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ci: pre-commit hook to auto-format yaml files (#2112)
* ci: pre-commit hook to auto-format yaml files * fix test (#2113) --------- Co-authored-by: Juan Orduz <juanitorduz@gmail.com>
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‎.github/workflows/ci.yml‎

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@@ -4,9 +4,9 @@ name: CI
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on:
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push:
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branches: [ master ]
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branches: [master]
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pull_request:
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branches: [ master ]
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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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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9","3.10","3.13"]
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python-version: ["3.9", "3.10", "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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with:
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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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- name: Lint with mypy and ruff
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if: matrix.python-version != '3.9'
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run: |
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make lint
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- name: Build documentation
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if: matrix.python-version != '3.9'
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run: |
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make docs
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- name: Test documentation
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if: matrix.python-version != '3.9'
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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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- 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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with:
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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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- name: Lint with mypy and ruff
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if: matrix.python-version != '3.9'
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run: |
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make lint
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- name: Build documentation
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if: matrix.python-version != '3.9'
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run: |
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make docs
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- name: Test documentation
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if: matrix.python-version != '3.9'
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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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test-modeling:
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python-version: ["3.9", "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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with:
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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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- 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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- 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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- 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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- 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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- 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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with:
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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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- 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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- 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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- 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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- 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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test-inference:
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python-version: ["3.9", "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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with:
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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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# 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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- 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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- 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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- 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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- 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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- 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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- 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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- 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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with:
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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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# 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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- 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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- 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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- 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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- 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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- 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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- 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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examples:
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python-version: ["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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with:
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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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- 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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- 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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- 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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with:
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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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- 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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- 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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finish:
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needs: [test-modeling, test-inference, examples]
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runs-on: ubuntu-latest
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steps:
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- name: Coveralls finished
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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-finished: true
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carryforward: "test-modeling,test-inference,examples"
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- name: Coveralls finished
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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-finished: true
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carryforward: "test-modeling,test-inference,examples"
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‎.github/workflows/publish.yml‎

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on:
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release:
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types: [ published ]
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types: [published]
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jobs:
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deploy:

‎.pre-commit-config.yaml‎

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stages: [pre-commit, commit-msg]
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args: [--ignore-words-list, "Teh,aas,ans,dout", --check-filenames, --skip, "*.ipynb"]
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# Format yaml files
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- repo: https://github.com/google/yamlfmt
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rev: v0.20.0
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hooks:
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- id: yamlfmt
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args: [-formatter, retain_line_breaks=true]

‎.readthedocs.yaml‎

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python: "3.10"
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sphinx:
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configuration: docs/source/conf.py
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configuration: docs/source/conf.py
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formats:
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- pdf
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- pdf
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python:
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install:
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- requirements: docs/requirements.txt
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install:
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- requirements: docs/requirements.txt

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