Merge pull request #257 from jhlegarreta/LimitNumpyVersion #373
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| name: Build, test | |
| on: | |
| push: | |
| branches: ['main'] | |
| pull_request: | |
| # Allow a subsequently queued workflow run to interrupt previous runs | |
| concurrency: | |
| group: '${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}' | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| env: | |
| ANTSPATH: /opt/ants | |
| FSLPATH: /opt/fsl | |
| FSLDIR: /opt/fsl | |
| FSLOUTPUTTYPE: NIFTI_GZ | |
| FSLVERSION: 6.0.6.5 | |
| steps: | |
| - name: Cache Ubuntu dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| /var/lib/apt | |
| !/var/lib/apt/lists/partial | |
| !/var/lib/apt/lists/lock | |
| key: apt-cache-v1 | |
| restore-keys: | | |
| apt-cache-v1 | |
| - name: Install Ubuntu dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends \ | |
| bc \ | |
| bzip2 \ | |
| ca-certificates \ | |
| curl \ | |
| dc \ | |
| file \ | |
| libfontconfig1 \ | |
| libfreetype6 \ | |
| libgl1-mesa-dev \ | |
| libgl1-mesa-dri \ | |
| libglu1-mesa-dev \ | |
| libgomp1 \ | |
| libice6 \ | |
| libxcursor1 \ | |
| libxft2 \ | |
| libxinerama1 \ | |
| libxrandr2 \ | |
| libxrender1 \ | |
| libxt6 | |
| sudo apt-get clean | |
| - name: Cache ANTs install | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/ants | |
| key: ants-v1 | |
| restore-keys: | | |
| ants-v1 | |
| - name: Install ANTs | |
| run: | | |
| if [[ ! -d "${ANTSPATH}" ]]; then | |
| sudo mkdir -p $ANTSPATH | |
| 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 | |
| fi | |
| - name: Cache FSL install | |
| uses: actions/cache@v4 | |
| with: | |
| path: $FSLPATH | |
| key: fsl-v2 | |
| restore-keys: | | |
| fsl-v2 | |
| # Run with multiple Python versions | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install FSL | |
| run: | | |
| if [[ ! -d "${FSLPATH}" ]]; then | |
| sudo mkdir -p $FSLPATH | |
| curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -o /tmp/fslinstaller.py -s | |
| python /tmp/fslinstaller.py -d ${FSLPATH} -V ${FSLVERSION} -o | |
| sudo rm -rf ${FSLPATH}/data/atlases | |
| rm /tmp/fslinstaller.py | |
| fi | |
| - name: Checkout GitHub repository | |
| uses: actions/checkout@v4 | |
| - name: Install dependencies for headless display | |
| run: | | |
| ${{ github.workspace }}/.github/scripts/setup_headless.sh | |
| - name: Install Python requirements | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install pytest nbval | |
| - name: Download data | |
| run: | | |
| pushd `pwd` | |
| cd ${{ github.workspace }}/data | |
| osf -p cmq8a fetch ds000221_subject/ds000221_sub-010006.zip | |
| unzip ds000221_sub-010006.zip | |
| rm ds000221_sub-010006.zip | |
| popd | |
| - name: Run pytest on Jupyter notebooks | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:`realpath ${{ github.workspace }}` | |
| export PATH=$FSLPATH/bin:$ANTSPATH:$PATH | |
| pytest --nbval-lax -v code/introduction.ipynb | |
| pytest --nbval-lax -v code/preprocessing.ipynb | |
| pytest --nbval-lax -v code/diffusion_tensor_imaging.ipynb | |
| pytest --nbval-lax -v code/constrained_spherical_deconvolution.ipynb | |
| pytest --nbval-lax -v code/deterministic_tractography.ipynb | |
| pytest --nbval-lax -v code/probabilistic_tractography.ipynb |