Merge branch 'MultiQC:main' into master #1
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: "Windows tests" | |
| on: | |
| push: | |
| paths: | |
| # runs e.g. when version updated, module added, or dependency added | |
| - "pyproject.toml" | |
| pull_request: | |
| paths: | |
| - "pyproject.toml" | |
| jobs: | |
| unit_tests: | |
| runs-on: windows-latest | |
| timeout-minutes: 10 | |
| env: | |
| # GitHub currently has 4 cores available for Windows runners | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories | |
| worker_cores: 4 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # 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 }} | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" | |
| - name: "Cache pip" | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~\AppData\Local\pip\Cache | |
| ~\AppData\Local\Programs\Python\Python312\Lib\site-packages | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: "Install MultiQC" | |
| run: pip install '.[dev]' | |
| # 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/MultiQC/test-data/archive/main.zip -o test-data.zip | |
| 7z x test-data.zip -y -o"test-data" | |
| # Flat plot export doesn't work on Windows, so forcing modules like somalier and peddy write interactive. | |
| # Also, forcing selected modules to be run. Some modules don't work when dumping plot json: | |
| # UnicodeEncodeError: 'charmap' codec can't encode character '\u2265' in position 1: character maps to <undefined> | |
| - run: | | |
| multiqc --strict --interactive -m fastqc -m samtools -m kallisto -v test-data\test-data-main\data\modules\ |