paperlint 10.1.1 → 10.2.0

package/dist/domain/repro-layout.js

@@ -7,15 +7,21 @@
  * where a new run goes. The layout gives each kind of material one place:
  *
  *   repro/
- *   ├── README.md              the index: one line per study
- *   ├── <slug>-YYYY-MM-DD/     one folder per study or spike, with a README.md inside
+ *   ├── README.md              the index: one line per study, generated from studies.json
+ *   ├── studies.json           the study registry: one row per study (src/domain/study-registry.ts)
+ *   ├── <id>-<slug>/           one folder per study or spike, named by its row, with a README.md inside
  *   ├── tools/                 scripts used across the paper (numbers, figures, anonymity check, harnesses)
  *   └── data/                  shared data (tables, caches)
  *
  * plus `.gitignore`. A loose note belongs in its study's folder or in the paper's `research/`.
  *
- * ── THE DATE IN A STUDY'S NAME ────────────────────────────────────────────────────
- * `<slug>-YYYY-MM-DD` is the day the study began. `<slug>-YYYY-MM` is accepted too: a study that ran
+ * ── A STUDY'S NAME ───────────────────────────────────────────────────────────────
+ * `<id>-<slug>` (`P1-S03-baseline`): the id of the study's row in `repro/studies.json` — the paper's
+ * prefix, `-S`, two or more digits — then the slug. Whether the id has a row, and the row this folder,
+ * is `repro/study-registered`'s question; this layout only accepts the shape.
+ *
+ * The older form, `<slug>-YYYY-MM-DD`, stays accepted, so a paper that turned the registry off is not
+ * broken: the date is the day the study began. `<slug>-YYYY-MM` is accepted too: a study that ran
  * over weeks (labelling, a reading of a corpus) has a month as its honest date, and both forms sort
  * by time. The date must be a real one (no month 13, no 30 February). The slug is lowercase letters
  * and digits in words joined by single hyphens.
@@ -30,11 +36,20 @@ import { extname } from "node:path";
 import { leaf, renderTree } from "./layout-tree.js";
 /** The folder this layout governs, at the paper folder's root. */
 export const REPRO_DIR = "repro";
+/** The study registry, at the top of `repro/` (src/domain/study-registry.ts). */
+export const STUDIES_FILE = "studies.json";
 /** The index at the top of `repro/`, and the file every study folder holds. */
 export const README = "README.md";
 /** The files `repro/` may hold at its top, by exact name. */
 export const REPRO_FILE_NOTES = [
-    { name: README, note: "the index: one line per study" },
+    {
+        name: README,
+        note: "the index: one line per study, generated from studies.json",
+    },
+    {
+        name: STUDIES_FILE,
+        note: "the study registry: id, title, status and result of each study",
+    },
     { name: ".gitignore", note: "keeps the scripts' byproducts out of git" },
 ];
 export const REPRO_FILES = REPRO_FILE_NOTES.map((f) => f.name);
@@ -51,8 +66,8 @@ export const REPRO_DIR_NOTES = [
 export const REPRO_DIRS = REPRO_DIR_NOTES.map((d) => d.name);
 /** The study folder as the layout draws it: the name pattern, and the README.md it must hold. */
 const STUDY_NODE = {
-    name: "<slug>-YYYY-MM-DD/",
-    note: "one folder per study or spike (<slug>-YYYY-MM for one that ran over weeks)",
+    name: "<id>-<slug>/",
+    note: "one folder per study or spike, named by its row in studies.json (P1-S03-baseline)",
     children: [
         leaf(README, "required: what it asks, how to run it, what it found"),
     ],
@@ -80,13 +95,19 @@ export const REPRO_BYPRODUCTS = [
     ".DS_Store",
     "Thumbs.db",
 ];
-/** A study's name: a slug, then the year, the month, and optionally the day it began. */
+/** A slug: lowercase letters and digits, in words joined by single hyphens. */
+export const STUDY_SLUG = /^[a-z0-9]+(?:-[a-z0-9]+)*$/u;
+/** A dated study's name: a slug, then the year, the month, and optionally the day it began. */
 const STUDY_NAME = /^([a-z0-9]+(?:-[a-z0-9]+)*)-(\d{4})-(\d{2})(?:-(\d{2}))?$/u;
+/** A registered study's name: the id (a prefix, `-S`, two or more digits), then the slug. */
+const REGISTERED_STUDY_NAME = /^[A-Z][A-Z0-9]*-S\d{2,}-[a-z0-9]+(?:-[a-z0-9]+)*$/u;
+/** Whether `name` is a registered study folder's: `<id>-<slug>`, as `P1-S03-baseline`. */
+export const isRegisteredStudyName = (name) => REGISTERED_STUDY_NAME.test(name);
 const isLeapYear = (y) => (y % 4 === 0 && y % 100 !== 0) || y % 400 === 0;
 /** The days in month `m` (1–12) of year `y`. */
 const daysIn = (y, m) => m === 2 ? (isLeapYear(y) ? 29 : 28) : [4, 6, 9, 11].includes(m) ? 30 : 31;
-/** Whether `name` is a study folder's: `<slug>-YYYY-MM-DD` or `<slug>-YYYY-MM`, a real date. */
-export function isStudyName(name) {
+/** Whether `name` is a dated study folder's: `<slug>-YYYY-MM-DD` or `<slug>-YYYY-MM`, a real date. */
+function isDatedStudyName(name) {
     const m = STUDY_NAME.exec(name);
     if (m === null)
         return false;
@@ -95,6 +116,8 @@ export function isStudyName(name) {
     const day = m[4] === undefined ? 1 : Number(m[4]);
     return month >= 1 && month <= 12 && day >= 1 && day <= daysIn(year, month);
 }
+/** Whether `name` is a study folder's: `<id>-<slug>`, or the dated `<slug>-YYYY-MM-DD` / `<slug>-YYYY-MM`. */
+export const isStudyName = (name) => isRegisteredStudyName(name) || isDatedStudyName(name);
 /**
  * The study name to suggest for a folder named `name`: its name as a slug, with the date to fill in.
  * A name that becomes a study name once lowercased and hyphenated is suggested as it is.
@@ -104,10 +127,18 @@ export function suggestedStudyName(name) {
         .toLowerCase()
         .replace(/[^a-z0-9]+/gu, "-")
         .replace(/^-+|-+$/gu, "");
-    if (isStudyName(slug))
+    if (isDatedStudyName(slug))
         return slug;
-    const base = slug.replace(/(?:^|-)\d{4}(?:-\d{1,2}){0,2}$/u, "");
-    return `${base === "" ? "<slug>" : base}-YYYY-MM-DD`;
+    return `${suggestedSlug(name)}-YYYY-MM-DD`;
+}
+/** The slug to suggest for a folder named `name`: its name as a slug, any trailing date dropped. */
+export function suggestedSlug(name) {
+    const base = name
+        .toLowerCase()
+        .replace(/[^a-z0-9]+/gu, "-")
+        .replace(/^-+|-+$/gu, "")
+        .replace(/(?:^|-)\d{4}(?:-\d{1,2}){0,2}$/u, "");
+    return base === "" ? "<slug>" : base;
 }
 /** The extensions of a script: what a study or the paper's build runs. */
 export const SCRIPT_EXTENSIONS = [
@@ -169,9 +200,9 @@ export const SCRIPT_CURE = "repro/tools/ — the scripts used across the paper (
 /** Where data goes. */
 export const DATA_CURE = "repro/data/ — the data shared across the paper (tables, caches); what one study's run produced goes in that study's folder instead";
 /** Where a note goes. */
-export const NOTE_CURE = "the dated folder of the study it is about (repro/<slug>-YYYY-MM-DD/), or the paper's research/ when it is research or a decision rather than the record of a run";
+export const NOTE_CURE = "the folder of the study it is about (repro/<id>-<slug>/), or the paper's research/ when it is research or a decision rather than the record of a run";
 /** Where a file of any other kind goes. */
-export const FILE_CURE_BY_KIND = "decide by what it is — a script → repro/tools/; data → repro/data/; a note → the dated folder of its study, or the paper's research/; what one study produced → that study's folder";
+export const FILE_CURE_BY_KIND = "decide by what it is — a script → repro/tools/; data → repro/data/; a note → the folder of its study, or the paper's research/; what one study produced → that study's folder";
 /** The files paperlint itself once kept at the top of `repro/`, each with where it is read now. */
 export const MOVED_FILES = [
     {
@@ -202,7 +233,7 @@ function fileCure(name) {
     return FILE_CURE_BY_KIND;
 }
 /** Where a folder with no study name goes: renamed as a study, or emptied into the shared folders. */
-const folderCure = (name) => `rename it to \`${suggestedStudyName(name)}\`, one folder per study or spike, named for what it is and the date it began — the date of its first commit is a fine default (\`git log --reverse --format=%as -- repro/${name} | head -1\`, run in the paper folder) — and give it a README.md; if it holds scripts or data shared across the paper instead, move them into repro/tools/ or repro/data/`;
+const folderCure = (name) => `rename it to \`<id>-${suggestedSlug(name)}\` — the next free id in repro/${STUDIES_FILE}, then what it is — give it its row there and a README.md (\`npx paperlint studies new\` makes all three for a new study); in a paper with repro/study-registered off, \`${suggestedStudyName(name)}\` is accepted instead, dated by the day it began — its first commit is a fine default (\`git log --reverse --format=%as -- repro/${name} | head -1\`, run in the paper folder); if it holds scripts or data shared across the paper instead, move them into repro/tools/ or repro/data/`;
 const isAllowed = (e) => REPRO_BYPRODUCTS.includes(e.name) ||
     (e.kind === "file"
         ? REPRO_FILES.includes(e.name)
@@ -220,7 +251,7 @@ function judgeEntry(e) {
         return {
             path,
             problem: "no-readme",
-            cure: `add ${path}${README} — what the study asks, how to run it, what it found — and a line for it in repro/${README}`,
+            cure: `add ${path}${README} — what the study asks, how to run it, what it found — and give the study its row in repro/${STUDIES_FILE}`,
         };
     return null;
 }
@@ -235,7 +266,7 @@ export function judgeRepro(entries) {
  */
 export function reproMessage(f) {
     const head = f.problem === "stray"
-        ? `\`${f.path}\` is loose at the top of the paper's repro/ folder, which holds only an index, the shared tools and data, and one dated folder per study. Where it goes: ${f.cure}.`
+        ? `\`${f.path}\` is loose at the top of the paper's repro/ folder, which holds only an index, the study registry, the shared tools and data, and one folder per study. Where it goes: ${f.cure}.`
         : `\`${f.path}\` is a study folder without a ${README}, and every study in repro/ has one. What to do: ${f.cure}.`;
     return [
         head,

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package/dist/domain/scaffold-layout.d.ts

@@ -11,10 +11,11 @@ export declare const NOT_SCAFFOLDED: readonly {
 /** The folders at the paper's root that a new paper holds from the first commit, in layout order. */
 export declare const SCAFFOLD_DIRS: readonly string[];
 /**
- * The stub index of `repro/`: it makes the folder non-empty (no `.gitkeep`) and says what the rule
- * asks of it. A line per study is added when the first study is.
+ * The stub index of `repro/`: it makes the folder non-empty (no `.gitkeep`) and says what the rules
+ * ask of it. The table of studies is generated into it by `paperlint studies new` and
+ * `paperlint studies index`, from `repro/studies.json`.
  */
-export declare const REPRO_INDEX_STUB = "# Reproduction index\n\nOne line per study: `<slug>-YYYY-MM-DD/` \u2014 what it asks and what it found. Scripts used across the\npaper go in `tools/`, shared data in `data/`.\n";
+export declare const REPRO_INDEX_STUB = "# Reproduction index\n\nOne line per study, generated from `studies.json` \u2014 create a study with\n`npx paperlint studies new <paper-dir> \"<title>\"`, and after editing its row run\n`npx paperlint studies index <paper-dir>`. Scripts used across the paper go in `tools/`,\nshared data in `data/`.\n";
 /** A file `paperlint new` writes into a new paper folder, with its path from that folder. */
 export interface ScaffoldFile {
     readonly path: string;

package/dist/domain/scaffold-layout.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scaffold-layout.d.ts","sourceRoot":"","sources":["../../src/domain/scaffold-layout.ts"],"names":[],"mappings":"AAiCA,mEAAmE;AACnE,eAAO,MAAM,OAAO,aAAa,CAAC;AAElC;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS;IACpC,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;CACtB,EAqBA,CAAC;AAEF,qGAAqG;AACrG,eAAO,MAAM,aAAa,EAAE,SAAS,MAAM,EAEqB,CAAC;AAEjE;;;GAGG;AACH,eAAO,MAAM,gBAAgB,qLAI5B,CAAC;AAEF,6FAA6F;AAC7F,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACvB;AAED;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,YAAY,EAYjD,CAAC"}
+{"version":3,"file":"scaffold-layout.d.ts","sourceRoot":"","sources":["../../src/domain/scaffold-layout.ts"],"names":[],"mappings":"AAiCA,mEAAmE;AACnE,eAAO,MAAM,OAAO,aAAa,CAAC;AAElC;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS;IACpC,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;CACtB,EAqBA,CAAC;AAEF,qGAAqG;AACrG,eAAO,MAAM,aAAa,EAAE,SAAS,MAAM,EAEqB,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,gBAAgB,kTAM5B,CAAC;AAEF,6FAA6F;AAC7F,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACvB;AAED;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,YAAY,EAYjD,CAAC"}

package/dist/domain/scaffold-layout.js

@@ -55,13 +55,16 @@ export const NOT_SCAFFOLDED = [
 /** The folders at the paper's root that a new paper holds from the first commit, in layout order. */
 export const SCAFFOLD_DIRS = ROOT_DIR_NOTES.map((d) => d.name).filter((name) => !NOT_SCAFFOLDED.some((n) => n.name === name));
 /**
- * The stub index of `repro/`: it makes the folder non-empty (no `.gitkeep`) and says what the rule
- * asks of it. A line per study is added when the first study is.
+ * The stub index of `repro/`: it makes the folder non-empty (no `.gitkeep`) and says what the rules
+ * ask of it. The table of studies is generated into it by `paperlint studies new` and
+ * `paperlint studies index`, from `repro/studies.json`.
  */
 export const REPRO_INDEX_STUB = `# Reproduction index
 
-One line per study: \`<slug>-YYYY-MM-DD/\` — what it asks and what it found. Scripts used across the
-paper go in \`${TOOLS_DIR}/\`, shared data in \`${DATA_DIR}/\`.
+One line per study, generated from \`studies.json\` — create a study with
+\`npx paperlint studies new <paper-dir> "<title>"\`, and after editing its row run
+\`npx paperlint studies index <paper-dir>\`. Scripts used across the paper go in \`${TOOLS_DIR}/\`,
+shared data in \`${DATA_DIR}/\`.
 `;
 /**
  * Every file of the layout scaffold, relative to the paper folder, in a fixed order: a `.gitkeep` in

package/dist/domain/scaffold-layout.js.map

@@ -1 +1 @@
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package/dist/domain/study-registry.d.ts

@@ -0,0 +1,176 @@
+import { STUDIES_FILE } from "./repro-layout.ts";
+/** The registry, at the top of the paper's `repro/`; the layout allows it there. */
+export { STUDIES_FILE };
+export declare const STUDY_KINDS: readonly ["measurement", "spike", "tooling", "data", "artifact", "salvage"];
+export type StudyKind = (typeof STUDY_KINDS)[number];
+export declare const STUDY_STATUSES: readonly ["designing", "running", "done", "stopped", "superseded", "dropped"];
+export type StudyStatus = (typeof STUDY_STATUSES)[number];
+/** `registry`: listed in the registry only, not in the paper's text. */
+export declare const IN_PAPER: readonly ["yes", "no", "registry"];
+export type InPaper = (typeof IN_PAPER)[number];
+/** A title is a plain name, not a sentence. */
+export declare const MAX_TITLE_WORDS = 8;
+/** A paper's prefix: a capital letter, then capitals or digits (`P1`). */
+export declare const PREFIX_PATTERN: RegExp;
+/** The kind `paperlint studies new` gives a study when none is named. */
+export declare const DEFAULT_KIND: StudyKind;
+/** The markers around the generated index in `repro/README.md`. Fixed: the rule finds the block by them. */
+export declare const INDEX_BEGIN = "<!-- studies:begin \u2014 generated from studies.json by `paperlint studies index`; do not edit -->";
+export declare const INDEX_END = "<!-- studies:end -->";
+/**
+ * One study. The named fields are the registry's; a row may carry more (a paper merges its own
+ * measurement metadata into it), and they are kept as they are.
+ */
+export interface Study {
+    readonly id: string;
+    readonly folder: string;
+    readonly title: string;
+    readonly question: string;
+    readonly kind: StudyKind;
+    readonly status: StudyStatus;
+    readonly date: string;
+    readonly result?: string | undefined;
+    readonly result_file?: string | undefined;
+    readonly superseded_by?: string | undefined;
+    readonly in_paper: InPaper;
+    readonly [extra: string]: unknown;
+}
+export interface StudyRegistry {
+    readonly prefix: string;
+    readonly studies: readonly Study[];
+}
+/** A registry's text, parsed: the registry, or the one reason it is not one. */
+export type ParsedRegistry = {
+    readonly ok: true;
+    readonly registry: StudyRegistry;
+} | {
+    readonly ok: false;
+    readonly why: string;
+};
+/** What the paper's `repro/` holds of a registry. */
+export type RegistryState = {
+    readonly kind: "absent";
+} | {
+    readonly kind: "unreadable";
+    readonly why: string;
+} | {
+    readonly kind: "read";
+    readonly registry: StudyRegistry;
+};
+/** What the judge reads. */
+export interface StudyInput {
+    /** The study folders at the top of `repro/`: every folder but the shared ones and the byproducts. */
+    readonly folders: readonly string[];
+    readonly registry: RegistryState;
+    /** `repro/README.md`'s text; null when there is none. */
+    readonly readme: string | null;
+    /** Each `<folder>/<result_file>` of the registry that is a file. */
+    readonly existingResults: ReadonlySet<string>;
+}
+/** One defect of the registry, of a row, or of the index. */
+export type StudyFinding = {
+    readonly problem: "no-registry";
+    readonly folders: readonly string[];
+} | {
+    readonly problem: "unreadable";
+    readonly why: string;
+} | {
+    readonly problem: "unregistered";
+    readonly folder: string;
+    readonly next: string;
+} | {
+    readonly problem: "no-folder";
+    readonly id: string;
+    readonly folder: string;
+} | {
+    readonly problem: "two-rows";
+    readonly folder: string;
+    readonly ids: readonly string[];
+} | {
+    readonly problem: "bad-id";
+    readonly id: string;
+    readonly prefix: string;
+} | {
+    readonly problem: "duplicate-id";
+    readonly id: string;
+} | {
+    readonly problem: "folder-name";
+    readonly id: string;
+    readonly folder: string;
+} | {
+    readonly problem: "long-title";
+    readonly id: string;
+    readonly words: number;
+} | {
+    readonly problem: "no-result";
+    readonly id: string;
+    readonly missing: readonly ("result" | "result_file")[];
+} | {
+    readonly problem: "result-file";
+    readonly id: string;
+    readonly path: string;
+    readonly why: "missing" | "outside";
+} | {
+    readonly problem: "no-successor";
+    readonly id: string;
+    readonly superseded_by: string | null;
+} | {
+    readonly problem: "stale-index";
+    readonly why: "no-readme" | "no-markers" | "differs";
+};
+/** The id after the highest one in `r`, at least two digits: `P1-S01` in an empty registry. */
+export declare function nextStudyId(r: StudyRegistry): string;
+/** The slug of a title: lowercase Latin letters and digits, words joined by single hyphens; "" when none. */
+export declare const studySlug: (title: string) => string;
+/** The number of words in a title. */
+export declare const titleWords: (title: string) => number;
+/**
+ * Every defect of a paper's study registry, in a fixed order: the registry itself; the unregistered
+ * folders; each row's; the index. Pure.
+ */
+export declare function judgeStudies(input: StudyInput): readonly StudyFinding[];
+/**
+ * The index of `r`: a markdown table, a row per study in registry order, each column padded to its
+ * widest cell (at least 3), the way prettier writes a table — so formatting the README leaves it as
+ * it is.
+ */
+export declare function studyIndex(r: StudyRegistry): string;
+/** Whether `readme` holds the index of `r`, whatever padding a formatter gave its table. */
+export declare function indexInSync(readme: string | null, r: StudyRegistry): boolean;
+/** The index between its markers, a blank line on each side. */
+export declare const indexBlock: (r: StudyRegistry) => string;
+/** The text between the markers of `readme`; null when it has no begin marker followed by an end one. */
+export declare function embeddedIndex(readme: string): string | null;
+/**
+ * `readme` with its index regenerated from `r`: the block replaced in place, appended when the README
+ * has none, a README of its own when there is none.
+ */
+export declare function withIndex(readme: string | null, r: StudyRegistry): string;
+/** The registry's text as `paperlint studies new` writes it: JSON, two-space indented, a final newline. */
+export declare const registryText: (r: StudyRegistry) => string;
+/** The one text a finding is reported with: what is wrong, what to do, and the rule's page. */
+export declare const studyMessage: (f: StudyFinding) => string;
+/** Whether `s` names a kind of study. */
+export declare const isStudyKind: (s: string) => s is StudyKind;
+/** What a new study is made from. */
+export interface NewStudy {
+    readonly title: string;
+    readonly kind: StudyKind;
+    /** The day it is registered, `YYYY-MM-DD`. */
+    readonly date: string;
+}
+/**
+ * `r` with a new study appended: the next id, the folder `<id>-<slug>`, `status: designing`,
+ * `in_paper: no` and an empty question; or why the title cannot make one.
+ */
+export declare function addStudy(r: StudyRegistry, n: NewStudy): {
+    readonly ok: true;
+    readonly registry: StudyRegistry;
+    readonly study: Study;
+} | {
+    readonly ok: false;
+    readonly why: string;
+};
+/** The `README.md` a new study's folder starts with: its id and title in frontmatter, then the sections. */
+export declare const studyReadme: (s: Study) => string;
+//# sourceMappingURL=study-registry.d.ts.map

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

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