rbartpackages 0.1.0__tar.gz

rbartpackages-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024-2026 The rbartpackages Contributors
+
+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.

rbartpackages-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rbartpackages
+Version: 0.1.0
+Summary: Python wrappers of R BART packages via rpy2
+Author: Giacomo Petrillo
+Author-email: Giacomo Petrillo <info@giacomopetrillo.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Dist: rpy2>=3.6.0
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: jaxtyping>=0.3.2
+Requires-Dist: jax>=0.6.1 ; extra == 'jax'
+Requires-Dist: pandas>=2.2.3 ; extra == 'pandas'
+Requires-Dist: polars>=1.30.0 ; extra == 'polars'
+Requires-Dist: pandas>=2.2.3 ; extra == 'polars'
+Requires-Python: >=3.10
+Project-URL: Homepage, https://github.com/bartz-org/rbartpackages
+Project-URL: Documentation, https://bartz-org.github.io/rbartpackages/docs-dev
+Project-URL: Issues, https://github.com/bartz-org/rbartpackages/issues
+Provides-Extra: jax
+Provides-Extra: pandas
+Provides-Extra: polars
+Description-Content-Type: text/markdown
+
+# rbartpackages
+
+Python wrappers of R BART (Bayesian Additive Regression Trees) packages, built on [rpy2](https://rpy2.github.io).
+
+`rbartpackages` lets you call several R BART implementations from Python with a uniform, lightly-typed interface: arguments are converted to R, the fitted R object's components become Python attributes, and the original R documentation is attached to each wrapper class. It currently wraps:
+
+- [`BART`](https://cran.r-project.org/package=BART)
+- [`BART3`](https://github.com/rsparapa/bnptools) (the development superset of `BART`)
+- [`bartMachine`](https://cran.r-project.org/package=bartMachine)
+- [`dbarts`](https://cran.r-project.org/package=dbarts)
+
+## Installation
+
+```sh
+pip install rbartpackages
+```
+
+You also need R with the package(s) you want to use installed (`BART`, `dbarts`, `bartMachine` from CRAN; `BART3` from `rsparapa/bnptools` on GitHub). `bartMachine` additionally requires Java. Optional extras `pandas`, `polars`, and `jax` enable passing those array/frame types directly. See the documentation for details.
+
+## Usage
+
+```python
+import numpy as np
+from rbartpackages import BART3
+
+x_train = np.random.randn(100, 5)
+y_train = x_train[:, 0] + 0.1 * np.random.randn(100)
+
+bart = BART3.gbart(x_train=x_train, y_train=y_train, ndpost=200)
+y_pred = bart.predict(x_train)  # shape (ndpost, n)
+```
+
+R argument names with dots are passed with underscores (`x.train` → `x_train`).
+
+## Links
+
+- [Documentation](https://bartz-org.github.io/rbartpackages/docs-dev)
+- [Repository](https://github.com/bartz-org/rbartpackages)
+- [List of BART packages](https://bartz-org.github.io/bartz/docs-dev/pkglist.html) (maintained in the bartz docs)
+
+These wrappers originated in the [bartz](https://github.com/bartz-org/bartz) project, where they are used to validate against reference R implementations.

rbartpackages-0.1.0/README.md

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+# rbartpackages
+
+Python wrappers of R BART (Bayesian Additive Regression Trees) packages, built on [rpy2](https://rpy2.github.io).
+
+`rbartpackages` lets you call several R BART implementations from Python with a uniform, lightly-typed interface: arguments are converted to R, the fitted R object's components become Python attributes, and the original R documentation is attached to each wrapper class. It currently wraps:
+
+- [`BART`](https://cran.r-project.org/package=BART)
+- [`BART3`](https://github.com/rsparapa/bnptools) (the development superset of `BART`)
+- [`bartMachine`](https://cran.r-project.org/package=bartMachine)
+- [`dbarts`](https://cran.r-project.org/package=dbarts)
+
+## Installation
+
+```sh
+pip install rbartpackages
+```
+
+You also need R with the package(s) you want to use installed (`BART`, `dbarts`, `bartMachine` from CRAN; `BART3` from `rsparapa/bnptools` on GitHub). `bartMachine` additionally requires Java. Optional extras `pandas`, `polars`, and `jax` enable passing those array/frame types directly. See the documentation for details.
+
+## Usage
+
+```python
+import numpy as np
+from rbartpackages import BART3
+
+x_train = np.random.randn(100, 5)
+y_train = x_train[:, 0] + 0.1 * np.random.randn(100)
+
+bart = BART3.gbart(x_train=x_train, y_train=y_train, ndpost=200)
+y_pred = bart.predict(x_train)  # shape (ndpost, n)
+```
+
+R argument names with dots are passed with underscores (`x.train` → `x_train`).
+
+## Links
+
+- [Documentation](https://bartz-org.github.io/rbartpackages/docs-dev)
+- [Repository](https://github.com/bartz-org/rbartpackages)
+- [List of BART packages](https://bartz-org.github.io/bartz/docs-dev/pkglist.html) (maintained in the bartz docs)
+
+These wrappers originated in the [bartz](https://github.com/bartz-org/bartz) project, where they are used to validate against reference R implementations.

rbartpackages-0.1.0/pyproject.toml

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+# rbartpackages/pyproject.toml
+#
+# Copyright (c) 2024-2026, The rbartpackages Contributors
+#
+# This file is part of rbartpackages.
+#
+# 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 = "rbartpackages"
+version = "0.1.0"
+description = "Python wrappers of R BART packages via rpy2"
+authors = [{ name = "Giacomo Petrillo", email = "info@giacomopetrillo.com" }]
+license = "MIT"
+license-files = ["LICENSE"]
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "rpy2>=3.6.0",
+    "numpy>=2.2.6",
+    "jaxtyping>=0.3.2",
+]
+
+[project.optional-dependencies]
+# Each extra backs a soft-imported converter in `rbartpackages._base`.
+jax = ["jax>=0.6.1"]
+pandas = ["pandas>=2.2.3"]
+polars = ["polars>=1.30.0", "pandas>=2.2.3"]
+
+[project.urls]
+Homepage = "https://github.com/bartz-org/rbartpackages"
+Documentation = "https://bartz-org.github.io/rbartpackages/docs-dev"
+Issues = "https://github.com/bartz-org/rbartpackages/issues"
+
+[dependency-groups]
+dev = [
+    "ipython>=8.37.0",
+    "pre-commit>=4.2.0",
+    "rich>=14.0.0",
+    "virtualenv>=20.31.2",
+    "asv>=0.6.4",
+    "gitpython>=3.1.44",
+    "packaging>=25.0",
+    "pytest>=8.4.0",
+    "pytest-cov>=6.1.1",
+    # WORKAROUND(pytest<9): pytest 9 has built-in subtests support
+    "pytest-subtests>=0.14.1",
+    "pytest-timeout>=2.4.0",
+    "pytest-xdist>=3.7.0",
+    "sphinx>=8.1.3",
+    "sphinx-autodoc-typehints>=3.0.1",
+    "tomli>=2.2.1",
+    "myst-nb>=1.2.0",
+    "jupyterlab>=4.4.3",
+    "diff-cover>=9.3.2",
+    # the soft-imported converters, so they are exercised by the test suite
+    "jax>=0.6.1",
+    "polars[pandas,pyarrow]>=1.30.0",
+]
+
+# WORKAROUND(pytest<9): use [tool.pytest]
+[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 = 1024  # about 15 min, ci runners are slow
+timeout_method = "thread"  # signals do not always work with embedded R
+
+[tool.coverage.run]
+branch = true
+source_pkgs = ["rbartpackages", "tests"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = 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/rbartpackages/rbartpackages/src/rbartpackages/',
+    '/Users/runner/work/rbartpackages/rbartpackages/src/rbartpackages/',
+    'D:\a\rbartpackages\rbartpackages\src\rbartpackages\',
+    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/rbartpackages/',
+    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/rbartpackages/',
+    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/rbartpackages/',
+    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\rbartpackages\',
+]
+
+local = [
+    'src/rbartpackages/',
+    '/home/runner/work/rbartpackages/rbartpackages/src/rbartpackages/',
+    '/Users/runner/work/rbartpackages/rbartpackages/src/rbartpackages/',
+    'D:\a\rbartpackages\rbartpackages\src\rbartpackages\',
+    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/rbartpackages/',
+    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/rbartpackages/',
+    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/rbartpackages/',
+    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\rbartpackages\',
+]
+
+[tool.uv]
+exclude-newer = '1 week'
+
+[tool.ruff]
+exclude = [".asv", "*.ipynb"]
+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.flake8-annotations]
+allow-star-arg-any = true
+
+[tool.ruff.lint]
+select = [
+    "ICN",  # flake8-import-conventions
+    "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
+    "ANN",  # flake8-annotations
+]
+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/rbartpackages/_version.py" = [
+    "CPY001", # Missing copyright notice at top of file
+]
+"{config/*,docs/*,tests/*,benchmarks/*}" = [
+    "T201", # `print` found
+]
+"{tests/*,benchmarks/*}" = [
+    "SLF001", # Private member accessed: `*`
+    "TID253", # `{module}` is banned at the module level
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.flake8-copyright]
+min-file-size = 1
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"numpy.testing.assert_allclose".msg = "Use tests.util.assert_allclose (zero default tolerances)."
+"numpy.testing.assert_array_equal".msg = "Use tests.util.assert_array_equal (strict=True default)."
+
+[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
+allow-init-docstring = false
+check-class-attributes = false
+# do not check class attributes because pydoclint only supports them being
+# documented in the class docstring while we document them individually
+
+[tool.pydocstringformatter]
+# numpydoc-only style: this leaves out the pep257 `split-summary-body`
+# formatter, which mis-splits our wrapped attribute docstrings at the first
+# physical line (and then inserts mid-sentence periods via `final-period`).
+style = ["numpydoc"]
+# keep the closing `"""` inline on attribute docstrings, as is our convention.
+closing-quotes = false