Michael Freno
d0e8ad5571
All per-check artifacts, all-summary, and export move from pygienium/ to .pygienium/; ensureRunStateIgnored appends .pygienium/ to the target repo's .gitignore on first run (opt out with --no-gitignore), so a run never stages its own output. Export now reads a single canonical root.
177 lines
8.8 KiB
Markdown
177 lines
8.8 KiB
Markdown
# Pygienium
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Code hygiene for [pi](https://github.com/earendil-works/pi-coding-agent) — isolated
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sub-agent checks that scan a target, apply fixes, and emit a findings + changes
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report. Inspired by piolium's sub-agent loops.
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Pygienium runs **highly-structured hygiene passes** over a repo to clean up the
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common quality issues LLM-generated code accumulates: restating comments,
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shallow pass-through modules, dead exports/files, and redundant defensive
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guards. Each check is an isolated, resumable sub-agent run whose progress lands
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in a single inspectable run-state file.
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## Install
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Pygienium is a local pi extension under `~/.pi/agent/extensions/pygienium/`.
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Pi loads it via `pi.extensions` in `package.json` (entry `./src/index.ts`).
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```sh
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# from the extension root
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bun install # optional: only needed for typecheck/test dev deps
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bun run typecheck
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bun test
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```
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Pi auto-discovers the extension from this location via the `pi.extensions` entry in `package.json` — no settings.json config is needed. 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).
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## Commands
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Every command accepts a `[path]` target (default: the current directory) and is
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resumable — progress is persisted to `<cwd>/.pygienium/run-state.json`.
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| Command | What it does |
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| --- | --- |
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| `/pygienium-help` | Print every command, shipped check, and flag. |
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| `/pygienium-<check> [path] [--fix]` | Run one isolated sub-agent that scans a target, applies fixes with `--fix`, and emits a findings + changes report. |
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| `/pygienium-all [path] [--fix]` | Run every registered check in sequence under one resumable run-state. |
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| `/pygienium-status [path]` | Show per-check progress, artifact line counts, and errors for the latest run. |
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| `/pygienium-resume [path] [--fresh]` | Resume the latest in-progress/failed/partial run; complete/skipped checks skip unless `--fresh`. |
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| `/pygienium-export [path] [--check=] [--status=] [--out=md\|json]` | Bundle every check's `findings.md` + `changes.md` into `pygienium/export.{md\|json}`. |
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## Flags
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| Flag | Scope | Description |
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| --- | --- | --- |
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| `[path]` | all check commands | Target file or directory to scan (default: current dir). |
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| `--fix` | `<check>`, `all`, `resume` | Apply fixes (default: scan-only; emits findings only). |
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| `--fresh` | `resume` | Re-dispatch completed checks too — reset their run-state entries and re-run. |
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| `--check=` | `export` | Comma-separated check names to include in the bundle. |
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| `--status=` | `export` | Comma-separated statuses to include (e.g. `complete,failed,skipped`). |
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| `--out=` | `export` | Bundle format: `md` (default) or `json`. |
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## Checks
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The five shipped checks live in [`src/checks/`](./src/checks/) and self-register
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on load. `/pygienium-help` lists whichever checks are currently registered, so
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this table and the live help always agree on the registered set.
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| Command | Check | Agent | What it fixes |
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| --- | --- | --- | --- |
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| `/pygienium-comments` | comments | `scanner` / `fixer` | Remove low-value/restating comments, tighten verbose ones, keep "why" comments. |
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| `/pygienium-deep-modules` | deep-modules | `deep-modules` | Detect shallow modules (pass-throughs, trivial wrappers, re-export barrels) and consolidate the safe ones. |
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| `/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. |
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| `/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). |
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| `/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. |
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## Artifacts
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Every check writes its reports under `<cwd>/.pygienium/checks/<name>/` (run
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state lives at `<cwd>/.pygienium/run-state.json`):
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- `findings.md` — what the scan found (per-file line refs).
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- `changes.md` — what the fix phase changed + anything deferred for human review.
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`/pygienium-export` merges every check's artifacts into one
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`.pygienium/export.md` (or `export.json`).
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On first run in a git work tree, pygienium appends `.pygienium/` to the
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target repo's `.gitignore` so a run never stages its own state/artifacts into
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git (opt out with `--no-gitignore`).
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## Adding a check
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One file + one `registerCheck()` call. **No `index.ts` command-wiring changes.**
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`index.ts` auto-discovers every `checks/*.ts` (except the registry barrel) at
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startup, so a new file self-registers and `/pygienium-<name>` appears
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automatically.
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1. Create `src/checks/<name>.ts` from the template below.
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2. Edit the `name`, `label`, `description`, the rubric in the scan/fix task
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builders, and the `gate` precondition.
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3. Keep the trailing `registerCheck(<name>Check)`. Done.
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```ts
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import { registerCheck, type CheckScope } from "./registry.js";
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export const myCheck = {
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name: "my-check",
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label: "My check",
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description: "What it fixes (shown in /pygienium-help).",
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agentName: "scanner", // reuse a shipped agent, or add agents/<name>.md
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fixAgentName: "fixer",
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phaseId: "my-check",
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buildScanTask: (_cwd: string, scope: CheckScope) => `# Task: my-check scan\n…`,
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buildFixTask: (_cwd: string, scope: CheckScope, findings: string) => `# Task: my-check fix\n…`,
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gate: (cwd: string) => undefined,
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} as const;
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registerCheck(myCheck);
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```
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Reload pi (or `/reload`) and run `/pygienium-help` — `/pygienium-my-check` is
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listed and runnable. A `CheckDefinition` supplies the task builders and gate;
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the generic check-runner wires the phases together, so a new check never
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touches command plumbing.
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## Architecture
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Each check is a "mode" running a fixed phase pipeline:
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```
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registerCheck(def) ← checks/*.ts self-register on load
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│
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▼
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/pygienium-<check> ─► runCheck(def) (src/modes/check-runner.ts)
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│
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├─ Q0 recon (shared, run once per run) (src/recon.ts)
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│ git state + source-file inventory → .pygienium/recon.json
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├─ analysis sub-agent (buildScanTask) ← scanner/<check> agent
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│ writes .pygienium/checks/<name>/findings.md
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├─ fix sub-agent (buildFixTask) ← fixer, only with --fix
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│ writes .pygienium/checks/<name>/changes.md
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├─ verify gate (re-runs check.gate)
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└─ cleanup (drops transient scratch artifacts)
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```
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- **Sub-agents** are isolated in-memory `AgentSession`s scoped to the target
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`cwd` (see `src/agent-runner.ts`), with the agent definition's system prompt
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and tool allowlist applied. Agent definitions are plain editable markdown in
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[`agents/`](./agents/) (frontmatter `name` + `allowedTools`, body = system
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prompt) — tuning a sub-agent never needs TypeScript changes.
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- **Run-state** is a single JSON file at `<cwd>/.pygienium/run-state.json`
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(`src/run-state.ts`): per-check phase progress, captured findings/changes
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text, and recon status. `/pygienium-status`, `/pygienium-resume`, and
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`/pygienium-export` are pure reads over it; `/pygienium-all` shares one
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`RunState` across every check so phases accumulate in one record.
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- **The registry** (`src/checks/registry.ts`) is the extensibility seam: a
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module-level `Map` of `CheckDefinition`s. `index.ts` iterates it and binds
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one `/pygienium-<name>` command per entry, so adding a check is a file +
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one `registerCheck()` line.
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## Layout
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```
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pygienium/
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├─ src/
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│ ├─ index.ts ← entry: auto-discover checks, bind commands
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│ ├─ commands.ts ← slash-command handlers (thin binders)
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│ ├─ help.ts ← COMMANDS + CLI_FLAGS → /pygienium-help output
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│ ├─ agent-runner.ts ← isolated sub-agent sessions (injectable for tests)
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│ ├─ agents.ts ← markdown agent-definition loader
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│ ├─ recon.ts ← shared Q0 reconnaissance snapshot
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│ ├─ run-state.ts ← persistent, resumable run-state model
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│ ├─ status.ts ← /pygienium-status formatter (pure)
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│ ├─ export.ts ← /pygienium-export gatherer + md/json renderer
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│ ├─ phases.ts ← footer status-strip UI adapter
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│ ├─ modes/check-runner.ts ← the per-check phase pipeline
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│ └─ checks/ ← one file per check, self-registering
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│ ├─ registry.ts ← CheckDefinition + registerCheck
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│ ├─ comments.ts deep-modules.ts dead-code.ts
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│ ├─ defensive-guards.ts noop.ts
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└─ agents/ ← scanner.md fixer.md deep-modules.md defensive-guards.md
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```
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## License
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MIT
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