genotoxic

Genotoxic

Combines mutation testing and necessist (test statement removal) with code graph analysis to triage findings into actionable categories: false positives, missing unit tests, and fuzzing targets.

When to Use

• After mutation testing reveals survived mutants that need triage
• Identifying where unit tests would have the highest impact
• Finding functions that need fuzz harnesses instead of unit tests
• Prioritizing test improvements using data flow context
• Filtering out harmless mutants from actionable ones
• Finding unnecessary test statements that indicate weak assertions (necessist)

When NOT to Use

• Codebase has no existing test suite (write tests first)
• Pure documentation or configuration changes
• Single-file scripts with trivial logic

Prerequisites

• trailmark installed — if uv run trailmark fails, run:

  uv pip install trailmark

DO NOT fall back to "manual verification" or "manual analysis" as a substitute for running trailmark. Install it first. If installation fails, report the error instead of switching to manual analysis.

• A mutation testing framework for the target language — if the framework

command fails (not found, not installed), install it using the instructions in references/mutation-frameworks.md. DO NOT fall back to "manual mutation analysis" or skip mutation testing. Install the framework first. If installation fails, report the error instead of switching to manual mutation analysis.

• necessist (optional, recommended) — if the target language is

supported (Go, Rust, Solidity/Foundry, TypeScript/Hardhat, TypeScript/Vitest, Rust/Anchor), install with cargo install necessist. See references/mutation-frameworks.md for details.

• An existing test suite that passes
• macOS environment: Run ulimit -n 1024 before any mull-runner

invocation. macOS Tahoe (26+) sets unlimited file descriptors by default, which crashes Mull's subprocess spawning. See references/mutation-frameworks.md for details.

---

Rationalizations to Reject

---

Quick Start

# 1. Build the code graph
uv run trailmark analyze --language auto --summary {targetDir}

# 2. Run mutation testing (language-dependent)
# Python:
uv run mutmut run --paths-to-mutate {targetDir}/src
uv run mutmut results

# 2b. Run necessist (if language supported)
necessist

# 3. Analyze results with this skill's workflow (Phase 3)

---

Workflow Overview

Phase 1: Graph Build      → Parse codebase with trailmark
      ↓
Phase 2: Mutation Run     → Execute mutation testing framework
Phase 2b: Necessist Run   → Remove test statements (optional, parallel)
      ↓
Phase 3: Triage           → Classify findings using graph data
      ↓
Output: Categorized Report
  ├── Corroborated         (both tools flag same function — highest value)
  ├── False Positives      (harmless, skip)
  ├── Missing Tests        (write unit tests)
  └── Fuzzing Targets      (set up fuzz harnesses)

---

Decision Tree

├─ Need to set up mutation testing for a language?
│  └─ Read: references/mutation-frameworks.md
│
├─ Need to set up necessist or find weak test statements?
│  └─ Read: references/mutation-frameworks.md (Necessist section)
│
├─ Need to understand the triage criteria in depth?
│  └─ Read: references/triage-methodology.md
│
├─ Need to understand how graph data informs triage?
│  └─ Read: references/graph-analysis.md
│
└─ Already have results + graph? Use Phase 3 below.

---

Phase 1: Build Code Graph and Run Pre-Analysis

Parse the target codebase with trailmark and run pre-analysis before mutation testing. Pre-analysis computes blast radius, entry points, privilege boundaries, and taint propagation, which Phase 3 uses for triage.

uv run trailmark analyze --language auto --summary {targetDir}

Use the QueryEngine API to build the graph and run pre-analysis:

1. QueryEngine.from_directory("{targetDir}", language="auto")
2. Call engine.preanalysis() — mandatory before triage
3. Export with engine.to_json() for cross-referencing with mutation results

If auto-detection is wrong for the target, rerun with an explicit language or comma-separated list such as python,rust.

See references/graph-analysis.md for the full API: node mapping, reachability queries, blast radius, and pre-analysis subgraph lookups.

---

Phase 2: Run Mutation Testing

Select and run the appropriate framework. See references/mutation-frameworks.md for language-specific setup.

Capture survived mutants. Each framework reports differently, but extract these fields per mutant:

Filter to survived mutants only for Phase 3.

---

Phase 2b: Run Necessist (Optional)

If the target language is supported (Go, Rust, Solidity/Foundry, TypeScript/Hardhat, TypeScript/Vitest, Rust/Anchor), run necessist to find unnecessary test statements. This runs independently of Phase 2 and can execute in parallel.

# Auto-detect framework
necessist

# Or target specific test files
necessist tests/test_parser.rs

# Export results
necessist --dump

Filter to findings where the test passed after removal. See references/mutation-frameworks.md for framework-specific configuration and the normalized record format.

Map each removal to a production function using the algorithm in references/graph-analysis.md.

---

Phase 3: Triage Findings

For each survived mutant and each necessist removal, determine its triage bucket using graph data. Necessist removals must first be mapped to a production function (see references/graph-analysis.md).

Quick Classification (Mutation Testing)

Quick Classification (Necessist)

When both mutation testing and necessist flag the same production function, mark as corroborated — highest confidence finding.

For detailed criteria, see references/triage-methodology.md.

Graph Queries for Triage

For each mutant, map it to its containing graph node and use pre-analysis subgraphs (tainted, high_blast_radius, privilege_boundary) from Phase 1 to classify it. The classification logic checks: no callers → false positive, privilege boundary → fuzzing, high CC + tainted → fuzzing, high blast radius → fuzzing, otherwise → missing tests.

See references/graph-analysis.md for the batch_triage implementation and node mapping functions.

---

Output Format

Generate a markdown report:

# Genotoxic Triage Report

## Summary
- Total survived mutants: N
- Total necessist removals: N
- Corroborated findings: N
- False positives: N (N%)
- Missing test coverage: N (N%)
- Fuzzing targets: N (N%)

## Corroborated Findings
| File | Line | Function | Mutation Signal | Necessist Signal | Action |
|------|------|----------|----------------|------------------|--------|

## False Positives
| File | Line | Mutation | Reason | Source |
|------|------|----------|--------|--------|

## Missing Test Coverage
| File | Line | Function | CC | Callers | Suggested Test | Source |
|------|------|----------|----|---------|----------------|--------|

## Fuzzing Targets
| File | Line | Function | CC | Entrypoint Path | Blast Radius | Source |
|------|------|----------|----|-----------------|--------------|--------|

The Source column is mutation, necessist, or corroborated.

Write the report to GENOTOXIC_REPORT.md in the working directory.

---

Quality Checklist

Before delivering:

• [ ] Trailmark graph built for target language
• [ ] Mutation framework ran to completion
• [ ] Necessist ran (if language supported) or noted as not applicable
• [ ] All survived mutants triaged (none unclassified)
• [ ] All necessist removals triaged (if applicable)
• [ ] Corroborated findings identified (if both tools ran)
• [ ] False positives have clear justifications
• [ ] Missing test items include suggested test type
• [ ] Fuzzing targets include entrypoint paths and blast radius
• [ ] Report file written to GENOTOXIC_REPORT.md
• [ ] User notified with summary statistics

---

Integration

trailmark skill:

• Phase 1: Build code graph, query complexity and entrypoints
• Phase 3: Caller analysis, reachability, blast radius

property-based-testing skill:

• Missing test coverage items involving boundary conditions
• Roundtrip/idempotence properties for serialization mutants

testing-handbook-skills (fuzzing):

• Fuzzing target items: use harness-writing, cargo-fuzz, atheris

---

Supporting Documentation

• references/mutation-frameworks.md -

Language-specific framework setup, output parsing, and necessist configuration

• references/triage-methodology.md -

Detailed triage criteria, edge cases, and worked examples for both mutation testing and necessist

• references/graph-analysis.md -

Graph query patterns, test-to-production mapping, and result merging

---

First-time users: Start with Phase 1 (graph build), then run mutations, then use the Quick Classification table in Phase 3.

Experienced users: Jump to Phase 3 and use the Decision Tree to load specific reference material.