bartz 0.4.1__tar.gz → 0.6.0__tar.gz

{bartz-0.4.1 → bartz-0.6.0}/PKG-INFO

@@ -1,22 +1,20 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: bartz
-Version: 0.4.1
+Version: 0.6.0
 Summary: Super-fast BART (Bayesian Additive Regression Trees) in Python
-License: MIT
 Author: Giacomo Petrillo
-Author-email: info@giacomopetrillo.com
+Author-email: Giacomo Petrillo <info@giacomopetrillo.com>
+License-Expression: MIT
+Requires-Dist: equinox>=0.12.2
+Requires-Dist: jax>=0.4.35
+Requires-Dist: jaxlib>=0.4.35
+Requires-Dist: jaxtyping>=0.3.2
+Requires-Dist: numpy>=1.25.2
+Requires-Dist: scipy>=1.11.4
 Requires-Python: >=3.10
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: jax (>=0.4.35,<1)
-Requires-Dist: jaxlib (>=0.4.35,<1)
-Requires-Dist: numpy (>=1.25.2,<3)
-Requires-Dist: scipy (>=1.11.4,<2)
-Project-URL: Bug Tracker, https://github.com/Gattocrucco/bartz/issues
+Project-URL: Documentation, https://gattocrucco.github.io/bartz/docs-dev
+Project-URL: Homepage, https://github.com/Gattocrucco/bartz
+Project-URL: Issues, https://github.com/Gattocrucco/bartz/issues
 Description-Content-Type: text/markdown
 
 [![PyPI](https://img.shields.io/pypi/v/bartz)](https://pypi.org/project/bartz/)
@@ -42,6 +40,7 @@ On CPU, bartz runs at the speed of dbarts (the fastest implementation I know of)
 - [Documentation (development version)](https://gattocrucco.github.io/bartz/docs-dev)
 - [Repository](https://github.com/Gattocrucco/bartz)
 - [Code coverage](https://gattocrucco.github.io/bartz/coverage)
+- [Benchmarks](https://gattocrucco.github.io/bartz/benchmarks)
 - [List of BART packages](https://gattocrucco.github.io/bartz/docs-dev/pkglist.html)
 
 ## Citing bartz
@@ -49,4 +48,3 @@ On CPU, bartz runs at the speed of dbarts (the fastest implementation I know of)
 Article: Petrillo (2024), "Very fast Bayesian Additive Regression Trees on GPU", [arXiv:2410.23244](https://arxiv.org/abs/2410.23244).
 
 To cite the software directly, including the specific version, use [zenodo](https://doi.org/10.5281/zenodo.13931477).
-

{bartz-0.4.1 → bartz-0.6.0}/README.md

@@ -21,6 +21,7 @@ On CPU, bartz runs at the speed of dbarts (the fastest implementation I know of)
 - [Documentation (development version)](https://gattocrucco.github.io/bartz/docs-dev)
 - [Repository](https://github.com/Gattocrucco/bartz)
 - [Code coverage](https://gattocrucco.github.io/bartz/coverage)
+- [Benchmarks](https://gattocrucco.github.io/bartz/benchmarks)
 - [List of BART packages](https://gattocrucco.github.io/bartz/docs-dev/pkglist.html)
 
 ## Citing bartz

{bartz-0.4.1 → bartz-0.6.0}/pyproject.toml

@@ -23,12 +23,12 @@
 # SOFTWARE.
 
 [build-system]
-requires = ["poetry-core>=2.0.0,<3.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["uv_build>=0.7.3,<0.8.0"]
+build-backend = "uv_build"
 
 [project]
 name = "bartz"
-version = "0.4.1"
+version = "0.6.0"
 description = "Super-fast BART (Bayesian Additive Regression Trees) in Python"
 authors = [
     {name = "Giacomo Petrillo", email = "info@giacomopetrillo.com"},
@@ -36,42 +36,49 @@ authors = [
 license = "MIT"
 readme = "README.md"
 requires-python = ">=3.10"
-repository = "https://github.com/Gattocrucco/bartz"
-packages = [
-    { include = "bartz", from = "src" },
-]
 dependencies = [
-    "jax >=0.4.35,<1",
-    "jaxlib >=0.4.35,<1",
-    "numpy >=1.25.2,<3",
-    "scipy >=1.11.4,<2",
+    "equinox>=0.12.2",
+    "jax>=0.4.35",
+    "jaxlib>=0.4.35",
+    "jaxtyping>=0.3.2",
+    "numpy>=1.25.2",
+    "scipy>=1.11.4",
 ]
 
-[tool.poetry.urls]
-"Bug Tracker" = "https://github.com/Gattocrucco/bartz/issues"
-
-[tool.poetry.group.dev.dependencies]
-ipython = ">=8.22.2"
-matplotlib = "^3.8.3"
-appnope = "^0.1.4"
-tomli = "^2.0.1"
-packaging = "^24.0"
-xgboost = "^2.0.3"
-pre-commit = "^3.7.0"
-scikit-learn = "^1.4.2"
-matplotlib-label-lines = "^0.7.0"
-polars = {version = "^1.0.0", extras = ["pandas", "pyarrow"]}
-
-[tool.poetry.group.test.dependencies]
-coverage = "^7.4.3"
-pytest = "^8.1.1"
-
-[tool.poetry.group.docs.dependencies]
-Sphinx = ">=7.2.6,<9"
-numpydoc = "^1.6.0"
-myst-parser = "^4.0.1"
+[project.urls]
+Homepage = "https://github.com/Gattocrucco/bartz"
+Documentation = "https://gattocrucco.github.io/bartz/docs-dev"
+Issues = "https://github.com/Gattocrucco/bartz/issues"
+
+[dependency-groups]
+only-local = [
+    "appnope>=0.1.4",
+    "ipython>=8.36.0",
+    "matplotlib>=3.10.3",
+    "matplotlib-label-lines>=0.8.1",
+    "pre-commit>=4.2.0",
+    "pydoclint>=0.6.6",
+    "ruff>=0.11.9",
+    "scikit-learn>=1.6.1",
+    "tomli>=2.2.1",
+    "virtualenv>=20.31.2",
+    "xgboost>=3.0.0",
+]
+ci = [
+    "asv>=0.6.4",
+    "coverage>=7.8.0",
+    "myst-parser>=4.0.1",
+    "numpydoc>=1.8.0",
+    "packaging>=25.0",
+    "polars[pandas,pyarrow]>=1.29.0",
+    "pytest>=8.3.5",
+    "pytest-timeout>=2.4.0",
+    "sphinx>=8.1.3",
+    "sphinx-autodoc-typehints>=3.0.1",
+]
 
 [tool.pytest.ini_options]
+cache_dir = "config/pytest_cache"
 testpaths = ["tests"]
 filterwarnings = [
     'error:scatter inputs have incompatible types.*',
@@ -80,7 +87,10 @@ addopts = [
     "-r xXfE",
     "--pdbcls=IPython.terminal.debugger:TerminalPdb",
     "--durations=3",
+    "--verbose",
 ]
+timeout = 64
+timeout_method = "thread"  # when jax hangs, signals do not work
 
 # I wanted to use `--import-mode=importlib`, but it breaks importing submodules,
 # in particular `from . import util`.
@@ -94,6 +104,7 @@ show_missing = true
 
 [tool.coverage.html]
 show_contexts = true
+directory = "_site/coverage"
 
 [tool.coverage.paths]
 # the first path in each list must be the source directory in the machine that's
@@ -119,3 +130,56 @@ local = [
     '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/bartz/',
     'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\bartz\',
 ]
+
+[tool.ruff]
+exclude = [".asv", "*.ipynb"]
+cache-dir = "config/ruff_cache"
+
+[tool.ruff.format]
+quote-style = "single"
+
+[tool.ruff.lint]
+select = [
+    "B", # bugbear: grab bag of additional stuff
+    "UP", # pyupgrade: fix some outdated idioms
+    "I", # isort: sort and reformat import statements
+    "F", # pyflakes
+    "D", # pydocstyle
+    "PT", # flake8-pytest-style
+]
+ignore = [
+    "B028",  # warn with stacklevel = 2
+    "D105",  # Missing docstring in magic method
+    "F722",  # Syntax error in forward annotation. I ignore this because jaxtyping uses strings for shapes instead of for deferred annotations.
+    "F821",  # Undefined name. I ignore this because strings in jaxtyping.
+    "UP037",  # Remove quotes from type annotation. Ignore because jaxtyping.
+]
+
+[tool.ruff.lint.per-file-ignores]
+"{config/*,benchmarks/*,docs/*,src/bartz/debug.py,tests/rbartpackages/*,tests/__init__.py}" = [
+    "D100",  # Missing docstring in public module
+    "D101",  # Missing docstring in public class
+    "D102",  # Missing docstring in public method
+    "D103",  # Missing docstring in public function
+    "D104",  # Missing docstring in public package
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+ignore-decorators = ["functools.cached_property"]
+
+[tool.pydoclint]
+baseline = "config/pydoclint-baseline.txt"
+auto-regenerate-baseline = true
+arg-type-hints-in-signature = true
+arg-type-hints-in-docstring = false
+check-return-types = false
+check-yield-types = false
+treat-property-methods-as-class-attributes = true
+check-style-mismatch = true
+show-filenames-in-every-violation-message = true
+check-class-attributes = false
+
+[tool.uv]
+python-downloads = "never"
+python-preference = "only-system"