Backwards compatibility renaming #765
Workflow file for this run
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| name: TileDB-BioImaging CI | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 20 | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| run_coverage: ${{ github.ref == 'refs/heads/main' }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: test | |
| cache-downloads: true | |
| create-args: >- | |
| python=3.7 | |
| pre-commit | |
| pytest-cov | |
| pytest-mock | |
| - name: Install openslide for non-Win | |
| run: micromamba install openslide | |
| if: matrix.os != 'windows-latest' | |
| - name: Install openslide for Win | |
| run: | | |
| choco install wget --no-progress | |
| wget https://github.com/openslide/openslide-winbuild/releases/download/v20221217/openslide-win64-20221217.zip | |
| unzip ./openslide-win64-20221217.zip -d /usr/local/ | |
| mv /usr/local/openslide-win64-20221217/* /usr/local/ | |
| if: matrix.os == 'windows-latest' | |
| - name: Run pre-commit hooks | |
| run: pre-commit run -a | |
| - name: Install package | |
| run: | | |
| pip install tifffile@git+https://github.com/TileDB-Inc/tifffile.git@gsa/python-3.7 | |
| pip install -e .[full] | |
| - name: Run tests with coverage | |
| id: stats | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| run: | | |
| # This GITHUB_WORKSPACE is bydefault set to D: driver whereas pytest's tmp_dir | |
| # default is C: ,thus we create a temp_test folder for pytest's tmp_dir to run on D: as well | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| pytest -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ > coverage.txt | |
| cat coverage.txt | |
| TEST_COVERAGE="$(grep '^TOTAL' coverage.txt | awk -v N=4 '{print $N}')" | |
| echo "COVERAGE=$TEST_COVERAGE" >> $GITHUB_OUTPUT | |
| else | |
| mkdir test_temp | |
| pytest --basetemp=test_temp -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ | |
| fi | |
| - name: Run notebook examples | |
| run: | | |
| pip install opencv-python-headless matplotlib nbmake | |
| pytest --nbmake examples | |
| - name: Create Test Coverage Badge | |
| if: ${{ fromJSON(env.run_coverage) && matrix.os == 'ubuntu-latest'}} | |
| uses: schneegans/dynamic-badges-action@v1.1.0 | |
| with: | |
| auth: ${{ secrets.COVERAGE_SECRET }} | |
| gistID: 32d48185733a4e7375e80e3e35fab452 | |
| filename: gist_bioimg.json | |
| label: Test Coverage | |
| message: ${{ steps.stats.outputs.COVERAGE }} | |
| color: green | |
| namedLogo: pytest |