ci.yml

name: Continuous integration

on:
  - push

jobs:
  getVersionNumber:
    name: Get version number
    if: startsWith(github.ref, 'refs/tags/') && github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
    runs-on: ubuntu-20.04
    outputs:
      version: ${{ steps.get-version-number.outputs.version }}
    steps:
      - id: get-version-number
        name: Get version number
        env:
          TAG: ${{ github.ref }}
        run: |
          version="${TAG/refs\/tags\//}"
          echo "::set-output name=version::$version"

  build:
    name: Lint, test, and compile documentation
    if: github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Configure Git
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false

      - 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('requirements.txt') }}-${{ hashFiles('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

      - name: Install Java # for pyNeuroML
        uses: actions/setup-java@v2
        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 update -y
          sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev

          cd /tmp
          wget http://www.math.pitt.edu/~bard/bardware/xppaut_latest.tar.gz
          mkdir xpp
          tar zxvf xppaut_latest.tar.gz --directory xpp
          cd xpp
          make
          sudo make install

          cd /tmp
          rm xppaut_latest.tar.gz
          rm -r xpp

      - name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
        uses: eWaterCycle/setup-singularity@v6

      # install package
      - name: Install the package
        run: |
          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
          python -m pip install .[all]

      # zip COMBINE/OMEX archives
      - name: Zip COMBINE/OMEX archives
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends zipcmp
          python scripts/zip_examples.py

      - id: commit-archives
        name: Commit zipped COMBINE/OMEX archives
        if: startsWith(github.ref, 'refs/heads/')
        env:
          HEAD: ${{ github.ref }}
        run: |
          git stash || true
          git pull
          set +e
          git stash pop || true
          git add examples/**/*.omex
          git commit -m "chore: Updated COMBINE/OMEX archives [skip ci]"
          if [[ $? = 0 ]]; then
            archivesChanged=1
          else
            archivesChanged=0
          fi
          echo "::set-output name=archivesChanged::$archivesChanged"

          branch="${HEAD/refs\/heads\//}"
          echo "::set-output name=branch::$branch"

      - name: Push the zipped COMBINE/OMEX archives
        if: steps.commit-archives.outputs.archivesChanged == '1' && startsWith(github.ref, 'refs/heads/')
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ steps.commit-archives.outputs.branch }}

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

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

      # 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
        # env:
        #   BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to run tests using the dev deployment
        uses: GabrielBB/xvfb-action@v1
        with:
          run: python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml

      - name: Upload the coverage report to Codecov
        uses: codecov/codecov-action@v2
        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

  release:
    name: Release a new version
    needs: [getVersionNumber, build]
    runs-on: ubuntu-20.04
    outputs:
      docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
    steps:
      - name: Checkout code
        uses: actions/checkout@v2
        with:
          fetch-depth: 1
          ref: deploy

      - name: Configure Git
        run: |
          git config --local user.email "biosimulators.daemon@gmail.com"
          git config --local user.name "biosimulatorsdaemon"
          git config pull.rebase false

      - 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('requirements.txt') }}-${{ hashFiles('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

      # install package
      - name: Install the package
        run: |
          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
          python -m pip install .[all]

      # compile and push 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

      - id: commit-docs
        name: Commit the compiled documentation
        run: |
          git stash || true
          git pull
          set +e
          git stash pop || true
          git add docs
          git add docs-src
          git commit -m "chore: Updating compiled documentation [skip ci]"
          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: steps.commit-docs.outputs.docsChanged == '1'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: deploy

      # Create GitHub release
      - name: Create GitHub release
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          tag_name: ${{ needs.getVersionNumber.outputs.version }}
          release_name: Release ${{ needs.getVersionNumber.outputs.version }}

      # Create PyPI release
      - name: Install pandoc
        run: |
          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

      - name: Convert README to .rst format
        run: pandoc --from=gfm --output=README.rst --to=rst README.md

      - name: Install twine
        run: |
          python -m pip install wheel twine

      - name: Create packages to upload to PyPI
        run: |
          python setup.py sdist
          python setup.py bdist_wheel

      - name: Upload packages to PyPI
        env:
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
        run: |
          twine upload dist/*