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/skullTo3d | |
| - 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-macaque-petra: | |
| name: Running all existing pipelines in skullTo3d_CI.zip (ANTS macaque petra) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/skullto3d:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/swYxNZ3P6LjfqN4 --output skullTo3d_CI.zip | |
| unzip -o skullTo3d_CI.zip -d skullTo3d_CI | |
| pwd | |
| echo "" | |
| ls skullTo3d_CI | |
| echo "" | |
| ls skullTo3d_CI/cenir-macaque-petra | |
| ls skullTo3d_CI/cenir-macaque-petra/sub-Magneto/anat | |
| echo "" | |
| - name: Running all test pipelines (ANTS cenir macaque petra) | |
| run: | | |
| docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cenir-macaque-petra -out /data/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt petra -deriv -pad -nprocs 1 | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results/derivatives | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_petra_segbrain_t1_t2/sub-Magneto/anat | |
| - name: Cleaning dataset | |
| run: | | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_petra_segbrain_t1_t2 | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/result/macapype_crop_aladin_ants_skull_petra_segbrain_t1_t2 | |
| run-pretest-ants-macaque-ct: | |
| name: Running all existing pipelines in skullTo3d_CI.zip (ANTS macaque CT) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/skullto3d:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/swYxNZ3P6LjfqN4 --output skullTo3d_CI.zip | |
| unzip -o skullTo3d_CI.zip -d skullTo3d_CI | |
| pwd | |
| echo "" | |
| ls skullTo3d_CI | |
| echo "" | |
| ls skullTo3d_CI/cerimed-macaque-ct | |
| ls skullTo3d_CI/cerimed-macaque-ct/sub-Marvin/ses-01/anat | |
| echo "" | |
| - name: Running all test pipelines (ANTS cerimed macaque CT) | |
| run: | | |
| docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cerimed-macaque-ct -out /data/cerimed-macaque-ct/results -soft ANTS_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt CT -deriv -pad -nprocs 1 | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results/derivatives | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_CT_segbrain_t1_t2/sub-Marvin/ses-01/anat | |
| - name: Cleaning dataset | |
| run: | | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_CT_segbrain_t1_t2 | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/result/macapype_crop_aladin_ants_skull_CT_segbrain_t1_t2 | |
| run-pretest-ants-marmo-petra: | |
| name: Running all existing pipelines in skullTo3d_CI.zip (ANTS marmo petra) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/skullto3d:latest | |
| - name: Download dataset | |
| run: | | |
| curl https://amubox.univ-amu.fr/public.php/dav/files/swYxNZ3P6LjfqN4 --output skullTo3d_CI.zip | |
| unzip -o skullTo3d_CI.zip -d skullTo3d_CI | |
| pwd | |
| echo "" | |
| ls skullTo3d_CI | |
| echo "" | |
| ls skullTo3d_CI/cerimed-marmo-petra | |
| ls skullTo3d_CI/cerimed-marmo-petra/sub-Paolina/ses-01/anat | |
| echo "" | |
| - name: Running all test pipelines (ANTS cerimed marmo petra) | |
| run: | | |
| docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cerimed-marmo-petra -out /data/cerimed-marmo-petra/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad -nprocs 1 | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results/derivatives | |
| ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_segbrain_t1_t2/sub-Paolina/ses-01/anat | |
| - name: Cleaning dataset | |
| run: | | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_segbrain_t1_t2 | |
| sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/result/macapype_crop_aladin_ants_skull_t1_petra_segbrain_t1_t2 | |