extract shape of full-resolution image, estimate visium pixel size #354
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| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| tags: | |
| - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10, v1.0-rc.1, v2.1-alpha, v3.0-beta.3 | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: ["3.9", "3.10"] | |
| os: [ubuntu-latest] | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Get pip cache dir | |
| id: pip-cache-dir | |
| run: | | |
| echo "::set-output name=dir::$(pip cache dir)" | |
| - name: Restore pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ steps.pip-cache-dir.outputs.dir }} | |
| key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| pip-${{ runner.os }}-${{ env.pythonLocation }}- | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install pytest-cov | |
| - name: Install dependencies | |
| run: | | |
| pip install --pre -e ".[dev,test]" | |
| - name: Download artifact of test data | |
| if: matrix.python == '3.10' | |
| uses: dawidd6/action-download-artifact@v2 | |
| with: | |
| workflow: prepare_test_data.yaml | |
| name: data | |
| path: ./data | |
| - name: List the data directory | |
| if: matrix.python == '3.10' | |
| run: | | |
| ls -l ./data | |
| pwd | |
| - name: Test | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| pytest -v --cov --color=yes --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: coverage | |
| verbose: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |