code-quality-tools

Code Quality Tools

Overview

The Scientific Python community standard for code quality is:

• pre-commit (or prek): runs checks and auto-fixes on commit or CI
• Ruff: ultra-fast linter and formatter (replaces flake8, isort, black)
• mypy: static type checker

All three are configured in pyproject.toml (ruff, mypy) and .pre-commit-config.yaml. Run locally with pixi run pre-commit or pre-commit run --all-files.

When to Use

• Starting a new HEP Python package and need code quality gates
• Adding linting/formatting to an existing project
• Configuring CI to reject style violations automatically
• Adding type annotations to existing code incrementally

Key Concepts

Tool	Role	Config location
pre-commit	Orchestrates all hooks; runs in isolated envs	.pre-commit-config.yaml
ruff-format	Auto-formatter (Black-compatible, 30× faster)	[tool.ruff] in pyproject.toml
ruff-check	Linter; replaces flake8, isort, pyupgrade, etc	[tool.ruff.lint] in pyproject.toml
mypy	Static type checker	[tool.mypy] in pyproject.toml
codespell	Spell checker for code and docs	.pre-commit-config.yaml

Hook execution order matters: put auto-fixers (ruff-format, ruff-check --fix) before linters that may fail on unfixed code.

Canonical Patterns

Minimal .pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: "v5.0.0"
    hooks:
      - id: check-added-large-files
      - id: check-case-conflict
      - id: check-merge-conflict
      - id: check-yaml
      - id: debug-statements
      - id: end-of-file-fixer
      - id: mixed-line-ending
      - id: name-tests-test
        args: ["--pytest-test-first"]
      - id: trailing-whitespace

  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: "v0.11.0"
    hooks:
      - id: ruff-format
      - id: ruff-check
        args: ["--fix", "--show-fixes"]

  - repo: https://github.com/codespell-project/codespell
    rev: "v2.4.1"
    hooks:
      - id: codespell
        additional_dependencies: ["tomli; python_version<'3.11'"]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: "v1.15.0"
    hooks:
      - id: mypy
        files: src
        args: []

Keep rev: pinned to fixed tags; update with pre-commit autoupdate.

Ruff configuration in pyproject.toml

[tool.ruff]
src = ["src"]

[tool.ruff.lint]
extend-select = [
  "B",    # flake8-bugbear — catches common bug patterns
  "I",    # isort — sorted imports
  "UP",   # pyupgrade — modernize syntax
  "RUF",  # Ruff-specific rules
  "NPY",  # NumPy-specific rules
]
ignore = [
  "PLR2004",  # magic value comparisons (common in HEP cuts)
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20"]  # allow print() in tests

mypy configuration in pyproject.toml

[tool.mypy]
files = "src"
python_version = "3.11"
strict = true
warn_unreachable = true
enable_error_codes = ["ignore-without-code", "redundant-expr", "truthy-bool"]

[[tool.mypy.overrides]]
module = ["awkward.*", "uproot.*", "hist.*", "ROOT.*"]
ignore_missing_imports = true

Start with strict = false and enable incrementally if adding mypy to a large existing codebase. Add [[tool.mypy.overrides]] blocks for HEP libraries that lack type stubs.

Running locally

# With pixi
pixi run pre-commit run --all-files

# Without pixi
pre-commit run --all-files

# Update all hook versions
pre-commit autoupdate

Gotchas

• ruff-format before ruff-check: always list ruff-format first so the formatter fixes style before the linter sees the code.
• mypy needs stubs for external packages: most HEP libraries (awkward, uproot, hist) lack complete type stubs — add ignore_missing_imports = true per package.
• --fix in ruff-check is safe: it makes changes that you review via git diff; --show-fixes explains what it changed.
• pre-commit.ci: free service that auto-runs hooks on every PR and updates rev: pins weekly — worth enabling at pre-commit.ci for shared projects.
• HEP-specific linting suppressions: magic number comparisons (PLR2004) frequently false-positive on physics cuts like pt > 30; add to ignore or suppress per line with # noqa: PLR2004.
• codespell false positives: HEP terms like hist, gaus, Eta may be flagged. Suppress with [tool.codespell] ignore-words-list = ["hist", "gaus"] in pyproject.toml.

Interop

• pixi: pixi run pre-commit wraps the hook runner; define a task in pixi.toml so contributors don't need to install pre-commit globally
• nox: nox -s lint is an alternative entry point for CI that doesn't require pre-commit to be installed
• CI: GitHub Actions can run pre-commit run --all-files directly, or use the managed pre-commit.ci service

Docs

• pre-commit: https://pre-commit.com
• Ruff: https://docs.astral.sh/ruff/
• mypy: https://mypy.readthedocs.io/
• Scientific Python style guide: https://learn.scientific-python.org/development/guides/style/