[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

setup.cfg

@@ -15,7 +15,7 @@ long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
 url = https://github.com/biocpy/txdb
 # Add here related links, for example:
 project_urls =
-    Documentation = https://biocpy.github.io/txdb/ 
+    Documentation = https://biocpy.github.io/txdb/
     Source = https://github.com/biocpy/txdb
 #    Changelog = https://pyscaffold.org/en/latest/changelog.html
 #    Tracker = https://github.com/pyscaffold/pyscaffold/issues

setup.py

@@ -12,7 +12,7 @@
 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/txdb/__init__.py

@@ -19,4 +19,4 @@
 from .txdb import TxDb
 from .txdbregistry import TxDbRegistry
 
-__all__ = ["TxDb", "TxDbRegistry", "TxDbRecord"]
+__all__ = ["TxDb", "TxDbRecord", "TxDbRegistry"]

src/txdb/record.py

@@ -2,7 +2,6 @@
 
 from dataclasses import dataclass
 from datetime import date, datetime
-from typing import Optional
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
@@ -14,18 +13,18 @@ class TxDbRecord:
     """Container for a single TxDb entry."""
 
     txdb_id: str
-    release_date: Optional[date]
+    release_date: date | None
     url: str
 
-    organism: Optional[str] = None  # e.g. "Hsapiens"
-    source: Optional[str] = None  # e.g. "UCSC", "BioMart"
-    build: Optional[str] = None  # e.g. "hg38.knownGene"
+    organism: str | None = None  # e.g. "Hsapiens"
+    source: str | None = None  # e.g. "UCSC", "BioMart"
+    build: str | None = None  # e.g. "hg38.knownGene"
 
     # Parsed from URL path (e.g. .../3.22/TxDb...)
-    bioc_version: Optional[str] = None
+    bioc_version: str | None = None
 
     @classmethod
-    def from_config_entry(cls, txdb_id: str, entry: dict) -> "TxDbRecord":
+    def from_config_entry(cls, txdb_id: str, entry: dict) -> TxDbRecord:
         """Build a record from a TXDB_CONFIG entry:
         {
             "release_date": "YYYY-MM-DD",  # optional
@@ -35,7 +34,7 @@ def from_config_entry(cls, txdb_id: str, entry: dict) -> "TxDbRecord":
         url = entry["url"]
 
         date_str = entry.get("release_date")
-        rel_date: Optional[date]
+        rel_date: date | None
         if date_str:
             rel_date = datetime.strptime(date_str, "%Y-%m-%d").date()
         else:
@@ -62,10 +61,8 @@ def _parse_txdb_id(txdb_id: str):
     into (organism, source, build).
     """
     name = txdb_id
-    if name.startswith("TxDb."):
-        name = name[len("TxDb.") :]
-    if name.endswith(".sqlite"):
-        name = name[: -len(".sqlite")]
+    name = name.removeprefix("TxDb.")
+    name = name.removesuffix(".sqlite")
 
     parts = name.split(".")
     if len(parts) < 2:
@@ -77,7 +74,7 @@ def _parse_txdb_id(txdb_id: str):
     return organism, source, build
 
 
-def _parse_bioc_version(url: str) -> Optional[str]:
+def _parse_bioc_version(url: str) -> str | None:
     """Extract the Bioconductor/AnnotationHub-like version from URL.
 
     Example:

src/txdb/txdb.py

@@ -1,5 +1,4 @@
 import sqlite3
-from typing import List, Optional
 
 from biocframe import BiocFrame
 from genomicranges import GenomicRanges, SeqInfo
@@ -95,8 +94,8 @@ def _fetch_as_gr(
         self,
         table: str,
         prefix: str,
-        columns: Optional[List[str]] = None,
-        filter: Optional[dict] = None,
+        columns: list[str] | None = None,
+        filter: dict | None = None,
     ) -> GenomicRanges:
         """Internal helper to fetch a table and convert to GenomicRanges.
 
@@ -165,7 +164,7 @@ def _fetch_as_gr(
             seqinfo=self.seqinfo,
         )
 
-    def transcripts(self, filter: Optional[dict] = None) -> GenomicRanges:
+    def transcripts(self, filter: dict | None = None) -> GenomicRanges:
         """Retrieve transcripts as a GenomicRanges object.
 
         Args:
@@ -177,7 +176,7 @@ def transcripts(self, filter: Optional[dict] = None) -> GenomicRanges:
         """
         return self._fetch_as_gr("transcript", "tx", filter=filter)
 
-    def exons(self, filter: Optional[dict] = None) -> GenomicRanges:
+    def exons(self, filter: dict | None = None) -> GenomicRanges:
         """Retrieve exons as a GenomicRanges object.
 
         Args:
@@ -189,7 +188,7 @@ def exons(self, filter: Optional[dict] = None) -> GenomicRanges:
         """
         return self._fetch_as_gr("exon", "exon", filter=filter)
 
-    def cds(self, filter: Optional[dict] = None) -> GenomicRanges:
+    def cds(self, filter: dict | None = None) -> GenomicRanges:
         """Retrieve coding sequences (CDS) as a GenomicRanges object.
 
         Args:

src/txdb/txdbregistry.py

@@ -1,7 +1,7 @@
 import os
 import sqlite3
 from pathlib import Path
-from typing import Any, Dict, Optional, Union
+from typing import Any
 
 from pybiocfilecache import BiocFileCache
 
@@ -19,7 +19,7 @@ class TxDbRegistry:
 
     def __init__(
         self,
-        cache_dir: Optional[Union[str, Path]] = None,
+        cache_dir: str | Path | None = None,
         force: bool = False,
     ) -> None:
         """Initialize the TxDB registry.
@@ -39,7 +39,7 @@ def __init__(
         self._cache_dir.mkdir(parents=True, exist_ok=True)
         self._bfc = BiocFileCache(self._cache_dir)
 
-        self._registry_map: Dict[str, TxDbRecord] = {}
+        self._registry_map: dict[str, TxDbRecord] = {}
 
         self._initialize_registry(force=force)
 
@@ -195,7 +195,7 @@ def load_db(self, txdb_id: str, force: bool = False) -> TxDb:
         path = self.download(txdb_id, force=force)
         return TxDb(path)
 
-    def _get_filepath(self, resource: Any) -> Optional[str]:
+    def _get_filepath(self, resource: Any) -> str | None:
         """Helper to extract absolute path from a BiocFileCache resource."""
         if hasattr(resource, "rpath"):
             rel_path = str(resource.rpath)