[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]

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 ensembldb.
-    Use setup.cfg to configure your project.
+Setup file for ensembldb.
+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/ensembldb/__init__.py

@@ -17,4 +17,4 @@
 
 from .record import EnsDbRecord
 from .registry import EnsDbRegistry
-from .ensdb import EnsDb
+from .ensdb import EnsDb

src/ensembldb/ensdb.py

@@ -83,7 +83,7 @@ def genes(self, filter: Optional[Dict[str, Union[str, List[str]]]] = None) -> Ge
         entrez_col = ", g.entrezid" if has_entrez else ""
 
         query = f"""
-        SELECT 
+        SELECT
             g.gene_id, g.gene_name, g.gene_biotype,
             g.seq_name, g.gene_seq_start, g.gene_seq_end, g.seq_strand{entrez_col},
             c.seq_length
@@ -130,7 +130,7 @@ def transcripts(self, filter: Optional[Dict[str, Union[str, List[str]]]] = None)
             A GenomicRanges object containing transcript coordinates and metadata.
         """
         query = """
-        SELECT 
+        SELECT
             t.tx_id, t.tx_biotype, t.gene_id,
             t.tx_seq_start, t.tx_seq_end,
             g.seq_name, g.seq_strand, g.gene_name,

tests/conftest.py

@@ -1,10 +1,10 @@
 """
-    Dummy conftest.py for ensembldb.
+Dummy conftest.py for ensembldb.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest