docrev 0.9.5 → 0.9.7

package/dist/lib/commands/project-info.js

@@ -0,0 +1,187 @@
+/**
+ * Project information commands: word-count (wc), stats, search
+ *
+ * Read-only queries about the project state.
+ */
+import { chalk, fs, fmt, loadBuildConfig, getComments, countWords, } from './context.js';
+/**
+ * Register project-info commands with the program
+ */
+export function register(program) {
+    // ==========================================================================
+    // WORD-COUNT command - Per-section word counts
+    // ==========================================================================
+    program
+        .command('word-count')
+        .alias('wc')
+        .description('Show word counts per section')
+        .option('-l, --limit <number>', 'Warn if total exceeds limit', parseInt)
+        .option('-j, --journal <name>', 'Use journal word limit')
+        .action(async (options) => {
+        let config = {};
+        try {
+            config = loadBuildConfig('.') || {};
+        }
+        catch {
+            // Not in a rev project, that's ok
+        }
+        const sections = config.sections || [];
+        if (sections.length === 0) {
+            // Try to find .md files
+            const mdFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+            if (mdFiles.length === 0) {
+                console.error(chalk.red('No section files found. Run from a rev project directory.'));
+                process.exit(1);
+            }
+            sections.push(...mdFiles);
+        }
+        let total = 0;
+        const rows = [];
+        for (const section of sections) {
+            if (!fs.existsSync(section))
+                continue;
+            const text = fs.readFileSync(section, 'utf-8');
+            const words = countWords(text);
+            total += words;
+            rows.push([section, words.toLocaleString()]);
+        }
+        rows.push(['', '']);
+        rows.push([chalk.bold('Total'), chalk.bold(total.toLocaleString())]);
+        console.log(fmt.header('Word Count'));
+        console.log(fmt.table(['Section', 'Words'], rows));
+        // Check limit
+        let limit = options.limit;
+        if (options.journal) {
+            const { getJournalProfile } = await import('../journals.js');
+            const profile = getJournalProfile(options.journal);
+            if (profile?.requirements?.wordLimit?.main) {
+                limit = profile.requirements.wordLimit.main;
+                console.log(chalk.dim(`\nUsing ${profile.name} word limit: ${limit.toLocaleString()}`));
+            }
+        }
+        if (limit && total > limit) {
+            console.log(chalk.red(`\n⚠ Over limit by ${(total - limit).toLocaleString()} words`));
+        }
+        else if (limit) {
+            console.log(chalk.green(`\n✓ Within limit (${(limit - total).toLocaleString()} words remaining)`));
+        }
+    });
+    // ==========================================================================
+    // STATS command - Project dashboard
+    // ==========================================================================
+    program
+        .command('stats')
+        .description('Show project statistics dashboard')
+        .action(async (_options) => {
+        let config = {};
+        try {
+            config = loadBuildConfig('.') || {};
+        }
+        catch {
+            // Not in a rev project, that's ok
+        }
+        let sections = config.sections || [];
+        if (sections.length === 0) {
+            sections = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+        }
+        let totalWords = 0;
+        let totalFigures = 0;
+        let totalTables = 0;
+        let totalComments = 0;
+        let pendingComments = 0;
+        const citations = new Set();
+        for (const section of sections) {
+            if (!fs.existsSync(section))
+                continue;
+            const text = fs.readFileSync(section, 'utf-8');
+            totalWords += countWords(text);
+            totalFigures += (text.match(/!\[.*?\]\(.*?\)/g) || []).length;
+            totalTables += (text.match(/^\|[^|]+\|/gm) || []).length / 5; // Approximate
+            const comments = getComments(text);
+            totalComments += comments.length;
+            pendingComments += comments.filter(c => !c.resolved).length;
+            const cites = text.match(/@(\w+)(?![:\w])/g) || [];
+            cites.forEach(c => citations.add(c.slice(1)));
+        }
+        console.log(fmt.header('Project Statistics'));
+        console.log();
+        const stats = [
+            ['Sections', sections.length],
+            ['Words', totalWords.toLocaleString()],
+            ['Figures', Math.round(totalFigures)],
+            ['Tables', Math.round(totalTables)],
+            ['Citations', citations.size],
+            ['Comments', `${totalComments} (${pendingComments} pending)`],
+        ];
+        for (const [label, value] of stats) {
+            console.log(`  ${chalk.dim(label.padEnd(12))} ${chalk.bold(value)}`);
+        }
+        // Bibliography stats
+        const bibPath = config.bibliography || 'references.bib';
+        if (fs.existsSync(bibPath)) {
+            const bibContent = fs.readFileSync(bibPath, 'utf-8');
+            const bibEntries = (bibContent.match(/@\w+\s*\{/g) || []).length;
+            console.log(`  ${chalk.dim('Bib entries'.padEnd(12))} ${chalk.bold(bibEntries)}`);
+        }
+        console.log();
+    });
+    // ==========================================================================
+    // SEARCH command - Search across section files
+    // ==========================================================================
+    program
+        .command('search')
+        .description('Search across all section files')
+        .argument('<query>', 'Search query (supports regex)')
+        .option('-i, --ignore-case', 'Case-insensitive search')
+        .option('-c, --context <lines>', 'Show context lines', parseInt, 1)
+        .action((query, options) => {
+        let config = {};
+        try {
+            config = loadBuildConfig('.') || {};
+        }
+        catch {
+            // Not in a rev project, that's ok
+        }
+        let sections = config.sections || [];
+        if (sections.length === 0) {
+            sections = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f));
+        }
+        const flags = options.ignoreCase ? 'gi' : 'g';
+        let pattern;
+        try {
+            pattern = new RegExp(query, flags);
+        }
+        catch {
+            pattern = new RegExp(query.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'), flags);
+        }
+        let totalMatches = 0;
+        for (const section of sections) {
+            if (!fs.existsSync(section))
+                continue;
+            const text = fs.readFileSync(section, 'utf-8');
+            const lines = text.split('\n');
+            const matches = [];
+            for (let i = 0; i < lines.length; i++) {
+                if (pattern.test(lines[i])) {
+                    matches.push({ line: i + 1, text: lines[i] });
+                    pattern.lastIndex = 0;
+                }
+            }
+            if (matches.length > 0) {
+                console.log(chalk.cyan.bold(`\n${section}`));
+                for (const match of matches) {
+                    const highlighted = match.text.replace(pattern, (m) => chalk.yellow.bold(m));
+                    console.log(`  ${chalk.dim(match.line + ':')} ${highlighted}`);
+                }
+                totalMatches += matches.length;
+            }
+        }
+        if (totalMatches === 0) {
+            console.log(chalk.yellow(`No matches found for "${query}"`));
+        }
+        else {
+            console.log(chalk.dim(`\n${totalMatches} match${totalMatches === 1 ? '' : 'es'} found`));
+        }
+    });
+}
+//# sourceMappingURL=project-info.js.map

package/dist/lib/commands/project-info.js.map

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

@@ -0,0 +1,11 @@
+/**
+ * Quality commands: lint, grammar, check
+ *
+ * Commands for checking project quality before submission.
+ */
+import type { Command } from 'commander';
+/**
+ * Register quality commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=quality.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"quality.d.ts","sourceRoot":"","sources":["../../../lib/commands/quality.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA8EzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA6a/C"}

package/dist/lib/commands/quality.js

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+/**
+ * Quality commands: lint, grammar, check
+ *
+ * Commands for checking project quality before submission.
+ */
+import { chalk, fs, fmt, loadBuildConfig, getComments, } from './context.js';
+/**
+ * Register quality commands with the program
+ */
+export function register(program) {
+    // ==========================================================================
+    // LINT command - Check for common issues
+    // ==========================================================================
+    program
+        .command('lint')
+        .description('Check for common issues in the project')
+        .option('--fix', 'Auto-fix issues where possible')
+        .action(async (_options) => {
+        let config = {};
+        try {
+            config = loadBuildConfig('.') || {};
+        }
+        catch {
+            // Not in a rev project, that's ok
+        }
+        let sections = config.sections || [];
+        if (sections.length === 0) {
+            sections = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+        }
+        const issues = [];
+        const warnings = [];
+        // Collect all content
+        let allText = '';
+        for (const section of sections) {
+            if (fs.existsSync(section)) {
+                allText += fs.readFileSync(section, 'utf-8') + '\n';
+            }
+        }
+        // Check 1: Broken cross-references
+        const figAnchors = new Set();
+        const tblAnchors = new Set();
+        const eqAnchors = new Set();
+        const anchorPattern = /\{#(fig|tbl|eq):([^}]+)\}/g;
+        let match;
+        while ((match = anchorPattern.exec(allText)) !== null) {
+            if (match[1] === 'fig')
+                figAnchors.add(match[2]);
+            else if (match[1] === 'tbl')
+                tblAnchors.add(match[2]);
+            else if (match[1] === 'eq')
+                eqAnchors.add(match[2]);
+        }
+        const refPattern = /@(fig|tbl|eq):([a-zA-Z0-9_-]+)/g;
+        while ((match = refPattern.exec(allText)) !== null) {
+            const type = match[1];
+            const label = match[2];
+            const anchors = type === 'fig' ? figAnchors : type === 'tbl' ? tblAnchors : eqAnchors;
+            if (!anchors.has(label)) {
+                issues.push({
+                    type: 'error',
+                    message: `Broken reference: @${type}:${label}`,
+                    fix: null
+                });
+            }
+        }
+        // Check 2: Orphaned figures
+        for (const label of figAnchors) {
+            if (!allText.includes(`@fig:${label}`)) {
+                warnings.push({
+                    type: 'warning',
+                    message: `Unreferenced figure: {#fig:${label}}`,
+                });
+            }
+        }
+        // Check 3: Missing citations
+        const bibPath = config.bibliography || 'references.bib';
+        if (fs.existsSync(bibPath)) {
+            const bibContent = fs.readFileSync(bibPath, 'utf-8');
+            const bibKeys = new Set();
+            const bibPattern = /@\w+\s*\{\s*([^,]+)/g;
+            while ((match = bibPattern.exec(bibContent)) !== null) {
+                bibKeys.add(match[1].trim());
+            }
+            const citePattern = /@([a-zA-Z][a-zA-Z0-9_-]*)(?![:\w])/g;
+            while ((match = citePattern.exec(allText)) !== null) {
+                const key = match[1];
+                if (!bibKeys.has(key) && !['fig', 'tbl', 'eq'].includes(key)) {
+                    issues.push({
+                        type: 'error',
+                        message: `Missing citation: @${key}`,
+                    });
+                }
+            }
+        }
+        // Check 4: Unresolved comments
+        const comments = getComments(allText);
+        const pending = comments.filter(c => !c.resolved);
+        if (pending.length > 0) {
+            warnings.push({
+                type: 'warning',
+                message: `${pending.length} unresolved comment${pending.length === 1 ? '' : 's'}`,
+            });
+        }
+        // Check 5: Empty sections
+        for (const section of sections) {
+            if (fs.existsSync(section)) {
+                const content = fs.readFileSync(section, 'utf-8').trim();
+                if (content.length < 50) {
+                    warnings.push({
+                        type: 'warning',
+                        message: `Section appears empty: ${section}`,
+                    });
+                }
+            }
+        }
+        // Output results
+        console.log(fmt.header('Lint Results'));
+        console.log();
+        if (issues.length === 0 && warnings.length === 0) {
+            console.log(chalk.green('✓ No issues found'));
+            return;
+        }
+        for (const issue of issues) {
+            console.log(chalk.red(`  ✗ ${issue.message}`));
+        }
+        for (const warning of warnings) {
+            console.log(chalk.yellow(`  ⚠ ${warning.message}`));
+        }
+        console.log();
+        console.log(chalk.dim(`${issues.length} error${issues.length === 1 ? '' : 's'}, ${warnings.length} warning${warnings.length === 1 ? '' : 's'}`));
+        if (issues.length > 0) {
+            process.exit(1);
+        }
+    });
+    // ==========================================================================
+    // GRAMMAR command - Check grammar and style
+    // ==========================================================================
+    program
+        .command('grammar')
+        .description('Check grammar and style issues')
+        .argument('[files...]', 'Markdown files to check')
+        .option('--learn <word>', 'Add word to custom dictionary')
+        .option('--forget <word>', 'Remove word from custom dictionary')
+        .option('--list', 'List custom dictionary words')
+        .option('--rules', 'List available grammar rules')
+        .option('--no-scientific', 'Disable scientific writing rules')
+        .option('-s, --severity <level>', 'Minimum severity: error, warning, info', 'info')
+        .action(async (files, options) => {
+        const { checkGrammar, getGrammarSummary, loadDictionary, addToDictionary, removeFromDictionary, listRules, } = await import('../grammar.js');
+        // Handle dictionary management
+        if (options.learn) {
+            const added = addToDictionary(options.learn);
+            if (added) {
+                console.log(fmt.status('success', `Added "${options.learn}" to dictionary`));
+            }
+            else {
+                console.log(chalk.dim(`"${options.learn}" already in dictionary`));
+            }
+            return;
+        }
+        if (options.forget) {
+            const removed = removeFromDictionary(options.forget);
+            if (removed) {
+                console.log(fmt.status('success', `Removed "${options.forget}" from dictionary`));
+            }
+            else {
+                console.log(chalk.yellow(`"${options.forget}" not in dictionary`));
+            }
+            return;
+        }
+        if (options.list) {
+            const words = loadDictionary();
+            console.log(fmt.header('Custom Dictionary'));
+            console.log();
+            if (words.size === 0) {
+                console.log(chalk.dim('  No custom words defined'));
+                console.log(chalk.dim('  Use --learn <word> to add words'));
+            }
+            else {
+                const sorted = [...words].sort();
+                for (const word of sorted) {
+                    console.log(`  ${word}`);
+                }
+                console.log();
+                console.log(chalk.dim(`${words.size} word(s)`));
+            }
+            return;
+        }
+        if (options.rules) {
+            const rules = listRules(options.scientific);
+            console.log(fmt.header('Grammar Rules'));
+            console.log();
+            for (const rule of rules) {
+                const icon = rule.severity === 'error' ? chalk.red('●') :
+                    rule.severity === 'warning' ? chalk.yellow('●') :
+                        chalk.blue('●');
+                console.log(`  ${icon} ${chalk.bold(rule.id)}`);
+                console.log(chalk.dim(`     ${rule.message}`));
+            }
+            return;
+        }
+        // Get files to check
+        let mdFiles = files;
+        if (!mdFiles || mdFiles.length === 0) {
+            let config = {};
+            try {
+                config = loadBuildConfig('.') || {};
+            }
+            catch {
+                // Not in a rev project
+            }
+            mdFiles = config.sections || [];
+            if (mdFiles.length === 0) {
+                mdFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+            }
+        }
+        if (mdFiles.length === 0) {
+            console.error(chalk.red('No markdown files found'));
+            process.exit(1);
+        }
+        console.log(fmt.header('Grammar Check'));
+        console.log();
+        const severityLevels = { error: 3, warning: 2, info: 1 };
+        const minSeverity = severityLevels[options.severity || 'info'] || 1;
+        let allIssues = [];
+        for (const file of mdFiles) {
+            if (!fs.existsSync(file))
+                continue;
+            const text = fs.readFileSync(file, 'utf-8');
+            const issues = checkGrammar(text, { scientific: options.scientific });
+            // Filter by severity
+            const filtered = issues.filter((i) => severityLevels[i.severity] >= minSeverity);
+            if (filtered.length > 0) {
+                console.log(chalk.cyan.bold(file));
+                for (const issue of filtered) {
+                    const icon = issue.severity === 'error' ? chalk.red('●') :
+                        issue.severity === 'warning' ? chalk.yellow('●') :
+                            chalk.blue('●');
+                    console.log(`  ${chalk.dim(`L${issue.line}:`)} ${icon} ${issue.message}`);
+                    console.log(chalk.dim(`      "${issue.match}" in: ${issue.context.slice(0, 60)}...`));
+                }
+                console.log();
+                allIssues.push(...filtered.map(i => ({ ...i, file })));
+            }
+        }
+        const summary = getGrammarSummary(allIssues);
+        if (summary.total === 0) {
+            console.log(chalk.green('✓ No issues found'));
+        }
+        else {
+            console.log(chalk.dim(`Found ${summary.total} issue(s): ${summary.errors} errors, ${summary.warnings} warnings, ${summary.info} info`));
+            console.log();
+            console.log(chalk.dim('Tip: Use --learn <word> to add words to dictionary'));
+        }
+    });
+    // ==========================================================================
+    // CHECK command - Pre-submission check
+    // ==========================================================================
+    program
+        .command('check')
+        .description('Run all checks before submission (lint + grammar + citations)')
+        .option('--fix', 'Auto-fix issues where possible')
+        .option('-s, --severity <level>', 'Minimum grammar severity', 'warning')
+        .action(async (options) => {
+        const { validateCitations } = await import('../citations.js');
+        const { checkGrammar, getGrammarSummary } = await import('../grammar.js');
+        console.log(fmt.header('Pre-Submission Check'));
+        console.log();
+        let hasErrors = false;
+        let totalIssues = 0;
+        // 1. Run lint
+        console.log(chalk.cyan.bold('1. Linting...'));
+        let config = {};
+        try {
+            config = loadBuildConfig('.') || {};
+        }
+        catch {
+            // Not in a rev project
+        }
+        let sections = config.sections || [];
+        if (sections.length === 0) {
+            sections = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+        }
+        const lintIssues = [];
+        const lintWarnings = [];
+        for (const file of sections) {
+            if (!fs.existsSync(file))
+                continue;
+            const content = fs.readFileSync(file, 'utf-8');
+            // Check for broken cross-references
+            const refs = content.match(/@(fig|tbl|eq|sec):\w+/g) || [];
+            const anchors = content.match(/\{#(fig|tbl|eq|sec):[^}]+\}/g) || [];
+            const anchorLabels = anchors.map(a => a.match(/#([^}]+)/)[1]);
+            for (const ref of refs) {
+                const label = ref.slice(1);
+                if (!anchorLabels.includes(label)) {
+                    lintIssues.push({ file, message: `Broken reference: ${ref}` });
+                }
+            }
+            // Check for unresolved comments
+            const unresolvedComments = (content.match(/\{>>[^<]*<<\}/g) || [])
+                .filter(c => !c.includes('[RESOLVED]'));
+            if (unresolvedComments.length > 0) {
+                lintWarnings.push({ file, message: `${unresolvedComments.length} unresolved comment(s)` });
+            }
+        }
+        if (lintIssues.length > 0) {
+            for (const issue of lintIssues) {
+                console.log(chalk.red(`   ✗ ${issue.file}: ${issue.message}`));
+            }
+            hasErrors = true;
+            totalIssues += lintIssues.length;
+        }
+        for (const warning of lintWarnings) {
+            console.log(chalk.yellow(`   ⚠ ${warning.file}: ${warning.message}`));
+            totalIssues++;
+        }
+        if (lintIssues.length === 0 && lintWarnings.length === 0) {
+            console.log(chalk.green('   ✓ No lint issues'));
+        }
+        console.log();
+        // 2. Run grammar check
+        console.log(chalk.cyan.bold('2. Grammar check...'));
+        const severityLevels = { error: 3, warning: 2, info: 1 };
+        const minSeverity = severityLevels[options.severity || 'warning'] || 2;
+        let grammarIssues = [];
+        for (const file of sections) {
+            if (!fs.existsSync(file))
+                continue;
+            const text = fs.readFileSync(file, 'utf-8');
+            const issues = checkGrammar(text, { scientific: true });
+            const filtered = issues.filter((i) => severityLevels[i.severity] >= minSeverity);
+            grammarIssues.push(...filtered.map(i => ({ ...i, file })));
+        }
+        const grammarSummary = getGrammarSummary(grammarIssues);
+        if (grammarSummary.errors > 0) {
+            hasErrors = true;
+        }
+        totalIssues += grammarSummary.total;
+        if (grammarSummary.total > 0) {
+            console.log(chalk.yellow(`   ⚠ ${grammarSummary.total} grammar issue(s): ${grammarSummary.errors} errors, ${grammarSummary.warnings} warnings`));
+        }
+        else {
+            console.log(chalk.green('   ✓ No grammar issues'));
+        }
+        console.log();
+        // 3. Run citation check
+        console.log(chalk.cyan.bold('3. Citation check...'));
+        const bibFile = config.bibliography || 'references.bib';
+        if (fs.existsSync(bibFile)) {
+            const existingSections = sections.filter(f => fs.existsSync(f));
+            const result = validateCitations(existingSections, bibFile);
+            if (result.missing.length > 0) {
+                console.log(chalk.red(`   ✗ ${result.missing.length} missing citation(s): ${result.missing.slice(0, 3).join(', ')}${result.missing.length > 3 ? '...' : ''}`));
+                hasErrors = true;
+                totalIssues += result.missing.length;
+            }
+            if (result.unused.length > 0) {
+                console.log(chalk.yellow(`   ⚠ ${result.unused.length} unused citation(s)`));
+                totalIssues += result.unused.length;
+            }
+            if (result.missing.length === 0 && result.unused.length === 0) {
+                console.log(chalk.green('   ✓ All citations valid'));
+            }
+        }
+        else {
+            console.log(chalk.dim('   - No bibliography file found'));
+        }
+        console.log();
+        // Summary
+        console.log(chalk.bold('Summary'));
+        if (hasErrors) {
+            console.log(chalk.red(`   ${totalIssues} issue(s) found. Please fix before submission.`));
+            process.exit(1);
+        }
+        else if (totalIssues > 0) {
+            console.log(chalk.yellow(`   ${totalIssues} warning(s). Review before submission.`));
+        }
+        else {
+            console.log(chalk.green('   ✓ All checks passed! Ready for submission.'));
+        }
+    });
+}
+//# sourceMappingURL=quality.js.map

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

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

@@ -0,0 +1,22 @@
+/**
+ * Compute section boundaries in a DOCX from its real heading paragraphs.
+ *
+ * Given the configured `sections.yaml` and the headings extracted via
+ * `extractHeadings()`, return one boundary per section file with text
+ * positions in the same coordinate system as `CommentAnchorData.docPosition`.
+ *
+ * Matching is by heading text (primary header + aliases, case-insensitive).
+ * This replaces the older keyword-search-in-body-text approach which would
+ * pick up section names that happen to appear inside prose ("results across
+ * countries") or in structured-abstract labels where paragraph boundaries
+ * are lost in concatenation.
+ */
+import type { DocxHeading } from '../word-extraction.js';
+import type { SectionConfig } from '../types.js';
+export interface SectionBoundary {
+    file: string;
+    start: number;
+    end: number;
+}
+export declare function computeSectionBoundaries(sections: Record<string, SectionConfig>, headings: DocxHeading[]): SectionBoundary[];
+//# sourceMappingURL=section-boundaries.d.ts.map

package/dist/lib/commands/section-boundaries.d.ts.map

@@ -0,0 +1 @@
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