CI(gh-2126): transition to uv for dependency management and testing #4311
Workflow file for this run
This file contains hidden or 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
| # adapted from https://github.com/actions/starter-workflows/blob/master/ci/python-package.yml | |
| name: CI | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| env: | |
| PYTEST_ADDOPTS: "--cov=numpyro --cov-append" | |
| jobs: | |
| prek: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: prek check | |
| uses: j178/prek-action@v1 | |
| with: | |
| extra-args: --all-files --skip ruff --skip ruff-format --skip ty --skip mypy | |
| lint: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.13"] | |
| env: | |
| UV_PYTHON: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| enable-cache: true | |
| update-path: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt install -y pandoc gsfonts | |
| uv pip install --system --upgrade jaxlib jax | |
| uv pip install --system --upgrade '.[doc,test]' | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/funsor/archive/master.zip | |
| uv pip install --system --upgrade -r docs/requirements.txt | |
| uv pip freeze | |
| - name: Lint with mypy and ruff | |
| run: | | |
| uv run make lint | |
| - name: Build documentation | |
| run: | | |
| uv run make docs | |
| - name: Test documentation | |
| run: | | |
| uv run make doctest | |
| uv run python -m doctest -v README.md | |
| test-modeling: | |
| runs-on: ubuntu-latest | |
| needs: [lint, prek] | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.13"] | |
| env: | |
| UV_PYTHON: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| update-path: true | |
| enable-cache: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt install -y graphviz | |
| # Keep track of pyro-api master branch | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/pyro-api/archive/master.zip | |
| uv pip install --system --upgrade jaxlib jax | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/funsor/archive/master.zip | |
| uv pip install --system --upgrade -e '.[dev,test]' | |
| uv pip freeze | |
| - name: Test with pytest | |
| run: | | |
| CI=1 uv run pytest -vs -k "not test_example" --durations=100 --ignore=test/infer/ --ignore=test/contrib/ | |
| - name: Test x64 | |
| run: | | |
| JAX_ENABLE_X64=1 uv run pytest -vs test/test_distributions.py -k "powerLaw or Dagum" | |
| - name: Test tracer leak | |
| if: matrix.python-version == '3.13' | |
| env: | |
| JAX_CHECK_TRACER_LEAKS: 1 | |
| run: | | |
| uv run pytest -vs test/infer/test_mcmc.py::test_chain_inside_jit | |
| uv run pytest -vs test/infer/test_mcmc.py::test_chain_jit_args_smoke | |
| uv run pytest -vs test/infer/test_mcmc.py::test_reuse_mcmc_run | |
| uv run pytest -vs test/infer/test_mcmc.py::test_model_with_multiple_exec_paths | |
| uv run pytest -vs test/test_distributions.py::test_mean_var -k Gompertz | |
| - name: Coveralls | |
| if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13' | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel: true | |
| flag-name: test-modeling | |
| test-inference: | |
| runs-on: ubuntu-latest | |
| needs: [lint, prek] | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.13"] | |
| env: | |
| UV_PYTHON: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| enable-cache: true | |
| update-path: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/pyro-api/archive/master.zip | |
| uv pip install --system --upgrade jaxlib jax | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/funsor/archive/master.zip | |
| uv pip install --system --upgrade -e '.[dev,test]' | |
| uv pip freeze | |
| - name: Test with pytest | |
| run: | | |
| uv run pytest -vs --durations=20 test/infer/test_mcmc.py | |
| uv run pytest -vs --durations=20 test/infer --ignore=test/infer/test_mcmc.py --ignore=test/contrib/test_nested_sampling.py | |
| uv run pytest -vs --durations=20 test/contrib --ignore=test/contrib/stochastic_support/test_dcc.py | |
| - name: Test x64 | |
| run: | | |
| JAX_ENABLE_X64=1 uv run pytest -vs test/infer/test_mcmc.py -k x64 | |
| - name: Test chains | |
| run: | | |
| XLA_FLAGS="--xla_force_host_platform_device_count=2" uv run pytest -vs test/infer/test_mcmc.py -k "chain or pmap or vmap" | |
| XLA_FLAGS="--xla_force_host_platform_device_count=2" uv run pytest -vs test/contrib/test_tfp.py -k "chain" | |
| XLA_FLAGS="--xla_force_host_platform_device_count=2" uv run pytest -vs test/contrib/stochastic_support/test_dcc.py | |
| XLA_FLAGS="--xla_force_host_platform_device_count=2" uv run pytest -vs test/infer/test_hmc_gibbs.py -k "chain" | |
| - name: Test custom prng | |
| run: | | |
| JAX_ENABLE_CUSTOM_PRNG=1 uv run pytest -vs test/infer/test_mcmc.py | |
| - name: Test nested sampling | |
| run: | | |
| JAX_ENABLE_X64=1 uv run pytest -vs test/contrib/test_nested_sampling.py | |
| - name: Coveralls | |
| if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13' | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel: true | |
| flag-name: test-inference | |
| examples: | |
| runs-on: ubuntu-latest | |
| needs: [lint, prek] | |
| strategy: | |
| matrix: | |
| python-version: ["3.13"] | |
| env: | |
| UV_PYTHON: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| enable-cache: true | |
| update-path: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| uv pip install --system --upgrade jaxlib jax | |
| uv pip install --system --upgrade https://github.com/pyro-ppl/funsor/archive/master.zip | |
| uv pip install --system --upgrade -e '.[dev,examples,test]' | |
| uv pip freeze | |
| - name: Test with pytest | |
| run: | | |
| CI=1 XLA_FLAGS="--xla_force_host_platform_device_count=2" uv run pytest -vs -k test_example | |
| - name: Coveralls | |
| if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13' | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel: true | |
| flag-name: examples | |
| finish: | |
| needs: [test-modeling, test-inference, examples] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls finished | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true | |
| carryforward: "test-modeling,test-inference,examples" |