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.pre-commit-config.yaml
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.pre-commit-config.yaml
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default_language_version:
python: python3
exclude: "^forks/"
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
# list of supported hooks: https://pre-commit.com/hooks.html
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-docstring-first
- id: check-yaml
- id: debug-statements
- id: detect-private-key
- id: check-executables-have-shebangs
- id: check-toml
- id: check-case-conflict
- id: check-added-large-files
args: ["--maxkb=15000"]
# python code formatting
- repo: https://github.com/psf/black
rev: 23.1.0
hooks:
- id: black
args: [--line-length, "99"]
# python import sorting
- repo: https://github.com/PyCQA/isort
rev: 5.12.0
hooks:
- id: isort
args: ["--profile", "black", "--filter-files"]
# python upgrading syntax to newer version
- repo: https://github.com/asottile/pyupgrade
rev: v3.3.1
hooks:
- id: pyupgrade
args: [--py38-plus]
# python docstring formatting
- repo: https://github.com/myint/docformatter
rev: v1.7.4
hooks:
- id: docformatter
args:
[
--in-place,
--wrap-summaries=99,
--wrap-descriptions=99,
--style=sphinx,
--black,
]
# python docstring coverage checking
- repo: https://github.com/econchick/interrogate
rev: 1.5.0 # or master if you're bold
hooks:
- id: interrogate
args:
[
--verbose,
--fail-under=80,
--ignore-init-module,
--ignore-init-method,
--ignore-module,
--ignore-nested-functions,
-vv,
]
exclude: ^posebench/analysis/casp15_ligand_scoring/
# python check (PEP8), programming errors and code complexity
- repo: https://github.com/PyCQA/flake8
rev: 6.0.0
hooks:
- id: flake8
args:
[
"--extend-ignore",
"E203,E402,E501,F401,F841,RST2,RST301",
"--exclude",
"logs/*,data/*,posebench/analysis/casp15_ligand_scoring/*",
]
additional_dependencies: [flake8-rst-docstrings==0.3.0]
# python security linter
- repo: https://github.com/PyCQA/bandit
rev: "1.7.5"
hooks:
- id: bandit
args: ["-s", "B101"]
# yaml formatting
- repo: https://github.com/pre-commit/mirrors-prettier
rev: v3.0.0-alpha.6
hooks:
- id: prettier
types: [yaml]
exclude: "environment.yaml"
# shell scripts linter
- repo: https://github.com/shellcheck-py/shellcheck-py
rev: v0.9.0.2
hooks:
- id: shellcheck
# md formatting
- repo: https://github.com/executablebooks/mdformat
rev: 0.7.16
hooks:
- id: mdformat
args: ["--number"]
additional_dependencies:
- mdformat-gfm
- mdformat-tables
- mdformat_frontmatter
# - mdformat-toc
# - mdformat-black
# word spelling linter
- repo: https://github.com/codespell-project/codespell
rev: v2.2.4
hooks:
- id: codespell
args:
- --skip=logs/**,data/**,*.ipynb,posebench/utils/data_utils.py,posebench/utils/residue_utils.py,posebench/data/components/protein_fasta_preparation.py,posebench/models/minimize_energy.py,posebench/data/components/create_casp15_ensemble_input_csv.py,posebench/analysis/casp15_ligand_scoring/casp_parser.py
# - --ignore-words-list=abc,def
# jupyter notebook cell output clearing
- repo: https://github.com/kynan/nbstripout
rev: 0.6.1
hooks:
- id: nbstripout
# jupyter notebook linting
- repo: https://github.com/nbQA-dev/nbQA
rev: 1.6.3
hooks:
- id: nbqa-black
args: ["--line-length=99"]
- id: nbqa-isort
args: ["--profile=black"]
- id: nbqa-flake8
args:
[
"--extend-ignore=E203,E402,E501,F401,F841",
"--exclude=logs/*,data/*",
]