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/skullTo3d | |
| - 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-spm-macaque: | |
| name: Running all existing pipelines in skullTo3d_CI.zip (SPM_native macaque) | |
| needs: docker-build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 1440 | |
| steps: | |
| - name: Pull latest docker image | |
| run: | |
| docker pull macatools/skullTo3d:latest | |
| - name: Download dataset | |
| run: | | |
| wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O 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 "" | |
| ls skullTo3d_CI/cerimed-macaque-ct | |
| ls skullTo3d_CI/cerimed-macaque-ct/sub-Marvin/sub-01/anat | |
| echo "" | |
| ls skullTo3d_CI/cerimed-marmo-petra | |
| ls skullTo3d_CI/cerimed-marmo-petra/sub-Paolina/sub-01/anat | |
| echo "" | |
| - name: Running all test pipelines (ANTS deriv pad) | |
| run: | | |
| python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |
| ls skullTo3d_CI/cenir-macaque-petra/results | |
| ls skullTo3d_CI/cenir-macaque-petra/results/derivatives | |
| ls skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Magneto/anat | |
| python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad | |
| ls skullTo3d_CI/cerimed-macaque-ct/results | |
| ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives | |
| ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2/sub-Marvin/-ses-01/anat | |
| python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad | |
| ls skullTo3d_CI/cerimed-marmo-petra/results | |
| ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives | |
| ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Paolina/-ses-01/anat | |