Workflow file for this run
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| name: (Prerelease) Build Pipy, Dockerhub image and test | |
| on: | |
| release: | |
| types: [prereleased] | |
| jobs: | |
| build: | |
| name: Build documentation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Set up Python 3.10.5 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.10.5 | |
| - name: Install dependencies | |
| run: | | |
| pip install -e .[doc] | |
| sudo apt-get install build-essential graphviz libgraphviz-dev | |
| pip install --upgrade pygraphviz graphviz | |
| - name: Test with pytest | |
| run: | |
| py.test --cov macapype --ignore=examples/ --ignore=run_examples/ | |
| - name: Build the Doc 🔧 | |
| run: | | |
| cd docs | |
| make clean | |
| make html | |
| touch _build/html/.nojekyll | |
| - name: Deploy Github Pages 🚀 | |
| uses: JamesIves/[email protected] | |
| with: | |
| branch: gh-pages | |
| folder: docs/_build/html/ | |
| clean: true | |
| ssh-key: ${{ secrets.DEPLOY_KEY }} | |
| build-n-publish-testpypi: | |
| name: Build and publish Python to Test PyPI | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Set up Python 3.10.5 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.10.5 | |
| - name: Install pypa/build | |
| run: >- | |
| python -m | |
| pip install | |
| build | |
| --user | |
| - name: Build a binary wheel and a source tarball | |
| run: >- | |
| python -m | |
| build | |
| --sdist | |
| --wheel | |
| --outdir dist/ | |
| - name: Publish distribution to Test PyPI | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| docker-build: | |
| name: Build Docker image and Push to Docker Hub | |
| needs: build-n-publish-testpypi | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v2 | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| with: | |
| images: macatools/macapype | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| with: | |
| context: . | |
| file: Dockerfile_testpypi_nomcr | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| run-pretest-ants-t1-marmo: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS marmo T1) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| run-pretest-ants-marmo: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS marmo) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| run-pretest-ants-t1-baboon: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS T1 baboon) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| run-pretest-ants-baboon: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS baboon) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| run-pretest-ants-macaque-t1: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS macaque T1) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de ANTS_prep T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| run-pretest-ants-macaque: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS macaque) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip | |
| unzip -o macapype_CI.zip -d macapype_CI | |
| pwd | |
| echo "" | |
| ls macapype_CI | |
| echo "" | |
| ls macapype_CI/macaque_prime-de | |
| echo "" | |
| ls macapype_CI/marmo-marmobrain | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 -nprocs 1 | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2 | |