docrev 0.10.2 → 0.11.0

package/dist/lib/comment-realign.js

@@ -1,365 +1,57 @@
 /**
- * Realign comments from a reference DOCX to markdown
- * Uses paragraph-level matching with exact positions
+ * Realign comments from a reference DOCX onto markdown.
+ *
+ * This is the same job as `rev sync`: read the comments and their anchors from
+ * a docx, then place them into the current markdown. It therefore reuses the
+ * one extraction + placement engine rather than carrying a second docx parser
+ * and a proportional position-mapper.
  */
 import * as fs from 'fs';
-import AdmZip from 'adm-zip';
-import { parseStringPromise } from 'xml2js';
-/**
- * Extract paragraphs with their full text and comment positions from DOCX
- */
-export async function extractParagraphsWithComments(docxPath) {
-    const zip = new AdmZip(docxPath);
-    const doc = zip.readAsText('word/document.xml');
-    const commentsXml = zip.readAsText('word/comments.xml');
-    // Parse comments to get authors and texts
-    const parsed = await parseStringPromise(commentsXml, { explicitArray: false });
-    const commentNodes = parsed['w:comments']?.['w:comment'];
-    if (!commentNodes)
-        return [];
-    const nodes = Array.isArray(commentNodes) ? commentNodes : [commentNodes];
-    const commentData = {};
-    for (const c of nodes) {
-        const id = c.$?.['w:id'] ?? '';
-        const author = c.$?.['w:author'] ?? 'Unknown';
-        let text = '';
-        const extractT = (n) => {
-            if (!n)
-                return;
-            if (n['w:t']) {
-                const t = n['w:t'];
-                text += typeof t === 'string' ? t : (t._ || t);
-            }
-            if (n['w:r']) {
-                (Array.isArray(n['w:r']) ? n['w:r'] : [n['w:r']]).forEach(extractT);
-            }
-            if (n['w:p']) {
-                (Array.isArray(n['w:p']) ? n['w:p'] : [n['w:p']]).forEach(extractT);
-            }
-        };
-        extractT(c);
-        commentData[id] = { author, text: text.trim() };
-    }
-    // Extract paragraphs with comments
-    const paragraphs = [];
-    const paraPattern = /<w:p\b[^>]*>([\s\S]*?)<\/w:p>/g;
-    let match;
-    while ((match = paraPattern.exec(doc)) !== null) {
-        const paraContent = match[1];
-        const hasComments = /commentRangeStart/.test(paraContent);
-        // Build paragraph text and track comment positions
-        let text = '';
-        const comments = [];
-        const tokenPattern = /<w:t[^>]*>([^<]*)<\/w:t>|<w:commentRangeStart[^>]*w:id="(\d+)"[^>]*\/?>/g;
-        let tokenMatch;
-        while ((tokenMatch = tokenPattern.exec(paraContent)) !== null) {
-            if (tokenMatch[1] !== undefined) {
-                text += tokenMatch[1];
-            }
-            else if (tokenMatch[2] !== undefined) {
-                const cid = tokenMatch[2];
-                const data = commentData[cid];
-                if (data) {
-                    comments.push({
-                        id: cid,
-                        position: text.length,
-                        author: data.author,
-                        text: data.text,
-                    });
-                }
-            }
-        }
-        if (text.trim() || hasComments) {
-            paragraphs.push({ text: text.trim(), comments });
-        }
-    }
-    return paragraphs;
-}
-/**
- * Find best matching paragraph in markdown for a reference paragraph
- */
-function findMatchingParagraph(refText, mdParagraphs) {
-    // Normalize for comparison
-    const normalize = (s) => s.toLowerCase().replace(/\s+/g, ' ').trim();
-    const refNorm = normalize(refText);
-    if (refNorm.length < 20)
-        return null;
-    let bestMatch = null;
-    let bestScore = 0;
-    for (let i = 0; i < mdParagraphs.length; i++) {
-        const mdNorm = normalize(mdParagraphs[i].text);
-        // Calculate word overlap
-        const refWords = new Set(refNorm.split(' ').filter((w) => w.length > 3));
-        const mdWords = mdNorm.split(' ').filter((w) => w.length > 3);
-        const overlap = mdWords.filter((w) => refWords.has(w)).length;
-        const score = overlap / Math.max(refWords.size, 1);
-        // Also check for substring containment (for section headers)
-        const containsStart = mdNorm.includes(refNorm.slice(0, 50));
-        if (score > bestScore || (containsStart && score > 0.3)) {
-            bestScore = Math.max(score, containsStart ? 0.8 : score);
-            bestMatch = { index: i, score: bestScore, paragraph: mdParagraphs[i] };
-        }
-    }
-    return bestScore > 0.4 ? bestMatch : null;
-}
-/**
- * Extract paragraphs from markdown (split by blank lines)
- */
-function parseMdParagraphs(markdown) {
-    const paragraphs = [];
-    const parts = markdown.split(/\n\n+/);
-    let pos = 0;
-    for (const part of parts) {
-        const trimmed = part.trim();
-        if (trimmed) {
-            const partStart = markdown.indexOf(part, pos);
-            if (partStart !== -1) {
-                paragraphs.push({
-                    text: trimmed,
-                    start: partStart,
-                    end: partStart + part.length,
-                });
-                pos = partStart + part.length;
-            }
-        }
-    }
-    return paragraphs;
-}
-/**
- * Normalize text for matching (remove citations, extra whitespace)
- */
-function normalizeForMatching(text) {
-    return text
-        // Remove Word citation placeholders
-        .replace(/\(\s*\$+\s*\)/g, '')
-        .replace(/\$+/g, '')
-        // Remove markdown citations
-        .replace(/\[@[^\]]+\]/g, '')
-        .replace(/@[A-Z][a-z]+\d{4}/g, '')
-        // Remove rendered citations like "(Author et al. 2021)"
-        .replace(/\([A-Z][a-z]+(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?(?:[;,]\s*[A-Z][a-z]+(?:\s+et\s+al\.?)?\s+\d{4}[a-z]?)*\)/g, '')
-        // Remove figure references like "Fig. 1" or "(Fig. 1)"
-        .replace(/\(?Fig\.?\s*\d+[a-z]?\)?/gi, '')
-        // Normalize whitespace
-        .replace(/\s+/g, ' ')
-        .trim()
-        .toLowerCase();
-}
-/**
- * Find the word at or near a position in text
- */
-function getWordAtPosition(text, pos) {
-    const before = text.slice(Math.max(0, pos - 30), pos);
-    const after = text.slice(pos, pos + 30);
-    // Get the last complete word before position
-    const beforeWords = before.split(/\s+/).filter(w => w.length > 2);
-    const afterWords = after.split(/\s+/).filter(w => w.length > 2);
-    return {
-        before: beforeWords.slice(-3),
-        after: afterWords.slice(0, 3)
-    };
+import { extractWordComments, extractCommentAnchors } from './word-extraction.js';
+import { insertCommentsIntoMarkdown } from './import.js';
+/** Existing CriticMarkup comments, removed before the reference set is placed. */
+function stripExistingComments(markdown) {
+    return markdown.replace(/\s*\{>>[\s\S]+?<<\}/g, '');
 }
 /**
- * Find position in markdown paragraph matching reference position
- * Uses the anchor word (word immediately before the comment) for precise matching
+ * Realign the reference docx's comments onto an in-memory markdown string.
+ * Existing comments are cleared first so re-running is idempotent.
  */
-function findMdPosition(refText, refPos, mdText) {
-    // Get the word(s) immediately before the comment position in reference
-    const refWords = getWordAtPosition(refText, refPos);
-    const normalizedMd = normalizeForMatching(mdText);
-    // The "anchor word" is the last word before the comment
-    const anchorWords = refWords.before;
-    if (anchorWords.length === 0) {
-        const ratio = refPos / Math.max(refText.length, 1);
-        return Math.round(ratio * mdText.length);
-    }
-    // Try to find the anchor word(s) in markdown
-    // Start with the most specific (all words), fall back to fewer
-    for (let numWords = anchorWords.length; numWords >= 1; numWords--) {
-        const searchWords = anchorWords.slice(-numWords);
-        const pattern = searchWords.map(w => w.toLowerCase().replace(/[.*+?^${}()|[\]\\]/g, '\\$&')).join('\\s+');
-        const regex = new RegExp(pattern, 'g');
-        const matches = [...normalizedMd.matchAll(regex)];
-        if (matches.length === 1) {
-            // Unique match - use this position
-            const matchEnd = matches[0].index + matches[0][0].length;
-            // Map back to original markdown position
-            const ratio = matchEnd / Math.max(normalizedMd.length, 1);
-            return Math.round(ratio * mdText.length);
-        }
-        else if (matches.length > 1) {
-            // Multiple matches - use context after to disambiguate
-            const afterWords = refWords.after;
-            if (afterWords.length > 0) {
-                const afterPattern = afterWords[0].toLowerCase().replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
-                for (const match of matches) {
-                    const matchEnd = match.index + match[0].length;
-                    const afterContext = normalizedMd.slice(matchEnd, matchEnd + 50);
-                    if (afterContext.includes(afterPattern)) {
-                        const ratio = matchEnd / Math.max(normalizedMd.length, 1);
-                        return Math.round(ratio * mdText.length);
-                    }
-                }
-            }
-            // Fall back to first match
-            const matchEnd = matches[0].index + matches[0][0].length;
-            const ratio = matchEnd / Math.max(normalizedMd.length, 1);
-            return Math.round(ratio * mdText.length);
-        }
+export async function realignMarkdown(docxPath, markdown, options = {}) {
+    try {
+        let comments = await extractWordComments(docxPath);
+        const { anchors } = await extractCommentAnchors(docxPath);
+        if (options.author) {
+            const keep = new Set([options.author, options.replyAuthor].filter(Boolean));
+            comments = comments.filter((c) => keep.has(c.author));
+        }
+        const stripped = stripExistingComments(markdown);
+        const stats = { placed: 0, lowConfidence: 0, deduped: 0, unmatched: 0 };
+        const result = insertCommentsIntoMarkdown(stripped, comments, anchors, {
+            quiet: true,
+            wrapAnchor: false,
+            outStats: stats,
+        });
+        return { success: true, markdown: result, insertions: stats.placed + stats.lowConfidence };
     }
-    // Fallback: proportional position
-    const ratio = refPos / Math.max(refText.length, 1);
-    return Math.round(ratio * mdText.length);
-}
-/**
- * Extract reply comments that follow a parent comment
- * Returns map of parent comment text -> array of reply texts
- */
-function extractReplies(markdown, parentAuthor, replyAuthor) {
-    const replies = new Map();
-    const pattern = new RegExp(`\\{>>${parentAuthor}:\\s*([^<]+)<<\\}((?:\\s*\\{>>${replyAuthor}:[^<]+<<\\})*)`, 'g');
-    let match;
-    while ((match = pattern.exec(markdown)) !== null) {
-        const parentText = match[1].trim();
-        const replyBlock = match[2];
-        if (replyBlock) {
-            const replyPattern = new RegExp(`\\{>>${replyAuthor}:\\s*([^<]+)<<\\}`, 'g');
-            const replyTexts = [];
-            let replyMatch;
-            while ((replyMatch = replyPattern.exec(replyBlock)) !== null) {
-                replyTexts.push(replyMatch[1].trim());
-            }
-            if (replyTexts.length > 0) {
-                replies.set(parentText.slice(0, 50), replyTexts); // Use first 50 chars as key
-            }
-        }
+    catch (err) {
+        return { success: false, markdown, insertions: 0, error: err.message };
     }
-    return replies;
 }
 /**
- * Realign comments from reference DOCX to markdown
+ * Realign the reference docx's comments onto a markdown file in place.
  */
 export async function realignComments(docxPath, markdownPath, options = {}) {
-    const { dryRun = false, author = 'Guy Colling', replyAuthor = 'Gilles Colling' } = options;
-    // Read original markdown to extract replies before stripping
-    const originalMarkdown = fs.readFileSync(markdownPath, 'utf-8');
-    // Extract reply relationships
-    const replies = extractReplies(originalMarkdown, author, replyAuthor);
-    console.log(`Found ${replies.size} ${author} comments with ${replyAuthor} replies`);
-    // Extract reference paragraphs with comments
-    const refParagraphs = await extractParagraphsWithComments(docxPath);
-    const refWithComments = refParagraphs.filter((p) => p.comments.length > 0 && p.comments.some((c) => c.author === author));
-    console.log(`Found ${refWithComments.length} paragraphs with ${author} comments in reference`);
-    // Strip ALL comments (both authors) from markdown to start fresh
-    let markdown = originalMarkdown;
-    markdown = markdown.replace(/\s*\{>>[\s\S]+?<<\}/g, '');
-    console.log(`Stripped all comments from markdown`);
-    // Parse markdown paragraphs
-    const mdParagraphs = parseMdParagraphs(markdown);
-    // Track insertions (position, text) - will insert from end to start
-    const insertions = [];
-    let matched = 0;
-    let unmatched = 0;
-    for (const refPara of refWithComments) {
-        const match = findMatchingParagraph(refPara.text, mdParagraphs);
-        if (!match) {
-            console.log(`  No match for: "${refPara.text.slice(0, 60)}..."`);
-            unmatched++;
-            continue;
-        }
-        matched++;
-        const mdPara = match.paragraph;
-        // Get author's comments in this paragraph
-        const authorComments = refPara.comments.filter((c) => c.author === author);
-        for (const comment of authorComments) {
-            // Find corresponding position in markdown paragraph
-            const mdPos = findMdPosition(refPara.text, comment.position, mdPara?.text ?? '');
-            const absolutePos = (mdPara?.start ?? 0) + mdPos;
-            // Build comment mark with any replies
-            let commentMark = ` {>>${comment.author}: ${comment.text}<<}`;
-            // Check for replies
-            const replyKey = comment.text.trim().slice(0, 50);
-            const replyTexts = replies.get(replyKey);
-            if (replyTexts) {
-                for (const replyText of replyTexts) {
-                    commentMark += ` {>>${replyAuthor}: ${replyText}<<}`;
-                }
-            }
-            insertions.push({
-                position: absolutePos,
-                text: commentMark,
-                commentText: comment.text.slice(0, 30),
-                hasReplies: !!replyTexts,
-                debug: `"${(mdPara?.text ?? '').slice(Math.max(0, mdPos - 20), mdPos)}|HERE|${(mdPara?.text ?? '').slice(mdPos, mdPos + 20)}"`,
-            });
-        }
+    const { dryRun = false, author, replyAuthor } = options;
+    const original = fs.readFileSync(markdownPath, 'utf-8');
+    const realigned = await realignMarkdown(docxPath, original, { author, replyAuthor });
+    if (!realigned.success) {
+        return { success: false, insertions: 0, error: realigned.error };
     }
-    console.log(`Matched ${matched} paragraphs, ${unmatched} unmatched`);
-    console.log(`Inserting ${insertions.length} comments (${insertions.filter((i) => i.hasReplies).length} with replies)`);
     if (dryRun) {
-        console.log('\nDry run - would insert:');
-        for (const ins of insertions.slice(0, 10)) {
-            console.log(`  At ${ins.position}: ${ins.debug}`);
-            console.log(`    Comment: "${ins.commentText}..."${ins.hasReplies ? ' (+ replies)' : ''}`);
-        }
-        return { success: true, dryRun: true, insertions: insertions.length };
-    }
-    // Sort by position descending and insert
-    insertions.sort((a, b) => b.position - a.position);
-    for (const ins of insertions) {
-        markdown = markdown.slice(0, ins.position) + ins.text + markdown.slice(ins.position);
-    }
-    // Write result
-    fs.writeFileSync(markdownPath, markdown);
-    return { success: true, insertions: insertions.length, matched, unmatched };
-}
-/**
- * Realign comments in markdown string (in-memory, doesn't write to file)
- */
-export async function realignMarkdown(docxPath, markdown, options = {}) {
-    const { author = 'Guy Colling', replyAuthor = 'Gilles Colling' } = options;
-    try {
-        // Extract reply relationships from original markdown
-        const replies = extractReplies(markdown, author, replyAuthor);
-        // Extract reference paragraphs with comments
-        const refParagraphs = await extractParagraphsWithComments(docxPath);
-        const refWithComments = refParagraphs.filter((p) => p.comments.length > 0 && p.comments.some((c) => c.author === author));
-        // Strip ALL comments from markdown
-        let result = markdown.replace(/\s*\{>>[\s\S]+?<<\}/g, '');
-        // Parse markdown paragraphs
-        const mdParagraphs = parseMdParagraphs(result);
-        // Track insertions
-        const insertions = [];
-        for (const refPara of refWithComments) {
-            const match = findMatchingParagraph(refPara.text, mdParagraphs);
-            if (!match)
-                continue;
-            const mdPara = match.paragraph;
-            const authorComments = refPara.comments.filter((c) => c.author === author);
-            for (const comment of authorComments) {
-                const mdPos = findMdPosition(refPara.text, comment.position, mdPara?.text ?? '');
-                const absolutePos = (mdPara?.start ?? 0) + mdPos;
-                let commentMark = ` {>>${comment.author}: ${comment.text}<<}`;
-                // Check for replies
-                const replyKey = comment.text.trim().slice(0, 50);
-                const replyTexts = replies.get(replyKey);
-                if (replyTexts) {
-                    for (const replyText of replyTexts) {
-                        commentMark += ` {>>${replyAuthor}: ${replyText}<<}`;
-                    }
-                }
-                insertions.push({ position: absolutePos, text: commentMark });
-            }
-        }
-        // Sort by position descending and insert
-        insertions.sort((a, b) => b.position - a.position);
-        for (const ins of insertions) {
-            result = result.slice(0, ins.position) + ins.text + result.slice(ins.position);
-        }
-        return { success: true, markdown: result, insertions: insertions.length };
-    }
-    catch (err) {
-        return { success: false, markdown, insertions: 0, error: err.message };
+        return { success: true, dryRun: true, insertions: realigned.insertions };
     }
+    fs.writeFileSync(markdownPath, realigned.markdown);
+    return { success: true, insertions: realigned.insertions };
 }
 //# sourceMappingURL=comment-realign.js.map

package/dist/lib/comment-realign.js.map

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

@@ -9,6 +9,16 @@ export declare function hasPandocCrossref(): boolean;
  * Check if pandoc is available
  */
 export declare function hasPandoc(): boolean;
+/**
+ * Parsed pandoc version (e.g. "3.9"), or null when pandoc is unavailable.
+ */
+export declare function getPandocVersion(): string | null;
+/**
+ * Whether pandoc bundles citeproc and accepts `--citeproc`. That flag and the
+ * built-in citeproc arrived in pandoc 2.11; earlier versions need the separate
+ * pandoc-citeproc filter.
+ */
+export declare function pandocSupportsCiteproc(): boolean;
 /**
  * Check if LaTeX is available (for PDF generation)
  */

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

@@ -1 +1 @@
-{"version":3,"file":"dependencies.d.ts","sourceRoot":"","sources":["../../lib/dependencies.ts"],"names":[],"mappings":"AAAA;;GAEG;AAgBH;;GAEG;AACH,wBAAgB,iBAAiB,IAAI,OAAO,CAE3C;AAED;;GAEG;AACH,wBAAgB,SAAS,IAAI,OAAO,CAEnC;AAED;;GAEG;AACH,wBAAgB,QAAQ,IAAI,OAAO,CAElC;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAwBjE;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE,OAAO,CAAC;IACf,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,IAAI,gBAAgB,CAmBpD"}
+{"version":3,"file":"dependencies.d.ts","sourceRoot":"","sources":["../../lib/dependencies.ts"],"names":[],"mappings":"AAAA;;GAEG;AAqBH;;GAEG;AACH,wBAAgB,iBAAiB,IAAI,OAAO,CAE3C;AAED;;GAEG;AACH,wBAAgB,SAAS,IAAI,OAAO,CAEnC;AAED;;GAEG;AACH,wBAAgB,gBAAgB,IAAI,MAAM,GAAG,IAAI,CAKhD;AAED;;;;GAIG;AACH,wBAAgB,sBAAsB,IAAI,OAAO,CAOhD;AAED;;GAEG;AACH,wBAAgB,QAAQ,IAAI,OAAO,CAElC;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAwBjE;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE,OAAO,CAAC;IACf,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,IAAI,gBAAgB,CAwBpD"}

package/dist/lib/dependencies.js

@@ -1,36 +1,64 @@
 /**
  * Dependency checking utilities for pandoc, LaTeX, and related tools
  */
-import { execSync } from 'child_process';
+import { execFileSync } from 'child_process';
 /**
- * Check if a command is available by running it silently
+ * Run `<file> --version` without a shell and return its stdout, or null when
+ * the binary is absent (ENOENT) or exits non-zero (present but broken). Using
+ * execFileSync avoids shell quoting and treats both failure modes uniformly.
  */
-function commandExists(cmd) {
+function runVersion(file, args = ['--version']) {
     try {
-        execSync(cmd, { stdio: 'ignore' });
-        return true;
+        return execFileSync(file, args, { stdio: ['ignore', 'pipe', 'ignore'], encoding: 'utf-8' });
     }
     catch {
-        return false;
+        return null;
     }
 }
+function commandExists(file, args = ['--version']) {
+    return runVersion(file, args) !== null;
+}
 /**
  * Check if pandoc-crossref is available
  */
 export function hasPandocCrossref() {
-    return commandExists('pandoc-crossref --version');
+    return commandExists('pandoc-crossref');
 }
 /**
  * Check if pandoc is available
  */
 export function hasPandoc() {
-    return commandExists('pandoc --version');
+    return commandExists('pandoc');
+}
+/**
+ * Parsed pandoc version (e.g. "3.9"), or null when pandoc is unavailable.
+ */
+export function getPandocVersion() {
+    const out = runVersion('pandoc');
+    if (!out)
+        return null;
+    const m = out.match(/pandoc(?:\.exe)?\s+(\d+\.\d+(?:\.\d+)?)/i);
+    return m ? m[1] : null;
+}
+/**
+ * Whether pandoc bundles citeproc and accepts `--citeproc`. That flag and the
+ * built-in citeproc arrived in pandoc 2.11; earlier versions need the separate
+ * pandoc-citeproc filter.
+ */
+export function pandocSupportsCiteproc() {
+    const v = getPandocVersion();
+    if (!v)
+        return false;
+    const parts = v.split('.').map((n) => parseInt(n, 10));
+    const major = parts[0] ?? 0;
+    const minor = parts[1] ?? 0;
+    return major > 2 || (major === 2 && minor >= 11);
 }
 /**
  * Check if LaTeX is available (for PDF generation)
  */
 export function hasLatex() {
-    return commandExists('pdflatex --version') || commandExists('xelatex --version');
+    return commandExists('pdflatex') || commandExists('xelatex');
 }
 /**
  * Get installation instructions for missing dependencies
@@ -72,6 +100,10 @@ export function checkDependencies() {
     if (!status.pandoc) {
         status.messages.push(`Pandoc not found. Install with: ${getInstallInstructions('pandoc')}`);
     }
+    else if (!pandocSupportsCiteproc()) {
+        const version = getPandocVersion();
+        status.messages.push(`Pandoc ${version ?? '(unknown version)'} is older than 2.11; citation processing (--citeproc) needs 2.11+. Upgrade with: ${getInstallInstructions('pandoc')}`);
+    }
     if (!status.latex) {
         status.messages.push(`LaTeX not found (required for PDF). Install with: ${getInstallInstructions('latex')}`);
     }

package/dist/lib/dependencies.js.map

@@ -1 +1 @@
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