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

Rationalization	Why It's Wrong	Required Action
"All survived mutants need tests"	Many are harmless or equivalent	Triage before writing tests
"Mutation testing is too noisy"	Noise means you're not triaging	Use graph data to filter
"Unit tests cover everything"	Complex data flows need fuzzing	Check entrypoint reachability
"Dead code mutants don't matter"	Dead code should be removed	Flag for cleanup
"Low complexity = low risk"	Boundary bugs hide in simple code	Check mutant location
"Tool isn't installed, I'll do it manually"	Manual analysis misses what tooling catches	Install the tool first
"Necessist isn't mutation testing, skip it"	Necessist finds what mutation testing misses: weak tests	Run both when the language supports it

---

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:

Field	Description
File path	Source file containing the mutant
Line number	Line where mutation was applied
Mutation type	What was changed (operator, value, etc.)
Status	survived, killed, timeout, error

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)

Signal	Bucket	Reasoning
No callers in graph	False Positive	Dead code, mutant is unreachable
Only test callers	False Positive	Test infrastructure, not production
Logging/display string	False Positive	Cosmetic, no behavioral impact
Equivalent mutant	False Positive	Behavior unchanged despite mutation
Simple function, low CC, no entrypoint path	Missing Tests	Unit test is straightforward
Error handling path	Missing Tests	Should have negative test cases
Boundary condition (off-by-one)	Missing Tests	Property-based test candidate
Pure function, deterministic	Missing Tests	Easy to test, high value
High CC (>10), entrypoint reachable	Fuzzing Target	Complex + exposed = fuzz it
Parser/validator/deserializer	Fuzzing Target	Structured input handling
Many callers (>10) + moderate CC	Fuzzing Target	High blast radius
Binary/wire protocol handling	Fuzzing Target	Fuzzers excel at format testing

Quick Classification (Necessist)

Signal	Bucket	Reasoning
Redundant setup or debug call	False Positive	Statement genuinely unnecessary
Cannot map to production function	False Positive	No graph context for triage
Call removed, no assertion checks its effect	Missing Tests	Test has weak assertions
Assertion removed, test still passes	Missing Tests	Redundant or insufficient coverage
Maps to high-CC entrypoint-reachable function	Fuzzing Target	Complex + exposed + weak test

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.