Bump jupyter-server from 2.7.2 to 2.11.2 in /pythonCopasiOpt/vcell-opt #3579
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: CI/CD | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| - '*/*' | |
| - '**' | |
| release: | |
| types: [published, edited] | |
| env: | |
| python-version: "3.9" | |
| jobs: | |
| CI-Build: | |
| name: CI-build | |
| runs-on: ubuntu-20.04 | |
| if: ${{ github.event_name == 'push' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| 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: setup java 17 with maven cache | |
| uses: actions/setup-java@v3 | |
| 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-20.04 | |
| strategy: | |
| matrix: | |
| test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT] | |
| fail-fast: false | |
| if: ${{ github.event_name == 'push' }} | |
| name: CI-Test-group-${{ matrix.test-group }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install hdf5 tools needed for testing | |
| run: sudo apt-get -y update && sudo apt-get -y install hdf5-tools | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Add Linux dependencies | |
| shell: bash | |
| run: | | |
| mvn -version | |
| java -version | |
| mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="org.vcell.test.${{ matrix.test-group }}" | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ failure() }} | |
| CD: | |
| name: CD | |
| runs-on: ubuntu-20.04 | |
| if: ${{ github.event_name == 'release' }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Get the VCell version from tags | |
| id: version | |
| run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) | |
| - name: Add Linux dependencies | |
| shell: bash | |
| run: | | |
| mvn -version | |
| java -version | |
| mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="org.vcell.test.Fast" | |
| - name: Build Docker image and push with latest tag | |
| run: | | |
| set -ux | |
| REVISION=$(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.ACTION_TOKEN }} | docker login ghcr.io -u ${{ secrets.ACTION_USER }} --password-stdin | |
| docker build \ | |
| --no-cache \ | |
| --file Dockerfile \ | |
| --build-arg SIMULATOR_VERSION=${{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() }} |