run_regression_tests.yaml

name: Tests

on:
  push:
  pull_request:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}

jobs:
  static_tests:
    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        with:
            lfs: false

      - name: Install conda environment dependencies
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          miniforge-variant: Mambaforge
          python-version: "3.11"
          mamba-version: "*"
          channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144
          channel-priority: strict
          activate-environment: V-pipe
          auto-update-conda: true
          environment-file: tests/conda_lint_env.yaml

      - name: Code formatting
        run: snakefmt --check .

      - name: Setup project
        run: |
          mkdir -p lintest/config  # virus does not matter
          cd lintest/
          $GITHUB_WORKSPACE/init_project.sh -n
          # dummy content so pipeline is configured properly
          cp -vr $GITHUB_WORKSPACE/tests/data/hiv/ ./samples
          sed -E 's/(#*virus_base_config:) .*$/\1 hiv/;s/false$/true/g;s/(trim_primers:) .*$/\1 false/' $GITHUB_WORKSPACE/config/config.yaml | tee ./config.yaml

      - name: Snakemake linting
        env:
          PYTHONUNBUFFERED: 1
        uses: snakemake/snakemake-github-action@v1
        with:
          directory: lintest/
          snakefile: 'workflow/Snakefile'
          args: '--lint'
        continue-on-error: true  # HACK for now snakemake linting is considered non-critical

  runtime_tests:
    needs: static_tests

    strategy:
      max-parallel: 5
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.10", "3.11"]
        virus: ["hiv", "sars-cov-2"]

    runs-on: ${{ matrix.os }}

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v3
        with:
            lfs: false
            # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS

      - name: Install conda environment dependencies
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          miniforge-variant: Mambaforge
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144
          channel-priority: strict
          activate-environment: V-pipe
          auto-update-conda: true
          environment-file: tests/conda_test_env.yaml

      - name: Setup project
        run: |
          mkdir -p /tmp/project/${{ matrix.virus }}/
          cd /tmp/project/${{ matrix.virus }}/
          $GITHUB_WORKSPACE/init_project.sh -n

      - name: Run tests
        working-directory: ./tests
        run: ./regression_tests.sh ${{ matrix.virus }}

      - name: Archive code coverage results
        uses: actions/upload-artifact@v3
        with:
          name: regression test output and diffs
          path: |
            /tmp/v-pipe_tests/*
          if-no-files-found: ignore