add test workflow #11
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| # This workflow will build msyd as a python package, and call the CLI interface to check the install worked | |
| # adapted from | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Build and test msyd | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| # manually install syris dependencies | |
| # the python version spoofing requires the --no-deps flag, so this is necessary | |
| pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp | |
| # manually use pip to install syri from github, as it isn't on pypi | |
| # spoof python version to get around bounds check | |
| pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site) | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Build package | |
| run: pip install . | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Test installation | |
| run: | | |
| msyd -h | |
| msyd call -h | |
| msyd view -h | |
| - name: Test example_run.sh | |
| run: | | |
| # alias to a call launching the syri entrypoint from python | |
| # necessary, as the hacky git install does not install the CLI entrypoints | |
| alias syri='python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")' | |
| ./example |