ci.yml

name: Continuous integration

on:
  push:
  workflow_dispatch:
    inputs:
      simulatorVersion:
        description: New version of the underlying simulation tool (e.g., '1.5.6')
        required: true
      simulatorVersionLatest:
        description: Is this version the latest version of the underlying simulation tool ("true" or "false")?
        required: false

jobs:
  continuousIntegration:
    name: Update simulator version, lint, test, compile documentation, and release
    runs-on: ubuntu-latest
    outputs:
      mainBranch: ${{ steps.get-main-branch.outputs.mainBranch }}
      mainBranchRef: ${{ steps.get-main-branch.outputs.mainBranchRef }}
      mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
      version: ${{ steps.get-version-number.outputs.version }}
      simulatorId: ${{ steps.get-docker-image-tag.outputs.simulatorId }}
      simulatorVersion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
      simulatorName: ${{ steps.get-docker-image-tag.outputs.simulatorName }}
      dockerImageBaseUrl: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}
      dockerRegistry: ${{ steps.get-docker-image-tag.outputs.dockerRegistry }}
      release: ${{ steps.determine-if-release-needed.outputs.release }}
      docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
    steps:
      - name: Clone repository
        run: |
          git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} .

      - id: get-main-branch
        name: Determine main branch
        run: |
          mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4)
          mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
          echo "mainBranch=$mainBranch" >> $GITHUB_OUTPUT
          echo "mainBranchRef=refs/heads/$mainBranch" >> $GITHUB_OUTPUT
          echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT

      - name: Checkout ref
        run: |
          if [[ "${{ github.ref }}" =~ ^refs/heads/ ]]; then
            branch=$(echo "${{ github.ref }}" | cut -d'/' -f 3-)
            git checkout ${branch}
          else
            git checkout ${{ github.ref }}
          fi

      #############################################
      ## Update the version of the simulator
      #############################################0
      - name: Check that the version of the simulator is available from PyPI
        if: github.event.inputs.simulatorVersion
        uses: emilioschepis/wait-for-endpoint@v1.0.3
        with:
          url: https://pypi.org/pypi/pysces/${{ github.event.inputs.simulatorVersion }}/json
          method: GET
          expected-status: 200
          timeout: 3600000 # 1 hr
          interval: 60000 # 1 min

      - name: Update the version of the simulator
        if: github.event.inputs.simulatorVersion
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends jq moreutils

          IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
          jq ".version = \"${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json
          jq ".image.url = \"${IMAGE_BASE_URL}:${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json | sponge biosimulators.json

          sed -i -E \
            "s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${{ github.event.inputs.simulatorVersion }}\"/" \
            Dockerfile

      #############################################
      ## Install package and its dependencies
      #############################################
      - name: Install Python
        uses: actions/setup-python@v3
        with:
          python-version: '3.10'

      - name: Setup caching for Python packages
        uses: actions/cache@v3
        with:
          path: /opt/hostedtoolcache/Python
          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install SUNDIALS
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends libsundials-dev

      - name: Install Python requirements
        run: |
          pip install -U pip==23.0.0
          pip install "cython<1.0"
          pip install scipy matplotlib nose

      - name: Install Assimulo
        env:
          ASSIMULO_VERSION: 3.4.3
        run: |
          pip install --install-option="--optimize=1" \
            --install-option="--extra-fortran-link-flags=-shared" \
            --install-option="--sundials-home=/usr" \
            --install-option="--blas-home=/usr/lib/x86_64-linux-gnu" \
            --install-option="--lapack-home=/usr" \
            --install-option="--extra-fortran-compile-flags=-fallow-argument-mismatch"  \
            --install-option="--extra-c-flags=-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION" \
            git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}

      - name: Install PySCeS
        uses: nick-invision/retry@v2
        with:
          timeout_minutes: 20
          retry_on: error
          retry_wait_seconds: 300
          max_attempts: 4
          command: |
            sudo apt-get update -y
            sudo apt-get install -y --no-install-recommends jq

            SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json)

            pip install "pysces==${SIMULATOR_VERSION}"

      # install package
      - name: Install the package
        run: python -m pip install .[all]

      #############################################
      ## Lint
      #############################################
      - name: Install flake8
        run: python -m pip install flake8

      - name: Lint the package
        run: python -m flake8

      #############################################
      ## Build Docker image
      #############################################
      - id: get-version-number
        name: Get version number
        env:
          TAG: ${{ github.ref }}
        run: |
          if [[ "${TAG}" =~ ^refs/tags/ ]]; then
            version="${TAG/refs\/tags\//}"
          else
            version=$(python -c "import glob; import importlib.util; version_filename = glob.glob('**/_version.py', recursive=True)[0]; spec = importlib.util.spec_from_file_location('module.name', version_filename); module = importlib.util.module_from_spec(spec); spec.loader.exec_module(module); print(module.__version__)")
          fi

          echo "version=$version" >> $GITHUB_OUTPUT

      - id: get-docker-image-tag
        name: Determine Docker image tag
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends jq

          simulatorId=$(jq -r '.id' biosimulators.json)
          simulatorVersion=$(jq -r '.version' biosimulators.json)
          simulatorName=$(jq -r '.name' biosimulators.json)
          dockerImageBaseUrl=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
          dockerRegistry=$(echo $dockerImageBaseUrl | cut -d / -f 1)

          echo "simulatorId=$simulatorId" >> $GITHUB_OUTPUT
          echo "simulatorVersion=$simulatorVersion" >> $GITHUB_OUTPUT
          echo "simulatorName=$simulatorName" >> $GITHUB_OUTPUT
          echo "dockerImageBaseUrl=$dockerImageBaseUrl" >> $GITHUB_OUTPUT
          echo "dockerRegistry=$dockerRegistry" >> $GITHUB_OUTPUT

      - name: Set up context for building base Docker image
        run: |
          mkdir -p empty-docker-context
          cp Dockerfile-base empty-docker-context/

      - name: Build base Docker image
        uses: whoan/docker-build-with-cache-action@v5
        with:
            registry: ${{ steps.get-docker-image-tag.outputs.dockerRegistry }}
            username: ${{ secrets.DOCKER_REGISTRY_USERNAME }}
            password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}"
            image_name: biosimulators/biosimulators_pysces/pysces_base
            image_tag: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
            build_extra_args: "--build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }}"
            dockerfile: Dockerfile-base
            context: empty-docker-context

      - name: Build Docker image
        run: |
          docker image tag \
            ghcr.io/biosimulators/biosimulators_pysces/pysces_base:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
            ghcr.io/biosimulators/biosimulators_pysces/pysces_base:latest

          REVISION=$(git rev-parse HEAD)
          CREATED=$(date --rfc-3339=seconds | sed 's/ /T/')
          docker build \
            --label org.opencontainers.image.source=https://github.com/${{ github.repository }} \
            --label org.opencontainers.image.revision=${REVISION} \
            --label org.opencontainers.image.created=${CREATED} \
            --build-arg VERSION=${{ steps.get-version-number.outputs.version }} \
            --build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
            --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
            --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \
            .

      #############################################
      ## Test and upload coverage report to Codecov
      #############################################
      - name: Install pytest
        run: python -m pip install pytest pytest-cov

      - name: Install the requirements for the tests
        run: python -m pip install .[tests]

      - name: Run the tests
        run: python -m pytest tests/ --cov=./biosimulators_pysces/ --cov-report=xml

      - name: Upload the coverage report to Codecov
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          flags: unittests
          file: ./coverage.xml

      #############################################
      ## Compile documentation
      #############################################
      - name: Install the requirements for compiling the documentation
        run: python -m pip install -r docs-src/requirements.txt

      - name: Compile the documentation
        run: |
          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
          mkdir -p docs-src/_static
          sphinx-build docs-src docs

      #############################################
      ## Commit and push new version of simulator
      #############################################
      # If new version of simulator, commit and push the new version
      - name: Commit the revised version of the simulator
        if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false
          git stash -- biosimulators.json Dockerfile
          git clean -f -d
          git checkout .
          git pull
          git stash pop
          git add biosimulators.json Dockerfile
          git commit -m "Updating version of simulator"

      - name: Setup tmate session
        uses: mxschmitt/action-tmate@v3
        if: ${{ failure() }}

      - name: Push the revised version of the simulator
        if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ github.ref }}

      #############################################
      ## Release
      #############################################

      - id: determine-if-release-needed
        name: Determine if a release should be made
        run: |
          release="0"

          if [ ! -z "${{ github.event.inputs.simulatorVersion }}" ]; then
            if [ "${{ github.ref }}" == "${{ steps.get-main-branch.outputs.mainBranchRef }}" ]; then
              release="1"
            fi
          fi

          if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
            tag_hash=$(git rev-parse "${{ github.ref }}")
            if [ "$tag_hash" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then
              release="1"
            fi
          fi

          echo "release=$release" >> $GITHUB_OUTPUT
          echo "release=$release"

      - name: Setup tmate session
        uses: mxschmitt/action-tmate@v3
        if: steps.determine-if-release-needed.outputs.release == '0'

      # If new tag, commit and push documentation
      - id: commit-docs
        name: Commit the compiled documentation
        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false
          git stash
          git checkout ${{ steps.get-main-branch.outputs.mainBranch }}
          git pull
          set +e
          git stash pop
          git add docs
          git commit -m "Updating compiled documentation"
          git checkout .
          git clean -f -d
          if [[ $? = 0 ]]; then
            docsChanged=1
          else
            docsChanged=0
          fi
          echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT

      - name: Push the compiled documentation
        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1' && steps.commit-docs.outputs.docsChanged == '1'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ steps.get-main-branch.outputs.mainBranch }}

      # Create GitHub release
      - name: Create GitHub release
        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          tag_name: ${{ steps.get-version-number.outputs.version }}
          release_name: Release ${{ steps.get-version-number.outputs.version }}

      # Create PyPI release
      - name: Create PyPI release
        if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
        env:
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
        run: |
          # Install pandoc
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends wget
          wget "https://github.com/jgm/pandoc/releases/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb         
          sudo dpkg -i /tmp/pandoc.deb
          rm /tmp/pandoc.deb

          # Convert README to .rst format
          pandoc --from=gfm --output=README.rst --to=rst README.md

          # Install twine
          python -m pip install wheel twine

          # Create packages to upload to PyPI
          python setup.py sdist
          python setup.py bdist_wheel

          # Upload packages to PyPI
          twine upload dist/*

      # build Docker image and push to GitHub Container Registry
      - name: Push Docker image
        if: steps.determine-if-release-needed.outputs.release == '1'
        run: |
          docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \
            --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
            --password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
          docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}

          if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ github.event.inputs.simulatorVersionLatest }}" == "true" ]; then
            docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
          fi

      # Submit to BioSimulators registry
      - name: Submit to BioSimulators registry
        if: steps.determine-if-release-needed.outputs.release == '1'
        run: |
          REVISION=$(git rev-parse HEAD)
          IMAGE_DIGEST=$(docker image inspect ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-)
          curl \
            -X POST \
            -u ${{ secrets.GH_ISSUE_USERNAME }}:${{ secrets.GH_ISSUE_TOKEN }} \
            -H "Accept: application/vnd.github.v3+json" \
            https://api.github.com/repos/biosimulators/Biosimulators/issues \
            -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit ${{ steps.get-docker-image-tag.outputs.simulatorName }} ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\", \"body\": \"---\nid: ${{ steps.get-docker-image-tag.outputs.simulatorId }}\nversion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n  version: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n  image:\n    url: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n    digest: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"