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

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

Author: pre-commit-ci[bot]

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/experimenthub/__init__.py

@@ -15,5 +15,5 @@
 finally:
     del version, PackageNotFoundError
 
-from .registry import ExperimentHubRegistry
 from .record import ExperimentHubRecord
+from .registry import ExperimentHubRegistry

src/experimenthub/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"
@@ -15,16 +14,16 @@ class ExperimentHubRecord:
 
     ehub_id: str
     title: str
-    species: Optional[str]
-    taxonomy_id: Optional[str]
-    genome: Optional[str]
-    description: Optional[str]
+    species: str | None
+    taxonomy_id: str | None
+    genome: str | None
+    description: str | None
     url: str
-    release_date: Optional[date]
-    preparer_dataclass: Optional[str]
+    release_date: date | None
+    preparer_dataclass: str | None
 
     @classmethod
-    def from_db_row(cls, row: tuple) -> "ExperimentHubRecord":
+    def from_db_row(cls, row: tuple) -> ExperimentHubRecord:
         """Build a record from a database query row.
 
         Expected row format:
@@ -33,7 +32,7 @@ def from_db_row(cls, row: tuple) -> "ExperimentHubRecord":
         rid, title, species, tax_id, genome, desc, url, date_str, rdataclass = row
         ehub_id = f"EH{rid}"
 
-        rel_date: Optional[date] = None
+        rel_date: date | None = None
         if date_str:
             try:
                 rel_date = datetime.strptime(str(date_str).split(" ")[0], "%Y-%m-%d").date()

src/experimenthub/registry.py

@@ -1,7 +1,7 @@
 import os
 import sqlite3
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
 
 from pybiocfilecache import BiocFileCache
 
@@ -24,7 +24,6 @@ class ExperimentHubRegistry:
         "matrix",
         "numeric",
         "int",
-        "matrix",
         "dataframe",
         "data.frame",
         "data frame",
@@ -42,7 +41,7 @@ class ExperimentHubRegistry:
 
     def __init__(
         self,
-        cache_dir: Optional[Union[str, Path]] = None,
+        cache_dir: str | Path | None = None,
         force: bool = False,
     ) -> None:
         """Initialize the ExperimentHub registry.
@@ -62,7 +61,7 @@ def __init__(
         self._cache_dir.mkdir(parents=True, exist_ok=True)
         self._bfc = BiocFileCache(self._cache_dir)
 
-        self._registry_map: Dict[str, ExperimentHubRecord] = {}
+        self._registry_map: dict[str, ExperimentHubRecord] = {}
 
         self._initialize_registry(force=force)
 
@@ -135,7 +134,7 @@ def _initialize_registry(self, force: bool = False):
             record = ExperimentHubRecord.from_db_row(row)
             self._registry_map[record.ehub_id] = record
 
-    def list_ids(self) -> List[str]:
+    def list_ids(self) -> list[str]:
         """List all available ExperimentHub IDs (e.g., 'EH1', 'EH123')."""
         return sorted(list(self._registry_map.keys()), key=lambda x: int(x[2:]))
 
@@ -146,7 +145,7 @@ def get_record(self, ehub_id: str) -> ExperimentHubRecord:
 
         return self._registry_map[ehub_id]
 
-    def search(self, query: str) -> List[ExperimentHubRecord]:
+    def search(self, query: str) -> list[ExperimentHubRecord]:
         """Search for resources matching the query string."""
         q = query.lower()
         results = []
@@ -220,7 +219,7 @@ def load(self, ehub_id: str, force: bool = False) -> Any:
         except Exception as e:
             raise RuntimeError(f"Failed to load R data from {path}: {e}")
 
-    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)