ci.yml

name: Test and release

on:
  push:

jobs:
  test:
    name: Run unit tests on the ontology
    if: "!contains(github.event.head_commit.message, '[Skip CI]')"
    runs-on: ubuntu-latest
    steps:
      # Check out the repository
      - name: Checkout repo
        uses: actions/checkout@master
        with:
          fetch-depth: 1

      # Install the requirements for the tests
      - 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('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install pip and setuptools
        run: |
          python -m pip install --upgrade pip==23.0.0
          python -m pip install --upgrade pip==23.0.0

      - name: Install the Python KiSAO package
        working-directory: libkisao/python
        run: |
          cp ../../kisao.owl kisao/
          python -m pip install .[all]

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

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

      # Run the tests
      - name: Install the requirements for the tests
        working-directory: libkisao/python
        run: |
          python -m pip install pytest pytest-cov
          python -m pip install -r tests/requirements.txt

      - name: Run the tests
        working-directory: libkisao/python
        run: python -m pytest tests/ --cov

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

      - name: Compile the documentation
        working-directory: libkisao/python
        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

      - name: Compile a report of the substitutability among algorithms
        working-directory: libkisao/python
        shell: python
        run: |
          import kisao.utils
          import os
          report = kisao.utils.get_algorithm_substitution_matrix()
          report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv'))

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

  getMainBranchHeadRevision:
    name: Get the head revision of the main branch
    if: startsWith(github.ref, 'refs/tags/')
    runs-on: ubuntu-latest
    outputs:
      mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
    steps:
      - name: Clone repository
        run: |
          git clone https://${{ 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/${mainBranch})
          echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT

  determineIfReleaseNeeded:
    name: Determine if the package should be released
    needs:
      - getMainBranchHeadRevision
    if: startsWith(github.ref, 'refs/tags/')
    runs-on: ubuntu-latest
    outputs:
      release: ${{ steps.determine-if-release-needed.outputs.release }}
    steps:
      # Check out the repository
      - name: Checkout repo
        uses: actions/checkout@master
        with:
          fetch-depth: 1

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

          if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
            echo "First check passed"
            tag_hash=$(git rev-parse "${{ github.ref }}")
            echo "tag_hash: $tag_hash"
            if [ "$tag_hash" == "${{ needs.getMainBranchHeadRevision.outputs.mainBranchHeadRevision }}" ]; then
              echo "Second check passed"
              release="1"
            fi
          fi

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

  commitCompiledDocumentation:
    name: Commit and push compiled documentation to GitHub
    needs:
      - test
      - determineIfReleaseNeeded
    if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
    runs-on: ubuntu-latest
    steps:
      # Check out the repository
      - name: Checkout repo
        uses: actions/checkout@master
        with:
          fetch-depth: 1
#          ref: dev
#          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

      # Install the requirements for the tests
      - 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('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install pip and setuptools
        run: |
          python -m pip install --upgrade pip==23.0.0
          python -m pip install --upgrade pip==23.0.0

      - name: Install the Python KiSAO package
        working-directory: libkisao/python
        run: |
          cp ../../kisao.owl kisao/
          python -m pip install .[all]

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

      - name: Compile the documentation
        working-directory: libkisao/python
        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

      - name: Compile a report of the substitutability among algorithms
        working-directory: libkisao/python
        shell: python
        run: |
          import kisao.utils
          import os
          report = kisao.utils.get_algorithm_substitution_matrix()
          report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv'))

      # If new tag, commit and push documentation
      - name: Configure Git
        run: |
          git config --local user.email "bot@sed-ml.org"
          git config --local user.name "SED-ML bot"
          git config pull.rebase false

      - id: commit-docs
        name: Commit the compiled documentation
        working-directory: libkisao/python
        run: |
          git stash
          git pull
          set +e
          git stash pop
          git add docs
          git commit -m "Updated compiled documentation [Skip CI]"
          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.commit-docs.outputs.docsChanged == '1'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.ADMIN_GITHUB_TOKEN  }}
          branch: ${{ steps.get-main-branch.outputs.mainBranch }}

  createGitHubRelease:
    name: Create GitHub release
    needs:
      - test
      - determineIfReleaseNeeded
    if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repo
        uses: actions/checkout@master
        with:
          fetch-depth: 1
#          ref: dev
#          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

      - name: Merge dev branch into deploy branch
        uses: devmasx/merge-branch@v1.3.1
        with:
          type: now
          target_branch: deploy
          github_token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

      - id: get-version
        name: Get version number
        env:
          TAG: ${{ github.ref }}
        run: |
          version="${TAG/refs\/tags\//}"
          echo "version=$version" >> $GITHUB_OUTPUT

      - name: Create GitHub release
        uses: "marvinpinto/action-automatic-releases@latest"
        with:
          repo_token: "${{ secrets.ADMIN_GITHUB_TOKEN }}"
          draft: false
          prerelease: false
          automatic_release_tag: ${{ steps.get-version.outputs.version }}

  releaseToBioPortal:
    name: Release version to BioPortal
    needs:
      - test
      - determineIfReleaseNeeded
    if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repo
        uses: actions/checkout@master

      - name: Install jq
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends jq moreutils

      - name: Prepare BioPortal submission
        env:
          TAG: ${{ github.ref }}
        run: |
          version="${TAG/refs\/tags\//}"
          released=$(date --iso-8601=second)
          cp .github/workflows/BioPortal-submission.json .github/workflows/BioPortal-submission-version.json
          jq \
            ".pullLocation = \"https://raw.githubusercontent.com/SED-ML/KiSAO/${version}/kisao.owl\"" \
            .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json
          jq \
            ".version = \"${version}\"" \
            .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json
          jq \
            ".released = \"${released}\"" \
            .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json

      - name: Submit to BioPortal
        run: |
          curl -X POST \
            -H "Authorization: apikey token=${{ secrets.BIOPORTAL_API_KEY }}" \
            -H "Content-Type: application/json" \
            -H "Accept: application/json" \
            -d @.github/workflows/BioPortal-submission-version.json \
            http://data.bioontology.org/ontologies/KISAO/submissions
          echo

  releaseToPyPI:
    name: Release version to PyPI
    needs:
      - test
      - determineIfReleaseNeeded
    if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
    runs-on: ubuntu-latest
    steps:
      # Check out the repository
      - name: Checkout repo
        uses: actions/checkout@master
        with:
          fetch-depth: 1

      # Install the requirements for the tests
      - 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('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install pip
        run: |
          python -m pip install --upgrade pip==23.0.0
          python -m pip install --upgrade pip==23.0.0

      # Create PyPI release
      - name: Create PyPI release
        working-directory: libkisao/python
        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

          # Copy OWL file and LICENSE so it can be bundled into the Python package
          cp ../../kisao.owl kisao/
          cp ../../LICENSE .

          # 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/*