more ruff rules

Author: dhimmel

ensembl_genes/ensembl_genes.py

@@ -23,7 +23,7 @@ class Ensembl_Gene_Queries:
     Regex to separate source information from the gene description text.
     https://regex101.com/r/wbW1Qc/1
     """
-    _column_dtypes: dict[str, str] = {
+    _column_dtypes: ClassVar[dict[str, str]] = {
         "alt_allele_is_representative": "bool",
         "primary_assembly": "bool",
     }
@@ -464,7 +464,7 @@ class DatasetExport:
 
 
 class Ensembl_Gene_Catalog_Writer(Ensembl_Gene_Queries):
-    exports: list[DatasetExport] = [
+    exports: ClassVar[list[DatasetExport]] = [
         DatasetExport(
             name="genes",
             query_fxn="gene_df",
@@ -528,7 +528,7 @@ class Ensembl_Gene_Catalog_Writer(Ensembl_Gene_Queries):
             ),
         ),
     ]
-    ipynb_exports = [
+    ipynb_exports: ClassVar[list[str]] = [
         "ensembl_genes_output.ipynb",
         "ensembl_genes_eda.ipynb",
         "ensembl_database_tables.ipynb",

pyproject.toml

@@ -60,7 +60,11 @@ select = [
     "C90",  # mccabe
     "E",  # pycodestyle errors
     "F",  # pyflakes
+    "FURB",  # refurbish and modernize
     "I",  # isort
+    "PT",  # flake8-pytest-style
+    "RUF",  # ruff
+    "SIM",  # simplify
     "UP",  # pyupgrade
     "W",  # pycode warnings
 ]

tests/ensembl_gene_test.py

@@ -8,7 +8,7 @@ def test_ensembl_gene_queries() -> None:
 
 
 @pytest.mark.parametrize(
-    "raw_description,expect_description,expect_src,expect_id",
+    ("raw_description", "expect_description", "expect_src", "expect_id"),
     [
         (
             "G protein subunit gamma 5 pseudogene 3 [Source:HGNC Symbol;Acc:HGNC:33552]",

tests/releases_test.py

@@ -1,3 +1,5 @@
+import re
+
 import pytest
 
 from ensembl_genes.releases import check_ensembl_release, get_latest_ensembl_release
@@ -13,6 +15,8 @@ def test_check_ensembl_release() -> None:
     assert int(check_ensembl_release("latest")) >= 104
     with pytest.raises(
         ValueError,
-        match="release should be convertible to an int, like '104'. Received 'v104'",
+        match=re.escape(
+            "release should be convertible to an int, like '104'. Received 'v104'"
+        ),
     ):
         check_ensembl_release("v104")

tests/species_test.py

@@ -13,7 +13,7 @@ def test_get_species() -> None:
 
 
 @pytest.mark.parametrize(
-    "gene, category",
+    ("gene", "category"),
     [
         # from ENSG00000112493
         (Gene("6", 33_221_298, 33_235_989), "MHC"),