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MAINT: Move from TravisCI to GHA
Resolves: #103.
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‎.github/workflows/pythonpackage.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python package
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on:
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push:
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branches: [ '*' ]
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tags: [ '*' ]
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pull_request:
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branches: [ master, 'maint/*' ]
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jobs:
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build:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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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: ${{ matrix.python-version }}
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Build in confined, updated environment and interpolate version
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run: |
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python -m venv /tmp/buildenv
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source /tmp/buildenv/bin/activate
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python -m pip install -U setuptools pip wheel twine docutils
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python setup.py sdist bdist_wheel
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python -m twine check dist/nitransforms*
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# Interpolate version
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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TAG=${GITHUB_REF##*/}
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fi
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THISVERSION=$( python get_version.py )
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THISVERSION=${TAG:-$THISVERSION}
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echo "Expected VERSION: \"${THISVERSION}\""
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echo "THISVERSION=${THISVERSION}" >> ${GITHUB_ENV}
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- name: Install in confined environment [sdist]
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run: |
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python -m venv /tmp/install_sdist
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source /tmp/install_sdist/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install dist/nitransforms*.tar.gz
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [wheel]
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run: |
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python -m venv /tmp/install_wheel
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source /tmp/install_wheel/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install dist/nitransforms*.whl
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [pip install .]
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run: |
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python -m venv /tmp/setup_install
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source /tmp/setup_install/bin/activate
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python -m pip install --upgrade pip wheel
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python -m pip install .
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [pip install -e .]
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run: |
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python -m venv /tmp/setup_develop
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source /tmp/setup_develop/bin/activate
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python -m pip install pip
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python -m pip install --upgrade pip wheel
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python -m pip install -e .
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INSTALLED_VERSION=$(python -c 'import nitransforms; print(nitransforms.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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flake8:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- run: pip install flake8
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- run: flake8 nitransforms/

‎.github/workflows/travis.yml

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name: Deps & CI
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on: [push, pull_request]
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jobs:
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build-linux:
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if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
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runs-on: ubuntu-latest
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env:
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TEST_DATA_HOME: /home/runner/sdcflows-tests
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FSLDIR: /usr/share/fsl/5.0
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FSLOUTPUTTYPE: NIFTI_GZ
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FSLMULTIFILEQUIT: TRUE
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POSSUMDIR: /usr/share/fsl/5.0
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FSLTCLSH: /usr/bin/tclsh
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FSLWISH: /usr/bin/wish
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AFNI_HOME: /opt/afni
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AFNI_MODELPATH: /opt/afni/models
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AFNI_IMSAVE_WARNINGS: NO
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AFNI_TTATLAS_DATASET: /opt/afni/atlases
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AFNI_PLUGINPATH: /opt/afni/plugins
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ANTSPATH: /opt/ants
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strategy:
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max-parallel: 5
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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- uses: actions/cache@v2
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with:
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path: /var/lib/apt
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key: apt-cache-v2
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restore-keys: |
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apt-cache-v2
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y --no-install-recommends \
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curl bzip2 ca-certificates \
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tcsh gsl-bin netpbm \
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libjpeg62 xvfb xterm \
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libglu1-mesa-dev libglw1-mesa \
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libxm4 build-essential
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- name: Install FSL
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run: |
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sudo apt-get install -y --no-install-recommends fsl
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- uses: actions/cache@v2
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with:
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path: /opt/afni
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key: afni-v1
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restore-keys: |
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afni-v1
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- name: Install AFNI
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run: |
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if [[ ! -d "${AFNI_HOME}" ]]; then
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curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
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tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
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fi
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- uses: actions/cache@v2
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with:
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path: /opt/ants
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key: ants-v1
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restore-keys: |
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ants-v1
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- name: Install ANTS
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run: |
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if [[ ! -d "${ANTSPATH}" ]]; then
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sudo mkdir -p $ANTSPATH
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curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | sudo tar -xzC $ANTSPATH --strip-components 1
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fi
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- name: Git settings (pacify DataLad)
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run: |
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git config --global user.name 'NiPreps Bot'
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git config --global user.email '[email protected]'
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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: ${{ matrix.python-version }}
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- uses: actions/cache@v2
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id: conda
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with:
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path: |
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/usr/share/miniconda/pkgs
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/home/runner/.cache/pip
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key: python-${{ matrix.python-version }}-v2
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restore-keys: |
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python-${{ matrix.python-version }}-
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- name: Install DataLad
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run: |
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$CONDA/bin/conda install -c conda-forge git-annex datalad pip
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$CONDA/bin/pip install datalad-osf
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- uses: actions/checkout@v2
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- name: Install minimal dependencies
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run: |
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$CONDA/bin/pip install -r min-requirements.txt
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$CONDA/bin/pip install .[tests]
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- uses: actions/cache@v2
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with:
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path: ~/.cache/templateflow
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key: tf-cache-v1
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restore-keys: |
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tf-cache-
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- name: Get TemplateFlow's required objects
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run: |
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$CONDA/bin/python tools/cache_templateflow.py
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- uses: actions/cache@v2
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with:
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path: ${{ env.TEST_DATA_HOME }}
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key: data-cache-v1
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restore-keys: |
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data-cache-
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- name: Install test data
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run: |
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export PATH=$CONDA/bin:$PATH
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mkdir -p ${{ env.TEST_DATA_HOME }}
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cd ${{ env.TEST_DATA_HOME }}
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# ds001600
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datalad install -r https://github.com/nipreps-data/ds001600.git
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datalad update -r --merge -d ds001600/
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datalad get -r -d ds001600/ ds001600/sub-1/
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# HCP/sub-101006
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datalad install -r https://github.com/nipreps-data/HCP101006.git
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datalad update -r --merge -d HCP101006/
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datalad get -r -d HCP101006
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# ds001771
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datalad install -r https://github.com/nipreps-data/ds001771.git
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datalad update -r --merge -d ds001771/
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datalad get -r -d ds001771/ ds001771/sub-36/*
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datalad get -r -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*
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# ds000054
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datalad install -r https://github.com/nipreps-data/ds000054.git
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datalad update --merge -d ds000054/
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datalad get -r -d ds000054/ ds000054/sub-100185/*
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# ds000206
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datalad install -r https://github.com/nipreps-data/ds000206.git
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datalad update -r --merge -d ds000206/
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datalad get -r -d ds000206/ ds000206/sub-05/
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- name: Install FreeSurfer's mri_robust_template
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env:
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MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
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run: |
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curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
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sudo install mri_robust_template /usr/local/bin
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mkdir -p $HOME/.cache/freesurfer/
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echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $HOME/.cache/freesurfer/license.txt
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- name: Run pytest with coverage
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run: |
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export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
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export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
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$CONDA/bin/pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows
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- name: Submit code coverage
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run: |
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$CONDA/bin/conda install codecov
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$CONDA/bin/python -m codecov --flags travis --file cov.xml -e $GITHUB_RUN_NUMBER

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