fix: freshly formatted toml files (#2190)

* fix: freshly formatted toml files

* chore: update pre-commit hooks to their latest

Author: Qazalbash

.pre-commit-config.yaml

@@ -38,20 +38,20 @@ repos:
         exclude: notebooks/
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
         args: [--ignore-words-list, "Teh,aas,ans,dout", --check-filenames, --skip, "*.ipynb"]
 
   # Format yaml files
   - repo: https://github.com/google/yamlfmt
-    rev: v0.20.0
+    rev: v0.21.0
     hooks:
       - id: yamlfmt
         args: [-formatter, retain_line_breaks=true]
 
   - repo: https://github.com/tombi-toml/tombi-pre-commit
-    rev: v0.10.6
+    rev: v0.11.5
     hooks:
       - id: tombi-format

pyproject.toml

@@ -27,24 +27,17 @@ dependencies = [
     "tqdm",
 ]
 
-[tool.setuptools.dynamic]
-version = { attr = "numpyro.version.__version__" }
-
-[project.optional-dependencies]
-cpu = ["jax[cpu]>=0.7.0"]
-cuda12 = ["jax[cuda12]>=0.7.0"]
-cuda13 = ["jax[cuda13]>=0.7.0"]
-tpu = ["jax[tpu]>=0.7.0"]
-
 [project.urls]
 Changelog = "https://github.com/pyro-ppl/numpyro/blob/main/CHANGELOG.md"
 Discussion = "https://github.com/pyro-ppl/numpyro/discussions"
 Homepage = "https://github.com/pyro-ppl/numpyro"
 Issues = "https://github.com/pyro-ppl/numpyro/issues"
 
-[build-system]
-requires = ["setuptools>=61", "wheel"]
-build-backend = "setuptools.build_meta"
+[project.optional-dependencies]
+cpu = ["jax[cpu]>=0.7.0"]
+cuda12 = ["jax[cuda12]>=0.7.0"]
+cuda13 = ["jax[cuda13]>=0.7.0"]
+tpu = ["jax[tpu]>=0.7.0"]
 
 [dependency-groups]
 dev = [
@@ -95,12 +88,52 @@ test = [
     "ty>=0.0.4",
 ]
 
-# NOTE: this can be simplified using src-layout
-[tool.setuptools.packages.find]
-include = ["numpyro*"]
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
 
-[tool.setuptools]
-include-package-data = true
+[tool.mypy]
+ignore_errors = true
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = [
+    "examples.datasets",
+    "numpyro.contrib.control_flow.*",        # types missing
+    "numpyro.contrib.funsor.*",              # types missing
+    "numpyro.contrib.hsgp.*",
+    "numpyro.contrib.stochastic_support.*",
+    "numpyro.diagnostics.*",
+    "numpyro.handlers.*",
+    "numpyro.infer.elbo.*",
+    "numpyro.optim.*",
+    "numpyro.primitives.*",
+    "numpyro.patch.*",
+    "numpyro.util.*",
+    "numpyro.distributions.constraints",
+    "numpyro.distributions.distribution",
+    "numpyro.distributions.transforms",
+]
+ignore_errors = false
+
+[tool.pytest.ini_options]
+addopts = ["-v", "--color=yes"]
+doctest_optionflags = [
+    "ELLIPSIS",
+    "NORMALIZE_WHITESPACE",
+    "IGNORE_EXCEPTION_DETAIL",
+]
+filterwarnings = [
+    "error",
+    "ignore:.*Attempting to hash a tracer:FutureWarning",
+    "ignore:numpy.ufunc size changed,:RuntimeWarning",
+    "ignore:Using a non-tuple sequence:FutureWarning",
+    "ignore:jax.tree_structure is deprecated:FutureWarning",
+    "ignore:numpy.linalg support is experimental:UserWarning",
+    "ignore:scipy.linalg support is experimental:UserWarning",
+    "once:No GPU:UserWarning",
+    "once::DeprecationWarning",
+]
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
@@ -159,19 +192,6 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 [tool.ruff.lint.pycodestyle]
 max-line-length = 120
 
-[tool.ruff.format]
-# Like Black, use double quotes for strings.
-quote-style = "double"
-
-# Like Black, indent with spaces, rather than tabs.
-indent-style = "space"
-
-# Like Black, respect magic trailing commas.
-skip-magic-trailing-comma = false
-
-# Like Black, automatically detect the appropriate line ending.
-line-ending = "auto"
-
 [tool.ruff.lint.per-file-ignores]
 "!numpyro/{diagnostics.py,handlers.py,optim.py,patch.py,primitives.py,infer/elbo.py,distributions/distribution.py}" = [
     "ANN",
@@ -198,48 +218,28 @@ section-order = [
 [tool.ruff.lint.isort.sections]
 known-jax = ["flax", "jax", "optax", "tensorflow_probability"]
 
-[tool.pytest.ini_options]
-addopts = ["-v", "--color=yes"]
-filterwarnings = [
-    "error",
-    "ignore:.*Attempting to hash a tracer:FutureWarning",
-    "ignore:numpy.ufunc size changed,:RuntimeWarning",
-    "ignore:Using a non-tuple sequence:FutureWarning",
-    "ignore:jax.tree_structure is deprecated:FutureWarning",
-    "ignore:numpy.linalg support is experimental:UserWarning",
-    "ignore:scipy.linalg support is experimental:UserWarning",
-    "once:No GPU:UserWarning",
-    "once::DeprecationWarning",
-]
-doctest_optionflags = [
-    "ELLIPSIS",
-    "NORMALIZE_WHITESPACE",
-    "IGNORE_EXCEPTION_DETAIL",
-]
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
 
-[tool.mypy]
-ignore_errors = true
-ignore_missing_imports = true
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
 
-[[tool.mypy.overrides]]
-module = [
-    "examples.datasets",
-    "numpyro.contrib.control_flow.*",        # types missing
-    "numpyro.contrib.funsor.*",              # types missing
-    "numpyro.contrib.hsgp.*",
-    "numpyro.contrib.stochastic_support.*",
-    "numpyro.diagnostics.*",
-    "numpyro.handlers.*",
-    "numpyro.infer.elbo.*",
-    "numpyro.optim.*",
-    "numpyro.primitives.*",
-    "numpyro.patch.*",
-    "numpyro.util.*",
-    "numpyro.distributions.constraints",
-    "numpyro.distributions.distribution",
-    "numpyro.distributions.transforms",
-]
-ignore_errors = false
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = { attr = "numpyro.version.__version__" }
+
+# NOTE: this can be simplified using src-layout
+[tool.setuptools.packages.find]
+include = ["numpyro*"]
 
 [tool.uv.sources]
 funsor = { git = "https://github.com/pyro-ppl/funsor.git" }