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[pull] master from biopython:master #68

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merged 3 commits into from
Feb 27, 2025
Merged

[pull] master from biopython:master #68

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c8d1005
pre-commit autoupdate (except black)
peterjc Feb 27, 2025
44f7a0a
Fix typo spotted with updated codespell
peterjc Feb 27, 2025
d7143fd
Exlude .bb files from mixed newline fixer
peterjc Feb 27, 2025
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11 changes: 6 additions & 5 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,9 @@ repos:
- id: end-of-file-fixer
files: \.py$
- id: mixed-line-ending
exclude: \.bb$
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.9.1
rev: v0.9.7
hooks:
# Run the Ruff linter.
- id: ruff
Expand All @@ -34,14 +35,14 @@ repos:
- id: black
args: [--check,--target-version,py310]
- repo: https://github.com/PyCQA/flake8
rev: 7.1.1
rev: 7.1.2
hooks:
- id: flake8
additional_dependencies: [
'flake8-rst-docstrings>=0.2.3',
]
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.14.1
rev: v1.15.0
hooks:
- id: mypy
# equivalent to "files" in .mypy.ini
Expand All @@ -50,7 +51,7 @@ repos:
rev: 1.19.1
hooks:
- id: blacken-docs
additional_dependencies: [black==24.2.0]
additional_dependencies: [black==24.10.0]
exclude: ^.github/
- repo: https://github.com/rstcheck/rstcheck
rev: v6.2.4
Expand All @@ -74,7 +75,7 @@ repos:
'--ignore=D000,D001,D002,D004'
]
- repo: https://github.com/codespell-project/codespell
rev: v2.3.0
rev: v2.4.1
hooks:
- id: codespell
files: \.(rst|md)$
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2 changes: 1 addition & 1 deletion Doc/doc.rst
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Expand Up @@ -200,7 +200,7 @@ X.3 Build a Codon Alignment
---------------------------

Building a codon alignment is the first step of many evolutionary
anaysis. But how to do that? ``Bio.codonalign`` provides you an easy
analysis. But how to do that? ``Bio.codonalign`` provides you an easy
function ``build()`` to achieve all. The data you need to prepare in
advance is a protein alignment and a set of DNA sequences that can be
translated into the protein sequences in the alignment.
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