docrev 0.8.1 → 0.8.5

package/dist/lib/crossref.js

@@ -0,0 +1,597 @@
+/**
+ * Cross-reference handling - dynamic figure/table references
+ *
+ * Enables:
+ * - @fig:label syntax in source (auto-numbered)
+ * - Conversion to "Figure 1" in Word output
+ * - Auto-conversion back during import
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+import YAML from 'yaml';
+// =============================================================================
+// Constants
+// =============================================================================
+/** Characters of context to check before a reference for deduplication */
+const REF_CONTEXT_WINDOW = 100;
+/** Minimum word length for similarity calculations */
+const MIN_WORD_LENGTH = 2;
+// =============================================================================
+// Internal Helpers
+// =============================================================================
+/**
+ * Discover section files from a directory by reading config files
+ * Only returns files explicitly defined in rev.yaml or sections.yaml
+ * Returns empty array if no config found (caller should handle this)
+ */
+function discoverSectionFiles(directory) {
+    // Try rev.yaml first
+    const revYamlPath = path.join(directory, 'rev.yaml');
+    if (fs.existsSync(revYamlPath)) {
+        try {
+            const config = YAML.parse(fs.readFileSync(revYamlPath, 'utf-8'));
+            if (config.sections && Array.isArray(config.sections) && config.sections.length > 0) {
+                return config.sections.filter((f) => fs.existsSync(path.join(directory, f)));
+            }
+        }
+        catch (e) {
+            if (process.env.DEBUG) {
+                console.warn('crossref: YAML parse error in rev.yaml:', e.message);
+            }
+        }
+    }
+    // Try sections.yaml
+    const sectionsPath = path.join(directory, 'sections.yaml');
+    if (fs.existsSync(sectionsPath)) {
+        try {
+            const config = YAML.parse(fs.readFileSync(sectionsPath, 'utf-8'));
+            if (config.sections) {
+                const sectionOrder = Object.entries(config.sections)
+                    .sort((a, b) => (a[1].order ?? 999) - (b[1].order ?? 999))
+                    .map(([file]) => file);
+                return sectionOrder.filter((f) => fs.existsSync(path.join(directory, f)));
+            }
+        }
+        catch (e) {
+            if (process.env.DEBUG) {
+                console.warn('crossref: YAML parse error in sections.yaml:', e.message);
+            }
+        }
+    }
+    // No config found - return empty array
+    // Caller must handle this (either error or use explicit sections)
+    return [];
+}
+// =============================================================================
+// Detection Patterns
+// =============================================================================
+/**
+ * Patterns for detecting hardcoded references
+ * Matches complex patterns including:
+ * - Simple: "Figure 1", "Fig. 2a", "Table S1"
+ * - Ranges: "Figures 1-3", "Fig. 1a-c", "Figs. 1a-3b"
+ * - Lists: "Figures 1, 2, and 3", "Fig. 1a, b, c", "Tables 1 & 2"
+ * - Mixed: "Figs. 1, 3-5, and 7"
+ *
+ * Uses a simpler base pattern and parses the full match for lists
+ */
+const DETECTION_PATTERNS = {
+    // Captures the full reference including lists with "and"
+    // Group 1: type prefix (Figure, Fig., etc.)
+    // Group 2: reference list (parsed by parseReferenceList())
+    // Matches: "1", "1a", "1-3", "1a-c", "1, 2, 3", "1 and 2", "1, 2 and 3", "1, 2, and 3"
+    // Separator: comma/dash/ampersand, optionally followed by "and"
+    // Standalone letters must be followed by separator, punctuation, or word boundary
+    // Also handles: "see Figure 1", "(Fig. 1)", "in Figures 1–3"
+    // Note: 'gi' flag makes these case-insensitive, so "figure 1" is also matched
+    figure: /\b(Figures?|Figs?\.?)\s+((?:\d+|S\d+)[a-z]?(?:(?:\s*[-–—,&]\s*(?:and\s+)?|\s+and\s+)(?:(?:\d+|S\d+)[a-z]?|[a-z]\b))*)/gi,
+    table: /\b(Tables?|Tabs?\.?)\s+((?:\d+|S\d+)[a-z]?(?:(?:\s*[-–—,&]\s*(?:and\s+)?|\s+and\s+)(?:(?:\d+|S\d+)[a-z]?|[a-z]\b))*)/gi,
+    equation: /\b(Equations?|Eqs?\.?)\s+((?:\d+)[a-z]?(?:(?:\s*[-–—,&]\s*(?:and\s+)?|\s+and\s+)(?:(?:\d+)[a-z]?|[a-z]\b))*)/gi,
+};
+/**
+ * Patterns to EXCLUDE from detection (false positives)
+ * These look like references but aren't (e.g., "Table of Contents", "Figure skating")
+ */
+const EXCLUSION_PATTERNS = [
+    /\bTable\s+of\s+Contents?\b/gi,
+    /\bFigure\s+skating\b/gi,
+    /\bFigure\s+out\b/gi,
+    /\bFigure\s+it\b/gi,
+    /\bTable\s+setting/gi,
+    /\bEquation\s+editor\b/gi,
+];
+/**
+ * Pattern for extracting anchors from markdown: {#fig:label}, {#tbl:label}
+ */
+const ANCHOR_PATTERN = /\{#(fig|tbl|eq):([^}]+)\}/gi;
+/**
+ * Pattern for @-style references: @fig:label, @tbl:label
+ */
+const REF_PATTERN = /@(fig|tbl|eq):([a-zA-Z0-9_-]+)/gi;
+// =============================================================================
+// Public API
+// =============================================================================
+/**
+ * Normalize a reference type to standard form
+ */
+export function normalizeType(typeStr) {
+    if (typeof typeStr !== 'string') {
+        throw new TypeError(`typeStr must be a string, got ${typeof typeStr}`);
+    }
+    const lower = typeStr.toLowerCase().replace(/\.$/, '');
+    if (lower.startsWith('fig'))
+        return 'fig';
+    if (lower.startsWith('tab'))
+        return 'tbl';
+    if (lower.startsWith('eq'))
+        return 'eq';
+    return lower;
+}
+/**
+ * Parse a reference number, handling supplementary (S1, S2) and letter suffixes (1a, 1b)
+ */
+export function parseRefNumber(numStr, suffix = null) {
+    if (!numStr || typeof numStr !== 'string') {
+        return { isSupp: false, num: 0, suffix: suffix || null };
+    }
+    const isSupp = numStr.toUpperCase().startsWith('S');
+    const numPart = isSupp ? numStr.slice(1) : numStr;
+    // Extract suffix if embedded in numStr (e.g., "1a")
+    const match = numPart.match(/^(\d+)([a-z])?$/i);
+    const num = match && match[1] ? parseInt(match[1], 10) : parseInt(numPart, 10);
+    const extractedSuffix = suffix || (match && match[2]) || null;
+    return { isSupp, num, suffix: extractedSuffix ? extractedSuffix.toLowerCase() : null };
+}
+/**
+ * Parse a reference list string like "1, 2, and 3" or "1a-c" or "1a-3b"
+ * Returns an array of {num, isSupp, suffix} objects
+ */
+export function parseReferenceList(listStr) {
+    const results = [];
+    if (!listStr || typeof listStr !== 'string')
+        return results;
+    // Normalize: replace "and" with comma, normalize dashes
+    let normalized = listStr
+        .replace(/\s+and\s+/gi, ', ')
+        .replace(/[–—]/g, '-') // en-dash, em-dash → hyphen
+        .replace(/&/g, ', '); // & → comma
+    // Split by comma (but not by dash, which indicates ranges)
+    const parts = normalized.split(/\s*,\s*/).filter((p) => p.trim());
+    let lastFullRef = null; // Track the last full reference for implicit prefixes
+    for (const part of parts) {
+        const trimmed = part.trim();
+        if (!trimmed)
+            continue;
+        // Check if this is a range (contains -)
+        if (trimmed.includes('-')) {
+            const parts = trimmed.split('-').map((s) => s.trim());
+            const start = parts[0] || '';
+            const end = parts[1] || '';
+            // Check if end is just a letter (e.g., "1a-c" where end is "c")
+            const endIsLetterOnly = /^[a-z]$/i.test(end);
+            const startRef = parseRefNumber(start);
+            // For letter-only end, don't parse as number
+            const endRef = endIsLetterOnly
+                ? { num: startRef.num, isSupp: startRef.isSupp, suffix: end.toLowerCase() }
+                : parseRefNumber(end);
+            // Handle different range types:
+            // 1. Suffix-only range on same number: "1a-c" → 1a, 1b, 1c
+            // 2. Number range: "1-3" → 1, 2, 3
+            // 3. Cross-number suffix range: "1a-3b" → 1a...1z, 2a...2z, 3a, 3b (limited)
+            if (startRef.suffix && endRef.suffix && startRef.num !== endRef.num) {
+                // Cross-number suffix range: "1a-3b"
+                // For academic papers, limit intermediate figures to same suffix range
+                // e.g., "1a-3b" typically means 1a, 1b, 2a, 2b, 3a, 3b
+                const maxSuffix = Math.max(startRef.suffix.charCodeAt(0), endRef.suffix.charCodeAt(0));
+                for (let n = startRef.num; n <= endRef.num; n++) {
+                    const suffixStart = n === startRef.num ? startRef.suffix.charCodeAt(0) : 'a'.charCodeAt(0);
+                    const suffixEnd = n === endRef.num ? endRef.suffix.charCodeAt(0) : maxSuffix;
+                    for (let s = suffixStart; s <= suffixEnd; s++) {
+                        results.push({
+                            num: n,
+                            isSupp: startRef.isSupp,
+                            suffix: String.fromCharCode(s),
+                        });
+                    }
+                }
+                lastFullRef = { num: endRef.num, isSupp: startRef.isSupp };
+            }
+            else if (startRef.suffix || endRef.suffix) {
+                // Suffix range on same number: "1a-c"
+                const num = startRef.num !== 0 ? startRef.num : (lastFullRef ? lastFullRef.num : 1);
+                const isSupp = startRef.isSupp ? startRef.isSupp : (lastFullRef ? lastFullRef.isSupp : false);
+                const startCode = (startRef.suffix || 'a').charCodeAt(0);
+                const endCode = (endRef.suffix || 'a').charCodeAt(0);
+                for (let code = startCode; code <= endCode; code++) {
+                    results.push({
+                        num,
+                        isSupp,
+                        suffix: String.fromCharCode(code),
+                    });
+                }
+                lastFullRef = { num, isSupp };
+            }
+            else {
+                // Pure number range: "1-3"
+                for (let n = startRef.num; n <= endRef.num; n++) {
+                    results.push({
+                        num: n,
+                        isSupp: startRef.isSupp,
+                        suffix: null,
+                    });
+                }
+                lastFullRef = { num: endRef.num, isSupp: startRef.isSupp };
+            }
+        }
+        else {
+            // Single reference or implicit suffix
+            // Check if it's just a letter (implicit prefix from previous number)
+            if (/^[a-z]$/i.test(trimmed) && lastFullRef) {
+                // Implicit prefix: "b" after "1a" means "1b"
+                results.push({
+                    num: lastFullRef.num,
+                    isSupp: lastFullRef.isSupp,
+                    suffix: trimmed.toLowerCase(),
+                });
+            }
+            else {
+                // Full reference: "1", "1a", "S1", "S1a"
+                const ref = parseRefNumber(trimmed);
+                results.push(ref);
+                lastFullRef = { num: ref.num, isSupp: ref.isSupp };
+            }
+        }
+    }
+    return results;
+}
+/**
+ * Build a registry of figure/table labels from .md files
+ * Scans for {#fig:label} and {#tbl:label} anchors
+ *
+ * IMPORTANT: This function requires either explicit sections or a rev.yaml/sections.yaml config.
+ * It will NOT guess by scanning all .md files, as this leads to incorrect numbering
+ * when temporary files (paper_clean.md, etc.) exist in the directory.
+ */
+export function buildRegistry(directory, sections) {
+    if (typeof directory !== 'string') {
+        throw new TypeError(`directory must be a string, got ${typeof directory}`);
+    }
+    const figures = new Map();
+    const tables = new Map();
+    const equations = new Map();
+    // Counters for numbering (separate for main and supplementary)
+    let figNum = 0;
+    let figSuppNum = 0;
+    let tblNum = 0;
+    let tblSuppNum = 0;
+    let eqNum = 0;
+    let orderedFiles;
+    if (Array.isArray(sections) && sections.length > 0) {
+        // Use explicitly provided section files - most reliable
+        orderedFiles = sections.filter((f) => fs.existsSync(path.join(directory, f)));
+    }
+    else {
+        // Try to determine sections from config files (rev.yaml or sections.yaml)
+        orderedFiles = discoverSectionFiles(directory);
+        // If no config found, return empty registry rather than guessing
+        // This prevents bugs from scanning wrong files
+    }
+    // Determine if a file is supplementary
+    const isSupplementary = (filename) => filename.toLowerCase().includes('supp') || filename.toLowerCase().includes('appendix');
+    // Process each file in order
+    for (const file of orderedFiles) {
+        const filePath = path.join(directory, file);
+        const content = fs.readFileSync(filePath, 'utf-8');
+        const isSupp = isSupplementary(file);
+        // Find all anchors
+        let match;
+        ANCHOR_PATTERN.lastIndex = 0;
+        while ((match = ANCHOR_PATTERN.exec(content)) !== null) {
+            const typeRaw = match[1];
+            const labelRaw = match[2];
+            if (!typeRaw || !labelRaw)
+                continue;
+            const type = typeRaw.toLowerCase();
+            const label = labelRaw;
+            if (type === 'fig') {
+                if (isSupp) {
+                    figSuppNum++;
+                    figures.set(label, { label, num: figSuppNum, isSupp: true, file });
+                }
+                else {
+                    figNum++;
+                    figures.set(label, { label, num: figNum, isSupp: false, file });
+                }
+            }
+            else if (type === 'tbl') {
+                if (isSupp) {
+                    tblSuppNum++;
+                    tables.set(label, { label, num: tblSuppNum, isSupp: true, file });
+                }
+                else {
+                    tblNum++;
+                    tables.set(label, { label, num: tblNum, isSupp: false, file });
+                }
+            }
+            else if (type === 'eq') {
+                eqNum++;
+                equations.set(label, { label, num: eqNum, isSupp: false, file });
+            }
+        }
+    }
+    // Build reverse lookup: number → label
+    const byNumber = {
+        fig: new Map(),
+        figS: new Map(),
+        tbl: new Map(),
+        tblS: new Map(),
+        eq: new Map(),
+    };
+    for (const [label, info] of figures) {
+        const key = info.isSupp ? 'figS' : 'fig';
+        byNumber[key].set(info.num, label);
+    }
+    for (const [label, info] of tables) {
+        const key = info.isSupp ? 'tblS' : 'tbl';
+        byNumber[key].set(info.num, label);
+    }
+    for (const [label, info] of equations) {
+        byNumber.eq.set(info.num, label);
+    }
+    return { figures, tables, equations, byNumber };
+}
+/**
+ * Get the display string for a label (e.g., "Figure 1", "Table S2")
+ */
+export function labelToDisplay(type, label, registry) {
+    if (!registry || !registry.figures)
+        return null;
+    const collection = type === 'fig' ? registry.figures : type === 'tbl' ? registry.tables : registry.equations;
+    const info = collection.get(label);
+    if (!info)
+        return null;
+    const prefix = type === 'fig' ? 'Figure' : type === 'tbl' ? 'Table' : 'Equation';
+    const numStr = info.isSupp ? `S${info.num}` : `${info.num}`;
+    return `${prefix} ${numStr}`;
+}
+/**
+ * Get the label for a display number (e.g., "fig:heatmap" from Figure 1)
+ */
+export function numberToLabel(type, num, isSupp, registry) {
+    if (!registry || !registry.byNumber)
+        return null;
+    const key = isSupp ? `${type}S` : type;
+    return registry.byNumber[key]?.get(num) || null;
+}
+/**
+ * Detect all hardcoded references in text
+ */
+export function detectHardcodedRefs(text) {
+    if (typeof text !== 'string') {
+        throw new TypeError(`text must be a string, got ${typeof text}`);
+    }
+    const refs = [];
+    for (const [type, pattern] of Object.entries(DETECTION_PATTERNS)) {
+        pattern.lastIndex = 0;
+        let match;
+        while ((match = pattern.exec(text)) !== null) {
+            // Pattern groups:
+            // [1] = type prefix (Figure, Fig., etc.)
+            // [2] = reference list string (e.g., "1, 2, and 3" or "1a-3b")
+            const listStr = match[2];
+            if (!listStr)
+                continue;
+            const numbers = parseReferenceList(listStr);
+            // Skip if no valid numbers were parsed
+            if (numbers.length === 0)
+                continue;
+            refs.push({
+                type: normalizeType(type),
+                match: match[0],
+                numbers,
+                position: match.index,
+            });
+        }
+    }
+    // Sort by position
+    refs.sort((a, b) => a.position - b.position);
+    return refs;
+}
+/**
+ * Convert hardcoded references to @-style references
+ */
+export function convertHardcodedRefs(text, registry) {
+    // Input validation delegated to detectHardcodedRefs
+    const refs = detectHardcodedRefs(text);
+    const conversions = [];
+    const warnings = [];
+    // Process in reverse order to preserve positions
+    let result = text;
+    for (let i = refs.length - 1; i >= 0; i--) {
+        const ref = refs[i];
+        if (!ref)
+            continue;
+        // Build replacement
+        const labels = [];
+        for (const { num, isSupp } of ref.numbers) {
+            const label = numberToLabel(ref.type, num, isSupp, registry);
+            if (label) {
+                labels.push(`@${ref.type}:${label}`);
+            }
+            else {
+                const displayNum = isSupp ? `S${num}` : `${num}`;
+                warnings.push(`Unknown reference: ${ref.type} ${displayNum} (no matching label)`);
+                labels.push(ref.match); // Keep original if no match
+            }
+        }
+        if (labels.length > 0 && !labels.includes(ref.match)) {
+            const replacement = labels.join('; ');
+            // Skip if the @-syntax already appears in the preceding text
+            // This prevents duplication when import restores @fig:x and then we see "Fig. 1"
+            // e.g., "@fig:map@fig:map{++@fig:map++}" or "@fig:mapFigure 1" patterns
+            const textBefore = result.slice(Math.max(0, ref.position - REF_CONTEXT_WINDOW), ref.position);
+            const alreadyHasRef = labels.some((label) => textBefore.includes(label));
+            if (alreadyHasRef) {
+                continue; // Skip - ref already present nearby
+            }
+            result =
+                result.slice(0, ref.position) + replacement + result.slice(ref.position + ref.match.length);
+            conversions.push({
+                from: ref.match,
+                to: replacement,
+            });
+        }
+    }
+    return { converted: result, conversions, warnings };
+}
+/**
+ * Detect @-style references in text
+ */
+export function detectDynamicRefs(text) {
+    if (typeof text !== 'string') {
+        throw new TypeError(`text must be a string, got ${typeof text}`);
+    }
+    const refs = [];
+    REF_PATTERN.lastIndex = 0;
+    let match;
+    while ((match = REF_PATTERN.exec(text)) !== null) {
+        const type = match[1];
+        const label = match[2];
+        if (!type || !label)
+            continue;
+        refs.push({
+            type: type,
+            label: label,
+            match: match[0],
+            position: match.index,
+        });
+    }
+    return refs;
+}
+/**
+ * Get reference status for a file/text
+ */
+export function getRefStatus(text, registry) {
+    const dynamic = detectDynamicRefs(text);
+    const hardcoded = detectHardcodedRefs(text);
+    // Count anchors in this text
+    ANCHOR_PATTERN.lastIndex = 0;
+    let figCount = 0, tblCount = 0, eqCount = 0;
+    let match;
+    while ((match = ANCHOR_PATTERN.exec(text)) !== null) {
+        const type = match[1];
+        if (!type)
+            continue;
+        if (type === 'fig')
+            figCount++;
+        else if (type === 'tbl')
+            tblCount++;
+        else if (type === 'eq')
+            eqCount++;
+    }
+    return {
+        dynamic,
+        hardcoded,
+        anchors: { figures: figCount, tables: tblCount, equations: eqCount },
+    };
+}
+/**
+ * Detect forward references in combined text
+ * A forward reference is a @ref that appears before its {#anchor} definition
+ */
+export function detectForwardRefs(text) {
+    // Build map of anchor positions: "fig:label" -> position
+    const anchorPositions = new Map();
+    ANCHOR_PATTERN.lastIndex = 0;
+    let match;
+    while ((match = ANCHOR_PATTERN.exec(text)) !== null) {
+        const type = match[1];
+        const label = match[2];
+        if (!type || !label)
+            continue;
+        const key = `${type}:${label}`;
+        // Only store first occurrence (in case of duplicates)
+        if (!anchorPositions.has(key)) {
+            anchorPositions.set(key, match.index);
+        }
+    }
+    // Find all references
+    const refs = detectDynamicRefs(text);
+    // Filter to only forward references
+    const forwardRefs = refs.filter((ref) => {
+        const key = `${ref.type}:${ref.label}`;
+        const anchorPos = anchorPositions.get(key);
+        // Forward ref if anchor doesn't exist or appears after the reference
+        return anchorPos === undefined || ref.position < anchorPos;
+    });
+    return { forwardRefs, anchorPositions };
+}
+/**
+ * Resolve forward references to display format
+ * Only resolves refs that appear before their anchor definition
+ * Leaves other refs for pandoc-crossref to handle (preserves clickable links)
+ */
+export function resolveForwardRefs(text, registry) {
+    const { forwardRefs } = detectForwardRefs(text);
+    const resolved = [];
+    const unresolved = [];
+    // Process in reverse order to preserve positions
+    let result = text;
+    for (let i = forwardRefs.length - 1; i >= 0; i--) {
+        const ref = forwardRefs[i];
+        if (!ref)
+            continue;
+        const display = labelToDisplay(ref.type, ref.label, registry);
+        if (display) {
+            result =
+                result.slice(0, ref.position) + display + result.slice(ref.position + ref.match.length);
+            resolved.push({
+                from: ref.match,
+                to: display,
+                position: ref.position,
+            });
+        }
+        else {
+            unresolved.push({
+                ref: ref.match,
+                position: ref.position,
+            });
+        }
+    }
+    return { text: result, resolved, unresolved };
+}
+/**
+ * Format registry for display
+ */
+export function formatRegistry(registry) {
+    const lines = [];
+    if (registry.figures.size > 0) {
+        lines.push('Figures:');
+        for (const [label, info] of registry.figures) {
+            const num = info.isSupp ? `S${info.num}` : info.num;
+            lines.push(`  Figure ${num}: @fig:${label} (${info.file})`);
+        }
+    }
+    if (registry.tables.size > 0) {
+        if (lines.length > 0)
+            lines.push('');
+        lines.push('Tables:');
+        for (const [label, info] of registry.tables) {
+            const num = info.isSupp ? `S${info.num}` : info.num;
+            lines.push(`  Table ${num}: @tbl:${label} (${info.file})`);
+        }
+    }
+    if (registry.equations.size > 0) {
+        if (lines.length > 0)
+            lines.push('');
+        lines.push('Equations:');
+        for (const [label, info] of registry.equations) {
+            lines.push(`  Equation ${info.num}: @eq:${label} (${info.file})`);
+        }
+    }
+    if (lines.length === 0) {
+        lines.push('No figure/table anchors found.');
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=crossref.js.map

package/dist/lib/crossref.js.map

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

@@ -0,0 +1,30 @@
+/**
+ * Dependency checking utilities for pandoc, LaTeX, and related tools
+ */
+/**
+ * Check if pandoc-crossref is available
+ */
+export declare function hasPandocCrossref(): boolean;
+/**
+ * Check if pandoc is available
+ */
+export declare function hasPandoc(): boolean;
+/**
+ * Check if LaTeX is available (for PDF generation)
+ */
+export declare function hasLatex(): boolean;
+/**
+ * Get installation instructions for missing dependencies
+ */
+export declare function getInstallInstructions(dependency: string): string;
+export interface DependencyStatus {
+    pandoc: boolean;
+    latex: boolean;
+    crossref: boolean;
+    messages: string[];
+}
+/**
+ * Check dependencies and return status
+ */
+export declare function checkDependencies(): DependencyStatus;
+//# sourceMappingURL=dependencies.d.ts.map

package/dist/lib/dependencies.d.ts.map

@@ -0,0 +1 @@
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