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Markiewicz Christopher J. Johnson +Christopher J. Markiewicz Christopher J. Markiewicz +Christopher J. Markiewicz Christopher J. 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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" + }, + { + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" + }, + { + "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" +} 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/circle.yml b/circle.yml index b4fb288357..49497a2e1d 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 - - docker load --input $HOME/docker/cache.tar || true : + - (cd $HOME/docker && gzip -d cache.tar.gz && docker load --input $HOME/docker/cache.tar) || true : timeout: 6000 override: # Get data @@ -55,7 +51,7 @@ dependencies: done && [ "$e" -eq "0" ] : timeout: 6000 - - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 : + - 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: 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/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 ~~~~~~~~~~~ diff --git a/nipype/info.py b/nipype/info.py index 00323450d0..9f6b9a0082 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -4,12 +4,13 @@ """ 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 # version # Remove -dev for release -__version__ = '1.0.0-dev' +__version__ = '0.13.1' def get_nipype_gitversion(): @@ -18,7 +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 @@ -96,11 +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' @@ -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' diff --git a/setup.py b/setup.py index ef207ca9b7..331fa5905b 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 +137,12 @@ 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))