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| name: TileDB-ML CI | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-verison: ["3.7"] | |
| ml-deps: | |
| - "torch==1.11.0+cpu torchvision==0.12.0+cpu torchdata==0.3.0 tensorflow-cpu==2.8.1" | |
| - "torch==1.12.1+cpu torchvision==0.13.1+cpu torchdata==0.4.1 tensorflow-cpu==2.9.1" | |
| - "torch==1.13.0+cpu torchvision==0.14.0+cpu torchdata==0.5.0 tensorflow-cpu==2.10.0" | |
| - "torch==1.13.0+cpu torchvision==0.14.0+cpu torchdata==0.5.0 tensorflow-cpu==2.11.0" | |
| include: | |
| - ml-deps: "torch==1.13.0+cpu torchvision==0.14.0+cpu torchdata==0.5.0 tensorflow-cpu==2.12.0" | |
| python-version: "3.9" | |
| - ml-deps: "torch==1.13.0+cpu torchvision==0.14.0+cpu torchdata==0.5.0 tensorflow-cpu==2.13.0" | |
| python-version: "3.9" | |
| env: | |
| run_coverage: ${{ github.ref == 'refs/heads/master' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}:ml-deps=[${{ matrix.ml-deps }}] | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install -f https://download.pytorch.org/whl/torch_stable.html protobuf==3.* ${{ matrix.ml-deps }} | |
| pip install pytest-mock pytest-cov scikit-learn==1.0.2 | |
| pip install -e .[cloud] | |
| - name: Run pre-commit hooks | |
| run: | | |
| pip install pre-commit | |
| pre-commit run -a | |
| - name: Run notebook examples | |
| run: | | |
| pip install pytest-xdist nbmake matplotlib idx2numpy | |
| pytest --disable-warnings --nbmake examples/{models,readers} | |
| # Run tiledb-cloud in parallel | |
| if [[ "${{ secrets.TILEDB_API_TOKEN }}" != "" ]]; then | |
| TILEDB_API_TOKEN="${{ secrets.TILEDB_API_TOKEN }}" pytest --disable-warnings --nbmake -n3 examples/cloud | |
| fi | |
| - name: Run tests | |
| if: ${{ !fromJSON(env.run_coverage) }} | |
| run: pytest --disable-warnings tests/ | |
| - name: Run test coverage statistics | |
| id: stats | |
| if: ${{ fromJSON(env.run_coverage) }} | |
| run: | | |
| pytest --disable-warnings --cov-report=term-missing --cov=tiledb tests/ > coverage.txt | |
| cat coverage.txt | |
| TEST_COVERAGE="$(grep '^TOTAL' coverage.txt | awk -v N=4 '{print $N}')" | |
| echo "::set-output name=COVERAGE::$TEST_COVERAGE" | |
| - name: Create Test Coverage Badge | |
| if: ${{ fromJSON(env.run_coverage) }} | |
| uses: schneegans/dynamic-badges-action@v1.1.0 | |
| with: | |
| auth: ${{ secrets.COVERAGE_SECRET }} | |
| gistID: 2506f6c9d3375e2d636cf594340d11bf | |
| filename: gistfile.json | |
| label: Test Coverage | |
| message: ${{ steps.stats.outputs.COVERAGE }} | |
| color: green | |
| namedLogo: pytest |