From da88c278b1ef4401a5f0d16525965c512b3ccd8d Mon Sep 17 00:00:00 2001 From: nstarman Date: Sat, 12 Oct 2024 14:24:38 -0400 Subject: [PATCH] build: refactor build infrastruture Signed-off-by: nstarman --- .pre-commit-config.yaml | 4 +- .python-version | 1 + numpyro/version.py | 4 - pyproject.toml | 122 +- setup.py | 103 - {numpyro => src/numpyro}/__init__.py | 0 {numpyro => src/numpyro}/compat/__init__.py | 0 .../numpyro}/compat/distributions.py | 0 {numpyro => src/numpyro}/compat/handlers.py | 0 {numpyro => src/numpyro}/compat/infer.py | 0 {numpyro => src/numpyro}/compat/ops.py | 0 {numpyro => src/numpyro}/compat/optim.py | 0 {numpyro => src/numpyro}/compat/pyro.py | 0 {numpyro => src/numpyro}/compat/util.py | 0 {numpyro => src/numpyro}/contrib/__init__.py | 0 .../numpyro}/contrib/control_flow/__init__.py | 0 .../numpyro}/contrib/control_flow/cond.py | 0 .../numpyro}/contrib/control_flow/scan.py | 7 +- .../numpyro}/contrib/ecs_proxies.py | 0 .../numpyro}/contrib/einstein/__init__.py | 0 .../einstein/mixture_guide_predictive.py | 0 .../contrib/einstein/stein_kernels.py | 0 .../numpyro}/contrib/einstein/stein_loss.py | 0 .../numpyro}/contrib/einstein/stein_util.py | 0 .../numpyro}/contrib/einstein/steinvi.py | 0 .../numpyro}/contrib/funsor/__init__.py | 0 .../numpyro}/contrib/funsor/discrete.py | 0 .../numpyro}/contrib/funsor/enum_messenger.py | 0 .../numpyro}/contrib/funsor/infer_util.py | 0 .../numpyro}/contrib/hsgp/__init__.py | 0 .../numpyro}/contrib/hsgp/approximation.py | 0 .../numpyro}/contrib/hsgp/laplacian.py | 0 .../contrib/hsgp/spectral_densities.py | 0 {numpyro => src/numpyro}/contrib/hsgp/util.py | 0 {numpyro => src/numpyro}/contrib/module.py | 0 .../numpyro}/contrib/nested_sampling.py | 0 {numpyro => src/numpyro}/contrib/render.py | 0 .../contrib/stochastic_support/__init__.py | 0 .../contrib/stochastic_support/dcc.py | 0 .../contrib/stochastic_support/sdvi.py | 0 .../numpyro}/contrib/tfp/__init__.py | 0 .../numpyro}/contrib/tfp/distributions.py | 0 {numpyro => src/numpyro}/contrib/tfp/mcmc.py | 0 {numpyro => src/numpyro}/diagnostics.py | 0 .../numpyro}/distributions/__init__.py | 0 .../numpyro}/distributions/batch_util.py | 0 .../numpyro}/distributions/conjugate.py | 0 .../numpyro}/distributions/constraints.py | 0 .../numpyro}/distributions/continuous.py | 0 .../numpyro}/distributions/copula.py | 0 .../numpyro}/distributions/directional.py | 0 .../numpyro}/distributions/discrete.py | 0 .../numpyro}/distributions/distribution.py | 0 .../numpyro}/distributions/flows.py | 0 {numpyro => src/numpyro}/distributions/gof.py | 0 {numpyro => src/numpyro}/distributions/kl.py | 0 .../numpyro}/distributions/mixtures.py | 0 .../numpyro}/distributions/transforms.py | 0 .../numpyro}/distributions/truncated.py | 0 .../numpyro}/distributions/util.py | 0 {numpyro => src/numpyro}/examples/__init__.py | 0 {numpyro => src/numpyro}/examples/datasets.py | 0 {numpyro => src/numpyro}/handlers.py | 0 {numpyro => src/numpyro}/infer/__init__.py | 0 {numpyro => src/numpyro}/infer/autoguide.py | 15 +- {numpyro => src/numpyro}/infer/barker.py | 0 {numpyro => src/numpyro}/infer/elbo.py | 7 +- {numpyro => src/numpyro}/infer/ensemble.py | 0 .../numpyro}/infer/ensemble_util.py | 0 {numpyro => src/numpyro}/infer/hmc.py | 0 {numpyro => src/numpyro}/infer/hmc_gibbs.py | 0 {numpyro => src/numpyro}/infer/hmc_util.py | 0 .../numpyro}/infer/initialization.py | 0 {numpyro => src/numpyro}/infer/inspect.py | 11 +- {numpyro => src/numpyro}/infer/mcmc.py | 0 {numpyro => src/numpyro}/infer/mixed_hmc.py | 0 {numpyro => src/numpyro}/infer/reparam.py | 0 {numpyro => src/numpyro}/infer/sa.py | 0 {numpyro => src/numpyro}/infer/svi.py | 0 {numpyro => src/numpyro}/infer/util.py | 0 {numpyro => src/numpyro}/nn/__init__.py | 0 {numpyro => src/numpyro}/nn/auto_reg_nn.py | 0 .../numpyro}/nn/block_neural_arn.py | 0 {numpyro => src/numpyro}/nn/masked_dense.py | 0 {numpyro => src/numpyro}/ops/__init__.py | 0 {numpyro => src/numpyro}/ops/indexing.py | 0 {numpyro => src/numpyro}/ops/provenance.py | 0 {numpyro => src/numpyro}/ops/pytree.py | 0 {numpyro => src/numpyro}/optim.py | 0 {numpyro => src/numpyro}/patch.py | 0 {numpyro => src/numpyro}/primitives.py | 0 {numpyro => src/numpyro}/util.py | 0 test/infer/test_hmc_util.py | 5 +- test/test_distributions.py | 8 +- test/test_handlers.py | 6 +- uv.lock | 3580 +++++++++++++++++ 96 files changed, 3724 insertions(+), 149 deletions(-) create mode 100644 .python-version delete mode 100644 numpyro/version.py delete mode 100644 setup.py rename {numpyro => src/numpyro}/__init__.py (100%) rename {numpyro => src/numpyro}/compat/__init__.py (100%) rename {numpyro => src/numpyro}/compat/distributions.py (100%) rename {numpyro => src/numpyro}/compat/handlers.py (100%) rename {numpyro => src/numpyro}/compat/infer.py (100%) rename {numpyro => src/numpyro}/compat/ops.py (100%) rename {numpyro => src/numpyro}/compat/optim.py (100%) rename {numpyro => src/numpyro}/compat/pyro.py (100%) rename {numpyro => src/numpyro}/compat/util.py (100%) rename {numpyro => src/numpyro}/contrib/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/control_flow/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/control_flow/cond.py (100%) rename {numpyro => src/numpyro}/contrib/control_flow/scan.py (99%) rename {numpyro => src/numpyro}/contrib/ecs_proxies.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/mixture_guide_predictive.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/stein_kernels.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/stein_loss.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/stein_util.py (100%) rename {numpyro => src/numpyro}/contrib/einstein/steinvi.py (100%) rename {numpyro => src/numpyro}/contrib/funsor/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/funsor/discrete.py (100%) rename {numpyro => src/numpyro}/contrib/funsor/enum_messenger.py (100%) rename {numpyro => src/numpyro}/contrib/funsor/infer_util.py (100%) rename {numpyro => src/numpyro}/contrib/hsgp/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/hsgp/approximation.py (100%) rename {numpyro => src/numpyro}/contrib/hsgp/laplacian.py (100%) rename {numpyro => src/numpyro}/contrib/hsgp/spectral_densities.py (100%) rename {numpyro => src/numpyro}/contrib/hsgp/util.py (100%) rename {numpyro => src/numpyro}/contrib/module.py (100%) rename {numpyro => src/numpyro}/contrib/nested_sampling.py (100%) rename {numpyro => src/numpyro}/contrib/render.py (100%) rename {numpyro => src/numpyro}/contrib/stochastic_support/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/stochastic_support/dcc.py (100%) rename {numpyro => src/numpyro}/contrib/stochastic_support/sdvi.py (100%) rename {numpyro => src/numpyro}/contrib/tfp/__init__.py (100%) rename {numpyro => src/numpyro}/contrib/tfp/distributions.py (100%) rename {numpyro => src/numpyro}/contrib/tfp/mcmc.py (100%) rename {numpyro => src/numpyro}/diagnostics.py (100%) rename {numpyro => src/numpyro}/distributions/__init__.py (100%) rename {numpyro => src/numpyro}/distributions/batch_util.py (100%) rename {numpyro => src/numpyro}/distributions/conjugate.py (100%) rename {numpyro => src/numpyro}/distributions/constraints.py (100%) rename {numpyro => src/numpyro}/distributions/continuous.py (100%) rename {numpyro => src/numpyro}/distributions/copula.py (100%) rename {numpyro => src/numpyro}/distributions/directional.py (100%) rename {numpyro => src/numpyro}/distributions/discrete.py (100%) rename {numpyro => src/numpyro}/distributions/distribution.py (100%) rename {numpyro => src/numpyro}/distributions/flows.py (100%) rename {numpyro => src/numpyro}/distributions/gof.py (100%) rename {numpyro => src/numpyro}/distributions/kl.py (100%) rename {numpyro => src/numpyro}/distributions/mixtures.py (100%) rename {numpyro => src/numpyro}/distributions/transforms.py (100%) rename {numpyro => src/numpyro}/distributions/truncated.py (100%) rename {numpyro => src/numpyro}/distributions/util.py (100%) rename {numpyro => src/numpyro}/examples/__init__.py (100%) rename {numpyro => src/numpyro}/examples/datasets.py (100%) rename {numpyro => src/numpyro}/handlers.py (100%) rename {numpyro => src/numpyro}/infer/__init__.py (100%) rename {numpyro => src/numpyro}/infer/autoguide.py (99%) rename {numpyro => src/numpyro}/infer/barker.py (100%) rename {numpyro => src/numpyro}/infer/elbo.py (99%) rename {numpyro => src/numpyro}/infer/ensemble.py (100%) rename {numpyro => src/numpyro}/infer/ensemble_util.py (100%) rename {numpyro => src/numpyro}/infer/hmc.py (100%) rename {numpyro => src/numpyro}/infer/hmc_gibbs.py (100%) rename {numpyro => src/numpyro}/infer/hmc_util.py (100%) rename {numpyro => src/numpyro}/infer/initialization.py (100%) rename {numpyro => src/numpyro}/infer/inspect.py (98%) rename {numpyro => src/numpyro}/infer/mcmc.py (100%) rename {numpyro => src/numpyro}/infer/mixed_hmc.py (100%) rename {numpyro => src/numpyro}/infer/reparam.py (100%) rename {numpyro => src/numpyro}/infer/sa.py (100%) rename {numpyro => src/numpyro}/infer/svi.py (100%) rename {numpyro => src/numpyro}/infer/util.py (100%) rename {numpyro => src/numpyro}/nn/__init__.py (100%) rename {numpyro => src/numpyro}/nn/auto_reg_nn.py (100%) rename {numpyro => src/numpyro}/nn/block_neural_arn.py (100%) rename {numpyro => src/numpyro}/nn/masked_dense.py (100%) rename {numpyro => src/numpyro}/ops/__init__.py (100%) rename {numpyro => src/numpyro}/ops/indexing.py (100%) rename {numpyro => src/numpyro}/ops/provenance.py (100%) rename {numpyro => src/numpyro}/ops/pytree.py (100%) rename {numpyro => src/numpyro}/optim.py (100%) rename {numpyro => src/numpyro}/patch.py (100%) rename {numpyro => src/numpyro}/primitives.py (100%) rename {numpyro => src/numpyro}/util.py (100%) create mode 100644 uv.lock diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b22262c06..793b3603d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,12 +20,12 @@ repos: - id: debug-statements - id: check-yaml - id: check-added-large-files - exclude: notebooks/* + exclude: notebooks/ - repo: https://github.com/codespell-project/codespell rev: v2.3.0 hooks: - id: codespell - stages: [commit, commit-msg] + stages: [pre-commit, commit-msg] args: [--ignore-words-list, "Teh,aas", --check-filenames, --skip, "*.ipynb"] diff --git a/.python-version b/.python-version new file mode 100644 index 000000000..bd28b9c5c --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.9 diff --git a/numpyro/version.py b/numpyro/version.py deleted file mode 100644 index 601b211d8..000000000 --- a/numpyro/version.py +++ /dev/null @@ -1,4 +0,0 @@ -# Copyright Contributors to the Pyro project. -# SPDX-License-Identifier: Apache-2.0 - -__version__ = "0.15.3" diff --git a/pyproject.toml b/pyproject.toml index 8e4a9df63..44d0d9543 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,24 +1,101 @@ +[project] +name = "numpyro" +version = "0.15.3" +description = "Pyro PPL on NumPy" +readme = "README.md" +requires-python = ">=3.9" +authors = [ + { name = "Uber AI Labs", email = "npradhan@uber.com" }, +] +keywords = ["probabilistic", "machine learning", "bayesian", "statistics"] +license.file = "LICENSE.md" +classifiers=[ + "Intended Audience :: Developers", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: POSIX :: Linux", + "Operating System :: MacOS :: MacOS X", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +dependencies = [ + "jax>=0.4.25", + "jaxlib>=0.4.25", + "multipledispatch>=1.0.0", + "numpy>=2.0.2", + "tqdm>=4.66.5", +] + +[project.optional-dependencies] +doc = [ + "ipython", # sphinx needs this to render codes + "nbsphinx>=0.8.9", + "readthedocs-sphinx-search>=0.3.2", + "sphinx>=5", + "sphinx_rtd_theme", + "sphinx-gallery", +] +test = [ + "importlib-metadata<5.0", + "ruff>=0.1.8", + "pytest>=4.1", + "pyro-api>=0.1.1", + "scikit-learn", + "scipy>=1.9", +] +dev = [ + "dm-haiku", + "flax", + "funsor>=0.4.1", + "graphviz", + "jaxns==2.4.8", + "matplotlib", + "optax>=0.0.6", + "pylab-sdk", # jaxns dependency + "pyyaml", # flax dependency + "requests", # pylab dependency + "tensorflow_probability>=0.18.0", +] +examples = [ + "arviz", + "jupyter", + "matplotlib", + "pandas", + "seaborn", + "scikit-learn", + "wordcloud", +] +cpu = ["numpyro", "jax[cpu]"] +# gpu = ["numpyro", "jax[tpu]"] +# cuda = ["numpyro", "jax[cuda]"] + +[project.urls] +Documentation = "https://num.pyro.ai/en/stable/" +Repository = "https://github.com/pyro-ppl/numpyro" + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.hatch.build] +include = ["src/numpyro/version.py"] + +[tool.hatch.build.targets.sdist.hooks.custom] +hooks = ["write_version_file"] + +[tool.hatch.hooks.write_version_file] +path = "your_package/version.py" +template = ''' +# Auto-generated version file +__version__ = "{version}" +''' + [tool.ruff] # Exclude a variety of commonly ignored directories. exclude = [ - ".bzr", - ".direnv", - ".eggs", - ".git", - ".git-rewrite", - ".hg", - ".ipynb_checkpoints", - ".mypy_cache", - ".nox", - ".pants.d", - ".pyenv", - ".pytest_cache", - ".pytype", - ".ruff_cache", - ".svn", - ".tox", - ".venv", - ".vscode", + ".*", "__pypackages__", "_build", "buck-out", @@ -63,8 +140,8 @@ skip-magic-trailing-comma = false line-ending = "auto" [tool.ruff.lint.extend-per-file-ignores] -"numpyro/contrib/tfp/distributions.py" = ["F811"] -"numpyro/distributions/kl.py" = ["F811"] +"src/numpyro/contrib/tfp/distributions.py" = ["F811"] +"src/numpyro/distributions/kl.py" = ["F811"] [tool.ruff.lint.isort] combine-as-imports = true @@ -102,3 +179,8 @@ doctest_optionflags = [ "NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL", ] + +[tool.uv] +dev-dependencies = [ + "pre-commit>=4.0.1", +] diff --git a/setup.py b/setup.py deleted file mode 100644 index b47b0bc92..000000000 --- a/setup.py +++ /dev/null @@ -1,103 +0,0 @@ -# Copyright Contributors to the Pyro project. -# SPDX-License-Identifier: Apache-2.0 - -from __future__ import absolute_import, division, print_function - -import os -import sys - -from setuptools import find_packages, setup - -PROJECT_PATH = os.path.dirname(os.path.abspath(__file__)) -_jax_version_constraints = ">=0.4.25" -_jaxlib_version_constraints = ">=0.4.25" - -# Find version -for line in open(os.path.join(PROJECT_PATH, "numpyro", "version.py")): - if line.startswith("__version__ = "): - version = line.strip().split()[2][1:-1] - -# READ README.md for long description on PyPi. -try: - long_description = open("README.md", encoding="utf-8").read() -except Exception as e: - sys.stderr.write("Failed to read README.md:\n {}\n".format(e)) - sys.stderr.flush() - long_description = "" - -setup( - name="numpyro", - version=version, - description="Pyro PPL on NumPy", - packages=find_packages(include=["numpyro", "numpyro.*"]), - url="https://github.com/pyro-ppl/numpyro", - author="Uber AI Labs", - install_requires=[ - f"jax{_jax_version_constraints}", - f"jaxlib{_jaxlib_version_constraints}", - "multipledispatch", - "numpy", - "tqdm", - ], - extras_require={ - "doc": [ - "ipython", # sphinx needs this to render codes - "nbsphinx>=0.8.9", - "readthedocs-sphinx-search>=0.3.2", - "sphinx>=5", - "sphinx_rtd_theme", - "sphinx-gallery", - ], - "test": [ - "importlib-metadata<5.0", - "ruff>=0.1.8", - "pytest>=4.1", - "pyro-api>=0.1.1", - "scikit-learn", - "scipy>=1.9", - ], - "dev": [ - "dm-haiku", - "flax", - "funsor>=0.4.1", - "graphviz", - "jaxns==2.4.8", - "matplotlib", - "optax>=0.0.6", - "pylab-sdk", # jaxns dependency - "pyyaml", # flax dependency - "requests", # pylab dependency - "tensorflow_probability>=0.18.0", - ], - "examples": [ - "arviz", - "jupyter", - "matplotlib", - "pandas", - "seaborn", - "scikit-learn", - "wordcloud", - ], - "cpu": f"jax[cpu]{_jax_version_constraints}", - # TPU and CUDA installations, currently require to add package repository URL, i.e., - # pip install numpyro[cuda] -f https://storage.googleapis.com/jax-releases/jax_releases.html - "tpu": f"jax[tpu]{_jax_version_constraints}", - "cuda": f"jax[cuda]{_jax_version_constraints}", - }, - python_requires=">=3.9", - long_description=long_description, - long_description_content_type="text/markdown", - keywords="probabilistic machine learning bayesian statistics", - license="Apache License 2.0", - classifiers=[ - "Intended Audience :: Developers", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Operating System :: POSIX :: Linux", - "Operating System :: MacOS :: MacOS X", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - ], -) diff --git a/numpyro/__init__.py b/src/numpyro/__init__.py similarity index 100% rename from numpyro/__init__.py rename to src/numpyro/__init__.py diff --git a/numpyro/compat/__init__.py b/src/numpyro/compat/__init__.py similarity index 100% rename from numpyro/compat/__init__.py rename to src/numpyro/compat/__init__.py diff --git a/numpyro/compat/distributions.py b/src/numpyro/compat/distributions.py similarity index 100% rename from numpyro/compat/distributions.py rename to src/numpyro/compat/distributions.py diff --git a/numpyro/compat/handlers.py b/src/numpyro/compat/handlers.py similarity index 100% rename from numpyro/compat/handlers.py rename to src/numpyro/compat/handlers.py diff --git a/numpyro/compat/infer.py b/src/numpyro/compat/infer.py similarity index 100% rename from numpyro/compat/infer.py rename to src/numpyro/compat/infer.py diff --git a/numpyro/compat/ops.py b/src/numpyro/compat/ops.py similarity index 100% rename from numpyro/compat/ops.py rename to src/numpyro/compat/ops.py diff --git a/numpyro/compat/optim.py b/src/numpyro/compat/optim.py similarity index 100% rename from numpyro/compat/optim.py rename to src/numpyro/compat/optim.py diff --git a/numpyro/compat/pyro.py b/src/numpyro/compat/pyro.py similarity index 100% rename from numpyro/compat/pyro.py rename to src/numpyro/compat/pyro.py diff --git a/numpyro/compat/util.py b/src/numpyro/compat/util.py similarity index 100% rename from numpyro/compat/util.py rename to src/numpyro/compat/util.py diff --git a/numpyro/contrib/__init__.py b/src/numpyro/contrib/__init__.py similarity index 100% rename from numpyro/contrib/__init__.py rename to src/numpyro/contrib/__init__.py diff --git a/numpyro/contrib/control_flow/__init__.py b/src/numpyro/contrib/control_flow/__init__.py similarity index 100% rename from numpyro/contrib/control_flow/__init__.py rename to src/numpyro/contrib/control_flow/__init__.py diff --git a/numpyro/contrib/control_flow/cond.py b/src/numpyro/contrib/control_flow/cond.py similarity index 100% rename from numpyro/contrib/control_flow/cond.py rename to src/numpyro/contrib/control_flow/cond.py diff --git a/numpyro/contrib/control_flow/scan.py b/src/numpyro/contrib/control_flow/scan.py similarity index 99% rename from numpyro/contrib/control_flow/scan.py rename to src/numpyro/contrib/control_flow/scan.py index 7a2689cf1..957cebe6b 100644 --- a/numpyro/contrib/control_flow/scan.py +++ b/src/numpyro/contrib/control_flow/scan.py @@ -197,9 +197,10 @@ def body_fn(wrapped_carry, x, prefix=None): ) return (i + 1, rng_key, new_carry), (PytreeTrace(trace), y) - with handlers.block( - hide_fn=lambda site: not site["name"].startswith("_PREV_") - ), enum(first_available_dim=first_available_dim): + with ( + handlers.block(hide_fn=lambda site: not site["name"].startswith("_PREV_")), + enum(first_available_dim=first_available_dim), + ): wrapped_carry = (0, rng_key, init) y0s = [] # We run unroll_steps + 1 where the last step is used for rolling with `lax.scan` diff --git a/numpyro/contrib/ecs_proxies.py b/src/numpyro/contrib/ecs_proxies.py similarity index 100% rename from numpyro/contrib/ecs_proxies.py rename to src/numpyro/contrib/ecs_proxies.py diff --git a/numpyro/contrib/einstein/__init__.py b/src/numpyro/contrib/einstein/__init__.py similarity index 100% rename from numpyro/contrib/einstein/__init__.py rename to src/numpyro/contrib/einstein/__init__.py diff --git a/numpyro/contrib/einstein/mixture_guide_predictive.py b/src/numpyro/contrib/einstein/mixture_guide_predictive.py similarity index 100% rename from numpyro/contrib/einstein/mixture_guide_predictive.py rename to src/numpyro/contrib/einstein/mixture_guide_predictive.py diff --git a/numpyro/contrib/einstein/stein_kernels.py b/src/numpyro/contrib/einstein/stein_kernels.py similarity index 100% rename from numpyro/contrib/einstein/stein_kernels.py rename to src/numpyro/contrib/einstein/stein_kernels.py diff --git a/numpyro/contrib/einstein/stein_loss.py b/src/numpyro/contrib/einstein/stein_loss.py similarity index 100% rename from numpyro/contrib/einstein/stein_loss.py rename to src/numpyro/contrib/einstein/stein_loss.py diff --git a/numpyro/contrib/einstein/stein_util.py b/src/numpyro/contrib/einstein/stein_util.py similarity index 100% rename from numpyro/contrib/einstein/stein_util.py rename to src/numpyro/contrib/einstein/stein_util.py diff --git a/numpyro/contrib/einstein/steinvi.py b/src/numpyro/contrib/einstein/steinvi.py similarity index 100% rename from numpyro/contrib/einstein/steinvi.py rename to src/numpyro/contrib/einstein/steinvi.py diff --git a/numpyro/contrib/funsor/__init__.py b/src/numpyro/contrib/funsor/__init__.py similarity index 100% rename from numpyro/contrib/funsor/__init__.py rename to src/numpyro/contrib/funsor/__init__.py diff --git a/numpyro/contrib/funsor/discrete.py b/src/numpyro/contrib/funsor/discrete.py similarity index 100% rename from numpyro/contrib/funsor/discrete.py rename to src/numpyro/contrib/funsor/discrete.py diff --git a/numpyro/contrib/funsor/enum_messenger.py b/src/numpyro/contrib/funsor/enum_messenger.py similarity index 100% rename from numpyro/contrib/funsor/enum_messenger.py rename to src/numpyro/contrib/funsor/enum_messenger.py diff --git a/numpyro/contrib/funsor/infer_util.py b/src/numpyro/contrib/funsor/infer_util.py similarity index 100% rename from numpyro/contrib/funsor/infer_util.py rename to src/numpyro/contrib/funsor/infer_util.py diff --git a/numpyro/contrib/hsgp/__init__.py b/src/numpyro/contrib/hsgp/__init__.py similarity index 100% rename from numpyro/contrib/hsgp/__init__.py rename to src/numpyro/contrib/hsgp/__init__.py diff --git a/numpyro/contrib/hsgp/approximation.py b/src/numpyro/contrib/hsgp/approximation.py similarity index 100% rename from numpyro/contrib/hsgp/approximation.py rename to src/numpyro/contrib/hsgp/approximation.py diff --git a/numpyro/contrib/hsgp/laplacian.py b/src/numpyro/contrib/hsgp/laplacian.py similarity index 100% rename from numpyro/contrib/hsgp/laplacian.py rename to src/numpyro/contrib/hsgp/laplacian.py diff --git a/numpyro/contrib/hsgp/spectral_densities.py b/src/numpyro/contrib/hsgp/spectral_densities.py similarity index 100% rename from numpyro/contrib/hsgp/spectral_densities.py rename to src/numpyro/contrib/hsgp/spectral_densities.py diff --git a/numpyro/contrib/hsgp/util.py b/src/numpyro/contrib/hsgp/util.py similarity index 100% rename from numpyro/contrib/hsgp/util.py rename to src/numpyro/contrib/hsgp/util.py diff --git a/numpyro/contrib/module.py b/src/numpyro/contrib/module.py similarity index 100% rename from numpyro/contrib/module.py rename to src/numpyro/contrib/module.py diff --git a/numpyro/contrib/nested_sampling.py b/src/numpyro/contrib/nested_sampling.py similarity index 100% rename from numpyro/contrib/nested_sampling.py rename to src/numpyro/contrib/nested_sampling.py diff --git a/numpyro/contrib/render.py b/src/numpyro/contrib/render.py similarity index 100% rename from numpyro/contrib/render.py rename to src/numpyro/contrib/render.py diff --git a/numpyro/contrib/stochastic_support/__init__.py b/src/numpyro/contrib/stochastic_support/__init__.py similarity index 100% rename from numpyro/contrib/stochastic_support/__init__.py rename to src/numpyro/contrib/stochastic_support/__init__.py diff --git a/numpyro/contrib/stochastic_support/dcc.py b/src/numpyro/contrib/stochastic_support/dcc.py similarity index 100% rename from numpyro/contrib/stochastic_support/dcc.py rename to src/numpyro/contrib/stochastic_support/dcc.py diff --git a/numpyro/contrib/stochastic_support/sdvi.py b/src/numpyro/contrib/stochastic_support/sdvi.py similarity index 100% rename from numpyro/contrib/stochastic_support/sdvi.py rename to src/numpyro/contrib/stochastic_support/sdvi.py diff --git a/numpyro/contrib/tfp/__init__.py b/src/numpyro/contrib/tfp/__init__.py similarity index 100% rename from numpyro/contrib/tfp/__init__.py rename to src/numpyro/contrib/tfp/__init__.py diff --git a/numpyro/contrib/tfp/distributions.py b/src/numpyro/contrib/tfp/distributions.py similarity index 100% rename from numpyro/contrib/tfp/distributions.py rename to src/numpyro/contrib/tfp/distributions.py diff --git a/numpyro/contrib/tfp/mcmc.py b/src/numpyro/contrib/tfp/mcmc.py similarity index 100% rename from numpyro/contrib/tfp/mcmc.py rename to src/numpyro/contrib/tfp/mcmc.py diff --git a/numpyro/diagnostics.py b/src/numpyro/diagnostics.py similarity index 100% rename from numpyro/diagnostics.py rename to src/numpyro/diagnostics.py diff --git a/numpyro/distributions/__init__.py b/src/numpyro/distributions/__init__.py similarity index 100% rename from numpyro/distributions/__init__.py rename to src/numpyro/distributions/__init__.py diff --git a/numpyro/distributions/batch_util.py b/src/numpyro/distributions/batch_util.py similarity index 100% rename from numpyro/distributions/batch_util.py rename to src/numpyro/distributions/batch_util.py diff --git a/numpyro/distributions/conjugate.py b/src/numpyro/distributions/conjugate.py similarity index 100% rename from numpyro/distributions/conjugate.py rename to src/numpyro/distributions/conjugate.py diff --git a/numpyro/distributions/constraints.py b/src/numpyro/distributions/constraints.py similarity index 100% rename from numpyro/distributions/constraints.py rename to src/numpyro/distributions/constraints.py diff --git a/numpyro/distributions/continuous.py b/src/numpyro/distributions/continuous.py similarity index 100% rename from numpyro/distributions/continuous.py rename to src/numpyro/distributions/continuous.py diff --git a/numpyro/distributions/copula.py b/src/numpyro/distributions/copula.py similarity index 100% rename from numpyro/distributions/copula.py rename to src/numpyro/distributions/copula.py diff --git a/numpyro/distributions/directional.py b/src/numpyro/distributions/directional.py similarity index 100% rename from numpyro/distributions/directional.py rename to src/numpyro/distributions/directional.py diff --git a/numpyro/distributions/discrete.py b/src/numpyro/distributions/discrete.py similarity index 100% rename from numpyro/distributions/discrete.py rename to src/numpyro/distributions/discrete.py diff --git a/numpyro/distributions/distribution.py b/src/numpyro/distributions/distribution.py similarity index 100% rename from numpyro/distributions/distribution.py rename to src/numpyro/distributions/distribution.py diff --git a/numpyro/distributions/flows.py b/src/numpyro/distributions/flows.py similarity index 100% rename from numpyro/distributions/flows.py rename to src/numpyro/distributions/flows.py diff --git a/numpyro/distributions/gof.py b/src/numpyro/distributions/gof.py similarity index 100% rename from numpyro/distributions/gof.py rename to src/numpyro/distributions/gof.py diff --git a/numpyro/distributions/kl.py b/src/numpyro/distributions/kl.py similarity index 100% rename from numpyro/distributions/kl.py rename to src/numpyro/distributions/kl.py diff --git a/numpyro/distributions/mixtures.py b/src/numpyro/distributions/mixtures.py similarity index 100% rename from numpyro/distributions/mixtures.py rename to src/numpyro/distributions/mixtures.py diff --git a/numpyro/distributions/transforms.py b/src/numpyro/distributions/transforms.py similarity index 100% rename from numpyro/distributions/transforms.py rename to src/numpyro/distributions/transforms.py diff --git a/numpyro/distributions/truncated.py b/src/numpyro/distributions/truncated.py similarity index 100% rename from numpyro/distributions/truncated.py rename to src/numpyro/distributions/truncated.py diff --git a/numpyro/distributions/util.py b/src/numpyro/distributions/util.py similarity index 100% rename from numpyro/distributions/util.py rename to src/numpyro/distributions/util.py diff --git a/numpyro/examples/__init__.py b/src/numpyro/examples/__init__.py similarity index 100% rename from numpyro/examples/__init__.py rename to src/numpyro/examples/__init__.py diff --git a/numpyro/examples/datasets.py b/src/numpyro/examples/datasets.py similarity index 100% rename from numpyro/examples/datasets.py rename to src/numpyro/examples/datasets.py diff --git a/numpyro/handlers.py b/src/numpyro/handlers.py similarity index 100% rename from numpyro/handlers.py rename to src/numpyro/handlers.py diff --git a/numpyro/infer/__init__.py b/src/numpyro/infer/__init__.py similarity index 100% rename from numpyro/infer/__init__.py rename to src/numpyro/infer/__init__.py diff --git a/numpyro/infer/autoguide.py b/src/numpyro/infer/autoguide.py similarity index 99% rename from numpyro/infer/autoguide.py rename to src/numpyro/infer/autoguide.py index 72b2df3bf..6df31055a 100644 --- a/numpyro/infer/autoguide.py +++ b/src/numpyro/infer/autoguide.py @@ -1463,8 +1463,10 @@ def _sample_latent(self, *args, **kwargs): if self.global_guide is not None: global_latents = self.global_guide(*args, **kwargs) rng_key = numpyro.prng_key() - with handlers.block(), handlers.seed(rng_seed=rng_key), handlers.substitute( - data=global_latents + with ( + handlers.block(), + handlers.seed(rng_seed=rng_key), + handlers.substitute(data=global_latents), ): global_outputs = self.global_guide.model(*args, **kwargs) local_args = (global_outputs,) @@ -1575,9 +1577,12 @@ def fn(x): if self.local_guide is not None: key = numpyro.prng_key() subsample_guide = partial(_subsample_model, self.local_guide) - with handlers.block(), handlers.trace() as tr, handlers.seed( - rng_seed=key - ), handlers.substitute(data=local_guide_params): + with ( + handlers.block(), + handlers.trace() as tr, + handlers.seed(rng_seed=key), + handlers.substitute(data=local_guide_params), + ): with warnings.catch_warnings(): warnings.simplefilter("ignore") subsample_guide(*local_args, **local_kwargs) diff --git a/numpyro/infer/barker.py b/src/numpyro/infer/barker.py similarity index 100% rename from numpyro/infer/barker.py rename to src/numpyro/infer/barker.py diff --git a/numpyro/infer/elbo.py b/src/numpyro/infer/elbo.py similarity index 99% rename from numpyro/infer/elbo.py rename to src/numpyro/infer/elbo.py index c0aaa3118..4fcd97b67 100644 --- a/numpyro/infer/elbo.py +++ b/src/numpyro/infer/elbo.py @@ -874,8 +874,11 @@ def get_importance_trace_enum( trace as _trace, ) - with plate_to_enum_plate(), enum( - first_available_dim=(-max_plate_nesting - 1) if max_plate_nesting else None + with ( + plate_to_enum_plate(), + enum( + first_available_dim=(-max_plate_nesting - 1) if max_plate_nesting else None + ), ): guide = substitute(guide, data=params) with _without_rsample_stop_gradient(): diff --git a/numpyro/infer/ensemble.py b/src/numpyro/infer/ensemble.py similarity index 100% rename from numpyro/infer/ensemble.py rename to src/numpyro/infer/ensemble.py diff --git a/numpyro/infer/ensemble_util.py b/src/numpyro/infer/ensemble_util.py similarity index 100% rename from numpyro/infer/ensemble_util.py rename to src/numpyro/infer/ensemble_util.py diff --git a/numpyro/infer/hmc.py b/src/numpyro/infer/hmc.py similarity index 100% rename from numpyro/infer/hmc.py rename to src/numpyro/infer/hmc.py diff --git a/numpyro/infer/hmc_gibbs.py b/src/numpyro/infer/hmc_gibbs.py similarity index 100% rename from numpyro/infer/hmc_gibbs.py rename to src/numpyro/infer/hmc_gibbs.py diff --git a/numpyro/infer/hmc_util.py b/src/numpyro/infer/hmc_util.py similarity index 100% rename from numpyro/infer/hmc_util.py rename to src/numpyro/infer/hmc_util.py diff --git a/numpyro/infer/initialization.py b/src/numpyro/infer/initialization.py similarity index 100% rename from numpyro/infer/initialization.py rename to src/numpyro/infer/initialization.py diff --git a/numpyro/infer/inspect.py b/src/numpyro/infer/inspect.py similarity index 98% rename from numpyro/infer/inspect.py rename to src/numpyro/infer/inspect.py index 7b999ede5..1e4b52b75 100644 --- a/numpyro/infer/inspect.py +++ b/src/numpyro/infer/inspect.py @@ -58,8 +58,10 @@ def get_trace(): def _get_log_probs(model, model_args, model_kwargs, **sample): # Note: We use seed 0 for parameter initialization. - with handlers.trace() as tr, handlers.seed(rng_seed=0), handlers.substitute( - data=sample + with ( + handlers.trace() as tr, + handlers.seed(rng_seed=0), + handlers.substitute(data=sample), ): model(*model_args, **model_kwargs) return { @@ -370,8 +372,9 @@ def process_message(self, msg): # Note: We use seed 0 for parameter initialization. with handlers.trace() as tr, handlers.seed(rng_seed=0): - with handlers.substitute(data=sample), substitute_deterministic( - data=sample + with ( + handlers.substitute(data=sample), + substitute_deterministic(data=sample), ): model(*model_args, **model_kwargs) provenance_arrays = {} diff --git a/numpyro/infer/mcmc.py b/src/numpyro/infer/mcmc.py similarity index 100% rename from numpyro/infer/mcmc.py rename to src/numpyro/infer/mcmc.py diff --git a/numpyro/infer/mixed_hmc.py b/src/numpyro/infer/mixed_hmc.py similarity index 100% rename from numpyro/infer/mixed_hmc.py rename to src/numpyro/infer/mixed_hmc.py diff --git a/numpyro/infer/reparam.py b/src/numpyro/infer/reparam.py similarity index 100% rename from numpyro/infer/reparam.py rename to src/numpyro/infer/reparam.py diff --git a/numpyro/infer/sa.py b/src/numpyro/infer/sa.py similarity index 100% rename from numpyro/infer/sa.py rename to src/numpyro/infer/sa.py diff --git a/numpyro/infer/svi.py b/src/numpyro/infer/svi.py similarity index 100% rename from numpyro/infer/svi.py rename to src/numpyro/infer/svi.py diff --git a/numpyro/infer/util.py b/src/numpyro/infer/util.py similarity index 100% rename from numpyro/infer/util.py rename to src/numpyro/infer/util.py diff --git a/numpyro/nn/__init__.py b/src/numpyro/nn/__init__.py similarity index 100% rename from numpyro/nn/__init__.py rename to src/numpyro/nn/__init__.py diff --git a/numpyro/nn/auto_reg_nn.py b/src/numpyro/nn/auto_reg_nn.py similarity index 100% rename from numpyro/nn/auto_reg_nn.py rename to src/numpyro/nn/auto_reg_nn.py diff --git a/numpyro/nn/block_neural_arn.py b/src/numpyro/nn/block_neural_arn.py similarity index 100% rename from numpyro/nn/block_neural_arn.py rename to src/numpyro/nn/block_neural_arn.py diff --git a/numpyro/nn/masked_dense.py b/src/numpyro/nn/masked_dense.py similarity index 100% rename from numpyro/nn/masked_dense.py rename to src/numpyro/nn/masked_dense.py diff --git a/numpyro/ops/__init__.py b/src/numpyro/ops/__init__.py similarity index 100% rename from numpyro/ops/__init__.py rename to src/numpyro/ops/__init__.py diff --git a/numpyro/ops/indexing.py b/src/numpyro/ops/indexing.py similarity index 100% rename from numpyro/ops/indexing.py rename to src/numpyro/ops/indexing.py diff --git a/numpyro/ops/provenance.py b/src/numpyro/ops/provenance.py similarity index 100% rename from numpyro/ops/provenance.py rename to src/numpyro/ops/provenance.py diff --git a/numpyro/ops/pytree.py b/src/numpyro/ops/pytree.py similarity index 100% rename from numpyro/ops/pytree.py rename to src/numpyro/ops/pytree.py diff --git a/numpyro/optim.py b/src/numpyro/optim.py similarity index 100% rename from numpyro/optim.py rename to src/numpyro/optim.py diff --git a/numpyro/patch.py b/src/numpyro/patch.py similarity index 100% rename from numpyro/patch.py rename to src/numpyro/patch.py diff --git a/numpyro/primitives.py b/src/numpyro/primitives.py similarity index 100% rename from numpyro/primitives.py rename to src/numpyro/primitives.py diff --git a/numpyro/util.py b/src/numpyro/util.py similarity index 100% rename from numpyro/util.py rename to src/numpyro/util.py diff --git a/test/infer/test_hmc_util.py b/test/infer/test_hmc_util.py index f1a81e436..080c6a6f4 100644 --- a/test/infer/test_hmc_util.py +++ b/test/infer/test_hmc_util.py @@ -57,8 +57,9 @@ def optimize(f): @pytest.mark.parametrize("regularize", [True, False]) @pytest.mark.filterwarnings("ignore:numpy.linalg support is experimental:UserWarning") def test_welford_covariance(jitted, diagonal, regularize): - with optional(jitted, disable_jit()), optional( - jitted, control_flow_prims_disabled() + with ( + optional(jitted, disable_jit()), + optional(jitted, control_flow_prims_disabled()), ): np.random.seed(0) loc = np.random.randn(3) diff --git a/test/test_distributions.py b/test/test_distributions.py index 20da4165d..8ed9e78e5 100644 --- a/test/test_distributions.py +++ b/test/test_distributions.py @@ -2221,8 +2221,12 @@ def g(x): def test_beta_proportion_invalid_mean(): - with dist.distribution.validation_enabled(), pytest.raises( - ValueError, match=r"^BetaProportion distribution got invalid mean parameter\.$" + with ( + dist.distribution.validation_enabled(), + pytest.raises( + ValueError, + match=r"^BetaProportion distribution got invalid mean parameter\.$", + ), ): dist.BetaProportion(1.0, 1.0) diff --git a/test/test_handlers.py b/test/test_handlers.py index 4ef449237..15121eb46 100644 --- a/test/test_handlers.py +++ b/test/test_handlers.py @@ -372,8 +372,10 @@ def test_subsample_substitute(): data = jnp.arange(100.0) subsample_size = 7 subsample = jnp.array([13, 3, 30, 4, 1, 68, 5]) - with handlers.trace() as tr, handlers.seed(rng_seed=0), handlers.substitute( - data={"a": subsample} + with ( + handlers.trace() as tr, + handlers.seed(rng_seed=0), + handlers.substitute(data={"a": subsample}), ): with numpyro.plate("a", len(data), subsample_size=subsample_size) as idx: assert data[idx].shape == (subsample_size,) diff --git a/uv.lock b/uv.lock new file mode 100644 index 000000000..a26497f50 --- /dev/null +++ b/uv.lock @@ -0,0 +1,3580 @@ +version = 1 +requires-python = ">=3.9" +resolution-markers = [ + "python_full_version < '3.10'", + "python_full_version == '3.10.*'", + "python_full_version == '3.11.*'", + "python_full_version == '3.12.*'", + "python_full_version >= '3.13'", +] + +[[package]] +name = "absl-py" +version = "2.1.0" +source = { registry = 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