docrev 0.8.1 → 0.9.0

package/README.md

@@ -215,6 +215,39 @@ Configure your name for comment replies:
 rev config user "Your Name"
 ```
 
+### Table Formatting
+
+For PDF output, configure columns that should not wrap:
+
+```yaml
+tables:
+  nowrap:
+    - Prior              # column headers to keep on one line
+    - "$\\widehat{R}$"
+```
+
+Distribution notation in nowrap columns is auto-converted to LaTeX math:
+`Normal(0, 0.5)` → `$\mathcal{N}(0, 0.5)$`
+
+### Postprocess Scripts
+
+Run custom scripts after output generation:
+
+```yaml
+postprocess:
+  pdf: ./scripts/fix-tables.py    # runs after PDF
+  docx: ./scripts/add-meta.js     # runs after DOCX
+  all: ./scripts/notify.sh        # runs after any format
+```
+
+Scripts receive environment variables: `OUTPUT_FILE`, `OUTPUT_FORMAT`, `PROJECT_DIR`, `CONFIG_PATH`.
+
+Use `--verbose` to see script output:
+
+```bash
+rev build pdf --verbose
+```
+
 ## Annotation Syntax
 
 Track changes from Word appear as [CriticMarkup](http://criticmarkup.com/):

package/bin/rev.js

@@ -1,138 +1,19 @@
 #!/usr/bin/env node
 
-/**
- * rev - Revision workflow for Word ↔ Markdown round-trips
- *
- * Handles track changes and comments when collaborating on academic papers.
- * Preserves reviewer feedback through the Markdown editing workflow.
- */
+// Wrapper to run the TypeScript entry point via tsx
+// This allows `rev` command to work after npm link / npm install
 
-import { program } from 'commander';
-import chalk from 'chalk';
-import * as fs from 'fs';
+import { spawnSync } from 'child_process';
+import { fileURLToPath } from 'url';
+import { dirname, join } from 'path';
 
-// Import refactored command modules
-import {
-  registerAllCommands,
-  setQuietMode,
-  setJsonMode,
-} from '../lib/commands/index.js';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const tsEntry = join(__dirname, 'rev.ts');
 
-// Global flags
-let quietMode = false;
-let jsonMode = false;
-
-// Levenshtein distance for command suggestions
-function levenshtein(a, b) {
-  const matrix = Array(b.length + 1).fill(null).map(() => Array(a.length + 1).fill(null));
-  for (let i = 0; i <= a.length; i++) matrix[0][i] = i;
-  for (let j = 0; j <= b.length; j++) matrix[j][0] = j;
-  for (let j = 1; j <= b.length; j++) {
-    for (let i = 1; i <= a.length; i++) {
-      const cost = a[i - 1] === b[j - 1] ? 0 : 1;
-      matrix[j][i] = Math.min(
-        matrix[j][i - 1] + 1,
-        matrix[j - 1][i] + 1,
-        matrix[j - 1][i - 1] + cost
-      );
-    }
-  }
-  return matrix[b.length][a.length];
-}
-
-// Find similar commands for typo suggestions
-function suggestCommand(input, commands) {
-  const suggestions = commands
-    .map(cmd => ({ cmd, dist: levenshtein(input.toLowerCase(), cmd.toLowerCase()) }))
-    .filter(({ dist }) => dist <= 3)
-    .sort((a, b) => a.dist - b.dist)
-    .slice(0, 3)
-    .map(({ cmd }) => cmd);
-  return suggestions;
-}
-
-// Read version from package.json
-const pkgPath = new URL('../package.json', import.meta.url);
-const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
-
-program
-  .name('rev')
-  .description('Revision workflow for Word ↔ Markdown round-trips')
-  .version(`${pkg.version}\nNode ${process.version} | ${process.platform} ${process.arch}`, '-V, --version', 'Output version information')
-  .configureOutput({
-    outputError: (str, write) => write(chalk.red(str)),
-  })
-  .showHelpAfterError(chalk.dim('(use --help for usage information)'))
-  .option('--no-color', 'Disable colored output')
-  .option('-q, --quiet', 'Suppress non-essential output')
-  .option('--json', 'Output in JSON format (for scripting)')
-  .hook('preAction', (thisCommand) => {
-    const opts = thisCommand.opts();
-    if (opts.color === false) {
-      chalk.level = 0;
-    }
-    if (opts.quiet) {
-      quietMode = true;
-      setQuietMode(true);
-    }
-    if (opts.json) {
-      jsonMode = true;
-      setJsonMode(true);
-      chalk.level = 0; // Disable colors in JSON mode
-    }
-  });
-
-// Register all command modules
-// Commands organized by module:
-//   core.js: review, strip, status
-//   comments.js: comments, resolve, next, prev, first, last, todo, accept, reject, reply
-//   init.js: init, new, config
-//   sections.js: import, extract, split, sync, merge
-//   build.js: refs, migrate, install, doctor, build
-//   response.js: response, validate, profiles, anonymize
-//   citations.js: citations, figures, equations, pdf-comments
-//   doi.js: doi, orcid
-//   history.js: diff, history, contributors
-//   utilities.js: help, completions, word-count, stats, search, backup, archive,
-//                 export, preview, watch, lint, grammar, annotate, apply, comment,
-//                 clean, check, open, spelling, upgrade, batch, install-cli-skill
-registerAllCommands(program, pkg);
-
-// Get all command names for typo suggestions
-const allCommands = program.commands.map(cmd => cmd.name());
-const allAliases = program.commands.flatMap(cmd => cmd.aliases());
-const allCommandNames = [...allCommands, ...allAliases];
-
-// Handle unknown commands with suggestions
-program.on('command:*', (operands) => {
-  const unknown = operands[0];
-  console.error(chalk.red(`Unknown command: ${unknown}`));
-
-  const suggestions = suggestCommand(unknown, allCommandNames);
-  if (suggestions.length > 0) {
-    console.error();
-    console.error(chalk.yellow('Did you mean?'));
-    for (const s of suggestions) {
-      console.error(chalk.cyan(`  rev ${s}`));
-    }
-  }
-  console.error();
-  console.error(chalk.dim('Run "rev help" for available commands.'));
-  process.exit(1);
+// Run tsx with the TypeScript entry point
+const result = spawnSync('npx', ['tsx', tsEntry, ...process.argv.slice(2)], {
+  stdio: 'inherit',
+  shell: true
 });
 
-// Default to status when no command given
-const args = process.argv.slice(2);
-const globalOpts = ['--no-color', '-q', '--quiet', '--json', '-V', '--version', '-h', '--help'];
-const hasOnlyGlobalOpts = args.every(arg => globalOpts.includes(arg) || arg.startsWith('--no-') || arg.startsWith('-'));
-const hasCommand = args.some(arg => !arg.startsWith('-') && !globalOpts.includes(arg));
-
-if (args.length === 0 || (hasOnlyGlobalOpts && !hasCommand && !args.includes('-h') && !args.includes('--help') && !args.includes('-V') && !args.includes('--version'))) {
-  // Insert 'status' after any global options
-  const insertPos = process.argv.findIndex((arg, i) => i >= 2 && !arg.startsWith('-'));
-  if (insertPos === -1) {
-    process.argv.push('status');
-  }
-}
-
-program.parse();
+process.exit(result.status ?? 0);

package/bin/rev.ts

@@ -0,0 +1,145 @@
+#!/usr/bin/env tsx
+
+/**
+ * rev - Revision workflow for Word ↔ Markdown round-trips
+ *
+ * Handles track changes and comments when collaborating on academic papers.
+ * Preserves reviewer feedback through the Markdown editing workflow.
+ */
+
+import { program, Command } from 'commander';
+import chalk from 'chalk';
+import * as fs from 'fs';
+
+// Import refactored command modules
+import {
+  registerAllCommands,
+  setQuietMode,
+  setJsonMode,
+} from '../lib/commands/index.js';
+
+// Global flags
+let quietMode = false;
+let jsonMode = false;
+
+// Levenshtein distance for command suggestions
+function levenshtein(a: string, b: string): number {
+  const matrix: number[][] = Array(b.length + 1).fill(null).map(() => Array(a.length + 1).fill(0));
+  for (let i = 0; i <= a.length; i++) matrix[0]![i] = i;
+  for (let j = 0; j <= b.length; j++) matrix[j]![0] = j;
+  for (let j = 1; j <= b.length; j++) {
+    for (let i = 1; i <= a.length; i++) {
+      const cost = a[i - 1] === b[j - 1] ? 0 : 1;
+      matrix[j]![i] = Math.min(
+        matrix[j]![i - 1]! + 1,
+        matrix[j - 1]![i]! + 1,
+        matrix[j - 1]![i - 1]! + cost
+      );
+    }
+  }
+  return matrix[b.length]![a.length]!;
+}
+
+// Find similar commands for typo suggestions
+function suggestCommand(input: string, commands: string[]): string[] {
+  const suggestions = commands
+    .map(cmd => ({ cmd, dist: levenshtein(input.toLowerCase(), cmd.toLowerCase()) }))
+    .filter(({ dist }) => dist <= 3)
+    .sort((a, b) => a.dist - b.dist)
+    .slice(0, 3)
+    .map(({ cmd }) => cmd);
+  return suggestions;
+}
+
+interface PackageJson {
+  version: string;
+  name?: string;
+  description?: string;
+  [key: string]: unknown;
+}
+
+// Read version from package.json
+const pkgPath = new URL('../package.json', import.meta.url);
+const pkg: PackageJson = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
+
+program
+  .name('rev')
+  .description('Revision workflow for Word ↔ Markdown round-trips')
+  .version(`${pkg.version}\nNode ${process.version} | ${process.platform} ${process.arch}`, '-V, --version', 'Output version information')
+  .configureOutput({
+    outputError: (str: string, write: (str: string) => void) => write(chalk.red(str)),
+  })
+  .showHelpAfterError(chalk.dim('(use --help for usage information)'))
+  .option('--no-color', 'Disable colored output')
+  .option('-q, --quiet', 'Suppress non-essential output')
+  .option('--json', 'Output in JSON format (for scripting)')
+  .hook('preAction', (thisCommand: Command) => {
+    const opts = thisCommand.opts<{ color?: boolean; quiet?: boolean; json?: boolean }>();
+    if (opts.color === false) {
+      chalk.level = 0;
+    }
+    if (opts.quiet) {
+      quietMode = true;
+      setQuietMode(true);
+    }
+    if (opts.json) {
+      jsonMode = true;
+      setJsonMode(true);
+      chalk.level = 0; // Disable colors in JSON mode
+    }
+  });
+
+// Register all command modules
+// Commands organized by module:
+//   core.js: review, strip, status
+//   comments.js: comments, resolve, next, prev, first, last, todo, accept, reject, reply
+//   init.js: init, new, config
+//   sections.js: import, extract, split, sync, merge
+//   build.js: refs, migrate, install, doctor, build
+//   response.js: response, validate, profiles, anonymize
+//   citations.js: citations, figures, equations, pdf-comments
+//   doi.js: doi, orcid
+//   history.js: diff, history, contributors
+//   utilities.js: help, completions, word-count, stats, search, backup, archive,
+//                 export, preview, watch, lint, grammar, annotate, apply, comment,
+//                 clean, check, open, spelling, upgrade, batch, install-cli-skill
+registerAllCommands(program, pkg);
+
+// Get all command names for typo suggestions
+const allCommands = program.commands.map(cmd => cmd.name());
+const allAliases = program.commands.flatMap(cmd => cmd.aliases());
+const allCommandNames = [...allCommands, ...allAliases];
+
+// Handle unknown commands with suggestions
+program.on('command:*', (operands: string[]) => {
+  const unknown = operands[0];
+  console.error(chalk.red(`Unknown command: ${unknown}`));
+
+  const suggestions = suggestCommand(unknown!, allCommandNames);
+  if (suggestions.length > 0) {
+    console.error();
+    console.error(chalk.yellow('Did you mean?'));
+    for (const s of suggestions) {
+      console.error(chalk.cyan(`  rev ${s}`));
+    }
+  }
+  console.error();
+  console.error(chalk.dim('Run "rev help" for available commands.'));
+  process.exit(1);
+});
+
+// Default to status when no command given
+const args = process.argv.slice(2);
+const globalOpts = ['--no-color', '-q', '--quiet', '--json', '-V', '--version', '-h', '--help'];
+const hasOnlyGlobalOpts = args.every(arg => globalOpts.includes(arg) || arg.startsWith('--no-') || arg.startsWith('-'));
+const hasCommand = args.some(arg => !arg.startsWith('-') && !globalOpts.includes(arg));
+
+if (args.length === 0 || (hasOnlyGlobalOpts && !hasCommand && !args.includes('-h') && !args.includes('--help') && !args.includes('-V') && !args.includes('--version'))) {
+  // Insert 'status' after any global options
+  const insertPos = process.argv.findIndex((arg, i) => i >= 2 && !arg.startsWith('-'));
+  if (insertPos === -1) {
+    process.argv.push('status');
+  }
+}
+
+program.parse();

package/dist/bin/rev.d.ts

@@ -0,0 +1,9 @@
+#!/usr/bin/env tsx
+/**
+ * rev - Revision workflow for Word ↔ Markdown round-trips
+ *
+ * Handles track changes and comments when collaborating on academic papers.
+ * Preserves reviewer feedback through the Markdown editing workflow.
+ */
+export {};
+//# sourceMappingURL=rev.d.ts.map

package/dist/bin/rev.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"rev.d.ts","sourceRoot":"","sources":["../../bin/rev.ts"],"names":[],"mappings":";AAEA;;;;;GAKG"}

package/dist/bin/rev.js

@@ -0,0 +1,118 @@
+#!/usr/bin/env tsx
+/**
+ * rev - Revision workflow for Word ↔ Markdown round-trips
+ *
+ * Handles track changes and comments when collaborating on academic papers.
+ * Preserves reviewer feedback through the Markdown editing workflow.
+ */
+import { program } from 'commander';
+import chalk from 'chalk';
+import * as fs from 'fs';
+// Import refactored command modules
+import { registerAllCommands, setQuietMode, setJsonMode, } from '../lib/commands/index.js';
+// Global flags
+let quietMode = false;
+let jsonMode = false;
+// Levenshtein distance for command suggestions
+function levenshtein(a, b) {
+    const matrix = Array(b.length + 1).fill(null).map(() => Array(a.length + 1).fill(0));
+    for (let i = 0; i <= a.length; i++)
+        matrix[0][i] = i;
+    for (let j = 0; j <= b.length; j++)
+        matrix[j][0] = j;
+    for (let j = 1; j <= b.length; j++) {
+        for (let i = 1; i <= a.length; i++) {
+            const cost = a[i - 1] === b[j - 1] ? 0 : 1;
+            matrix[j][i] = Math.min(matrix[j][i - 1] + 1, matrix[j - 1][i] + 1, matrix[j - 1][i - 1] + cost);
+        }
+    }
+    return matrix[b.length][a.length];
+}
+// Find similar commands for typo suggestions
+function suggestCommand(input, commands) {
+    const suggestions = commands
+        .map(cmd => ({ cmd, dist: levenshtein(input.toLowerCase(), cmd.toLowerCase()) }))
+        .filter(({ dist }) => dist <= 3)
+        .sort((a, b) => a.dist - b.dist)
+        .slice(0, 3)
+        .map(({ cmd }) => cmd);
+    return suggestions;
+}
+// Read version from package.json
+const pkgPath = new URL('../package.json', import.meta.url);
+const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
+program
+    .name('rev')
+    .description('Revision workflow for Word ↔ Markdown round-trips')
+    .version(`${pkg.version}\nNode ${process.version} | ${process.platform} ${process.arch}`, '-V, --version', 'Output version information')
+    .configureOutput({
+    outputError: (str, write) => write(chalk.red(str)),
+})
+    .showHelpAfterError(chalk.dim('(use --help for usage information)'))
+    .option('--no-color', 'Disable colored output')
+    .option('-q, --quiet', 'Suppress non-essential output')
+    .option('--json', 'Output in JSON format (for scripting)')
+    .hook('preAction', (thisCommand) => {
+    const opts = thisCommand.opts();
+    if (opts.color === false) {
+        chalk.level = 0;
+    }
+    if (opts.quiet) {
+        quietMode = true;
+        setQuietMode(true);
+    }
+    if (opts.json) {
+        jsonMode = true;
+        setJsonMode(true);
+        chalk.level = 0; // Disable colors in JSON mode
+    }
+});
+// Register all command modules
+// Commands organized by module:
+//   core.js: review, strip, status
+//   comments.js: comments, resolve, next, prev, first, last, todo, accept, reject, reply
+//   init.js: init, new, config
+//   sections.js: import, extract, split, sync, merge
+//   build.js: refs, migrate, install, doctor, build
+//   response.js: response, validate, profiles, anonymize
+//   citations.js: citations, figures, equations, pdf-comments
+//   doi.js: doi, orcid
+//   history.js: diff, history, contributors
+//   utilities.js: help, completions, word-count, stats, search, backup, archive,
+//                 export, preview, watch, lint, grammar, annotate, apply, comment,
+//                 clean, check, open, spelling, upgrade, batch, install-cli-skill
+registerAllCommands(program, pkg);
+// Get all command names for typo suggestions
+const allCommands = program.commands.map(cmd => cmd.name());
+const allAliases = program.commands.flatMap(cmd => cmd.aliases());
+const allCommandNames = [...allCommands, ...allAliases];
+// Handle unknown commands with suggestions
+program.on('command:*', (operands) => {
+    const unknown = operands[0];
+    console.error(chalk.red(`Unknown command: ${unknown}`));
+    const suggestions = suggestCommand(unknown, allCommandNames);
+    if (suggestions.length > 0) {
+        console.error();
+        console.error(chalk.yellow('Did you mean?'));
+        for (const s of suggestions) {
+            console.error(chalk.cyan(`  rev ${s}`));
+        }
+    }
+    console.error();
+    console.error(chalk.dim('Run "rev help" for available commands.'));
+    process.exit(1);
+});
+// Default to status when no command given
+const args = process.argv.slice(2);
+const globalOpts = ['--no-color', '-q', '--quiet', '--json', '-V', '--version', '-h', '--help'];
+const hasOnlyGlobalOpts = args.every(arg => globalOpts.includes(arg) || arg.startsWith('--no-') || arg.startsWith('-'));
+const hasCommand = args.some(arg => !arg.startsWith('-') && !globalOpts.includes(arg));
+if (args.length === 0 || (hasOnlyGlobalOpts && !hasCommand && !args.includes('-h') && !args.includes('--help') && !args.includes('-V') && !args.includes('--version'))) {
+    // Insert 'status' after any global options
+    const insertPos = process.argv.findIndex((arg, i) => i >= 2 && !arg.startsWith('-'));
+    if (insertPos === -1) {
+        process.argv.push('status');
+    }
+}
+program.parse();
+//# sourceMappingURL=rev.js.map

package/dist/bin/rev.js.map

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

@@ -0,0 +1,91 @@
+/**
+ * CriticMarkup annotation parsing and manipulation
+ *
+ * Syntax:
+ *   {++inserted text++}     - Insertions
+ *   {--deleted text--}      - Deletions
+ *   {~~old~>new~~}          - Substitutions
+ *   {>>Author: comment<<}   - Comments
+ *   {==text==}              - Highlights
+ */
+import type { Annotation, AnnotationCounts, StripOptions, CommentFilterOptions } from './types.js';
+/**
+ * Parse all annotations from text
+ * @param text - Markdown text containing CriticMarkup annotations
+ * @returns Array of parsed annotations sorted by position
+ * @throws TypeError If text is not a string
+ */
+export declare function parseAnnotations(text: string): Annotation[];
+/**
+ * Strip annotations from text, applying changes
+ * Handles nested annotations by iterating until stable
+ * @param text - Markdown text with CriticMarkup annotations
+ * @param options - Strip options
+ * @returns Clean text with annotations applied/removed
+ * @throws TypeError If text is not a string
+ */
+export declare function stripAnnotations(text: string, options?: StripOptions): string;
+/**
+ * Collapse multiple spaces to single space, preserving table formatting
+ * Useful for cleaning up messy Word imports
+ * @param text - Text to normalize
+ * @returns Text with multiple spaces collapsed to single spaces
+ * @throws TypeError If text is not a string
+ */
+export declare function stripToSingleSpace(text: string): string;
+/**
+ * Check if text contains any CriticMarkup annotations
+ * @param text - Text to check
+ * @returns True if text contains any annotations
+ * @throws TypeError If text is not a string
+ */
+export declare function hasAnnotations(text: string): boolean;
+/**
+ * Apply a decision to a single annotation (accept or reject)
+ * @param text - Document text containing the annotation
+ * @param annotation - Annotation object from parseAnnotations()
+ * @param accept - True to accept the change, false to reject
+ * @returns Updated text with the decision applied
+ * @throws TypeError If text is not a string or annotation is invalid
+ */
+export declare function applyDecision(text: string, annotation: Annotation, accept: boolean): string;
+/**
+ * Get track changes only (no comments)
+ * @param text - Markdown text with CriticMarkup annotations
+ * @returns Array of insert/delete/substitute annotations
+ * @throws TypeError If text is not a string
+ */
+export declare function getTrackChanges(text: string): Annotation[];
+/**
+ * Get comments only
+ * @param text - Markdown text with CriticMarkup annotations
+ * @param options - Filter options
+ * @returns Array of comment annotations
+ * @throws TypeError If text is not a string
+ */
+export declare function getComments(text: string, options?: CommentFilterOptions): Annotation[];
+/**
+ * Mark a comment as resolved or pending
+ * @param text - Document text containing the comment
+ * @param comment - Comment annotation object from getComments()
+ * @param resolved - True to mark resolved, false to mark pending
+ * @returns Updated text with status marker applied
+ * @throws TypeError If text is not a string or comment is invalid
+ */
+export declare function setCommentStatus(text: string, comment: Annotation, resolved: boolean): string;
+/**
+ * Count annotations by type
+ * @param text - Markdown text with CriticMarkup annotations
+ * @returns Counts by annotation type
+ * @throws TypeError If text is not a string
+ */
+export declare function countAnnotations(text: string): AnnotationCounts;
+/**
+ * Clean up orphaned/malformed CriticMarkup markers
+ * This can happen when track changes span across comment boundaries
+ * @param text - Document text with potentially malformed markers
+ * @returns Cleaned text with orphaned markers removed
+ * @throws TypeError If text is not a string
+ */
+export declare function cleanupOrphanedMarkers(text: string): string;
+//# sourceMappingURL=annotations.d.ts.map

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