.pre-commit-config.yaml

# DiffBio Pre-commit Configuration
# Aligned with the avitai-org pre-commit conventions used across datarax, artifex,
# opifex, and calibrax — same anchor-based excludes, same local hook pattern, with
# DiffBio-specific architecture and complexity gates layered on top.

repos:
  # TOML formatting
  - repo: local
    hooks:
      - id: sort_pyproject
        name: sort_pyproject
        entry: toml-sort
        language: python
        args: [-i, --sort-table-keys, --sort-inline-tables, pyproject.toml]
        files: ^pyproject\.toml$
        additional_dependencies: ["toml-sort==0.23.1"]

  # Standard pre-commit hooks
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: trailing-whitespace
        exclude: &repo_non_source_exclude ^(?:memory-bank|notebooks|\.deprecated)/|^uv\.lock$
      - id: end-of-file-fixer
        exclude: *repo_non_source_exclude
      - id: check-yaml
        exclude: &repo_yaml_syntax_exclude ^(?:memory-bank|notebooks|\.deprecated)/(?:.*)|mkdocs\.yml$
      - id: check-added-large-files
        args: ["--maxkb=2000"]
        exclude: *repo_non_source_exclude
      - id: check-merge-conflict
      - id: check-toml
      - id: check-json
        exclude: *repo_non_source_exclude
      - id: debug-statements
        exclude: *repo_non_source_exclude
      - id: mixed-line-ending
        exclude: *repo_non_source_exclude

  # Python linting and formatting with auto-fix
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.14.8
    hooks:
      - id: ruff
        args: [--fix, --unsafe-fixes]
        exclude: *repo_non_source_exclude
        types_or: [python, pyi, jupyter, toml]
      - id: ruff-format
        types_or: [python, pyi, jupyter, toml]
        exclude: *repo_non_source_exclude

  # GitHub Actions simulation - exact mirror of CI checks
  - repo: local
    hooks:
      - id: ruff-docstring-whitespace
        name: ruff-docstring-whitespace (auto-fix whitespace)
        entry: ruff check --select=W291,W292,W293,F841 --fix --unsafe-fixes
        language: system
        types: [python]
        exclude: *repo_non_source_exclude
        pass_filenames: true
      - id: ruff-github-actions-check
        name: ruff-github-actions-check (mirrors CI)
        entry: uv run ruff check --output-format=github
        language: system
        types: [python]
        exclude: *repo_non_source_exclude
        pass_filenames: false
        always_run: true
      - id: ruff-critical-check
        name: ruff-critical-check (fast CI-critical rules only)
        # F821 excluded due to false positives from jaxtyping dimension annotations
        entry: uv run ruff check --select=RUF005,B904,F822,F823 --output-format=github
        language: system
        types: [python]
        exclude: *repo_non_source_exclude
        pass_filenames: false
        always_run: true

  # Manual-stage strict checks (run with: pre-commit run --hook-stage manual)
  - repo: local
    hooks:
      - id: flake8-functions-names
        name: flake8-functions-names (FNE)
        entry: uv run flake8 --select=FNE src tests
        language: system
        types: [python]
        stages: [manual]
        pass_filenames: false
      - id: flake8-wemake-wps233
        name: flake8-wemake WPS233
        entry: uv run flake8 --select=WPS233 src tests
        language: system
        types: [python]
        stages: [manual]
        pass_filenames: false
      - id: pylint-targeted-guide-checks
        name: pylint targeted guide checks
        entry: >-
          uv run pylint --disable=all
          --enable=duplicate-code,too-many-public-methods,too-many-instance-attributes,too-few-public-methods,too-many-ancestors,inconsistent-return-statements
          --reports=no --score=no src/diffbio
        language: system
        types: [python]
        stages: [manual]
        pass_filenames: false

  # Type checking - reuse the project venv so pre-commit stays hermetic
  - repo: local
    hooks:
      - id: pyright
        name: pyright (project environment)
        entry: uv run pyright --warnings
        language: system
        types_or: [python, pyi]
        files: ^src/.*\.py$
        pass_filenames: true

  # Security scanning
  - repo: https://github.com/PyCQA/bandit
    rev: 1.8.6
    hooks:
      - id: bandit
        args: ["-c", "pyproject.toml"]
        exclude: &repo_non_source_and_tests_exclude ^(?:memory-bank|notebooks|\.deprecated|tests)/
        additional_dependencies: ["bandit[toml]"]
        log_file: /dev/null

  # Documentation quality
  - repo: https://github.com/pycqa/pydocstyle
    rev: 6.3.0
    hooks:
      - id: pydocstyle
        exclude: &repo_non_source_tests_examples_exclude ^(?:memory-bank|notebooks|\.deprecated|tests|examples)/
        additional_dependencies: ["pydocstyle[toml]"]
        args: ["--config=pyproject.toml"]

  # Architecture and code quality gates from SWE standards
  - repo: local
    hooks:
      - id: lint-imports
        name: lint-imports (architecture contracts)
        entry: uv run lint-imports
        language: system
        pass_filenames: false
        always_run: true
      - id: radon-complexity
        name: radon-complexity (cyclomatic complexity)
        entry: uv run radon cc src -a -nc
        language: system
        pass_filenames: false
        always_run: true
      - id: interrogate
        name: interrogate (docstring coverage)
        entry: uv run interrogate src -v
        language: system
        pass_filenames: false
        always_run: true

  # Notebook quality
  - repo: https://github.com/nbQA-dev/nbQA
    rev: 1.9.1
    hooks:
      - id: nbqa-ruff
        exclude: *repo_non_source_exclude
        args: [--fix]

  # Shell script quality
  - repo: local
    hooks:
      - id: shellcheck
        name: shellcheck
        entry: shellcheck
        language: system
        types: [shell]
        exclude: *repo_non_source_exclude
        args: ["-e", "SC1091"]
        pass_filenames: true
        always_run: false

  # File length check
  - repo: local
    hooks:
      - id: check-file-length
        name: check-file-length (warn >1500, fail >2000 lines)
        entry: bash
        args:
          - -c
          - |
            for file in "$@"; do
              lines=$(wc -l < "$file" 2>/dev/null || echo 0)
              if [ "$lines" -gt 2000 ]; then
                echo "ERROR: $file has $lines lines (limit: 2000)"
                exit 1
              elif [ "$lines" -gt 1500 ]; then
                echo "WARNING: $file has $lines lines (approaching limit of 2000)"
              fi
            done
          - --
        language: system
        types: [python]
        exclude: *repo_non_source_and_tests_exclude

# CI configuration - no autofix, manual testing before commits
ci:
  autofix_commit_msg: |
    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci
  autofix_prs: false
  autoupdate_branch: ""
  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
  autoupdate_schedule: weekly
  skip: []
  submodules: false