ci.yml

name: Continuous integration and deployment

on:
  push:

  schedule:
    - cron: '0 0 * * 0' # weekly

  workflow_dispatch:

jobs:
  testExamples:
    name: Test example SED-ML files (in COMBINE archives)
    if: "!contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - 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('site_creator/requirements.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 requirements
        run: python -m pip install -r tests/requirements.txt

      - name: Compile example COMBINE archives
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends zipcmp
          python scripts/compile_examples_combine_archives.py

      - name: Test examples
        run: python -m pytest tests/

  compileStaticWebsite:
    name: Compile static website
    if: "!contains(github.event.head_commit.message, '[skip ci]')"
    needs: testExamples
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - 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('site_creator/requirements.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 requirements
        working-directory: site_creator
        run: python -m pip install -r requirements.txt

      - name: Setup Git
        run: |
          git config --global user.email "bot@sed-ml.org"
          git config --global user.name "SED-ML Bot"
          git config pull.rebase false

      - name: Compile website
        working-directory: site_creator
        run: python create_static_html.py

      - id: commit-compiled-website
        name: Commit changes to the compiled web pages
        run: |
          git stash
          git pull
          set +e
          git stash pop
          git add *.html
          git commit -m "Updated compiled files for website [skip ci]"
          if [[ $? = 0 ]]; then
            websiteChanged=1
          else
            websiteChanged=0
          fi
          echo "::set-output name=websiteChanged::$websiteChanged"

      - name: Compile example COMBINE archives
        run: |
          sudo apt-get update -y
          sudo apt-get install -y --no-install-recommends zipcmp
          python scripts/compile_examples_combine_archives.py

      - id: commit-example-combine-archives
        name: Commit compiled example COMBINE archives
        run: |
          git stash
          git pull
          set +e
          git stash pop
          git add examples/*.omex
          git commit -m "Updated example COMBINE archives [skip ci]"
          if [[ $? = 0 ]]; then
            examplesChanged=1
          else
            examplesChanged=0
          fi
          echo "::set-output name=examplesChanged::$examplesChanged"

      - name: Bundle examples
        id: bundle-examples
        working-directory: examples/L1V3
        run: |
          zip SED-ML_L1V3_examples-new.zip *.omex
          zipcmp SED-ML_L1V3_examples.zip SED-ML_L1V3_examples-new.zip
          if [[ $? = 0 ]]; then
            changed=0
            rm SED-ML_L1V3_examples-new.zip
          else
            changed=1
            mv SED-ML_L1V3_examples-new.zip SED-ML_L1V3_examples.zip
          fi
          echo "::set-output name=changed::$changed"

      - id: commit-bundled-examples
        if: steps.bundle-examples.outputs.changed == '1'
        name: Commit changes to the bundled examples
        working-directory: examples/L1V3
        run: |
          git stash
          git pull
          set +e
          git stash pop
          git add SED-ML_L1V3_examples.zip
          git commit -m "Updated bundle of example files [skip ci]"

      - name: Determine branch to push compiled website to
        id: get-push-branch
        run: |
          if [ "${{ github.ref }}" == "refs/heads/master" ]; then
            echo "::set-output name=branch::ci-compiled-website"
          else
            echo "::set-output name=branch::${{ github.ref }}"
          fi

      - name: Push the changes to the compiled website
        if: steps.commit-compiled-website.outputs.websiteChanged == '1' || steps.commit-example-combine-archives.outputs.examplesChanged == '1' || steps.bundle-examples.outputs.changed == '1'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          branch: ${{ steps.get-push-branch.outputs.branch }}
          force: ${{ steps.get-push-branch.outputs.branch == 'ci-compiled-website' }}

      - name: Create pull request
        if: steps.get-push-branch.outputs.branch == 'ci-compiled-website'
        uses: peter-evans/create-pull-request@v3
        with:
          branch: ${{ steps.get-push-branch.outputs.branch }}