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.pre-commit-config.yaml
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.pre-commit-config.yaml
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default_language_version:
python: python3.10
exclude: "docs/index.md"
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
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, "800"]
# python code formatting
- repo: https://github.com/psf/black
rev: 23.7.0
hooks:
- id: black
args: [--line-length, "110"]
# python import sorting
- repo: https://github.com/PyCQA/isort
rev: 5.12.0
hooks:
- id: isort
args: ["--profile", "black", "--filter-files", "-o", "wandb"]
- repo: https://github.com/PyCQA/autoflake
rev: v2.2.0
hooks:
- id: autoflake
args: [--in-place, --remove-all-unused-imports]
# python upgrading syntax to newer version
- repo: https://github.com/asottile/pyupgrade
rev: v3.10.1
hooks:
- id: pyupgrade
args: [--py310-plus]
# python docstring formatting
# - repo: https://github.com/myint/docformatter
# rev: v1.7.5
# hooks:
# - id: docformatter
# args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]
# python check (PEP8), programming errors and code complexity
- repo: https://github.com/PyCQA/flake8
rev: 6.1.0
hooks:
- id: flake8
args:
[
"--max-complexity=10",
"--extend-ignore",
"E402,E701,E251,E226,E302,W504,E704,E402,E401,C901,E203",
"--max-line-length=110",
"--exclude",
"logs/*,data/*",
"--per-file-ignores",
"__init__.py:F401",
]
# yaml formatting
- repo: https://github.com/pre-commit/mirrors-prettier
rev: v3.0.3
hooks:
- id: prettier
types: [yaml]
# shell scripts linter
- repo: https://github.com/shellcheck-py/shellcheck-py
rev: v0.9.0.5
hooks:
- id: shellcheck
# md formatting
- repo: https://github.com/executablebooks/mdformat
rev: 0.7.17
hooks:
- id: mdformat
args: ["--number"]
additional_dependencies:
- mdformat-gfm
- mdformat-tables
- mdformat_frontmatter
- mdformat-black
- mdformat-config
- mdformat-shfmt
- mdformat-mkdocs
- mdformat-toc
- mdformat-admon
# word spelling linter
- repo: https://github.com/codespell-project/codespell
rev: v2.2.5
hooks:
- id: codespell
args:
- --skip=logs/**,data/**,*.ipynb,*.bib,env.yml,env_cpu.yml,*.svg,poetry.lock
- --ignore-words-list=ehr,crate,infarction
# 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: 1.7.0
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/*",
]