Submit VCell 7.7.0.7 #2718
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| name: Validate and/or commit simulator | |
| on: | |
| issues: | |
| types: [labeled, edited] | |
| jobs: | |
| validateCommit: | |
| name: Validate and/or commit simulator | |
| runs-on: ubuntu-22.04 # includes Docker | |
| if: | | |
| github.event.issue.state == 'open' | |
| && contains(github.event.issue.labels.*.name, 'Validate/submit simulator') | |
| && ( | |
| github.event.action == 'edited' | |
| || ( | |
| github.event.action == 'labeled' | |
| && github.event.label.name == 'Validate/submit simulator' | |
| ) | |
| || ( | |
| github.event.action == 'labeled' | |
| && github.event.label.name == 'Approved' | |
| && github.event.sender.login != 'biosimulators-daemon' | |
| ) | |
| ) | |
| steps: | |
| - name: Install Python | |
| # uses: actions/setup-python@v3 | |
| # with: | |
| # python-version: '3.11-dev' | |
| run: | | |
| sudo apt-get install -y python3.11-dev python3-pip python3-venv python3.11-venv | |
| #- name: Setup pip cache | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: /opt/hostedtoolcache/Python | |
| # key: ${{ runner.os }}-pip-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.txt') }}-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.optional.txt') }} | |
| # restore-keys: | | |
| # ${{ runner.os }}-pip- | |
| - name: Install pip and setuptools | |
| run: | | |
| python3.11 -m pip install --upgrade setuptools | |
| # wget https://bootstrap.pypa.io/get-pip.py | |
| # python get-pip.py pip==20.3.4 | |
| python3.11 -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 HDF5 and H5PY | |
| # run: | | |
| # sudo apt-get install -y libhdf5-serial-dev hdf5-tools libhdf5-dev | |
| # sudo apt-get install -y zlib1g-dev zip libjpeg8-dev liblapack-dev libblas-dev build-essential | |
| # #python3.11 -m pip install -U pip testresources | |
| # #ln -s /usr/include/locale.h /usr/include/xlocale.h | |
| # python3.11 -m pip install Cython==0.29.36 | |
| # python3.11 -m pip install numpy==1.23.5 | |
| # #python3.11 -m pip install pkgconfig | |
| # echo '---' | |
| # echo $(python3.11 --version) | |
| # echo $(which python3.11) | |
| # echo '---' | |
| # python3.11 -m pip install --no-binary=h5py h5py | |
| - name: Check Docker Version | |
| run: | | |
| docker version | |
| - name: Install Go (for Singularity) | |
| uses: actions/setup-go@v3 | |
| with: | |
| go-version: '^1.13.1' # The Go version to download (if necessary) and use. | |
| - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image | |
| env: | |
| GO_VERSION: 1.17.2 | |
| SINGULARITY_VERSION: 3.11.5 | |
| OS: linux | |
| ARCH: amd64 | |
| run: | | |
| sudo apt-get install -y --no-install-recommends \ | |
| build-essential \ | |
| libseccomp-dev \ | |
| pkg-config \ | |
| squashfs-tools \ | |
| cryptsetup | |
| wget https://dl.google.com/go/go$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 BioSimulators test suite | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: biosimulators/biosimulators_test_suite | |
| fetch-depth: 1 | |
| ref: 0.2 | |
| # - name: Install simulator validation utilities | |
| # working-directory: ${{ github.workspace }} | |
| # run: | | |
| # # python3.11 -m pip cache purge | |
| # # python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy | |
| # python3.11 -m pip install docker python-libsbml "urllib3<2.0" | |
| # python3.11 -m pip install --no-cache-dir "biosimulators_utils @ git+https://github.com/biosimulators/Biosimulators_utils@depFixes#egg=biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn]" | |
| # - name: Intall BioSimulators Test Suite | |
| # run: | | |
| # python3.11 -m pip install -e .[all] | |
| # python3.11 --version | |
| # python3.11 -m pip freeze | |
| # - name: Install Poetry | |
| # env: | |
| # POETRY_VERSION: "1.7.1" | |
| # shell: bash | |
| # run: | | |
| # curl -sSL https://install.python-poetry.org | python - -y | |
| # echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| # poetry config virtualenvs.in-project true | |
| # Since we may have projects that use poetry, and singularity containers are not fully self-contained | |
| # we need to avoid accidentally using the test-suite's poetry installation, and not the one intended | |
| # to be used in the singularity container | |
| - name: Install Virtualized Poetry | |
| shell: bash | |
| run: | | |
| mkdir -p /home/runner/poetry-install-dir | |
| python3.11 -m venv /home/runner/poetry-install-dir | |
| /home/runner/poetry-install-dir/bin/python -m pip install -U pip setuptools | |
| /home/runner/poetry-install-dir/bin/python -m pip install poetry | |
| - name: Install BioSimulators Test Suite with Poetry | |
| shell: bash | |
| run: /home/runner/poetry-install-dir/bin/poetry install --all-extras | |
| - name: Login into Docker registries | |
| run: | | |
| # Docker Hub | |
| docker login \ | |
| --username ${{ secrets.DOCKER_HUB_USERNAME }} \ | |
| --password ${{ secrets.DOCKER_HUB_TOKEN }} | |
| # BioSimulators Docker registry (GHCR) | |
| docker login ${{ secrets.DOCKER_REGISTRY_URL }} \ | |
| --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \ | |
| --password ${{ secrets.DOCKER_REGISTRY_TOKEN }} | |
| - 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: | |
| # run: | | |
| # python3.11 -m pip install --force-reinstall "requests==2.31.0" | |
| # python3.11 -m pip install --force-reinstall "urllib3==1.26.20" | |
| # python3.11 -c "from biosimulators_test_suite.exec_gh_action import ValidateCommitSimulatorGitHubAction; ValidateCommitSimulatorGitHubAction().run(); exit();" | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| /home/runner/poetry-install-dir/bin/poetry run python -c "from biosimulators_test_suite.exec_gh_action import ValidateCommitSimulatorGitHubAction; ValidateCommitSimulatorGitHubAction().run(); exit();" | |
| - 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@v4 | |
| if: success() || failure() | |
| with: | |
| name: Validation test results | |
| path: ${{ github.workspace }}/.biosimulators-test-suite-results.json | |
| if-no-files-found: warn |