baseline from /biosimulators/Biosimulators validateCommitSimulator.yml

.github/workflows/bsts_local.yml

@@ -0,0 +1,169 @@
+name: Validate and/or commit simulator
+
+on:
+  issues:
+    types: [labeled, edited]
+
+jobs:
+  validateCommit:
+    name: Validate and/or commit simulator
+    runs-on: ubuntu-20.04 # 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'
+
+      #- 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: |
+      #      ${{ runner.os }}-pip-
+
+      - name: Install pip and setuptools
+        run: |
+          python -m pip install --upgrade setuptools
+          # wget https://bootstrap.pypa.io/get-pip.py
+          # python get-pip.py pip==20.3.4
+          python -m pip install pip==20.3.4
+
+      - name: Install Java # for pyNeuroML
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'adopt'
+          java-version: '15'
+
+      - name: Install Perl # for BioNetGen
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y --no-install-recommends perl
+
+      - name: Install XPP
+        run: |
+          sudo apt-get install -y --no-install-recommends xppaut
+
+      - name: Install Go (for Singularity)
+        uses: actions/setup-go@v3
+        with:
+          go-version: '^1.13.1' # The Go version to download (if necessary) and use.
+
+      - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
+        env:
+          GO_VERSION: 1.17.2
+          SINGULARITY_VERSION: 3.9.5
+          OS: linux
+          ARCH: amd64
+        run: |
+          sudo apt-get install -y --no-install-recommends \
+            build-essential \
+            libseccomp-dev \
+            pkg-config \
+            squashfs-tools \
+            cryptsetup
+
+          wget https://dl.google.com/go/go$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 BioSimulators test suite
+        uses: actions/checkout@v3
+        with:
+          repository: biosimulators/biosimulators_test_suite
+          fetch-depth: 1
+          ref: depFixes
+
+      - 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
+
+      - 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:
+          working-directory: ${{ github.workspace }}
+          run: |
+            python -m pip install --upgrade biosimulators_utils
+            python -c "from biosimulators_test_suite.exec_gh_action import ValidateCommitSimulatorGitHubAction; ValidateCommitSimulatorGitHubAction().run(); exit();"
+
+      # If tmate is useful for a particular debugging issue, comment this back in:
+      # - 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