Removing the valid metadata KV on each run before termination #1021
Workflow file for this run
This file contains 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: TileDB-BioImaging CI | |
| on: [push] | |
| jobs: | |
| build: | |
| name: ${{ matrix.sys.os }} | |
| runs-on: ${{ matrix.sys.os }} | |
| timeout-minutes: 25 | |
| strategy: | |
| matrix: | |
| sys: | |
| - { os: windows-latest, shell: 'cmd /C call {0}' } | |
| - { os: ubuntu-latest, shell: "bash -l {0}" } | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: ${{ matrix.sys.shell }} | |
| env: | |
| run_coverage: ${{ github.ref == 'refs/heads/main' }} | |
| outputs: | |
| coverage: ${{ steps.stats.outputs.coverage }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1.9.0 | |
| with: | |
| micromamba-version: 1.5.10-0 | |
| environment-name: test | |
| cache-downloads: true | |
| create-args: >- | |
| python=3.9 | |
| pre-commit | |
| pytest-cov | |
| pytest-mock | |
| - name: Install openslide for non-Win | |
| run: | | |
| sudo apt install openslide-tools | |
| micromamba install openslide | |
| echo ${{ matrix.sys.os }} | |
| if: ${{ matrix.sys.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 | |
| 7z x openslide-win64-20221217.zip -oD:\openslide\ | |
| mklink /D C:\openslide-win64\ D:\openslide\openslide-win64-20221217\ | |
| cd C:\openslide-win64\ | |
| dir | |
| set openslide_path=%cd% | |
| echo %openslide_path% | |
| if: ${{ matrix.sys.os == 'windows-latest' }} | |
| - name: Run pre-commit hooks | |
| run: | | |
| micromamba run -n test pre-commit run -a | |
| - name: Install package | |
| shell: "bash -l {0}" | |
| run: | | |
| pip install --no-cache-dir --upgrade tifffile "imagecodecs>=2023.7.10" | |
| pip install .[full] | |
| - name: Run tests with coverage | |
| id: stats | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| run: | | |
| : # This GITHUB_WORKSPACE is bydefault set to D: driver whereas pytest's tmp_dir | |
| : # default is C: ,thus we create a temp_test folder for pytest's tmp_dir to run on D: as well | |
| pytest -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ > coverage.txt | |
| exit_code=$? | |
| TEST_COVERAGE="$(grep '^TOTAL' coverage.txt | awk -v N=4 '{print $N}')" | |
| echo "coverage=$TEST_COVERAGE" >> $GITHUB_OUTPUT | |
| exit $exit_code | |
| if: ${{ matrix.sys.os != 'windows-latest' }} | |
| - name: Run tests with coverage WINDOWS | |
| id: stats-win | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| run: | | |
| mkdir test_temp | |
| micromamba run -n test pytest --basetemp=test_temp -v --cov=tiledb --cov-report=term-missing --durations=0 tests/ --ignore=tests/integration/converters/test_ome_tiff_experimental.py | |
| if: ${{ matrix.sys.os == 'windows-latest' }} | |
| - name: Run notebook examples | |
| run: | | |
| micromamba run -n test pip install opencv-python-headless matplotlib nbmake | |
| micromamba run -n test pytest --nbmake examples | |
| - name: Create Test Coverage Badge | |
| if: ${{ fromJSON(env.run_coverage) && matrix.sys.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 |