cargo-mutants

name	cargo-mutants
description	Configure and run cargo-mutants for Rust mutation testing — invoking runs, reading mutants.out, writing exclude_re patterns matching cargo-mutants' mutant-name format, and choosing exclude_re vs

cargo-mutants

cargo-mutants mutates Rust source and re-runs the test suite to find spec gaps. The trap is not the tool itself but the gap between what you think a mutant is named and what cargo-mutants actually emits — that gap silently turns exclude_re entries into dead config.

Running mutation runs

Command	Purpose
cargo mutants --file <path>	Run mutations on one file (fast iteration)
cargo mutants --regex '<pattern>'	Restrict to mutants whose name matches
cargo mutants --list	Print every mutant name after exclude_re filtering — your single source of truth for valid regex targets when authoring a new exclude
cargo mutants --list --config <stripped-toml>	Print mutants using <stripped-toml> (a copy of mutants.toml with exclude_re emptied, every other key kept) — the validation universe for checking that existing exclude_re anchors still match; diff against --list to see exactly what exclude_re removed
cargo mutants --list --config <stripped-toml> --exclude-re='<pattern>'	Add the pattern back on top of the stripped universe — a live pattern shrinks that universe by at least one line; the per-pattern liveness cross-check (must run against the stripped config, not the normal one; use the = form so a --leading pattern is not read as a flag)
cargo mutants --jobs N	Parallelize across N rebuilds (CPU-bound)
cargo mutants --no-shuffle	Stable order; required when comparing two runs
cargo mutants --baseline=skip	Skip the unmutated baseline (only safe if you ran it manually)

Output lives in mutants.out/:

File	Meaning
caught.txt	Test suite failed — mutant killed
missed.txt	Test suite passed — spec gap (or equivalent mutant)
unviable.txt	Code didn't compile — usually a type-system save
timeout.txt	Tests hung — most often LAPACK/BLAS on garbage matrices; tune timeout_multiplier
outcomes.json	Machine-readable outcomes for the whole run
mutants.json	All mutants the planner generated, including filtered ones

Forbidden flag: --in-place

Never pass --in-place. It mutates the working tree directly, so any abnormal termination leaves the source holding the last applied mutation, and subsequent cargo commands operate on corrupted source. Default mode copies the workspace to a temp directory before mutating, leaving the original tree untouched.

Mutant name format — the trap

exclude_re matches against the full mutant name string as printed by cargo mutants --list. The string format depends on the mutation kind:

Mutation kind	Mutant name format	Example
Binary operator in fn body (+ → -, && → ||, == → !=, < → >, etc.)	replace X with Y in <fn>	replace == with != in einsum_pair
delete ! (boolean negation)	delete ! in <fn>	delete ! in contract_to_tensor
delete match arm <pat>	delete match arm <pat> in <fn>	delete match arm 0 in einsum
Free fn / private fn returning a primitive — replace whole body with constant	replace <fn> -> <Ret> with <const> (no in <fn>)	replace is_identity_perm -> bool with false
Inherent method (impl T) — replace body with default value	replace <T>::<method> -> <Ret> with <default>	replace NativeBackend::shared -> Arc<NativeBackend> with Arc::new(Default::default())
Trait method body — replace body with default value	replace <X as Trait>::<method> -> <Ret> with <default>	replace <NativeBackend as ComputeBackend>::is_available -> bool with true

Each line is prefixed with the source location: path:line:col: <name>.

The most common mistake is assuming in <fn> always appears. It does not — it only appears for body-internal mutations (binary ops, delete !, match arms). Whole-body replacements name the function as part of the subject of replace, not after in.

Concrete failure: a pattern like

"replace .* with false in is_identity_perm"

matches nothing, because cargo-mutants emits

replace is_identity_perm -> bool with false

— note the absence of in is_identity_perm. The pattern is dead config; the mutant survives forever and the regex looks reasonable in code review.

Verification protocol

Before adding any exclude_re entry, prove it matches the intended mutant(s) and only those:

1. Run cargo mutants --list and grep for the intended target string.
2. Apply the exclude_re change.
3. Run cargo mutants --list again — the targeted mutants should be gone from the list, and only the targeted ones should be gone.

A useful diff:

cargo mutants --list 2>/dev/null | sort > /tmp/before.txt
# (edit mutants.toml)
cargo mutants --list 2>/dev/null | sort > /tmp/after.txt
diff /tmp/before.txt /tmp/after.txt   # only the lines you intended to remove should appear

If a regex looks plausible but matches nothing in --list, it's dead config — usually a format-mismatch trap.

Pre-run anchor validation

exclude_re anchors rot between runs: a renamed or deleted function kills a function-name anchor, and any line shift kills a file:line:col anchor. Mutation runs are infrequent (heavy, costly triage), so nothing visits the config between them — the invariant that matters is the excludes are valid at the moment a run starts. Validate them just before a run. This is a consumption-time activity, not a per-diff obligation: a refactor that shifts lines does not have to fix the anchors immediately, only the next run does.

This is a different check from the Verification protocol above: that one confirms a newly authored exclude takes effect (its target disappears from --list); this one confirms already-authored excludes have not since gone stale. The two use different commands because --list cannot answer the second question, as below.

Validate each exclude_re against the mutants that would exist without exclude_re — not against cargo mutants --list:

• cargo mutants --list is post-exclude_re. A live entry removes its own targets, so grepping --list for a live pattern returns zero hits — indistinguishable from a stale pattern that matches nothing. Validating against --list flags every working entry as stale.
• --no-config is also wrong: it drops config-generated mutants. A -> Result fn with error_values set yields replace <fn> -> <Ret> with Err(<value>) mutants that vanish under --no-config, so an exclude targeting one is falsely flagged stale.

Build the universe by stripping only exclude_re, keeping every other key:

# 1. Copy the config and empty its exclude_re (keep error_values / examine_re / etc.).
cp .cargo/mutants.toml /tmp/mutants-noexclude.toml
# edit /tmp/mutants-noexclude.toml so that: exclude_re = []
# 2. The validation universe: every mutant in scope of the config, minus the exclude filter.
#    Add --workspace so a member crate's mutants are listed (an unscoped --list shows only
#    the root package when the root is itself a package). Drop --workspace if not a workspace.
#    Do NOT suppress stderr — a config-parse or build failure must surface, not silently
#    leave an empty universe that makes every pattern look stale.
cargo mutants --list --workspace --config /tmp/mutants-noexclude.toml > /tmp/universe.txt
test -s /tmp/universe.txt || { echo "empty universe (the run failed?) — fix before validating"; exit 1; }
# 3. Each exclude_re pattern must match at least one line. rg uses the same Rust regex
#    crate as cargo-mutants, so the match semantics agree (BRE grep does not).
#    Use `rg --` so a pattern beginning with `-` (e.g. `-> bool with true`) is not read as a flag.
rg -- '<pattern>' /tmp/universe.txt

The universe must cover every package any exclude_re targets — staleness is a global property, so the universe has to be at least as broad as the set of excludes you are validating. In a multi-crate workspace, pass --workspace (and enumerate --package if some members are excluded from the default set): an unscoped cargo mutants --list lists only the root package when the root is itself a package, so a valid exclude for a member crate would read as stale. Do not narrow the universe with --file or a single --package — that drops the out-of-scope excludes and falsely flags them stale. An anchor is stale only if it matches nothing in this complete set, regardless of which scoped run later consumes it.

Zero hits means a stale anchor — fix it before running. The remedy depends on the cause: if a line shift moved a file:line:col anchor, refresh the coordinate (the equivalence rationale already lives in the comment next to the regex). If the function was renamed or deleted, or cargo-mutants changed its name format, the named mutant is gone — re-point the pattern to the current mutant name or remove it, and re-assess whether the equivalence claim still holds.

A nonzero match is necessary but not sufficient. For a file:line:col anchor, confirm the matched mutant is the one the adjacent equivalence comment describes: a moved coordinate can match a different identically named mutant and silently exclude the wrong target — the same "intended mutant(s) and only those" requirement as the Verification protocol. The cargo-mutants-native cross-check is to add the pattern back on top of the stripped universe: cargo mutants --list --config <stripped-toml> --exclude-re='<pattern>' should drop exactly the mutants the pattern is meant to exclude — at least one line, and more when the anchor intentionally covers several (a function-name anchor over a multi-mutant function). Compare the removed lines against the intended target set, not against a fixed count. Run it against the stripped config, not the normal one — under the normal config the pattern's own targets are already filtered out, so it would never shrink. Use the --exclude-re=<pattern> (equals) form: cargo-mutants rejects a space-separated value beginning with - (e.g. -> bool with true) as an unknown flag.

Pattern style: line:col vs function-name

Two anchoring strategies, with different trade-offs:

Function-name-based (replace X with Y in <fn>$ or <T>::<method>):

• Stable across line-number drift.
• Fails when multiple operands on the same expression generate identical names — e.g., let x = !a && !b; produces two delete ! in <fn> mutants whose names are identical aside from the :line:col prefix. A function-name regex would unintentionally exclude both.

Line:col-anchored (<file>:<line>:<col>: <suffix>):

• Surgical: kills exactly one mutant.
• Fragile: silently breaks on line/column shifts. Always pair with a comment explaining what's at that location and why it's equivalent, so a future editor can re-anchor after a refactor.

Rule of thumb: prefer function-name when the mutant name is unique within its function. Fall back to line:col when multiple equivalent positions share a name. Group line:col patterns under a clearly labeled "fragile / line-anchored" section in mutants.toml to signpost the maintenance burden.

When a line:col anchor is forced this way, consider extracting the equivalent-mutant expression into a small named helper function instead. cargo-mutants then names that mutant after the helper (replace <helper> -> <Ret> with <const> or replace X with Y in <helper>), so a stable function-name anchor replaces the fragile coordinate and survives line shifts. The cost is a one-line refactor; the payoff is an anchor that does not need re-validating after every nearby edit. Worth it when the equivalent position is otherwise indistinguishable from a live one by name alone.

exclude_re vs #[mutants::skip]

Both suppress mutants. They are not interchangeable.

Use exclude_re (config) when	Use #[mutants::skip] (attribute) when
The fn or expression has specific mutations that are equivalent, but others are still in scope	The fn is wholly equivalent (e.g., a stub, or all paths inside it are invariants under all operator mutations)
You want surgical line:col anchoring	You want function-level granularity and don't care about precision
The fn is downstream code you don't want to annotate	You own the fn and want the rationale to live next to the code

#[mutants::skip] requires a regular mutants dependency (not dev-dependency, since the attribute lives on non-test code). exclude_re requires no dependency.

For optimization-gate predicates — predicates whose with true is dangerous (false-positive enables an unsafe shortcut) but with false is safe (false-negative falls back to a slower, correct path) — prefer direct unit tests on the predicate over either skip mechanism. A unit test pins the predicate's spec rather than papering over the asymmetry, and it kills both with true and with false mutants in one assertion.

Equivalent mutant criteria

A mutant is "equivalent" when it cannot be distinguished from the original by any test that respects the program's specification. Common categories:

• Optimization-only: a predicate that gates a fast path; the mutant disables the fast path but the slow path is correct (e.g., is_identity_perm -> false always physically permutes — slower but correct).
• Unreachable: code path the type system / parser guarantees never fires (e.g., a 0-arity match arm in code that always parses ≥1 input). "Unreachable under the current test or feature configuration" does not qualify — reachability under a supported config (or a test you could write) only refutes this unreachable rationale; the mutant is a coverage gap only if a specification-respecting test can then distinguish it, and may still be equivalent under one of the other criteria here (see Equivalence soundness).
• Default-equivalent values: a real type whose Default matches the function's return on the documented domain (e.g., <Scalar for f64>::im returning 0.0 is the same as Default::default() for the real subset).
• Same-output-different-path: two implementations of the same operation produce identical numerical output by design (e.g., transpose-then-GEMM and GEMM-with-trans-flag over the same data).
• Tie-breaking-only: a comparison whose ordering doesn't affect downstream observable state (e.g., > vs >= when picking the max of equal values).

When you label a mutant equivalent, document the reason next to the regex. Equivalence claims rot when the surrounding code changes; a comment lets a future editor decide whether the claim still holds.

When missed doesn't mean "untested"

A mutant in missed.txt means the test suite passed when the mutation was applied. That can mean:

1. Spec gap — there is no test that observes the mutated behavior at all.
2. Test gap — tests exist but use degenerate inputs (size-1, zero, identity) that don't visit the mutated path.
3. Equivalent mutant — every observable behavior is preserved by the mutation; the test suite is correct to pass.

Distinguish them before reaching for exclude_re. The default is to kill the mutant by writing a stronger test, not to exclude it. Reach for exclude_re only when you can articulate why no test can distinguish the mutation — and stress-test that articulation against the Equivalence soundness checks before trusting it.

A pattern: when both with true and with false survive on the same predicate, that's almost always two different reasons (one is a coverage gap, one is genuinely equivalent). Don't bulk-exclude — handle each direction independently.

Equivalence soundness

The criteria above define what equivalence is; the checks below stress-test an equivalence claim before you add an equivalence exclude_re. They are falsification attempts — each tries to expose the mutant as a killable coverage gap — and they are necessary, not sufficient: clearing all of them rules out the common coverage-gap signatures, not every one. Crucially, absence from caught.txt is never itself evidence of equivalence: a mutant you are weighing sits in missed.txt, so it is absent from caught.txt by definition, whether it is a true equivalent or an as-yet-uncovered coverage gap. The exclusion bar therefore stays the positive standard from When missed doesn't mean "untested": you must be able to prove that no specification-respecting test can distinguish the mutation — a type/parser guarantee of unreachability, an algebraic same-output identity, or an exhaustive argument over a finite input domain. A distinguishing-input search that came up empty only raises confidence: on a non-exhaustively-searchable domain it never establishes that no distinguishing input exists. These checks narrow and pressure that proof; they do not replace it.

This is also a different axis from anchor validity: the Verification protocol and Pre-run anchor validation confirm a regex hits the intended mutant, whereas these checks probe whether the mutant it hits is truly unkillable. A pattern can be perfectly anchored and still exclude a killable mutant.

Step 1 is a mechanical, command-checkable assertion. Steps 2–4 are judgment-based heuristics — tells and standards that route the decision, deliberately not hard mechanical gates.

1. Over-exclusion cross-check (mechanical). The removed set — the mutants an exclude_re pattern strips — must contain nothing the test suite kills. Compute it as a set difference, the way Pre-run anchor validation diffs to see what a pattern removes: list the stripped universe U (cargo mutants --list --config <stripped-toml>, plus --workspace per that section), list it again with the candidate pattern applied as K (cargo mutants --list --config <stripped-toml> --exclude-re='<pattern>'), and take removed_set = U \ K (e.g. comm -23 over the two sorted listings). K is the kept set — the universe minus the pattern's targets — so do not intersect K itself with caught.txt; K is non-empty for any healthy config and would falsely read as a swarm of over-exclusions. Intersect removed_set with caught.txt; the intersection must be empty. A mutant in the intersection was killed by some test — so, provided that test is specification-respecting (not flaky, and not asserting an implementation detail such as a mock expecting the fast path), the mutant is not equivalent: an over-exclusion, usually an over-broad function-name anchor sweeping in killable siblings. A hit killed only by a flaky or implementation-detail test is the exception — inspect the failing test before ruling the mutant non-equivalent, since equivalence is defined against specification-respecting tests only. Two provenance requirements make the intersection sound:
   • caught.txt must come from a run capable of killing every mutant in removed_set — one that actually tested each, under a configuration in which a distinguishing test, if one exists, would execute and fail. The single failure mode to rule out: any mutant left untested by a run-configuration difference is absent from both caught.txt and missed.txt, so removed_set ∩ caught.txt is empty for the trivial reason that it was never exercised — not because it is equivalent (a false pass). Match U's full run configuration: source revision, workspace/package scope, feature flags, cargo / test arguments, and test tooling, and empty all exclude_re (a stripped-config run) so no pre-existing exclude masks a candidate target. Each common slip — a run with the candidate exclude already applied, a narrower --file / single---package scope, a different feature set, a different test filter — reduces to the same untested-mutant defect.
   • Run --list at its default --line-col=true so both sides carry the path:line:col: prefix and the exact-string intersection holds; caught.txt always carries that prefix. A line:col-stripped bare-name comparison is a fallback only when locations are genuinely unavailable: identical bare names recur at distinct locations, so it over-reports — its hits are suspects to confirm by location, not a clean verdict.
2. Sibling-asymmetry tell. If a structurally symmetric sibling of the target is in caught.txt while the target is in missed.txt, treat the equivalence claim as suspect: a true equivalence usually makes both siblings equivalent, so the asymmetry signals a coverage gap. This is a tell that warrants investigation, not a verdict that the target is killable.
3. Guard-gates-an-index check. If the mutated predicate guards a slice or index access (shape[..n], v[i]), a mutation that disables the guard may reach the access with an out-of-range value and panic instead of returning the guarded error. A panic is observable, so a test feeding such an input kills the mutant — a coverage gap. When the mutated predicate guards an index, flip the default to coverage-gap; the equivalence claim survives only if the index is otherwise guaranteed in range (an earlier validation, a type bound), making the guard genuinely redundant. Identify which slice the disabled guard actually reaches and whether its index can exceed the length: the original audit's error was justifying the mutant via shape[nrow..] (the empty, product-1 case — which holds only when nrow == shape.len()) when the disabled guard in fact reaches shape[..nrow], out-of-range and panicking once nrow > shape.len(). shape[nrow..] panics on nrow > shape.len() too, so neither slice form is automatically safe — pin the actual access and its reachable index range.
4. Reachability standard. "Unreachable under the current test or feature configuration" is not equivalence. Reachability only disproves the Unreachable rationale; it does not by itself prove a coverage gap, because a reachable mutant can still be equivalent under another criterion (optimization-only, default-equivalent, same-output, tie-breaking). A reachable mutant is a coverage gap precisely when a specification-respecting test can distinguish it — exhibit an input on which the mutated and original code observably differ. Reachability is necessary but not sufficient: an optimization-only or same-output mutant executes the reachable path yet leaves every observable identical, so it stays equivalent. When you can produce such a distinguishing input — reachable by a supported config, an in-tree fixture, or a test you could write — it is a coverage gap: leave the mutant in scope and kill it (wire the fixture, enable the feature). Only a type- or parser-guaranteed-unreachable path, or a mutation with mathematically identical output, qualifies as equivalent. An optimization-gate predicate that fails these checks routes to the unit-test remedy in exclude_re vs #[mutants::skip], not to an exclude.

Clearing steps 1–4 means no common coverage-gap signature fired; it does not discharge the positive argument. If you cannot state why every specification-respecting test must agree with the original — a type/parser unreachability, a proven same-output identity, or an exhaustive argument over the input domain — the default stands: kill the mutant with a test, do not exclude it. A distinguishing-input search that merely came up empty is not such an argument.

Killing surviving mutants — type-axis parametrization

When the stronger-test response above must cover multiple trait impls of an identical algebraic property (e.g., Scalar for f32 / f64 / Complex<f32> / Complex<f64>), the right shape is a generic test parameterized over the type, not N copy-paste functions.

fn conj_involutive<T: Scalar>(x: T) {
    assert_eq!(T::conj(T::conj(x)), x);
}

#[test] fn conj_involutive_f32() { conj_involutive::<f32>(1.5); }
#[test] fn conj_involutive_f64() { conj_involutive::<f64>(1.5); }
#[test] fn conj_involutive_c32() { conj_involutive::<Complex<f32>>(Complex::new(1.5, 2.5)); }
#[test] fn conj_involutive_c64() { conj_involutive::<Complex<f64>>(Complex::new(1.5, 2.5)); }

This is type-axis parametrization, not test-logic abstraction. The algebraic identity is the same statement for all T; only the type varies. Per-type copy-paste of the same assert_eq! is duplication along a single axis, not the "tests document behavior independently" pattern that argues against DRY-in-tests.

Reserve this for properties that genuinely hold across the type set with the same shape. If f32 and f64 need different tolerances, or Complex needs an additional im check, write the test fully per type — type-axis parametrization is only the right tool when the property is the same statement for every T.

mutants.toml knobs

Beyond exclude_re:

Key	Purpose
examine_re	Allowlist: only test mutants whose names match. Inverse of exclude_re.
examine_globs / exclude_globs	File-pathname filters (independent of mutant names).
timeout_multiplier	Multiply baseline test time. Default 5.0; for FFI-heavy crates 2.0 is often enough and saves cycles.
additional_cargo_args / test_tool	Customize the test runner invocation.
minimum_test_timeout	Floor for the auto-tuned timeout, in seconds.

timeout_multiplier should be tuned only after observing actual baseline test time; setting it too low produces false-positive timeouts (timeout.txt entries that aren't really runaway).

Audit workflow

When inheriting an existing mutants.toml, audit it:

1. Build the validation universe — a copy of mutants.toml with exclude_re emptied, every other key kept — and capture it: cargo mutants --list --config <stripped-toml> > /tmp/universe.txt (see Pre-run anchor validation for why --list and --no-config are both the wrong universe).
2. For each exclude_re entry, rg -- '<pattern>' /tmp/universe.txt (the -- keeps a --leading pattern from being read as a flag). Entries matching nothing are dead config (the regex matches no current mutant). For each match, confirm it is the intended target, not a same-named mutant a shifted coordinate now points at.
3. For each entry that does match, re-evaluate the equivalence claim against the current code via the Equivalence soundness checks.
4. Remove dead entries; rewrite or re-anchor entries whose claims no longer hold.

A regex that worked when written can rot in two ways: the underlying code changed (mutant no longer exists), or cargo-mutants' name format evolved between versions. Both produce silent dead patterns.