Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: (Prerelease) Build Pipy, Dockerhub image and test | |
| on: | |
| release: | |
| types: [prereleased] | |
| jobs: | |
| 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 | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| docker-pull: | |
| name: Running all existing pipelines in macapype_CI.zip (SPM_native) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/macapype:latest | |
| - name: Download dataset | |
| run: | | |
| 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 "" | |
| run-pretest-spm-macaque: | |
| name: Running all existing pipelines in macapype_CI.zip (SPM_native macaque) | |
| needs: docker-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Running test pipeline macaque_prime-de SPM_native_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 SPM_native_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 | |
| 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_spm_t1_t2_native/ | |
| ls /home/runner/work/macapype/macapype/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/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/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/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/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/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_spm_t1_t2_native | |
| run-pretest-spm-marmo: | |
| name: Running all existing pipelines in macapype_CI.zip (SPM_native marmo) | |
| needs: docker-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Running test pipeline marmo-marmobrain SPM_native_prep 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 SPM_native_prep -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_spm_t1_t2_native/ | |
| ls /home/runner/work/macapype/macapype/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/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/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/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/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/ | |
| run-pretest-ants-t1-marmo: | |
| name: Running all existing pipelines in macapype_CI.zip (ANTS marmo T1) | |
| needs: docker-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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: Running test pipeline marmo-marmobrain ANTS 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 -species marmo -sub Percy -ses 01 -deriv -pad -dt 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-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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/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/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/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-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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-pull | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - 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 | |
| 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 | |