releaseToBioSimulators.yml

name: Build test BioSimulators interface and release to BioSimulators registry

on:
  push:

jobs:
  buildTestDeploy:
    name: Build, test, and deploy BioSimulators interface
    runs-on: ubuntu-latest
    steps:
      #############################################
      ## Checkout repository
      #############################################
      - 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/${mainBranch})
          echo "::set-output name=mainBranch::$mainBranch"
          echo "::set-output name=mainBranchRef::refs/heads/$mainBranch"
          echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision"

      - 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

      #############################################
      ## Install package and its dependencies
      #############################################
      - name: Install Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.9'

      - name: Setup pip cache
        uses: actions/cache@v2
        with:
          path: /opt/hostedtoolcache/Python
          key: ${{ runner.os }}-pip-${{ hashFiles('biosimulators/requirements.txt') }}-${{ hashFiles('biosimulators/requirements.optional.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install pip and setuptools
        run: |
          python -m pip install --upgrade pip
          python -m pip install --upgrade setuptools

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

      - name: Lint the package
        working-directory: biosimulators
        run: python -m flake8

      #############################################
      ## Get and sync version number
      #############################################
      - id: get-version-number
        name: Get version number
        run: |
          SIMULATOR_VERSION=$(cat src/libsbmlsim/version.h | grep LIBSBMLSIM_DOTTED_VERSION | cut -d '"' -f 2)
          echo "::set-output name=simulatorVersion::$SIMULATOR_VERSION"

          VERSION=$(cat biosimulators/biosimulators_libsbmlsim/_version.py | grep __version__ | cut -d "'" -f 2)
          echo "::set-output name=version::$VERSION"

      #############################################
      ## Build Docker image
      #############################################
      - name: Build Docker image
        run: |
          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=${{ steps.get-version-number.outputs.simulatorVersion }} \
            --tag ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:${{ steps.get-version-number.outputs.simulatorVersion }} \
            --tag ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:latest \
            -f biosimulators/Dockerfile \
            .

      #############################################
      ## Test
      #############################################
      - name: Run the tests
        run: |
          cwd=$(pwd)
          docker run \
              --rm \
              --entrypoint bash \
              --mount type=bind,source=${cwd},target=/root/Biosimulators_LibSBMLSim \
              --workdir /root/Biosimulators_LibSBMLSim/biosimulators \
              ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:latest \
              -c "
                  pip install pytest pytest-cov \
                  && pip install -r tests/requirements.txt \
                  && python -m pytest tests/ --cov biosimulators_libsbmlsim --cov-report=xml
              "
          sudo chown ${UID} ./biosimulators/coverage.xml

      - name: Upload the coverage report to Codecov
        uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          flags: unittests
          file: ./biosimulators/coverage.xml

      #############################################
      ## Compile documentation
      #############################################
      - name: Compile documentation
        run: |
          cwd=$(pwd)
          docker run \
              --rm \
              --entrypoint bash \
              --mount type=bind,source=${cwd},target=/root/Biosimulators_LibSBMLSim \
              --workdir /root/Biosimulators_LibSBMLSim/biosimulators \
              ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:1.4.0 \
              -c "
                  pip install -r docs-src/requirements.txt \
                  && sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc \
                  && mkdir -p docs-src/_static \
                  && sphinx-build docs-src ../docs
              "
          sudo chown ${UID} -R docs
          sudo chown ${UID} -R biosimulators/docs-src

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

      # If new tag, commit and push documentation
      - id: commit-docs
        name: Commit the compiled documentation
        if: startsWith(github.ref, 'refs/tags/')
        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 [[ $? = 0 ]]; then
            docsChanged=1
          else
            docsChanged=0
          fi
          echo "::set-output name=docsChanged::$docsChanged"

      - name: Push the compiled documentation
        if: startsWith(github.ref, 'refs/tags/') && 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/')
        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/')
        env:
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
        working-directory: biosimulators
        run: |
          # Install pandoc
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends wget

          wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
          urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
          wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
          sudo dpkg -i /tmp/pandoc.deb
          rm /tmp/pandocVersions.html
          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: startsWith(github.ref, 'refs/tags/')
        run: |
          docker login ghcr.io \
            --username ${{ secrets.GHCR_USERNAME }} \
            --password ${{ secrets.GHCR_TOKEN }}
          docker push ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:${{ steps.get-version-number.outputs.simulatorVersion }}
          docker push ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:latest

      # Submit to BioSimulators registry
      - name: Submit to BioSimulators registry
        if: startsWith(github.ref, 'refs/tags/')
        run: |
          REVISION=$(git rev-parse HEAD)
          IMAGE_DIGEST=$(docker image inspect ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:${{ steps.get-version-number.outputs.simulatorVersion }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-)
          curl \
            -X POST \
            -u ${{ secrets.BIOSIMULATORS_GH_USERNAME }}:${{ secrets.BIOSIMULATORS_GH_TOKEN }} \
            -H "Accept: application/vnd.github.v3+json" \
            https://api.github.com/repos/biosimulators/Biosimulators/issues \
            -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit LibSBMLsim ${{ steps.get-version-number.outputs.simulatorVersion }}\", \"body\": \"---\nid: libsbmlsim\nversion: ${{ steps.get-version-number.outputs.simulatorVersion }}\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n  version: ${{ steps.get-version-number.outputs.simulatorVersion }}\n  image:\n    url: ghcr.io/biosimulators/biosimulators_libsbmlsim/libsbmlsim:${{ steps.get-version-number.outputs.simulatorVersion }}\n    digest: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"