qc.yml

name: Code quality

on:
  pull_request:
    branches_ignore: []

jobs:
  formatting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Setup mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: fmt
          channels: "conda-forge, bioconda"
          miniforge-variant: Mambaforge
          miniforge-version: latest

      - name: Setup environment
        shell: bash -el {0}
        run: |
          conda config --set channel_priority strict
          mamba install -n fmt -y black snakefmt

      - name: Check Python formatting
        shell: bash -el {0}
        run: |
          black --check */*/*/wrapper.py */*/wrapper.py

      # TODO reactivate once comment errors are fixed
      # - name: Check Snakemake formatting
      #   run: |
      #     export PATH="/usr/share/miniconda/bin:$PATH"
      #     source activate fmt
      #     snakefmt --check $(git diff origin/master --name-only | grep Snakefile)

  linting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v1

      - name: Setup mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: snakemake
          channels: "conda-forge, bioconda"
          miniforge-variant: Mambaforge
          miniforge-version: latest

      - name: Setup Snakemake environment
        shell: bash -el {0}
        run: |
          conda config --set channel_priority strict
          mamba install -n snakemake -y snakemake-minimal snakemake

      - name: Fetch master
        run: |
          git fetch origin master

      - name: Linting
        shell: bash -el {0}
        run: |
          declare -i ERRORS=0
          # get all modified and added files, not those that are deleted
          for f in $(git diff origin/master --name-only --diff-filter=d | grep Snakefile)
          do 
            snakemake -s $f --lint
            ERRORS+=$?
          done
          if (( $ERRORS > 0 ))
          then
            echo "There are some lints above. Please fix them."
            exit 1
          fi