docrev 0.11.2 → 0.12.0

package/lib/commands/context.ts

@@ -1,176 +0,0 @@
-/**
- * Shared context for command modules
- *
- * This module provides shared utilities and state that command modules need.
- */
-
-import chalk from 'chalk';
-import * as fs from 'fs';
-import * as path from 'path';
-import * as fmt from '../format.js';
-
-// Global flags (set by main CLI)
-export let quietMode = false;
-export let jsonMode = false;
-
-export function setQuietMode(value: boolean): void {
-  quietMode = value;
-}
-
-export function setJsonMode(value: boolean): void {
-  jsonMode = value;
-  if (value) {
-    chalk.level = 0;
-  }
-}
-
-// JSON output helper
-export function jsonOutput(data: unknown): void {
-  console.log(JSON.stringify(data, null, 2));
-}
-
-// Find files by extension
-export function findFiles(ext: string, cwd: string = process.cwd()): string[] {
-  try {
-    return fs.readdirSync(cwd)
-      .filter(f => f.endsWith(ext) && !f.startsWith('.'));
-  } catch {
-    return [];
-  }
-}
-
-// Re-export common dependencies
-export { chalk, fs, path, fmt };
-
-// Re-export from lib modules
-export {
-  parseAnnotations,
-  stripAnnotations,
-  countAnnotations,
-  getComments,
-  setCommentStatus,
-  hasAnnotations,
-  getTrackChanges,
-  applyDecision,
-  cleanupOrphanedMarkers,
-} from '../annotations.js';
-
-export {
-  interactiveReview,
-  listComments,
-  interactiveCommentReview,
-} from '../review.js';
-
-export {
-  generateConfig,
-  loadConfig,
-  saveConfig,
-  deriveSectionsFromRev,
-  resolveSectionsConfig,
-  matchHeading,
-  extractSectionsFromText,
-  splitAnnotatedPaper,
-  getOrderedSections,
-} from '../sections.js';
-
-export {
-  buildRegistry,
-  detectHardcodedRefs,
-  convertHardcodedRefs,
-  getRefStatus,
-  formatRegistry,
-} from '../crossref.js';
-
-export {
-  build,
-  loadConfig as loadBuildConfig,
-  formatBuildResults,
-} from '../build.js';
-
-export {
-  hasPandoc,
-  hasPandocCrossref,
-  hasLatex,
-  checkDependencies,
-  getInstallInstructions,
-} from '../dependencies.js';
-
-export {
-  getTemplate,
-  listTemplates,
-  generateCustomTemplate,
-} from '../templates.js';
-
-export {
-  getUserName,
-  setUserName,
-  getConfigPath,
-  getDefaultSections,
-  setDefaultSections,
-  loadUserConfig,
-  saveUserConfig,
-} from '../config.js';
-
-export { inlineDiffPreview } from '../format.js';
-
-export { countWords } from '../utils.js';
-
-export {
-  parseCommentsWithReplies,
-  collectComments,
-  generateResponseLetter,
-  groupByReviewer,
-} from '../response.js';
-
-export {
-  validateCitations,
-  getCitationStats,
-} from '../citations.js';
-
-export {
-  extractEquations,
-  getEquationStats,
-  createEquationsDoc,
-  extractEquationsFromWord,
-  getWordEquationStats,
-} from '../equations.js';
-
-export {
-  parseBibEntries,
-  checkBibDois,
-  fetchBibtex,
-  addToBib,
-  isValidDoiFormat,
-  lookupDoi,
-  lookupMissingDois,
-} from '../doi.js';
-
-export {
-  clearDoiCache,
-  getDoiCacheStats,
-} from '../doi-cache.js';
-
-export {
-  formatError,
-  getFileNotFoundSuggestions,
-  getDependencySuggestions,
-  getAnnotationSuggestions,
-  getBuildSuggestions,
-  exitWithError,
-  requireFile,
-} from '../errors.js';
-
-export {
-  listJournals,
-  getJournalProfile,
-  validateManuscript,
-  validateProject,
-} from '../journals.js';
-
-export {
-  listCustomProfiles,
-  saveProfileTemplate,
-  getPluginDirs,
-} from '../plugins.js';
-
-export { tuiCommentReview } from '../tui.js';

package/lib/commands/core.ts

@@ -1,309 +0,0 @@
-/**
- * Core commands: review, strip, status
- *
- * Basic annotation operations for track changes workflow.
- */
-
-import type { Command } from 'commander';
-import type { Comment } from '../types.js';
-import {
-  chalk,
-  fs,
-  path,
-  fmt,
-  quietMode,
-  jsonMode,
-  jsonOutput,
-  findFiles,
-  parseAnnotations,
-  stripAnnotations,
-  countAnnotations,
-  getComments,
-  interactiveReview,
-  exitWithError,
-  getFileNotFoundSuggestions,
-  requireFile,
-} from './context.js';
-
-interface StripOptions {
-  output?: string;
-  keepComments?: boolean;
-}
-
-/**
- * Register core commands with the program
- */
-export function register(program: Command): void {
-  // ==========================================================================
-  // REVIEW command - Interactive track change review
-  // ==========================================================================
-
-  program
-    .command('review')
-    .description('Interactively review and accept/reject track changes')
-    .argument('<file>', 'Markdown file to review')
-    .action(async (file: string) => {
-      requireFile(file, 'Markdown file');
-
-      const text = fs.readFileSync(file, 'utf-8');
-      const result = await interactiveReview(text);
-
-      if (result.accepted > 0 || result.rejected > 0) {
-        // Confirm save
-        const rl = await import('readline');
-        const readline = rl.createInterface({
-          input: process.stdin,
-          output: process.stdout,
-        });
-
-        readline.question(chalk.cyan(`\nSave changes to ${file}? [y/N] `), (answer) => {
-          readline.close();
-          if (answer.toLowerCase() === 'y') {
-            fs.writeFileSync(file, result.text, 'utf-8');
-            console.log(chalk.green(`Saved ${file}`));
-          } else {
-            console.log(chalk.yellow('Changes not saved.'));
-          }
-        });
-      }
-    });
-
-  // ==========================================================================
-  // STRIP command - Remove annotations
-  // ==========================================================================
-
-  program
-    .command('strip')
-    .description('Strip annotations, outputting clean Markdown')
-    .argument('<file>', 'Markdown file to strip')
-    .option('-o, --output <file>', 'Output file (default: stdout)')
-    .option('-c, --keep-comments', 'Keep comment annotations')
-    .action((file: string, options: StripOptions) => {
-      requireFile(file, 'Markdown file');
-
-      const text = fs.readFileSync(file, 'utf-8');
-      const clean = stripAnnotations(text, { keepComments: options.keepComments });
-
-      if (options.output) {
-        fs.writeFileSync(options.output, clean, 'utf-8');
-        console.error(chalk.green(`Written to ${options.output}`));
-      } else {
-        process.stdout.write(clean);
-      }
-    });
-
-  // ==========================================================================
-  // STATUS command - Show annotation statistics
-  // ==========================================================================
-
-  program
-    .command('status')
-    .alias('s')
-    .description('Show project overview or file annotation statistics')
-    .argument('[file]', 'Markdown file to analyze (default: project overview)')
-    .action(async (file?: string) => {
-      // If a specific file is given, show its annotations
-      if (file) {
-        if (!fs.existsSync(file)) {
-          if (jsonMode) {
-            jsonOutput({ error: `File not found: ${file}` });
-          } else {
-            exitWithError(`File not found: ${file}`, getFileNotFoundSuggestions(file));
-          }
-        }
-
-        const text = fs.readFileSync(file, 'utf-8');
-        const counts = countAnnotations(text);
-        const comments = getComments(text);
-
-        if (jsonMode) {
-          jsonOutput({
-            file: path.basename(file),
-            annotations: counts,
-            comments: comments.map((c) => ({
-              author: c.author || null,
-              content: c.content,
-              line: c.line,
-              resolved: c.resolved || false,
-            })),
-          });
-          return;
-        }
-
-        if (counts.total === 0) {
-          console.log(fmt.status('success', 'No annotations found.'));
-          return;
-        }
-
-        console.log(fmt.header(`Annotations in ${path.basename(file)}`));
-        console.log();
-
-        // Build stats table
-        const rows: string[][] = [];
-        if (counts.inserts > 0) rows.push([chalk.green('+'), 'Insertions', chalk.green(counts.inserts.toString())]);
-        if (counts.deletes > 0) rows.push([chalk.red('-'), 'Deletions', chalk.red(counts.deletes.toString())]);
-        if (counts.substitutes > 0) rows.push([chalk.yellow('~'), 'Substitutions', chalk.yellow(counts.substitutes.toString())]);
-        if (counts.comments > 0) rows.push([chalk.blue('#'), 'Comments', chalk.blue(counts.comments.toString())]);
-        rows.push([chalk.dim('Σ'), chalk.dim('Total'), chalk.dim(counts.total.toString())]);
-
-        console.log(fmt.table(['', 'Type', 'Count'], rows, { align: ['center', 'left', 'right'] }));
-
-        // List comments with authors in a table
-        if (comments.length > 0) {
-          console.log();
-          console.log(fmt.header('Comments'));
-          console.log();
-
-          const commentRows = comments.map((c, i: number) => [
-            chalk.dim((i + 1).toString()),
-            c.author ? chalk.blue(c.author) : chalk.dim('Anonymous'),
-            c.content.length > 45 ? c.content.slice(0, 45) + '...' : c.content,
-            chalk.dim(`L${c.line}`),
-          ]);
-
-          console.log(fmt.table(['#', 'Author', 'Comment', 'Line'], commentRows, {
-            align: ['right', 'left', 'left', 'right'],
-          }));
-        }
-        return;
-      }
-
-      // Project overview mode
-      // Find all markdown files
-      const mdFiles = findFiles('.md');
-      if (mdFiles.length === 0) {
-        if (jsonMode) {
-          jsonOutput({ error: 'No markdown files found', files: [] });
-        } else {
-          console.log(fmt.status('warning', 'No markdown files found in current directory.'));
-        }
-        return;
-      }
-
-      // Gather stats across all files
-      let totalWords = 0;
-      let totalComments = 0;
-      let pendingComments = 0;
-      let totalInserts = 0;
-      let totalDeletes = 0;
-      let totalSubstitutes = 0;
-      const fileStats: Array<{
-        file: string;
-        words: number;
-        inserts: number;
-        deletes: number;
-        substitutions: number;
-        comments: number;
-        pending: number;
-      }> = [];
-
-      for (const f of mdFiles) {
-        const text = fs.readFileSync(f, 'utf-8');
-        const counts = countAnnotations(text);
-        const comments = getComments(text);
-        const pending = comments.filter((c) => c.resolved === false).length;
-
-        // Simple word count (excluding annotations)
-        const stripped = stripAnnotations(text);
-        const words = stripped.split(/\s+/).filter(w => w.length > 0).length;
-
-        totalWords += words;
-        totalComments += comments.length;
-        pendingComments += pending;
-        totalInserts += counts.inserts;
-        totalDeletes += counts.deletes;
-        totalSubstitutes += counts.substitutes;
-
-        if (counts.total > 0 || words > 0) {
-          fileStats.push({
-            file: f,
-            words,
-            inserts: counts.inserts,
-            deletes: counts.deletes,
-            substitutions: counts.substitutes,
-            comments: comments.length,
-            pending,
-          });
-        }
-      }
-
-      // JSON output
-      if (jsonMode) {
-        const docxFiles = findFiles('.docx');
-        const latestDocx = docxFiles.length > 0
-          ? docxFiles
-              .map(f => ({ name: f, mtime: fs.statSync(f).mtime }))
-              .sort((a, b) => b.mtime.getTime() - a.mtime.getTime())[0]
-          : null;
-
-        jsonOutput({
-          summary: {
-            words: totalWords,
-            files: mdFiles.length,
-            comments: totalComments,
-            pendingComments,
-            insertions: totalInserts,
-            deletions: totalDeletes,
-            substitutions: totalSubstitutes,
-          },
-          files: fileStats,
-          latestDocx: latestDocx ? { name: latestDocx.name, mtime: latestDocx.mtime.toISOString() } : null,
-        });
-        return;
-      }
-
-      // Normal output
-      console.log(fmt.header('Project Status'));
-      console.log();
-
-      // Summary
-      console.log(`  ${chalk.bold(totalWords.toLocaleString())} words across ${mdFiles.length} files`);
-
-      if (totalComments > 0) {
-        console.log(`  ${chalk.blue(totalComments.toString())} comments (${chalk.yellow(pendingComments.toString())} pending)`);
-      }
-
-      const totalChanges = totalInserts + totalDeletes + totalSubstitutes;
-      if (totalChanges > 0) {
-        console.log(`  ${chalk.green(`+${totalInserts}`)} insertions, ${chalk.red(`-${totalDeletes}`)} deletions, ${chalk.yellow(`~${totalSubstitutes}`)} substitutions`);
-      }
-
-      // Per-file breakdown if there are annotations
-      if (totalChanges > 0 || totalComments > 0) {
-        console.log();
-        const rows = fileStats
-          .filter(f => f.inserts + f.deletes + f.substitutions + f.comments > 0)
-          .map(f => [
-            f.file,
-            f.words.toLocaleString(),
-            f.inserts > 0 ? chalk.green(`+${f.inserts}`) : chalk.dim('-'),
-            f.deletes > 0 ? chalk.red(`-${f.deletes}`) : chalk.dim('-'),
-            f.substitutions > 0 ? chalk.yellow(`~${f.substitutions}`) : chalk.dim('-'),
-            f.pending > 0 ? chalk.yellow(f.pending.toString()) : (f.comments > 0 ? chalk.dim(f.comments.toString()) : chalk.dim('-')),
-          ]);
-
-        if (rows.length > 0) {
-          console.log(fmt.table(
-            ['File', 'Words', 'Ins', 'Del', 'Sub', 'Cmt'],
-            rows,
-            { align: ['left', 'right', 'right', 'right', 'right', 'right'] }
-          ));
-        }
-      }
-
-      // Check for recent docx files
-      const docxFiles = findFiles('.docx');
-      if (docxFiles.length > 0) {
-        const sorted = docxFiles
-          .map(f => ({ name: f, mtime: fs.statSync(f).mtime }))
-          .sort((a, b) => b.mtime.getTime() - a.mtime.getTime());
-        const latest = sorted[0];
-        const age = Date.now() - latest.mtime.getTime();
-        const ageStr = age < 3600000 ? `${Math.round(age / 60000)}m ago` :
-                       age < 86400000 ? `${Math.round(age / 3600000)}h ago` :
-                       `${Math.round(age / 86400000)}d ago`;
-        console.log();
-        console.log(chalk.dim(`  Latest DOCX: ${latest.name} (${ageStr})`));
-      }
-    });
-}