@alisio/plugin-thesis 0.1.0

package/dist/styles/xml.js

@@ -0,0 +1,179 @@
+/**
+ * Minimal, non-entity-expanding XML reader for CSL files (spec 10.4.1). It exists so that no style
+ * from the workspace ever reaches an XML parser that could resolve entities or external subsets:
+ * any DOCTYPE or ENTITY declaration is rejected before anything is parsed, and only the five
+ * predefined entities and numeric character references are accepted in text and attributes.
+ */
+export class XmlError extends Error {
+}
+const maxBytes = 2 * 1024 * 1024;
+const maxDepth = 64;
+const maxNodes = 200_000;
+const nameStart = /[A-Za-z_:]/;
+const nameChar = /[A-Za-z0-9_:.-]/;
+const predefined = {
+    lt: "<",
+    gt: ">",
+    amp: "&",
+    quot: '"',
+    apos: "'",
+};
+function decode(text) {
+    return text.replace(/&(#x[0-9A-Fa-f]{1,6}|#[0-9]{1,7}|[A-Za-z]+);/g, (_match, body) => {
+        if (body.startsWith("#x") || body.startsWith("#")) {
+            const code = body.startsWith("#x")
+                ? Number.parseInt(body.slice(2), 16)
+                : Number(body.slice(1));
+            if (!Number.isInteger(code) ||
+                (code < 0x20 && code !== 9 && code !== 10 && code !== 13) ||
+                code > 0x10ffff)
+                throw new XmlError(`Invalid character reference &${body};`);
+            return String.fromCodePoint(code);
+        }
+        const value = predefined[body];
+        if (value === undefined)
+            throw new XmlError(`Entity &${body}; is not allowed`);
+        return value;
+    });
+}
+/** Parse a document; throws XmlError for DOCTYPE, entities, malformed markup or oversize input. */
+export function parseXml(source) {
+    if (Buffer.byteLength(source) > maxBytes)
+        throw new XmlError("The XML file is larger than 2 MB");
+    if (/<!DOCTYPE|<!ENTITY/i.test(source)) {
+        throw new XmlError("A DOCTYPE or ENTITY declaration is not allowed (entity expansion is disabled)");
+    }
+    if (source.includes("\0"))
+        throw new XmlError("The XML file contains a NUL character");
+    let pos = source.charCodeAt(0) === 0xfeff ? 1 : 0;
+    let nodes = 0;
+    const fail = (message) => {
+        const line = source.slice(0, pos).split("\n").length;
+        throw new XmlError(`${message} (line ${line})`);
+    };
+    const skipSpace = () => {
+        while (pos < source.length && /\s/.test(source[pos]))
+            pos += 1;
+    };
+    const readName = () => {
+        const start = pos;
+        if (!nameStart.test(source[pos] ?? ""))
+            fail("Expected a name");
+        while (pos < source.length && nameChar.test(source[pos]))
+            pos += 1;
+        return source.slice(start, pos);
+    };
+    /** Skip comments and processing instructions; true when something was skipped. */
+    const skipMisc = () => {
+        if (source.startsWith("<!--", pos)) {
+            const end = source.indexOf("-->", pos + 4);
+            if (end === -1)
+                fail("Unterminated comment");
+            pos = end + 3;
+            return true;
+        }
+        if (source.startsWith("<?", pos)) {
+            const end = source.indexOf("?>", pos + 2);
+            if (end === -1)
+                fail("Unterminated processing instruction");
+            pos = end + 2;
+            return true;
+        }
+        return false;
+    };
+    const element = (depth) => {
+        if (depth > maxDepth)
+            fail("The XML nesting is too deep");
+        nodes += 1;
+        if (nodes > maxNodes)
+            fail("The XML file has too many elements");
+        pos += 1; // <
+        const name = readName();
+        const attrs = {};
+        for (;;) {
+            skipSpace();
+            const current = source[pos];
+            if (current === "/" || current === ">")
+                break;
+            const attribute = readName();
+            skipSpace();
+            if (source[pos] !== "=")
+                fail(`Attribute ${attribute} has no value`);
+            pos += 1;
+            skipSpace();
+            const quote = source[pos];
+            if (quote !== '"' && quote !== "'")
+                fail(`Attribute ${attribute} must be quoted`);
+            const end = source.indexOf(quote, pos + 1);
+            if (end === -1)
+                fail("Unterminated attribute value");
+            const raw = source.slice(pos + 1, end);
+            if (raw.includes("<"))
+                fail(`Attribute ${attribute} contains <`);
+            if (attribute in attrs)
+                fail(`Duplicate attribute ${attribute}`);
+            attrs[attribute] = decode(raw);
+            pos = end + 1;
+        }
+        const node = { name, attrs, children: [], text: "" };
+        if (source[pos] === "/") {
+            if (source[pos + 1] !== ">")
+                fail("Malformed empty element");
+            pos += 2;
+            return node;
+        }
+        pos += 1; // >
+        let text = "";
+        for (;;) {
+            const next = source.indexOf("<", pos);
+            if (next === -1)
+                fail(`Element <${name}> is not closed`);
+            text += decode(source.slice(pos, next));
+            pos = next;
+            if (skipMisc())
+                continue;
+            if (source.startsWith("<![CDATA[", pos)) {
+                const end = source.indexOf("]]>", pos);
+                if (end === -1)
+                    fail("Unterminated CDATA section");
+                text += source.slice(pos + 9, end);
+                pos = end + 3;
+                continue;
+            }
+            if (source.startsWith("</", pos)) {
+                pos += 2;
+                const closing = readName();
+                skipSpace();
+                if (source[pos] !== ">")
+                    fail("Malformed closing tag");
+                pos += 1;
+                if (closing !== name)
+                    fail(`Closing tag </${closing}> does not match <${name}>`);
+                node.text = text.trim();
+                return node;
+            }
+            node.children.push(element(depth + 1));
+        }
+    };
+    skipSpace();
+    while (skipMisc())
+        skipSpace();
+    if (source[pos] !== "<")
+        fail("The document has no root element");
+    const root = element(1);
+    skipSpace();
+    while (skipMisc())
+        skipSpace();
+    if (pos < source.length)
+        fail("Unexpected content after the root element");
+    return root;
+}
+export const child = (node, name) => node.children.find((entry) => entry.name === name);
+export const childrenNamed = (node, name) => node.children.filter((entry) => entry.name === name);
+/** Depth-first visit of every element. */
+export function walkXml(node, visit) {
+    visit(node);
+    for (const entry of node.children)
+        walkXml(entry, visit);
+}
+//# sourceMappingURL=xml.js.map

package/dist/styles/xml.js.map

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

@@ -0,0 +1,285 @@
+import type { Question } from "@alisio/sdk";
+/** Identifier patterns from spec section 4.1. */
+export declare const idPatterns: {
+    readonly section: RegExp;
+    readonly objective: RegExp;
+    readonly evidence: RegExp;
+    readonly claim: RegExp;
+    readonly finding: RegExp;
+    readonly figure: RegExp;
+    readonly table: RegExp;
+    readonly equation: RegExp;
+    readonly citationKey: RegExp;
+};
+export type SectionId = string;
+export declare const roles: readonly ["thesis-coordinator", "thesis-methodologist", "thesis-librarian", "thesis-evidence-auditor", "thesis-architect", "thesis-writer", "thesis-editor", "thesis-reviewer"];
+export type ResourceRole = (typeof roles)[number];
+export declare const gates: readonly ["G0", "G1", "G2", "G3", "G4", "G5", "G6", "G7", "G8", "G9", "G10"];
+export type Gate = (typeof gates)[number];
+export interface Finding {
+    code: string;
+    gate: Gate;
+    severity: "error" | "warning" | "info";
+    file?: string;
+    line?: number;
+    /** Outline section the finding belongs to, when it has one. */
+    section?: string;
+    message: string;
+    hint?: string;
+}
+export interface CheckReport {
+    at: string;
+    ok: boolean;
+    counts: {
+        error: number;
+        warning: number;
+        info: number;
+    };
+    findings: Finding[];
+}
+export declare const phases: readonly ["intake", "design", "outline", "sections", "review", "final", "submitted"];
+export type Phase = (typeof phases)[number];
+export declare const gateNames: readonly ["A", "B", "OUTLINE", "C"];
+export type HumanGateName = (typeof gateNames)[number];
+export interface HumanGate {
+    status: "pending" | "approved";
+    at?: string;
+    notes?: string;
+}
+export declare const sectionStatuses: readonly ["planned", "researching", "research_review", "research_approved", "drafting", "draft_review", "approved", "revising"];
+export type SectionStatus = (typeof sectionStatuses)[number];
+export interface SectionState {
+    status: SectionStatus;
+    updatedAt?: string;
+    /** Evidence ids of CONTEXTUAL_ONLY records the user explicitly approved for this section (spec 8.4). */
+    contextualApprovals?: string[];
+    /** When the research dossier was last written. */
+    dossierAt?: string;
+    /** Copied from the approved outline so progress can be planned from state alone. */
+    title?: string;
+    dependsOn?: SectionId[];
+    /** When the section was last drafted (or revised) and its chapter file, relative to the root. */
+    draftAt?: string;
+    chapter?: string;
+    /** File role of the section (abstract, ai-declaration, ...); absent for ordinary body sections. */
+    role?: string;
+}
+/** Sections with no research phase: they are written from the thesis itself, not from sources. */
+export declare const frontSectionRoles: readonly string[];
+/** Written last: an abstract summarizes sections that must be approved first. */
+export declare const summarySectionRoles: readonly string[];
+/** One interview round that is waiting for answers (headless continuation). */
+export interface PendingQuestions {
+    round: number;
+    createdAt: string;
+    questions: Question[];
+}
+export interface IntakeState {
+    /** Option values and `<id>:text` free-text answers collected so far. */
+    answers: Record<string, string>;
+    completedRounds: number[];
+    /** Conversation language detected when the interview started (BCP-47). */
+    languageHint?: string;
+}
+export interface ThesisState {
+    schemaVersion: 1;
+    root: string;
+    phase: Phase;
+    humanGates: Record<HumanGateName, HumanGate>;
+    sections: Record<SectionId, SectionState>;
+    intake: IntakeState;
+    pendingQuestions?: PendingQuestions;
+    /** When research/protocol.md and outline/outline.json were last drafted. */
+    protocolAt?: string;
+    outlineAt?: string;
+    counters: {
+        evidence: number;
+        claim: number;
+        finding: number;
+    };
+    /** Resolutions of triggered ethics requirements, by requirement id (spec 11.4, ETH-001). */
+    ethicsResolutions?: Record<string, {
+        text: string;
+        at: string;
+    }>;
+    /** Workspace citation styles the user approved through `/thesis:style new`. */
+    styles?: Record<string, {
+        approvedAt: string;
+    }>;
+    /** The last independent review (spec 7.5). */
+    lastReview?: {
+        at: string;
+        scope: string;
+        sections: SectionId[];
+        findings: number;
+        /** Open critical or major findings, kept in step with reviews/. */
+        blocking?: number;
+    };
+    /** The PDF/A build made by `/thesis:finalize` (FIN-001). */
+    finalBuild?: {
+        at: string;
+        pdf: string;
+        sha256: string;
+    };
+    submittedAt?: string;
+    lastCheck?: {
+        at: string;
+        errors: number;
+        warnings: number;
+    };
+    lastBuild?: {
+        at: string;
+        engine: "typst-cli" | "typst-node" | "chrome";
+        pdf: string;
+        ms: number;
+    };
+}
+export declare const workTypes: readonly ["undergraduate_thesis", "degree_project", "monograph", "master_thesis", "doctoral_dissertation"];
+export type WorkType = (typeof workTypes)[number];
+export declare const approaches: readonly ["quantitative", "qualitative", "mixed", "design_science", "theoretical", "systematic_review"];
+export type Approach = (typeof approaches)[number];
+export declare const shippedCitationStyles: readonly ["apa-7", "ieee", "icontec-ntc1486-2022"];
+export declare const shippedPresentationStandards: readonly ["apa-7", "ieee", "icontec-ntc1486-2022", "generic"];
+export declare const paletteNames: readonly ["okabe-ito", "tol-bright", "tol-muted", "tol-high-contrast", "viridis", "cividis"];
+export interface Brief {
+    schemaVersion: 1;
+    language: string;
+    secondaryAbstractLanguage: string | null;
+    searchLanguages: string[];
+    workType: WorkType;
+    title: string | null;
+    subtitle: string | null;
+    authors: {
+        name: string;
+        id: string | null;
+    }[];
+    advisors: {
+        name: string;
+        role: string;
+    }[];
+    institution: {
+        name: string | null;
+        faculty: string | null;
+        program: string | null;
+        city: string | null;
+        country: string;
+    };
+    year: number;
+    domain: {
+        primary: string;
+        secondary: string[];
+    };
+    approach: Approach;
+    studyDesign: string | null;
+    citationStyle: string;
+    presentation: {
+        standard: string;
+        paper: "letter" | "a4";
+        fontProfile: "serif" | "sans" | "institutional";
+        palette: string;
+        diagramTheme: "neutral" | "grayscale";
+        /** Body font family chosen in the interview (for example ICONTEC's Arial or Times New Roman). */
+        bodyFont?: string;
+        /** Body line spacing multiple chosen in the interview (1 or 1.5). */
+        lineSpacing?: number;
+    };
+    targets: {
+        pages: number | null;
+        words: number | null;
+    };
+    aiUse: {
+        assisted: boolean;
+        declaration: "auto" | "always" | "never";
+    };
+    policy: {
+        packs: "auto" | string[];
+    };
+}
+/** Study designs that route reporting guidelines. Superset of the spec list plus the pack drafts. */
+export declare const studyDesigns: readonly ["rct", "observational", "qualitative_interview", "systematic_review", "scoping_review", "case_study", "experiment", "survey", "health_economic_evaluation", "diagnostic_accuracy", "prediction_model", "quality_improvement", "other"];
+export declare const evidenceTypes: readonly ["journal_article", "book", "chapter", "conference_paper", "thesis", "report", "standard", "law", "dataset", "web_page", "preprint"];
+export type EvidenceType = (typeof evidenceTypes)[number];
+export declare const evidenceStatuses: readonly ["VERIFIED_PRIMARY", "VERIFIED_PEER_REVIEWED", "VERIFIED_AUTHORITATIVE_GREY", "CONTEXTUAL_ONLY", "UNVERIFIED", "REJECTED"];
+export type EvidenceStatus = (typeof evidenceStatuses)[number];
+export declare const citableStatuses: readonly EvidenceStatus[];
+export declare const permittedUses: readonly ["background", "argument", "method", "results_comparison"];
+export type PermittedUse = (typeof permittedUses)[number];
+export type EvidenceId = string;
+/** Spec section 8.3. */
+export interface EvidenceRecord {
+    id: EvidenceId;
+    citeKey: string;
+    type: EvidenceType;
+    title: string;
+    authors: {
+        family: string;
+        given?: string;
+        orcid?: string;
+    }[];
+    year: number;
+    containerTitle?: string;
+    volume?: string;
+    issue?: string;
+    pages?: string;
+    publisher?: string;
+    /** City of publication, printed by styles that need it (for example ICONTEC). */
+    placeOfPublication?: string;
+    doi?: string;
+    isbn?: string;
+    issn?: string;
+    url?: string;
+    language?: string;
+    retrievedAt: string;
+    verification: {
+        method: "crossref" | "openalex" | "arxiv" | "official_domain" | "user_supplied";
+        metadataMatch: number;
+        retracted: boolean;
+        checkedAt: string;
+    };
+    status: EvidenceStatus;
+    appraisal: {
+        relevance: "high" | "medium" | "low";
+        evidenceType: string;
+        limitations: string[];
+        supports: string[];
+        location?: string;
+    };
+    permittedUse: PermittedUse[];
+    sections: SectionId[];
+}
+export declare const claimKinds: readonly ["background", "argument", "result", "conclusion"];
+export type ClaimKind = (typeof claimKinds)[number];
+/** Spec 8.5. Ids are allocated by code; `anchor` is the `<!-- claim:anchor -->` id in the chapter. */
+export interface ClaimRecord {
+    id: string;
+    section: SectionId;
+    anchor: string;
+    text: string;
+    kind: ClaimKind;
+    evidence: EvidenceId[];
+    /** Ids of the claims a conclusion rests on. */
+    results?: string[];
+    objectives: string[];
+}
+export type FindingSeverity = "critical" | "major" | "minor";
+export declare const reviewCategories: readonly ["source", "concept", "method", "statistics", "argument", "wording", "format"];
+export type ReviewCategory = (typeof reviewCategories)[number];
+export declare const reviewRoutes: readonly ["evidence-auditor", "methodologist", "writer", "architect", "editor", "build"];
+export type ReviewRoute = (typeof reviewRoutes)[number];
+/** Spec 7.5 routing table (source notes section 23). */
+export declare const routeOfCategory: Record<ReviewCategory, ReviewRoute>;
+/** A reviewer finding stored as `reviews/FND-xxxx.json`. */
+export interface ReviewFinding {
+    id: string;
+    severity: FindingSeverity;
+    category: ReviewCategory;
+    target: SectionId;
+    evidence: string;
+    description: string;
+    routeTo: ReviewRoute;
+    status: "open" | "resolved" | "dismissed" | "superseded";
+    createdAt: string;
+    resolvedAt?: string;
+    notes?: string;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/types.d.ts.map

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package/dist/types.js

@@ -0,0 +1,155 @@
+/** Identifier patterns from spec section 4.1. */
+export const idPatterns = {
+    section: /^SEC-\d{2}(\.\d{2}){0,2}$/,
+    objective: /^OBJ-(G|\d{2})$/,
+    evidence: /^EVD-\d{5}$/,
+    claim: /^CLM-\d{4}$/,
+    finding: /^FND-\d{4}$/,
+    figure: /^fig-[a-z0-9-]{1,48}$/,
+    table: /^tbl-[a-z0-9-]{1,48}$/,
+    equation: /^eq-[a-z0-9-]{1,48}$/,
+    citationKey: /^[a-z][a-z0-9]{1,30}\d{4}[a-z]?$/,
+};
+export const roles = [
+    "thesis-coordinator",
+    "thesis-methodologist",
+    "thesis-librarian",
+    "thesis-evidence-auditor",
+    "thesis-architect",
+    "thesis-writer",
+    "thesis-editor",
+    "thesis-reviewer",
+];
+export const gates = ["G0", "G1", "G2", "G3", "G4", "G5", "G6", "G7", "G8", "G9", "G10"];
+export const phases = [
+    "intake",
+    "design",
+    "outline",
+    "sections",
+    "review",
+    "final",
+    "submitted",
+];
+export const gateNames = ["A", "B", "OUTLINE", "C"];
+export const sectionStatuses = [
+    "planned",
+    "researching",
+    "research_review",
+    "research_approved",
+    "drafting",
+    "draft_review",
+    "approved",
+    "revising",
+];
+/** Sections with no research phase: they are written from the thesis itself, not from sources. */
+export const frontSectionRoles = [
+    "abstract",
+    "abstract-secondary",
+    "dedication",
+    "acknowledgments",
+    "ai-declaration",
+];
+/** Written last: an abstract summarizes sections that must be approved first. */
+export const summarySectionRoles = ["abstract", "abstract-secondary"];
+export const workTypes = [
+    "undergraduate_thesis",
+    "degree_project",
+    "monograph",
+    "master_thesis",
+    "doctoral_dissertation",
+];
+export const approaches = [
+    "quantitative",
+    "qualitative",
+    "mixed",
+    "design_science",
+    "theoretical",
+    "systematic_review",
+];
+export const shippedCitationStyles = ["apa-7", "ieee", "icontec-ntc1486-2022"];
+export const shippedPresentationStandards = [
+    "apa-7",
+    "ieee",
+    "icontec-ntc1486-2022",
+    "generic",
+];
+export const paletteNames = [
+    "okabe-ito",
+    "tol-bright",
+    "tol-muted",
+    "tol-high-contrast",
+    "viridis",
+    "cividis",
+];
+/** Study designs that route reporting guidelines. Superset of the spec list plus the pack drafts. */
+export const studyDesigns = [
+    "rct",
+    "observational",
+    "qualitative_interview",
+    "systematic_review",
+    "scoping_review",
+    "case_study",
+    "experiment",
+    "survey",
+    "health_economic_evaluation",
+    "diagnostic_accuracy",
+    "prediction_model",
+    "quality_improvement",
+    "other",
+];
+export const evidenceTypes = [
+    "journal_article",
+    "book",
+    "chapter",
+    "conference_paper",
+    "thesis",
+    "report",
+    "standard",
+    "law",
+    "dataset",
+    "web_page",
+    "preprint",
+];
+export const evidenceStatuses = [
+    "VERIFIED_PRIMARY",
+    "VERIFIED_PEER_REVIEWED",
+    "VERIFIED_AUTHORITATIVE_GREY",
+    "CONTEXTUAL_ONLY",
+    "UNVERIFIED",
+    "REJECTED",
+];
+export const citableStatuses = [
+    "VERIFIED_PRIMARY",
+    "VERIFIED_PEER_REVIEWED",
+    "VERIFIED_AUTHORITATIVE_GREY",
+];
+export const permittedUses = ["background", "argument", "method", "results_comparison"];
+export const claimKinds = ["background", "argument", "result", "conclusion"];
+export const reviewCategories = [
+    "source",
+    "concept",
+    "method",
+    "statistics",
+    "argument",
+    "wording",
+    "format",
+];
+export const reviewRoutes = [
+    "evidence-auditor",
+    "methodologist",
+    "writer",
+    "architect",
+    "editor",
+    "build",
+];
+/** Spec 7.5 routing table (source notes section 23). */
+export const routeOfCategory = {
+    source: "evidence-auditor",
+    concept: "methodologist",
+    method: "methodologist",
+    statistics: "writer",
+    argument: "architect",
+    wording: "editor",
+    format: "build",
+};
+//# sourceMappingURL=types.js.map

package/dist/types.js.map

@@ -0,0 +1 @@
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package/dist/typst-pins.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Pinned Typst release (spec 16.1, P0.5). `/thesis:setup` downloads exactly these assets and
+ * verifies the SHA-256 before extracting anything. CI installs the same pins.
+ */
+export declare const typstVersion = "0.15.1";
+export interface TypstPin {
+    asset: string;
+    sha256: string;
+    /** Name of the executable inside the extracted archive. */
+    executable: "typst" | "typst.exe";
+}
+export declare const typstPins: Record<string, TypstPin>;
+export declare const typstReleaseBase = "https://github.com/typst/typst/releases/download/v0.15.1/";
+/** Pin key for a Node platform/arch pair, or undefined when no pinned asset exists. */
+export declare function pinKey(platform: string, arch: string): string | undefined;
+//# sourceMappingURL=typst-pins.d.ts.map