lint.yml

name: Linting

on: 
  pull_request:
    paths_ignore:
      - "docs/**"

defaults:
  run:
    # This is needed for miniconda, see:
    # https://github.com/marketplace/actions/setup-miniconda#important
    shell: bash -l {0}  

jobs:
  lint:
    runs-on: ubuntu-latest
    name: Linting checks
    steps:
      - uses: actions/checkout@v2.3.4
        with:
          submodules: recursive
      
      - name: Set cache date
        run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV

      - name: Cache conda environment
        # Use an always upload cache to prevent solving conda environment again and again on failing linting.
        uses: pat-s/always-upload-cache@v2.1.5
        env:
          # Increase this value to manually invalidate the cache
          CACHE_NUMBER: 0
        with:
          path: /usr/share/miniconda/envs/biowdl-lint
          key:
            ${{runner.os}}-biowdl-lint-${{ env.CACHE_NUMBER }}-${{env.DATE}}-${{ hashFiles('.github/lint-environment.yml') }}
        id: env_cache
      
      # Use the builtin conda. This is the fastest installation. It may not be
      # the fastest for resolving, but the package cache mitigates that problem.
      # Since this installs fastest, it is fastest for all runs where a cache
      # hit occurs.
      - name: install miniconda
        uses: conda-incubator/setup-miniconda@v2.1.1
        with:
          channels: conda-forge,bioconda,defaults
          channel-priority: strict
          auto-activate-base: false
          use-only-tar-bz2: true  # Needed for proper caching according to the documentation.
        # activate-environment is broken! This always seems to create a new environment.
        # Activation is therefore done separately.
      
      - name: Create test environment if no cache is present
        run: conda env create -n biowdl-lint -f .github/lint-environment.yml
        if: steps.env_cache.outputs.cache-hit != 'true'
      
      - name: Activate test environment
        # The new PATH should be passed to the environment, otherwise it won't register.
        run: |
          conda activate biowdl-lint
          echo "PATH=$PATH" >> $GITHUB_ENV
      
      - name: Fetch develop branch for comparisons
        run: git fetch --depth=1 origin develop

      - name: run womtool validate
        # Only check files that have changed from the base reference.
        # Womtool validate checks very slowly, so this saves a lot of time.
        run: |
          set -x
          for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do
            womtool validate $WDL_FILE
          done
      - name: run miniwdl check
        run: |
          set -x
          bash -c 'miniwdl check $(git ls-files *.wdl)'

      - name: Check copyright headers
        run: | 
          set -x
          for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do
            grep Copyright $WDL_FILE || bash -c "echo No copyright header in $WDL_FILE && exit 1"
          done
      - name: Check parameter_meta for inputs
        run: |
          set -x
          for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do
            wdl-aid --strict $WDL_FILE > /dev/null 2> wdl-aid_stderr || 
            if grep -z  'ValueError: Missing parameter_meta for inputs:' wdl-aid_stderr
            then
                exit 1
            fi
          done