[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: v0.15.7
   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

@@ -1,10 +1,10 @@
 """
-    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

src/orgdb/orgdb.py

@@ -543,7 +543,7 @@ def genes(self) -> GenomicRanges:
             return GenomicRanges.empty()
 
         query = """
-        SELECT 
+        SELECT
             g.gene_id,
             c.seqname,
             c.start_location,

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"