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Establish Pingvin streaming image reconstruction framework. * Upgrade all tested Gadgets/Toolboxes to use MRDv2 instead of ISMRMRD * Remove all socket networking code, including `gadgetron_ismrmrd_client` * Remove all Readers and Writers * Refactor end-to-end tests to use PyTest, removing Siemens dat conversion * Remove everything Windows-related * Port the CI pipeline to GitHub Actions * Rename from Gadgetron to Pingvin
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,14 @@ | ||
| #! /bin/bash | ||
| # shellcheck source=/dev/null | ||
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| source /opt/conda/etc/profile.d/conda.sh | ||
| conda activate pingvin | ||
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| if command -v just >/dev/null ; then | ||
| source <(just --completions bash) | ||
| fi | ||
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| if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then | ||
| # We don't want subshells to unnecessarily source this again. | ||
| unset BASH_ENV | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,149 @@ | ||
| name: Pingvin CI | ||
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| on: | ||
| push: | ||
| branches: [main] | ||
| tags: ["v*.*.*"] | ||
| pull_request: | ||
| branches: [main] | ||
| workflow_dispatch: | ||
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| permissions: | ||
| id-token: write | ||
| contents: read | ||
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| env: | ||
| imageBaseName: ghcr.io/gadgetron/pingvin/ubuntu22.04 | ||
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| defaults: | ||
| run: | ||
| # See https://github.com/marketplace/actions/setup-miniconda#important | ||
| shell: bash -el {0} | ||
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| jobs: | ||
| build-and-test: | ||
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | ||
| strategy: | ||
| matrix: | ||
| flavor: [cuda, nocuda] | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/[email protected] | ||
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| - name: Check GPU availability | ||
| run: docker run --rm --gpus=all ghcr.io/gadgetron/gadgetron/cuda:12.3.0-base-ubuntu22.04 nvidia-smi | ||
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| - name: Build Docker images | ||
| run: ./docker/build-images.sh --type dev --type build --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" | ||
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| - name: Unit Test | ||
| run: |- | ||
| image_name="${{env.imageBaseName}}_build_${{matrix.flavor}}" | ||
| test_command=". /opt/conda/etc/profile.d/conda.sh \ | ||
| && conda activate pingvin \ | ||
| && /opt/code/pingvin/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 Pingvin entrypoint | ||
| docker run --rm -i --gpus=all "${image_name}" --info | ||
| # Test Pingvin end-to-end | ||
| test_command=". /opt/conda/etc/profile.d/conda.sh \ | ||
| && conda activate pingvin \ | ||
| && cd /opt/e2e-test/ \ | ||
| && pytest --echo-log-on-failure" | ||
| docker run --rm --gpus=all --entrypoint /bin/bash "${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] | ||
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| - name: Log into ghcr.io | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| registry: ghcr.io | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Publish Docker images | ||
| run: |- | ||
| PINGVIN_VERSION_MAJOR=$(grep -Po '(?<=set\(PINGVIN_VERSION_MAJOR )([^\)]+)' CMakeLists.txt) | ||
| PINGVIN_VERSION_MINOR=$(grep -Po '(?<=set\(PINGVIN_VERSION_MINOR )([^\)]+)' CMakeLists.txt) | ||
| PINGVIN_VERSION_PATCH=$(grep -Po '(?<=set\(PINGVIN_VERSION_PATCH )([^\)]+)' CMakeLists.txt) | ||
| PINGVIN_VERSION="${PINGVIN_VERSION_MAJOR}.${PINGVIN_VERSION_MINOR}.${PINGVIN_VERSION_PATCH}" | ||
| ./docker/build-images.sh --type dev --type rt --flavor ${{matrix.flavor}} --base-name "${{env.imageBaseName}}" --tag "${PINGVIN_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] | ||
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| - 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: pingvin-build | ||
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| - name: Build conda package | ||
| run: ./conda/package.sh | ||
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| - name: Upload Conda package | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: conda-packages | ||
| path: conda/build_pkg/**/pingvin*.tar.bz2 | ||
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| publish-conda-package: | ||
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | ||
| needs: [build-conda-package] | ||
| runs-on: ["self-hosted", "1ES.Pool=biomedsigproc-pingvin-NC6s_v3"] | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/[email protected] | ||
|
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| - name: Setup Miniforge | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| miniforge-version: latest | ||
| environment-file: conda/environment.yml | ||
| activate-environment: pingvin-build | ||
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| - name: Download Conda package | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: conda-packages | ||
| path: conda/build_pkg/ | ||
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| - name: Publish conda package | ||
| env: | ||
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | ||
| run: | | ||
| for p in $(find conda/build_pkg -name pingvin*.tar.bz2) | ||
| do | ||
| ./conda/publish_package.sh -u gadgetron -t "$ANACONDA_TOKEN" -p "$p" | ||
| done |
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