docrev 0.6.13 → 0.7.6

package/lib/commands/context.js

@@ -0,0 +1,165 @@
+/**
+ * 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) {
+  quietMode = value;
+}
+
+export function setJsonMode(value) {
+  jsonMode = value;
+  if (value) {
+    chalk.level = 0;
+  }
+}
+
+// JSON output helper
+export function jsonOutput(data) {
+  console.log(JSON.stringify(data, null, 2));
+}
+
+// Find files by extension
+export function findFiles(ext, cwd = process.cwd()) {
+  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,
+} from '../annotations.js';
+
+export {
+  interactiveReview,
+  listComments,
+  interactiveCommentReview,
+} from '../review.js';
+
+export {
+  generateConfig,
+  loadConfig,
+  saveConfig,
+  matchHeading,
+  extractSectionsFromText,
+  splitAnnotatedPaper,
+  getOrderedSections,
+} from '../sections.js';
+
+export {
+  buildRegistry,
+  detectHardcodedRefs,
+  convertHardcodedRefs,
+  getRefStatus,
+  formatRegistry,
+} from '../crossref.js';
+
+export {
+  build,
+  loadConfig as loadBuildConfig,
+  hasPandoc,
+  hasPandocCrossref,
+  formatBuildResults,
+  hasLatex,
+  checkDependencies,
+  getInstallInstructions,
+} from '../build.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 {
+  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,
+  clearDoiCache,
+  getDoiCacheStats,
+} from '../doi.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.js

@@ -0,0 +1,295 @@
+/**
+ * Core commands: review, strip, status
+ *
+ * Basic annotation operations for track changes workflow.
+ */
+
+import {
+  chalk,
+  fs,
+  path,
+  fmt,
+  quietMode,
+  jsonMode,
+  jsonOutput,
+  findFiles,
+  parseAnnotations,
+  stripAnnotations,
+  countAnnotations,
+  getComments,
+  interactiveReview,
+  exitWithError,
+  getFileNotFoundSuggestions,
+  requireFile,
+} from './context.js';
+
+/**
+ * Register core commands with the program
+ * @param {import('commander').Command} program
+ */
+export function register(program) {
+  // ==========================================================================
+  // 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) => {
+      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, options) => {
+      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) => {
+      // 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 ${path.basename(file)}`));
+        console.log();
+
+        // Build stats table
+        const rows = [];
+        if (counts.inserts > 0) rows.push([chalk.green('+'), 'Insertions', chalk.green(counts.inserts)]);
+        if (counts.deletes > 0) rows.push([chalk.red('-'), 'Deletions', chalk.red(counts.deletes)]);
+        if (counts.substitutes > 0) rows.push([chalk.yellow('~'), 'Substitutions', chalk.yellow(counts.substitutes)]);
+        if (counts.comments > 0) rows.push([chalk.blue('#'), 'Comments', chalk.blue(counts.comments)]);
+        rows.push([chalk.dim('Σ'), chalk.dim('Total'), chalk.dim(counts.total)]);
+
+        console.log(fmt.table(['', 'Type', 'Count'], rows, { align: ['center', 'left', 'right'] }));
+
+        // List comments with authors in a table
+        if (comments.length > 0) {
+          console.log();
+          console.log(fmt.header('Comments'));
+          console.log();
+
+          const commentRows = comments.map((c, i) => [
+            chalk.dim(i + 1),
+            c.author ? chalk.blue(c.author) : chalk.dim('Anonymous'),
+            c.content.length > 45 ? c.content.slice(0, 45) + '...' : c.content,
+            chalk.dim(`L${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 = [];
+
+      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).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 - a.mtime)[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(`  ${chalk.blue(totalComments)} comments (${chalk.yellow(pendingComments)} 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(`~${f.substitutions}`) : chalk.dim('-'),
+            f.pending > 0 ? chalk.yellow(f.pending) : (f.comments > 0 ? chalk.dim(f.comments) : chalk.dim('-')),
+          ]);
+
+        if (rows.length > 0) {
+          console.log(fmt.table(
+            ['File', 'Words', 'Ins', 'Del', 'Sub', 'Cmt'],
+            rows,
+            { align: ['left', 'right', 'right', 'right', 'right', 'right'] }
+          ));
+        }
+      }
+
+      // Check for recent docx files
+      const docxFiles = findFiles('.docx');
+      if (docxFiles.length > 0) {
+        const sorted = docxFiles
+          .map(f => ({ name: f, mtime: fs.statSync(f).mtime }))
+          .sort((a, b) => b.mtime - a.mtime);
+        const latest = sorted[0];
+        const age = Date.now() - latest.mtime.getTime();
+        const ageStr = age < 3600000 ? `${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})`));
+      }
+    });
+}