fix OligoMiner support #12
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| name: Build and Test | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| conda-build: | |
| name: Conda Installation | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: setup/environment.yml | |
| auto-activate-base: false | |
| activate-environment: probest | |
| channels: conda-forge,bioconda,defaults | |
| - name: Install PROBEst in editable mode | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| pytest | |
| pip-build: | |
| name: Pip Installation | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Install PROBEst in editable mode | |
| run: | | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test package installation and imports | |
| run: | | |
| # Verify package can be imported | |
| python -c "import PROBESt; print('PROBESt imported successfully')" | |
| python -c "from PROBESt.args import arguments_parse; print('Args module imported successfully')" | |
| python -c "from PROBESt.evolution import mutate_position; print('Evolution module imported successfully')" | |
| - name: Test with pytest (basic tests only) | |
| run: | | |
| # Run tests that don't require external tools | |
| pytest tests/PROBESt/test_merge.py tests/PROBESt/test_dedegeneration.py -v || echo "Some tests skipped (external tools required)" |