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CI: Move from Travis to GitHub actions
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‎.github/workflows/tests.yml

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name: Stable tests
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# This file tests the claimed support range of nipype including
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#
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# * Operating systems: Linux, OSX
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# * Dependencies: minimum requirements, optional requirements
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# * Installation methods: setup.py, sdist, wheel, archive
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on:
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push:
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branches:
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- master
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- maint/*
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pull_request:
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branches:
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- master
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- maint/*
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-latest']
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python-version: [3.7]
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check: ['test']
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pip-flags: ['']
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depends: ['REQUIREMENTS']
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deb-depends: [false]
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nipype-extras: ['doc,tests,profiler']
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optional-depends: ['DEFAULT_OPT_DEPENDS']
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include:
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- os: ubuntu-latest
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python-version: 3.8
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check: test
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pip-flags: ''
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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env:
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DEPENDS: ${{ matrix.depends }}
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OPTIONAL_DEPENDS: ${{ matrix.optional-depends }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-latest' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install NiBabel
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v1
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with:
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file: for_testing/coverage.xml
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if: ${{ always() }}
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: for_testing/test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎tools/ci/activate.sh

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if [ -e virtenv/bin/activate ]; then
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source virtenv/bin/activate
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elif [ -e virtenv/Scripts/activate ]; then
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source virtenv/Scripts/activate
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else
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echo Cannot activate virtual environment
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ls -R virtenv
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false
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fi

‎tools/ci/build_archive.sh

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#!/bin/bash
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echo "Building archive"
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source tools/ci/activate.sh
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set -eu
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# Required dependencies
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echo "INSTALL_TYPE = $INSTALL_TYPE"
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set -x
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if [ "$INSTALL_TYPE" == "sdist" ]; then
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python setup.py egg_info # check egg_info while we're here
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python setup.py sdist
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export ARCHIVE=$( ls dist/*.tar.gz )
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elif [ "$INSTALL_TYPE" == "wheel" ]; then
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python setup.py bdist_wheel
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export ARCHIVE=$( ls dist/*.whl )
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elif [ "$INSTALL_TYPE" == "archive" ]; then
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export ARCHIVE="package.tar.gz"
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git archive -o $ARCHIVE HEAD
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fi
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set +eux

‎tools/ci/check.sh

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#!/bin/bash
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echo Running tests
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source tools/ci/activate.sh
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set -eu
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# Required variables
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echo CHECK_TYPE = $CHECK_TYPE
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set -x
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if [ "${CHECK_TYPE}" == "test" ]; then
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pytest --capture=no --verbose --doctest-modules -c nipype/pytest.ini \
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--cov-config .coveragerc --cov nipype --cov-report xml:cov.xml \
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--junitxml=test-results.xml nipype
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else
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false
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fi
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set +eux
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echo Done running tests

‎tools/ci/create_venv.sh

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#!/bin/bash
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echo Creating isolated virtual environment
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source tools/ci/env.sh
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set -eu
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# Required variables
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echo SETUP_REQUIRES = $SETUP_REQUIRES
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set -x
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python -m pip install --upgrade pip virtualenv
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virtualenv --python=python virtenv
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source tools/ci/activate.sh
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python --version
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python -m pip install -U $SETUP_REQUIRES
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which python
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which pip
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set +eux
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echo Done creating isolated virtual environment

‎tools/ci/env.sh

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SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
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# Minimum requirements
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REQUIREMENTS="-r requirements.txt"
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# Minimum versions of minimum requirements
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MIN_REQUIREMENTS="-r min-requirements.txt"
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# Numpy and scipy upload nightly/weekly/intermittent wheels
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NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple"
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STAGING_WHEELS="https://pypi.anaconda.org/multibuild-wheels-staging/simple"
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PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS --extra-index-url $STAGING_WHEELS"
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for CONF in (/etc/fsl/fsl.sh /etc/afni/afni.sh); do
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if [ -r $CONF ]; then source $CONF; fi
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done
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FSLOUTPUTTYPE=NIFTI_GZ

‎tools/ci/install.sh

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#!/bin/bash
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echo Installing nibabel
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source tools/ci/activate.sh
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source tools/ci/env.sh
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set -eu
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# Required variables
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echo INSTALL_TYPE = $INSTALL_TYPE
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echo CHECK_TYPE = $CHECK_TYPE
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echo NIPYPE_EXTRAS = $NIPYPE_EXTRAS
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echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
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set -x
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if [ -n "$EXTRA_PIP_FLAGS" ]; then
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EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
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fi
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if [ "$INSTALL_TYPE" == "setup" ]; then
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python setup.py install
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else
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pip install $EXTRA_PIP_FLAGS $ARCHIVE
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fi
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# Basic import check
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python -c 'import nipype; print(nipype.__version__)'
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if [ "$CHECK_TYPE" == "skiptests" ]; then
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exit 0
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fi
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pip install $EXTRA_PIP_FLAGS "nipype[$NIPYPE_EXTRAS]"
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set +eux
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echo Done installing nibabel

‎tools/ci/install_deb_dependencies.sh

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#!/bin/bash
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echo "Installing NeuroDebian dependencies"
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set -eu
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echo "INSTALL_DEB_DEPENDENCIES = $INSTALL_DEB_DEPENDENCIES"
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if $INSTALL_DEB_DEPENDENCIES; then
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sudo rm -rf /dev/shm
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sudo ln -s /run/shm /dev/shm
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bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
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sudo apt update
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sudo apt install -y -qq fsl afni elastix fsl-atlases xvfb fusefat graphviz
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fi

‎tools/ci/install_dependencies.sh

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#!/bin/bash
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echo Installing dependencies
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source tools/ci/activate.sh
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source tools/ci/env.sh
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set -eu
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# Required variables
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echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
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echo DEPENDS = $DEPENDS
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echo OPTIONAL_DEPENDS = $OPTIONAL_DEPENDS
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set -x
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if [ -n "$EXTRA_PIP_FLAGS" ]; then
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EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
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fi
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if [ -n "$DEPENDS" ]; then
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pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS}
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if [ -n "$OPTIONAL_DEPENDS" ]; then
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for DEP in ${!OPTIONAL_DEPENDS}; do
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pip install ${EXTRA_PIP_FLAGS} --prefer-binary $DEP || true
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done
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fi
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fi
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set +eux
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echo Done installing dependencies

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