "name": "Loney, Fred" + }, + { + "name": "Madison, Cindee" + }, + { + "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay", + "name": "Gramfort, Alexandre", + "orcid": "0000-0001-9791-4404" + }, + { + "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", + "name": "Keshavan, Anisha", + "orcid": "0000-0003-3554-043X" + }, + { + "name": "Berleant, Shoshana" + }, + { + "name": "Pinsard, Basile" + }, + { + "affiliation": "MIT", + "name": "Goncalves, Mathias" + }, + { + "affiliation": "UC Berkeley", + "name": "Clark, Dav", + "orcid": "0000-0002-3982-4416" + }, + { + "affiliation": "UC San Diego", + "name": "Cipollini, Ben", + "orcid": "0000-0002-7782-0790" + }, + { + "affiliation": "INRIA", + "name": "Varoquaux, Gael", + "orcid": "0000-0003-1076-5122" + }, + { + "affiliation": "Athena EPI, Inria Sophia-Antipolis", + "name": "Wassermann , Demian", + "orcid": "0000-0001-5194-6056" + }, + { + "affiliation": "The University of Washington eScience Institute", + "name": "Rokem, Ariel", + "orcid": "0000-0003-0679-1985" + }, + { + "affiliation": "Dartmouth College: Hanover, NH, United States", + "name": "Halchenko, Yaroslav O.", + "orcid": "0000-0003-3456-2493" + }, + { + "name": "Forbes, Jessica" + }, + { + "name": "Moloney, Brendan" + }, + { + "affiliation": "University College London", + "name": "Malone, Ian B.", + "orcid": "0000-0001-7512-7856" + }, + { + "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", + "name": "Hanke, Michael", + "orcid": "0000-0001-6398-6370" + }, + { + "name": "Mordom, David" + }, + { + "name": "Buchanan, Colin" + }, + { + "affiliation": "California Institute of Technology", + "name": "PAULI, WOLFGANG M.", + "orcid": "0000-0002-0966-0254" + }, + { + "affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", + "name": "Huntenburg, Julia M.", + "orcid": "0000-0003-0579-9811" + }, + { + "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", + "name": "Horea, Christian", + "orcid": "0000-0001-7037-2449" + }, + { + "name": "Schwartz, Yannick" + }, + { + "name": "Tungaraza, Rosalia" + }, + { + "affiliation": "Duke University", + "name": "Iqbal, Shariq", + "orcid": "0000-0003-2766-8425" + }, + { + "affiliation": "UniversityHospital Heidelberg, Germany", + "name": "Kleesiek, Jens" + }, + { + "affiliation": "Nathan s Kline institute for psychiatric research", + "name": "Sikka, Sharad" + }, + { + "affiliation": "Child Mind Institute", + "name": "Frohlich, Caroline" + }, + { + "name": "Kent, James" + }, + { + "name": "Perez-Guevara, Martin" + }, + { + "name": "Watanabe, Aimi" + }, + { + "affiliation": "University of Iowa", + "name": "Welch, David" + }, + { + "name": "Cumba, Chad" + }, + { + "name": "Ginsburg, Daniel" + }, + { + "affiliation": "University College London", + "name": "Eshaghi, Arman", + "orcid": "0000-0002-6652-3512" + }, + { + "affiliation": "Harvard University - Psychology", + "name": "Kastman, Erik", + "orcid": "0000-0001-7221-9042" + }, + { + "affiliation": "Molecular Imaging Research Center, CEA, France", + "name": "Bougacha, Salma" + }, + { + "name": "Blair, Ross" + }, + { + "affiliation": "Washington University in St Louis", + "name": "Acland, Benjamin", + "orcid": "0000-0001-6392-6634" + }, + { + "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", + "name": "Gillman, Ashley", + "orcid": "0000-0001-9130-1092" + }, + { + "affiliation": "National University Singapore", + "name": "Schaefer, Alexander", + "orcid": "0000-0001-6488-4739" + }, + { + "affiliation": "SRI International", + "name": "Nichols, B. Nolan", + "orcid": "0000-0003-1099-3328" + }, + { + "affiliation": "Child Mind Institute", + "name": "Giavasis, Steven" + }, + { + "name": "Erickson, Drew" + }, + { + "name": "Correa, Carlos" + }, + { + "name": "Ghayoor, Ali" + }, + { + "name": "K\u00fcttner, Ren\u00e9" + }, + { + "name": "Haselgrove, Christian" + }, + { + "name": "Zhou, Dale" + }, + { + "affiliation": "Child Mind Institute", + "name": "Craddock, R. Cameron", + "orcid": "0000-0002-4950-1303" + }, + { + "name": "Haehn, Daniel" + }, + { + "affiliation": "MPI CBS Leipzig, Germany", + "name": "Lampe, Leonie" + }, + { + "name": "Millman, Jarrod" + }, + { + "name": "Lai, Jeff" + }, + { + "name": "Renfro, Mandy" + }, + { + "affiliation": "The University of Sydney", + "name": "Liu, Siqi" + }, + { + "affiliation": "Leibniz Institute for Neurobiology", + "name": "Stadler, J\u00f6rg", + "orcid": "0000-0003-4313-129X" + }, + { + "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.", + "name": "Glatard, Tristan", + "orcid": "0000-0003-2620-5883" + }, + { + "affiliation": "University of Pennsylvania", + "name": "Kahn, Ari E.", + "orcid": "0000-0002-2127-0507" + }, + { + "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands", + "name": "Kong, Xiang-Zhen", + "orcid": "0000-0002-0805-1350" + }, + { + "affiliation": "Department of Psychology, Stanford University", + "name": "Triplett, William", + "orcid": "0000-0002-9546-1306" + }, + { + "name": "Park, Anne" + }, + { + "name": "McDermottroe, Conor" + }, + { + "name": "Hallquist, Michael" + }, + { + "name": "Poldrack, Russell" + }, + { + "affiliation": "Boston University", + "name": "Perkins, L. Nathan" + }, + { + "name": "Noel, Maxime" + }, + { + "affiliation": "Institute of Neuroinformatics, ETH/University of Zurich", + "name": "Gerhard, Stephan", + "orcid": "0000-0003-4454-6171" + }, + { + "name": "Salvatore, John" + }, + { + "name": "Mertz, Fred" + }, + { + "affiliation": "Duke University", + "name": "Broderick, William", + "orcid": "0000-0002-8999-9003" + }, + { + "name": "Inati, Souheil" + }, + { + "name": "Hinds, Oliver" + }, + { + "name": "Brett, Matthew" + }, + { + "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", + "name": "Durnez, Joke", + "orcid": "0000-0001-9030-2202" + }, + { + "name": "Tambini, Arielle" + }, + { + "name": "Rothmei, Simon" + }, + { + "affiliation": "University of Helsinki", + "name": "Andberg, Sami Kristian", + "orcid": "0000-0002-5650-3964" + }, + { + "affiliation": "University of Newcastle, Australia", + "name": "Cooper, Gavin", + "orcid": "0000-0002-7186-5293" + }, + { + "name": "Marina, Ana" + }, + { + "name": "Mattfeld, Aaron" + }, + { + "name": "Urchs, Sebastian" + }, + { + "affiliation": "University of illinois urbana champaign", + "name": "Sharp, Paul" + }, + { + "name": "Matsubara, K" + }, + { + "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", + "name": "Geisler, Daniel", + "orcid": "0000-0003-2076-5329" + }, + { + "name": "Cheung, Brian" + }, + { + "affiliation": "The University of Texas at Austin", + "name": "Floren, Andrew", + "orcid": "0000-0003-3618-2056" + }, + { + "name": "Nickson, Thomas" + }, + { + "affiliation": "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", + "name": "Pannetier, Nicolas", + "orcid": "0000-0002-0744-5155" + }, + { + "name": "Weinstein, Alejandro" + }, + { + "name": "Dubois, Mathieu" + }, + { + "name": "Arias, Jaime" + }, + { + "name": "Tarbert, Claire" + }, + { + "name": "Schlamp, Kai" + }, + { + "name": "Jordan, Kesshi" + }, + { + "name": "Liem, Franz" + }, + { + "name": "Saase, Victor" + }, + { + "name": "Harms, Robbert" + }, + { + "name": "Khanuja, Ranjeet" + }, + { + "name": "Podranski, Kornelius" + }, + { + "name": "Flandin, Guillaume" + }, + { + "affiliation": "CEA", + "name": "Papadopoulos Orfanos, Dimitri", + "orcid": "0000-0002-1242-8990" + }, + { + "name": "Schwabacher, Isaac" + }, + { + "affiliation": "University of Cambridge", + "name": "McNamee, Daniel", + "orcid": "0000-0001-9928-4960" + }, + { + "name": "Falkiewicz, Marcel" + }, + { + "affiliation": "Child Mind Institute / Nathan Kline Institute", + "name": "Pellman, John", + "orcid": "0000-0001-6810-4461" + }, + { + "affiliation": "German Institute for International Educational Research", + "name": "Linkersd\u00f6rfer, Janosch", + "orcid": "0000-0002-1577-1233" + }, + { + "name": "Varada, Jan" + }, + { + "affiliation": "Stereotaxy Core, Brain & Spine Institute", + "name": "P\u00e9rez-Garc\u00eda, Fernando", + "orcid": "0000-0001-9090-3024" + }, + { + "name": "Davison, Andrew" + }, + { + "name": "Shachnev, Dmitry" + }, + { + "affiliation": "MIT, HMS", + "name": "Ghosh, Satrajit", + "orcid": "0000-0002-5312-6729" + } + ], + "keywords": [ + "neuroimaging", + "workflow", + "pipeline" + ], + "license": "Apache-2.0", + "upload_type": "software" +} \ No newline at end of file From 127272b94a5e09a1158668003631bb7b82497ac2 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Thu, 18 May 2017 12:05:48 -0700 Subject: [PATCH 08/20] fix: test if gzipping the docker tar image works --- circle.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/circle.yml b/circle.yml index b4fb288357..c4634a595a 100644 --- a/circle.yml +++ b/circle.yml @@ -27,7 +27,7 @@ dependencies: - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR - mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/ - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi - - docker load --input $HOME/docker/cache.tar || true : + - gzcat $HOME/docker/cache.tar.gz | docker loaddocker load || true : timeout: 6000 override: # Get data @@ -55,7 +55,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 : + - docker save ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 | gzip > -o $HOME/docker/cache.tar.gz : timeout: 6000 test: From ec4bf7437e3faca59abafb2ee4108d03290f5b07 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Thu, 18 May 2017 12:07:49 -0700 Subject: [PATCH 09/20] fix: typo --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index c4634a595a..9942cd0260 100644 --- a/circle.yml +++ b/circle.yml @@ -27,7 +27,7 @@ dependencies: - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR - mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/ - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi - - gzcat $HOME/docker/cache.tar.gz | docker loaddocker load || true : + - gzcat $HOME/docker/cache.tar.gz | docker load || true : timeout: 6000 override: # Get data From 09c3f7c1ec34cf4ce685d6317bbbb3efb29c2909 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 18 May 2017 15:31:27 -0700 Subject: [PATCH 10/20] Update circle.yml --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index 9942cd0260..449eea6db4 100644 --- a/circle.yml +++ b/circle.yml @@ -55,7 +55,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 | gzip > -o $HOME/docker/cache.tar.gz : + - docker save ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 && gzip -9 $HOME/docker/cache.tar : timeout: 6000 test: From 303b982c6b69bedbf66a68e518eae9c8ac9906a8 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 18 May 2017 18:30:51 -0700 Subject: [PATCH 11/20] Update circle.yml --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index 449eea6db4..c2400b3715 100644 --- a/circle.yml +++ b/circle.yml @@ -55,7 +55,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 && gzip -9 $HOME/docker/cache.tar : + - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 && gzip -9 $HOME/docker/cache.tar : timeout: 6000 test: From e881288e00178285bdb385716703992d8885ce32 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Thu, 18 May 2017 21:18:10 -0700 Subject: [PATCH 12/20] fix: change to gunzip --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index c2400b3715..b6318cb5b3 100644 --- a/circle.yml +++ b/circle.yml @@ -27,7 +27,7 @@ dependencies: - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR - mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/ - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi - - gzcat $HOME/docker/cache.tar.gz | docker load || true : + - gunzip $HOME/docker/cache.tar.gz && docker load --input $HOME/docker/cache.tar || true : timeout: 6000 override: # Get data From 373c3b9772914246ddd638bcead01aa51fa0ca6c Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 19 May 2017 08:31:02 -0400 Subject: [PATCH 13/20] tst: some more checks --- circle.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/circle.yml b/circle.yml index b6318cb5b3..202f3fdcb2 100644 --- a/circle.yml +++ b/circle.yml @@ -1,7 +1,4 @@ machine: - pre: - - sudo curl -L -o /usr/bin/docker 'https://s3-external-1.amazonaws.com/circle-downloads/docker-1.9.1-circleci' - - sudo chmod 0755 /usr/bin/docker environment: OSF_NIPYPE_URL: "https://files.osf.io/v1/resources/nefdp/providers/osfstorage" DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21" @@ -17,7 +14,6 @@ dependencies: - "~/docker" - "~/examples" - "~/.apt-cache" - - "~/bin" pre: # Let CircleCI cache the apt archive @@ -27,7 +23,7 @@ dependencies: - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR - mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/ - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi - - gunzip $HOME/docker/cache.tar.gz && docker load --input $HOME/docker/cache.tar || true : + - docker load --input $HOME/docker/cache.tar || true : timeout: 6000 override: # Get data @@ -55,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 && gzip -9 $HOME/docker/cache.tar : + - docker save -o $HOME/docker/cache.tar nipype/base:latest : timeout: 6000 test: From 4bb54d9232bcba79e2cd15e667076c376acba30c Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 19 May 2017 18:35:19 -0400 Subject: [PATCH 14/20] fix: save ubuntu and nipype base but use compression --- circle.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/circle.yml b/circle.yml index 202f3fdcb2..fb7b8be193 100644 --- a/circle.yml +++ b/circle.yml @@ -23,7 +23,7 @@ dependencies: - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR - mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/ - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi - - docker load --input $HOME/docker/cache.tar || true : + - (cd $HOME/docker && gzip -d cache.tar.gz && docker load --input $HOME/docker/cache.tar) || true : timeout: 6000 override: # Get data @@ -51,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar nipype/base:latest : + - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest && gzip cache.tar : timeout: 6000 test: From 43a0b0b016851a5ad27595b387c17497d6467468 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 19 May 2017 19:28:55 -0400 Subject: [PATCH 15/20] fix: compression location --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index fb7b8be193..f650b2fd9f 100644 --- a/circle.yml +++ b/circle.yml @@ -51,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest && gzip cache.tar : + - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest && (cd $HOME/docker && gzip cache.tar) : timeout: 6000 test: From 0a02b1dde22c17288bc3eebafd42bdad2bd3bdea Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 19 May 2017 19:34:03 -0400 Subject: [PATCH 16/20] fix: white spaces --- doc/about.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/about.rst b/doc/about.rst index 94afabe08c..df498a47da 100644 --- a/doc/about.rst +++ b/doc/about.rst @@ -13,13 +13,13 @@ Citation Gorgolewski, Krzysztof J.; Esteban, Oscar; Burns, Christopher; Ziegler, Erik; Pinsard, Basile; Madison, Cindee; Waskom, Michael; Ellis, David Gage; Clark, Dav; Wong, Jason; Dayan, Michael; Manhães-Savio, Alexandre; Notter, Michael Philipp; Johnson, Hans; Dewey, Blake E; Halchenko, Yaroslav O.; Hamalainen, Carlo; Keshavan, Anisha; Clark, Daniel; Huntenburg, Julia M.; Hanke, Michael; - Nichols, B. Nolan; Wassermann , Demian; Eshaghi, Arman; Markiewicz, Christopher J.; Varoquaux, Gael; Acland, Benjamin; + Nichols, B. Nolan; Wassermann , Demian; Eshaghi, Arman; Markiewicz, Christopher J.; Varoquaux, Gael; Acland, Benjamin; Forbes, Jessica; Rokem, Ariel; Kong, Xiang-Zhen; Gramfort, Alexandre; Kleesiek, Jens; Schaefer, Alexander; Sikka, Sharad; Perez-Guevara, Martin Felipe; Glatard, Tristan; Iqbal, Shariq; Liu, Siqi; Welch, David; Sharp, Paul; Warner, Joshua; Kastman, Erik; Lampe, Leonie; Perkins, L. Nathan; Craddock, R. Cameron; Küttner, René; Bielievtsov, Dmytro; Geisler, Daniel; Gerhard, Stephan; Liem, Franziskus; Linkersdörfer, Janosch; Margulies, Daniel S.; Andberg, Sami Kristian; Stadler, Jörg; Steele, Christopher John; Broderick, William; Cipollini, Ben; Cooper, Gavin; Floren, Andrew; Huang, Lijie; Gonzalez, Ivan; McNamee, Daniel; - Papadopoulos Orfanos, Dimitri; Pellman, John; Triplett, William; Goncalves, Mathias; Durnez, Joke; Ghosh, Satrajit (2017). Nipype: + Papadopoulos Orfanos, Dimitri; Pellman, John; Triplett, William; Goncalves, Mathias; Durnez, Joke; Ghosh, Satrajit (2017). Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.0 Zenodo. `10.5281/zenodo.50186 `_ @@ -94,7 +94,7 @@ Citation Goncalves, Mathias and Durnez, Joke and Ghosh, Satrajit}, - title = {{Nipype: a flexible, lightweight and extensible + title = {{Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.0}}, month = may, From fe08e185d9873327d1c86fada386e95aebb8e687 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 19 May 2017 19:35:17 -0400 Subject: [PATCH 17/20] fix: add kesshi's details --- .zenodo.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index 802d0f41c7..2104092581 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -452,7 +452,9 @@ "name": "Schlamp, Kai" }, { - "name": "Jordan, Kesshi" + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" }, { "name": "Liem, Franz" From b4e6a51687600c99dc3f7128b1a7adb8ef825bb4 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 20 May 2017 09:25:22 -0400 Subject: [PATCH 18/20] doc: update changes and point to neurodocker --- CHANGES | 17 +++++++++++++++-- doc/users/install.rst | 3 +++ 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/CHANGES b/CHANGES index b61e8cdc37..ac16200d85 100644 --- a/CHANGES +++ b/CHANGES @@ -1,5 +1,18 @@ -Upcoming Release -================ +0.13.1 (May 20, 2017) +===================== + +* FIX: Make release compatible with conda-forge build process (https://github.com/nipy/nipype/pull/2017) +* ENH: Update some minimum versions in compliance with Debian Jessie (https://github.com/nipy/nipype/pull/2017) +* ENH: Circle builds use cached docker layers (https://github.com/nipy/nipype/pull/2017) +* ENH: Base docker to use FS6 and ANTS 2.2.0 (https://github.com/nipy/nipype/pull/2024) +* FIX: Mailmap and contributor acknowledgment (https://github.com/nipy/nipype/pull/2017) +* FIX: Preserve node properties in sub nodes of MapNode (https://github.com/nipy/nipype/pull/2019) +* FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister, + AffineInitializer (https://github.com/nipy/nipype/pull/2025, https://github.com/nipy/nipype/pull/2027, + https://github.com/nipy/nipype/pull/2036, https://github.com/nipy/nipype/pull/2037, + https://github.com/nipy/nipype/pull/2031, https://github.com/nipy/nipype/pull/2010) +* ENH: Add Anisotropic Power interface (https://github.com/nipy/nipype/pull/2039) +* FIX: Bayesian estimation in SPM (https://github.com/nipy/nipype/pull/2030) 0.13.0 (May 11, 2017) ===================== diff --git a/doc/users/install.rst b/doc/users/install.rst index bdd649df00..2e38122c68 100644 --- a/doc/users/install.rst +++ b/doc/users/install.rst @@ -13,6 +13,9 @@ You can follow the `Nipype tutorial or use this docker container: `docker pull nipype/nipype` +or if you want to build custom docker containers with specific versions of +software see `Neurodocker `_ + Using conda ~~~~~~~~~~~ From bd0ddd7bd240cc991e895098a4bb040a8e1ee3fd Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 20 May 2017 09:30:58 -0400 Subject: [PATCH 19/20] fix: add nipype latest to cache --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index f650b2fd9f..db2b5f8fcc 100644 --- a/circle.yml +++ b/circle.yml @@ -51,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest && (cd $HOME/docker && gzip cache.tar) : + - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:latest && (cd $HOME/docker && gzip cache.tar) : timeout: 6000 test: From 1d3d1183cf970953b91c0d8172a5044509b7b8c7 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 20 May 2017 10:07:33 -0400 Subject: [PATCH 20/20] fix: add nipype py36 to cache --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index db2b5f8fcc..49497a2e1d 100644 --- a/circle.yml +++ b/circle.yml @@ -51,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:latest && (cd $HOME/docker && gzip cache.tar) : + - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 && (cd $HOME/docker && gzip cache.tar) : timeout: 6000 test: