paperlint 10.1.1 → 10.2.0

package/dist/studies.js

@@ -0,0 +1,160 @@
+/**
+ * `paperlint studies new|index <paper-dir>` — the two commands that write a paper's study registry,
+ * `repro/studies.json`, and its index in `repro/README.md` (docs/design/study-registry.md).
+ *
+ *   new <paper-dir> "<title>" [--kind <kind>]
+ *            the next id; `repro/<id>-<slug>/README.md` with the id and title in its frontmatter; the
+ *            row, `status: designing`, today's date; the index regenerated
+ *   index <paper-dir>
+ *            the index block of `repro/README.md`, regenerated from the registry
+ *
+ * Nothing else changes a row: a study's status, result and `in_paper` are edited in `studies.json`, and
+ * `repro/study-registered` checks them. The prefix is the paper's own choice, so a paper without a
+ * registry is refused with the file to write rather than given a guessed one.
+ */
+import { join, relative, resolve } from "node:path";
+import { callerPath } from "./caller-path.js";
+import { README, REPRO_DIR } from "./domain/repro-layout.js";
+import { DEFAULT_KIND, STUDIES_FILE, STUDY_KINDS, addStudy, indexInSync, isStudyKind, registryText, studyReadme, withIndex, } from "./domain/study-registry.js";
+import { registryOf } from "./study-registry-rule.js";
+const NEW_USAGE = 'npx paperlint studies new <paper-dir> "<title>" [--kind <kind>]';
+const INDEX_USAGE = "npx paperlint studies index <paper-dir>";
+const SUBS = `new or index — ${NEW_USAGE} · ${INDEX_USAGE}`;
+const STATUS_FILE = "PIPELINE-STATUS.md";
+const refuse = (code, line) => ({ code, line });
+/** The paper folder's registry, or the refusal naming why there is none to write to. */
+function registryIn(p, deps) {
+    const r = registryOf(p.dir, deps);
+    const file = `${p.shown}/${REPRO_DIR}/${STUDIES_FILE}`;
+    switch (r.kind) {
+        case "absent":
+            return refuse(1, `${file} does not exist. Its prefix is the paper's own choice — a capital letter, then capitals or digits, one per paper (P1) — so write the file, then run this again:\n\n{ "prefix": "P1", "studies": [] }`);
+        case "unreadable":
+            return refuse(1, `${file} is not a study registry: ${r.why}`);
+        case "read":
+            return r.registry;
+    }
+}
+const isRefusal = (v) => typeof v === "object" && v !== null && "code" in v && "line" in v;
+const text = (s) => new TextEncoder().encode(s);
+/** The README's text; null when there is none. */
+const readmeOf = (dir, files) => {
+    const b = files.readBytes(callerPath(join(dir, REPRO_DIR, README)));
+    return b === null ? null : new TextDecoder().decode(b);
+};
+const studiesCount = (r) => `${String(r.studies.length)} ${r.studies.length === 1 ? "study" : "studies"}`;
+/**
+ * Write the index of `r` into the README; whether it wrote. A block already in sync is left as it
+ * is, so the padding a formatter gave the table is never undone.
+ */
+function writeIndex(dir, r, files) {
+    const before = readmeOf(dir, files);
+    if (indexInSync(before, r))
+        return false;
+    files.writeAtomic(callerPath(join(dir, REPRO_DIR, README)), text(withIndex(before, r)));
+    return true;
+}
+/** The refusal when something that is not a file sits where `repro/README.md` goes; null when none. */
+function readmeBlocked(p, deps) {
+    const listed = deps.listDir(callerPath(join(p.dir, REPRO_DIR)));
+    const path = callerPath(join(p.dir, REPRO_DIR, README));
+    return listed.includes(README) && !deps.files.isFile(path)
+        ? refuse(1, `${p.shown}/${REPRO_DIR}/${README} is not a file, so the index cannot be written there. Move it, then run this again.`)
+        : null;
+}
+/** `studies index`: the README's block regenerated from the registry. */
+function runIndex(p, a, deps) {
+    const [surplus] = [...(a.title === undefined ? [] : [a.title]), ...a.extra];
+    if (surplus !== undefined)
+        return refuse(2, `studies index takes only the paper's folder — \`${surplus}\` is one argument too many`);
+    const r = registryIn(p, deps);
+    if (isRefusal(r))
+        return r;
+    const blocked = readmeBlocked(p, deps);
+    if (blocked !== null)
+        return blocked;
+    const readme = `${p.shown}/${REPRO_DIR}/${README}`;
+    return [
+        writeIndex(p.dir, r, deps.files)
+            ? `wrote the index of ${studiesCount(r)} in ${readme}`
+            : `the index in ${readme} is in sync with ${studiesCount(r)}`,
+    ];
+}
+/** `new`'s title and kind from the command line, or the refusal. */
+function newArgs(a) {
+    if (a.title === undefined)
+        return refuse(2, `studies new needs the study's title: ${NEW_USAGE}`);
+    const [surplus] = a.extra;
+    if (surplus !== undefined)
+        return refuse(2, `studies new takes the paper's folder and one title — \`${surplus}\` is one argument too many (quote a title of several words)`);
+    const kind = a.kind ?? DEFAULT_KIND;
+    return isStudyKind(kind)
+        ? { title: a.title, kind }
+        : refuse(2, `--kind ${kind} is not a kind of study: one of ${STUDY_KINDS.join(", ")}`);
+}
+/** Write a new study's README.md, the registry, and the index; the lines that say so. */
+function writeStudy(p, added, files) {
+    const { study, registry } = added;
+    const at = (...names) => callerPath(join(p.dir, REPRO_DIR, ...names));
+    files.writeAtomic(at(study.folder, README), text(studyReadme(study)));
+    files.writeAtomic(at(STUDIES_FILE), text(registryText(registry)));
+    writeIndex(p.dir, registry, files);
+    const repro = `${p.shown}/${REPRO_DIR}`;
+    return [
+        `created ${repro}/${study.folder}/${README}`,
+        `added ${study.id} to ${repro}/${STUDIES_FILE}: kind ${study.kind}, status ${study.status}, ${study.date}`,
+        `wrote the index of ${studiesCount(registry)} in ${repro}/${README}`,
+        `Next: write the study's one-sentence question in its row (\`question\`) and in its README.md. When it ends, set \`status\`, \`result\`, \`result_file\` and \`in_paper\` in its row, then run \`npx paperlint studies index ${p.shown}\`.`,
+    ];
+}
+/** `studies new`: the folder, its README.md, the row, the index. */
+function runNew(p, a, deps) {
+    const args = newArgs(a);
+    if (isRefusal(args))
+        return args;
+    const r = registryIn(p, deps);
+    if (isRefusal(r))
+        return r;
+    const blocked = readmeBlocked(p, deps);
+    if (blocked !== null)
+        return blocked;
+    const added = addStudy(r, { ...args, date: deps.today });
+    if (!added.ok)
+        return refuse(2, added.why);
+    const folder = added.study.folder;
+    return deps.listDir(callerPath(join(p.dir, REPRO_DIR))).includes(folder)
+        ? refuse(1, `${p.shown}/${REPRO_DIR}/${folder}/ already exists; it is never overwritten. Register it by hand, or remove it and run this again.`)
+        : writeStudy(p, added, deps.files);
+}
+/** The paper folder the command line names, or the refusal. */
+function paperOf(a, deps) {
+    if (a.sub === undefined)
+        return refuse(2, `studies needs a subcommand: ${SUBS}`);
+    if (a.sub !== "new" && a.sub !== "index")
+        return refuse(2, `unknown subcommand \`studies ${a.sub}\`: ${SUBS}`);
+    if (a.paperDir === undefined)
+        return refuse(2, `studies ${a.sub} needs the paper's folder: ${a.sub === "new" ? NEW_USAGE : INDEX_USAGE}`);
+    const dir = resolve(deps.cwd, a.paperDir);
+    const shown = relative(deps.cwd, dir) || ".";
+    return deps.files.isFile(callerPath(join(dir, STATUS_FILE)))
+        ? { dir, shown }
+        : refuse(2, `${shown} is not a paper folder: it has no ${STATUS_FILE}`);
+}
+/** The run: 0 done, 1 refused by the paper's state, 2 refused by the command line. */
+export function runStudies(a, deps) {
+    const p = paperOf(a, deps);
+    const out = isRefusal(p)
+        ? p
+        : a.sub === "new"
+            ? runNew(p, a, deps)
+            : runIndex(p, a, deps);
+    if (isRefusal(out)) {
+        deps.err(out.line);
+        return out.code;
+    }
+    out.forEach((line) => {
+        deps.log(line);
+    });
+    return 0;
+}
+//# sourceMappingURL=studies.js.map

package/dist/studies.js.map

@@ -0,0 +1 @@
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package/dist/study-registry-rule.d.ts

@@ -0,0 +1,17 @@
+import { type RegistryState, type StudyFinding } from "./domain/study-registry.ts";
+import type { FolderLayoutDeps } from "./folder-layout-rule.ts";
+import type { FolderRuleModule } from "./folder-venue-rule.ts";
+import type { StudyRegistryCodec } from "./ports/study-registry-codec.ts";
+/** What the rule reads with: the disk, its listings, and the registry's parser. */
+export interface StudyRegistryDeps extends FolderLayoutDeps {
+    readonly codec: StudyRegistryCodec;
+}
+/** The registry of the paper folder `dir`: absent, unreadable with why, or read. */
+export declare function registryOf(dir: string, deps: Pick<StudyRegistryDeps, "files" | "codec">): RegistryState;
+/** Every finding of the paper folder `dir`'s study registry — THE function behind the rule. */
+export declare function studyFindings(dir: string, deps: StudyRegistryDeps): readonly StudyFinding[];
+/** The rule, reading the folder through `deps`. */
+export declare function studyRegistryRules(deps: StudyRegistryDeps): Readonly<Record<"study-registered", FolderRuleModule>>;
+/** The level it is on at in paperlint's own config, for every paper's `PIPELINE-STATUS.md`. */
+export declare const STUDY_REGISTRY_RULE_LEVELS: Readonly<Record<"repro/study-registered", "error">>;
+//# sourceMappingURL=study-registry-rule.d.ts.map

package/dist/study-registry-rule.d.ts.map

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package/dist/study-registry-rule.js

@@ -0,0 +1,115 @@
+/**
+ * `repro/study-registered` — every study folder at the top of a paper's `repro/` has exactly one row in
+ * `repro/studies.json`, every row names a folder that exists, and the index in `repro/README.md` is the
+ * one the registry generates.
+ *
+ * What is judged, and why, is `src/domain/study-registry.ts` and docs/rules/repro/study-registered.md.
+ * This file lists `repro/`, reads the registry, the README and the result files, and reports.
+ *
+ * ── WHY A RULE OF ITS OWN, NOT MORE OF `repro/allowed-files-only` ─────────────────────
+ * `repro/allowed-files-only` judges what may stand at the top of `repro/`, by name, and accepts the
+ * dated `<slug>-YYYY-MM-DD` folders of a paper that predates the registry. This rule judges the
+ * registry against the folders. A paper that keeps its dated folders turns this one off and keeps
+ * its layout judged.
+ *
+ * ── WHICH FILE IT REPORTS ON ─────────────────────────────────────────────────────
+ * `PIPELINE-STATUS.md`, first line, like the layout rules: every paper has it, and ESLint lints no
+ * file in `repro/`.
+ */
+import { basename, dirname, join } from "node:path";
+import { callerPath } from "./caller-path.js";
+import { README, REPRO_BYPRODUCTS, REPRO_DIR, REPRO_DIRS, } from "./domain/repro-layout.js";
+import { STUDIES_FILE, judgeStudies, studyMessage, } from "./domain/study-registry.js";
+import { reproEntriesOf } from "./repro-layout-rule.js";
+import { rulePageUrl } from "./venue-rules.js";
+const STATUS_FILE = "PIPELINE-STATUS.md";
+/** The text of the file at `p`; null when there is none, or a directory sits there. */
+const textAt = (files, p) => {
+    const b = files.isFile(callerPath(p)) ? files.readBytes(callerPath(p)) : null;
+    return b === null ? null : new TextDecoder().decode(b);
+};
+/** The registry of the paper folder `dir`: absent, unreadable with why, or read. */
+export function registryOf(dir, deps) {
+    const text = textAt(deps.files, join(dir, REPRO_DIR, STUDIES_FILE));
+    if (text === null)
+        return { kind: "absent" };
+    const parsed = deps.codec.parse(text);
+    return parsed.ok
+        ? { kind: "read", registry: parsed.registry }
+        : { kind: "unreadable", why: parsed.why };
+}
+/** The study folders at the top of `<dir>/repro/`: every folder but the shared ones and the byproducts. */
+const studyFolders = (dir, deps) => reproEntriesOf(dir, deps)
+    .filter((e) => e.kind === "dir" &&
+    !REPRO_DIRS.includes(e.name) &&
+    !REPRO_BYPRODUCTS.includes(e.name))
+    .map((e) => e.name);
+/** Each `<folder>/<result_file>` of `r` that is a file. */
+const existingResults = (dir, r, files) => new Set((r.kind === "read" ? r.registry.studies : [])
+    .flatMap((s) => s.result_file === undefined ? [] : [`${s.folder}/${s.result_file}`])
+    // A NUL is no path the disk can hold, and probing one throws: such a row reads as missing.
+    .filter((p) => !p.includes("\0") &&
+    files.isFile(callerPath(join(dir, REPRO_DIR, p)))));
+/** Every finding of the paper folder `dir`'s study registry — THE function behind the rule. */
+export function studyFindings(dir, deps) {
+    const registry = registryOf(dir, deps);
+    return judgeStudies({
+        folders: studyFolders(dir, deps),
+        registry,
+        readme: textAt(deps.files, join(dir, REPRO_DIR, README)),
+        existingResults: existingResults(dir, registry, deps.files),
+    });
+}
+/** The problems a finding can be, each its own message id; the text is `studyMessage`. */
+const PROBLEMS = [
+    "no-registry",
+    "unreadable",
+    "unregistered",
+    "no-folder",
+    "two-rows",
+    "bad-id",
+    "duplicate-id",
+    "folder-name",
+    "long-title",
+    "no-result",
+    "result-file",
+    "no-successor",
+    "stale-index",
+];
+const META = {
+    type: "suggestion",
+    docs: {
+        description: "every study folder at the top of a paper's repro/ has exactly one row in repro/studies.json, every row names a folder that exists, and repro/README.md's index is the one the registry generates",
+        url: rulePageUrl("repro/study-registered"),
+    },
+    schema: [],
+    // The whole text is `studyMessage` (src/domain/study-registry.ts).
+    messages: Object.fromEntries(PROBLEMS.map((p) => [p, "{{text}}"])),
+};
+/** The rule, reading the folder through `deps`. */
+export function studyRegistryRules(deps) {
+    return {
+        "study-registered": {
+            meta: META,
+            create(context) {
+                if (basename(context.filename) !== STATUS_FILE)
+                    return {};
+                return {
+                    root() {
+                        const at = context.sourceCode.getLocFromIndex(0);
+                        studyFindings(dirname(context.filename), deps).forEach((f) => {
+                            context.report({
+                                loc: { start: at, end: at },
+                                messageId: f.problem,
+                                data: { text: studyMessage(f) },
+                            });
+                        });
+                    },
+                };
+            },
+        },
+    };
+}
+/** The level it is on at in paperlint's own config, for every paper's `PIPELINE-STATUS.md`. */
+export const STUDY_REGISTRY_RULE_LEVELS = { "repro/study-registered": "error" };
+//# sourceMappingURL=study-registry-rule.js.map

package/dist/study-registry-rule.js.map

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package/docs/design/study-registry.md

@@ -0,0 +1,130 @@
+# The study registry — design
+
+A paper's `repro/` holds one folder per study. Named `<slug>-YYYY-MM-DD`, they sort by date and say
+nothing else: a real paper reached 79 study folders, and nobody could tell which one a number in the
+paper came from, which ones had ended, or which were current. This note fixes the shape of the
+registry that gives every study a stable number and a plain name, the lint rule that holds it, and the
+two commands that write it.
+
+## What is decided
+
+1. **One registry, `repro/studies.json`, JSON with a schema.** Never markdown: a table in a README is
+   what people edit by hand and what a parser has to guess at. The schema (zod, in
+   `src/adapters/study-registry/`) is checked where the file is read; nothing after that re-validates.
+
+   ```json
+   {
+     "prefix": "P1",
+     "studies": [
+       {
+         "id": "P1-S01",
+         "folder": "P1-S01-baseline-pass-rate",
+         "title": "Baseline pass rate",
+         "question": "How often does the unmodified agent pass the task?",
+         "kind": "measurement",
+         "status": "done",
+         "date": "2026-10-15",
+         "result": "41 of 60 runs pass",
+         "result_file": "results.tsv",
+         "in_paper": "yes"
+       }
+     ]
+   }
+   ```
+
+   | field           | values                                                                    |
+   | --------------- | ------------------------------------------------------------------------- |
+   | `prefix`        | the paper's prefix: a capital letter, then capitals or digits (`P1`)      |
+   | `id`            | `<prefix>-S<two or more digits>`, unique                                  |
+   | `folder`        | `<id>-<slug>`: the study's folder at the top of `repro/`                  |
+   | `title`         | a plain name, at most 8 words                                             |
+   | `question`      | one sentence: what the study asks                                         |
+   | `kind`          | `measurement`, `spike`, `tooling`, `data`, `artifact`, `salvage`          |
+   | `status`        | `designing`, `running`, `done`, `stopped`, `superseded`, `dropped`        |
+   | `date`          | `YYYY-MM-DD`, the day it was registered                                   |
+   | `result`        | optional; one line. Required when `done`                                  |
+   | `result_file`   | optional; a path inside the folder. Required, and must exist, when `done` |
+   | `superseded_by` | optional; an id in the registry. Required when `superseded`               |
+   | `in_paper`      | `yes`, `no`, `registry` (listed only in the registry, not in the text)    |
+
+   **A row may carry more fields**, and they are kept: a paper merges its own measurement metadata
+   into the rows (`role`, `frame`, `method`, `outcome`, …). The top level is closed: a misspelt
+   `prefix` is an error, not an ignored key.
+
+2. **The rule `repro/study-registered`, an error,** reported on the first line of
+   `PIPELINE-STATUS.md` like `repro/allowed-files-only`, once per finding:
+
+   - every folder at the top of `repro/` that is not `tools/`, `data/` or a byproduct the layout
+     ignores (`__pycache__/`, `node_modules/`, …) has exactly one row, and every row's folder exists;
+   - the folder is `<id>-<slug>`, the id is `<prefix>-S<digits>`, ids are unique;
+   - `done` has a `result` and an existing `result_file`; `superseded` names an existing id in
+     `superseded_by`; a title has at most 8 words;
+   - **the index is in sync:** the block of `repro/README.md` between the two markers below equals the
+     text generated from `studies.json`. The comparison is of strings. The markdown is output only and
+     is never parsed.
+
+     ```
+     <!-- studies:begin — generated from studies.json by `paperlint studies index`; do not edit -->
+     <!-- studies:end -->
+     ```
+
+   - a paper with study folders and no `repro/studies.json` gets one finding naming the file.
+   - a `studies.json` that is not JSON, or not of the schema, gets one finding with the reasons.
+
+3. **Two commands**, in `src/studies.ts`, wired in `src/cli.ts`:
+
+   - `paperlint studies new <paper-dir> "<title>" [--kind measurement]` takes the next id, creates
+     `repro/<id>-<slug>/README.md` (frontmatter `id:` and `title:`), appends the row with
+     `status: designing`, `in_paper: no` and today's date, and regenerates the index block. It refuses a
+     title over 8 words, a title with no letter or digit to make a slug from, an unknown kind, a folder
+     that already exists, and a paper with no `studies.json` (the prefix is the author's choice, so the
+     refusal names the file to write and does not guess one).
+   - `paperlint studies index <paper-dir>` regenerates the index block: a table with the columns id ·
+     title · status · result · in paper · folder. With no markers in `repro/README.md` the block is
+     appended; with no `repro/README.md` the file is written.
+
+4. **The layout accepts `<id>-<slug>` beside `<slug>-YYYY-MM-DD`.** `repro/allowed-files-only` keeps
+   accepting the dated form, so a paper that turns the registry off is not broken by this change; it
+   also allows `studies.json` at the top of `repro/`. A folder in the dated form is still reported by
+   `repro/study-registered` as unregistered — that is the point of the registry — and the paper decides
+   whether to register it or turn the rule off.
+
+5. **Skills.** `build-benchmark`, `run-agent-grid` and `build-label-page` create a study only with
+   `paperlint studies new`, and update its row (status, result, result file, in paper) when it ends,
+   then run `paperlint studies index`.
+
+## Where each part lives
+
+| part                                    | file                                | layer   |
+| --------------------------------------- | ----------------------------------- | ------- |
+| the types, the judge, the index, ids    | `src/domain/study-registry.ts`      | domain  |
+| the schema (zod), parsing the text      | `src/adapters/study-registry/`      | adapter |
+| what the app asks of a parser           | `src/ports/study-registry-codec.ts` | port    |
+| the rule: list the folder, read, report | `src/study-registry-rule.ts`        | app     |
+| the two commands                        | `src/studies.ts`                    | app     |
+| wiring, the clock for today's date      | `src/cli.ts`                        | root    |
+
+The judge is pure: it takes the folder names, the parsed registry (or why it is absent or unreadable),
+the README's text, and which result files exist, and returns findings. The rule and the commands are
+the only places that touch the disk, through the `Files` and `ListDir` ports.
+
+## Generated index, and prettier
+
+The index is a table whose columns are padded to their widest cell, the way prettier writes a
+markdown table, so formatting `repro/README.md` with prettier does not make the block stale. A `|` in
+a cell is escaped and a line break becomes a space.
+
+## Rejected, by the author on 2026-10-15
+
+- Commands that change a study's status: the row is edited in `studies.json`, the rule checks it.
+- Detecting automatically whether a study is cited in the paper: `in_paper` is declared.
+- An adopt or migration command for existing folders: there are no other users; the folders are
+  renamed by hand once.
+- A PreToolUse hook for the registry: the lint is the guarantee, and the layout hook already refuses
+  a loose entry.
+
+## What it does not check
+
+- Whether the `question` is one sentence, or the `result` one line, beyond their being strings.
+- What a study's `README.md` says, or whether its frontmatter matches the row.
+- Files inside a study folder other than `result_file`.