Workflow file for this run
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| name: (Release) Build Pipy, Dockerhub image and test | |
| on: | |
| release: | |
| types: [released] | |
| jobs: | |
| 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: . | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| run-pretest-spm: | |
| name: Running all existing pipelines in macapype_CI.zip (SPM_native) | |
| 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: | | |
| mkdir SPM_native | |
| cd SPM_native | |
| wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O 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 SPM_native_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de SPM_native_noseg T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native_noseg -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de SPM_native T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain SPM_native_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native_prep -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/ | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ | |
| - name: Running test pipeline marmo-marmobrain SPM_native_noseg T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain SPM_native T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Cleaning dataset | |
| run: | |
| sudo rm -rf /home/runner/work/macapype/macapype/SPM_native | |
| run-pretest: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS) | |
| 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: | | |
| mkdir ANTS | |
| cd ANTS | |
| wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O 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 "" | |
| ls macapype_CI/baboon-cerimed-adrien | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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/ANTS/macapype_CI/marmo-marmobrain/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline marmo-marmobrain ANTS T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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/ANTS/macapype_CI/baboon-cerimed-adrien/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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/ANTS/macapype_CI/baboon-cerimed-adrien/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/ | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de ANTS_prep T1 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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/ANTS/macapype_CI/macaque_prime-de/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/ | |
| echo "" | |
| - name: Running test pipeline macaque_prime-de ANTS_prep T1 T2 | |
| run: | | |
| docker run -i -v /home/runner/work/macapype/macapype/ANTS/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 | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/ | |
| ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/ | |
| ls /home/runner/work/macapype/macapype/ANTS/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 /home/runner/work/macapype/macapype/ANTS | |