From fcdff71a461bc1411e780610eed0f88a456f070a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 20 Jul 2026 20:16:59 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0)
- [github.com/astral-sh/ruff-pre-commit: v0.11.7 → v0.15.22](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.7...v0.15.22)
- [github.com/pycqa/flake8: 7.2.0 → 7.3.0](https://github.com/pycqa/flake8/compare/7.2.0...7.3.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dec7023..554570c 100644
--- a/.pre-commit-config.yaml
+++ b/.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]

From 5bd3b4b17aaa5930129d178785910c4551f11ce9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 20 Jul 2026 20:17:06 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/serpent/convert/amino.py   | 3 +--
 src/serpent/io/files.py        | 1 -
 src/serpent/lab.py             | 2 +-
 src/serpent/visual/__init__.py | 1 -
 4 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/serpent/convert/amino.py b/src/serpent/convert/amino.py
index 238474d..03c5d38 100644
--- a/src/serpent/convert/amino.py
+++ b/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
diff --git a/src/serpent/io/files.py b/src/serpent/io/files.py
index 366a58a..17ec093 100644
--- a/src/serpent/io/files.py
+++ b/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")
 
 
diff --git a/src/serpent/lab.py b/src/serpent/lab.py
index 04abce6..573cadd 100644
--- a/src/serpent/lab.py
+++ b/src/serpent/lab.py
@@ -1,5 +1,5 @@
 """Lab for interactive work."""
-# ruff: noqa: F401, F403
+# ruff: noqa: F403
 
 from __future__ import annotations
 
diff --git a/src/serpent/visual/__init__.py b/src/serpent/visual/__init__.py
index da87c65..16d092e 100644
--- a/src/serpent/visual/__init__.py
+++ b/src/serpent/visual/__init__.py
@@ -1,4 +1,3 @@
 """Visual things."""
-# flake8: noqa: F401
 
 from __future__ import annotations