BSTS local #18
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| name: BSTS local | |
| # derived from https://raw.githubusercontent.com/biosimulators/Biosimulators/dev/.github/workflows/validateCommitSimulator.yml | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| biosimulators_vcell_tag: | |
| description: 'version.major.minor.patch' | |
| required: true | |
| default: '7.5.0.127' | |
| # vcell_build: | |
| # description: 'build number' | |
| # required: true | |
| # default: '23' | |
| # vcell_site: | |
| # description: 'rel or alpha' | |
| # required: true | |
| # default: 'alpha' | |
| # server_only: | |
| # description: 'Deploy only the server components?' | |
| # required: true | |
| # default: 'false' | |
| jobs: | |
| validateCommit: | |
| name: Validate and/or commit simulator | |
| runs-on: ubuntu-22.04 # includes Docker | |
| steps: | |
| - name: Install Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.11' | |
| - name: Install pip and setuptools | |
| run: | | |
| python -m pip install --upgrade setuptools | |
| # wget https://bootstrap.pypa.io/get-pip.py | |
| # python get-pip.py pip==20.3.4 | |
| python -m pip install pip==20.3.4 | |
| - name: Install Java # for pyNeuroML | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '15' | |
| - name: Install Perl # for BioNetGen | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends perl | |
| - name: Install XPP | |
| run: | | |
| sudo apt-get install -y --no-install-recommends xppaut | |
| - name: Install Go (for Singularity) | |
| uses: actions/setup-go@v3 | |
| with: | |
| go-version: '^1.13.1' # The Go version to download (if necessary) and use. | |
| - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image | |
| env: | |
| GO_VERSION: 1.17.2 | |
| SINGULARITY_VERSION: 3.9.5 | |
| OS: linux | |
| ARCH: amd64 | |
| run: | | |
| sudo apt-get install -y --no-install-recommends \ | |
| build-essential \ | |
| libseccomp-dev \ | |
| pkg-config \ | |
| squashfs-tools \ | |
| cryptsetup | |
| wget https://dl.google.com/go/go$GO_VERSION.$OS-$ARCH.tar.gz | |
| sudo tar -C /usr/local -xzvf go$GO_VERSION.$OS-$ARCH.tar.gz | |
| rm go$GO_VERSION.$OS-$ARCH.tar.gz | |
| echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc | |
| source ~/.bashrc | |
| echo "/usr/local/go/bin" >> $GITHUB_PATH | |
| wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | |
| tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz | |
| cd singularity-ce-${SINGULARITY_VERSION} | |
| ./mconfig | |
| make -C builddir | |
| sudo make -C builddir install | |
| - name: checkout vcell | |
| uses: actions/checkout@v3 | |
| - name: Login into Docker registries | |
| run: | | |
| # VCell Docker registry (GHCR) | |
| echo ${{ secrets.ACTION_TOKEN }} | docker login ghcr.io -u ${{ secrets.ACTION_USER }} --password-stdin | |
| - name: configure biosimulations.json | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| docker pull ghcr.io/virtualcell/biosimulators_vcell:${{ github.event.inputs.biosimulators_vcell_tag }} | |
| IMAGE_DIGEST=$(docker image inspect ghcr.io/virtualcell/biosimulators_vcell:${{ github.event.inputs.biosimulators_vcell_tag }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-) | |
| sed -i "s/_VC_DIGEST_TAG_/${IMAGE_DIGEST}/g" biosimulators.json | |
| sed -i 's/_VC_VERSION_TAG_/${{github.event.inputs.biosimulators_vcell_tag}}/g' biosimulators.json | |
| - name: save updated biosimulators.json | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: biosimulators.json | |
| path: ${{ github.workspace }}/biosimulators.json | |
| overwrite: true | |
| - name: Checkout BioSimulators test suite | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: biosimulators/biosimulators_test_suite | |
| fetch-depth: 1 | |
| ref: depFixes | |
| - name: retrieve updated biosimulators.json | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: biosimulators.json | |
| path: ${{ github.workspace }} | |
| - name: Install simulator validation utilities | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| # python -m pip cache purge | |
| # python -m pip install --no-cache-dir "biosimulators_utils @ git+https://github.com/biosimulators/Biosimulators_utils@depFixes#egg=biosimulators_utils[containers,sbml]" | |
| # python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy | |
| python -m pip install docker python-libsbml "urllib3<2.0" "biosimulations-test-suite[containers,sbml]" | |
| # python -m pip install -e .[all] | |
| python --version | |
| python -m pip freeze | |
| - id: validateCommitSimulator | |
| name: Validate and commit simulator | |
| uses: GabrielBB/xvfb-action@v1 | |
| env: | |
| GH_REPO: ${{ github.repository }} | |
| GH_ACTION_RUN_ID: ${{ github.run_id }} | |
| GH_ISSUE_NUMBER: ${{ github.event.issue.number }} | |
| GH_ISSUES_USER: ${{ secrets.GH_ISSUES_USER }} | |
| GH_ISSUES_ACCESS_TOKEN: ${{ secrets.GH_ISSUES_ACCESS_TOKEN }} | |
| DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }} | |
| DOCKER_REGISTRY_URL: ${{ secrets.DOCKER_REGISTRY_URL }} | |
| DOCKER_REGISTRY_USERNAME: ${{ secrets.DOCKER_REGISTRY_USERNAME }} | |
| DOCKER_REGISTRY_TOKEN: ${{ secrets.DOCKER_REGISTRY_TOKEN }} | |
| BIOSIMULATORS_API_CLIENT_ID: ${{ secrets.BIOSIMULATORS_API_CLIENT_ID }} | |
| BIOSIMULATORS_API_CLIENT_SECRET: ${{ secrets.BIOSIMULATORS_API_CLIENT_SECRET }} | |
| # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to use the dev deployment of the BioSimulators API | |
| RUNBIOSIMULATIONS_API_CLIENT_ID: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_ID }} | |
| RUNBIOSIMULATIONS_API_CLIENT_SECRET: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_SECRET }} | |
| # RUNBIOSIMULATIONS_API_ENDPOINT: https://api.biosimulations.dev/ # uncomment to use the dev deployment of the BioSimulators API | |
| with: | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python -m pip install --upgrade biosimulators_utils | |
| biosimulators-test-suite --verbose biosimulators.json | |
| - name: Setup tmate session 3 (if failed) | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |
| timeout-minutes: 40 | |
| - name: Save test results | |
| uses: actions/upload-artifact@v2 | |
| if: success() || failure() | |
| with: | |
| name: Validation test results | |
| path: ${{ github.workspace }}/.biosimulators-test-suite-results.json | |
| if-no-files-found: warn |