Pre-commit Hooks¶

CytoScnPy provides several pre-commit hooks to automate code analysis in your local development workflow. This ensures that unused code, security vulnerabilities, and quality issues are caught before they reach your repository.

Installation¶

Install pre-commit:
```
pip install pre-commit
```

Add Configuration: Create or update .pre-commit-config.yaml in your project root:

repos:
  - repo: https://github.com/djinn09/CytoScnPy
    rev: v1.2.1 # Use the latest release tag
    hooks:
      - id: cytoscnpy-check
        # Optional: custom arguments
        # args: ['--confidence', '60', '--danger', '--quality']

Install Hooks:
```
pre-commit install
```

Available Hooks¶

Hook ID	Description	Recommended For
`cytoscnpy-check`	Full analysis (security + quality + dead code)	General protection
`cytoscnpy-danger`	Scans for dangerous patterns (SQLi, XSS, etc.)	Security-focused projects
`cytoscnpy-secrets`	Scans for hardcoded credentials/API keys	All projects
`cytoscnpy-quality`	Checks CC, MI, and unused code	Maintaining code health
`cytoscnpy-security`	`cytoscnpy-danger` + `cytoscnpy-secrets`	Security hardening

Usage & Best Practices¶

Selective Analysis¶

If you only want to fail on security issues but want to see quality warnings, use separate hooks:

- id: cytoscnpy-security
  args: ["--fail-threshold", "0"]
- id: cytoscnpy-quality
  args: ["--fail-on-quality", "false"]

Strictness Levels¶

You can enforce strict quality gates using these flags in args:

--fail-on-quality: Exit with code 1 if any quality issues are found.
--fail-threshold <N>: Fail if unused code percentage exceeds N.
--max-complexity <N>: Fail if any function exceeds complexity N.

Performance¶

CytoScnPy is built in Rust and is designed to be extremely fast. However, for very large monorepos, you may want to limit the frequency:

- id: cytoscnpy-check
  stages: [push] # Only run on push instead of every commit

Troubleshooting¶

"Too many open files"¶

If running on thousands of files at once, you might hit OS limits. You can limit the hook to specific directories:

hooks:
  - id: cytoscnpy-check
    files: ^src/

Suppression¶

To ignore a specific finding on a line, use any of these formats:

def legacy_function():  # noqa
    pass  # bare noqa suppresses all

unused_var = 1  # ignore
    # bare ignore also suppresses all

secret_key = "..."  # pragma: no cytoscnpy
    # legacy format, still supported

other_var = value  # noqa: E501, CSP
    # mixed codes: suppresses CytoScnPy because CSP is in the list

[!NOTE] Inline suppression comments (# noqa, # ignore, # pragma: no cytoscnpy) apply to dead code, security, quality, and clone findings on a specific line. For ignoring rules across the entire project, use the ignore list in your .cytoscnpy.toml configuration file.