Provide JAX Ops from Optional tfp dependency #23
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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@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: dorny/paths-filter@v2 | |
| 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' | |
| style: | |
| name: Check code style | |
| needs: changes | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changes.outputs.changes == 'true' }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: pre-commit/action@v3.0.0 | |
| test_ubuntu: | |
| name: "Test py${{ matrix.python-version }} : fast-compile ${{ matrix.fast-compile }} : float32 ${{ matrix.float32 }} : ${{ matrix.part }}" | |
| needs: | |
| - changes | |
| - style | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.11"] | |
| fast-compile: [0,1] | |
| float32: [0,1] | |
| install-numba: [0] | |
| install-jax: [0] | |
| part: | |
| - "tests --ignore=tests/tensor --ignore=tests/scan --ignore=tests/sparse" | |
| - "tests/scan" | |
| - "tests/sparse" | |
| - "tests/tensor --ignore=tests/tensor/conv --ignore=tests/tensor/rewriting --ignore=tests/tensor/test_math.py --ignore=tests/tensor/test_basic.py --ignore=tests/tensor/test_blas.py --ignore=tests/tensor/test_math_scipy.py --ignore=tests/tensor/test_inplace.py --ignore=tests/tensor/test_elemwise.py" | |
| - "tests/tensor/conv" | |
| - "tests/tensor/rewriting" | |
| - "tests/tensor/test_math.py" | |
| - "tests/tensor/test_basic.py tests/tensor/test_inplace.py" | |
| - "tests/tensor/test_blas.py tests/tensor/test_elemwise.py tests/tensor/test_math_scipy.py" | |
| exclude: | |
| - python-version: "3.9" | |
| fast-compile: 1 | |
| - python-version: "3.9" | |
| float32: 1 | |
| - python-version: "3.9" | |
| part: "tests/tensor/test_math.py" | |
| - fast-compile: 1 | |
| float32: 1 | |
| include: | |
| - install-numba: 1 | |
| python-version: "3.9" | |
| fast-compile: 0 | |
| float32: 0 | |
| part: "tests/link/numba" | |
| - install-numba: 1 | |
| python-version: "3.11" | |
| fast-compile: 0 | |
| float32: 0 | |
| part: "tests/link/numba" | |
| - install-jax: 1 | |
| python-version: "3.9" | |
| fast-compile: 0 | |
| float32: 0 | |
| part: "tests/link/jax" | |
| - install-jax: 1 | |
| python-version: "3.11" | |
| fast-compile: 0 | |
| float32: 0 | |
| part: "tests/link/jax" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ 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 | md5sum | cut -c 1-32` | |
| echo $MATRIX_ID | |
| echo "id=$MATRIX_ID" >> $GITHUB_OUTPUT | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| mamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock sympy | |
| # numba-scipy downgrades the installed scipy to 1.7.3 in Python 3.9, but | |
| # not numpy, even though scipy 1.7 requires numpy<1.23. When installing | |
| # PyTensor next, pip installs a lower version of numpy via the PyPI. | |
| if [[ $INSTALL_NUMBA == "1" ]] && [[ $PYTHON_VERSION == "3.9" ]]; then mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numpy<1.23" "numba>=0.57" numba-scipy; fi | |
| if [[ $INSTALL_NUMBA == "1" ]] && [[ $PYTHON_VERSION != "3.9" ]]; then mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numba>=0.57" numba-scipy; fi | |
| if [[ $INSTALL_JAX == "1" ]]; then mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" jax jaxlib numpyro && pip install tensorflow-probability; fi | |
| pip install -e ./ | |
| mamba 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: ${{ matrix.python-version }} | |
| INSTALL_NUMBA: ${{ matrix.install-numba }} | |
| INSTALL_JAX: ${{ matrix.install-jax }} | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| if [[ $FAST_COMPILE == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,mode=FAST_COMPILE; fi | |
| if [[ $FLOAT32 == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,floatX=float32; fi | |
| export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe | |
| python -m pytest -r A --verbose --runslow --cov=pytensor/ --cov-report=xml:coverage/coverage-${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 }} | |
| FAST_COMPILE: ${{ matrix.fast-compile }} | |
| FLOAT32: ${{ matrix.float32 }} | |
| - name: Upload coverage file | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml | |
| benchmarks: | |
| name: "Benchmarks" | |
| needs: | |
| - changes | |
| - style | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| mamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" numba-scipy jax jaxlib pytest-benchmark | |
| pip install -e ./ | |
| mamba 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: 3.9 | |
| - name: Download previous benchmark data | |
| uses: actions/cache@v3 | |
| with: | |
| path: ./cache | |
| key: ${{ runner.os }}-benchmark | |
| - name: Run benchmarks | |
| shell: bash -l {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@v1 | |
| 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_ubuntu] | |
| steps: | |
| - name: Check build matrix status | |
| if: ${{ needs.changes.outputs.changes == 'true' && (needs.style.result != 'success' || needs.test_ubuntu.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@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -U coverage>=5.1 coveralls | |
| - name: Download coverage file | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage | |
| path: coverage | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| directory: ./coverage/ | |
| fail_ci_if_error: true |