BSTS local #11
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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-20.04 # 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: ${{ github.workspace }} | ||
| run: | | ||
|
Check failure on line 100 in .github/workflows/bsts_local.yml
|
||
| docker pull ghcr.io/virtualcell/biosimulators_vcell:${{ github.event.inputs.biosimulators_vcell_tag }} | ||
| export 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_VERSION_TAG_/${{github.event.inputs.biosimulators_vcell_tag}}/g' biosimulators.json | ||
| sed -i 's/_VC_DIGEST_TAG_/${{IMAGE_DIGEST}}/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" | ||
| 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 | ||
