[FIX] Fix tests #2
Workflow file for this run
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| name: abagen-tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| env: | |
| ABAGEN_DATA: ~/abagen-data | |
| jobs: | |
| check_style: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 | |
| - name: Run style checks | |
| run: flake8 abagen | |
| fetch_ahba: | |
| needs: check_style | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements.txt | |
| - name: Install abagen | |
| run: python -m pip install -e . | |
| - name: Print abagen version | |
| run: python -c "import abagen; print(abagen.__version__)" | |
| - name: Fetch AHBA data | |
| run: python -c "import abagen; abagen.fetch_microarray(data_dir='$ABAGEN_DATA', donors=['12876', '15496'], n_proc=2)" | |
| - name: Upload AHBA data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: abagen-data | |
| path: ${{ env.ABAGEN_DATA }} | |
| run_tests: | |
| needs: [check_style, fetch_ahba] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-latest'] | |
| python-version: ['3.7', '3.8', '3.9', '3.10'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov | |
| python -m pip install -r requirements.txt | |
| - name: Install abagen | |
| run: python -m pip install -e . | |
| - name: Print abagen version | |
| run: python -c "import abagen; print(abagen.__version__)" | |
| - name: Fetch AHBA data | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: abagen-data | |
| path: ${{ env.ABAGEN_DATA }} | |
| - name: Run tests | |
| run: pytest --doctest-modules --cov=abagen --cov-report=xml --junitxml=junit/test-results.xml --verbose --pyargs abagen | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: junit/test-results.xml |