[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: v0.16.5
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -71,7 +71,9 @@ To create a `SummarizedExperiment`,
 from summarizedexperiment import SummarizedExperiment
 
 tse = SummarizedExperiment(
-    assays={"counts": counts}, row_data=row_data, column_data=col_data,
+    assays={"counts": counts},
+    row_data=row_data,
+    column_data=col_data,
     metadata={"seq_platform": "Illumina NovaSeq 6000"},
 )
 ```
@@ -93,8 +95,10 @@ from summarizedexperiment import RangedSummarizedExperiment
 from genomicranges import GenomicRanges
 
 trse = RangedSummarizedExperiment(
-    assays={"counts": counts}, row_data=row_data,
-    row_ranges=GenomicRanges.from_pandas(row_data.to_pandas()), column_data=col_data
+    assays={"counts": counts},
+    row_data=row_data,
+    row_ranges=GenomicRanges.from_pandas(row_data.to_pandas()),
+    column_data=col_data,
 )
 ```
 

docs/extend_se.md

@@ -10,6 +10,7 @@ As a simple example, let's create a new class called `BioSampleSE` that stores b
 ```python
 from summarizedexperiment import SummarizedExperiment
 
+
 class BioSampleSE(SummarizedExperiment):
     pass
 ```
@@ -25,8 +26,8 @@ from summarizedexperiment import SummarizedExperiment
 import biocframe
 from typing import Dict, Any, List, Optional
 
-class BioSampleSE(SummarizedExperiment):
 
+class BioSampleSE(SummarizedExperiment):
     def __init__(
         self,
         assays: Dict[str, Any] = None,
@@ -35,7 +36,7 @@ class BioSampleSE(SummarizedExperiment):
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
         metadata: Optional[dict] = None,
-        bio_sample_information: Optional[biocframe.BiocFrame] = None, # NEW SLOT
+        bio_sample_information: Optional[biocframe.BiocFrame] = None,  # NEW SLOT
         validate: bool = True,
     ) -> None:
         super().__init__(
@@ -66,7 +67,6 @@ Our class now validates the new slot:
 
 ```python
 class BioSampleSE(SummarizedExperiment):
-
     def __init__(
         self,
         assays: Dict[str, Any] = None,
@@ -75,7 +75,7 @@ class BioSampleSE(SummarizedExperiment):
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
         metadata: Optional[dict] = None,
-        bio_sample_information: Optional[biocframe.BiocFrame] = None, # NEW SLOT
+        bio_sample_information: Optional[biocframe.BiocFrame] = None,  # NEW SLOT
         validate: bool = True,
     ) -> None:
         super().__init__(
@@ -108,6 +108,7 @@ def get_bio_sample_information(self) -> Optional[biocframe.BiocFrame]:
     """
     return self._bio_sample_information
 
+
 def set_bio_sample_information(
     self, bio_sample_information: Optional[biocframe.BiocFrame], in_place: bool = False
 ) -> "BioSampleSE":
@@ -126,7 +127,7 @@ def set_bio_sample_information(
     """
     _validate_bio_sample_information(bio_sample_info)
 
-    output = self._define_output(in_place) # MAKES A SHALLOW COPY
+    output = self._define_output(in_place)  # MAKES A SHALLOW COPY
     output._bio_sample_information = bio_sample_info
     return output
 ```
@@ -139,6 +140,7 @@ def bio_sample_information(self) -> biocframe.BiocFrame:
     """Alias for :py:meth:`~get_bio_sample_info`."""
     return self.get_bio_sample_info()
 
+
 @bio_sample_information.setter
 def bio_sample_information(self, bio_sample_info: biocframe.BiocFrame) -> None:
     """Alias for :py:meth:`~set_bio_sample_info`."""
@@ -147,7 +149,6 @@ def bio_sample_information(self, bio_sample_info: biocframe.BiocFrame) -> None:
         UserWarning,
     )
     return self.set_bio_sample_information(row_ranges=row_ranges, in_place=True)
-
 ```
 
 This allows users to easily access the new property using the **dot** notation on an instance, for example, `obj.bio_sample_info` provides access to the attribute.
@@ -183,6 +184,7 @@ def __deepcopy__(self, memo=None, _nil=[]):
         metadata=_metadata_copy,
     )
 
+
 def __copy__(self):
     """
     Returns:
@@ -199,6 +201,7 @@ def __copy__(self):
         metadata=self._metadata,
     )
 
+
 def copy(self):
     """Alias for :py:meth:`~__copy__`."""
     return self.__copy__()
@@ -241,13 +244,12 @@ def get_slice(
 
 
 ```python
-
 def _validate_bio_sample_information(bio_sample_info):
     if not isinstance(bio_sample_info, biocframe.BiocFrame):
         raise Exception("Biosample information must be a BiocFrame object.")
 
-class BioSampleSE(SummarizedExperiment):
 
+class BioSampleSE(SummarizedExperiment):
     def __init__(
         self,
         assays: Dict[str, Any] = None,
@@ -256,7 +258,7 @@ class BioSampleSE(SummarizedExperiment):
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
         metadata: Optional[dict] = None,
-        bio_sample_information: Optional[biocframe.BiocFrame] = None, # NEW SLOT
+        bio_sample_information: Optional[biocframe.BiocFrame] = None,  # NEW SLOT
         validate: bool = True,
     ) -> None:
         super().__init__(
@@ -320,7 +322,6 @@ class BioSampleSE(SummarizedExperiment):
         """Alias for :py:meth:`~__copy__`."""
         return self.__copy__()
 
-
     def get_bio_sample_information(self) -> Optional[biocframe.BiocFrame]:
         """Get biosample information.
 
@@ -347,11 +348,10 @@ class BioSampleSE(SummarizedExperiment):
         """
         _validate_bio_sample_information(bio_sample_info)
 
-        output = self._define_output(in_place) # MAKES A SHALLOW COPY
+        output = self._define_output(in_place)  # MAKES A SHALLOW COPY
         output._bio_sample_information = bio_sample_info
         return output
 
-
     @property
     def bio_sample_information(self) -> biocframe.BiocFrame:
         """Alias for :py:meth:`~get_bio_sample_info`."""
@@ -365,8 +365,6 @@ class BioSampleSE(SummarizedExperiment):
             UserWarning,
         )
         return self.set_bio_sample_information(row_ranges=row_ranges, in_place=True)
-
-
 ```
 
 That's the minimum required to extend a `SummarizedExperiment` and adapt it to new use cases. Please follow the [developer guide](https://github.com/BiocPy/developer_guide), which provides information on class design, package setup, and documentation to ensure consistency in how BiocPy-related packages are developed.

setup.py

@@ -10,7 +10,7 @@
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/summarizedexperiment/RangedSummarizedExperiment.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Any, Dict, List, Literal, Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Any, Literal, Union
 from warnings import warn
 
 import biocframe
@@ -92,13 +93,13 @@ class RangedSummarizedExperiment(SummarizedExperiment):
 
     def __init__(
         self,
-        assays: Dict[str, Any] = None,
-        row_ranges: Optional[GRangesOrGRangesList] = None,
-        row_data: Optional[biocframe.BiocFrame] = None,
-        column_data: Optional[biocframe.BiocFrame] = None,
-        row_names: Optional[List[str]] = None,
-        column_names: Optional[List[str]] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        assays: dict[str, Any] = None,
+        row_ranges: GRangesOrGRangesList | None = None,
+        row_data: biocframe.BiocFrame | None = None,
+        column_data: biocframe.BiocFrame | None = None,
+        row_names: list[str] | None = None,
+        column_names: list[str] | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         _validate: bool = True,
     ) -> None:
         """Initialize a `RangedSummarizedExperiment` (RSE) object.
@@ -274,7 +275,7 @@ def __str__(self) -> str:
         )
         output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n"
 
-        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}"
+        output += f"metadata({len(self.metadata)!s}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}"
 
         return output
 
@@ -291,7 +292,7 @@ def get_row_ranges(self) -> GRangesOrGRangesList:
         return self._row_ranges
 
     def set_row_ranges(
-        self, row_ranges: Optional[GRangesOrGRangesList], in_place: bool = False
+        self, row_ranges: GRangesOrGRangesList | None, in_place: bool = False
     ) -> RangedSummarizedExperiment:
         """Set new genomic features.
 
@@ -351,7 +352,7 @@ def start(self) -> np.ndarray:
         return self.row_ranges.start
 
     @property
-    def seqnames(self) -> List[str]:
+    def seqnames(self) -> list[str]:
         """Get sequence or chromosome names.
 
         Returns:
@@ -392,21 +393,18 @@ def seq_info(self) -> SeqInfo:
 
     # rest of them are inherited from BaseSE.
 
-    def _normalize_row_slice(self, rows: Union[str, int, bool, Sequence]):
+    def _normalize_row_slice(self, rows: str | int | bool | Sequence):
 
-        if isinstance(rows, (GenomicRanges, CompressedGenomicRangesList)):
-            hits = self.row_ranges.find_overlaps(query=rows)
-            rows = hits.get_column("self_hits")
-        elif hasattr(rows, "find_overlaps"):
+        if isinstance(rows, (GenomicRanges, CompressedGenomicRangesList)) or hasattr(rows, "find_overlaps"):
             hits = self.row_ranges.find_overlaps(query=rows)
             rows = hits.get_column("self_hits")
 
         return super()._normalize_row_slice(rows)
 
     def get_slice(
         self,
-        rows: Optional[Union[str, int, bool, Sequence]],
-        columns: Optional[Union[str, int, bool, Sequence]],
+        rows: str | int | bool | Sequence | None,
+        columns: str | int | bool | Sequence | None,
     ) -> RangedSummarizedExperiment:
         """Alias for :py:attr:`~__getitem__`, for back-compatibility."""
 
@@ -431,7 +429,7 @@ def get_slice(
     ######>> range ops <<#######
     ############################
 
-    def coverage(self, shift: int = 0, width: Optional[int] = None, weight: int = 1) -> Dict[str, np.ndarray]:
+    def coverage(self, shift: int = 0, width: int | None = None, weight: int = 1) -> dict[str, np.ndarray]:
         """Calculate coverage for each chromosome.
 
         Args:
@@ -456,7 +454,7 @@ def nearest(
         query: GRangesOrRangeSE,
         select: Literal["all", "arbitrary"] = "all",
         ignore_strand: bool = False,
-    ) -> Optional[List[Optional[int]]]:
+    ) -> list[int | None] | None:
         """Search nearest positions both upstream and downstream that overlap with each range in ``query``.
 
         Args:
@@ -496,7 +494,7 @@ def precede(
         query: GRangesOrRangeSE,
         select: Literal["all", "arbitrary"] = "all",
         ignore_strand: bool = False,
-    ) -> Optional[List[Optional[int]]]:
+    ) -> list[int | None] | None:
         """Search nearest positions only downstream that overlap with each range in ``query``.
 
         Args:
@@ -536,7 +534,7 @@ def follow(
         query: GRangesOrRangeSE,
         select: Literal["all", "arbitrary"] = "all",
         ignore_strand: bool = False,
-    ) -> Optional[List[Optional[int]]]:
+    ) -> list[int | None] | None:
         """Search nearest positions only upstream that overlap with each range in ``query``.
 
         Args:
@@ -617,7 +615,7 @@ def flank(
 
     def resize(
         self,
-        width: Union[int, List[int], np.ndarray],
+        width: int | list[int] | np.ndarray,
         fix: Literal["start", "end", "center"] = "start",
         ignore_strand: bool = False,
         in_place: bool = False,
@@ -654,7 +652,7 @@ def resize(
         output._row_ranges = new_ranges
         return output
 
-    def shift(self, shift: Union[int, List[int], np.ndarray] = 0, in_place: bool = False) -> RangedSummarizedExperiment:
+    def shift(self, shift: int | list[int] | np.ndarray = 0, in_place: bool = False) -> RangedSummarizedExperiment:
         """Shift all intervals.
 
         ``shift`` may be be negative.
@@ -708,8 +706,8 @@ def promoters(
 
     def restrict(
         self,
-        start: Optional[Union[int, List[int], np.ndarray]] = None,
-        end: Optional[Union[int, List[int], np.ndarray]] = None,
+        start: int | list[int] | np.ndarray | None = None,
+        end: int | list[int] | np.ndarray | None = None,
         keep_all_ranges: bool = False,
         in_place: bool = False,
     ) -> RangedSummarizedExperiment:
@@ -742,9 +740,9 @@ def restrict(
 
     def narrow(
         self,
-        start: Optional[Union[int, List[int], np.ndarray]] = None,
-        width: Optional[Union[int, List[int], np.ndarray]] = None,
-        end: Optional[Union[int, List[int], np.ndarray]] = None,
+        start: int | list[int] | np.ndarray | None = None,
+        width: int | list[int] | np.ndarray | None = None,
+        end: int | list[int] | np.ndarray | None = None,
         in_place: bool = False,
     ) -> RangedSummarizedExperiment:
         """Narrow genomic positions by provided ``start``, ``width`` and ``end`` parameters.

src/summarizedexperiment/SummarizedExperiment.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
 from warnings import warn
 
 import biocframe
@@ -30,12 +30,12 @@ class SummarizedExperiment(BaseSE):
 
     def __init__(
         self,
-        assays: Dict[str, Any] = None,
-        row_data: Optional[biocframe.BiocFrame] = None,
-        column_data: Optional[biocframe.BiocFrame] = None,
-        row_names: Optional[List[str]] = None,
-        column_names: Optional[List[str]] = None,
-        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
+        assays: dict[str, Any] = None,
+        row_data: biocframe.BiocFrame | None = None,
+        column_data: biocframe.BiocFrame | None = None,
+        row_names: list[str] | None = None,
+        column_names: list[str] | None = None,
+        metadata: dict[str, Any] | ut.NamedList | None = None,
         _validate: bool = True,
     ) -> None:
         """Initialize a Summarized Experiment (SE).

src/summarizedexperiment/__init__.py

@@ -15,5 +15,5 @@
 finally:
     del version, PackageNotFoundError
 
-from .SummarizedExperiment import SummarizedExperiment
 from .RangedSummarizedExperiment import RangedSummarizedExperiment
+from .SummarizedExperiment import SummarizedExperiment