Run whole test suite on numba backend #5767
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| # Cancels all previous workflow runs for pull requests that have not completed. | |
| concurrency: | |
| # The concurrency group contains the workflow name and the branch name for pull requests | |
| # or the commit hash for any other events. | |
| group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }} | |
| cancel-in-progress: true | |
| jobs: | |
| changes: | |
| name: "Check for changes" | |
| runs-on: ubuntu-latest | |
| outputs: | |
| changes: ${{ steps.changes.outputs.src }} | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3.0.2 | |
| id: changes | |
| with: | |
| filters: | | |
| python: &python | |
| - 'pytensor/**/*.py' | |
| - 'tests/**/*.py' | |
| - 'pytensor/**/*.pyx' | |
| - 'tests/**/*.pyx' | |
| - '*.py' | |
| src: | |
| - *python | |
| - 'pytensor/**/*.c' | |
| - 'tests/**/*.c' | |
| - 'pytensor/**/*.h' | |
| - 'tests/**/*.h' | |
| - '.github/workflows/*.yml' | |
| - 'setup.cfg' | |
| - 'requirements.txt' | |
| - '.pre-commit-config.yaml' | |
| style: | |
| name: Check code style | |
| needs: changes | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changes.outputs.changes == 'true' }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.14"] | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 | |
| with: | |
| persist-credentials: false | |
| - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| test: | |
| name: "mode ${{ matrix.default-mode }} : py${{ matrix.python-version }} : ${{ matrix.os }} : ${{ matrix.part[0] }}" | |
| needs: | |
| - changes | |
| - style | |
| runs-on: ${{ matrix.os }} | |
| if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| default-mode: ["C", "NUMBA", "FAST_COMPILE"] | |
| python-version: ["3.11", "3.14"] | |
| os: ["ubuntu-latest"] | |
| install-jax: [0] | |
| install-torch: [0] | |
| install-mlx: [0] | |
| install-xarray: [0] | |
| part: | |
| - [ "*rest", "tests --ignore=tests/scan --ignore=tests/tensor --ignore=tests/xtensor --ignore=tests/link/numba" ] | |
| - [ "scan", "tests/scan" ] | |
| - [ "tensor *rest", "tests/tensor --ignore=tests/tensor/test_basic.py --ignore=tests/tensor/test_elemwise.py --ignore=tests/tensor/test_math.py --ignore=tests/tensor/test_math_scipy.py --ignore=tests/tensor/test_blas.py --ignore=tests/tensor/conv --ignore=tests/tensor/rewriting --ignore=tests/tensor/linalg --ignore=tests/tensor/test_nlinalg.py --ignore=tests/tensor/test_slinalg.py --ignore=tests/tensor/test_pad.py" ] | |
| - [ "tensor basic+elemwise", "tests/tensor/test_basic.py tests/tensor/test_elemwise.py" ] | |
| - [ "tensor math", "tests/tensor/test_math.py" ] | |
| - [ "tensor scipy+blas+conv+pad", "tests/tensor/test_math_scipy.py tests/tensor/test_blas.py tests/tensor/conv tests/tensor/test_pad.py" ] | |
| - [ "tensor rewriting", "tests/tensor/rewriting" ] | |
| - [ "tensor linalg", "tests/tensor/linalg tests/tensor/test_nlinalg.py tests/tensor/test_slinalg.py" ] | |
| exclude: | |
| - python-version: "3.11" | |
| default-mode: "FAST_COMPILE" | |
| include: | |
| - part: ["doctests", "--doctest-modules pytensor --ignore=pytensor/misc/check_duplicate_key.py --ignore=pytensor/link --ignore=pytensor/ipython.py"] | |
| default-mode: "C" | |
| python-version: "3.12" | |
| os: "ubuntu-latest" | |
| - part: ["numba link", "tests/link/numba --ignore=tests/link/numba/test_slinalg.py"] | |
| default-mode: "C" | |
| python-version: "3.12" | |
| os: "ubuntu-latest" | |
| - part: ["numba link slinalg", "tests/link/numba/test_slinalg.py"] | |
| default-mode: "C" | |
| python-version: "3.13" | |
| os: "ubuntu-latest" | |
| - part: ["jax link", "tests/link/jax"] | |
| install-jax: 1 | |
| default-mode: "C" | |
| python-version: "3.14" | |
| os: "ubuntu-latest" | |
| - part: ["pytorch link", "tests/link/pytorch"] | |
| install-torch: 1 | |
| default-mode: "C" | |
| python-version: "3.11" | |
| os: "ubuntu-latest" | |
| - part: ["xtensor", "tests/xtensor"] | |
| install-xarray: 1 | |
| default-mode: "C" | |
| python-version: "3.14" | |
| os: "ubuntu-latest" | |
| - part: ["mlx link", "tests/link/mlx"] | |
| install-mlx: 1 | |
| default-mode: "C" | |
| python-version: "3.11" | |
| os: "macos-15" | |
| - part: ["macos smoke test", "tests/tensor/test_elemwise.py tests/tensor/test_math_scipy.py tests/tensor/test_blas.py"] | |
| default-mode: "C" | |
| python-version: "3.14" | |
| os: "macos-15" | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7 | |
| with: | |
| environment-name: pytensor-test | |
| micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved | |
| init-shell: bash | |
| post-cleanup: "all" | |
| create-args: python=${{ matrix.python-version }} | |
| - name: Create matrix id | |
| id: matrix-id | |
| env: | |
| MATRIX_CONTEXT: ${{ toJson(matrix) }} | |
| run: | | |
| echo $MATRIX_CONTEXT | |
| export MATRIX_ID=`echo $MATRIX_CONTEXT | sha256sum | cut -c 1-32` | |
| echo $MATRIX_ID | |
| echo "id=$MATRIX_ID" >> $GITHUB_OUTPUT | |
| - name: Install dependencies | |
| shell: micromamba-shell {0} | |
| run: | | |
| if [[ $OS == "macos-15" ]]; then | |
| micromamba install --yes -q "python~=${PYTHON_VERSION}" numpy scipy "numba>=0.63" pip graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock pytest-sphinx libblas=*=*accelerate; | |
| else | |
| micromamba install --yes -q "python~=${PYTHON_VERSION}" numpy scipy "numba>=0.63" pip graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock pytest-sphinx mkl mkl-service; | |
| fi | |
| if [[ $INSTALL_JAX == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}" jax jaxlib numpyro equinox && pip install tfp-nightly; fi | |
| if [[ $INSTALL_TORCH == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}" pytorch pytorch-cuda=12.1 "mkl<=2024.0" -c pytorch -c nvidia; fi | |
| if [[ $INSTALL_MLX == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}" "mlx<0.29.4"; fi | |
| if [[ $INSTALL_XARRAY == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}" xarray xarray-einstats; fi | |
| pip install -e ./ | |
| micromamba list && pip freeze | |
| python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))' | |
| if [[ $OS == "macos-15" ]]; then | |
| python -c 'import pytensor; assert pytensor.config.blas__ldflags.startswith("-framework Accelerate"), "Blas flags are not set to MacOS Accelerate"'; | |
| else | |
| python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"'; | |
| fi | |
| env: | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| INSTALL_JAX: ${{ matrix.install-jax }} | |
| INSTALL_TORCH: ${{ matrix.install-torch }} | |
| INSTALL_XARRAY: ${{ matrix.install-xarray }} | |
| INSTALL_MLX: ${{ matrix.install-mlx }} | |
| OS: ${{ matrix.os}} | |
| - name: Run tests | |
| shell: micromamba-shell {0} | |
| run: | | |
| if [[ $DEFAULT_MODE == "FAST_COMPILE" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,mode=FAST_COMPILE; fi | |
| if [[ $DEFAULT_MODE == "NUMBA" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,linker=numba; fi | |
| export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe | |
| python -m pytest -r A --verbose --runslow --durations=50 --cov=pytensor/ --cov-report=xml:coverage/coverage-${MATRIX_ID}.xml --no-cov-on-fail $PART --benchmark-skip | |
| env: | |
| MATRIX_ID: ${{ steps.matrix-id.outputs.id }} | |
| MKL_THREADING_LAYER: GNU | |
| MKL_NUM_THREADS: 1 | |
| OMP_NUM_THREADS: 1 | |
| PART: ${{ matrix.part[1] }} | |
| DEFAULT_MODE: ${{ matrix.default-mode }} | |
| - name: Upload coverage file | |
| uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 | |
| with: | |
| name: coverage-${{ steps.matrix-id.outputs.id }} | |
| path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml | |
| benchmarks: | |
| name: "Benchmarks" | |
| needs: | |
| - changes | |
| - style | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - name: Set up Python 3.11 | |
| uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7 | |
| with: | |
| environment-name: pytensor-test | |
| micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved | |
| init-shell: bash | |
| post-cleanup: "all" | |
| - name: Install dependencies | |
| shell: micromamba-shell {0} | |
| run: | | |
| micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark | |
| pip install -e ./ | |
| micromamba list && pip freeze | |
| python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))' | |
| python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"' | |
| env: | |
| PYTHON_VERSION: 3.11 | |
| - name: Download previous benchmark data | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0 | |
| with: | |
| path: ./cache | |
| key: ${{ runner.os }}-benchmark | |
| - name: Run benchmarks | |
| shell: micromamba-shell {0} | |
| run: | | |
| export PYTENSOR_FLAGS=mode=FAST_COMPILE,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe | |
| python -m pytest --runslow --benchmark-only --benchmark-json output.json | |
| - name: Store benchmark result | |
| uses: benchmark-action/github-action-benchmark@4bdcce38c94cec68da58d012ac24b7b1155efe8b # v1.20.7 | |
| with: | |
| name: Python Benchmark with pytest-benchmark | |
| tool: "pytest" | |
| output-file-path: output.json | |
| external-data-json-path: ./cache/benchmark-data.json | |
| alert-threshold: "200%" | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| comment-on-alert: false | |
| fail-on-alert: false | |
| auto-push: false | |
| all-checks: | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| name: "All tests" | |
| needs: [changes, style, test] | |
| steps: | |
| - name: Check build matrix status | |
| if: ${{ needs.changes.outputs.changes == 'true' && (needs.style.result != 'success' || needs.test.result != 'success') }} | |
| run: exit 1 | |
| upload-coverage: | |
| runs-on: ubuntu-latest | |
| name: "Upload coverage" | |
| needs: [changes, all-checks] | |
| if: ${{ needs.changes.outputs.changes == 'true' && needs.all-checks.result == 'success' }} | |
| steps: | |
| - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 | |
| with: | |
| persist-credentials: false | |
| - name: Set up Python | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0 | |
| with: | |
| python-version: "3.14" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -U coverage>=5.1 coveralls | |
| - name: Download coverage file | |
| uses: actions/download-artifact@018cc2cf5baa6db3ef3c5f8a56943fffe632ef53 # v6.0.0 | |
| with: | |
| pattern: coverage-* | |
| path: coverage | |
| merge-multiple: true | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1 | |
| with: | |
| directory: ./coverage/ | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |