Update tiledb-ml package to work with python 3.12 #1411
Workflow file for this run
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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-version: ["3.12"] | ||
| ml-deps: | ||
| # - "torch==2.1.2+cpu torchvision==0.16.2+cpu torchdata==0.7.1 tensorflow-cpu==2.15.1 " | ||
| # - "torch==2.3.1+cpu torchvision==0.18.1+cpu torchdata==0.8.0 'tensorflow-cpu<2.16'" | ||
| env: | ||
| run_coverage: ${{ github.ref == 'refs/heads/master' }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Cache dependencies | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: ~/.cache/pip | ||
| key: ${{ runner.os }} # :ml-deps=[${{ matrix.ml-deps }}] | ||
| - name: Install dependencies | ||
| run: | | ||
| pip install --upgrade pip | ||
| pip install pytest-mock pytest-cov scikit-learn==1.0.2 | ||
| pip install -e .[full] | ||
| - 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 "numpy<2" | ||
| 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/[email protected] | ||
| with: | ||
| auth: ${{ secrets.COVERAGE_SECRET }} | ||
| gistID: 2506f6c9d3375e2d636cf594340d11bf | ||
| filename: gistfile.json | ||
| label: Test Coverage | ||
| message: ${{ steps.stats.outputs.COVERAGE }} | ||
| color: green | ||
| namedLogo: pytest | ||
