docrev 0.8.1 → 0.8.5

package/dist/lib/commands/response.js

@@ -0,0 +1,317 @@
+/**
+ * Response commands: response, validate, profiles, anonymize
+ *
+ * Commands for generating reviewer responses and validating manuscripts.
+ */
+import { chalk, fs, path, fmt, collectComments, generateResponseLetter, groupByReviewer, getUserName, } from './context.js';
+/**
+ * Register response commands with the program
+ */
+export function register(program) {
+    // ==========================================================================
+    // RESPONSE command - Generate response letter for reviewers
+    // ==========================================================================
+    program
+        .command('response')
+        .description('Generate response letter from reviewer comments')
+        .argument('[files...]', 'Markdown files to process (default: all section files)')
+        .option('-o, --output <file>', 'Output file (default: response-letter.md)')
+        .option('-a, --author <name>', 'Author name for identifying replies')
+        .option('--no-context', 'Omit context snippets')
+        .option('--no-location', 'Omit file:line references')
+        .action(async (files, options) => {
+        let mdFiles = files;
+        if (!mdFiles || mdFiles.length === 0) {
+            const allFiles = fs.readdirSync('.').filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f));
+            mdFiles = allFiles;
+        }
+        if (mdFiles.length === 0) {
+            console.error(fmt.status('error', 'No markdown files found'));
+            process.exit(1);
+        }
+        const spin = fmt.spinner('Collecting comments...').start();
+        const comments = collectComments(mdFiles);
+        spin.stop();
+        if (comments.length === 0) {
+            console.log(fmt.status('info', 'No comments found in files'));
+            return;
+        }
+        const letter = generateResponseLetter(comments, {
+            authorName: options.author || getUserName() || 'Author',
+            includeContext: options.context !== false,
+            includeLocation: options.location !== false,
+        });
+        const outputPath = options.output || 'response-letter.md';
+        fs.writeFileSync(outputPath, letter, 'utf-8');
+        const grouped = groupByReviewer(comments);
+        const reviewers = [...grouped.keys()].filter(r => !r.toLowerCase().includes('claude') &&
+            r.toLowerCase() !== (options.author || '').toLowerCase());
+        console.log(fmt.header('Response Letter Generated'));
+        console.log();
+        const rows = reviewers.map(r => [r, grouped.get(r).length.toString()]);
+        console.log(fmt.table(['Reviewer', 'Comments'], rows));
+        console.log();
+        console.log(fmt.status('success', `Created ${outputPath}`));
+    });
+    // ==========================================================================
+    // VALIDATE command - Check manuscript against journal requirements
+    // ==========================================================================
+    program
+        .command('validate')
+        .description('Validate manuscript against journal requirements')
+        .argument('[files...]', 'Markdown files to validate (default: all section files)')
+        .option('-j, --journal <name>', 'Journal profile (e.g., nature, plos-one, science)')
+        .option('--list', 'List available journal profiles')
+        .action(async (files, options) => {
+        const { listJournals, validateProject, getJournalProfile } = await import('../journals.js');
+        if (options.list) {
+            console.log(fmt.header('Available Journal Profiles'));
+            console.log();
+            const journals = listJournals();
+            const builtIn = journals.filter(j => !j.custom);
+            const custom = journals.filter(j => j.custom);
+            for (const j of builtIn) {
+                console.log(`  ${chalk.bold(j.id)} - ${j.name}`);
+                if (j.url)
+                    console.log(chalk.dim(`    ${j.url}`));
+            }
+            if (custom.length > 0) {
+                console.log();
+                console.log(chalk.cyan('  Custom Profiles:'));
+                for (const j of custom) {
+                    console.log(`  ${chalk.bold(j.id)} - ${j.name} ${chalk.cyan('[custom]')}`);
+                    if (j.url)
+                        console.log(chalk.dim(`    ${j.url}`));
+                }
+            }
+            console.log();
+            console.log(chalk.dim('Usage: rev validate --journal <name>'));
+            console.log(chalk.dim('Manage custom profiles: rev profiles'));
+            return;
+        }
+        if (!options.journal) {
+            console.error(fmt.status('error', 'Please specify a journal with --journal <name>'));
+            console.error(chalk.dim('Use --list to see available profiles'));
+            process.exit(1);
+        }
+        const profile = getJournalProfile(options.journal);
+        if (!profile) {
+            console.error(fmt.status('error', `Unknown journal: ${options.journal}`));
+            console.error(chalk.dim('Use --list to see available profiles'));
+            process.exit(1);
+        }
+        let mdFiles = files;
+        if (!mdFiles || 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(fmt.status('error', 'No markdown files found'));
+            process.exit(1);
+        }
+        console.log(fmt.header(`Validating for ${profile.name}`));
+        console.log(chalk.dim(`  ${profile.url}`));
+        console.log();
+        const result = validateProject(mdFiles, options.journal);
+        if (result.stats) {
+            console.log(chalk.cyan('Manuscript Stats:'));
+            console.log(fmt.table(['Metric', 'Value'], [
+                ['Word count', result.stats.wordCount.toString()],
+                ['Abstract', `${result.stats.abstractWords} words`],
+                ['Title', `${result.stats.titleChars} chars`],
+                ['Figures', result.stats.figures.toString()],
+                ['Tables', result.stats.tables.toString()],
+                ['References', result.stats.references.toString()],
+            ]));
+            console.log();
+        }
+        if (result.errors.length > 0) {
+            console.log(chalk.red('Errors:'));
+            for (const err of result.errors) {
+                console.log(chalk.red(`  ✗ ${err}`));
+            }
+            console.log();
+        }
+        if (result.warnings.length > 0) {
+            console.log(chalk.yellow('Warnings:'));
+            for (const warn of result.warnings) {
+                console.log(chalk.yellow(`  ⚠ ${warn}`));
+            }
+            console.log();
+        }
+        if (result.valid) {
+            console.log(fmt.status('success', `Manuscript meets ${profile.name} requirements`));
+        }
+        else {
+            console.log(fmt.status('error', `Manuscript has ${result.errors.length} error(s)`));
+            process.exit(1);
+        }
+    });
+    // ==========================================================================
+    // PROFILES command - Manage custom journal profiles
+    // ==========================================================================
+    program
+        .command('profiles')
+        .description('Manage custom journal profiles')
+        .option('--list', 'List all custom profiles')
+        .option('--new <name>', 'Create a new profile template')
+        .option('--project', 'Create profile in project directory (with --new)')
+        .option('--dirs', 'Show profile directory locations')
+        .action(async (options) => {
+        const { listCustomProfiles, saveProfileTemplate, getPluginDirs, } = await import('../plugins.js');
+        const { listJournals } = await import('../journals.js');
+        if (options.dirs) {
+            const dirs = getPluginDirs();
+            console.log(fmt.header('Profile Directories'));
+            console.log();
+            console.log(`  User:    ${dirs.user}`);
+            console.log(chalk.dim(`           ${dirs.userExists ? 'exists' : 'not created'}`));
+            console.log();
+            console.log(`  Project: ${dirs.project}`);
+            console.log(chalk.dim(`           ${dirs.projectExists ? 'exists' : 'not created'}`));
+            console.log();
+            console.log(chalk.dim('Use --new <name> to create a profile template'));
+            return;
+        }
+        if (options.new) {
+            try {
+                const filePath = saveProfileTemplate(options.new, options.project);
+                console.log(fmt.status('success', `Created profile template: ${filePath}`));
+                console.log(chalk.dim('Edit the file to customize journal requirements'));
+            }
+            catch (err) {
+                console.error(fmt.status('error', err.message));
+                process.exit(1);
+            }
+            return;
+        }
+        console.log(fmt.header('Custom Journal Profiles'));
+        console.log();
+        const customProfiles = listCustomProfiles();
+        if (customProfiles.length === 0) {
+            console.log(chalk.dim('  No custom profiles found'));
+            console.log();
+            console.log(chalk.dim('  Create one with: rev profiles --new "Journal Name"'));
+            console.log();
+            const dirs = getPluginDirs();
+            console.log(chalk.dim(`  User profiles:    ${dirs.user}`));
+            console.log(chalk.dim(`  Project profiles: ${dirs.project}`));
+        }
+        else {
+            for (const p of customProfiles) {
+                const source = p.source === 'project' ? chalk.cyan('[project]') : chalk.dim('[user]');
+                console.log(`  ${chalk.bold(p.id)} - ${p.name} ${source}`);
+                console.log(chalk.dim(`    ${p.path}`));
+            }
+            console.log();
+            console.log(chalk.dim(`  ${customProfiles.length} custom profile(s)`));
+        }
+        console.log();
+        const allJournals = listJournals();
+        const builtIn = allJournals.filter(j => !j.custom).length;
+        console.log(chalk.dim(`  ${builtIn} built-in profiles available (rev validate --list)`));
+    });
+    // ==========================================================================
+    // ANONYMIZE command - Prepare document for blind review
+    // ==========================================================================
+    program
+        .command('anonymize')
+        .description('Prepare document for blind review')
+        .argument('<input>', 'Input markdown file or directory')
+        .option('-o, --output <file>', 'Output file (default: input-anonymous.md)')
+        .option('--authors <names>', 'Author names to redact (comma-separated)')
+        .option('--dry-run', 'Show what would be changed without writing')
+        .action(async (input, options) => {
+        const { default: YAML } = await import('yaml');
+        const isDir = fs.existsSync(input) && fs.statSync(input).isDirectory();
+        const files = isDir
+            ? fs.readdirSync(input)
+                .filter(f => f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f))
+                .map(f => path.join(input, f))
+            : [input];
+        if (files.length === 0) {
+            console.error(fmt.status('error', 'No markdown files found'));
+            process.exit(1);
+        }
+        let authorNames = [];
+        if (options.authors) {
+            authorNames = options.authors.split(',').map(n => n.trim());
+        }
+        else {
+            const configPath = isDir ? path.join(input, 'rev.yaml') : 'rev.yaml';
+            if (fs.existsSync(configPath)) {
+                try {
+                    const config = YAML.parse(fs.readFileSync(configPath, 'utf-8'));
+                    if (config.authors) {
+                        authorNames = config.authors.map((a) => typeof a === 'string' ? a : a.name).filter(Boolean);
+                    }
+                }
+                catch { /* ignore */ }
+            }
+        }
+        console.log(fmt.header('Anonymizing Document'));
+        console.log();
+        let totalChanges = 0;
+        for (const file of files) {
+            if (!fs.existsSync(file)) {
+                console.error(chalk.yellow(`  Skipping: ${file} (not found)`));
+                continue;
+            }
+            let text = fs.readFileSync(file, 'utf-8');
+            let changes = 0;
+            text = text.replace(/^---\n([\s\S]*?)\n---/, (match, fm) => {
+                let modified = fm;
+                modified = modified.replace(/^author:.*(?:\n(?:  |\t).*)*$/m, '');
+                modified = modified.replace(/^authors:.*(?:\n(?:  |\t|-\s+).*)*$/m, '');
+                modified = modified.replace(/^affiliation:.*$/m, '');
+                modified = modified.replace(/^email:.*$/m, '');
+                if (modified !== fm)
+                    changes++;
+                return '---\n' + modified.replace(/\n{3,}/g, '\n\n').trim() + '\n---';
+            });
+            const ackPatterns = [
+                /^#+\s*Acknowledgments?[\s\S]*?(?=^#|\Z)/gmi,
+                /^#+\s*Funding[\s\S]*?(?=^#|\Z)/gmi,
+            ];
+            for (const pattern of ackPatterns) {
+                const before = text;
+                text = text.replace(pattern, '');
+                if (text !== before)
+                    changes++;
+            }
+            for (const name of authorNames) {
+                const namePattern = new RegExp(`\\b${name.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\b`, 'gi');
+                const before = text;
+                text = text.replace(namePattern, '[AUTHOR]');
+                if (text !== before)
+                    changes++;
+            }
+            for (const name of authorNames) {
+                const lastName = name.split(/\s+/).pop();
+                if (lastName && lastName.length > 2) {
+                    const citePat = new RegExp(`@${lastName}(\\d{4})`, 'gi');
+                    const before = text;
+                    text = text.replace(citePat, '@AUTHOR$1');
+                    if (text !== before)
+                        changes++;
+                }
+            }
+            totalChanges += changes;
+            if (options.dryRun) {
+                console.log(chalk.dim(`  ${path.basename(file)}: ${changes} change(s)`));
+            }
+            else {
+                const outPath = options.output || file.replace(/\.md$/, '-anonymous.md');
+                fs.writeFileSync(outPath, text, 'utf-8');
+                console.log(fmt.status('success', `${path.basename(file)} → ${path.basename(outPath)} (${changes} changes)`));
+            }
+        }
+        console.log();
+        if (options.dryRun) {
+            console.log(chalk.dim(`  Total: ${totalChanges} change(s) would be made`));
+        }
+        else {
+            console.log(fmt.status('success', `Anonymized ${files.length} file(s)`));
+        }
+    });
+}
+//# sourceMappingURL=response.js.map

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

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package/dist/lib/commands/sections.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Section commands: import, extract, split, sync, merge
+ *
+ * Commands for importing Word documents, splitting/syncing section files.
+ */
+import type { Command } from 'commander';
+/**
+ * Register section commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=sections.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"sections.d.ts","sourceRoot":"","sources":["../../../lib/commands/sections.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAgBH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoRzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAu9B/C"}