bartz 0.6.0__tar.gz → 0.8.0__tar.gz

{bartz-0.6.0 → bartz-0.8.0}/PKG-INFO

@@ -1,20 +1,23 @@
 Metadata-Version: 2.4
 Name: bartz
-Version: 0.6.0
+Version: 0.8.0
 Summary: Super-fast BART (Bayesian Additive Regression Trees) in Python
 Author: Giacomo Petrillo
 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: jax>=0.5.3
 Requires-Dist: jaxtyping>=0.3.2
 Requires-Dist: numpy>=1.25.2
 Requires-Dist: scipy>=1.11.4
+Requires-Dist: jax[cuda12] ; extra == 'cuda12'
+Requires-Dist: jax[cuda13] ; extra == 'cuda13'
 Requires-Python: >=3.10
-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
+Project-URL: Documentation, https://bartz-org.github.io/bartz/docs-dev
+Project-URL: Homepage, https://github.com/bartz-org/bartz
+Project-URL: Issues, https://github.com/bartz-org/bartz/issues
+Provides-Extra: cuda12
+Provides-Extra: cuda13
 Description-Content-Type: text/markdown
 
 [![PyPI](https://img.shields.io/pypi/v/bartz)](https://pypi.org/project/bartz/)
@@ -32,16 +35,18 @@ This Python module provides an implementation of BART that runs on GPU, to proce
 
 On CPU, bartz runs at the speed of dbarts (the fastest implementation I know of) if n > 20,000, but using 1/20 of the memory. On GPU, the speed premium depends on sample size; it is convenient over CPU only for n > 10,000. The maximum speedup is currently 200x, on an Nvidia A100 and with at least 2,000,000 observations.
 
-[This Colab notebook](https://colab.research.google.com/github/Gattocrucco/bartz/blob/main/docs/examples/basic_simdata.ipynb) runs bartz with n = 100,000 observations, p = 1000 predictors, 10,000 trees, for 1000 MCMC iterations, in 5 minutes.
+[This Colab notebook](https://colab.research.google.com/github/bartz-org/bartz/blob/main/docs/examples/basic_simdata.ipynb) runs bartz with n = 100,000 observations, p = 1000 predictors, 10,000 trees, for 1000 MCMC iterations, in 10 minutes.
+
+BART is a very flexible method with many variants. This implementation provides only a small subset of the possible features. If you need a feature from [another BART implementation](https://bartz-org.github.io/bartz/docs-dev/pkglist.html) or from the BART literature, please [open an issue on github](https://github.com/bartz-org/bartz/issues).
 
 ## Links
 
-- [Documentation (latest release)](https://gattocrucco.github.io/bartz/docs)
-- [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)
+- [Documentation (latest release)](https://bartz-org.github.io/bartz/docs)
+- [Documentation (development version)](https://bartz-org.github.io/bartz/docs-dev)
+- [Repository](https://github.com/bartz-org/bartz)
+- [Code coverage](https://bartz-org.github.io/bartz/coverage)
+- [Benchmarks](https://bartz-org.github.io/bartz/benchmarks)
+- [List of BART packages](https://bartz-org.github.io/bartz/docs-dev/pkglist.html)
 
 ## Citing bartz
 

{bartz-0.6.0 → bartz-0.8.0}/README.md

@@ -13,16 +13,18 @@ This Python module provides an implementation of BART that runs on GPU, to proce
 
 On CPU, bartz runs at the speed of dbarts (the fastest implementation I know of) if n > 20,000, but using 1/20 of the memory. On GPU, the speed premium depends on sample size; it is convenient over CPU only for n > 10,000. The maximum speedup is currently 200x, on an Nvidia A100 and with at least 2,000,000 observations.
 
-[This Colab notebook](https://colab.research.google.com/github/Gattocrucco/bartz/blob/main/docs/examples/basic_simdata.ipynb) runs bartz with n = 100,000 observations, p = 1000 predictors, 10,000 trees, for 1000 MCMC iterations, in 5 minutes.
+[This Colab notebook](https://colab.research.google.com/github/bartz-org/bartz/blob/main/docs/examples/basic_simdata.ipynb) runs bartz with n = 100,000 observations, p = 1000 predictors, 10,000 trees, for 1000 MCMC iterations, in 10 minutes.
+
+BART is a very flexible method with many variants. This implementation provides only a small subset of the possible features. If you need a feature from [another BART implementation](https://bartz-org.github.io/bartz/docs-dev/pkglist.html) or from the BART literature, please [open an issue on github](https://github.com/bartz-org/bartz/issues).
 
 ## Links
 
-- [Documentation (latest release)](https://gattocrucco.github.io/bartz/docs)
-- [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)
+- [Documentation (latest release)](https://bartz-org.github.io/bartz/docs)
+- [Documentation (development version)](https://bartz-org.github.io/bartz/docs-dev)
+- [Repository](https://github.com/bartz-org/bartz)
+- [Code coverage](https://bartz-org.github.io/bartz/coverage)
+- [Benchmarks](https://bartz-org.github.io/bartz/benchmarks)
+- [List of BART packages](https://bartz-org.github.io/bartz/docs-dev/pkglist.html)
 
 ## Citing bartz
 

bartz-0.8.0/pyproject.toml

@@ -0,0 +1,250 @@
+# bartz/pyproject.toml
+#
+# Copyright (c) 2024-2026, The Bartz Contributors
+#
+# This file is part of bartz.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+[build-system]
+requires = ["uv_build>=0.9.5,<0.10.0"]
+build-backend = "uv_build"
+
+[project]
+name = "bartz"
+version = "0.8.0"
+description = "Super-fast BART (Bayesian Additive Regression Trees) in Python"
+authors = [{ name = "Giacomo Petrillo", email = "info@giacomopetrillo.com" }]
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "equinox>=0.12.2",
+    "jax>=0.5.3",
+    "jaxtyping>=0.3.2",
+    "numpy>=1.25.2",
+    "scipy>=1.11.4",
+]
+
+[project.optional-dependencies]
+cuda12 = ["jax[cuda12]"]
+cuda13 = ["jax[cuda13]"]
+
+[project.urls]
+Homepage = "https://github.com/bartz-org/bartz"
+Documentation = "https://bartz-org.github.io/bartz/docs-dev"
+Issues = "https://github.com/bartz-org/bartz/issues"
+
+[dependency-groups]
+dev = [
+    "appnope>=0.1.4",
+    "ipython>=8.36.0",
+    "matplotlib>=3.10.3",
+    "matplotlib-label-lines>=0.8.1",
+    "pre-commit>=4.2.0",
+    "rich>=13.9.4",
+    "snakeviz>=2.2.2",
+    "tqdm>=4.67.1",
+    "virtualenv>=20.31.2",
+    "asv>=0.6.4",
+    "beartype>=0.20.2",
+    "flaky>=3.8.1",
+    "gitpython>=3.1.43",
+    "packaging>=25.0",
+    "polars[pandas,pyarrow]>=1.29.0",
+    "pytest>=8.3.5",
+    "pytest-cov>=6.1.1",
+    "pytest-subtests>=0.14.1",
+    "pytest-timeout>=2.4.0",
+    "pytest-xdist>=3.6.1",
+    "rpy2>=3.5.17",
+    "sphinx>=8.1.3",
+    "sphinx-autodoc-typehints>=3.0.1",
+    "tomli>=2.2.1",
+    "myst-nb>=1.2.0",
+    "jupyterlab>=4.4.2",
+]
+
+[tool.pytest.ini_options]
+cache_dir = "config/pytest_cache"
+testpaths = ["tests"]
+addopts = [
+    "-r xXfE",
+    "--pdbcls=IPython.terminal.debugger:TerminalPdb",
+    "--durations=3",
+    "--verbose",
+    "--import-mode=importlib",
+]
+filterwarnings = [
+    "ignore:unclosed database:ResourceWarning",
+]
+timeout = 512
+timeout_method = "thread" # when jax hangs, signals do not work
+
+[tool.coverage.run]
+branch = true
+source_pkgs = ["bartz", "tests"]
+
+[tool.coverage.report]
+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
+# generating the coverage report
+
+github = [
+    '/home/runner/work/bartz/bartz/src/bartz/',
+    '/Users/runner/work/bartz/bartz/src/bartz/',
+    'D:\a\bartz\bartz\src\bartz\',
+    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/bartz/',
+    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/bartz/',
+    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/bartz/',
+    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\bartz\',
+]
+
+local = [
+    'src/bartz/',
+    '/home/runner/work/bartz/bartz/src/bartz/',
+    '/Users/runner/work/bartz/bartz/src/bartz/',
+    'D:\a\bartz\bartz\src\bartz\',
+    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/bartz/',
+    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/bartz/',
+    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/bartz/',
+    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\bartz\',
+]
+
+[tool.ruff]
+exclude = [".asv", "*.ipynb", "benchmarks/latest_bartz"]
+cache-dir = "config/ruff_cache"
+
+[tool.ruff.format]
+quote-style = "single"
+skip-magic-trailing-comma = true
+
+[tool.ruff.lint.isort]
+split-on-trailing-comma = false
+
+[tool.ruff.lint]
+select = [
+    "ERA",  # eradicate
+    "S",    # flake8-bandit
+    "BLE",  # flake8-blind-except
+    "B",    # bugbear
+    "A",    # flake8-builtins
+    "C4",   # flake8-comprehensions
+    "CPY",  # flake8-copyright
+    "DTZ",  # flake8-datetimez
+    "T10",  # flake8-debugger
+    "EM",   # flake8-errmsg
+    "EXE",  # flake8-executable
+    "FIX",  # flake8-fixme
+    "ISC",  # flake8-implicit-str-concat
+    "INP",  # flake8-no-pep420
+    "PIE",  # flake8-pie
+    "T20",  # flake8-print
+    "PT",   # flake8-pytest-style
+    "RSE",  # flake8-raise
+    "RET",  # flake8-return
+    "SLF",  # flake8-self
+    "SIM",  # flake8-simplify
+    "TID",  # flake8-tidy-imports
+    "ARG",  # flake8-unused-arguments
+    "PTH",  # flake8-use-pathlib
+    "FLY",  # flynt
+    "I",    # isort
+    "C90",  # mccabe
+    "NPY",  # NumPy-specific rules
+    "PERF", # Perflint
+    "W",    # pycodestyle Warning
+    "F",    # pyflakes
+    "D",    # pydocstyle
+    "PGH",  # pygrep-hooks
+    "PLC",  # Pylint Convention
+    "PLE",  # Pylint Error
+    "PLR",  # Pylint Refactor
+    "PLW",  # Pyling Warning
+    "UP",   # pyupgrade
+    "FURB", # refurb
+    "RUF",  # Ruff-specific rules
+    "TRY",  # tryceratops
+]
+ignore = [
+    "B028",    # warn with stacklevel = 2
+    "C408",    # Unnecessary `dict()` call (rewrite as a literal), it's too convenient for kwargs
+    "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.
+    "PIE790",  # Unnecessary ... or pass. Ignored because sometimes I use ... as sentinel to tell the rest of ruff and pyright that an implementation is a stub.
+    "PLR0912", # Too many branches; ignore bc C901 already handles this
+    "PLR0913", # Too many arguments in function definition. Maybe I should do something about this?
+    "PLR2004", # Magic value used in comparison, consider replacing `*` with a constant variable
+    "RET505",  # Unnecessary `{branch}` after `return` statement. I ignore this because I like to keep branches for readability.
+    "RET506",  # Unnecessary `else` after `raise` statement. I ignore this because I like to keep branches for readability.
+    "S101",    # Use of `assert` detected. Too annoying.
+    "SIM108",  # SIM108 Use ternary operator `*` instead of `if`-`else`-block, I find blocks more readable
+    "UP037",   # Remove quotes from type annotation. Ignore because jaxtyping.
+]
+
+[tool.ruff.lint.per-file-ignores]
+"{config/*,docs/*}" = [
+    "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
+    "INP001", # File * is part of an implicit namespace package. Add an `__init__.py`.
+]
+"src/bartz/_version.py" = [
+    "CPY001", # Missing copyright notice at top of file
+]
+"{config/*,docs/*,tests/*,benchmarks/_vendor_latest_bartz.py,scripts/*}" = [
+    "T201", # `print` found
+]
+"{tests/*,benchmarks/*}" = [
+    "SLF001", # Private member accessed: `*`
+    "TID253", # `{module}` is banned at the module level
+]
+"docs/conf.py" = [
+    "S607", # Starting a process with a partial executable path. Ignored because for a build script it makes more sense to use PATH.
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.flake8-copyright]
+min-file-size = 1
+
+[tool.ruff.lint.flake8-tidy-imports]
+banned-module-level-imports = ["bartz.debug"]
+ban-relative-imports = "all"
+
+[tool.pydoclint]
+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
+# do not check class attributes because in dataclasses I document them as
+# init parameters because they are duplicated in the html docs otherwise.

bartz-0.8.0/src/bartz/BART/__init__.py

@@ -0,0 +1,27 @@
+# bartz/src/bartz/BART/__init__.py
+#
+# Copyright (c) 2026, The Bartz Contributors
+#
+# This file is part of bartz.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+"""Implement classes `mc_gbart` and `gbart` that mimic the R BART3 package."""
+
+from bartz.BART._gbart import gbart, mc_gbart  # noqa: F401