[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.0
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

setup.py

@@ -5,13 +5,14 @@
 Learn more under: https://pyscaffold.org/
 """
 
-from setuptools import setup, Extension
-from setuptools.command.build_ext import build_ext as build_ext_orig
-import pathlib
 import os
+import pathlib
 import shutil
 import sys
+
 import pybind11
+from setuptools import Extension, setup
+from setuptools.command.build_ext import build_ext as build_ext_orig
 
 
 ###  Adapted from dolomite_base: https://github.com/ArtifactDB/dolomite-base/blob/master/setup.py
@@ -72,7 +73,7 @@ def build_cmake(self, ext):
             ext_modules=[CMakeExtension("rds2py")],
             cmdclass={"build_ext": build_ext},
         )
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/rds2py/PyRdaReader.py

@@ -5,7 +5,7 @@
 by higher-level functions.
 """
 
-from typing import Any, Dict
+from typing import Any
 
 from .lib_rds_parser import RdaObject, RdsReader
 from .PyRdsReader import PyRdsParser
@@ -18,8 +18,6 @@
 class PyRdaParserError(Exception):
     """Exception raised for errors during RData parsing."""
 
-    pass
-
 
 class PyRdaParser:
     """Parser for reading RData files.
@@ -43,7 +41,7 @@ def __init__(self, file_path: str):
         try:
             self.rda_object = RdaObject(file_path)
         except Exception as e:
-            raise PyRdaParserError(f"Error initializing 'PyRdaParser': {str(e)}")
+            raise PyRdaParserError(f"Error initializing 'PyRdaParser': {e!s}")
 
     def get_object_names(self):
         """Get the names of all objects stored in the RData file.
@@ -61,7 +59,7 @@ def get_object_count(self) -> int:
         """
         return self.rda_object.get_object_count()
 
-    def parse(self) -> Dict[str, Dict[str, Any]]:
+    def parse(self) -> dict[str, dict[str, Any]]:
         """Parse all objects in the RData file.
 
         Returns:
@@ -81,9 +79,9 @@ def parse(self) -> Dict[str, Dict[str, Any]]:
 
             return result
         except Exception as e:
-            raise PyRdaParserError(f"Error parsing RData file: {str(e)}")
+            raise PyRdaParserError(f"Error parsing RData file: {e!s}")
 
-    def parse_object(self, name: str) -> Dict[str, Any]:
+    def parse_object(self, name: str) -> dict[str, Any]:
         """Parse a single named object from the RData file.
 
         Args:
@@ -98,7 +96,7 @@ def parse_object(self, name: str) -> Dict[str, Any]:
             reader = self.rda_object.get_object_by_name(name)
             return helper._process_object(reader)
         except Exception as e:
-            raise PyRdaParserError(f"Error parsing object '{name}': {str(e)}")
+            raise PyRdaParserError(f"Error parsing object '{name}': {e!s}")
 
 
 class _RdsProcessorHelper(PyRdsParser):
@@ -107,5 +105,5 @@ class _RdsProcessorHelper(PyRdsParser):
     def __init__(self):
         self.R_MIN = -2147483648
 
-    def _process_object(self, obj: RdsReader) -> Dict[str, Any]:
+    def _process_object(self, obj: RdsReader) -> dict[str, Any]:
         return super()._process_object(obj)

src/rds2py/PyRdsReader.py

@@ -4,7 +4,7 @@
 dictionary representation that can be further processed by higher-level functions.
 """
 
-from typing import Any, Dict, List, Union
+from typing import Any
 from warnings import warn
 
 import numpy as np
@@ -15,8 +15,6 @@
 class PyRdsParserError(Exception):
     """Exception raised for errors during RDS parsing."""
 
-    pass
-
 
 class PyRdsParser:
     """Parser for reading RDS files.
@@ -55,9 +53,9 @@ def __init__(self, file_path: str):
 
             self.root_object = robject
         except Exception as e:
-            raise PyRdsParserError(f"Error initializing 'PyRdsParser': {str(e)}")
+            raise PyRdsParserError(f"Error initializing 'PyRdsParser': {e!s}")
 
-    def parse(self) -> Dict[str, Any]:
+    def parse(self) -> dict[str, Any]:
         """Parse the entire RDS file into a dictionary structure.
 
         Returns:
@@ -74,12 +72,12 @@ def parse(self) -> Dict[str, Any]:
         try:
             return self._process_object(self.root_object)
         except Exception as e:
-            raise PyRdsParserError(f"Error parsing RDS object: {str(e)}")
+            raise PyRdsParserError(f"Error parsing RDS object: {e!s}")
 
-    def _process_object(self, obj: RdsReader) -> Dict[str, Any]:
+    def _process_object(self, obj: RdsReader) -> dict[str, Any]:
         try:
             rtype = obj.get_rtype()
-            result: Dict[str, Any] = {"type": rtype}
+            result: dict[str, Any] = {"type": rtype}
 
             if rtype == "S4":
                 result["package_name"] = obj.get_package_name()
@@ -116,9 +114,9 @@ def _process_object(self, obj: RdsReader) -> Dict[str, Any]:
 
             return result
         except Exception as e:
-            raise PyRdsParserError(f"Error processing object: {str(e)}")
+            raise PyRdsParserError(f"Error processing object: {e!s}")
 
-    def _handle_r_special_cases(self, data: np.ndarray, rtype: str, size: int) -> Union[np.ndarray, range]:
+    def _handle_r_special_cases(self, data: np.ndarray, rtype: str, size: int) -> np.ndarray | range:
         """Handle special R data representations."""
         try:
             # Special handling for R integer containing NA
@@ -137,7 +135,7 @@ def _handle_r_special_cases(self, data: np.ndarray, rtype: str, size: int) -> Un
 
             return data
         except Exception as e:
-            raise PyRdsParserError(f"Error handling R special cases: {str(e)}")
+            raise PyRdsParserError(f"Error handling R special cases: {e!s}")
 
     def _get_numeric_data(self, obj: RdsReader, rtype: str) -> np.ndarray:
         try:
@@ -155,12 +153,12 @@ def _get_numeric_data(self, obj: RdsReader, rtype: str) -> np.ndarray:
 
             return data
         except Exception as e:
-            raise PyRdsParserError(f"Error getting numeric data: {str(e)}")
+            raise PyRdsParserError(f"Error getting numeric data: {e!s}")
 
-    def _process_vector(self, obj: RdsReader) -> List[Dict[str, Any]]:
+    def _process_vector(self, obj: RdsReader) -> list[dict[str, Any]]:
         return [self._process_object(obj.load_vec_element(i)) for i in range(obj.get_rsize())]
 
-    def _process_attributes(self, obj: RdsReader) -> Dict[str, Dict[str, Any]]:
+    def _process_attributes(self, obj: RdsReader) -> dict[str, dict[str, Any]]:
         try:
             attributes = {}
             for name in obj.get_attribute_names():
@@ -169,10 +167,10 @@ def _process_attributes(self, obj: RdsReader) -> Dict[str, Dict[str, Any]]:
 
             return attributes
         except Exception as e:
-            raise PyRdsParserError(f"Error processing attributes: {str(e)}")
+            raise PyRdsParserError(f"Error processing attributes: {e!s}")
 
-    def get_dimensions(self) -> Union[tuple, None]:
+    def get_dimensions(self) -> tuple | None:
         try:
             return self.root_object.get_dimensions()
         except Exception as e:
-            raise PyRdsParserError(f"Error getting dimensions: {str(e)}")
+            raise PyRdsParserError(f"Error getting dimensions: {e!s}")

src/rds2py/__init__.py

@@ -16,5 +16,5 @@
     del version, PackageNotFoundError
 
 
-from .generics import read_rds, read_rda, save_rds, register_parser
-from .rdsutils import parse_rds, parse_rda, write_rds, write_rda
+from .generics import read_rda, read_rds, register_parser, save_rds
+from .rdsutils import parse_rda, parse_rds, write_rda, write_rds

src/rds2py/generics.py

@@ -17,7 +17,7 @@
 
 from functools import singledispatch
 from importlib import import_module
-from typing import Any, List, Optional
+from typing import Any
 from warnings import warn
 
 from .rdsutils import get_class, parse_rda, parse_rds
@@ -92,7 +92,7 @@ def read_rds(path: str, **kwargs):
     return _dispatcher(_robj, **kwargs)
 
 
-def read_rda(path: str, objects: Optional[List[str]] = None, **kwargs) -> dict:
+def read_rda(path: str, objects: list[str] | None = None, **kwargs) -> dict:
     """Read an RData file and convert each object to an appropriate Python type.
 
     This function parses all (or selected) objects and dispatches each one
@@ -153,7 +153,7 @@ def _dispatcher(robject: dict, **kwargs):
             return command(robject, **kwargs)
         except Exception as e:
             warn(
-                f"Failed to coerce RDS object to class: '{_class_name}', returning the dictionary, {str(e)}",
+                f"Failed to coerce RDS object to class: '{_class_name}', returning the dictionary, {e!s}",
                 RuntimeWarning,
             )
     else:
@@ -182,7 +182,7 @@ def decorator(func):
 
 
 @singledispatch
-def save_rds(x: Any, path: Optional[str] = None):
+def save_rds(x: Any, path: str | None = None):
     """Save a Python object as RDS file.
 
     Args:
@@ -196,7 +196,7 @@ def save_rds(x: Any, path: Optional[str] = None):
 
 
 # Import all modules with save_rds registrations to ensure they are loaded
-from . import (  # noqa: E402
+from . import (
     save_atomic,  # noqa: F401
     save_compressed_list,  # noqa: F401
     save_delayed_matrix,  # noqa: F401

src/rds2py/rdsutils.py

@@ -4,7 +4,7 @@
 information from parsed objects.
 """
 
-from typing import Any, Dict, List, Optional
+from typing import Any
 
 from .lib_rds_parser import write_rda as _write_rda_native
 from .PyRdaReader import PyRdaParser
@@ -32,7 +32,7 @@ def parse_rds(path: str) -> dict:
     return realized
 
 
-def parse_rda(path: str, objects: Optional[List[str]] = None) -> Dict[str, dict]:
+def parse_rda(path: str, objects: list[str] | None = None) -> dict[str, dict]:
     """Parse an RData file into a dictionary of named objects.
 
     Args:
@@ -73,7 +73,7 @@ def write_rds(obj: Any, path: str) -> None:
     save_rds(obj, path)
 
 
-def write_rda(objects: Dict[str, Any], path: str) -> None:
+def write_rda(objects: dict[str, Any], path: str) -> None:
     """Write multiple named Python objects to a gzip-compressed RData file.
 
     Each value is converted using :py:func:`~.write_rds`.

src/rds2py/save_atomic.py

@@ -1,7 +1,5 @@
 """Functions for saving atomic R vector types from Python objects."""
 
-from typing import Optional
-
 import numpy as np
 from biocutils import BooleanList, FloatList, IntegerList, Names, StringList
 
@@ -17,7 +15,7 @@
 @save_rds.register(float)
 @save_rds.register(str)
 @save_rds.register(type(None))
-def _save_rds_primitives(x, path: Optional[str] = None):
+def _save_rds_primitives(x, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     if path is not None:
@@ -27,12 +25,12 @@ def _save_rds_primitives(x, path: Optional[str] = None):
 
 
 @save_rds.register(np.generic)
-def _save_rds_numpy_scalars(x: np.generic, path: Optional[str] = None):
+def _save_rds_numpy_scalars(x: np.generic, path: str | None = None):
     return save_rds(x.item(), path=path)
 
 
 @save_rds.register(BooleanList)
-def _save_rds_booleanlist(x: BooleanList, path: Optional[str] = None):
+def _save_rds_booleanlist(x: BooleanList, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     cleaned = [-2147483648 if val is None else (1 if val else 0) for val in x]
@@ -44,7 +42,7 @@ def _save_rds_booleanlist(x: BooleanList, path: Optional[str] = None):
 
 
 @save_rds.register(IntegerList)
-def _save_rds_integerlist(x: IntegerList, path: Optional[str] = None):
+def _save_rds_integerlist(x: IntegerList, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     cleaned = [-2147483648 if val is None else val for val in x]
@@ -56,7 +54,7 @@ def _save_rds_integerlist(x: IntegerList, path: Optional[str] = None):
 
 
 @save_rds.register(FloatList)
-def _save_rds_floatlist(x: FloatList, path: Optional[str] = None):
+def _save_rds_floatlist(x: FloatList, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     cleaned = [np.nan if val is None else val for val in x]
@@ -68,7 +66,7 @@ def _save_rds_floatlist(x: FloatList, path: Optional[str] = None):
 
 
 @save_rds.register(StringList)
-def _save_rds_stringlist(x: StringList, path: Optional[str] = None):
+def _save_rds_stringlist(x: StringList, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     converted = list(x)
@@ -79,7 +77,7 @@ def _save_rds_stringlist(x: StringList, path: Optional[str] = None):
 
 
 @save_rds.register(Names)
-def _save_rds_names(x: Names, path: Optional[str] = None):
+def _save_rds_names(x: Names, path: str | None = None):
     from .lib_rds_parser import write_rds as _write_rds_native
 
     converted = list(x)

src/rds2py/save_compressed_list.py

@@ -1,7 +1,5 @@
 """Functions and classes for parsing Compressed List data structures."""
 
-from typing import Optional
-
 from biocutils.package_utils import is_package_installed
 
 from .generics import save_rds
@@ -14,7 +12,7 @@
     from compressed_lists import CompressedList, Partitioning
 
     @save_rds.register(CompressedList)
-    def _save_rds_compressedlist(x: CompressedList, path: Optional[str] = None):
+    def _save_rds_compressedlist(x: CompressedList, path: str | None = None):
         from .lib_rds_parser import write_rds as _write_rds_native
 
         def _get(obj, name):
@@ -63,7 +61,7 @@ def _get(obj, name):
         return converted
 
     @save_rds.register(Partitioning)
-    def _save_rds_partitioning(x: Partitioning, path: Optional[str] = None):
+    def _save_rds_partitioning(x: Partitioning, path: str | None = None):
         from .lib_rds_parser import write_rds as _write_rds_native
 
         def _get(obj, name):

src/rds2py/save_delayed_matrix.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from biocutils.package_utils import is_package_installed
 
 from .generics import save_rds
@@ -13,7 +11,7 @@
     from delayedarray import DelayedArray
 
     @save_rds.register(DelayedArray)
-    def _save_rds_delayedarray(x: DelayedArray, path: Optional[str] = None):
+    def _save_rds_delayedarray(x: DelayedArray, path: str | None = None):
         from .lib_rds_parser import write_rds as _write_rds_native
 
         def _get(obj, name):
@@ -41,7 +39,7 @@ def _get(obj, name):
     from hdf5array import Hdf5CompressedSparseMatrixSeed
 
     @save_rds.register(Hdf5CompressedSparseMatrixSeed)
-    def _save_rds_h5sparse_seed(x: Hdf5CompressedSparseMatrixSeed, path: Optional[str] = None):
+    def _save_rds_h5sparse_seed(x: Hdf5CompressedSparseMatrixSeed, path: str | None = None):
         from .lib_rds_parser import write_rds as _write_rds_native
 
         converted = {