[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -17,12 +17,12 @@ repos:
       # - id: requirements-txt-fixer
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.7
+    rev: v0.15.22
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
   - repo: https://github.com/pycqa/flake8
-    rev: 7.2.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         additional_dependencies: [flake8-tabs]

src/serpent/convert/amino.py

@@ -24,7 +24,6 @@
 def codon_to_amino(codon, table=1):
 	return degenerate_amino.get(codon) or genetic_code[table][codon]
 
-# ruff: noqa: F601
 # multi-value-repeated-key-literal
 # TODO: Use degenerate nucleotide codes
 def amino_to_codon(amino, table=1):
@@ -51,7 +50,7 @@ def num_to_amino(number: int, table: int=1) -> str:
 aminos_inverse = inverse_od(aminos)
 
 
-# ruff: noqa: ARG001 # Unused function argument: `table`
+# Unused function argument: `table`
 def decode_aminos(
 	dna,
 	# table=1

src/serpent/io/files.py

@@ -92,7 +92,6 @@ def write_iterable(lines, outfile):
 
 def openfile(filename):
 	"""Open stdin or a file to be used in a context handler."""
-	# ruff: noqa: SIM115
 	return stdin if filename == '-' else Path(filename).open("r", encoding="UTF-8")
 
 

src/serpent/lab.py

@@ -1,5 +1,5 @@
 """Lab for interactive work."""
-# ruff: noqa: F401, F403
+# ruff: noqa: F403
 
 from __future__ import annotations
 

src/serpent/visual/__init__.py

@@ -1,4 +1,3 @@
 """Visual things."""
-# flake8: noqa: F401
 
 from __future__ import annotations