docrev 0.8.1 → 0.8.5

package/dist/lib/commands/build.js.map

@@ -0,0 +1 @@
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package/dist/lib/commands/citations.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Citation commands: citations, figures, equations, pdf-comments
+ *
+ * Commands for validating citations, managing figures/tables, and equation handling.
+ */
+import type { Command } from 'commander';
+/**
+ * Register citation commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=citations.d.ts.map

package/dist/lib/commands/citations.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"citations.d.ts","sourceRoot":"","sources":["../../../lib/commands/citations.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkBzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAie/C"}

package/dist/lib/commands/citations.js

@@ -0,0 +1,428 @@
+/**
+ * Citation commands: citations, figures, equations, pdf-comments
+ *
+ * Commands for validating citations, managing figures/tables, and equation handling.
+ */
+import { chalk, fs, path, fmt, } from './context.js';
+/**
+ * Register citation commands with the program
+ */
+export function register(program) {
+    // ==========================================================================
+    // CITATIONS command - Validate citations against .bib file
+    // ==========================================================================
+    program
+        .command('citations')
+        .alias('cite')
+        .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) => {
+        const { getCitationStats } = await import('../citations.js');
+        // If no files specified, find all .md files
+        let mdFiles = files;
+        if (!mdFiles || mdFiles.length === 0) {
+            mdFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f));
+        }
+        if (!fs.existsSync(options.bib)) {
+            console.error(fmt.status('error', `Bibliography not found: ${options.bib}`));
+            process.exit(1);
+        }
+        const stats = getCitationStats(mdFiles, options.bib);
+        console.log(fmt.header('Citation Check'));
+        console.log();
+        // Summary table
+        const rows = [
+            ['Total citations', stats.totalCitations.toString()],
+            ['Unique keys cited', stats.uniqueCited.toString()],
+            ['Bib entries', stats.bibEntries.toString()],
+            [chalk.green('Valid'), chalk.green(stats.valid.toString())],
+            [stats.missing > 0 ? chalk.red('Missing') : 'Missing', stats.missing > 0 ? chalk.red(stats.missing.toString()) : '0'],
+            [chalk.dim('Unused in bib'), chalk.dim(stats.unused.toString())],
+        ];
+        console.log(fmt.table(['Metric', 'Count'], rows));
+        // Show missing keys
+        if (stats.missingKeys.length > 0) {
+            console.log();
+            console.log(fmt.status('error', 'Missing citations:'));
+            for (const key of stats.missingKeys) {
+                console.log(chalk.red(`  - ${key}`));
+            }
+        }
+        // Show unused (if verbose)
+        if (stats.unusedKeys.length > 0 && stats.unusedKeys.length <= 10) {
+            console.log();
+            console.log(chalk.dim('Unused bib entries:'));
+            for (const key of stats.unusedKeys.slice(0, 10)) {
+                console.log(chalk.dim(`  - ${key}`));
+            }
+            if (stats.unusedKeys.length > 10) {
+                console.log(chalk.dim(`  ... and ${stats.unusedKeys.length - 10} more`));
+            }
+        }
+        console.log();
+        if (stats.missing === 0) {
+            console.log(fmt.status('success', 'All citations valid'));
+        }
+        else {
+            console.log(fmt.status('warning', `${stats.missing} citation(s) missing from ${options.bib}`));
+            process.exit(1);
+        }
+    });
+    // ==========================================================================
+    // FIGURES command - Figure/table inventory
+    // ==========================================================================
+    program
+        .command('figures')
+        .alias('figs')
+        .description('List all figures and tables with reference counts')
+        .argument('[files...]', 'Markdown files to scan')
+        .action(async (files) => {
+        const { buildRegistry } = await import('../crossref.js');
+        // If no files specified, find all .md files
+        let mdFiles = files;
+        if (!mdFiles || mdFiles.length === 0) {
+            mdFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f));
+        }
+        // Build registry
+        const registry = buildRegistry('.');
+        // Count references in files
+        const refCounts = new Map();
+        for (const file of mdFiles) {
+            if (!fs.existsSync(file))
+                continue;
+            const text = fs.readFileSync(file, 'utf-8');
+            // Count @fig: and @tbl: references
+            const figRefs = text.matchAll(/@fig:([a-zA-Z0-9_-]+)/g);
+            for (const match of figRefs) {
+                const key = `fig:${match[1]}`;
+                refCounts.set(key, (refCounts.get(key) || 0) + 1);
+            }
+            const tblRefs = text.matchAll(/@tbl:([a-zA-Z0-9_-]+)/g);
+            for (const match of tblRefs) {
+                const key = `tbl:${match[1]}`;
+                refCounts.set(key, (refCounts.get(key) || 0) + 1);
+            }
+        }
+        console.log(fmt.header('Figure & Table Inventory'));
+        console.log();
+        // Figures
+        if (registry.figures.size > 0) {
+            const figRows = [...registry.figures.entries()].map(([label, info]) => {
+                const key = `fig:${label}`;
+                const refs = refCounts.get(key) || 0;
+                const num = info.isSupp ? `S${info.num}` : info.num.toString();
+                return [
+                    `Figure ${num}`,
+                    chalk.cyan(`@fig:${label}`),
+                    info.file,
+                    refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
+                ];
+            });
+            console.log(fmt.table(['#', 'Label', 'File', 'Refs'], figRows));
+            console.log();
+        }
+        // Tables
+        if (registry.tables.size > 0) {
+            const tblRows = [...registry.tables.entries()].map(([label, info]) => {
+                const key = `tbl:${label}`;
+                const refs = refCounts.get(key) || 0;
+                const num = info.isSupp ? `S${info.num}` : info.num.toString();
+                return [
+                    `Table ${num}`,
+                    chalk.cyan(`@tbl:${label}`),
+                    info.file,
+                    refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
+                ];
+            });
+            console.log(fmt.table(['#', 'Label', 'File', 'Refs'], tblRows));
+            console.log();
+        }
+        if (registry.figures.size === 0 && registry.tables.size === 0) {
+            console.log(chalk.dim('No figures or tables found.'));
+            console.log(chalk.dim('Add anchors like {#fig:label} to your figures.'));
+        }
+        // Warn about unreferenced
+        const unreferenced = [];
+        for (const [label] of registry.figures) {
+            if (!refCounts.get(`fig:${label}`))
+                unreferenced.push(`@fig:${label}`);
+        }
+        for (const [label] of registry.tables) {
+            if (!refCounts.get(`tbl:${label}`))
+                unreferenced.push(`@tbl:${label}`);
+        }
+        if (unreferenced.length > 0) {
+            console.log(fmt.status('warning', `${unreferenced.length} unreferenced figure(s)/table(s)`));
+        }
+    });
+    // ==========================================================================
+    // EQUATIONS command - Extract and convert equations
+    // ==========================================================================
+    program
+        .command('equations')
+        .alias('eq')
+        .description('Extract equations or convert to Word')
+        .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) => {
+        const { extractEquations, getEquationStats, createEquationsDoc, extractEquationsFromWord, getWordEquationStats } = await import('../equations.js');
+        if (action === 'from-word') {
+            // Extract equations from Word document
+            if (!input) {
+                console.error(fmt.status('error', 'Word document required'));
+                process.exit(1);
+            }
+            if (!input.endsWith('.docx')) {
+                console.error(fmt.status('error', 'Input must be a .docx file'));
+                process.exit(1);
+            }
+            const spin = fmt.spinner(`Extracting equations from ${path.basename(input)}...`).start();
+            const result = await extractEquationsFromWord(input);
+            if (!result.success) {
+                spin.error(result.error);
+                process.exit(1);
+            }
+            spin.stop();
+            console.log(fmt.header('Equations from Word'));
+            console.log();
+            if (result.equations.length === 0) {
+                console.log(chalk.dim('No equations found in document.'));
+                return;
+            }
+            const display = result.equations.filter(e => e.type === 'display');
+            const inline = result.equations.filter(e => e.type === 'inline');
+            console.log(chalk.dim(`Found ${result.equations.length} equations (${display.length} display, ${inline.length} inline)`));
+            console.log();
+            // Show equations
+            for (let i = 0; i < result.equations.length; i++) {
+                const eq = result.equations[i];
+                const typeLabel = eq.type === 'display' ? chalk.cyan('[display]') : chalk.yellow('[inline]');
+                if (eq.latex) {
+                    console.log(`${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).toString())}. ${typeLabel} ${chalk.red('[conversion failed]')}`);
+                }
+            }
+            // Optionally save to file
+            if (options.output) {
+                const latex = result.equations
+                    .filter(e => e.latex)
+                    .map((e, i) => `%% Equation ${i + 1} (${e.type})\n${e.type === 'display' ? '$$' : '$'}${e.latex}${e.type === 'display' ? '$$' : '$'}`)
+                    .join('\n\n');
+                fs.writeFileSync(options.output, latex, 'utf-8');
+                console.log();
+                console.log(fmt.status('success', `Saved ${result.equations.filter(e => e.latex).length} equations to ${options.output}`));
+            }
+        }
+        else if (action === 'list') {
+            // List equations in all section files
+            const mdFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f));
+            const stats = getEquationStats(mdFiles);
+            console.log(fmt.header('Equations'));
+            console.log();
+            if (stats.byFile.length === 0) {
+                console.log(chalk.dim('No equations found.'));
+                return;
+            }
+            const rows = stats.byFile.map(f => [
+                f.file,
+                f.display > 0 ? chalk.cyan(f.display.toString()) : chalk.dim('-'),
+                f.inline > 0 ? chalk.yellow(f.inline.toString()) : chalk.dim('-'),
+            ]);
+            rows.push([
+                chalk.bold('Total'),
+                chalk.bold.cyan(stats.display.toString()),
+                chalk.bold.yellow(stats.inline.toString()),
+            ]);
+            console.log(fmt.table(['File', 'Display', 'Inline'], rows));
+        }
+        else if (action === 'extract') {
+            if (!input) {
+                console.error(fmt.status('error', 'Input file required'));
+                process.exit(1);
+            }
+            const output = options.output || input.replace('.md', '-equations.md');
+            const result = await createEquationsDoc(input, output);
+            if (result.success) {
+                console.log(fmt.status('success', result.message));
+                console.log(chalk.dim(`  ${result.stats.display} display, ${result.stats.inline} inline equations`));
+            }
+            else {
+                console.error(fmt.status('error', result.message));
+                process.exit(1);
+            }
+        }
+        else if (action === 'convert') {
+            if (!input) {
+                console.error(fmt.status('error', 'Input file required'));
+                process.exit(1);
+            }
+            const output = options.output || input.replace('.md', '.docx');
+            const spin = fmt.spinner(`Converting ${path.basename(input)} to Word...`).start();
+            try {
+                const { exec } = await import('child_process');
+                const { promisify } = await import('util');
+                const execAsync = promisify(exec);
+                await execAsync(`pandoc "${input}" -o "${output}" --mathml`);
+                spin.success(`Created ${output}`);
+            }
+            catch (err) {
+                const error = err;
+                spin.error(error.message);
+                process.exit(1);
+            }
+        }
+        else {
+            console.error(fmt.status('error', `Unknown action: ${action}`));
+            console.log(chalk.dim('Actions: list, extract, convert, from-word'));
+            process.exit(1);
+        }
+    });
+    // ==========================================================================
+    // PDF-COMMENTS command - Extract comments from PDF
+    // ==========================================================================
+    program
+        .command('pdf-comments')
+        .alias('pdf')
+        .description('Extract and manage comments from annotated PDFs')
+        .argument('<pdf>', 'PDF file with annotations')
+        .option('-a, --append <file>', 'Append comments to markdown file')
+        .option('--json', 'Output as JSON')
+        .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) => {
+        if (!fs.existsSync(pdf)) {
+            console.error(fmt.status('error', `File not found: ${pdf}`));
+            process.exit(1);
+        }
+        if (!pdf.toLowerCase().endsWith('.pdf')) {
+            console.error(fmt.status('error', 'File must be a PDF'));
+            process.exit(1);
+        }
+        const { extractPdfComments, extractPdfAnnotationsWithText, formatPdfComments, getPdfCommentStats, insertPdfCommentsIntoMarkdown, formatAnnotationWithText, } = await import('../pdf-import.js');
+        const spin = fmt.spinner(`Extracting comments from ${path.basename(pdf)}...`).start();
+        try {
+            let comments;
+            if (options.withText) {
+                // Use the new text extraction feature
+                const annotations = await extractPdfAnnotationsWithText(pdf);
+                spin.stop();
+                if (annotations.length === 0) {
+                    console.log(fmt.status('info', 'No annotations found in PDF.'));
+                    return;
+                }
+                // Convert to comment format with highlighted text
+                comments = annotations.map(a => ({
+                    author: a.author || 'Reviewer',
+                    text: a.highlightedText
+                        ? `"${a.highlightedText}"${a.contents ? ' → ' + a.contents : ''}`
+                        : a.contents,
+                    page: a.page,
+                    type: a.type,
+                    date: a.date,
+                    highlightedText: a.highlightedText,
+                })).filter(c => c.text);
+            }
+            else {
+                comments = await extractPdfComments(pdf);
+                spin.stop();
+            }
+            if (comments.length === 0) {
+                console.log(fmt.status('info', 'No comments found in PDF.'));
+                return;
+            }
+            const stats = getPdfCommentStats(comments);
+            // JSON output
+            if (options.json) {
+                console.log(JSON.stringify({ comments, stats }, null, 2));
+                return;
+            }
+            // Append to markdown file
+            if (options.append) {
+                if (!fs.existsSync(options.append)) {
+                    console.error(fmt.status('error', `Markdown file not found: ${options.append}`));
+                    process.exit(1);
+                }
+                const markdown = fs.readFileSync(options.append, 'utf-8');
+                const updated = insertPdfCommentsIntoMarkdown(markdown, comments);
+                fs.writeFileSync(options.append, updated, 'utf-8');
+                console.log(fmt.status('success', `Added ${comments.length} comments to ${options.append}`));
+                return;
+            }
+            // Display comments
+            console.log(fmt.header(`PDF Comments: ${path.basename(pdf)}`));
+            console.log();
+            if (options.byAuthor) {
+                // Group by author
+                const byAuthor = {};
+                for (const c of comments) {
+                    const author = c.author || 'Unknown';
+                    if (!byAuthor[author])
+                        byAuthor[author] = [];
+                    byAuthor[author].push(c);
+                }
+                for (const [author, authorComments] of Object.entries(byAuthor)) {
+                    console.log(chalk.bold(`${author} (${authorComments.length}):`));
+                    for (const c of authorComments) {
+                        if (c.highlightedText) {
+                            console.log(`  [p.${c.page}] ${chalk.yellow(`"${c.highlightedText}"`)}${c.text !== c.highlightedText ? ` → ${c.text.replace(`"${c.highlightedText}" → `, '')}` : ''}`);
+                        }
+                        else {
+                            console.log(`  [p.${c.page}] ${c.text}`);
+                        }
+                    }
+                    console.log();
+                }
+            }
+            else {
+                // Default: by page
+                if (options.withText) {
+                    let currentPage = 0;
+                    for (const c of comments) {
+                        if (c.page !== currentPage) {
+                            if (currentPage > 0)
+                                console.log();
+                            console.log(`Page ${c.page}:`);
+                            currentPage = c.page;
+                        }
+                        if (c.highlightedText) {
+                            console.log(`  ${chalk.yellow(`"${c.highlightedText}"`)} → ${c.text.replace(`"${c.highlightedText}" → `, '')}`);
+                        }
+                        else {
+                            console.log(`  ${c.text}`);
+                        }
+                    }
+                    console.log();
+                }
+                else {
+                    console.log(formatPdfComments(comments));
+                    console.log();
+                }
+            }
+            // Summary
+            const authorList = Object.entries(stats.byAuthor)
+                .map(([author, count]) => `${author} (${count})`)
+                .join(', ');
+            console.log(chalk.dim(`Total: ${stats.total} comments from ${authorList}`));
+            console.log();
+            if (!options.withText) {
+                console.log(chalk.dim(`Tip: Use --with-text to extract the highlighted text content`));
+            }
+            console.log(chalk.dim(`Tip: Use --append <file.md> to add comments to your markdown`));
+        }
+        catch (err) {
+            spin.stop();
+            const error = err;
+            console.error(fmt.status('error', `Failed to extract PDF comments: ${error.message}`));
+            if (process.env.DEBUG)
+                console.error(error.stack);
+            process.exit(1);
+        }
+    });
+}
+//# sourceMappingURL=citations.js.map

package/dist/lib/commands/citations.js.map

@@ -0,0 +1 @@
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package/dist/lib/commands/comments.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Comment commands: comments, resolve, next, prev, first, last, todo, accept, reject, reply
+ *
+ * Commands for viewing, navigating, and managing reviewer comments and track changes.
+ */
+import { Command } from 'commander';
+/**
+ * Register comment commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=comments.d.ts.map

package/dist/lib/commands/comments.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"comments.d.ts","sourceRoot":"","sources":["../../../lib/commands/comments.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkJpC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAm4B/C"}