paperlint 10.3.0 → 10.4.0

package/dist/domain/decide-first.js

@@ -0,0 +1,102 @@
+/**
+ * DECIDE FIRST — the default mode of a measurement study (src/domain/study-mode.ts): the author's
+ * decisions on the inputs are committed before any output exists, and git's history is the proof of
+ * order. `repro/outputs-before-decision` judges it here, from facts git gave (src/adapters/git/):
+ *
+ *   - each output in the tree or ever committed while the decision file was never committed;
+ *   - each output whose FIRST commit is not a strict descendant of the decision file's FIRST commit —
+ *     earlier, on a line of history the decision is not on, or in the very same commit (which says
+ *     nothing about which came first);
+ *   - a decision file the outputs match (it would be "produced" by the run it gates);
+ *   - a decision file committed and since deleted: it is not in HEAD, so there is no decision;
+ *   - a history that cannot be read: no git, or a shallow clone, whose every file starts at the clone.
+ *
+ * Outputs that were committed and later deleted count: an output that existed before the decision is
+ * evidence after it is gone. Pure.
+ */
+import { README } from "./repro-layout.js";
+import { decisionAsOutput, inStudy, isOutput, } from "./study-mode.js";
+/** Whether `path` (relative to the study's folder) is an output and none of the study's own files. */
+const outputOf = (s) => (path) => ![README, s.plan, inStudy(s.folder, s.mode.decision.file)].includes(path) &&
+    isOutput(s.mode.outputs, path);
+/** The files of a read history that are outputs of the study, oldest first commit first. */
+export const outputCommits = (s, files) => files.filter((f) => outputOf(s)(f.path));
+/** The findings of a history that was read. */
+const ordered = (s, decision, files) => {
+    const isOut = outputOf(s);
+    const at = { id: s.id, folder: s.folder };
+    if (decision === null)
+        // The tree's outputs, then those only history holds: deleting an output does not erase it.
+        return [...new Set([...s.tree, ...files.map((f) => f.path)])]
+            .filter(isOut)
+            .map((path) => ({
+            problem: "undecided-output",
+            ...at,
+            path,
+            decision: s.mode.decision.file,
+        }));
+    return files
+        .filter((f) => isOut(f.path) && f.order !== "after")
+        .map((f) => ({
+        problem: "output-before-decision",
+        ...at,
+        path: f.path,
+        output: { commit: f.commit, date: f.date },
+        decision,
+        same: f.order === "same",
+    }));
+};
+/** Every defect of a decide-first study, in a fixed order: the plan's, then the history's. */
+export const judgeOrder = (s) => {
+    const glob = decisionAsOutput(s.folder, s.mode);
+    const clash = glob === null
+        ? []
+        : [
+            {
+                problem: "decision-is-output",
+                id: s.id,
+                file: s.mode.decision.file,
+                glob,
+            },
+        ];
+    return [...clash, ...historyFindings(s)];
+};
+/** The findings of a decide-first study's history, whatever git could say of it. */
+const historyFindings = (s) => {
+    const file = s.mode.decision.file;
+    switch (s.facts.kind) {
+        case "not-a-file":
+            return [
+                { problem: "decision-not-file", id: s.id, file, what: s.facts.what },
+            ];
+        case "unknown":
+            return [{ problem: "no-history", id: s.id, why: s.facts.why }];
+        case "shallow":
+            return [{ problem: "shallow", id: s.id }];
+        case "read":
+            // A decision deleted since is no decision: the order is not judged against it.
+            return s.facts.decisionDeleted
+                ? [{ problem: "decision-deleted", id: s.id, file }]
+                : ordered(s, s.facts.decision, s.facts.files);
+    }
+};
+const RULE = "repro/outputs-before-decision";
+/** Why git's history says nothing of a decision that is not a file. */
+const NOT_A_FILE = {
+    directory: "git answers for a directory with the commits of anything under it",
+    "symbolic link": "git records the link, not the file it points to",
+};
+const short = (c) => `${c.commit.slice(0, 12)} (${c.date})`;
+const HEADS = {
+    "decision-is-output": (f) => `The decision of \`${f.id}\`, \`${f.file}\`, is matched by its output \`${f.glob}\`: the decision would be one of the files its own run produces. What to do: keep the decision out of the outputs — a file the globs do not match, or one elsewhere in the paper — and set \`mode.decision.file\`.`,
+    "decision-deleted": (f) => `The decision of \`${f.id}\`, \`${f.file}\`, was committed and then deleted: it is not in HEAD, so the study has no decision its outputs could follow. What to do: restore the decision file as it was decided and commit it — never write a new one after the outputs; if the decision no longer holds, declare the study \`exploratory\` with the reason.`,
+    "decision-not-file": (f) => `The decision of \`${f.id}\`, \`${f.file}\`, is a ${f.what}, not a file: ${NOT_A_FILE[f.what]}, so no order can be read from it. What to do: name the decision file itself in \`mode.decision.file\`.`,
+    "no-history": (f) => `\`${f.id}\` is decided before its run, and git's history is the proof of that order, but git could not answer: ${f.why}. What to do: lint the paper inside its git repository, with git installed.`,
+    shallow: (f) => `\`${f.id}\` is decided before its run, and this clone is shallow: every file's first commit is the clone's first, so the order of decision and outputs cannot be read. What to do: fetch the whole history (\`git fetch --unshallow\`; in GitHub Actions, \`actions/checkout\` with \`fetch-depth: 0\`).`,
+    "undecided-output": (f) => `\`repro/${f.folder}/${f.path}\` is an output of \`${f.id}\` — in the tree, or in its history — and the study is decided before its run, but its decision \`${f.decision}\` was never committed. What to do: write and commit the decision, check it with \`npx paperlint studies gate <paper-dir> ${f.id}\`, then run the study again; if the output was made before any decision, declare the study \`exploratory\` with the reason. Deleting the output does not undo it: history keeps it.`,
+    "output-before-decision": (f) => `\`repro/${f.folder}/${f.path}\`, an output of \`${f.id}\`, entered history in ${short(f.output)}, ${f.same ? "the very commit" : "not after the commit"} that first recorded its decision, ${short(f.decision)}. The study is declared decided before its run, and its history does not show that order. What to do: if the decision really came first, nothing in this history can prove it — declare the study \`exploratory\` with the reason, or run it again after the decision; never rewrite the history to make it pass.`,
+};
+const headOf = (p, f) => HEADS[p](f);
+/** The one text a finding is reported with: what is wrong, what to do, and the rule's page. */
+export const orderMessage = (f) => `${headOf(f.problem, f)}\nRule ${RULE}: https://github.com/zernie/paperlint/blob/main/docs/rules/${RULE}.md`;
+//# sourceMappingURL=decide-first.js.map

package/dist/domain/decide-first.js.map

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package/dist/domain/index-columns.d.ts

@@ -0,0 +1,45 @@
+/**
+ * THE MODE COLUMNS OF THE INDEX — three columns of `repro/README.md`'s study index beyond the row:
+ * the study's mode, as its plan declares it, and for a study decided before its run the commit that
+ * first recorded its decision and the commit that first recorded an output (docs/design/study-modes.md).
+ *
+ * The mode comes from the plan, which is in the tree, so `repro/study-registered` compares it. The
+ * two commits come from git's history as `paperlint studies index` read it when it ran: a squash merge
+ * or a rebase gives the same files new commits, and a shallow CI clone has none to read, so the lint
+ * never compares those two columns. `repro/outputs-before-decision` judges the order itself. Pure.
+ */
+import { type CommitAt, type DecideFirstStudy } from "./decide-first.ts";
+import type { StudyMode } from "./study-mode.ts";
+/** What git's history says of a decide-first study's decision and outputs. */
+export type IndexHistory = 
+/** No order could be read: why, in a few words (`shallow clone`). */
+{
+    readonly kind: "unread";
+    readonly why: string;
+} | {
+    readonly kind: "read";
+    /** The decision file's first commit; null: never committed. */
+    readonly decision: CommitAt | null;
+    /** The decision was committed, then deleted: it is not in HEAD. */
+    readonly decisionDeleted: boolean;
+    /** The first commit of the oldest output; null: no output was ever committed. */
+    readonly firstOutput: CommitAt | null;
+};
+/** What the index shows of a study beyond its row. */
+export interface IndexFacts {
+    /** The mode its plan declares; null when its plan declares none, or there is no plan to read. */
+    readonly mode: StudyMode | null;
+    /** For a decide-first study, its history; null when it was not asked (the lint does not ask). */
+    readonly history: IndexHistory | null;
+}
+/** The cell of a column that does not apply to a study. */
+export declare const NOT_APPLICABLE = "\u2014";
+/** The mode cell: `decide_before_run`, `exploratory: <reason>`, or `—`. */
+export declare const modeCell: (f: IndexFacts) => string;
+/** The decision cell: its first commit and date (`, deleted since` when it is not in HEAD), or `not committed`. */
+export declare const decisionCell: (f: IndexFacts) => string;
+/** The first-output cell: the commit and date of the first output, or `none`. */
+export declare const firstOutputCell: (f: IndexFacts) => string;
+/** The history the index shows of a decide-first study, from the facts git gave. */
+export declare const indexHistory: (s: DecideFirstStudy) => IndexHistory;
+//# sourceMappingURL=index-columns.d.ts.map

package/dist/domain/index-columns.d.ts.map

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package/dist/domain/index-columns.js

@@ -0,0 +1,62 @@
+/**
+ * THE MODE COLUMNS OF THE INDEX — three columns of `repro/README.md`'s study index beyond the row:
+ * the study's mode, as its plan declares it, and for a study decided before its run the commit that
+ * first recorded its decision and the commit that first recorded an output (docs/design/study-modes.md).
+ *
+ * The mode comes from the plan, which is in the tree, so `repro/study-registered` compares it. The
+ * two commits come from git's history as `paperlint studies index` read it when it ran: a squash merge
+ * or a rebase gives the same files new commits, and a shallow CI clone has none to read, so the lint
+ * never compares those two columns. `repro/outputs-before-decision` judges the order itself. Pure.
+ */
+import { outputCommits, } from "./decide-first.js";
+/** The cell of a column that does not apply to a study. */
+export const NOT_APPLICABLE = "—";
+/** A commit as a cell: its first twelve characters, and its date. */
+const commitCell = (c) => `${c.commit.slice(0, 12)} ${c.date.slice(0, 10)}`;
+/** The mode cell: `decide_before_run`, `exploratory: <reason>`, or `—`. */
+export const modeCell = (f) => {
+    if (f.mode === null)
+        return NOT_APPLICABLE;
+    return f.mode.kind === "exploratory"
+        ? `exploratory: ${f.mode.reason}`
+        : f.mode.kind;
+};
+/** A history cell of a decide-first study: the text `pick` makes of it, `absent` when it makes none. */
+const historyCell = (pick, absent) => (f) => {
+    if (f.mode?.kind !== "decide_before_run")
+        return NOT_APPLICABLE;
+    if (f.history === null)
+        return "not read";
+    if (f.history.kind === "unread")
+        return `unknown (${f.history.why})`;
+    return pick(f.history) ?? absent;
+};
+/** The decision cell: its first commit and date (`, deleted since` when it is not in HEAD), or `not committed`. */
+export const decisionCell = historyCell((h) => h.decision === null
+    ? null
+    : `${commitCell(h.decision)}${h.decisionDeleted ? ", deleted since" : ""}`, "not committed");
+/** The first-output cell: the commit and date of the first output, or `none`. */
+export const firstOutputCell = historyCell((h) => (h.firstOutput === null ? null : commitCell(h.firstOutput)), "none");
+/** The history the index shows of a decide-first study, from the facts git gave. */
+export const indexHistory = (s) => {
+    switch (s.facts.kind) {
+        case "not-a-file":
+            return { kind: "unread", why: `the decision is a ${s.facts.what}` };
+        case "unknown":
+            return { kind: "unread", why: "git could not answer" };
+        case "shallow":
+            return { kind: "unread", why: "shallow clone" };
+        case "read": {
+            const [first] = outputCommits(s, s.facts.files);
+            return {
+                kind: "read",
+                decision: s.facts.decision,
+                decisionDeleted: s.facts.decisionDeleted,
+                firstOutput: first === undefined
+                    ? null
+                    : { commit: first.commit, date: first.date },
+            };
+        }
+    }
+};
+//# sourceMappingURL=index-columns.js.map

package/dist/domain/index-columns.js.map

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package/dist/domain/study-mode.d.ts

@@ -0,0 +1,37 @@
+import type { StudyKind } from "./study-registry.ts";
+/** A decision recorded in a file: where, and what it decides. */
+export interface Decision {
+    /** Relative to the paper's folder. */
+    readonly file: string;
+    readonly note: string;
+}
+/** Decide first: the decision on the inputs is committed before any output exists. */
+export interface DecideFirst {
+    readonly kind: "decide_before_run";
+    /** Globs relative to the study's folder: the files the run produces. */
+    readonly outputs: readonly string[];
+    readonly decision: Decision;
+}
+/** Exploratory: no gate, and reported as exploratory. */
+export interface Exploratory {
+    readonly kind: "exploratory";
+    readonly reason: string;
+}
+export type StudyMode = DecideFirst | Exploratory;
+/**
+ * The kinds of study whose plan must declare a mode: the ones that measure. A spike, a tool, a data
+ * set, an artifact or a salvage may omit it.
+ */
+export declare const MODE_REQUIRED: readonly StudyKind[];
+/** Whether a study of `kind` must declare its mode. */
+export declare const needsMode: (kind: StudyKind) => boolean;
+/** `paperPath` relative to the study folder `folder`, when it lies inside it; else null. */
+export declare const inStudy: (folder: string, paperPath: string) => string | null;
+/** Whether the file at `path` (relative to the study's folder) is one of `outputs`. */
+export declare const isOutput: (outputs: readonly string[], path: string) => boolean;
+/**
+ * The output glob that matches the study's own decision file, when the file lies in the study's
+ * folder: the decision would be "produced" by the run it gates.
+ */
+export declare const decisionAsOutput: (folder: string, m: DecideFirst) => string | null;
+//# sourceMappingURL=study-mode.d.ts.map

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

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package/dist/domain/study-mode.js

@@ -0,0 +1,45 @@
+/**
+ * A STUDY'S MODE — how its outcomes are kept from the decisions about its inputs. A measurement study
+ * declares exactly one (docs/design/study-modes.md):
+ *
+ *   decide_before_run   the default: the author's decisions on the inputs (exclusions, veto, the
+ *                       sample's approval) are committed BEFORE any output exists. No key, no extra
+ *                       tool: git's history is the proof of order, and
+ *                       `repro/outputs-before-decision` re-checks it on every lint.
+ *   exploratory         no gate: the study is exploratory and is reported as such, with its reason.
+ *
+ * "None" and "two at once" cannot be written: the plan holds one `mode`, a union on its `kind`, and a
+ * measurement study's plan is not ready without it (the parser, `src/adapters/study-registry/`).
+ *
+ * Paths: `outputs` are globs relative to the study's folder (the study's results live there); the
+ * decision's `file` is relative to the PAPER's folder, so a decision may live beside the study or
+ * anywhere in the paper (`research/decisions.md`). Pure.
+ */
+import { posix } from "node:path";
+import { REPRO_DIR } from "./repro-layout.js";
+/**
+ * The kinds of study whose plan must declare a mode: the ones that measure. A spike, a tool, a data
+ * set, an artifact or a salvage may omit it.
+ */
+export const MODE_REQUIRED = ["measurement"];
+/** Whether a study of `kind` must declare its mode. */
+export const needsMode = (kind) => MODE_REQUIRED.includes(kind);
+/** `paperPath` relative to the study folder `folder`, when it lies inside it; else null. */
+export const inStudy = (folder, paperPath) => {
+    const prefix = `${REPRO_DIR}/${folder}/`;
+    const n = posix.normalize(paperPath);
+    return n.startsWith(prefix) ? n.slice(prefix.length) : null;
+};
+/** Whether the file at `path` (relative to the study's folder) is one of `outputs`. */
+export const isOutput = (outputs, path) => outputs.some((g) => posix.matchesGlob(path, g));
+/**
+ * The output glob that matches the study's own decision file, when the file lies in the study's
+ * folder: the decision would be "produced" by the run it gates.
+ */
+export const decisionAsOutput = (folder, m) => {
+    const rel = inStudy(folder, m.decision.file);
+    return rel === null
+        ? null
+        : (m.outputs.find((g) => posix.matchesGlob(rel, g)) ?? null);
+};
+//# sourceMappingURL=study-mode.js.map

package/dist/domain/study-mode.js.map

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

@@ -1,4 +1,6 @@
 import { STUDIES_FILE } from "./repro-layout.ts";
+import { type StudyMode } from "./study-mode.ts";
+import { type IndexHistory } from "./index-columns.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"];
@@ -115,6 +117,11 @@ export interface StudyPlan {
     readonly author_check: AuthorCheck | null;
     /** The paper's own keys: hypotheses, models, budget … Kept, never read; none is a plan field. */
     readonly extra?: Readonly<Record<string, unknown>> | undefined;
+    /**
+     * How the outcomes are kept from the decisions on the inputs: decided before the run, or
+     * exploratory (src/domain/study-mode.ts). A measurement study's plan is not ready without it.
+     */
+    readonly mode?: StudyMode | undefined;
 }
 /**
  * How the sample is drawn from the population: a seeded draw, whose seed is part of it, or all of
@@ -132,13 +139,13 @@ export type Draw = {
     readonly method: string;
 };
 /** The top-level fields of a plan: none of them may be a key of `extra`. */
-export declare const PLAN_FIELDS: readonly ["question", "population", "arms", "primary_outcome", "author_check", "extra"];
+export declare const PLAN_FIELDS: readonly ["question", "population", "arms", "primary_outcome", "author_check", "extra", "mode"];
 /** A plan with empty required texts: the author has not approved it. */
 export type DraftPlan = StudyPlan & {
     readonly author_check: null;
 };
 /** The texts a plan must fill before the study runs, in the order they are named. */
-export declare const PLAN_TEXT_FIELDS: readonly ["question", "population.source", "population.draw.method", "primary_outcome"];
+export declare const PLAN_TEXT_FIELDS: readonly ["question", "population.source", "population.draw.method", "primary_outcome", "mode", "mode.outputs", "mode.decision.file", "mode.decision.note", "mode.reason"];
 export type PlanTextField = (typeof PLAN_TEXT_FIELDS)[number];
 /**
  * A plan's text, parsed: ready (every required text filled), a draft (its empty texts named, and
@@ -159,11 +166,17 @@ export type ParsedPlan = {
 export type PlanState = {
     readonly kind: "absent";
 } | ParsedPlan;
+/** The decision file `paperlint studies new` names for a study in `folder`, relative to the paper. */
+export declare const decisionPath: (folder: string) => string;
+/** The decision file's name, beside the plan. */
+export declare const DECISION_FILE = "decision.md";
 /**
- * The plan `paperlint studies new` writes: every field present, its value to fill. Its draw is of
- * all the population (a census); a sampled study changes it to `{ "kind": "seeded", "method", "seed" }`.
+ * The plan `paperlint studies new` writes for a study of `kind` in `folder`: every field present, its
+ * value to fill. Its draw is of all the population (a census); a sampled study changes it to
+ * `{ "kind": "seeded", "method", "seed" }`. A study that must declare its mode gets the default one,
+ * decided before the run, its decision file named and its outputs and note to fill.
  */
-export declare const planTemplate: () => DraftPlan;
+export declare const planTemplate: (kind: StudyKind, folder: string) => DraftPlan;
 /** A plan's text as `paperlint studies new` writes it: JSON, two-space indented, a final newline. */
 export declare const planText: (p: StudyPlan) => string;
 /** A registry's text, parsed: the registry, or the one reason it is not one. */
@@ -313,33 +326,67 @@ export declare function nextStudyId(r: StudyRegistry): string;
 export declare const studySlug: (title: string) => string;
 /** The number of words in a title. */
 export declare const titleWords: (title: string) => number;
+/**
+ * Whether `path` stays inside the folder it is relative to. A backslash or a Windows absolute path
+ * is refused outright: `posix.normalize` does not resolve `..\\`, while the host's `join` may.
+ */
+export declare const isInside: (path: string) => boolean;
+/**
+ * Whether `folder` names one folder directly inside `repro/`: not empty, not `.` or `..`, and no
+ * separator or NUL. Every command and rule that reads a study's folder reads only such a one: a row
+ * naming `../x` would have them read and write outside the paper.
+ */
+export declare const isFolderName: (folder: string) => boolean;
 /**
  * The `<folder>/<plan>` of each row whose plan lies inside its folder: the files the judge needs read
  * (`StudyInput.plans`). A plan outside its folder is reported without being read.
  */
 export declare const planKeys: (r: StudyRegistry) => readonly string[];
+/** Each plan `planKeys` names, with the kind of the study whose row names it: what its parser needs. */
+export declare const planRefs: (r: StudyRegistry) => readonly {
+    readonly key: string;
+    readonly folder: string;
+    readonly kind: StudyKind;
+}[];
 /**
  * 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[];
+/**
+ * What the index is generated from beyond the registry: the plans by `<folder>/<plan>` (as
+ * `StudyInput.plans`), and the history of each decide-first study by id. A study with no history
+ * listed shows `not read` — the lint, which never compares those columns, asks none.
+ */
+export interface IndexInput {
+    readonly plans: ReadonlyMap<string, PlanState>;
+    readonly history: ReadonlyMap<string, IndexHistory>;
+}
 /**
  * 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;
+export declare function studyIndex(r: StudyRegistry, at: IndexInput): string;
+/**
+ * Whether `readme` holds the index of `r`, whatever padding a formatter gave its table and whatever
+ * its two columns read from git say: what `repro/study-registered` checks.
+ */
+export declare const indexInSync: (readme: string | null, r: StudyRegistry, at: IndexInput) => boolean;
+/**
+ * Whether `readme` holds the index of `r` in every column, whatever its padding: when it does,
+ * `studies index` leaves the README as it is, so the padding a formatter gave the table stays.
+ */
+export declare const indexCurrent: (readme: string | null, r: StudyRegistry, at: IndexInput) => boolean;
 /** The index between its markers, a blank line on each side. */
-export declare const indexBlock: (r: StudyRegistry) => string;
+export declare const indexBlock: (r: StudyRegistry, at: IndexInput) => 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;
+export declare function withIndex(readme: string | null, r: StudyRegistry, at: IndexInput): 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. */

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

@@ -1 +1 @@
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