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CI(gh-2126): transition to uv for dependency management and testing (#2129)
* CI(gh-2126): transition to uv for dependency management and testing * fix: install packages in system * fix: update path * fix: specify uv python version in enviornment variable * chore: `setup.py` -> `pyproject.toml` Co-authored-by: nstarman <nstarman@users.noreply.github.com> * Revert "chore: `setup.py` -> `pyproject.toml`" This reverts commit c3ce49f. * chore: remove `UV_PYTHON` from env variable * chore: explicit python installation * fix: remove `--system` flag * fix: avoid installing pyro-api pyro-ppl/pyro-api#26 * fix: sync enviorment * chore: update logic for code coverage * fix: remove run from coverage * fix: remove run from coverage * ci: fix coveralls integration and coverage reporting - Add --cov-report=lcov to pytest commands for Coveralls compatibility. - Use --cov-append to aggregate coverage results across multiple test runs within jobs. - Explicitly point the Coveralls action to the generated LCOV files. - Synchronize the finish job condition with parallel test jobs. * fix: using uv to create env for readthedocs reference: https://docs.readthedocs.com/platform/stable/build-customization.html#install-dependencies-with-uv * fix: pinning jax version until #2154 is resolved * chore: use env variable for pytest flags * Revert "fix: pinning jax version until #2154 is resolved" This reverts commit 7202cc4. --------- Co-authored-by: nstarman <nstarman@users.noreply.github.com>
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‎.github/workflows/ci.yml‎

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

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uv.lock
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numpyro.egg-info
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__pycache__/
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.ipynb_checkpoints/

‎.readthedocs.yaml‎

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os: ubuntu-24.04
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tools:
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python: "3.13"
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jobs: # https://docs.readthedocs.com/platform/stable/build-customization.html#install-dependencies-with-uv
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pre_create_environment:
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- asdf plugin add uv
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- asdf install uv latest
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- asdf global uv latest
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create_environment:
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- uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
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install:
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- UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --extra cpu --group dev --group docs --group test
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sphinx:
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configuration: docs/source/conf.py
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formats:
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- pdf
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python:
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install:
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- requirements: docs/requirements.txt

‎docs/requirements.txt‎

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