docrev 0.9.13 → 0.9.15

package/dev_notes/stresstest_pstyle.ts

@@ -1,55 +1,55 @@
-// Inspect the document.xml paragraph styles to find true headings.
-import AdmZip from 'adm-zip';
-import * as fs from 'fs';
-
-const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
-const zip = new AdmZip(docx);
-const xml = zip.getEntry('word/document.xml')!.getData().toString('utf8');
-
-// Build text-position map from <w:t> runs the same way extractCommentAnchors does
-const textNodePattern = /<w:t[^>]*>([^<]*)<\/w:t>/g;
-const textNodes: Array<{ xmlStart: number; xmlEnd: number; textStart: number; textEnd: number; text: string }> = [];
-let textPosition = 0;
-let m;
-function decode(s: string): string {
-  return s.replace(/&amp;/g, '&').replace(/&lt;/g, '<').replace(/&gt;/g, '>').replace(/&quot;/g, '"').replace(/&apos;/g, "'");
-}
-while ((m = textNodePattern.exec(xml)) !== null) {
-  const decoded = decode(m[1]);
-  textNodes.push({ xmlStart: m.index, xmlEnd: m.index + m[0].length, textStart: textPosition, textEnd: textPosition + decoded.length, text: decoded });
-  textPosition += decoded.length;
-}
-
-function xmlToText(xmlPos: number): number {
-  for (const n of textNodes) {
-    if (xmlPos >= n.xmlStart && xmlPos < n.xmlEnd) return n.textStart;
-    if (xmlPos < n.xmlStart) return n.textStart;
-  }
-  return textNodes.length ? textNodes[textNodes.length - 1].textEnd : 0;
-}
-
-// Now walk paragraphs; each <w:p ...>...</w:p>. Inside, find <w:pStyle w:val="..."/> if present, and concatenate text runs.
-const paraPattern = /<w:p\b[^>]*>([\s\S]*?)<\/w:p>/g;
-const headings: Array<{ style: string; text: string; xmlStart: number; textPos: number }> = [];
-let pm;
-while ((pm = paraPattern.exec(xml)) !== null) {
-  const inner = pm[1];
-  const styleMatch = inner.match(/<w:pStyle[^>]*w:val="([^"]+)"/);
-  if (!styleMatch) continue;
-  const style = styleMatch[1];
-  if (!/heading/i.test(style)) continue;
-  // Extract text from runs
-  const textInRange = /<w:t[^>]*>([^<]*)<\/w:t>/g;
-  let txt = '';
-  let tm;
-  while ((tm = textInRange.exec(inner)) !== null) txt += decode(tm[1]);
-  if (!txt.trim()) continue;
-  const xmlStart = pm.index;
-  const textPos = xmlToText(xmlStart);
-  headings.push({ style, text: txt.trim(), xmlStart, textPos });
-}
-
-console.log(`Found ${headings.length} heading paragraphs:`);
-for (const h of headings) {
-  console.log(`  [${h.style.padEnd(8)}] textPos=${String(h.textPos).padStart(6)} "${h.text.slice(0, 60)}"`);
-}
+// Inspect the document.xml paragraph styles to find true headings.
+import AdmZip from 'adm-zip';
+import * as fs from 'fs';
+
+const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
+const zip = new AdmZip(docx);
+const xml = zip.getEntry('word/document.xml')!.getData().toString('utf8');
+
+// Build text-position map from <w:t> runs the same way extractCommentAnchors does
+const textNodePattern = /<w:t[^>]*>([^<]*)<\/w:t>/g;
+const textNodes: Array<{ xmlStart: number; xmlEnd: number; textStart: number; textEnd: number; text: string }> = [];
+let textPosition = 0;
+let m;
+function decode(s: string): string {
+  return s.replace(/&amp;/g, '&').replace(/&lt;/g, '<').replace(/&gt;/g, '>').replace(/&quot;/g, '"').replace(/&apos;/g, "'");
+}
+while ((m = textNodePattern.exec(xml)) !== null) {
+  const decoded = decode(m[1]);
+  textNodes.push({ xmlStart: m.index, xmlEnd: m.index + m[0].length, textStart: textPosition, textEnd: textPosition + decoded.length, text: decoded });
+  textPosition += decoded.length;
+}
+
+function xmlToText(xmlPos: number): number {
+  for (const n of textNodes) {
+    if (xmlPos >= n.xmlStart && xmlPos < n.xmlEnd) return n.textStart;
+    if (xmlPos < n.xmlStart) return n.textStart;
+  }
+  return textNodes.length ? textNodes[textNodes.length - 1].textEnd : 0;
+}
+
+// Now walk paragraphs; each <w:p ...>...</w:p>. Inside, find <w:pStyle w:val="..."/> if present, and concatenate text runs.
+const paraPattern = /<w:p\b[^>]*>([\s\S]*?)<\/w:p>/g;
+const headings: Array<{ style: string; text: string; xmlStart: number; textPos: number }> = [];
+let pm;
+while ((pm = paraPattern.exec(xml)) !== null) {
+  const inner = pm[1];
+  const styleMatch = inner.match(/<w:pStyle[^>]*w:val="([^"]+)"/);
+  if (!styleMatch) continue;
+  const style = styleMatch[1];
+  if (!/heading/i.test(style)) continue;
+  // Extract text from runs
+  const textInRange = /<w:t[^>]*>([^<]*)<\/w:t>/g;
+  let txt = '';
+  let tm;
+  while ((tm = textInRange.exec(inner)) !== null) txt += decode(tm[1]);
+  if (!txt.trim()) continue;
+  const xmlStart = pm.index;
+  const textPos = xmlToText(xmlStart);
+  headings.push({ style, text: txt.trim(), xmlStart, textPos });
+}
+
+console.log(`Found ${headings.length} heading paragraphs:`);
+for (const h of headings) {
+  console.log(`  [${h.style.padEnd(8)}] textPos=${String(h.textPos).padStart(6)} "${h.text.slice(0, 60)}"`);
+}

package/dev_notes/stresstest_section_debug.ts

@@ -1,23 +1,23 @@
-import { extractCommentAnchors } from '../lib/import.js';
-
-const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
-const { fullDocText } = await extractCommentAnchors(docx);
-
-const keywords = ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion', 'Conclusion', 'References'];
-for (const kw of keywords) {
-  const lower = fullDocText.toLowerCase();
-  const needle = kw.toLowerCase();
-  const occ: Array<{ idx: number; ctx: string; afterChar: string }> = [];
-  let idx = 0;
-  while ((idx = lower.indexOf(needle, idx)) !== -1) {
-    const ctx = fullDocText.slice(Math.max(0, idx - 20), idx + needle.length + 20).replace(/\s+/g, ' ');
-    const afterChar = fullDocText.slice(idx + needle.length, idx + needle.length + 1);
-    occ.push({ idx, ctx, afterChar });
-    idx++;
-  }
-  console.log(`\n--- ${kw} (${occ.length} occurrences) ---`);
-  for (const o of occ.slice(0, 6)) {
-    console.log(`  @${o.idx} after="${o.afterChar}" ctx: ...${o.ctx}...`);
-  }
-  if (occ.length > 6) console.log(`  ... and ${occ.length - 6} more`);
-}
+import { extractCommentAnchors } from '../lib/import.js';
+
+const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
+const { fullDocText } = await extractCommentAnchors(docx);
+
+const keywords = ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion', 'Conclusion', 'References'];
+for (const kw of keywords) {
+  const lower = fullDocText.toLowerCase();
+  const needle = kw.toLowerCase();
+  const occ: Array<{ idx: number; ctx: string; afterChar: string }> = [];
+  let idx = 0;
+  while ((idx = lower.indexOf(needle, idx)) !== -1) {
+    const ctx = fullDocText.slice(Math.max(0, idx - 20), idx + needle.length + 20).replace(/\s+/g, ' ');
+    const afterChar = fullDocText.slice(idx + needle.length, idx + needle.length + 1);
+    occ.push({ idx, ctx, afterChar });
+    idx++;
+  }
+  console.log(`\n--- ${kw} (${occ.length} occurrences) ---`);
+  for (const o of occ.slice(0, 6)) {
+    console.log(`  @${o.idx} after="${o.afterChar}" ctx: ...${o.ctx}...`);
+  }
+  if (occ.length > 6) console.log(`  ... and ${occ.length - 6} more`);
+}

package/dev_notes/stresstest_split.ts

@@ -1,70 +1,70 @@
-import * as fs from 'fs';
-import * as path from 'path';
-
-const ROOT = 'C:/GillesC/tmp/docrev-stress/project';
-fs.mkdirSync(ROOT, { recursive: true });
-
-const full = fs.readFileSync('C:/GillesC/tmp/docrev-stress/full.md', 'utf-8');
-const lines = full.split(/\r?\n/);
-
-interface Section { file: string; header: string; lines: string[]; }
-
-const sections: Section[] = [];
-
-// Map H1 heading text to section file
-const headerToFile: Record<string, string> = {
-  'Abstract': 'abstract.md',
-  'Introduction': 'introduction.md',
-  'Methods': 'methods.md',
-  'Results': 'results.md',
-  'Discussion': 'discussion.md',
-  'Conclusion': 'conclusion.md',
-  'References': 'references.md',
-  'Supplementary Materials': 'supplement.md',
-};
-
-let current: Section | null = null;
-const preambleLines: string[] = [];
-
-for (const line of lines) {
-  const m = line.match(/^# (.+)$/);
-  if (m && headerToFile[m[1].trim()]) {
-    if (current) sections.push(current);
-    current = { file: headerToFile[m[1].trim()], header: m[1].trim(), lines: [line] };
-  } else if (current) {
-    current.lines.push(line);
-  } else {
-    preambleLines.push(line);
-  }
-}
-if (current) sections.push(current);
-
-// Write sections
-for (const s of sections) {
-  const out = path.join(ROOT, s.file);
-  fs.writeFileSync(out, s.lines.join('\n'), 'utf-8');
-  console.log(`wrote ${out} (${s.lines.length} lines)`);
-}
-
-// Write sections.yaml
-const yaml: string[] = ['version: 1', 'sections:'];
-for (const s of sections) {
-  yaml.push(`  ${s.file}:`);
-  yaml.push(`    header: "${s.header}"`);
-  yaml.push(`    aliases: []`);
-}
-fs.writeFileSync(path.join(ROOT, 'sections.yaml'), yaml.join('\n') + '\n', 'utf-8');
-console.log(`wrote sections.yaml`);
-
-// Minimal rev.yaml so commands that look for project root don't choke
-const revYaml = `title: "Stress Test"
-authors:
-  - name: Gilles Colling
-output:
-  docx: {}
-  pdf: {}
-`;
-fs.writeFileSync(path.join(ROOT, 'rev.yaml'), revYaml, 'utf-8');
-
-console.log();
-console.log(`section files: ${sections.length}`);
+import * as fs from 'fs';
+import * as path from 'path';
+
+const ROOT = 'C:/GillesC/tmp/docrev-stress/project';
+fs.mkdirSync(ROOT, { recursive: true });
+
+const full = fs.readFileSync('C:/GillesC/tmp/docrev-stress/full.md', 'utf-8');
+const lines = full.split(/\r?\n/);
+
+interface Section { file: string; header: string; lines: string[]; }
+
+const sections: Section[] = [];
+
+// Map H1 heading text to section file
+const headerToFile: Record<string, string> = {
+  'Abstract': 'abstract.md',
+  'Introduction': 'introduction.md',
+  'Methods': 'methods.md',
+  'Results': 'results.md',
+  'Discussion': 'discussion.md',
+  'Conclusion': 'conclusion.md',
+  'References': 'references.md',
+  'Supplementary Materials': 'supplement.md',
+};
+
+let current: Section | null = null;
+const preambleLines: string[] = [];
+
+for (const line of lines) {
+  const m = line.match(/^# (.+)$/);
+  if (m && headerToFile[m[1].trim()]) {
+    if (current) sections.push(current);
+    current = { file: headerToFile[m[1].trim()], header: m[1].trim(), lines: [line] };
+  } else if (current) {
+    current.lines.push(line);
+  } else {
+    preambleLines.push(line);
+  }
+}
+if (current) sections.push(current);
+
+// Write sections
+for (const s of sections) {
+  const out = path.join(ROOT, s.file);
+  fs.writeFileSync(out, s.lines.join('\n'), 'utf-8');
+  console.log(`wrote ${out} (${s.lines.length} lines)`);
+}
+
+// Write sections.yaml
+const yaml: string[] = ['version: 1', 'sections:'];
+for (const s of sections) {
+  yaml.push(`  ${s.file}:`);
+  yaml.push(`    header: "${s.header}"`);
+  yaml.push(`    aliases: []`);
+}
+fs.writeFileSync(path.join(ROOT, 'sections.yaml'), yaml.join('\n') + '\n', 'utf-8');
+console.log(`wrote sections.yaml`);
+
+// Minimal rev.yaml so commands that look for project root don't choke
+const revYaml = `title: "Stress Test"
+authors:
+  - name: Gilles Colling
+output:
+  docx: {}
+  pdf: {}
+`;
+fs.writeFileSync(path.join(ROOT, 'rev.yaml'), revYaml, 'utf-8');
+
+console.log();
+console.log(`section files: ${sections.length}`);

package/dev_notes/stresstest_trace.ts

@@ -1,19 +1,19 @@
-import { extractCommentAnchors } from '../lib/import.js';
-
-const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
-const { fullDocText } = await extractCommentAnchors(docx);
-
-const needle = 'methods';
-const lower = fullDocText.toLowerCase();
-let idx = 0;
-const trace: Array<{idx:number, after:string, skipped:boolean}> = [];
-while ((idx = lower.indexOf(needle, idx)) !== -1 && trace.length < 10) {
-  const after = fullDocText.slice(idx + needle.length, idx + needle.length + 5);
-  const skip = after.startsWith(':') || after.startsWith(' :');
-  trace.push({ idx, after, skipped: skip });
-  if (!skip) break;
-  idx++;
-}
-for (const t of trace) console.log(`idx=${t.idx} after="${t.after}" skipped=${t.skipped}`);
-console.log();
-console.log(`first non-:-prefixed Methods idx = ${trace.find(t => !t.skipped)?.idx ?? -1}`);
+import { extractCommentAnchors } from '../lib/import.js';
+
+const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
+const { fullDocText } = await extractCommentAnchors(docx);
+
+const needle = 'methods';
+const lower = fullDocText.toLowerCase();
+let idx = 0;
+const trace: Array<{idx:number, after:string, skipped:boolean}> = [];
+while ((idx = lower.indexOf(needle, idx)) !== -1 && trace.length < 10) {
+  const after = fullDocText.slice(idx + needle.length, idx + needle.length + 5);
+  const skip = after.startsWith(':') || after.startsWith(' :');
+  trace.push({ idx, after, skipped: skip });
+  if (!skip) break;
+  idx++;
+}
+for (const t of trace) console.log(`idx=${t.idx} after="${t.after}" skipped=${t.skipped}`);
+console.log();
+console.log(`first non-:-prefixed Methods idx = ${trace.find(t => !t.skipped)?.idx ?? -1}`);

package/dev_notes/stresstest_verify_no_overwrite.ts

@@ -1,40 +1,40 @@
-// Verify sync --comments-only didn't touch existing prose, only inserted comments.
-import * as fs from 'fs';
-import { stripCriticMarkup } from '../lib/anchor-match.js';
-
-const original = 'C:/GillesC/tmp/docrev-stress/project';
-const synced = 'C:/GillesC/tmp/docrev-stress/project-sync';
-const files = ['abstract.md', 'introduction.md', 'methods.md', 'results.md', 'discussion.md', 'conclusion.md', 'references.md', 'supplement.md'];
-
-let totalComments = 0;
-let mismatches = 0;
-for (const f of files) {
-  const orig = fs.readFileSync(`${original}/${f}`, 'utf-8');
-  const synd = fs.readFileSync(`${synced}/${f}`, 'utf-8');
-
-  // Count comments inserted
-  const commentMatches = synd.match(/\{>>.*?<<\}/gs) || [];
-  totalComments += commentMatches.length;
-
-  // The originals may already contain CriticMarkup (Word highlights -> [X]{.mark}),
-  // so strip both sides to compare just the underlying prose.
-  const synStripped = stripCriticMarkup(synd);
-  const origNorm = stripCriticMarkup(orig);
-
-  if (synStripped !== origNorm) {
-    // Find first difference
-    let i = 0;
-    while (i < origNorm.length && i < synStripped.length && origNorm[i] === synStripped[i]) i++;
-    const ctxOrig = origNorm.slice(Math.max(0, i - 30), i + 50).replace(/\n/g, '\\n');
-    const ctxSyn = synStripped.slice(Math.max(0, i - 30), i + 50).replace(/\n/g, '\\n');
-    console.log(`✗ ${f}: prose differs at byte ${i} (lengths orig=${origNorm.length} stripped=${synStripped.length})`);
-    console.log(`    orig: ${ctxOrig}`);
-    console.log(`    syn:  ${ctxSyn}`);
-    mismatches++;
-  } else {
-    console.log(`✓ ${f}: prose preserved (${commentMatches.length} comments inserted)`);
-  }
-}
-console.log();
-console.log(`total comments inserted: ${totalComments}`);
-console.log(`prose mismatches:        ${mismatches}/${files.length}`);
+// Verify sync --comments-only didn't touch existing prose, only inserted comments.
+import * as fs from 'fs';
+import { stripCriticMarkup } from '../lib/anchor-match.js';
+
+const original = 'C:/GillesC/tmp/docrev-stress/project';
+const synced = 'C:/GillesC/tmp/docrev-stress/project-sync';
+const files = ['abstract.md', 'introduction.md', 'methods.md', 'results.md', 'discussion.md', 'conclusion.md', 'references.md', 'supplement.md'];
+
+let totalComments = 0;
+let mismatches = 0;
+for (const f of files) {
+  const orig = fs.readFileSync(`${original}/${f}`, 'utf-8');
+  const synd = fs.readFileSync(`${synced}/${f}`, 'utf-8');
+
+  // Count comments inserted
+  const commentMatches = synd.match(/\{>>.*?<<\}/gs) || [];
+  totalComments += commentMatches.length;
+
+  // The originals may already contain CriticMarkup (Word highlights -> [X]{.mark}),
+  // so strip both sides to compare just the underlying prose.
+  const synStripped = stripCriticMarkup(synd);
+  const origNorm = stripCriticMarkup(orig);
+
+  if (synStripped !== origNorm) {
+    // Find first difference
+    let i = 0;
+    while (i < origNorm.length && i < synStripped.length && origNorm[i] === synStripped[i]) i++;
+    const ctxOrig = origNorm.slice(Math.max(0, i - 30), i + 50).replace(/\n/g, '\\n');
+    const ctxSyn = synStripped.slice(Math.max(0, i - 30), i + 50).replace(/\n/g, '\\n');
+    console.log(`✗ ${f}: prose differs at byte ${i} (lengths orig=${origNorm.length} stripped=${synStripped.length})`);
+    console.log(`    orig: ${ctxOrig}`);
+    console.log(`    syn:  ${ctxSyn}`);
+    mismatches++;
+  } else {
+    console.log(`✓ ${f}: prose preserved (${commentMatches.length} comments inserted)`);
+  }
+}
+console.log();
+console.log(`total comments inserted: ${totalComments}`);
+console.log(`prose mismatches:        ${mismatches}/${files.length}`);

package/dist/lib/build.d.ts

@@ -97,6 +97,12 @@ export interface BuildConfig {
     pptx: PptxConfig;
     tables: TablesConfig;
     postprocess: PostprocessConfig;
+    /**
+     * Directory (relative to the project) where final outputs land. Created on
+     * demand. Set to null/empty to keep outputs alongside paper.md (legacy
+     * behavior).
+     */
+    outputDir?: string | null;
     _configPath?: string | null;
 }
 export interface BuildResult {
@@ -128,6 +134,18 @@ interface FullBuildResult {
     forwardRefsResolved: number;
     refsAutoInjected?: boolean;
 }
+interface Registry {
+    figures: Map<string, unknown>;
+    tables: Map<string, unknown>;
+    equations: Map<string, unknown>;
+    byNumber: {
+        fig?: Map<number, string>;
+        figS?: Map<number, string>;
+        tbl?: Map<number, string>;
+        tblS?: Map<number, string>;
+        eq?: Map<number, string>;
+    };
+}
 /**
  * Default rev.yaml configuration
  */
@@ -166,14 +184,33 @@ export declare function combineSections(directory: string, config: BuildConfig,
  * @returns processed content
  */
 export declare function processTablesForFormat(content: string, tablesConfig: TablesConfig, format: string): string;
+/**
+ * Apply format-specific transforms (table normalization, author blocks,
+ * crossref display conversion, slide syntax). Caller is responsible for
+ * stripping annotations beforehand — the dual-output paths keep comments
+ * in the markdown stream and need to apply these transforms separately
+ * from annotation handling.
+ *
+ * @param content - Markdown content (annotations already stripped as needed)
+ * @param format - Output format
+ * @param config - Build config
+ * @param registry - Crossref registry for the project
+ * @returns Transformed markdown
+ */
+export declare function applyFormatTransforms(content: string, format: string, config: BuildConfig, registry: Registry): string;
 /**
  * Prepare paper.md for specific output format
  */
-export declare function prepareForFormat(paperPath: string, format: string, config: BuildConfig, options?: BuildOptions): string;
+export declare function prepareForFormat(paperPath: string, format: string, config: BuildConfig, _options?: BuildOptions): string;
 /**
  * Build pandoc arguments for format
  */
 export declare function buildPandocArgs(format: string, config: BuildConfig, outputPath: string): string[];
+/**
+ * Resolve the absolute directory where final outputs should land.
+ * Honors config.outputDir; falls back to the project directory when null/empty.
+ */
+export declare function resolveOutputDir(directory: string, config: BuildConfig): string;
 /**
  * Run pandoc build
  */

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

@@ -1 +1 @@
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