[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

@@ -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/pybiocfilecache/cache.py

@@ -1,9 +1,10 @@
 import logging
+from collections.abc import Iterator
 from contextlib import contextmanager
 from datetime import datetime
 from pathlib import Path
 from time import sleep, time
-from typing import Any, Dict, Iterator, List, Literal, Optional, Tuple, Union
+from typing import Any, Literal
 
 from biocframe import BiocFrame
 from sqlalchemy import create_engine, func, text
@@ -39,7 +40,7 @@ class BiocFileCache:
     - Cleanup of expired resources
     """
 
-    def __init__(self, cache_dir: Optional[Union[str, Path]] = None, config: Optional[CacheConfig] = None):
+    def __init__(self, cache_dir: str | Path | None = None, config: CacheConfig | None = None):
         """Initialize cache with optional configuration.
 
         Args:
@@ -106,7 +107,7 @@ def _setup_database(self) -> None:
 
             return SCHEMA_VERSION
 
-    def _get_detached_resource(self, session: Session, obj: Union[Resource, Metadata]) -> Optional[dict]:
+    def _get_detached_resource(self, session: Session, obj: Resource | Metadata) -> dict | None:
         """Get a detached copy of a resource."""
         if obj is None:
             return None
@@ -205,7 +206,7 @@ def cleanup(self) -> int:
     ######>> get resources <<######
     ###############################
 
-    def get(self, rname: str = None, rid: str = None) -> Optional[dict]:
+    def get(self, rname: str = None, rid: str = None) -> dict | None:
         """Get resource by name from cache.
 
         Args:
@@ -244,10 +245,10 @@ def get(self, rname: str = None, rid: str = None) -> Optional[dict]:
     def add(
         self,
         rname: str,
-        fpath: Union[str, Path],
+        fpath: str | Path,
         rtype: Literal["local", "web", "relative"] = "relative",
         action: Literal["copy", "move", "asis"] = "copy",
-        expires: Optional[datetime] = None,
+        expires: datetime | None = None,
         download: bool = True,
         ext: bool = True,
     ) -> dict:
@@ -334,7 +335,7 @@ def add(
                 session.commit()
                 raise Exception("Failed to add resource") from e
 
-    def add_batch(self, resources: List[Dict[str, Any]]) -> BiocFrame:
+    def add_batch(self, resources: list[dict[str, Any]]) -> BiocFrame:
         """Add multiple resources in a single transaction.
 
         Args:
@@ -356,7 +357,7 @@ def add_batch(self, resources: List[Dict[str, Any]]) -> BiocFrame:
     def update(
         self,
         rname: str,
-        fpath: Union[str, Path],
+        fpath: str | Path,
         action: Literal["copy", "move", "asis"] = "copy",
     ) -> dict:
         """Update an existing resource.
@@ -430,7 +431,7 @@ def remove(self, rname: str) -> None:
                     session.rollback()
                     raise Exception(f"Failed to remove resource '{rname}'") from e
 
-    def list_resources(self, rtype: Optional[str] = None, expired: Optional[bool] = None) -> BiocFrame:
+    def list_resources(self, rtype: str | None = None, expired: bool | None = None) -> BiocFrame:
         """List resources in the cache with optional filtering.
 
         Args:
@@ -521,7 +522,7 @@ def validate_resource(self, resource: Resource) -> bool:
     #                 session.merge(resource)
     #         session.commit()
 
-    def verify_cache(self) -> Tuple[int, int]:
+    def verify_cache(self) -> tuple[int, int]:
         """Verify integrity of all cached resources.
 
         Returns:
@@ -559,7 +560,7 @@ def search(self, query: str, field: str = "rname", exact: bool = False) -> BiocF
 
             return BiocFrame(convert_to_columnar([self._get_detached_resource(session, r) for r in resources]))
 
-    def get_stats(self) -> Dict[str, Any]:
+    def get_stats(self) -> dict[str, Any]:
         """Get statistics about the cache."""
         with self.get_session() as session:
             total = session.query(Resource).count()

src/pybiocfilecache/config.py

@@ -1,7 +1,6 @@
 from dataclasses import dataclass
 from datetime import timedelta
 from pathlib import Path
-from typing import Optional
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
@@ -28,6 +27,6 @@ class CacheConfig:
     """
 
     cache_dir: Path
-    cleanup_interval: Optional[timedelta] = None  # timedelta(days=30)
+    cleanup_interval: timedelta | None = None  # timedelta(days=30)
     rname_pattern: str = r"^[a-zA-Z0-9_-]+$"
     hash_algorithm: str = "md5"

src/pybiocfilecache/utils.py

@@ -7,7 +7,7 @@
 import zlib
 from pathlib import Path
 from shutil import copy2, move
-from typing import List, Literal
+from typing import Literal
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
@@ -99,7 +99,7 @@ def download_web_file(url: str, filename: str, download: bool):
     return outpath
 
 
-def convert_to_columnar(list_of_dicts: List[dict]):
+def convert_to_columnar(list_of_dicts: list[dict]):
     if not list_of_dicts:
         return {}