switch tests to build in conda env #23
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| # This workflow will use the build action to build the msyd python package, and call the CLI interface to check the install worked | |
| name: Test build | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| # Cancel if a newer run is started | |
| # taken from https://github.com/nf-core/modules/blob/master/.github/workflows/nf-test.yml | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| # use old install manually | |
| # since switching to conda no longer supports different python version | |
| # - name: Build msyd | |
| # uses: schneebergerlab/msyd@main | |
| # # with: | |
| # # python-version: ${{ matrix.python-version }} | |
| - name: Set up Python ${{ inputs.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ inputs.python-version }} | |
| cache: pip | |
| - name: Update pip | |
| run: python -m pip install --upgrade pip setuptools | |
| shell: bash | |
| - name: Install SyRI manually | |
| run: | | |
| # 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) | |
| shell: bash | |
| - name: Install other dependencies | |
| run: pip install -r requirements.txt | |
| shell: bash | |
| - name: Test installation | |
| run: | | |
| msyd --version | |
| msyd -h | |
| msyd call -h | |
| msyd view -h |