bartz 0.6.0__tar.gz → 0.7.0__tar.gz

{bartz-0.6.0 → bartz-0.7.0}/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: bartz
-Version: 0.6.0
+Version: 0.7.0
 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

{bartz-0.6.0 → bartz-0.7.0}/pyproject.toml

@@ -28,7 +28,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bartz"
-version = "0.6.0"
+version = "0.7.0"
 description = "Super-fast BART (Bayesian Additive Regression Trees) in Python"
 authors = [
     {name = "Giacomo Petrillo", email = "info@giacomopetrillo.com"},
@@ -38,8 +38,7 @@ readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
     "equinox>=0.12.2",
-    "jax>=0.4.35",
-    "jaxlib>=0.4.35",
+    "jax>=0.5.3",
     "jaxtyping>=0.3.2",
     "numpy>=1.25.2",
     "scipy>=1.11.4",
@@ -68,7 +67,6 @@ 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",
@@ -80,21 +78,16 @@ ci = [
 [tool.pytest.ini_options]
 cache_dir = "config/pytest_cache"
 testpaths = ["tests"]
-filterwarnings = [
-    'error:scatter inputs have incompatible types.*',
-]
 addopts = [
     "-r xXfE",
     "--pdbcls=IPython.terminal.debugger:TerminalPdb",
     "--durations=3",
     "--verbose",
+    "--import-mode=importlib",
 ]
-timeout = 64
+timeout = 256
 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`.
-
 [tool.coverage.run]
 branch = true
 source = ["bartz"]
@@ -137,40 +130,110 @@ 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 = [
-    "B", # bugbear: grab bag of additional stuff
-    "UP", # pyupgrade: fix some outdated idioms
-    "I", # isort: sort and reformat import statements
+    "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
-    "PT", # flake8-pytest-style
+    "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.
-    "F821",  # Undefined name. I ignore this because strings in jaxtyping.
+    "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.
+    "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.
+    "S603",  # `subprocess` call: check for execution of untrusted input. Too many false positives.
+    "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/*,benchmarks/*,docs/*,src/bartz/debug.py,tests/rbartpackages/*,tests/__init__.py}" = [
+"{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/*}" = [
+    "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"
-ignore-decorators = ["functools.cached_property"]
+
+[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]
 baseline = "config/pydoclint-baseline.txt"
-auto-regenerate-baseline = true
+auto-regenerate-baseline = false
+# auto-regenerate = false because in pre-commit pydoclint does not see the
+# unmodified files, thinks those errors are gone, and removes them from the
+# baseline.
 arg-type-hints-in-signature = true
 arg-type-hints-in-docstring = false
 check-return-types = false
@@ -179,6 +242,8 @@ 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 otherwise.
 
 [tool.uv]
 python-downloads = "never"