pytest fix #18
This file contains hidden or 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: conda build | |
| 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')" |