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PR #58 was closed unmerged during branch cleanup; its review findings were still valid against main. This PR resurrects them on a fresh branch from current origin/main:
@qodo-code-review[bot] (valid bug): stdout WARNING now carries the error detail (FileNotFoundError: [Errno 2] ...), matching stderr — permission-denied vs missing-file are now distinguishable on both channels.
@codacy-production[bot] (nitpick): trigger is now \bweak assertions?\b (plural).
@codacy-production[bot] (MEDIUM): Stryker --incremental doc now says cache reports/stryker-incremental.json in CI, not commit it; the Universal CI pattern item reworded to match (CI cache, not the repo).
Verification
Hook behavior suite (echo-based): plural "weak assertions" fires; "are my tests passing?" stays silent; "are my tests actually good" fires; unreadable skill file now emits the error detail on BOTH stdout WARNING and stderr.
codacy-analysis analyze --files on all 6 changed files — 0 issues.
npm run test — 371 passed. npm run check — 0/0. npm run build — clean.
Installed copy re-synced to ~/.agents/skills/mutation-testing (diff-verified).
CodeAnt-AI Description
Make mutation-testing guidance accurate and hook failures visible
What Changed
Mutation-testing hook failures now show a warning and the specific error in user-visible output while still allowing prompts to continue.
The hook only activates for explicit mutation-testing or meaningful test-quality questions, avoiding unrelated prompts such as “are my tests passing?”
Guidance now matches current mutmut 3.x, PIT, and Stryker behavior, including updated commands, result locations, diff-run support, and CI caching.
Research claims and equivalent-mutant estimates are qualified with source context instead of presenting fixed results as universal.
Skill files and repository guidance now include the required licensing notices and clarify that hook errors are reported through both output channels.
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This PR tightens when the mutation-testing skill is injected and makes skill-loading failures visible to both the user-facing context and server logs while preserving prompt flow.
sequenceDiagram
participant User
participant Hook
participant SkillFile
participant Harness
User->>Harness: Submit prompt
Harness->>Hook: Run prompt hook
Hook->>Hook: Match mutation testing trigger
alt Trigger matches and skill file is readable
Hook->>SkillFile: Read skill content
SkillFile-->>Hook: Return skill content
Hook-->>Harness: Inject skill guidance
else Trigger matches and skill file cannot be read
Hook-->>Harness: Show warning and fallback path
Hook-->>Harness: Log failure to server output
end
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This PR successfully resurrects the review fixes from closed PR #58 with clean improvements to the mutation-testing skill. All changes are correct and well-implemented:
Key improvements:
License headers properly added to all mutation-testing skill files per repository standards
Research citations refined with precise attributions (Yao, Harman & Jia study; Dakhel et al. MuTAP reference)
Tool documentation updated for current versions (mutmut 3.x CLI changes, PIT's removed scmMutationCoverage goal)
Error handling enhanced in prehook to ensure failures are visible on both stdout and stderr
Trigger patterns tightened (plural "weak assertions" support, more precise "are my tests" matching)
CI guidance clarified on caching state files rather than committing them
The changes align with the repo's "fail loudly" rule and maintain consistency across all skill documentation. No defects found that would block merge.
You can now have the agent implement changes and create commits directly on your pull request's source branch. Simply comment with /q followed by your request in natural language to ask the agent to make changes.
• Make mutation-testing prehook failures visible on stdout (and still logged to stderr).
• Tighten prehook trigger phrases to avoid noisy matches while catching “weak assertions”.
• Update mutation-testing docs for current mutmut/PIT/Stryker behavior and cite research/limits.
Diagram
graph TD
U{{"User prompt"}} --> H["Prehook script"] --> SK["Skill doc"] --> IC(("Injected context"))
H --> SO(("Stdout WARNING"))
H --> SE(("Stderr log"))
R["Reference docs"] --> SK
subgraph Legend
direction LR
_ext{{"External"}} ~~~ _mod["Hook/module"] ~~~ _doc["Markdown doc"] ~~~ _io(("Output channel"))
end
Loading
High-Level Assessment
The following are alternative approaches to this PR:
1. Shared hook error-reporting wrapper
➕ Removes duplicated try/except + warning formatting across multiple skills
➕ Enforces consistent stdout/stderr behavior and message format repo-wide
➖ Requires introducing and distributing a shared helper module (and updating other hooks to use it)
➖ Slightly higher coordination cost than a targeted fix in one hook
2. Structured (JSON) diagnostic output channel
➕ Machine-parseable warnings (severity/code/path) for tooling/CI aggregation
➕ Avoids mixing human warnings into injected text streams if a runner can route them separately
➖ Only useful if the hook runner/tooling is prepared to handle a structured side-channel
➖ More complexity than needed for a simple visibility fix
Recommendation: Current approach (emit a concise stdout WARNING in addition to stderr) is the best fit given stdout-injecting harnesses may hide stderr. If multiple skills adopt similar logic, consider extracting a small shared wrapper to standardize formatting and reduce repetition.
• Adds AGPL license comment and expands guidance on tool-specific mutant status semantics. Updates Stryker incremental docs to recommend CI caching of the incremental JSON rather than committing it. Refreshes mutmut guidance for 3.x config keys and workflow (browse/TUI, mutants/ state), and corrects PIT PR-diff guidance to reflect removal of scmMutationCoverage and the need for alternative git integration or version pinning. Updates the universal CI pattern to prefer CI caches over repo commits for state files.
skill_prehook.pyMake prehook failures visible on stdout and tighten trigger regexes+35/-6
Make prehook failures visible on stdout and tighten trigger regexes
• Adds license header and clarifies stdout contract to include loud warnings on failures. Tightens keyword triggers (avoids broad "are my tests" matches; supports plural "weak assertions"). On file-read and runtime failures, now emits detailed WARNING messages to stdout while still logging to stderr; exit behavior remains non-breaking (always 0).
SKILL.mdAdd license header and refine equivalent-mutant ceiling guidance+19/-1
Add license header and refine equivalent-mutant ceiling guidance
• Adds an AGPL license notice comment after YAML front matter (to preserve loader requirements). Updates the equivalent-mutant discussion to avoid a single hard-coded rate and references the classic manual-analysis study contextually.
agent-mutation-loop.mdAdd license header and polish research/cost-control guidance+18/-3
Add license header and polish research/cost-control guidance
• Adds AGPL license comment and updates the research-support bullets to be less numerically assertive while naming sources. Adjusts fenced block to explicit text formatting and refines cost-control wording, including updated mutmut guidance.
AGENTS.mdDocument dual-channel (stdout+stderr) loud failure policy for hooks+4/-2
Document dual-channel (stdout+stderr) loud failure policy for hooks
• Updates repo guidance to specify that hook failures must be visible to users via a stdout WARNING line in addition to stderr logging, while still always exiting 0 to avoid breaking prompt flow.
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Pull Request Overview
This PR successfully updates the mutation-testing skill to align with modern toolchains (mutmut 3.x, PIT 1.7+, and StrykerJS) and improves reliability through a 'fail-loudly' error reporting mechanism in the pre-hook. While the implementation of the dual-channel error reporting (stdout/stderr) and the placement of license headers are correct, there is a significant gap in verification: no unit or integration tests were provided to validate the updated regex triggers or the exception-handling logic. Additionally, the qualitative triggers should be expanded to handle singular nouns to ensure consistent behavior when users query the quality of a single test.
About this PR
No new or updated test files were included in the diff to verify the refined regex triggers or the dual-channel error reporting logic, despite the verification steps listed in the PR description.
Test suggestions
Verify that the keyword trigger matches plural 'weak assertions'\n- [ ] Verify that the trigger stays silent for 'are my tests passing?' while firing for 'are my tests actually good'\n- [ ] Verify that a FileNotFoundError during skill read emits a WARNING with error details to stdout\n- [ ] Verify that a generic Exception in the hook's main loop emits a WARNING to stdout
Prompt proposal for missing tests
Consider implementing these tests if applicable:
1. Verify that the keyword trigger matches plural 'weak assertions'\n- [ ] Verify that the trigger stays silent for 'are my tests passing?' while firing for 'are my tests actually good'\n- [ ] Verify that a FileNotFoundError during skill read emits a WARNING with error details to stdout\n- [ ] Verify that a generic Exception in the hook's main loop emits a WARNING to stdout
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⚪ LOW RISK
Suggestion: The trigger for evaluating test quality only matches the plural form ("are my tests"). Users often ask questions in the singular (e.g., "is my test good?"). Expanding the regex to handle both singular and plural forms ensures the mutation-testing skill is correctly injected for both cases.\n\nsuggestion\n r"\b(is|are) my tests? (actually )?(good|catching|enough|worth|strong)\b", r"\bweak assertions?\b",\n
The top-level exception handler writes to stdout/stderr without guarding write failures; if the
original error was caused by a broken output stream (e.g., stdout pipe closed), the handler can
raise again before sys.exit(0), violating the documented “hooks always exit 0” contract.
ⓘ Recommendations generated based on similar findings in past PRs
Evidence
The new exception handler unconditionally writes a WARNING to stdout during failure handling, so if
stdout is the source of the failure the handler can throw again and never reach sys.exit(0). The
repo documentation explicitly states hooks must always exit 0 and failures should be loud on
stdout/stderr.
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution
## Issue description
The mutation-testing prehook promises to always exit 0, but the new failure-reporting code writes to stdout/stderr inside exception paths without handling write errors. If stdout/stderr is broken/closed (or the triggering exception is itself a BrokenPipeError from an earlier write), the handler can throw again and terminate before reaching `sys.exit(0)`.
## Issue Context
This PR intentionally makes failures “loud on both channels” by adding `sys.stdout.write(...)` warnings in error paths. That increases the chance of a second exception during error handling.
## Fix Focus Areas
- .agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py[122-134]
- .agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py[147-158]
## Suggested fix
- Wrap stdout/stderr writes in a small helper like `safe_write(stream, text)` that catches `BrokenPipeError`/`OSError` and returns.
- Use that helper for **all** diagnostic writes (both the OSError fallback warning and the top-level exception handler), so the process reliably reaches `sys.exit(0)` even when output streams are unavailable.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
2. skill_prehook.py uses space indentation 📘 Rule violation⚙ Maintainability
Description
The updated prehook script includes indented lines that start with spaces rather than tabs. This
violates the repository rule requiring tab-only indentation in changed source files.
+ sys.stdout.write(+ f"[mutation-testing prehook WARNING: could not read the skill "+ f"file at {skill_path} ({type(file_error).__name__}: {file_error}); "+ "falling back to a path directive.]\n"
Relevance
● Weak
Similar “replace spaces with tabs” findings were rejected (tabs-only enforcement not followed).
ⓘ Recommendations generated based on similar findings in past PRs
Evidence
PR Compliance ID 2401137 requires that changed source files use tabs for indentation, not spaces.
The modified block around sys.stdout.write(...) in skill_prehook.py is indented with spaces.
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution
## Issue description
The file `.agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py` contains indentation using leading spaces on indented lines, but the repo compliance rule requires tabs for indentation.
## Issue Context
This PR modified the file and added/changed indented lines in the `except OSError` block; those lines currently begin with spaces.
## Fix Focus Areas
- .agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py[117-158]
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
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2. Hook may exit non-zero 🐞 Bug☼ Reliability
The top-level exception handler writes to stdout/stderr without guarding write failures; if the
original error was caused by a broken output stream (e.g., stdout pipe closed), the handler can
raise again before sys.exit(0), violating the documented “hooks always exit 0” contract.
Agent Prompt
## Issue description
The mutation-testing prehook promises to always exit 0, but the new failure-reporting code writes to stdout/stderr inside exception paths without handling write errors. If stdout/stderr is broken/closed (or the triggering exception is itself a BrokenPipeError from an earlier write), the handler can throw again and terminate before reaching `sys.exit(0)`.
## Issue Context
This PR intentionally makes failures “loud on both channels” by adding `sys.stdout.write(...)` warnings in error paths. That increases the chance of a second exception during error handling.
## Fix Focus Areas
- .agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py[122-134]
- .agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py[147-158]
## Suggested fix
- Wrap stdout/stderr writes in a small helper like `safe_write(stream, text)` that catches `BrokenPipeError`/`OSError` and returns.
- Use that helper for **all** diagnostic writes (both the OSError fallback warning and the top-level exception handler), so the process reliably reaches `sys.exit(0)` even when output streams are unavailable.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Post-merge review triage — all bot comments addressed
This PR merged before every finding was triaged; the valid ones are fixed in follow-up PR #96.
@qodo-code-review
Hook may exit non-zero (bug, skill_prehook.py) — valid, fixed in fix: PR #59/#60 review — FAQ channel-read disclosure; prehook broken-stream guard #96 (81866bb). Reproduced before the fix: a triggering prompt with stdout closed exited 1, breaking the documented always-exit-0 contract — the exception handler's own stream writes were unguarded. Both writes are now individually guarded; verified broken-stdout → exit 0, broken-stderr → exit 0, and the trigger / no-match / garbage-stdin paths unchanged. Installed copy re-synced to ~/.agents/skills/mutation-testing.
skill_prehook.py uses spaces, not tabs (rule violation) — declined. It is a Python file, space-indented per PEP 8 since its creation in chore: mutation-testing skill source + pre-hook + role docs #55; the repo's tabs convention targets the Svelte/TypeScript codebase.
@codacy-production — Trigger only matches the plural "are my tests" (low) — valid, fixed in #96 (72d102f). The trigger is now \b(is|are) my tests? (actually )?(good|catching|enough|worth|strong)\b. Verified: "is my test good?" and the plural forms inject the skill; "how are my tests today" and unrelated prompts stay silent.
@CodeAnt-AI — quality gate passed; sequence diagram and review status comments are informational, nothing actionable. @coderabbitai — rate-limited, no actionable comments. @netlify — deploy preview, informational. @sonarqubecloud — quality gate passed.
Question: a triggering prompt with stdout closed exited 1, breaking the documented always-exit-0 contract — the exception handler's own stream writes were unguarded. both writes are now individually guarded; verified broken-stdout → exit 0, broken-stderr → exit 0, and the trigger / no-match / garbage-stdin paths unchanged. installed copy re-synced to ~/.agents/skills/mutation-testing.
skill_prehook.py uses spaces, not tabs (rule violation) — declined. it is a python file, space-indented per pep 8 since its creation in chore: mutation-testing skill source + pre-hook + role docs #55; the repo's tabs convention targets the svelte/typescript codebase.
@codacy-production — trigger only matches the plural "are my tests" (low) — valid, fixed in #96 (72d102f). the trigger is now \b(is|are) my tests? (actually )?(good|catching|enough|worth|strong)\b. verified: "is my test good?" and the plural forms inject the skill; "how are my tests today" and unrelated prompts stay silent.
@CodeAnt-AI — quality gate passed; sequence diagram and review status comments are informational, nothing actionable. @coderabbitai — rate-limited, no actionable comments. @netlify — deploy preview, informational. @sonarqubecloud — quality gate passed.
Answer:
The always exit 0 contract is still broken for a triggering prompt when stdout is closed.
In the outer exception handler, both writes remain unguarded:
sys.stderr.write(...)
sys.stdout.write(...)
If main() raises because stdout is unavailable, the first stderr write may succeed, but the subsequent stdout.write() raises BrokenPipeError. That exception escapes the handler, so Python exits nonzero instead of reaching sys.exit(0). If stderr is also unavailable, the first write can fail for the same reason.
Guard each diagnostic stream independently, for example:
The same principle should be applied to the OSError fallback branch if the hook must guarantee exit 0 under broken stdout/stderr in all failure paths. After that, the final sys.exit(0) can execute reliably.
Commit 81866bb guards each output-stream write in skill_prehook.py. The handler can now reach sys.exit(0) when either stdout or stderr is broken.
Commit 72d102f supports both is my test good? and plural forms with \b(is|are) my tests? (actually )?(good|catching|enough|worth|strong)\b.
The space indentation in this Python file is appropriate. It does not require a tabs-based change.
PR #96 is still open. The fixes are not merged yet, but the inspected changes address the stated findings.
✏️ Learnings added
Learnt from: Bonobo791
URL: https://github.com/Bonobo791/Moderaty/pull/60
Timestamp: 2026-08-05T14:10:21.672Z
Learning: In the Moderaty repository, the tabs convention applies to the Svelte/TypeScript codebase. Python files, including `.agents/skills-src/mutation-testing/assets/hooks/skill_prehook.py`, use spaces according to PEP 8.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
Post-merge review triage — all bot comments addressed
This PR merged before every finding was triaged; the valid ones are fixed in follow-up PR #96.
@qodo-code-review
Hook may exit non-zero (bug, skill_prehook.py) — valid, fixed in fix: PR #59/#60 review — FAQ channel-read disclosure; prehook broken-stream guard #96 (81866bb). Reproduced before the fix: a triggering prompt with stdout closed exited 1, breaking the documented always-exit-0 contract — the exception handler's own stream writes were unguarded. Both writes are now individually guarded; verified broken-stdout → exit 0, broken-stderr → exit 0, and the trigger / no-match / garbage-stdin paths unchanged. Installed copy re-synced to ~/.agents/skills/mutation-testing.
skill_prehook.py uses spaces, not tabs (rule violation) — declined. It is a Python file, space-indented per PEP 8 since its creation in chore: mutation-testing skill source + pre-hook + role docs #55; the repo's tabs convention targets the Svelte/TypeScript codebase.
@codacy-production — Trigger only matches the plural "are my tests" (low) — valid, fixed in #96 (72d102f). The trigger is now \b(is|are) my tests? (actually )?(good|catching|enough|worth|strong)\b. Verified: "is my test good?" and the plural forms inject the skill; "how are my tests today" and unrelated prompts stay silent.
@CodeAnt-AI — quality gate passed; sequence diagram and review status comments are informational, nothing actionable. @coderabbitai — rate-limited, no actionable comments. @netlify — deploy preview, informational. @sonarqubecloud — quality gate passed.
Thanks for the post-merge triage. Based on the details provided:
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User description
Why
PR #58 was closed unmerged during branch cleanup; its review findings were still valid against
main. This PR resurrects them on a fresh branch from currentorigin/main:6e8c18b— cherry-pick of the unmerged fix: PR #55 review round 3 — coderabbit findings on the mutation-testing skill #58 head (19ea615): stdout failure visibility, tightenedare my teststrigger, mutmut 3.x / PIT scm / Stryker corrections, cited research claims, license headers. AGENTS.md auto-merged cleanly with the docs: bullet the rules list, add PR-review triage and no-default-branch rules #57 rules changes.d03a6d6— the round-3 fixes that were uncommitted when fix: PR #55 review round 3 — coderabbit findings on the mutation-testing skill #58 closed:FileNotFoundError: [Errno 2] ...), matching stderr — permission-denied vs missing-file are now distinguishable on both channels.\bweak assertions?\b(plural).--incrementaldoc now says cachereports/stryker-incremental.jsonin CI, not commit it; theUniversal CI patternitem reworded to match (CI cache, not the repo).Verification
codacy-analysis analyze --fileson all 6 changed files — 0 issues.npm run test— 371 passed.npm run check— 0/0.npm run build— clean.~/.agents/skills/mutation-testing(diff-verified).CodeAnt-AI Description
Make mutation-testing guidance accurate and hook failures visible
What Changed
Impact
✅ Visible mutation-testing hook failures✅ Fewer unintended skill injections✅ Accurate current-tool setup guidance💡 Usage Guide
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