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| default_language_version: | |
| python: python3.12 | |
| default_stages: [pre-commit] | |
| repos: | |
| - repo: https://github.com/hakancelikdev/unimport | |
| rev: 1.3.0 | |
| hooks: | |
| - id: unimport | |
| args: | |
| - --remove | |
| - repo: https://github.com/astral-sh/ruff-pre-commit | |
| rev: v0.13.1 | |
| hooks: | |
| - id: ruff-format | |
| - id: ruff-check | |
| args: [--fix, --exit-non-zero-on-fix] | |
| - repo: https://github.com/kynan/nbstripout | |
| rev: 0.8.1 | |
| hooks: | |
| - id: nbstripout | |
| - repo: https://github.com/codespell-project/codespell | |
| rev: v2.4.1 | |
| hooks: | |
| - id: codespell | |
| name: codespell | |
| description: Checks for common misspellings in text files. | |
| entry: codespell --skip="*.js,*.html,*.css, *.svg" --ignore-words=.codespell-ignore.txt | |
| language: python | |
| types: [text] | |
| - repo: https://github.com/pre-commit/pre-commit-hooks | |
| rev: v6.0.0 | |
| hooks: | |
| - id: debug-statements | |
| - id: check-ast # Simply check whether the files parse as valid python | |
| - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems | |
| - id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types | |
| - id: check-docstring-first # Check a common error of defining a docstring after code | |
| - id: check-merge-conflict # Check for files that contain merge conflict strings | |
| - id: check-yaml # Check yaml files | |
| args: ["--unsafe"] # Allows special tags in mkdocs.yaml | |
| - id: end-of-file-fixer # Ensure that a file is either empty, or ends with one newline | |
| exclude: end-to-end-pipeline/web/.* | |
| - id: mixed-line-ending # Replace or checks mixed line ending | |
| - id: trailing-whitespace # This hook trims trailing whitespace | |
| - id: file-contents-sorter # Sort the lines in specified files | |
| files: .*requirements*\.txt$ | |
| - repo: https://github.com/google/yamlfmt | |
| rev: v0.17.2 | |
| hooks: | |
| - id: yamlfmt | |
| args: ["-formatter", "retain_line_breaks_single=true,pad_line_comments=2"] | |
| - repo: https://github.com/asottile/pyupgrade | |
| rev: v3.20.0 | |
| hooks: | |
| - id: pyupgrade | |
| args: [--py312-plus] | |
| # The following hook sorts and formats toml files | |
| - repo: https://github.com/pappasam/toml-sort | |
| rev: v0.24.3 | |
| hooks: | |
| - id: toml-sort | |
| description: "Sort and format toml files." | |
| args: | |
| - --all | |
| - --in-place | |
| # The following hook checks for secrets in the code | |
| - repo: https://github.com/zricethezav/gitleaks | |
| rev: v8.28.0 | |
| hooks: | |
| - id: gitleaks | |
| # The following hook checks for secrets in the code | |
| - repo: https://github.com/trufflesecurity/trufflehog | |
| rev: v3.90.8 | |
| hooks: | |
| - id: trufflehog | |
| - repo: local | |
| hooks: | |
| - id: pylint | |
| name: pylint | |
| entry: pylint | |
| language: python | |
| additional_dependencies: ["pylint"] | |
| types: [python] | |
| args: ["--disable=all", "--enable=missing-docstring,unused-argument"] | |
| exclude: 'test_\.py$' | |
| # The following hook check docstrings quality | |
| - repo: https://github.com/terrencepreilly/darglint | |
| rev: v1.8.1 | |
| hooks: | |
| - id: darglint | |
| args: ["--docstring-style=google"] | |
| exclude: 'src/sentinel/risk_models/qcancer\.py$' | |
| # The following hook checks for docstring in functions | |
| - repo: https://github.com/pycqa/pydocstyle | |
| rev: 6.3.0 | |
| hooks: | |
| - id: pydocstyle | |
| args: ["--select=D103", "--match-dir=(genomics_research|projects)"] | |