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Merge pull request #10 from poldracklab/rel/0.0.1
REL: 0.0.1
2 parents a02a183 + d925c6b commit b8a4a89

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‎.circleci/config.yml‎

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@@ -3,27 +3,125 @@ jobs:
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build:
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docker:
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- image: docker:18.01.0-ce-git
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working_directory: /home/circleci/fitlins
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working_directory: /tmp/src/fitlins
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steps:
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- checkout:
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path: /home/circleci/fitlins
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- run:
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name: Install parallel gzip
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command: |
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apk add --no-cache pigz
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- checkout
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- setup_remote_docker
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- run:
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name: Build image
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no_output_timeout: 30m
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command: |
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docker build \
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--tag fitlins \
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--tag poldracklab/fitlins:latest \
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--build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
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--build-arg VCS_REF="$(git rev-parse --short HEAD)" \
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--build-arg VERSION="${CIRCLE_TAG}" /home/circleci/fitlins
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--build-arg VERSION="${CIRCLE_TAG}" .
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- run:
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name: Verify executable can be run
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command: docker run --rm -it fitlins --help
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command: docker run --rm -it poldracklab/fitlins:latest --help
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- run:
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name: Docker save
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no_output_timeout: 40m
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command: |
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mkdir -p /tmp/cache
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docker save poldracklab/fitlins:latest \
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| pigz -8 -p 3 > /tmp/cache/docker.tar.gz
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- persist_to_workspace:
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root: /tmp
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paths:
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- cache/docker.tar.gz
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- src/fitlins
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deploy_test:
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machine:
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image: circleci/classic:201711-01
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working_directory: /tmp/src/fitlins
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steps:
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- attach_workspace:
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at: /tmp
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- run:
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name: Load Docker image layer cache
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no_output_timeout: 30m
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command: |
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docker info
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set +o pipefail
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if [ -f /tmp/cache/docker.tar.gz ]; then
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sudo apt update && sudo apt -y install pigz
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pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
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docker images
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fi
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- run:
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name: Deploy to Docker Hub
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no_output_timeout: 40m
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command: |
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if [[ -n "$DOCKER_PASS" ]]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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fi
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- run:
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name: Deploy to PyPi
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command: |
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pip install "setuptools>=27.0" twine
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echo "${CIRCLE_TAG}" > fitlins/VERSION
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python setup.py sdist
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deploy:
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machine:
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image: circleci/classic:201711-01
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working_directory: /tmp/src/fitlins
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steps:
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- attach_workspace:
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at: /tmp
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- run:
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name: Load Docker image layer cache
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no_output_timeout: 30m
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command: |
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docker info
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set +o pipefail
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if [ -f /tmp/cache/docker.tar.gz ]; then
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sudo apt update && sudo apt -y install pigz
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pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
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docker images
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fi
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- run:
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name: Deploy to Docker Hub
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no_output_timeout: 40m
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command: |
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if [[ -n "$DOCKER_PASS" ]]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker push poldracklab/fitlins:latest
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docker tag poldracklab/fitlins poldracklab/fitlins:$CIRCLE_TAG
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docker push poldracklab/fitlins:$CIRCLE_TAG
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fi
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- run:
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name: Deploy to PyPi
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command: |
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pip install "setuptools>=27.0" twine
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echo "${CIRCLE_TAG}" > fitlins/VERSION
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python setup.py sdist
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twine upload dist/*
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workflows:
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version: 2
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fitlins_tests:
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jobs:
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- build
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- deploy_test:
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requires:
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- build
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filters:
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branches:
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only: /rel\/[\d\.]+/
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tags:
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ignore: /.*/
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- deploy:
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requires:
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- build
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filters:
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branches:
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ignore: /.*/
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tags:
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only: /.*/

‎.dockerignore‎

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./work*
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./out*
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data
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.git
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.gitignore
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*.rst
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*.md
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*.egg-info/
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.circleci/

‎Dockerfile‎

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@@ -7,10 +7,7 @@ RUN conda install -y mkl=2018.0.1 mkl-service git=2.9.3; sync &&\
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scikit-learn=0.19.1 \
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matplotlib=2.1.2 \
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seaborn=0.8.1 \
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pandas=0.22.0 \
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libxml2=2.9.7 \
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libxslt=1.1.29\
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traits=4.6.0; sync && \
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pandas=0.22.0; sync && \
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chmod +x /opt/conda/bin/*; sync && \
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conda clean --all -y; sync && \
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conda clean -tipsy && sync

‎README.rst‎

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@@ -61,7 +61,7 @@ Similarly the outputs (or derivatives) are subject to change, as experience
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and user feedback prompt.
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The command-line interface outlined above should be fairly stable, however.
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.. _"BIDS Model": https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M/
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.. _"BIDS Derivatives": https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/
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.. _`BIDS Model`: https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M/
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.. _`BIDS Derivatives`: https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/
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.. _BIDS-Apps: http://bids-apps.neuroimaging.io
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.. _FMRIPREP: https://fmriprep.readthedocs.io

‎fitlins/info.py‎

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Base module variables
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"""
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__version__ = '0.0.1-dev'
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__version__ = '0.0.1'
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__author__ = 'The CRN developers'
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__copyright__ = 'Copyright 2017, Center for Reproducible Neuroscience, Stanford University'
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__credits__ = ['Christopher J. Markiewicz', 'Chris Gorgolewski', 'Russell A. Poldrack']
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__copyright__ = ('Copyright 2018, Center for Reproducible Neuroscience, '
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'Stanford University')
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__credits__ = ['Christopher J. Markiewicz', 'Chris Gorgolewski',
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'Russell A. Poldrack']
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__license__ = '3-clause BSD'
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__maintainer__ = 'Christopher J. Markiewicz'
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__email__ = '[email protected]'
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__status__ = 'Prototype'
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__url__ = 'https://github.com/poldracklab/fitlins'
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__packagename__ = 'fitlins'
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__description__ = ''
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__description__ = 'Fit Linear Models to fMRI Data'
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__longdesc__ = ''
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DOWNLOAD_URL = (
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'https://github.com/effigies/{name}/archive/{ver}.tar.gz'.format(
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'https://github.com/poldracklab/{name}/archive/{ver}.tar.gz'.format(
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name=__packagename__, ver=__version__))
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SETUP_REQUIRES = [
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'setuptools>=18.0',
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'setuptools>=27.0',
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]
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REQUIRES = [
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'nistats',
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'nibabel>=2.0',
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'seaborn>=0.7.1',
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'numpy>=1.11',
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'nilearn>=0.4.0',
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'pandas>=0.19',
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'nistats>=0.0.1a',
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'pybids>=0.3',
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'niworkflows>=0.1.8',
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'jinja2',
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]
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LINKS_REQUIRES = [
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'git+https://github.com/grabbles/grabbit.git@'
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'f317224f90f572ec35899a43f19cb82b870ff772#egg=grabbit-0.1.1-dev',
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'git+https://github.com/INCF/pybids.git@'
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'ea6cf9db042f25dfcae907bd535e9dcabcf2bd55#egg=pybids-0.4.3-dev',
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'git+https://github.com/effigies/nistats.git@'
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'd5b63e0ce1ea817bacd9117b9d729b3ca62c9352#egg=nistats-0.0.1b-dev',
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]
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TESTS_REQUIRES = [
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]
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EXTRA_REQUIRES = {
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'doc': ['sphinx>=1.5.3', 'pydotplus', 'pydot>=1.2.3', 'sphinx_rtd_theme', 'sphinx-argparse'],
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'tests': TESTS_REQUIRES,
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'duecredit': ['duecredit'],
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}

‎requirements.txt‎

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nibabel>2.0
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seaborn>0.7.1
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numpy>1.11
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nibabel>=2.0
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seaborn>=0.7.1
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numpy>=1.11
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nilearn>=0.4.0
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pandas>0.19
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niworkflows>0.3
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PyYAML>3
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pandas>=0.19
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git+https://github.com/grabbles/grabbit.git@f317224f90f572ec35899a43f19cb82b870ff772#egg=grabbit-0.1.1-dev
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git+https://github.com/INCF/pybids.git@ea6cf9db042f25dfcae907bd535e9dcabcf2bd55#egg=pybids-0.4.3-dev
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git+https://github.com/effigies/nistats.git@d5b63e0ce1ea817bacd9117b9d729b3ca62c9352#egg=nistats-0.0.1b-dev

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