set pybids config (#174) #94
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| --- | |
| name: docker | |
| on: | |
| push: | |
| branches: ['main'] | |
| tags: ['*'] | |
| pull_request: | |
| branches: ['*'] | |
| paths: | |
| - 'Dockerfile' | |
| - 'requirements.txt' | |
| - '.github/workflows/docker.yml' | |
| - 'tools/*' | |
| release: | |
| types: [published] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| env: | |
| USER_NAME: bids | |
| REPO_NAME: giga_connectome | |
| DATA: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| IMAGE: /home/runner/work/giga_connectome/giga_connectome/docker | |
| jobs: | |
| download-test-data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: ${{ env.DATA }} | |
| key: data | |
| - if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| uses: actions/setup-python@v5 | |
| - if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| name: Download fmriprep derivative of ds000017 | |
| run: | | |
| pip install tox | |
| tox -e test_data | |
| docker-build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build the Docker image | |
| run: | | |
| docker build . --file Dockerfile --tag ${{env.USER_NAME}}/${{env.REPO_NAME}} | |
| mkdir -p ${{ env.IMAGE }} | |
| docker save "${{env.USER_NAME}}/${{env.REPO_NAME}}" > "${{ env.IMAGE }}/image.tar" | |
| - name: Check image size and version | |
| run: | | |
| docker images | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --version | |
| - name: Upload docker artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| docker-run: | |
| runs-on: ubuntu-latest | |
| needs: [download-test-data, docker-build] | |
| strategy: | |
| matrix: | |
| atlas: ['Schaefer2018', 'MIST', 'DiFuMo', 'HarvardOxfordCortical', 'HarvardOxfordCorticalSymmetricSplit', 'HarvardOxfordSubcortical'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Restore docker image | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| - name: Restore cached data ds000017 | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ${{ env.DATA }} | |
| key: data | |
| - name: Test the Docker image | |
| run: | | |
| docker load -i ${{ env.IMAGE }}/image.tar | |
| docker run --rm \ | |
| -v ${{ env.DATA }}:/test_data \ | |
| -v ./outputs:/outputs \ | |
| -v ./outputs/atlases:/atlases \ | |
| ${{env.USER_NAME}}/${{env.REPO_NAME}} \ | |
| /test_data/ds000017-fmriprep22.0.1-downsampled-nosurface \ | |
| /outputs \ | |
| participant \ | |
| -a /atlases \ | |
| --atlas ${{ matrix.atlas }} \ | |
| --participant_label 1 \ | |
| --reindex-bids | |
| - name: Upload output artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: connectome_${{ matrix.atlas }} | |
| path: ./outputs/ | |
| docker-push: | |
| runs-on: ubuntu-latest | |
| needs: [docker-run] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| if: ${{ github.ref == 'refs/heads/main' || github.ref_type == 'tag' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Restore docker image | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Load image | |
| run: docker load -i ${{ env.IMAGE }}/image.tar | |
| - name: Push unstable to dockerhub on tags or on main | |
| run: | | |
| echo "Pushing unstable versions to DockerHub" | |
| unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable" | |
| docker tag "${{env.USER_NAME}}/${{env.REPO_NAME}}" "${unstable}" | |
| docker push "${unstable}" | |
| - name: Push stable release to dockerhub on tags only | |
| if: ${{ github.ref_type == 'tag' }} | |
| run: | | |
| echo "Pushing stable and latest versions to DockerHub for latest and ${{ github.ref_name }}" | |
| unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable" | |
| latest="${{env.USER_NAME}}/${{env.REPO_NAME}}:latest" | |
| docker tag "${unstable}" "${latest}" | |
| docker push "${latest}" | |
| tagged_release="${{env.USER_NAME}}/${{env.REPO_NAME}}:${{ github.ref_name }}" | |
| docker tag "${unstable}" "${tagged_release}" | |
| docker push "${tagged_release}" |