InstaNovo/.pre-commit-config.yaml at main · instadeepai/InstaNovo · GitHub

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default_stages: [pre-commit]

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: debug-statements # Check for debugger imports
      - id: requirements-txt-fixer # Order requirements alphabetically
      - 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"]
      - id: end-of-file-fixer # Ensure that a file is either empty, or ends with one newline
        exclude: |
          (?x)(
              ^docs/|
              ^notebooks/|
          )

      - id: mixed-line-ending # Replace or checks mixed line ending
        exclude: |
          (?x)(
              ^docs/|
              ^notebooks/|
          )

      - id: trailing-whitespace # This hook trims trailing whitespace
        exclude: |
          (?x)(
              ^docs/|
              ^notebooks/|
          )

  - repo: https://github.com/compilerla/conventional-pre-commit
    rev: v4.2.0
    hooks:
      - id: conventional-pre-commit
        stages:
          - commit-msg
        args:
          [
            "ci",
            "build",
            "docs",
            "feat",
            "fix",
            "perf",
            "refactor",
            "style",
            "test",
            "exp",
            "chore",
          ]

  #   - repo: https://github.com/asottile/pyupgrade
  #     rev: v3.15.0
  #     hooks:
  #       - id: pyupgrade
  #         args:
  #           - --py38-plus

  - repo: https://github.com/pycqa/pydocstyle
    rev: 6.3.0
    hooks:
      - id: pydocstyle
        additional_dependencies: ["toml"]
        args:
          - --convention=google
          - --add-ignore=D100,D104,D105,D107,D417

  - 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 --toml pyproject.toml
        language: python
        types: [text]
        additional_dependencies:
          - tomli
        exclude: |
          ^(docs/.venv|dist|build)/

  - repo: https://github.com/kynan/nbstripout
    rev: 0.8.1
    hooks:
      - id: nbstripout
        exclude: ^notebooks/introducing_the_next_generation_of_InstaNovo_models\.ipynb$

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.13.0
    hooks:
      # Run the linter.
      - id: ruff
        args:
          [
            "--select",
            "A,B,C,D,E,F,G,I,N,T,W",
            "--fix",
            "--ignore",
            "B008,C901,D100,D103,D104,D105,D107,D417,F722,G004,N812",
          ]
        types_or: [python, pyi]
      # Run the formatter.
      - id: ruff-format
        types_or: [python, pyi]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: "v1.17.1"
    hooks:
      - id: mypy
        additional_dependencies: [types-requests, types-PyYAML, types-tqdm] # TODO: pandas-stubs
        args:
          [
            --ignore-missing-imports,
            "--exclude=(notebooks|tests)",
            --disable-error-code,
            "name-defined",
          ]

  - repo: https://github.com/astral-sh/uv-pre-commit
    # uv version.
    rev: 0.8.17
    hooks:
      # Update the uv lockfile
      - id: uv-lock