docrev 0.11.3 → 0.12.0

package/lib/commands/response.ts

@@ -1,454 +0,0 @@
-/**
- * Response commands: response, validate, profiles, anonymize
- *
- * Commands for generating reviewer responses and validating manuscripts.
- */
-
-import type { Command } from 'commander';
-import {
-  chalk,
-  fs,
-  path,
-  fmt,
-  collectComments,
-  generateResponseLetter,
-  groupByReviewer,
-  getUserName,
-} from './context.js';
-
-interface ResponseOptions {
-  output?: string;
-  author?: string;
-  context?: boolean;
-  location?: boolean;
-}
-
-interface ValidateOptions {
-  journal?: string;
-  list?: boolean;
-}
-
-interface ProfilesOptions {
-  list?: boolean;
-  new?: string;
-  project?: boolean;
-  dirs?: boolean;
-  fetchCsl?: string;
-  listCsl?: boolean;
-}
-
-interface AnonymizeOptions {
-  output?: string;
-  authors?: string;
-  dryRun?: boolean;
-}
-
-/**
- * Register response commands with the program
- */
-export function register(program: Command): void {
-  // ==========================================================================
-  // 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: string[] | undefined, options: ResponseOptions) => {
-      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 = await 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: string[] | undefined, options: ValidateOptions) => {
-      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) {
-          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}`));
-        }
-
-        if (custom.length > 0) {
-          console.log();
-          console.log(chalk.cyan('  Custom Profiles:'));
-          for (const j of 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;
-      }
-
-      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')
-    .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,
-        saveProfileTemplate,
-        getPluginDirs,
-      } = 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'));
-        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 as Error).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: string, options: AnonymizeOptions) => {
-      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: string[] = [];
-      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: string | { name: string }) => 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)`));
-      }
-    });
-}

package/lib/commands/section-boundaries.ts

@@ -1,82 +0,0 @@
-/**
- * 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 function computeSectionBoundaries(
-  sections: Record<string, SectionConfig>,
-  headings: DocxHeading[],
-  docLength?: number,
-): SectionBoundary[] {
-  const matched: SectionBoundary[] = [];
-
-  // Only consider top-level (Heading1-style) when level info is available;
-  // when level==0 (unparseable style), fall back to all headings.
-  const haveLevels = headings.some(h => h.level > 0);
-  const candidates = haveLevels ? headings.filter(h => h.level === 1) : headings;
-
-  for (const [file, cfg] of Object.entries(sections)) {
-    const targets = [cfg.header, ...(cfg.aliases || [])]
-      .filter(Boolean)
-      .map(s => s.toLowerCase().trim());
-
-    let firstMatch = -1;
-    for (const h of candidates) {
-      const text = h.text.toLowerCase().trim();
-      if (targets.includes(text)) {
-        firstMatch = h.docPosition;
-        break;
-      }
-    }
-
-    // Fallback: if no level-1 hit, allow any-level match (handles single-level docs)
-    if (firstMatch < 0 && haveLevels) {
-      for (const h of headings) {
-        const text = h.text.toLowerCase().trim();
-        if (targets.includes(text)) {
-          firstMatch = h.docPosition;
-          break;
-        }
-      }
-    }
-
-    if (firstMatch >= 0) {
-      matched.push({ file, start: firstMatch, end: Number.MAX_SAFE_INTEGER });
-    }
-  }
-
-  // Sort by start position and tighten each end to the next start.
-  // The last section's end is capped at docLength when known, otherwise
-  // left at MAX_SAFE_INTEGER. Without the cap, single-section configs
-  // produce a sectionLength of ~9e15, collapsing proportional-position
-  // math in insertCommentsIntoMarkdown to 0 and stacking every comment
-  // at the document start.
-  matched.sort((a, b) => a.start - b.start);
-  for (let i = 0; i < matched.length - 1; i++) {
-    matched[i].end = matched[i + 1].start;
-  }
-  if (matched.length > 0 && docLength !== undefined) {
-    const last = matched[matched.length - 1];
-    if (last.end > docLength) last.end = docLength;
-  }
-
-  return matched;
-}