Workflow file for this run
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| name: (Release) Build Pipy, Dockerhub image and test | |
| on: | |
| release: | |
| types: [released] | |
| 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/github-pages-deploy-action@v4.4.3 | |
| with: | |
| branch: gh-pages | |
| folder: docs/_build/html/ | |
| clean: true | |
| ssh-key: ${{ secrets.DEPLOY_KEY }} | |
| build-n-publish-pypi: | |
| name: Build and publish Python to 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 PyPI | |
| if: startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| docker-build: | |
| name: Build Docker image and Push to Docker Hub | |
| needs: build-n-publish-pypi | |
| 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_nomcr | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| run-pretest-ants-marmo: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_marmo | |
| echo "" | |
| - name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/sub-Tresor/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results | |
| run-pretest-ants-marmoT2: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_marmo | |
| echo "" | |
| - name: Running test pipeline cerimed_marmo ANTS_noseg T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmoT2 -sub Tresor -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/derivatives/macapype_ants/sub-Tresor/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results | |
| run-pretest-ants-baboon: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_baboon | |
| echo "" | |
| - name: Running test pipeline cerimed_baboon ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results -soft ANTS_prep -species baboon -sub Prune -ses 3 -deriv -pad -dt T1 T2 -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results/derivatives/macapype_ants/sub-Prune/ses-3/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results | |
| run-pretest-ants-baboon3: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_baboon | |
| echo "" | |
| - name: Running test pipeline cerimed_baboon ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_prep -species baboon3 -sub Prune -ses 3 -deriv -pad -dt T1 T2 -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3/derivatives/macapype_ants/sub-Prune/ses-3/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3 | |
| run-pretest-ants-baboon2: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_baboon | |
| echo "" | |
| - name: Running test pipeline cerimed_baboon ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_prep -species baboon2 -sub Prune -ses 2 -deriv -pad -dt T1 T2 -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2/derivatives/macapype_ants/sub-Prune/ses-2/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2 | |
| run-pretest-ants-baboon1: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_baboon | |
| echo "" | |
| - name: Running test pipeline cerimed_baboon ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_prep -species baboon1 -sub Prune -ses 1 -deriv -pad -dt T1 T2 -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1/derivatives/macapype_ants/sub-Prune/ses-1/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1 | |
| run-pretest-ants-baboon0: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_baboon | |
| echo "" | |
| - name: Running test pipeline cerimed_baboon ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2 -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0 | |
| run-pretest-ants-macaque: | |
| name: Running all existing pipelines in macapype_CI_v2.1.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/CoSC5w5ATZextme --output macapype_CI_v2.1.zip | |
| unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1 | |
| pwd | |
| echo "" | |
| ls macapype_CI_v2.1 | |
| echo "" | |
| ls macapype_CI_v2.1/cerimed_macaque | |
| echo "" | |
| - name: Running test pipeline cerimed_macaque ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_macaque/ -out /data/cerimed_macaque/results -soft ANTS_robustreg_prep -species macaque -sub Stevie -ses 01 -deriv -pad -dt T1 T2 -nprocs 1 | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/ | |
| ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results/derivatives/macapype_ants/sub-Stevie/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results | |