@alisio/plugin-thesis 0.1.0

package/dist/checks/project.d.ts

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+import { type LoadBriefResult } from "../brief.js";
+import type { PackSelection } from "../policy/packs.js";
+import { type ComplianceProfile, type LoadedPack, type LoadedRule, type PackProblem } from "../policy/resolver.js";
+import { type WorkspaceStyleFile } from "../styles/discovery.js";
+import type { WorkspaceProfileFile } from "../styles/profile.js";
+import type { SectionState, ThesisState } from "../types.js";
+export interface ProjectFile {
+    /** Path relative to the thesis root, `/`-separated. */
+    path: string;
+    content: string;
+}
+/** Everything a pure check needs, loaded once. */
+export interface LoadedProject {
+    root: string;
+    briefText: string | undefined;
+    brief: LoadBriefResult | undefined;
+    workspaceCitationStyles: string[];
+    workspacePresentationStandards: string[];
+    /** Workspace CSL styles, presentation profiles and style fixtures (spec 10.4.1). */
+    styleFiles: WorkspaceStyleFile[];
+    profileFiles: WorkspaceProfileFile[];
+    styleFixtures: Record<string, string>;
+    /** Chart specs under figures/charts and the files under data/, for the FIG checks. */
+    chartSpecs: ProjectFile[];
+    dataFiles: string[];
+    /** Every shipped and workspace pack found, active or not. */
+    allPacks: LoadedPack[];
+    selection: PackSelection | undefined;
+    overrides: LoadedRule[];
+    policyProblems: PackProblem[];
+    /** Fresh resolution; undefined while the brief has errors. */
+    profile: ComplianceProfile | undefined;
+    /** Raw text of compliance-profile.json, when present. */
+    profileOnDisk: string | undefined;
+    chapters: ProjectFile[];
+    /** Raw text of research/protocol.md, outline/outline.json and the evidence files, when present. */
+    protocolText: string | undefined;
+    outlineText: string | undefined;
+    libraryText: string | undefined;
+    rejectedText: string | undefined;
+    bibliographyText: string | undefined;
+    /** Raw text of claims/claims.jsonl and the `reviews/FND-*.json` files, when present. */
+    claimsText: string | undefined;
+    reviewFiles: ProjectFile[];
+    /** Raw text of i18n.yaml (user label overrides) and build/build-report.json, when present. */
+    i18nText: string | undefined;
+    buildReportText: string | undefined;
+    /** Section states from state.json; undefined when the caller has no state (e.g. a bare folder). */
+    sections: Record<string, SectionState> | undefined;
+    /** Whole workspace state, for the checks that depend on gates and progress (ETH, POL-AI, REV, FIN). */
+    state: ThesisState | undefined;
+    now: Date;
+}
+export interface LoadProjectOptions {
+    packsRoot?: string;
+    /** Defaults to `<root>/policy-packs`. */
+    workspacePacksRoot?: string;
+    /** Section states from state.json, for the checks that depend on progress (EVD-010). */
+    sections?: Record<string, SectionState>;
+    /** The whole state; implies `sections`. */
+    state?: ThesisState;
+    now?: Date;
+}
+export declare function loadProject(root: string, options?: LoadProjectOptions): Promise<LoadedProject>;
+//# sourceMappingURL=project.d.ts.map

package/dist/checks/project.d.ts.map

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package/dist/checks/project.js

@@ -0,0 +1,203 @@
+import { readdir, readFile, stat } from "node:fs/promises";
+import { join } from "node:path";
+import { loadBrief } from "../brief.js";
+import { packagePath } from "../package-paths.js";
+import { crossValidate, loadOverrides, loadPacks, resolve, selectPacks, } from "../policy/resolver.js";
+import { loadWorkspaceStyleAssets } from "../styles/discovery.js";
+const maxChapterFiles = 500;
+const maxFileBytes = 2 * 1024 * 1024;
+async function readIfPresent(path) {
+    try {
+        return await readFile(path, "utf8");
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return undefined;
+        throw error;
+    }
+}
+async function listStyleIds(directory, suffix) {
+    try {
+        return (await readdir(directory, { withFileTypes: true }))
+            .filter((entry) => entry.isFile() && entry.name.endsWith(suffix))
+            .map((entry) => entry.name.slice(0, -suffix.length))
+            .sort();
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+}
+const maxChartSpecs = 200;
+const maxDataFiles = 2000;
+/** Chart spec texts (`*.vl.json` files under figures/). */
+async function collectChartSpecs(root) {
+    const base = join(root, "figures");
+    let entries;
+    try {
+        entries = await readdir(base, { withFileTypes: true, recursive: true });
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+    const files = [];
+    const sorted = entries
+        .filter((entry) => entry.isFile() && entry.name.endsWith(".vl.json"))
+        .map((entry) => join(entry.parentPath ?? base, entry.name))
+        .sort();
+    for (const absolute of sorted.slice(0, maxChartSpecs)) {
+        if ((await stat(absolute)).size > 1024 * 1024)
+            continue;
+        files.push({
+            path: absolute
+                .slice(root.length + 1)
+                .split("\\")
+                .join("/"),
+            content: await readFile(absolute, "utf8"),
+        });
+    }
+    return files;
+}
+/** Regular files under data/, relative to it. */
+async function collectDataFiles(root) {
+    const base = join(root, "data");
+    let entries;
+    try {
+        entries = await readdir(base, { withFileTypes: true, recursive: true });
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+    return entries
+        .filter((entry) => entry.isFile())
+        .map((entry) => join(entry.parentPath ?? base, entry.name)
+        .slice(base.length + 1)
+        .split("\\")
+        .join("/"))
+        .sort()
+        .slice(0, maxDataFiles);
+}
+const maxReviewFiles = 500;
+/** `reviews/FND-*.json`, sorted. */
+async function collectReviews(root) {
+    const base = join(root, "reviews");
+    let names;
+    try {
+        names = (await readdir(base)).filter((name) => /^FND-\d{4}\.json$/.test(name)).sort();
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+    const files = [];
+    for (const name of names.slice(0, maxReviewFiles)) {
+        const absolute = join(base, name);
+        if ((await stat(absolute)).size > 64 * 1024)
+            continue;
+        files.push({ path: `reviews/${name}`, content: await readFile(absolute, "utf8") });
+    }
+    return files;
+}
+async function collectChapters(root) {
+    const base = join(root, "chapters");
+    let entries;
+    try {
+        entries = await readdir(base, { withFileTypes: true, recursive: true });
+    }
+    catch (error) {
+        if (error.code === "ENOENT")
+            return [];
+        throw error;
+    }
+    const files = [];
+    const sorted = entries
+        .filter((entry) => entry.isFile() && entry.name.endsWith(".md"))
+        .map((entry) => join(entry.parentPath ?? base, entry.name))
+        .sort();
+    for (const absolute of sorted.slice(0, maxChapterFiles)) {
+        if ((await stat(absolute)).size > maxFileBytes)
+            continue;
+        files.push({
+            path: absolute
+                .slice(root.length + 1)
+                .split("\\")
+                .join("/"),
+            content: await readFile(absolute, "utf8"),
+        });
+    }
+    return files;
+}
+export async function loadProject(root, options = {}) {
+    const briefText = await readIfPresent(join(root, "thesis.yaml"));
+    const workspaceCitationStyles = await listStyleIds(join(root, "styles"), ".csl");
+    const workspacePresentationStandards = await listStyleIds(join(root, "styles"), ".profile.yaml");
+    const styleAssets = await loadWorkspaceStyleAssets(root);
+    const brief = briefText === undefined
+        ? undefined
+        : loadBrief(briefText, {
+            citationStyles: workspaceCitationStyles,
+            presentationStandards: workspacePresentationStandards,
+        });
+    const shipped = await loadPacks(options.packsRoot ?? packagePath("policy-packs"), "shipped");
+    const workspacePacks = await loadPacks(options.workspacePacksRoot ?? join(root, "policy-packs"), "workspace");
+    const allPacks = [...shipped.packs, ...workspacePacks.packs];
+    const loadedOverrides = await loadOverrides(join(root, "policy"));
+    const policyProblems = [
+        ...shipped.problems,
+        ...workspacePacks.problems,
+        ...crossValidate(allPacks),
+        ...loadedOverrides.problems,
+    ];
+    if (!allPacks.some((pack) => pack.scope === "global")) {
+        policyProblems.push({
+            code: "PCK-001",
+            severity: "error",
+            file: "policy-packs/global",
+            message: "The global policy pack is missing",
+        });
+    }
+    const selection = brief?.brief ? selectPacks(allPacks, brief.brief) : undefined;
+    if (selection)
+        policyProblems.push(...selection.problems);
+    const profile = brief?.brief && selection
+        ? resolve(brief.brief, selection.active, loadedOverrides.rules)
+        : undefined;
+    return {
+        root,
+        briefText,
+        brief,
+        workspaceCitationStyles,
+        workspacePresentationStandards,
+        styleFiles: styleAssets.styles,
+        profileFiles: styleAssets.profiles,
+        styleFixtures: styleAssets.fixtures,
+        chartSpecs: await collectChartSpecs(root),
+        dataFiles: await collectDataFiles(root),
+        allPacks,
+        selection,
+        overrides: loadedOverrides.rules,
+        policyProblems,
+        profile,
+        profileOnDisk: await readIfPresent(join(root, "compliance-profile.json")),
+        chapters: await collectChapters(root),
+        protocolText: await readIfPresent(join(root, "research", "protocol.md")),
+        outlineText: await readIfPresent(join(root, "outline", "outline.json")),
+        libraryText: await readIfPresent(join(root, "evidence", "library.jsonl")),
+        rejectedText: await readIfPresent(join(root, "evidence", "rejected.jsonl")),
+        bibliographyText: await readIfPresent(join(root, "bibliography", "references.bib")),
+        claimsText: await readIfPresent(join(root, "claims", "claims.jsonl")),
+        reviewFiles: await collectReviews(root),
+        i18nText: await readIfPresent(join(root, "i18n.yaml")),
+        buildReportText: await readIfPresent(join(root, "build", "build-report.json")),
+        sections: options.sections ?? options.state?.sections,
+        state: options.state,
+        now: options.now ?? new Date(),
+    };
+}
+//# sourceMappingURL=project.js.map

package/dist/checks/project.js.map

@@ -0,0 +1 @@
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package/dist/checks/styles.d.ts

@@ -0,0 +1,12 @@
+import type { Finding } from "../types.js";
+import type { LoadedProject } from "./project.js";
+/**
+ * Workspace styles and profiles, and the notes about the selected citation style (spec 9.2 and
+ * 10.4.1): CSL-001 (style structure, DOCTYPE/entity guard, id rules, no shadowing), PRF-001
+ * (profile schema), CSL-020 (provisional style selected) and CSL-021 (types without a source).
+ * CSL-010 needs the Typst engine and is run by `style check` and by the build (`styles/golden.ts`).
+ */
+export type StyleScope = "all" | "selected";
+export declare function styleFindings(project: LoadedProject, scope?: StyleScope): Finding[];
+export declare const checkStyles: (project: LoadedProject) => Finding[];
+//# sourceMappingURL=styles.d.ts.map

package/dist/checks/styles.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"styles.d.ts","sourceRoot":"","sources":["../../src/checks/styles.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAElD;;;;;GAKG;AAEH,MAAM,MAAM,UAAU,GAAG,KAAK,GAAG,UAAU,CAAC;AAE5C,wBAAgB,aAAa,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,GAAE,UAAkB,GAAG,OAAO,EAAE,CA+D1F;AAKD,eAAO,MAAM,WAAW,YAAa,aAAa,KAAG,OAAO,EAAmC,CAAC"}

package/dist/checks/styles.js

@@ -0,0 +1,67 @@
+import { parseLibraryText } from "../research/library.js";
+import { inspectCsl, loadCatalog, shippedStyleIds } from "../styles/csl.js";
+import { resolveCitationStyle } from "../styles/discovery.js";
+import { resolveWorkspaceProfile } from "../styles/profile.js";
+export function styleFindings(project, scope = "all") {
+    const findings = [];
+    const brief = project.brief?.brief;
+    const selectedStyle = project.profile?.citationStyle.value ?? brief?.citationStyle;
+    const selectedStandard = project.profile?.presentationStandard.value;
+    const shipped = shippedStyleIds();
+    for (const style of project.styleFiles) {
+        if (scope === "selected" && style.id !== selectedStyle)
+            continue;
+        for (const issue of inspectCsl(style.text, { stem: style.id, shipped }).issues) {
+            findings.push({
+                code: issue.code,
+                gate: "G0",
+                severity: "error",
+                file: style.file,
+                message: issue.message,
+                ...(issue.hint ? { hint: issue.hint } : {}),
+            });
+        }
+    }
+    for (const profile of project.profileFiles) {
+        if (scope === "selected" && profile.id !== selectedStandard)
+            continue;
+        for (const issue of resolveWorkspaceProfile(profile).issues) {
+            findings.push({
+                code: issue.code,
+                gate: "G0",
+                severity: "error",
+                file: profile.file,
+                message: `${issue.path ? `${issue.path}: ` : ""}${issue.message}`,
+            });
+        }
+    }
+    const resolved = selectedStyle
+        ? resolveCitationStyle(selectedStyle, project.styleFiles).style
+        : undefined;
+    if (resolved?.provisional) {
+        findings.push({
+            code: "CSL-020",
+            gate: "G0",
+            severity: "warning",
+            message: `The citation style "${resolved.title}" is provisional: only one source documents its citation and reference format`,
+            hint: "Confirm the result with your program, or drop a program-approved style into thesis/styles/ and select it.",
+        });
+        const fallback = new Set((resolved.source === "shipped" ? (shippedFallback(resolved.id) ?? []) : []));
+        if (fallback.size > 0) {
+            const records = parseLibraryText(project.libraryText).records.filter((record) => record.status !== "REJECTED" && fallback.has(record.type));
+            if (records.length > 0) {
+                findings.push({
+                    code: "CSL-021",
+                    gate: "G0",
+                    severity: "warning",
+                    message: `${records.length} ${[...fallback].join("/")} reference(s) have no format in the "${resolved.title}" style and use the closest type`,
+                    hint: "Check how those references print and correct them by hand if your program requires another format.",
+                });
+            }
+        }
+    }
+    return findings;
+}
+const shippedFallback = (id) => loadCatalog().find((entry) => entry.id === id)?.fallbackTypes;
+export const checkStyles = (project) => styleFindings(project, "all");
+//# sourceMappingURL=styles.js.map

package/dist/checks/styles.js.map

@@ -0,0 +1 @@
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package/dist/checks/writing.d.ts

@@ -0,0 +1,6 @@
+import type { Finding } from "../types.js";
+import type { LoadedProject } from "./project.js";
+export declare const longSentenceWords = 45;
+export declare function sentencesOf(text: string): string[];
+export declare function checkWriting(project: LoadedProject): Finding[];
+//# sourceMappingURL=writing.d.ts.map

package/dist/checks/writing.d.ts.map

@@ -0,0 +1 @@
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package/dist/checks/writing.js

@@ -0,0 +1,115 @@
+import { flattenOutline, parseOutline } from "../outline.js";
+import { countWords, proseOf, wordsOf } from "../render/text.js";
+import { allSections } from "../render/walk.js";
+import { documentOf } from "./document.js";
+/** WRT checks (G7, spec 9.2): word count, abstract limit, long sentences, repeated openings. */
+const targetTolerance = 0.25;
+export const longSentenceWords = 45;
+const maxSentenceFindings = 5;
+const sentencePattern = /(?<=[.!?…])\s+(?=[\p{Lu}\d¿¡"“(])/u;
+export function sentencesOf(text) {
+    return text.split(sentencePattern).filter((sentence) => sentence.trim().length > 0);
+}
+export function checkWriting(project) {
+    const assembled = documentOf(project);
+    if (!assembled)
+        return [];
+    const findings = [];
+    const targets = new Map();
+    if (project.outlineText !== undefined) {
+        const outline = parseOutline(project.outlineText).outline;
+        for (const node of flattenOutline(outline?.sections ?? []))
+            targets.set(node.id, node.targetWords);
+    }
+    const limit = project.profile?.rules.find((rule) => rule.kind === "length_limit" && rule.values.section === "abstract");
+    const maxAbstract = typeof limit?.values.maxWords === "number" ? limit.values.maxWords : undefined;
+    const limitSeverity = limit?.values.severity === "error" ? "error" : "warning";
+    for (const section of allSections(assembled.document)) {
+        const prose = proseOf(section.blocks);
+        const body = prose.filter((paragraph) => !paragraph.heading);
+        const base = {
+            file: section.path,
+            ...(section.section ? { section: section.section } : {}),
+        };
+        const words = body.reduce((sum, paragraph) => sum + countWords(paragraph.text), 0);
+        // WRT-001: the word count of a chapter against its outline target.
+        const target = section.section ? targets.get(section.section) : undefined;
+        if (section.role === "body" && target !== undefined && target > 0 && words > 0) {
+            const low = Math.floor(target * (1 - targetTolerance));
+            const high = Math.ceil(target * (1 + targetTolerance));
+            if (words < low || words > high)
+                findings.push({
+                    code: "WRT-001",
+                    gate: "G7",
+                    severity: "warning",
+                    ...base,
+                    message: `${words} words against a target of ${target} (allowed ${low} to ${high})`,
+                    hint: "Adjust the section, or change targetWords in the outline when the target was wrong.",
+                });
+        }
+        // WRT-002: abstract word limit from the policy.
+        if ((section.role === "abstract" || section.role === "abstract-secondary") &&
+            maxAbstract !== undefined &&
+            words > maxAbstract)
+            findings.push({
+                code: "WRT-002",
+                gate: "G7",
+                severity: limitSeverity,
+                ...base,
+                message: `The abstract has ${words} words; the policy limit is ${maxAbstract}`,
+                hint: `Rule ${limit?.ruleId}; see /thesis:pack explain ${limit?.ruleId}.`,
+            });
+        // WRT-003: very long sentences.
+        let long = 0;
+        let longTotal = 0;
+        for (const paragraph of body) {
+            for (const sentence of sentencesOf(paragraph.text)) {
+                const count = wordsOf(sentence).length;
+                if (count <= longSentenceWords)
+                    continue;
+                longTotal += 1;
+                if (long >= maxSentenceFindings)
+                    continue;
+                long += 1;
+                findings.push({
+                    code: "WRT-003",
+                    gate: "G7",
+                    severity: "warning",
+                    ...base,
+                    ...(paragraph.line === undefined ? {} : { line: paragraph.line }),
+                    message: `A sentence has ${count} words (more than ${longSentenceWords}): "${sentence.slice(0, 60).trim()}..."`,
+                    hint: "Split it into two sentences.",
+                });
+            }
+        }
+        if (longTotal > long)
+            findings.push({
+                code: "WRT-003",
+                gate: "G7",
+                severity: "info",
+                ...base,
+                message: `${longTotal - long} more long sentence(s) not listed`,
+            });
+        // WRT-004: paragraphs that open with the same three words.
+        const openings = new Map();
+        for (const paragraph of body) {
+            const opening = wordsOf(paragraph.text.toLowerCase()).slice(0, 3);
+            if (opening.length < 3)
+                continue;
+            const key = opening.join(" ");
+            openings.set(key, (openings.get(key) ?? 0) + 1);
+        }
+        for (const [opening, count] of openings)
+            if (count >= 2)
+                findings.push({
+                    code: "WRT-004",
+                    gate: "G7",
+                    severity: "warning",
+                    ...base,
+                    message: `${count} paragraphs open with "${opening}"`,
+                    hint: "Vary how paragraphs begin; each should open with its own topic sentence.",
+                });
+    }
+    return findings;
+}
+//# sourceMappingURL=writing.js.map

package/dist/checks/writing.js.map

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package/dist/chrome/detect.d.ts

@@ -0,0 +1,19 @@
+/**
+ * Chrome-family detection ported from scripts/render-diagrams.mjs: explicit overrides, known
+ * install locations, then a PATH lookup that never opens a shell. Nothing is ever downloaded.
+ */
+export interface ChromeDeps {
+    env: NodeJS.ProcessEnv;
+    platform: NodeJS.Platform;
+    home: string;
+    exists(path: string): boolean;
+    which(name: string): Promise<string | undefined>;
+}
+export interface ChromeDetection {
+    browser: string | null;
+    source: "ALISIO_THESIS_CHROME" | "PUPPETEER_EXECUTABLE_PATH" | "known-path" | "path" | null;
+}
+export declare function knownBrowserPaths(platform: NodeJS.Platform, env: NodeJS.ProcessEnv, home: string): string[];
+export declare function pathBrowserNames(platform: NodeJS.Platform): string[];
+export declare function detectChrome(overrides?: Partial<ChromeDeps>): Promise<ChromeDetection>;
+//# sourceMappingURL=detect.d.ts.map

package/dist/chrome/detect.d.ts.map

@@ -0,0 +1 @@
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