Pygienium

Code hygiene for pi — isolated sub-agent checks that scan a target, apply fixes, and emit a findings + changes report. Inspired by piolium's sub-agent loops.

Pygienium runs highly-structured hygiene passes over a repo to clean up the common quality issues LLM-generated code accumulates: restating comments, shallow pass-through modules, dead exports/files, and redundant defensive guards. Each check is an isolated, resumable sub-agent run whose progress lands in a single inspectable run-state file.

Install

pi install npm:@mikefreno/pygienium

On load it emits a TUI notification Pygienium loaded. Run /pygienium-help for available checks and flags. (only when a dialog-capable UI is available).

Configuration

Pygienium reads its chat-rendering style from pi's settings.json (~/.pi/agent/settings.json) under a pygienium key:

{
  "pygienium": {
    "chatStyle": "verbose"
  }
}

| Setting | Default | Values | Description | | --- | --- | --- | --- | | pygienium.chatStyle | "verbose" | "verbose" | "compact" | Chat rendering for sub-agent tool calls. verbose (piolium-style) streams each tool event live as its own chat line ([Comments: Scanning] → bash ... / ← (ok)). compact (ralpi-style) suppresses the per-event stream and shows only the final completion message with its expandable phase tree. |

No entry means "verbose" (the default). An unreadable or missing settings.json also falls back to "verbose".

Environment variable (read at run time):

| Env var | Default | Description | | --- | --- | --- | | PYGIENIUM_AGENT_TIMEOUT_MS | 3600000 (60 min) | Per-agent-phase settle deadline. A sub-agent session that never settles (stalled provider stream, hung retry/auto-compaction after its last tool call) is aborted and the phase fails with a visible error instead of hanging the run mid-transition with no state update and no completion message. Lower it (e.g. 1200000) to fail fast on flaky providers; raise it for very large repos.

Commands

Every command accepts a [path] target (default: the current directory) and is resumable — progress is persisted to <cwd>/.pygienium/run-state.json.

| Command | What it does | | --- | --- | | /pygienium-help | Print every command, shipped check, and flag. | | /pygienium-<check> [path] [--fix] | Run one isolated sub-agent that scans a target, applies fixes with --fix, and emits a findings + changes report. | | /pygienium-all [path] [--fix] | Run every registered check in sequence under one resumable run-state. | | /pygienium-status [path] | Show per-check progress, artifact line counts, and errors for the latest run. | | /pygienium-resume [path] [--fresh] | Resume the latest in-progress/failed/partial run; complete/skipped checks skip unless --fresh. | | /pygienium-export [path] [--check=] [--status=] [--out=md\|json] | Bundle every check's findings.md + changes.md into pygienium/export.{md\|json}. |

Flags

| Flag | Scope | Description | | --- | --- | --- | | [path] | all check commands | Target file or directory to scan (default: current dir). | | --fix | <check>, all, resume | Apply fixes (default: scan-only; emits findings only). | | --fresh | resume | Re-dispatch completed checks too — reset their run-state entries and re-run. | | --check= | export | Comma-separated check names to include in the bundle. | | --status= | export | Comma-separated statuses to include (e.g. complete,failed,skipped). | | --out= | export | Bundle format: md (default) or json. |

Checks

The five shipped checks live in src/checks/ and self-register on load. /pygienium-help lists whichever checks are currently registered, so this table and the live help always agree on the registered set.

| Command | Check | Agent | What it fixes | | --- | --- | --- | --- | | /pygienium-comments | comments | scanner / fixer | Remove low-value/restating comments, tighten verbose ones, keep "why" comments. | | /pygienium-deep-modules | deep-modules | deep-modules | Detect shallow modules (pass-throughs, trivial wrappers, re-export barrels) and consolidate the safe ones. | | /pygienium-dead-code | dead-code | scanner / fixer | Find unreferenced exports, dead files, obsolete compat shims, migration helpers, and unused dependencies; remove clearly-dead items and flag dynamic ones. | | /pygienium-defensive-guards | defensive-guards | defensive-guards | Remove redundant defensive guarding (null checks on non-nullable types, swallowing try/catch, masking fallbacks) while keeping boundary guards (IO, parsing, untrusted input). | | /pygienium-todos | todos | todos / fixer | Inventory TODO/FIXME markers and stub implementations; with --fix, convert silent stubs (placeholder returns, empty bodies) into loud failures — never implementing TODOs or deleting markers. |

Artifacts

Every check writes its reports under <cwd>/.pygienium/checks/<name>/ (run state lives at <cwd>/.pygienium/run-state.json):

• findings.md — what the scan found (per-file line refs).
• changes.md — what the fix phase changed + anything deferred for human review.

/pygienium-export merges every check's artifacts into one .pygienium/export.md (or export.json).

On first run in a git work tree, pygienium appends .pygienium/ to the target repo's .gitignore so a run never stages its own state/artifacts into git (opt out with --no-gitignore).

Adding a check

One file + one registerCheck() call. No index.ts command-wiring changes. index.ts auto-discovers every checks/*.ts (except the registry barrel) at startup, so a new file self-registers and /pygienium-<name> appears automatically.

1. Create src/checks/<name>.ts from the template below.
2. Edit the name, label, description, the rubric in the scan/fix task builders, and the gate precondition.
3. Keep the trailing registerCheck(<name>Check). Done.

import { registerCheck, type CheckScope } from "./registry.js";

export const myCheck = {
  name: "my-check",
  label: "My check",
  description: "What it fixes (shown in /pygienium-help).",
  agentName: "scanner",       // reuse a shipped agent, or add agents/<name>.md
  fixAgentName: "fixer",
  phaseId: "my-check",
  buildScanTask: (_cwd: string, scope: CheckScope) => `# Task: my-check scan\n…`,
  buildFixTask: (_cwd: string, scope: CheckScope, findings: string) => `# Task: my-check fix\n…`,
  gate: (cwd: string) => undefined,
} as const;

registerCheck(myCheck);

Reload pi (or /reload) and run /pygienium-help — /pygienium-my-check is listed and runnable. A CheckDefinition supplies the task builders and gate; the generic check-runner wires the phases together, so a new check never touches command plumbing.

Architecture

Each check is a "mode" running a fixed phase pipeline:

registerCheck(def)            ← checks/*.ts self-register on load
        │
        ▼
/pygienium-<check> ─► runCheck(def)        (src/modes/check-runner.ts)
        │
        ├─ Q0 recon (shared, run once per run)   (src/recon.ts)
        │     git state + source-file inventory → .pygienium/recon.json
        ├─ analysis sub-agent  (buildScanTask)    ← scanner/<check> agent
        │     writes .pygienium/checks/<name>/findings.md
        ├─ fix sub-agent       (buildFixTask)     ← fixer, only with --fix
        │     writes .pygienium/checks/<name>/changes.md
        ├─ verify gate         (re-runs check.gate)
        └─ cleanup             (drops transient scratch artifacts)

• Sub-agents are isolated in-memory AgentSessions scoped to the target cwd (see src/agent-runner.ts), with the agent definition's system prompt and tool allowlist applied. Agent definitions are plain editable markdown in agents/ (frontmatter name + allowedTools, body = system prompt) — tuning a sub-agent never needs TypeScript changes. A scanned project can ship its own agents/*.md at its root: those are loaded as overrides (repo agent wins on name collision), so teams can tune prompts or add project-specific agents without touching the extension.
• Run-state is a single JSON file at <cwd>/.pygienium/run-state.json (src/run-state.ts): per-check phase progress, captured findings/changes text, and recon status. /pygienium-status, /pygienium-resume, and /pygienium-export are pure reads over it; /pygienium-all shares one RunState across every check so phases accumulate in one record.
• The registry (src/checks/registry.ts) is the extensibility seam: a module-level Map of CheckDefinitions. index.ts iterates it and binds one /pygienium-<name> command per entry, so adding a check is a file + one registerCheck() line.
• The footer (src/footer.ts) is the piolium-style pipeline-overview status strip: a single static line in the TUI footer (via ui.setStatus(key, text)) listing the full ordered pipeline with the cursor on the current phase and what's to come. For a single check the items are the phases; for /pygienium-all they're the checks (the full todo list), and the per-check footer is suppressed so two overviews never compete over the same status slot. The chat widget (phases.ts) remains the animated detail view (spinner + tool-call tree + completion tree); the footer is the overview — the two never overlap. In print/JSON mode the footer is a no-op.

Layout

pygienium/
├─ src/
│  ├─ index.ts            ← entry: auto-discover checks, bind commands
│  ├─ commands.ts          ← slash-command handlers (thin binders)
│  ├─ help.ts              ← COMMANDS + CLI_FLAGS → /pygienium-help output
│  ├─ agent-runner.ts      ← isolated sub-agent sessions (injectable for tests)
│  ├─ agents.ts            ← markdown agent-definition loader
│  ├─ recon.ts             ← shared Q0 reconnaissance snapshot
│  ├─ run-state.ts         ← persistent, resumable run-state model
│  ├─ status.ts            ← /pygienium-status formatter (pure)
│  ├─ export.ts            ← /pygienium-export gatherer + md/json renderer
│  ├─ phases.ts            ← live chat progress widget + completion-tree helpers
│  ├─ footer.ts            ← pipeline-overview status strip (TUI footer)
│  ├─ modes/check-runner.ts ← the per-check phase pipeline
│  └─ checks/              ← one file per check, self-registering
│     ├─ registry.ts       ← CheckDefinition + registerCheck
│     ├─ comments.ts  deep-modules.ts  dead-code.ts
│     ├─ defensive-guards.ts
└─ agents/                 ← scanner.md  fixer.md  deep-modules.md  defensive-guards.md

Development

The omp port at ~/.omp/agent/extensions/pygienium is regenerated only by CI on push (.gitea/workflows/port-to-omp.yml) — never by hand.

The source repo's own tsconfig.json extends the host harness tsconfig, so the reliable typecheck target is the regenerated port (self-contained tsconfig + pinned @oh-my-pi SDK devDependency). A committed pre-commit hook runs exactly what CI runs — regenerate the port into a temp dir and tsc --noEmit it — and fails the commit on any error:

git config core.hooksPath .githooks

License

MIT