docrev 0.8.5 → 0.9.3

package/lib/annotations.ts

@@ -281,6 +281,9 @@ export function stripAnnotations(text: string, options: StripOptions = {}): stri
       text = text.replace(PATTERNS.comment, '');
     }
 
+    // Strip pandoc highlight spans: [text]{.mark} → text
+    text = text.replace(/\[([^\]]*)\]\{\.mark\}/g, '$1');
+
     // Clean up partial/orphaned markers within the loop
     // This handles cases where nested annotations leave behind fragments
 
@@ -319,6 +322,11 @@ export function stripAnnotations(text: string, options: StripOptions = {}): stri
   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, '');
+
   return text;
 }
 

package/lib/build.ts

@@ -21,7 +21,9 @@ import { getThemePath, getThemeNames, PPTX_THEMES } from './pptx-themes.js';
 import { runPostprocess } from './postprocess.js';
 import { hasPandoc, hasPandocCrossref, hasLatex } from './dependencies.js';
 import { buildImageRegistry, writeImageRegistry } from './image-registry.js';
-import type { Author } from './types.js';
+import type { Author, JournalFormatting } from './types.js';
+import { getJournalProfile } from './journals.js';
+import { resolveCSL } from './csl.js';
 
 // =============================================================================
 // Constants
@@ -250,6 +252,69 @@ export const DEFAULT_CONFIG: BuildConfig = {
 // Public API
 // =============================================================================
 
+/**
+ * Merge journal formatting defaults into a config.
+ * Priority: DEFAULT_CONFIG < journal formatting < rev.yaml explicit settings
+ */
+export function mergeJournalFormatting(config: BuildConfig, formatting: JournalFormatting, directory: string): BuildConfig {
+  const merged = { ...config };
+
+  // CSL: only apply if user hasn't set one
+  if (formatting.csl && !config.csl) {
+    const resolved = resolveCSL(formatting.csl, directory);
+    if (resolved) {
+      merged.csl = resolved;
+    }
+    // If not resolved locally, store the name — pandoc --citeproc
+    // can sometimes resolve it, and the user can fetch with rev profiles --fetch-csl
+    if (!resolved) {
+      merged.csl = formatting.csl;
+    }
+  }
+
+  // PDF settings: merge only unset fields
+  if (formatting.pdf) {
+    const userPdf = config.pdf || {};
+    const defaults = DEFAULT_CONFIG.pdf;
+    merged.pdf = { ...config.pdf };
+    for (const [key, value] of Object.entries(formatting.pdf)) {
+      const k = key as keyof PdfConfig;
+      // Apply journal value only if user config matches the default (i.e., wasn't explicitly set)
+      if (value !== undefined && JSON.stringify(userPdf[k]) === JSON.stringify(defaults[k])) {
+        (merged.pdf as Record<string, unknown>)[k] = value;
+      }
+    }
+  }
+
+  // DOCX settings: merge only unset fields
+  if (formatting.docx) {
+    const userDocx = config.docx || {};
+    const defaults = DEFAULT_CONFIG.docx;
+    merged.docx = { ...config.docx };
+    for (const [key, value] of Object.entries(formatting.docx)) {
+      const k = key as keyof DocxConfig;
+      if (value !== undefined && JSON.stringify(userDocx[k]) === JSON.stringify(defaults[k])) {
+        (merged.docx as Record<string, unknown>)[k] = value;
+      }
+    }
+  }
+
+  // Crossref settings: merge only unset fields
+  if (formatting.crossref) {
+    const userCrossref = config.crossref || {};
+    const defaults = DEFAULT_CONFIG.crossref;
+    merged.crossref = { ...config.crossref };
+    for (const [key, value] of Object.entries(formatting.crossref)) {
+      const k = key as keyof CrossrefConfig;
+      if (value !== undefined && JSON.stringify(userCrossref[k]) === JSON.stringify(defaults[k])) {
+        (merged.crossref as Record<string, unknown>)[k] = value;
+      }
+    }
+  }
+
+  return merged;
+}
+
 /**
  * Load rev.yaml config from directory
  * @param directory - Project directory path
@@ -273,7 +338,7 @@ export function loadConfig(directory: string): BuildConfig {
     const userConfig = YAML.parse(content) || {};
 
     // Deep merge with defaults
-    const config: BuildConfig = {
+    let config: BuildConfig = {
       ...DEFAULT_CONFIG,
       ...userConfig,
       crossref: { ...DEFAULT_CONFIG.crossref, ...userConfig.crossref },
@@ -287,6 +352,14 @@ export function loadConfig(directory: string): BuildConfig {
       _configPath: configPath,
     };
 
+    // Apply journal formatting defaults (between DEFAULT_CONFIG and user settings)
+    if (userConfig.journal) {
+      const profile = getJournalProfile(userConfig.journal);
+      if (profile?.formatting) {
+        config = mergeJournalFormatting(config, profile.formatting, directory);
+      }
+    }
+
     return config;
   } catch (err) {
     const error = err as Error;

package/lib/commands/build.ts

@@ -42,6 +42,7 @@ interface InstallOptions {
 
 interface BuildOptions {
   dir: string;
+  journal?: string;
   crossref?: boolean;
   toc?: boolean;
   showChanges?: boolean;
@@ -270,13 +271,6 @@ export function register(program: Command, pkg?: { version?: string }): void {
         console.log(chalk.yellow('  ✗ pandoc-crossref not found'));
       }
 
-      try {
-        await import('mammoth');
-        console.log(chalk.green('  ✓ mammoth (Word parsing)'));
-      } catch {
-        console.log(chalk.red('  ✗ mammoth not found - run: npm install'));
-      }
-
       console.log('');
 
       if (hasPandocInstalled && hasCrossref) {
@@ -484,6 +478,7 @@ export function register(program: Command, pkg?: { version?: string }): void {
     .description('Build PDF/DOCX/TEX/PPTX/Beamer from sections')
     .argument('[formats...]', 'Output formats: pdf, docx, tex, beamer, pptx, all', ['pdf', 'docx'])
     .option('-d, --dir <directory>', 'Project directory', '.')
+    .option('-j, --journal <name>', 'Use journal profile for build formatting defaults')
     .option('--no-crossref', 'Skip pandoc-crossref filter')
     .option('--toc', 'Include table of contents')
     .option('--show-changes', 'Export DOCX with visible track changes (audit mode)')
@@ -515,11 +510,34 @@ export function register(program: Command, pkg?: { version?: string }): void {
         process.exit(1);
       }
 
+      // Apply journal formatting from CLI flag (overrides rev.yaml journal field)
+      let journalName: string | undefined;
+      if (options.journal) {
+        const { getJournalProfile } = await import('../journals.js');
+        const { mergeJournalFormatting } = await import('../build.js');
+        const profile = getJournalProfile(options.journal);
+        if (!profile) {
+          console.error(fmt.status('error', `Unknown journal: ${options.journal}`));
+          console.error(chalk.dim('Use "rev validate --list" to see available profiles'));
+          process.exit(1);
+        }
+        journalName = profile.name;
+        if (profile.formatting) {
+          Object.assign(config, mergeJournalFormatting(config, profile.formatting, dir));
+        }
+      } else if ((config as unknown as { journal?: string }).journal) {
+        // Journal set in rev.yaml — already applied by loadConfig, just get name for display
+        const { getJournalProfile } = await import('../journals.js');
+        const profile = getJournalProfile((config as unknown as { journal?: string }).journal!);
+        if (profile) journalName = profile.name;
+      }
+
       console.log(fmt.header(`Building ${config.title || 'document'}`));
       console.log();
 
       const targetFormats = formats.length > 0 ? formats : ['pdf', 'docx'];
       const tocEnabled = options.toc || config.pdf?.toc || config.docx?.toc;
+      if (journalName) console.log(chalk.dim(`  Journal: ${journalName}`));
       console.log(chalk.dim(`  Formats: ${targetFormats.join(', ')}`));
       console.log(chalk.dim(`  Crossref: ${hasPandocCrossref() && options.crossref !== false ? 'enabled' : 'disabled'}`));
       if (tocEnabled) console.log(chalk.dim(`  TOC: enabled`));

package/lib/commands/response.ts

@@ -33,6 +33,8 @@ interface ProfilesOptions {
   new?: string;
   project?: boolean;
   dirs?: boolean;
+  fetchCsl?: string;
+  listCsl?: boolean;
 }
 
 interface AnonymizeOptions {
@@ -126,7 +128,9 @@ export function register(program: Command): void {
         const custom = journals.filter(j => j.custom);
 
         for (const j of builtIn) {
-          console.log(`  ${chalk.bold(j.id)} - ${j.name}`);
+          const profile = getJournalProfile(j.id);
+          const fmtTag = profile?.formatting ? chalk.green(' [formatting]') : '';
+          console.log(`  ${chalk.bold(j.id)} - ${j.name}${fmtTag}`);
           if (j.url) console.log(chalk.dim(`    ${j.url}`));
         }
 
@@ -134,13 +138,16 @@ export function register(program: Command): void {
           console.log();
           console.log(chalk.cyan('  Custom Profiles:'));
           for (const j of custom) {
-            console.log(`  ${chalk.bold(j.id)} - ${j.name} ${chalk.cyan('[custom]')}`);
+            const profile = getJournalProfile(j.id);
+            const fmtTag = profile?.formatting ? chalk.green(' [formatting]') : '';
+            console.log(`  ${chalk.bold(j.id)} - ${j.name} ${chalk.cyan('[custom]')}${fmtTag}`);
             if (j.url) console.log(chalk.dim(`    ${j.url}`));
           }
         }
 
         console.log();
         console.log(chalk.dim('Usage: rev validate --journal <name>'));
+        console.log(chalk.dim('Profiles with [formatting] can also be used with: rev build -j <name>'));
         console.log(chalk.dim('Manage custom profiles: rev profiles'));
         return;
       }
@@ -224,6 +231,8 @@ export function register(program: Command): void {
     .option('--new <name>', 'Create a new profile template')
     .option('--project', 'Create profile in project directory (with --new)')
     .option('--dirs', 'Show profile directory locations')
+    .option('--fetch-csl <name>', 'Download a CSL citation style to cache')
+    .option('--list-csl', 'List cached CSL citation styles')
     .action(async (options: ProfilesOptions) => {
       const {
         listCustomProfiles,
@@ -232,6 +241,50 @@ export function register(program: Command): void {
       } = await import('../plugins.js');
       const { listJournals } = await import('../journals.js');
 
+      if (options.listCsl) {
+        const { listCachedCSL, getCSLCacheDir } = await import('../csl.js');
+        const cached = listCachedCSL();
+        console.log(fmt.header('Cached CSL Styles'));
+        console.log(chalk.dim(`  ${getCSLCacheDir()}`));
+        console.log();
+        if (cached.length === 0) {
+          console.log(chalk.dim('  No cached styles. Download with: rev profiles --fetch-csl <name>'));
+        } else {
+          for (const c of cached) {
+            console.log(`  ${chalk.bold(c.name)}`);
+          }
+          console.log();
+          console.log(chalk.dim(`  ${cached.length} cached style(s)`));
+        }
+        return;
+      }
+
+      if (options.fetchCsl) {
+        const { fetchCSL, resolveCSL, getCSLAliases } = await import('../csl.js');
+
+        // Check if already cached
+        const existing = resolveCSL(options.fetchCsl);
+        if (existing) {
+          console.log(fmt.status('info', `Already cached: ${existing}`));
+          return;
+        }
+
+        const spin = fmt.spinner(`Downloading CSL style "${options.fetchCsl}"...`).start();
+        const result = await fetchCSL(options.fetchCsl);
+        spin.stop();
+
+        if (result) {
+          console.log(fmt.status('success', `Downloaded: ${result}`));
+        } else {
+          console.error(fmt.status('error', `Could not download CSL style "${options.fetchCsl}"`));
+          const aliases = getCSLAliases();
+          const names = Object.keys(aliases).sort().join(', ');
+          console.error(chalk.dim(`  Known short names: ${names}`));
+          process.exit(1);
+        }
+        return;
+      }
+
       if (options.dirs) {
         const dirs = getPluginDirs();
         console.log(fmt.header('Profile Directories'));

package/lib/commands/sections.ts

@@ -204,11 +204,10 @@ async function bootstrapFromWord(docx: string, options: BootstrapOptions): Promi
   console.log(chalk.cyan(`Bootstrapping project from ${path.basename(docx)}...\n`));
 
   try {
-    const mammoth = await import('mammoth');
+    const { extractTextFromWord } = await import('../word.js');
     const { default: YAML } = await import('yaml');
 
-    const result = await mammoth.extractRawText({ path: docx });
-    const text = result.value;
+    const text = await extractTextFromWord(docx);
 
     const sections = detectSectionsFromWord(text);
 
@@ -328,6 +327,13 @@ export function register(program: Command): void {
 
       console.log(chalk.cyan(`Comparing ${path.basename(docx)} against ${path.basename(original)}...`));
 
+      // Warn if pandoc is missing
+      const { hasPandoc: hasPandocImport, getInstallInstructions: getInstallImport } = await import('../dependencies.js');
+      if (!hasPandocImport()) {
+        console.log(chalk.yellow(`\n  Warning: Pandoc not installed. Track changes extracted from XML (formatting may differ).`));
+        console.log(chalk.dim(`  Install for best results: ${getInstallImport('pandoc')}\n`));
+      }
+
       try {
         const { importFromWord } = await import('../import.js');
         const { annotated, stats } = await importFromWord(docx, original, {
@@ -386,14 +392,14 @@ export function register(program: Command): void {
       }
 
       try {
-        const mammoth = await import('mammoth');
-        const result = await mammoth.extractRawText({ path: docx });
+        const { extractTextFromWord } = await import('../word.js');
+        const text = await extractTextFromWord(docx);
 
         if (options.output) {
-          fs.writeFileSync(options.output, result.value, 'utf-8');
+          fs.writeFileSync(options.output, text, 'utf-8');
           console.error(chalk.green(`Extracted to ${options.output}`));
         } else {
-          process.stdout.write(result.value);
+          process.stdout.write(text);
         }
       } catch (err) {
         const error = err as Error;
@@ -564,6 +570,14 @@ export function register(program: Command): void {
         process.exit(1);
       }
 
+      // Check pandoc availability upfront and warn
+      const { hasPandoc, getInstallInstructions } = await import('../dependencies.js');
+      if (!hasPandoc()) {
+        console.log(fmt.status('warning', `Pandoc not installed. Track changes will be extracted from XML (formatting may differ).`));
+        console.log(chalk.dim(`  Install for best results: ${getInstallInstructions('pandoc')}`));
+        console.log();
+      }
+
       const spin = fmt.spinner(`Importing ${path.basename(docx)}...`).start();
 
       try {
@@ -579,12 +593,20 @@ export function register(program: Command): void {
         const comments = await extractWordComments(docx);
         const { anchors, fullDocText: xmlDocText } = await extractCommentAnchors(docx);
 
-        // Use pandoc for extraction to preserve markdown formatting (bold, tables, etc.)
-        // Mammoth only extracts plain text which loses all formatting
+        // Extract Word text (uses pandoc if available, falls back to XML extraction)
         const wordExtraction = await extractFromWord(docx, { mediaDir: options.dir });
         let wordText = wordExtraction.text;
         const wordTables = wordExtraction.tables || [];
 
+        // Log extraction messages (warnings about pandoc, track change stats, etc.)
+        for (const msg of wordExtraction.messages || []) {
+          if (msg.type === 'warning') {
+            spin.stop();
+            console.log(fmt.status('warning', msg.message));
+            spin.start();
+          }
+        }
+
         // Restore crossref on FULL text BEFORE splitting into sections
         // This ensures duplicate labels from track changes are handled correctly
         // (the same figure may appear multiple times in old/new versions)

package/lib/csl.ts

@@ -0,0 +1,191 @@
+/**
+ * CSL citation style resolution and caching
+ *
+ * Resolves short CSL names (e.g. "nature") to local file paths,
+ * downloading from the CSL repository if needed.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import * as https from 'https';
+
+// =============================================================================
+// Constants
+// =============================================================================
+
+/** Cache directory for downloaded CSL files */
+const CSL_CACHE_DIR = path.join(os.homedir(), '.rev', 'csl');
+
+/** GitHub raw URL for the CSL styles repository */
+const CSL_REPO_BASE = 'https://raw.githubusercontent.com/citation-style-language/styles/master';
+
+/**
+ * Short name → CSL filename mapping for common styles.
+ * Names that match their filename exactly don't need an entry here.
+ */
+const CSL_ALIASES: Record<string, string> = {
+  'apa': 'apa',
+  'chicago': 'chicago-author-date',
+  'vancouver': 'vancouver',
+  'ieee': 'ieee',
+  'nature': 'nature',
+  'science': 'science',
+  'cell': 'cell',
+  'pnas': 'pnas',
+  'plos': 'plos',
+  'elife': 'elife',
+  'ecology-letters': 'ecology-letters',
+  'ecology': 'ecology',
+  'ama': 'american-medical-association',
+  'acs': 'american-chemical-society',
+  'rsc': 'royal-society-of-chemistry',
+  'harvard': 'harvard-cite-them-right',
+  'mla': 'modern-language-association',
+  'elsevier': 'elsevier-harvard',
+  'springer': 'springer-basic-author-date',
+  'biomed-central': 'biomed-central',
+};
+
+// =============================================================================
+// Public API
+// =============================================================================
+
+/**
+ * Get the CSL cache directory path
+ */
+export function getCSLCacheDir(): string {
+  return CSL_CACHE_DIR;
+}
+
+/**
+ * Resolve a CSL name or path to a local file path.
+ *
+ * Resolution order:
+ * 1. If it's an absolute path or relative path that exists, return it
+ * 2. Check project directory for <name>.csl
+ * 3. Check ~/.rev/csl/ cache
+ * 4. Return null (caller can then use fetchCSL to download)
+ */
+export function resolveCSL(nameOrPath: string, projectDir?: string): string | null {
+  // Already a file path that exists
+  if (path.isAbsolute(nameOrPath) && fs.existsSync(nameOrPath)) {
+    return nameOrPath;
+  }
+
+  // Relative path in project directory
+  if (projectDir) {
+    const projectPath = path.join(projectDir, nameOrPath);
+    if (fs.existsSync(projectPath)) {
+      return projectPath;
+    }
+    // Try with .csl extension
+    const projectPathCsl = projectPath.endsWith('.csl') ? projectPath : `${projectPath}.csl`;
+    if (fs.existsSync(projectPathCsl)) {
+      return projectPathCsl;
+    }
+  }
+
+  // Resolve short name to filename
+  const baseName = resolveCSLName(nameOrPath);
+  const fileName = baseName.endsWith('.csl') ? baseName : `${baseName}.csl`;
+
+  // Check cache
+  const cachePath = path.join(CSL_CACHE_DIR, fileName);
+  if (fs.existsSync(cachePath)) {
+    return cachePath;
+  }
+
+  return null;
+}
+
+/**
+ * Download a CSL style from the CSL repository to the local cache.
+ *
+ * @returns Path to the cached file, or null on failure
+ */
+export async function fetchCSL(name: string): Promise<string | null> {
+  const baseName = resolveCSLName(name);
+  const fileName = baseName.endsWith('.csl') ? baseName : `${baseName}.csl`;
+  const url = `${CSL_REPO_BASE}/${fileName}`;
+  const cachePath = path.join(CSL_CACHE_DIR, fileName);
+
+  // Ensure cache directory exists
+  if (!fs.existsSync(CSL_CACHE_DIR)) {
+    fs.mkdirSync(CSL_CACHE_DIR, { recursive: true });
+  }
+
+  try {
+    const content = await httpGet(url);
+    if (content) {
+      fs.writeFileSync(cachePath, content, 'utf-8');
+      return cachePath;
+    }
+    return null;
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * List all cached CSL files
+ */
+export function listCachedCSL(): Array<{ name: string; path: string }> {
+  if (!fs.existsSync(CSL_CACHE_DIR)) {
+    return [];
+  }
+
+  return fs.readdirSync(CSL_CACHE_DIR)
+    .filter(f => f.endsWith('.csl'))
+    .sort()
+    .map(f => ({
+      name: path.basename(f, '.csl'),
+      path: path.join(CSL_CACHE_DIR, f),
+    }));
+}
+
+/**
+ * Get the list of known CSL short name aliases
+ */
+export function getCSLAliases(): Record<string, string> {
+  return { ...CSL_ALIASES };
+}
+
+// =============================================================================
+// Internal helpers
+// =============================================================================
+
+/**
+ * Resolve a short name to a CSL filename (without extension)
+ */
+function resolveCSLName(name: string): string {
+  const normalized = name.toLowerCase().replace(/\.csl$/, '');
+  return CSL_ALIASES[normalized] || normalized;
+}
+
+/**
+ * Simple HTTPS GET that follows redirects
+ */
+function httpGet(url: string, redirectCount = 0): Promise<string | null> {
+  if (redirectCount > 5) return Promise.resolve(null);
+
+  return new Promise((resolve) => {
+    https.get(url, (res) => {
+      // Follow redirects
+      if ((res.statusCode === 301 || res.statusCode === 302) && res.headers.location) {
+        resolve(httpGet(res.headers.location, redirectCount + 1));
+        return;
+      }
+
+      if (res.statusCode !== 200) {
+        resolve(null);
+        return;
+      }
+
+      let data = '';
+      res.on('data', chunk => { data += chunk; });
+      res.on('end', () => resolve(data));
+      res.on('error', () => resolve(null));
+    }).on('error', () => resolve(null));
+  });
+}

package/lib/import.ts

@@ -743,13 +743,27 @@ export async function extractFromWord(
       }
     }
   } catch (pandocErr: any) {
-    // Fall back to mammoth if pandoc fails
-    messages.push({ type: 'warning', message: 'Pandoc failed, using mammoth (equations and images may not be preserved)' });
-    const mammoth = await import('mammoth');
-    const textResult = await mammoth.extractRawText({ path: docxPath });
-    const htmlResult = await mammoth.convertToHtml({ path: docxPath });
-    text = textResult.value;
-    messages = [...textResult.messages, ...htmlResult.messages].map(m => ({ type: 'warning' as const, message: String(m) }));
+    // Pandoc not available — use XML-based extraction with track change support
+    const { extractPlainTextWithTrackChanges } = await import('./word.js');
+    const { getInstallInstructions } = await import('./dependencies.js');
+    const installCmd = getInstallInstructions('pandoc');
+
+    const xmlResult = await extractPlainTextWithTrackChanges(docxPath);
+    text = xmlResult.text;
+    hasTrackChanges = xmlResult.hasTrackChanges;
+    trackChangeStats = xmlResult.stats;
+
+    if (hasTrackChanges) {
+      messages.push({
+        type: 'warning',
+        message: `Pandoc not installed. Using built-in XML extractor (${trackChangeStats.insertions} insertions, ${trackChangeStats.deletions} deletions preserved). Formatting may differ. Install pandoc for best results: ${installCmd}`
+      });
+    } else {
+      messages.push({
+        type: 'warning',
+        message: `Pandoc not installed. Using built-in XML extractor (no track changes found). Install pandoc for better formatting: ${installCmd}`
+      });
+    }
   }
 
   // Extract comments directly from docx XML

package/lib/journals.ts

@@ -5,7 +5,7 @@
 
 import * as fs from 'fs';
 import * as path from 'path';
-import type { JournalProfile, JournalRequirements, ValidationResult } from './types.js';
+import type { JournalProfile, JournalRequirements, JournalFormatting, ValidationResult } from './types.js';
 import { loadCustomProfiles } from './plugins.js';
 import { countWords } from './utils.js';
 
@@ -23,6 +23,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       figures: { max: 6 },
       sections: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
     },
+    formatting: {
+      csl: 'nature',
+      pdf: { fontsize: '11pt', geometry: 'margin=2.5cm', linestretch: 2 },
+    },
   },
 
   science: {
@@ -34,6 +38,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       figures: { max: 4 },
       sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
     },
+    formatting: {
+      csl: 'science',
+      pdf: { fontsize: '12pt', geometry: 'margin=1in', linestretch: 2 },
+    },
   },
 
   'plos-one': {
@@ -44,6 +52,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       references: { doiRequired: false },
       sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
     },
+    formatting: {
+      csl: 'plos',
+      pdf: { fontsize: '12pt', geometry: 'margin=1in', linestretch: 2 },
+    },
   },
 
   'pnas': {
@@ -55,6 +67,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       figures: { max: 6 },
       sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
     },
+    formatting: {
+      csl: 'pnas',
+      pdf: { documentclass: 'article', fontsize: '9pt', geometry: 'margin=2cm', linestretch: 1.2, numbersections: false },
+    },
   },
 
   'ecology-letters': {
@@ -97,6 +113,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       references: { doiRequired: true },
       sections: ['Abstract', 'Introduction', 'Results', 'Discussion', 'Methods'],
     },
+    formatting: {
+      csl: 'elife',
+      pdf: { fontsize: '11pt', geometry: 'margin=2.5cm', linestretch: 1.5 },
+    },
   },
 
   'cell': {
@@ -108,6 +128,10 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       figures: { max: 7 },
       sections: ['Abstract', 'Introduction', 'Results', 'Discussion'],
     },
+    formatting: {
+      csl: 'cell',
+      pdf: { fontsize: '12pt', geometry: 'margin=2.5cm', linestretch: 2 },
+    },
   },
 
   'current-biology': {