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default_language_version:
python: python3
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
- id: double-quote-string-fixer
# python code formatting
- repo: https://github.com/pre-commit/mirrors-autopep8
rev: v2.0.2
hooks:
- id: autopep8
name: autopep8-default
args: [--max-line-length, "110", --in-place]
exclude: tests/.*
- repo: https://github.com/pre-commit/mirrors-autopep8
rev: v2.0.2
hooks:
- id: autopep8
name: autopep8-unit-tests
args: ["-i", "--ignore=E226,E24,W50,W690,E402"]
# python import sorting
- repo: https://github.com/PyCQA/isort
rev: 5.12.0
hooks:
- id: isort
args: ["--skip-gitignore", "--line-length", "110"]
# 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: v1.5.1
hooks:
- id: docformatter
args: [--in-place, --wrap-summaries, "100", --wrap-descriptions, "110"]
# python check (PEP8), programming errors and code complexity
- repo: https://github.com/PyCQA/flake8
rev: 6.0.0
hooks:
- id: flake8
args: ["--extend-ignore", "E402,E501", "--exclude", "logs/*,data/*"]
# 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
# - --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=110"]
- id: nbqa-isort
args: ["--profile=black"]
- id: nbqa-flake8
args:
[
"--extend-ignore=E203,E402,E501,F401,F841",
"--exclude=logs/*,data/*",
]
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