docrev 0.8.1 → 0.8.5

package/lib/{citations.js → citations.ts}

@@ -5,15 +5,17 @@
 
 import * as fs from 'fs';
 import * as path from 'path';
+import type { Citation, CitationValidation, CitationStats } from './types.js';
 
 /**
  * Extract all citation keys from markdown text
  * Handles: [@Key], [@Key1; @Key2], @Key (inline)
- * @param {string} text
- * @returns {Array<{key: string, line: number, file: string}>}
+ * @param text - Markdown text to parse
+ * @param file - Optional filename for context
+ * @returns Array of citation objects
  */
-export function extractCitations(text, file = '') {
-  const citations = [];
+export function extractCitations(text: string, file: string = ''): Citation[] {
+  const citations: Citation[] = [];
   const lines = text.split('\n');
 
   // Pattern for bracketed citations: [@Key] or [@Key1; @Key2]
@@ -23,15 +25,18 @@ export function extractCitations(text, file = '') {
 
   for (let lineNum = 0; lineNum < lines.length; lineNum++) {
     const line = lines[lineNum];
+    if (!line) continue;
 
     // Skip code blocks and comments
     if (line.trim().startsWith('```') || line.trim().startsWith('<!--')) continue;
 
     // Bracketed citations
-    let match;
+    let match: RegExpExecArray | null;
     while ((match = bracketPattern.exec(line)) !== null) {
       // Split by ; for multiple citations
-      const keys = match[1].split(';').map(k => k.trim().replace(/^@/, ''));
+      const citationGroup = match[1];
+      if (!citationGroup) continue;
+      const keys = citationGroup.split(';').map(k => k.trim().replace(/^@/, ''));
       for (const key of keys) {
         if (key) {
           citations.push({ key, line: lineNum + 1, file });
@@ -42,7 +47,10 @@ export function extractCitations(text, file = '') {
     // Inline citations (reset lastIndex)
     inlinePattern.lastIndex = 0;
     while ((match = inlinePattern.exec(line)) !== null) {
-      citations.push({ key: match[1], line: lineNum + 1, file });
+      const citationKey = match[1];
+      if (citationKey) {
+        citations.push({ key: citationKey, line: lineNum + 1, file });
+      }
     }
   }
 
@@ -51,11 +59,11 @@ export function extractCitations(text, file = '') {
 
 /**
  * Parse .bib file and extract all entry keys
- * @param {string} bibPath
- * @returns {Set<string>}
+ * @param bibPath - Path to bibliography file
+ * @returns Set of citation keys found in the bib file
  */
-export function parseBibFile(bibPath) {
-  const keys = new Set();
+export function parseBibFile(bibPath: string): Set<string> {
+  const keys = new Set<string>();
 
   if (!fs.existsSync(bibPath)) {
     return keys;
@@ -66,9 +74,12 @@ export function parseBibFile(bibPath) {
   // Pattern for bib entries: @type{key,
   const entryPattern = /@\w+\s*\{\s*([^,\s]+)\s*,/g;
 
-  let match;
+  let match: RegExpExecArray | null;
   while ((match = entryPattern.exec(content)) !== null) {
-    keys.add(match[1]);
+    const key = match[1];
+    if (key) {
+      keys.add(key);
+    }
   }
 
   return keys;
@@ -76,13 +87,13 @@ export function parseBibFile(bibPath) {
 
 /**
  * Validate citations against bib file
- * @param {string[]} mdFiles - Markdown files to check
- * @param {string} bibPath - Path to .bib file
- * @returns {{valid: Array, missing: Array, unused: Array, duplicates: Array}}
+ * @param mdFiles - Markdown files to check
+ * @param bibPath - Path to .bib file
+ * @returns Validation result with valid, missing, unused, and duplicate citations
  */
-export function validateCitations(mdFiles, bibPath) {
+export function validateCitations(mdFiles: string[], bibPath: string): CitationValidation {
   // Collect all citations from markdown
-  const allCitations = [];
+  const allCitations: Citation[] = [];
   for (const file of mdFiles) {
     if (!fs.existsSync(file)) continue;
     const text = fs.readFileSync(file, 'utf-8');
@@ -94,10 +105,10 @@ export function validateCitations(mdFiles, bibPath) {
   const bibKeys = parseBibFile(bibPath);
 
   // Categorize
-  const valid = [];
-  const missing = [];
-  const citedKeys = new Set();
-  const keyOccurrences = new Map();
+  const valid: Citation[] = [];
+  const missing: Citation[] = [];
+  const citedKeys = new Set<string>();
+  const keyOccurrences = new Map<string, Citation[]>();
 
   for (const citation of allCitations) {
     citedKeys.add(citation.key);
@@ -106,7 +117,7 @@ export function validateCitations(mdFiles, bibPath) {
     if (!keyOccurrences.has(citation.key)) {
       keyOccurrences.set(citation.key, []);
     }
-    keyOccurrences.get(citation.key).push(citation);
+    keyOccurrences.get(citation.key)!.push(citation);
 
     if (bibKeys.has(citation.key)) {
       valid.push(citation);
@@ -128,11 +139,11 @@ export function validateCitations(mdFiles, bibPath) {
 
 /**
  * Get citation statistics
- * @param {string[]} mdFiles
- * @param {string} bibPath
- * @returns {object}
+ * @param mdFiles - Markdown files to analyze
+ * @param bibPath - Path to bibliography file
+ * @returns Statistics object
  */
-export function getCitationStats(mdFiles, bibPath) {
+export function getCitationStats(mdFiles: string[], bibPath: string): CitationStats {
   const result = validateCitations(mdFiles, bibPath);
   const bibKeys = parseBibFile(bibPath);
 

package/lib/commands/{build.js → build.ts}

@@ -23,13 +23,40 @@ import {
   formatBuildResults,
   getUserName,
 } from './context.js';
+import type { Command } from 'commander';
+import * as readline from 'readline';
+
+interface RefsOptions {
+  dir: string;
+}
+
+interface MigrateOptions {
+  dir: string;
+  auto?: boolean;
+  dryRun?: boolean;
+}
+
+interface InstallOptions {
+  check?: boolean;
+}
+
+interface BuildOptions {
+  dir: string;
+  crossref?: boolean;
+  toc?: boolean;
+  showChanges?: boolean;
+  dual?: boolean;
+  reference?: string;
+  theme?: string;
+  colortheme?: string;
+  aspectratio?: string;
+  verbose?: boolean;
+}
 
 /**
  * Register build commands with the program
- * @param {import('commander').Command} program
- * @param {object} pkg - Package.json object for version info
  */
-export function register(program, pkg) {
+export function register(program: Command, pkg?: { version?: string }): void {
   // ==========================================================================
   // REFS command - Show figure/table reference status
   // ==========================================================================
@@ -39,7 +66,7 @@ export function register(program, pkg) {
     .description('Show figure/table reference registry and status')
     .argument('[file]', 'Optional file to analyze for references')
     .option('-d, --dir <directory>', 'Directory to scan for anchors', '.')
-    .action((file, options) => {
+    .action((file: string | undefined, options: RefsOptions) => {
       const dir = path.resolve(options.dir);
 
       if (!fs.existsSync(dir)) {
@@ -103,7 +130,7 @@ export function register(program, pkg) {
     .option('-d, --dir <directory>', 'Directory for registry', '.')
     .option('--auto', 'Auto-convert without prompting')
     .option('--dry-run', 'Preview without saving')
-    .action(async (file, options) => {
+    .action(async (file: string, options: MigrateOptions) => {
       if (!fs.existsSync(file)) {
         console.error(chalk.red(`File not found: ${file}`));
         process.exit(1);
@@ -141,8 +168,7 @@ export function register(program, pkg) {
           console.log(chalk.green(`\nConverted ${conversions.length} reference(s) in ${file}`));
         }
       } else {
-        const rl = await import('readline');
-        const readline = rl.createInterface({
+        const rl = readline.createInterface({
           input: process.stdin,
           output: process.stdout,
         });
@@ -151,8 +177,8 @@ export function register(program, pkg) {
         let converted = 0;
         let skipped = 0;
 
-        const askQuestion = (prompt) =>
-          new Promise((resolve) => readline.question(prompt, resolve));
+        const askQuestion = (prompt: string): Promise<string> =>
+          new Promise((resolve) => rl.question(prompt, resolve));
 
         const sortedRefs = [...refs].sort((a, b) => b.position - a.position);
 
@@ -198,7 +224,7 @@ export function register(program, pkg) {
           }
         }
 
-        readline.close();
+        rl.close();
 
         console.log(chalk.cyan(`\nConverted: ${converted}, Skipped: ${skipped}`));
 
@@ -219,7 +245,7 @@ export function register(program, pkg) {
     .command('install')
     .description('Check and install dependencies (pandoc-crossref)')
     .option('--check', 'Only check, don\'t install')
-    .action(async (options) => {
+    .action(async (options: InstallOptions) => {
       const os = await import('os');
       const { execSync } = await import('child_process');
       const platform = os.platform();
@@ -303,7 +329,7 @@ export function register(program, pkg) {
           execSync('conda --version', { encoding: 'utf-8', stdio: 'pipe' });
           console.log(chalk.cyan('Conda detected. Install missing dependencies? [y/N] '));
 
-          const rl = (await import('readline')).createInterface({
+          const rl = readline.createInterface({
             input: process.stdin,
             output: process.stdout,
           });
@@ -323,7 +349,8 @@ export function register(program, pkg) {
                 }
                 console.log(chalk.green('\nDone! Run "rev install --check" to verify.'));
               } catch (err) {
-                console.log(chalk.red(`\nInstallation failed: ${err.message}`));
+                const error = err as Error;
+                console.log(chalk.red(`\nInstallation failed: ${error.message}`));
                 console.log(chalk.dim('Try installing manually with the commands above.'));
               }
             }
@@ -421,7 +448,8 @@ export function register(program, pkg) {
             }
           }
         } catch (e) {
-          console.log(chalk.red('  ✗') + ` rev.yaml parse error: ${e.message}`);
+          const error = e as Error;
+          console.log(chalk.red('  ✗') + ` rev.yaml parse error: ${error.message}`);
           issues++;
         }
       } else {
@@ -453,15 +481,19 @@ export function register(program, pkg) {
   program
     .command('build')
     .alias('b')
-    .description('Build PDF/DOCX/TEX from sections')
-    .argument('[formats...]', 'Output formats: pdf, docx, tex, all', ['pdf', 'docx'])
+    .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('--no-crossref', 'Skip pandoc-crossref filter')
     .option('--toc', 'Include table of contents')
     .option('--show-changes', 'Export DOCX with visible track changes (audit mode)')
     .option('--dual', 'Output both clean version and annotated version (with comments)')
     .option('--reference <docx>', 'Reference DOCX for comment position alignment (use with --dual)')
-    .action(async (formats, options) => {
+    .option('--theme <name>', 'Beamer theme (default, metropolis, etc.)')
+    .option('--colortheme <name>', 'Beamer color theme')
+    .option('--aspectratio <ratio>', 'Beamer aspect ratio (169, 43)')
+    .option('--verbose', 'Show detailed output including postprocess scripts')
+    .action(async (formats: string[], options: BuildOptions) => {
       const dir = path.resolve(options.dir);
 
       if (!fs.existsSync(dir)) {
@@ -496,14 +528,31 @@ export function register(program, pkg) {
       console.log('');
 
       if (options.toc) {
+        config.pdf = config.pdf || {};
         config.pdf.toc = true;
+        config.docx = config.docx || {};
         config.docx.toc = true;
       }
 
       if (options.dual) {
+        config.docx = config.docx || {};
         config.docx.keepComments = false;
       }
 
+      // Apply beamer CLI options
+      if (options.theme) {
+        config.beamer = config.beamer || {};
+        config.beamer.theme = options.theme;
+      }
+      if (options.colortheme) {
+        config.beamer = config.beamer || {};
+        config.beamer.colortheme = options.colortheme;
+      }
+      if (options.aspectratio) {
+        config.beamer = config.beamer || {};
+        config.beamer.aspectratio = options.aspectratio;
+      }
+
       if (options.showChanges) {
         if (!targetFormats.includes('docx') && !targetFormats.includes('all')) {
           console.error(fmt.status('error', '--show-changes only applies to DOCX output'));
@@ -545,8 +594,9 @@ export function register(program, pkg) {
           }
         } catch (err) {
           spin.stop();
-          console.error(fmt.status('error', err.message));
-          if (process.env.DEBUG) console.error(err.stack);
+          const error = err as Error;
+          console.error(fmt.status('error', error.message));
+          if (process.env.DEBUG) console.error(error.stack);
           process.exit(1);
         }
         return;
@@ -558,6 +608,7 @@ export function register(program, pkg) {
         const { results, paperPath, forwardRefsResolved, refsAutoInjected } = await build(dir, targetFormats, {
           crossref: options.crossref,
           config,
+          verbose: options.verbose,
         });
 
         spin.stop();
@@ -632,7 +683,7 @@ export function register(program, pkg) {
               if (!pandocResult.success) {
                 console.error(chalk.yellow(`\nWarning: Could not build marked DOCX: ${pandocResult.error}`));
               } else {
-                const commentsDocxPath = docxResult.outputPath.replace(/\.docx$/, '_comments.docx');
+                const commentsDocxPath = docxResult.outputPath!.replace(/\.docx$/, '_comments.docx');
                 const spinInject = fmt.spinner('Injecting comments at markers...').start();
                 const commentResult = await injectCommentsAtMarkers(markedDocxPath, comments, commentsDocxPath);
                 spinInject.stop();
@@ -646,7 +697,7 @@ export function register(program, pkg) {
 
                 if (commentResult.success) {
                   console.log(chalk.cyan('\nDual output:'));
-                  console.log(`  Clean:    ${path.basename(docxResult.outputPath)}`);
+                  console.log(`  Clean:    ${path.basename(docxResult.outputPath!)}`);
                   console.log(`  Comments: ${path.basename(commentsDocxPath)} (${commentResult.commentCount} comments)`);
                   if (commentResult.skippedComments > 0) {
                     console.log(chalk.yellow(`  Warning: ${commentResult.skippedComments} comments could not be anchored (markers not found)`));
@@ -684,7 +735,7 @@ export function register(program, pkg) {
               annotatedConfig.pdf['header-includes'] = (annotatedConfig.pdf['header-includes'] || '') + preamble;
               annotatedConfig.pdf.geometry = 'left=2.5cm,right=4.5cm,top=2.5cm,bottom=2.5cm,marginparwidth=3.5cm';
 
-              const annotatedPdfPath = pdfResult.outputPath.replace(/\.pdf$/, '_comments.pdf');
+              const annotatedPdfPath = pdfResult.outputPath!.replace(/\.pdf$/, '_comments.pdf');
               spinPdf.text = 'Building annotated PDF...';
               const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, { ...options, outputPath: annotatedPdfPath });
               spinPdf.stop();
@@ -695,7 +746,7 @@ export function register(program, pkg) {
 
               if (pandocResult.success) {
                 console.log(chalk.cyan('\nPDF dual output:'));
-                console.log(`  Clean:    ${path.basename(pdfResult.outputPath)}`);
+                console.log(`  Clean:    ${path.basename(pdfResult.outputPath!)}`);
                 console.log(`  Comments: ${path.basename(annotatedPdfPath)} (${commentCount} margin notes)`);
               } else {
                 console.error(chalk.yellow(`\nWarning: Could not create annotated PDF: ${pandocResult.error}`));
@@ -709,12 +760,13 @@ export function register(program, pkg) {
         if (docxResult && !options.dual) {
           try {
             const { storeBaseDocument } = await import('../merge.js');
-            storeBaseDocument(dir, docxResult.outputPath);
+            storeBaseDocument(dir, docxResult.outputPath!);
             console.log(chalk.dim(`\n  Saved as .rev/base.docx for merge`));
           } catch (err) {
             // Non-fatal - just log if DEBUG
             if (process.env.DEBUG) {
-              console.log(chalk.dim(`\n  Could not store base document: ${err.message}`));
+              const error = err as Error;
+              console.log(chalk.dim(`\n  Could not store base document: ${error.message}`));
             }
           }
         }
@@ -722,8 +774,9 @@ export function register(program, pkg) {
         console.log(chalk.green('\nBuild complete!'));
       } catch (err) {
         spin.stop();
-        console.error(fmt.status('error', err.message));
-        if (process.env.DEBUG) console.error(err.stack);
+        const error = err as Error;
+        console.error(fmt.status('error', error.message));
+        if (process.env.DEBUG) console.error(error.stack);
         process.exit(1);
       }
     });

package/lib/commands/{citations.js → citations.ts}

@@ -10,12 +10,28 @@ import {
   path,
   fmt,
 } from './context.js';
+import type { Command } from 'commander';
+
+interface CitationsOptions {
+  bib: string;
+}
+
+interface EquationsOptions {
+  output?: string;
+}
+
+interface PdfCommentsOptions {
+  append?: string;
+  json?: boolean;
+  byPage?: boolean;
+  byAuthor?: boolean;
+  withText?: boolean;
+}
 
 /**
  * Register citation commands with the program
- * @param {import('commander').Command} program
  */
-export function register(program) {
+export function register(program: Command): void {
   // ==========================================================================
   // CITATIONS command - Validate citations against .bib file
   // ==========================================================================
@@ -26,7 +42,7 @@ export function register(program) {
     .description('Validate citations against bibliography')
     .argument('[files...]', 'Markdown files to check (default: all section files)')
     .option('-b, --bib <file>', 'Bibliography file', 'references.bib')
-    .action(async (files, options) => {
+    .action(async (files: string[], options: CitationsOptions) => {
       const { getCitationStats } = await import('../citations.js');
 
       // If no files specified, find all .md files
@@ -48,7 +64,7 @@ export function register(program) {
       console.log();
 
       // Summary table
-      const rows = [
+      const rows: string[][] = [
         ['Total citations', stats.totalCitations.toString()],
         ['Unique keys cited', stats.uniqueCited.toString()],
         ['Bib entries', stats.bibEntries.toString()],
@@ -97,7 +113,7 @@ export function register(program) {
     .alias('figs')
     .description('List all figures and tables with reference counts')
     .argument('[files...]', 'Markdown files to scan')
-    .action(async (files) => {
+    .action(async (files: string[]) => {
       const { buildRegistry } = await import('../crossref.js');
 
       // If no files specified, find all .md files
@@ -112,7 +128,7 @@ export function register(program) {
       const registry = buildRegistry('.');
 
       // Count references in files
-      const refCounts = new Map();
+      const refCounts = new Map<string, number>();
       for (const file of mdFiles) {
         if (!fs.existsSync(file)) continue;
         const text = fs.readFileSync(file, 'utf-8');
@@ -174,7 +190,7 @@ export function register(program) {
       }
 
       // Warn about unreferenced
-      const unreferenced = [];
+      const unreferenced: string[] = [];
       for (const [label] of registry.figures) {
         if (!refCounts.get(`fig:${label}`)) unreferenced.push(`@fig:${label}`);
       }
@@ -198,7 +214,7 @@ export function register(program) {
     .argument('<action>', 'Action: list, extract, convert, from-word')
     .argument('[input]', 'Input file (.md for extract/convert, .docx for from-word)')
     .option('-o, --output <file>', 'Output file')
-    .action(async (action, input, options) => {
+    .action(async (action: string, input: string | undefined, options: EquationsOptions) => {
       const { extractEquations, getEquationStats, createEquationsDoc, extractEquationsFromWord, getWordEquationStats } = await import('../equations.js');
 
       if (action === 'from-word') {
@@ -218,7 +234,7 @@ export function register(program) {
         const result = await extractEquationsFromWord(input);
 
         if (!result.success) {
-          spin.error(result.error);
+          spin.error(result.error!);
           process.exit(1);
         }
 
@@ -243,10 +259,10 @@ export function register(program) {
           const typeLabel = eq.type === 'display' ? chalk.cyan('[display]') : chalk.yellow('[inline]');
 
           if (eq.latex) {
-            console.log(`${chalk.bold(i + 1)}. ${typeLabel}`);
+            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel}`);
             console.log(chalk.dim('   LaTeX:'), eq.latex.length > 80 ? eq.latex.substring(0, 77) + '...' : eq.latex);
           } else {
-            console.log(`${chalk.bold(i + 1)}. ${typeLabel} ${chalk.red('[conversion failed]')}`);
+            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel} ${chalk.red('[conversion failed]')}`);
           }
         }
 
@@ -302,7 +318,7 @@ export function register(program) {
 
         if (result.success) {
           console.log(fmt.status('success', result.message));
-          console.log(chalk.dim(`  ${result.stats.display} display, ${result.stats.inline} inline equations`));
+          console.log(chalk.dim(`  ${result.stats!.display} display, ${result.stats!.inline} inline equations`));
         } else {
           console.error(fmt.status('error', result.message));
           process.exit(1);
@@ -326,7 +342,8 @@ export function register(program) {
           await execAsync(`pandoc "${input}" -o "${output}" --mathml`);
           spin.success(`Created ${output}`);
         } catch (err) {
-          spin.error(err.message);
+          const error = err as Error;
+          spin.error(error.message);
           process.exit(1);
         }
       } else {
@@ -350,7 +367,7 @@ export function register(program) {
     .option('--by-page', 'Group comments by page')
     .option('--by-author', 'Group comments by author')
     .option('--with-text', 'Extract highlighted text (slower but shows what was highlighted)')
-    .action(async (pdf, options) => {
+    .action(async (pdf: string, options: PdfCommentsOptions) => {
       if (!fs.existsSync(pdf)) {
         console.error(fmt.status('error', `File not found: ${pdf}`));
         process.exit(1);
@@ -373,7 +390,7 @@ export function register(program) {
       const spin = fmt.spinner(`Extracting comments from ${path.basename(pdf)}...`).start();
 
       try {
-        let comments;
+        let comments: any[];
 
         if (options.withText) {
           // Use the new text extraction feature
@@ -435,7 +452,7 @@ export function register(program) {
 
         if (options.byAuthor) {
           // Group by author
-          const byAuthor = {};
+          const byAuthor: Record<string, any[]> = {};
           for (const c of comments) {
             const author = c.author || 'Unknown';
             if (!byAuthor[author]) byAuthor[author] = [];
@@ -489,8 +506,9 @@ export function register(program) {
 
       } catch (err) {
         spin.stop();
-        console.error(fmt.status('error', `Failed to extract PDF comments: ${err.message}`));
-        if (process.env.DEBUG) console.error(err.stack);
+        const error = err as Error;
+        console.error(fmt.status('error', `Failed to extract PDF comments: ${error.message}`));
+        if (process.env.DEBUG) console.error(error.stack);
         process.exit(1);
       }
     });