Updated KiSAO OBO and added parsing for 694 #5070
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| name: CI/CD | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| - '*/*' | |
| - '**' | |
| release: | |
| types: [published, edited] | |
| env: | |
| python-version: "3.10" | |
| jobs: | |
| CI-Build: | |
| name: CI-build | |
| runs-on: ubuntu-22.04 | |
| if: ${{ github.event_name == 'push' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build python-restclient package | |
| run: | | |
| cd python-restclient | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcelldata package | |
| run: | | |
| cd pythonData | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Add Linux dependencies | |
| shell: bash | |
| run: | | |
| mvn -version | |
| java -version | |
| mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true | |
| - name: Test building of docker image | |
| run: | | |
| docker build \ | |
| --file Dockerfile \ | |
| . | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |
| CI-Test: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT, Quarkus] | |
| fail-fast: false | |
| if: ${{ github.event_name == 'push' }} | |
| name: CI-Test-group-${{ matrix.test-group }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install hdf5 tools needed for testing | |
| run: sudo apt -y update && sudo apt -y install hdf5-tools | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build python-restclient package | |
| run: | | |
| cd python-restclient | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcelldata package | |
| run: | | |
| cd pythonData | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Maven Build and run Test group ${{ matrix.test-group }} | |
| shell: bash | |
| run: | | |
| mvn -version | |
| java -version | |
| if [ "${{ matrix.test-group }}" == "Quarkus" ]; then | |
| mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true | |
| cd vcell-rest | |
| mvn test | |
| else | |
| mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="${{ matrix.test-group }}" | |
| fi | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ failure() }} | |
| CD: | |
| name: CD | |
| runs-on: ubuntu-22.04 | |
| if: ${{ github.event_name == 'release' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build python-restclient package | |
| run: | | |
| cd python-restclient | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcelldata package | |
| run: | | |
| cd pythonData | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Get the VCell version from tags | |
| id: version | |
| run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) | |
| - name: Add Linux dependencies | |
| shell: bash | |
| run: | | |
| mvn -version | |
| java -version | |
| mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="Fast" | |
| - name: Build Docker image and push with latest tag | |
| run: | | |
| set -ux | |
| REVISION=$(git rev-parse HEAD) | |
| CREATED=$(date --rfc-3339=seconds | sed 's/ /T/') | |
| sed -i 's/_VC_VERSION_TAG_/${{steps.version.outputs.tag}}/g' biosimulators.json | |
| echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin | |
| docker build \ | |
| --no-cache \ | |
| --file Dockerfile \ | |
| --build-arg SIMULATOR_VERSION=${{steps.version.outputs.tag}} \ | |
| --tag ghcr.io/virtualcell/biosimulators_vcell:latest \ | |
| --label org.opencontainers.image.revision=${REVISION} \ | |
| --label org.opencontainers.image.created=${CREATED} \ | |
| --label org.opencontainers.image.version=${{steps.version.outputs.tag}} \ | |
| --label org.opencontainers.image.license=MIT \ | |
| . | |
| docker tag ghcr.io/virtualcell/biosimulators_vcell:latest ghcr.io/virtualcell/biosimulators_vcell:${{steps.version.outputs.tag}} | |
| docker push --all-tags ghcr.io/virtualcell/biosimulators_vcell | |
| - name: Get release upload URL | |
| id: get_url | |
| uses: pdamianik/[email protected] | |
| with: | |
| tag: ${{ steps.version.outputs.tag }} | |
| token: ${{ github.token }} | |
| - name: Upload edited specifications file | |
| uses: shogo82148/actions-upload-release-asset@v1 | |
| with: | |
| upload_url: ${{ steps.get_url.outputs.uploadUrl }} | |
| asset_path: biosimulators.json | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} |