multiqc_windows.yml

name: "MultiQC - Windows"
on:
  push:
    branches:
      - master
    paths-ignore:
      - "docs/**"
      - "*.md"
  pull_request:
    paths-ignore:
      - "docs/**"
      - "*.md"

jobs:
  changes:
    name: Check for changes
    runs-on: ubuntu-latest
    outputs:
      files_changed: ${{ steps.filter.outputs.changes }}
      n_files_changes: ${{ steps.filter.outputs.changes.all_files_count}}
      modules: ${{ steps.filter.outputs.changes.modules }}
      n_modules: ${{ steps.filter.outputs.changes.modules_count }}
      base_module: ${{ steps.filter.outputs.changes.base_module }}
      changelog: ${{ steps.filter.outputs.changes.changelog }}

    steps:
      - uses: actions/checkout@v2

      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: |
            modules:
              - "multiqc/modules/**"
            base_module:
              - "multiqc/modules/base_module.py"
            changelog:
              - "CHANGELOG.md"
            all_files:
              - "**"

  run_multiqc:
    name: Windows - Python ${{ matrix.python-version }}
    runs-on: windows-latest
    needs: changes
    strategy:
      matrix:
        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
    timeout-minutes: 10

    steps:
      # Check out MultiQC code
      - uses: actions/checkout@v2

      # Set up Windows with C++ for numpy
      - name: Visual Studio Command Prompt tool
        run: cmd "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" ${{ matrix.platform-vcvars }}

      # Set up Python
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      # Update core packages
      - name: Install dependencies for CI tests
        run: |
          python -m pip install --upgrade pip setuptools

      # Install MultiQC
      - name: Install MultiQC
        run: pip install .

      # Fetch the MultiQC test data
      # NB: Download zip file instead of git clone, as Windows complains about reserved filenames and certain characters
      - name: Download test data
        run: |
          curl -fsSL https://github.com/ewels/MultiQC_TestData/archive/master.zip -o test_data.zip
          7z x test_data.zip -y -o"test_data"
          dir test_data\MultiQC_TestData-master

        # Set the `-m` flag if only one module has changed
      - name: "Get a `-m` flag for the `multiqc` if only one module has changed"
        uses: haya14busa/action-cond@v1
        id: single_module
        with:
          cond: ${{ ! needs.changes.outputs.base_module && needs.changes.outputs.n_modules == 1 && (needs.changes.outputs.n_files == 1 || needs.changes.outputs.n_files == 2 && needs.changes.outputs.changelog)}}
          if_true: "-m ${{ needs.changes.outputs.modules[0] }}"
          if_false: ""

      # Run all of the tests! Remember the BACKslash path separator!
      - name: Special case input data
        run: multiqc ${{ steps.single_module.outputs.value }} test_data\MultiQC_TestData-master\data --ignore test_data\MultiQC_TestData-master\data\modules\

      - name: All modules / Custom report filename
        run: multiqc ${{ steps.single_module.outputs.value }} --lint test_data\MultiQC_TestData-master\data\modules\ --filename full_report.html

      - name: File-list input of dirs
        run: |
          cd test_data\MultiQC_TestData-master
          multiqc ${{ steps.single_module.outputs.value }} --file-list data\special_cases\dir_list.txt

      - name: Specific module / Force overwrite / Prepend dirnames / Name and comment / No data dir
        run: multiqc --lint test_data\MultiQC_TestData-master\data\modules\ -m fastqc -f -d -dd 1 -i "Forced Report" -b "This command has lots of options" --filename custom_fn --no-data-dir

      - name: For overwrite / Flat plots / Tagged modules only / Exclude module / Ignore samples / Full names / zip data dir / config file
        run: multiqc ${{ steps.single_module.outputs.value }} --lint test_data\MultiQC_TestData-master\data\modules\ -f --flat --tag methylation --exclude clusterflow --ignore-samples ngi --fullnames --zip-data-dir -c test\config_example.yaml

      - name: Specfic module / named output dir / dev template / JSON data / File list
        run: |
          cd test_data\MultiQC_TestData-master
          multiqc -m star -o testsmultiqc_report_dev -t default_dev -k json --file-list data\special_cases\file_list.txt