[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -19,7 +19,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.2
+  rev: v0.16.0
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Version 0.0.1 
+## Version 0.0.1
 
-- Initial implementation to access OrgDB objects. 
+- Initial implementation to access OrgDB objects.
 - This also fetches the annotation hub sqlite file and queries for available org sqlite files instead of a static registry used in the txdb package.

docs/requirements.txt

@@ -1,9 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-furo
 sphinx-autodoc-typehints

setup.py

@@ -1,18 +1,18 @@
 """
-    Setup file for orgdb.
-    Use setup.cfg to configure your project.
+Setup file for orgdb.
+Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.6.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.6.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 
 from setuptools import setup
 
 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/orgdb/__init__.py

@@ -19,4 +19,4 @@
 from .orgdbregistry import OrgDbRegistry
 from .record import OrgDbRecord
 
-__all__ = ["OrgDb", "OrgDbRegistry", "OrgDbRecord"]
+__all__ = ["OrgDb", "OrgDbRecord", "OrgDbRegistry"]

src/orgdb/orgdb.py

@@ -1,5 +1,4 @@
 import sqlite3
-from typing import Dict, List, Union
 
 from biocframe import BiocFrame
 from genomicranges import GenomicRanges
@@ -68,7 +67,7 @@ def species(self) -> str:
                     return v
         return "Unknown"
 
-    def _define_tables(self) -> Dict[str, tuple]:
+    def _define_tables(self) -> dict[str, tuple]:
         """Define the mapping between column names and (table, field).
 
         Mirrors .definePossibleTables from R/methods-geneCentricDbs.R
@@ -111,8 +110,7 @@ def _define_tables(self) -> Dict[str, tuple]:
         }
 
         if db_class == "OrgDb":
-            if "ALIAS2PROBE" in mapping:
-                del mapping["ALIAS2PROBE"]
+            mapping.pop("ALIAS2PROBE", None)
 
         if db_class == "ChipDb":
             mapping["PROBEID"] = ("c.probes", "probe_id")
@@ -379,15 +377,15 @@ def _define_tables(self) -> Dict[str, tuple]:
 
         return mapping
 
-    def columns(self) -> List[str]:
+    def columns(self) -> list[str]:
         """List all available columns/keytypes."""
         return list(self._table_map.keys())
 
-    def keytypes(self) -> List[str]:
+    def keytypes(self) -> list[str]:
         """List all available keytypes (same as columns)."""
         return self.columns()
 
-    def keys(self, keytype: str) -> List[str]:
+    def keys(self, keytype: str) -> list[str]:
         """Return keys for the given keytype."""
         if keytype not in self._table_map:
             raise ValueError(f"Invalid keytype: {keytype}. Use columns() to see valid options.")
@@ -404,7 +402,7 @@ def keys(self, keytype: str) -> List[str]:
         except sqlite3.OperationalError:
             return []
 
-    def _expand_cols(self, cols: List[str]) -> List[str]:
+    def _expand_cols(self, cols: list[str]) -> list[str]:
         """Expand columns like GO into GO, EVIDENCE, ONTOLOGY."""
         new_cols = []
         for c in cols:
@@ -419,7 +417,7 @@ def _expand_cols(self, cols: List[str]) -> List[str]:
                     new_cols.append("CHRLOCCHR")
         return list(set(new_cols))  # remove duplicates
 
-    def select(self, keys: Union[List[str], str], columns: Union[List[str], str], keytype: str) -> BiocFrame:
+    def select(self, keys: list[str] | str, columns: list[str] | str, keytype: str) -> BiocFrame:
         """Retrieve data from the database.
 
         Args:
@@ -482,9 +480,7 @@ def select(self, keys: Union[List[str], str], columns: Union[List[str], str], ke
 
         return self._query_as_biocframe(sql, tuple(keys))
 
-    def mapIds(
-        self, keys: Union[List[str], str], column: str, keytype: str, multiVals: str = "first"
-    ) -> Union[dict, list]:
+    def mapIds(self, keys: list[str] | str, column: str, keytype: str, multiVals: str = "first") -> dict | list:
         """Map keys to a specific column. A wrapper around select.
 
         Args:
@@ -543,7 +539,7 @@ def genes(self) -> GenomicRanges:
             return GenomicRanges.empty()
 
         query = """
-        SELECT 
+        SELECT
             g.gene_id,
             c.seqname,
             c.start_location,

src/orgdb/orgdbregistry.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
 
@@ -19,7 +19,7 @@ class OrgDbRegistry:
 
     def __init__(
         self,
-        cache_dir: Optional[Union[str, Path]] = None,
+        cache_dir: str | Path | None = None,
         force: bool = False,
     ) -> None:
         """Initialize the OrgDb 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, OrgDbRecord] = {}
+        self._registry_map: dict[str, OrgDbRecord] = {}
 
         self._initialize_registry(force=force)
 
@@ -108,7 +108,7 @@ def _initialize_registry(self, force: bool = False):
             record = OrgDbRecord.from_config_entry(orgdb_id, entry)
             self._registry_map[orgdb_id] = record
 
-    def list_orgdb(self) -> List[str]:
+    def list_orgdb(self) -> list[str]:
         """List all available OrgDb IDs (e.g., 'org.Hs.eg.db').
 
         Returns:
@@ -205,7 +205,7 @@ def load_db(self, orgdb_id: str, force: bool = False) -> OrgDb:
         path = self.download(orgdb_id, force=force)
         return OrgDb(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)

src/orgdb/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"
@@ -14,16 +13,16 @@ class OrgDbRecord:
     """Container for a single OrgDb entry."""
 
     orgdb_id: str
-    release_date: Optional[date]
+    release_date: date | None
     url: str
 
-    species: Optional[str] = None  # e.g. "Hs" or "Hsapiens"
-    id_type: Optional[str] = None  # e.g. "eg" (Entrez Gene) or "tair"
+    species: str | None = None  # e.g. "Hs" or "Hsapiens"
+    id_type: str | None = None  # e.g. "eg" (Entrez Gene) or "tair"
 
-    bioc_version: Optional[str] = None
+    bioc_version: str | None = None
 
     @classmethod
-    def from_config_entry(cls, orgdb_id: str, entry: dict) -> "OrgDbRecord":
+    def from_config_entry(cls, orgdb_id: str, entry: dict) -> OrgDbRecord:
         """Build a record from a ORGDB_CONFIG entry:
         {
             "release_date": "YYYY-MM-DD",  # optional
@@ -33,7 +32,7 @@ def from_config_entry(cls, orgdb_id: str, entry: dict) -> "OrgDbRecord":
         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:
@@ -59,14 +58,11 @@ def _parse_orgdb_id(orgdb_id: str):
     into (species, id_type).
     """
     name = orgdb_id
-    if name.startswith("org."):
-        name = name[len("org.") :]
+    name = name.removeprefix("org.")
 
-    if name.endswith(".db"):
-        name = name[: -len(".db")]
+    name = name.removesuffix(".db")
 
-    if name.endswith(".sqlite"):
-        name = name[: -len(".sqlite")]
+    name = name.removesuffix(".sqlite")
 
     parts = name.split(".")
 
@@ -79,7 +75,7 @@ def _parse_orgdb_id(orgdb_id: str):
     return species, id_type
 
 
-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:

tests/conftest.py

@@ -7,7 +7,7 @@
     - https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
-import sqlite3 
+import sqlite3
 from orgdb import OrgDb
 import pytest
 
@@ -102,4 +102,4 @@ def mock_orgdb(mock_orgdb_path):
     """Return an open OrgDb instance using the mock database."""
     db = OrgDb(mock_orgdb_path)
     yield db
-    db.close()
+    db.close()

tests/test_orgdb.py

@@ -41,19 +41,19 @@ def test_select_simple(mock_orgdb):
 def test_select_multikey(mock_orgdb):
     res = mock_orgdb.select(keys=["1", "10"], columns=["SYMBOL"], keytype="ENTREZID")
     assert len(res) == 2
-    
+
     symbols = res.get_column("SYMBOL")
     assert "A1BG" in symbols
     assert "NAT2" in symbols
 
 def test_select_go_expansion(mock_orgdb):
     res = mock_orgdb.select(keys="1", columns=["GO"], keytype="ENTREZID")
-    
+
     col_names = list(res.column_names)
     assert "GO" in col_names
     assert "EVIDENCE" in col_names
     assert "ONTOLOGY" in col_names
-    
+
     assert len(res) == 2
     go_ids = res.get_column("GO")
     assert "GO:0000001" in go_ids
@@ -66,12 +66,12 @@ def test_select_many_to_one(mock_orgdb):
 
 def test_mapIds(mock_orgdb):
     keys = ["1", "10", "100"]
-    
+
     res = mock_orgdb.mapIds(keys, column="SYMBOL", keytype="ENTREZID")
     assert isinstance(res, dict)
     assert res["1"] == "A1BG"
     assert res["10"] == "NAT2"
-    
+
     res_list = mock_orgdb.mapIds(["1"], column="GO", keytype="ENTREZID", multiVals="list")
     assert isinstance(res_list["1"], list)
     assert len(res_list["1"]) == 2
@@ -81,12 +81,12 @@ def test_genes_genomicranges(mock_orgdb):
     gr = mock_orgdb.genes()
     assert isinstance(gr, GenomicRanges)
     assert len(gr) == 2
-    
+
     names = list(gr.names)
     idx = names.index("1")
     assert str(gr.seqnames[idx]) == "chr19"
     assert gr.start[idx] == 58346806
     assert gr.end[idx] == 58353492
-    
+
     assert "gene_id" in gr.mcols.column_names
-    assert gr.mcols.get_column("gene_id")[idx] == "1"
+    assert gr.mcols.get_column("gene_id")[idx] == "1"

tests/test_real.py

@@ -21,6 +21,6 @@ def test_real_orgdb_workflow(tmp_path):
              "GO:0048699",
              "GO:0048143"],
         columns="SYMBOL")
-    
+
     assert res.shape == (104, 4)
     orgdb.close()

tests/test_registry.py

@@ -9,7 +9,7 @@ def registry(tmp_path):
 def test_registry_init(registry):
     assert isinstance(registry, OrgDbRegistry)
     assert "org.Hs.eg.db" in registry.list_orgdb()
-    
+
 def test_get_record(registry):
     rec = registry.get_record("org.Hs.eg.db")
     assert rec.orgdb_id == "org.Hs.eg.db"