Reintroduce linting of docs/modules/*.md
#2515
Workflow file for this run
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| 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@v3 | |
| - 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", "3.11"] | |
| timeout-minutes: 10 | |
| steps: | |
| # Check out MultiQC code | |
| - uses: actions/checkout@v3 | |
| # 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@v3 | |
| 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:/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 |