docrev 0.9.7 → 0.9.13

package/dev_notes/stresstest_inspect.ts

@@ -0,0 +1,54 @@
+import { extractWordComments, extractCommentAnchors } from '../lib/import.js';
+
+const docx = 'C:/GillesC/tmp/docrev-stress/reviewed.docx';
+
+const comments = await extractWordComments(docx);
+const { anchors, fullDocText } = await extractCommentAnchors(docx);
+
+console.log(`comments: ${comments.length}`);
+console.log(`anchors:  ${anchors.size}`);
+console.log(`docText:  ${fullDocText.length} chars`);
+console.log();
+
+const byAuthor: Record<string, number> = {};
+for (const c of comments) byAuthor[c.author] = (byAuthor[c.author] || 0) + 1;
+console.log('by author:', byAuthor);
+console.log();
+
+console.log('first 5 comments:');
+for (const c of comments.slice(0, 5)) {
+  const a = anchors.get(c.id);
+  const pos = a?.docPosition ?? -1;
+  const anchor = (a?.anchor || '').slice(0, 60);
+  const text = c.text.replace(/\s+/g, ' ').slice(0, 80);
+  console.log(`  #${c.id} [${c.author}] pos=${pos} anchor="${anchor}" text="${text}"`);
+}
+console.log();
+console.log('last 3 comments:');
+for (const c of comments.slice(-3)) {
+  const a = anchors.get(c.id);
+  const pos = a?.docPosition ?? -1;
+  const anchor = (a?.anchor || '').slice(0, 60);
+  const text = c.text.replace(/\s+/g, ' ').slice(0, 80);
+  console.log(`  #${c.id} [${c.author}] pos=${pos} anchor="${anchor}" text="${text}"`);
+}
+console.log();
+
+const sectionKeywords = ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion', 'Conclusion', 'References', 'Acknowledgements', 'Data Availability', 'Author Contributions'];
+console.log('candidate headings:');
+for (const kw of sectionKeywords) {
+  const idx = fullDocText.indexOf(kw);
+  if (idx >= 0) {
+    const context = fullDocText.slice(idx, idx + 80).replace(/\s+/g, ' ');
+    console.log(`  ${kw} @ ${idx}: "${context}"`);
+  }
+}
+
+// Check anchor distribution to understand section spans
+const positions = [...anchors.values()].map(a => a.docPosition).sort((a, b) => a - b);
+console.log();
+console.log(`anchor positions: min=${positions[0]} max=${positions[positions.length-1]} median=${positions[Math.floor(positions.length/2)]}`);
+
+// Check for empty anchors
+const empty = [...anchors.values()].filter(a => a.isEmpty).length;
+console.log(`empty anchors: ${empty}`);

package/dev_notes/stresstest_pstyle.ts

@@ -0,0 +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)}"`);
+}

package/dev_notes/stresstest_section_debug.ts

@@ -0,0 +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`);
+}

package/dev_notes/stresstest_split.ts

@@ -0,0 +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}`);

package/dev_notes/stresstest_trace.ts

@@ -0,0 +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}`);

package/dev_notes/stresstest_verify_no_overwrite.ts

@@ -0,0 +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}`);

package/dist/lib/anchor-match.d.ts

@@ -22,6 +22,16 @@ export declare function stripCriticMarkup(text: string): string;
  * Empty needles return no occurrences (empty matches are not useful
  * for anchor placement).
  */
+/**
+ * Score how well the docx-side `before` / `after` context matches the
+ * surroundings of a candidate position in the target text. Used by
+ * `verify-anchors` to tell apart "multiple hits but context picks one
+ * cleanly" (sync will place it correctly) from "multiple hits, context
+ * doesn't help" (truly ambiguous, needs human placement).
+ *
+ * Returns 0 if no context was provided.
+ */
+export declare function scoreContextAt(pos: number, text: string, before: string, after: string, anchorLen: number): number;
 export declare function findAllOccurrences(haystack: string, needle: string): number[];
 /**
  * Find candidate positions for `anchor` in `text`, falling back through

package/dist/lib/anchor-match.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"anchor-match.d.ts","sourceRoot":"","sources":["../../lib/anchor-match.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,MAAM,cAAc,GACtB,QAAQ,GACR,YAAY,GACZ,UAAU,GACV,eAAe,GACf,wBAAwB,GACxB,cAAc,GACd,gBAAgB,GAChB,eAAe,GACf,aAAa,GACb,cAAc,GACd,QAAQ,CAAC;AAEb,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,QAAQ,EAAE,cAAc,CAAC;IACzB,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAOtD;AAED;;;;GAIG;AACH;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,GAChB,MAAM,CAqBR;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,CAS7E;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,MAAM,GAAE,MAAW,EACnB,KAAK,GAAE,MAAW,GACjB,kBAAkB,CA2IpB;AAED;;;GAGG;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,GAAG,OAAO,GAAG,cAAc,GAAG,WAAW,CAAC;AAElF,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,GAAG,kBAAkB,CAoBlG"}

package/dist/lib/anchor-match.js

@@ -22,6 +22,41 @@ export function stripCriticMarkup(text) {
  * Empty needles return no occurrences (empty matches are not useful
  * for anchor placement).
  */
+/**
+ * Score how well the docx-side `before` / `after` context matches the
+ * surroundings of a candidate position in the target text. Used by
+ * `verify-anchors` to tell apart "multiple hits but context picks one
+ * cleanly" (sync will place it correctly) from "multiple hits, context
+ * doesn't help" (truly ambiguous, needs human placement).
+ *
+ * Returns 0 if no context was provided.
+ */
+export function scoreContextAt(pos, text, before, after, anchorLen) {
+    let score = 0;
+    if (before) {
+        const contextBefore = text.slice(Math.max(0, pos - before.length - 20), pos).toLowerCase();
+        const beforeLower = before.toLowerCase();
+        const beforeWords = beforeLower.split(/\s+/).filter(w => w.length > 3);
+        for (const word of beforeWords) {
+            if (contextBefore.includes(word))
+                score += 2;
+        }
+        if (contextBefore.includes(beforeLower.slice(-30)))
+            score += 5;
+    }
+    if (after) {
+        const contextAfter = text.slice(pos + anchorLen, pos + anchorLen + after.length + 20).toLowerCase();
+        const afterLower = after.toLowerCase();
+        const afterWords = afterLower.split(/\s+/).filter(w => w.length > 3);
+        for (const word of afterWords) {
+            if (contextAfter.includes(word))
+                score += 2;
+        }
+        if (contextAfter.includes(afterLower.slice(0, 30)))
+            score += 5;
+    }
+    return score;
+}
 export function findAllOccurrences(haystack, needle) {
     if (!needle || needle.length === 0)
         return [];

package/dist/lib/anchor-match.js.map

@@ -1 +1 @@
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@@ -1 +1 @@
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+{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../lib/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,YAAY,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAC;AAuHnG;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CA6G3D;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,MAAM,CAyFjF;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAqDvD;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAUpD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAiD3F;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CAG1D;AAED;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,UAAU,EAAE,CAyB1F;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,GAAG,MAAM,CAmB7F;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,gBAAgB,CAwB/D;AAED;;;;;;GAMG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CA6C3D"}

package/dist/lib/annotations.js

@@ -249,8 +249,16 @@ export function stripAnnotations(text, options = {}) {
         if (!keepComments) {
             text = text.replace(PATTERNS.comment, '');
         }
-        // Strip pandoc highlight spans: [text]{.mark} → text
-        text = text.replace(/\[([^\]]*)\]\{\.mark\}/g, '$1');
+        // Strip pandoc highlight spans: [text]{.mark} → text.
+        // When `keepComments=true`, preserve `[anchor]{.mark}` that is the
+        // anchor of a kept `{>>...<<}` comment. The dual-build flow runs
+        // stripAnnotations() before prepareMarkdownWithMarkers(), and stripping
+        // the anchor span here would leave the marker generator with no anchor
+        // text — collapsing every multi-word anchor to a single fallback word
+        // in the rebuilt docx.
+        text = keepComments
+            ? text.replace(/(?<!<<\}\s{0,3})\[([^\]]*)\]\{\.mark\}/g, '$1')
+            : text.replace(/\[([^\]]*)\]\{\.mark\}/g, '$1');
         // Clean up partial/orphaned markers within the loop
         // This handles cases where nested annotations leave behind fragments
         // Empty annotations (from nested stripping)
@@ -283,9 +291,11 @@ export function stripAnnotations(text, options = {}) {
     text = text.replace(/\{~~/g, '');
     text = text.replace(/~>/g, '');
     // Remove orphan [ from stripped {.mark} spans where the closing ]{.mark}
-    // was inside a comment. A [ is orphan if no matching ] follows before
-    // the next [ or end of line.
-    text = text.replace(/\[(?![^\[\]]*\])/g, '');
+    // was inside a comment. A [ is orphan if no `]` follows before end of line.
+    // We deliberately allow other `[` between the candidate and the matching `]`
+    // — otherwise nested forms like `[[0..9]]{.mark}` would have their outer
+    // `[` stripped because the lookahead saw the inner `[` as a barrier.
+    text = text.replace(/\[(?![^\]\n]*\])/g, '');
     return text;
 }
 /**
@@ -377,7 +387,7 @@ export function applyDecision(text, annotation, accept) {
     let replacement;
     // Extract any comments embedded in the annotation content
     // These should be preserved when accepting deletions or rejecting insertions
-    const commentPattern = /\{>>[^<]*<<\}/g;
+    const commentPattern = /\{>>[\s\S]*?<<\}/g;
     const embeddedComments = (annotation.match || '').match(commentPattern) || [];
     switch (annotation.type) {
         case 'insert':

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package/dist/lib/build.d.ts

@@ -25,6 +25,18 @@ export interface PdfConfig {
     linestretch?: number;
     numbersections?: boolean;
     toc?: boolean;
+    /**
+     * LaTeX engine: pdflatex (default), xelatex, lualatex, tectonic, etc.
+     * xelatex/lualatex are required for native UTF-8 rendering of Latin-Extended
+     * diacritics (Czech/Polish/Croatian/Spanish author names, species epithets).
+     */
+    engine?: string;
+    /** Roman/serif main font (xelatex/lualatex only — uses fontspec). */
+    mainfont?: string;
+    /** Sans-serif font (xelatex/lualatex only). */
+    sansfont?: string;
+    /** Monospace font (xelatex/lualatex only). */
+    monofont?: string;
 }
 export interface DocxConfig {
     reference?: string | null;

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

@@ -1 +1 @@
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package/dist/lib/build.js

@@ -648,6 +648,18 @@ export function buildPandocArgs(format, config, outputPath) {
         if (config.pdf.template) {
             args.push('--template', config.pdf.template);
         }
+        if (config.pdf.engine) {
+            args.push(`--pdf-engine=${config.pdf.engine}`);
+        }
+        if (config.pdf.mainfont) {
+            args.push('-V', `mainfont=${config.pdf.mainfont}`);
+        }
+        if (config.pdf.sansfont) {
+            args.push('-V', `sansfont=${config.pdf.sansfont}`);
+        }
+        if (config.pdf.monofont) {
+            args.push('-V', `monofont=${config.pdf.monofont}`);
+        }
         args.push('-V', `documentclass=${config.pdf.documentclass}`);
         args.push('-V', `fontsize=${config.pdf.fontsize}`);
         args.push('-V', `geometry:${config.pdf.geometry}`);