Upgrade from ISMRMRD to MRD v2 #5
Workflow file for this run
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| name: Pingvin CI | |
| on: | |
| push: | |
| branches: [main] | |
| tags: ["v*.*.*"] | |
| pull_request: | |
| branches: [main] | |
| workflow_dispatch: | |
| permissions: | |
| id-token: write | |
| contents: read | |
| env: | |
| imageBaseName: ghcr.io/gadgetron/pingvin/ubuntu22.04 | |
| defaults: | |
| run: | |
| # See https://github.com/marketplace/actions/setup-miniconda#important | |
| shell: bash -el {0} | |
| jobs: | |
| build-and-test: | |
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | |
| strategy: | |
| matrix: | |
| include: | |
| - flavor: cuda | |
| requirements: python,cuda | |
| - flavor: nocuda | |
| requirements: python | |
| steps: | |
| - name: checkout | |
| uses: actions/[email protected] | |
| - name: Check GPU availability | |
| run: docker run --rm --gpus=all ghcr.io/gadgetron/gadgetron/cuda:12.3.0-base-ubuntu22.04 nvidia-smi | |
| - name: Build Docker images | |
| run: ./docker/build-images.sh --type dev --type build --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" | |
| - name: Unit Test | |
| run: |- | |
| image_name="${{env.imageBaseName}}_build_${{matrix.flavor}}" | |
| test_command=". /opt/conda/etc/profile.d/conda.sh \ | |
| && conda activate gadgetron \ | |
| && /opt/code/gadgetron/build/test/test_all" | |
| docker run --rm --gpus=all "${image_name}" /bin/bash -c "$test_command" | |
| - name: End-to-End Test | |
| run: |- | |
| image_name="${{env.imageBaseName}}_rt_${{matrix.flavor}}" | |
| # Check Gadgetron entrypoint | |
| docker run --rm -i --gpus=all "${image_name}" --info | |
| # Test Gadgetron end-to-end | |
| test_command=". /opt/conda/etc/profile.d/conda.sh \ | |
| && conda activate gadgetron \ | |
| && cd /opt/e2e-test/ \ | |
| && pytest --ignore-requirements ${{matrix.requirements}} --echo-log-on-failure" | |
| docker run --rm --gpus=all --entrypoint /bin/bash "${image_name}" -c "$test_command" | |
| publish-docker-images: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| needs: [build-and-test] | |
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | |
| strategy: | |
| matrix: | |
| flavor: [cuda, nocuda] | |
| permissions: | |
| packages: write | |
| steps: | |
| - name: checkout | |
| uses: actions/[email protected] | |
| - name: Log into ghcr.io | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Publish Docker images | |
| run: |- | |
| GADGETRON_VERSION_MAJOR=$(grep -Po '(?<=set\(GADGETRON_VERSION_MAJOR )([^\)]+)' CMakeLists.txt) | |
| GADGETRON_VERSION_MINOR=$(grep -Po '(?<=set\(GADGETRON_VERSION_MINOR )([^\)]+)' CMakeLists.txt) | |
| GADGETRON_VERSION_PATCH=$(grep -Po '(?<=set\(GADGETRON_VERSION_PATCH )([^\)]+)' CMakeLists.txt) | |
| GADGETRON_VERSION="${GADGETRON_VERSION_MAJOR}.${GADGETRON_VERSION_MINOR}.${GADGETRON_VERSION_PATCH}" | |
| ./docker/build-images.sh --type dev --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" --tag "${GADGETRON_VERSION}" --push | |
| ./docker/build-images.sh --type dev --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" --tag latest --push | |
| build-conda-package: | |
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | |
| steps: | |
| - name: checkout | |
| uses: actions/[email protected] | |
| - name: Install Yardl | |
| run: |- | |
| YARDL_VERSION=$(grep -Po '(?<=YARDL_VERSION=)(.+)' Dockerfile) | |
| mkdir -p "/tmp/yardl_${YARDL_VERSION}_linux_x86_64" | |
| cd "/tmp/yardl_${YARDL_VERSION}_linux_x86_64" | |
| wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" | |
| tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" | |
| pwd >> $GITHUB_PATH | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| environment-file: conda/environment.yml | |
| activate-environment: gadgetron-build | |
| - name: Build conda package | |
| run: ./conda/package.sh | |
| - name: Upload Conda package | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: conda-packages | |
| path: conda/build_pkg/**/gadgetron*.tar.bz2 | |
| publish-conda-package: | |
| # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| # Publishing a Pingvin conda package will overwrite Gadgetron packages. | |
| # Enable this job once Pingvin is ready for release. | |
| if: false | |
| needs: [build-conda-package] | |
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | |
| steps: | |
| - name: checkout | |
| uses: actions/[email protected] | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| environment-file: conda/environment.yml | |
| activate-environment: gadgetron-build | |
| - name: Download Conda package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: conda-packages | |
| path: conda/build_pkg/ | |
| - name: Publish conda package | |
| env: | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| run: | | |
| for p in $(find conda/build_pkg -name gadgetron*.tar.bz2) | |
| do | |
| ./conda/publish_package.sh -u gadgetron -t "$ANACONDA_TOKEN" -p "$p" | |
| done |