docrev 0.9.18 → 0.10.1

package/lib/types.ts

@@ -1,550 +1,550 @@
-/**
- * Shared TypeScript type definitions for docrev
- * Extracted from types/index.d.ts for internal use
- */
-
-// ============================================
-// Annotations
-// ============================================
-
-export interface Annotation {
-  type: 'insert' | 'delete' | 'substitute' | 'comment' | 'highlight';
-  match: string;
-  content: string;
-  replacement?: string;
-  author?: string;
-  position: number;
-  line: number;
-  before?: string;
-  after?: string;
-  resolved?: boolean;
-}
-
-export interface Comment extends Annotation {
-  type: 'comment';
-  author: string;
-  resolved: boolean;
-}
-
-export interface AnnotationCounts {
-  inserts: number;
-  deletes: number;
-  substitutes: number;
-  comments: number;
-  total: number;
-}
-
-export interface StripOptions {
-  keepComments?: boolean;
-}
-
-export interface CommentFilterOptions {
-  pendingOnly?: boolean;
-  resolvedOnly?: boolean;
-}
-
-// ============================================
-// Build
-// ============================================
-
-export interface Author {
-  name: string;
-  affiliation?: string;
-  affiliations?: string[];
-  corresponding?: boolean;
-  email?: string;
-  orcid?: string;
-}
-
-export interface CrossrefConfig {
-  figureTitle?: string;
-  tableTitle?: string;
-  figPrefix?: string | string[];
-  tblPrefix?: string | string[];
-}
-
-export interface PdfConfig {
-  documentclass?: string;
-  fontsize?: string;
-  geometry?: string;
-  linestretch?: number;
-  toc?: boolean;
-  /**
-   * LaTeX engine to use for PDF output. One of `pdflatex` (default),
-   * `xelatex`, `lualatex`, `tectonic`, etc. xelatex/lualatex are required
-   * for native UTF-8 rendering of diacritics in author names, place
-   * names, and species epithets.
-   */
-  engine?: string;
-  /** Roman/serif main font (xelatex/lualatex only — uses fontspec). */
-  mainfont?: string;
-  /** Sans-serif font (xelatex/lualatex only). */
-  sansfont?: string;
-  /** Monospace font (xelatex/lualatex only). */
-  monofont?: string;
-  numbersections?: boolean;
-  template?: string;
-  headerIncludes?: string;
-}
-
-export interface DocxConfig {
-  reference?: string;
-  keepComments?: boolean;
-  toc?: boolean;
-}
-
-export interface BuildConfig {
-  title?: string;
-  authors?: Author[];
-  sections?: string[];
-  bibliography?: string;
-  csl?: string;
-  crossref?: CrossrefConfig;
-  pdf?: PdfConfig;
-  docx?: DocxConfig;
-  postprocess?: { [key: string]: string };
-  _configPath?: string;
-  [key: string]: unknown;
-}
-
-export interface BuildResult {
-  format: string;
-  output: string;
-  success: boolean;
-  error?: string;
-}
-
-// ============================================
-// Citations
-// ============================================
-
-export interface Citation {
-  key: string;
-  line: number;
-  file: string;
-}
-
-export interface CitationValidation {
-  valid: Citation[];
-  missing: Citation[];
-  unused: string[];
-  duplicates: Array<{ key: string; count: number; locations: Citation[] }>;
-}
-
-export interface CitationStats {
-  totalCitations: number;
-  uniqueCited: number;
-  valid: number;
-  missing: number;
-  missingKeys: string[];
-  bibEntries: number;
-  unused: number;
-  unusedKeys: string[];
-}
-
-// ============================================
-// Crossref
-// ============================================
-
-export interface RefNumber {
-  num: number;
-  isSupp: boolean;
-  suffix: string | null;
-}
-
-export interface HardcodedRef {
-  type: 'fig' | 'tbl' | 'eq';
-  match: string;
-  numbers: RefNumber[];
-  position: number;
-}
-
-export interface DynamicRef {
-  type: 'fig' | 'tbl' | 'eq';
-  label: string;
-  match: string;
-  position: number;
-}
-
-export interface FigureInfo {
-  label: string;
-  num: number;
-  isSupp: boolean;
-  file: string;
-}
-
-export interface Registry {
-  figures: Map<string, FigureInfo>;
-  tables: Map<string, FigureInfo>;
-  equations: Map<string, FigureInfo>;
-  byNumber: {
-    fig: Map<number, string>;
-    figS: Map<number, string>;
-    tbl: Map<number, string>;
-    tblS: Map<number, string>;
-    eq: Map<number, string>;
-  };
-}
-
-export interface RefStatus {
-  dynamic: DynamicRef[];
-  hardcoded: HardcodedRef[];
-  anchors: { figures: number; tables: number; equations: number };
-}
-
-export interface ConversionResult {
-  converted: string;
-  conversions: Array<{ from: string; to: string }>;
-  warnings: string[];
-}
-
-// ============================================
-// DOI
-// ============================================
-
-export interface BibEntry {
-  key: string;
-  type: string;
-  doi: string | null;
-  title: string;
-  authorRaw: string;
-  year: number | null;
-  journal: string;
-  skip: boolean;
-  expectDoi: boolean;
-  noDoi: boolean;
-  line: number;
-}
-
-export interface DoiCheckResult {
-  valid: boolean;
-  source?: 'crossref' | 'datacite';
-  metadata?: {
-    title: string;
-    authors: string[];
-    year: number;
-    journal: string;
-    type?: string;
-  };
-  error?: string;
-}
-
-export interface BibtexFetchResult {
-  success: boolean;
-  bibtex?: string;
-  error?: string;
-}
-
-export interface DoiLookupResult {
-  found: boolean;
-  doi?: string;
-  confidence?: 'low' | 'medium' | 'high';
-  score?: number;
-  metadata?: {
-    title: string;
-    authors: string[];
-    year: number;
-    journal: string;
-  };
-  alternatives?: Array<{
-    doi: string;
-    title: string;
-    score: number;
-  }>;
-  error?: string;
-}
-
-export interface BibCheckResult {
-  entries: Array<BibEntry & { status: string; message?: string; metadata?: object }>;
-  valid: number;
-  invalid: number;
-  missing: number;
-  skipped: number;
-}
-
-// ============================================
-// Equations
-// ============================================
-
-export interface Equation {
-  type: 'inline' | 'display';
-  content: string;
-  line: number;
-  file: string;
-}
-
-export interface EquationStats {
-  total: number;
-  display: number;
-  inline: number;
-  byFile: Array<{ file: string; display: number; inline: number }>;
-}
-
-export interface WordEquationResult {
-  success: boolean;
-  equations: Array<{
-    type: 'inline' | 'display' | 'unknown';
-    latex: string | null;
-    position: number;
-    line?: number;
-    raw?: string;
-    error?: string;
-  }>;
-  error?: string;
-}
-
-// ============================================
-// Git
-// ============================================
-
-export interface FileChange {
-  added: number;
-  removed: number;
-  changes: Array<{ added?: boolean; removed?: boolean; value: string }>;
-}
-
-export interface CommitInfo {
-  hash: string;
-  date: string;
-  author: string;
-  message: string;
-}
-
-export interface ChangedFile {
-  file: string;
-  status: 'added' | 'deleted' | 'modified';
-}
-
-export interface BlameEntry {
-  line: number;
-  author: string;
-  date: string;
-  hash: string;
-  content: string;
-}
-
-export interface AuthorStats {
-  lines: number;
-  percentage: number;
-}
-
-export interface ContributorStats {
-  lines: number;
-  files: number;
-}
-
-// ============================================
-// Journals
-// ============================================
-
-export interface JournalRequirements {
-  wordLimit?: { main?: number; abstract?: number };
-  references?: { max?: number; doiRequired?: boolean };
-  figures?: { max?: number };
-  tables?: { max?: number };
-  sections?: string[];
-}
-
-export interface JournalFormatting {
-  csl?: string;
-  pdf?: {
-    documentclass?: string;
-    fontsize?: string;
-    geometry?: string;
-    linestretch?: number;
-    template?: string;
-    numbersections?: boolean;
-    engine?: string;
-    mainfont?: string;
-    sansfont?: string;
-    monofont?: string;
-  };
-  docx?: {
-    reference?: string;
-  };
-  crossref?: {
-    figPrefix?: string | string[];
-    tblPrefix?: string | string[];
-  };
-}
-
-export interface JournalProfile {
-  name: string;
-  url: string;
-  requirements: JournalRequirements;
-  formatting?: JournalFormatting;
-}
-
-export interface ValidationResult {
-  journal: string;
-  valid: boolean;
-  wordCount: { main: number; abstract: number; limit: { main: number; abstract: number } };
-  figures: { count: number; max: number };
-  tables: { count: number; max: number };
-  references: { count: number; max: number };
-  sections: { found: string[]; missing: string[]; required: string[] };
-  errors: string[];
-  warnings: string[];
-}
-
-// ============================================
-// Merge
-// ============================================
-
-export interface ReviewerChange {
-  reviewer: string;
-  type: 'insert' | 'delete' | 'replace';
-  start: number;
-  end: number;
-  oldText: string;
-  newText: string;
-}
-
-export interface Conflict {
-  id: string;
-  start: number;
-  end: number;
-  original: string;
-  changes: ReviewerChange[];
-  section?: string;
-  line?: number;
-  resolved: string | null;
-}
-
-export interface MergeResult {
-  merged: string;
-  conflicts: Conflict[];
-  stats: {
-    reviewers: number;
-    totalChanges: number;
-    nonConflicting: number;
-    conflicts: number;
-    comments: number;
-  };
-  originalText: string;
-}
-
-// ============================================
-// Sections
-// ============================================
-
-export interface SectionConfig {
-  header: string;
-  aliases?: string[];
-  order?: number;
-}
-
-export interface SectionsConfig {
-  version: number;
-  description?: string;
-  sections: Record<string, SectionConfig>;
-}
-
-export interface ExtractedSection {
-  file: string;
-  header: string;
-  content: string;
-  matched: boolean;
-}
-
-// ============================================
-// Word
-// ============================================
-
-export interface WordComment {
-  id: string;
-  author: string;
-  date?: string;
-  text: string;
-}
-
-export interface WordMetadata {
-  title?: string;
-  author?: string;
-  created?: string;
-  modified?: string;
-}
-
-export interface CommentAnchor {
-  text: string;
-  context: string;
-}
-
-export interface WordContent {
-  text: string;
-  html: string;
-}
-
-export interface TrackChangesResult {
-  hasTrackChanges: boolean;
-  content: string | null;
-  stats: { insertions: number; deletions: number };
-}
-
-// ============================================
-// TrackChanges
-// ============================================
-
-export interface TrackChangeMarker {
-  id: number;
-  type: 'insert' | 'delete' | 'substitute' | 'comment';
-  content: string;
-  author: string;
-  replacement?: string;
-}
-
-// ============================================
-// Spelling
-// ============================================
-
-export interface SpellingIssue {
-  word: string;
-  line: number;
-  column: number;
-  file?: string;
-  suggestions?: string[];
-}
-
-export interface SpellingResult {
-  misspelled: SpellingIssue[];
-  possibleNames: SpellingIssue[];
-}
-
-// ============================================
-// Config
-// ============================================
-
-export interface UserConfig {
-  userName?: string;
-  defaultSections?: string[];
-}
-
-// ============================================
-// DOI Cache
-// ============================================
-
-export interface DoiCacheEntry {
-  result: DoiCheckResult | DoiLookupResult;
-  timestamp: number;
-}
-
-export interface DoiCache {
-  entries: Record<string, DoiCacheEntry>;
-  version: number;
-}
-
-export interface DoiCacheStats {
-  size: number;
-  path: string;
-}
-
-// ============================================
-// Errors
-// ============================================
-
-export interface ErrorInfo {
-  code: string;
-  message: string;
-  help?: string;
-  cause?: Error;
-}
+/**
+ * Shared TypeScript type definitions for docrev
+ * Extracted from types/index.d.ts for internal use
+ */
+
+// ============================================
+// Annotations
+// ============================================
+
+export interface Annotation {
+  type: 'insert' | 'delete' | 'substitute' | 'comment' | 'highlight';
+  match: string;
+  content: string;
+  replacement?: string;
+  author?: string;
+  position: number;
+  line: number;
+  before?: string;
+  after?: string;
+  resolved?: boolean;
+}
+
+export interface Comment extends Annotation {
+  type: 'comment';
+  author: string;
+  resolved: boolean;
+}
+
+export interface AnnotationCounts {
+  inserts: number;
+  deletes: number;
+  substitutes: number;
+  comments: number;
+  total: number;
+}
+
+export interface StripOptions {
+  keepComments?: boolean;
+}
+
+export interface CommentFilterOptions {
+  pendingOnly?: boolean;
+  resolvedOnly?: boolean;
+}
+
+// ============================================
+// Build
+// ============================================
+
+export interface Author {
+  name: string;
+  affiliation?: string;
+  affiliations?: string[];
+  corresponding?: boolean;
+  email?: string;
+  orcid?: string;
+}
+
+export interface CrossrefConfig {
+  figureTitle?: string;
+  tableTitle?: string;
+  figPrefix?: string | string[];
+  tblPrefix?: string | string[];
+}
+
+export interface PdfConfig {
+  documentclass?: string;
+  fontsize?: string;
+  geometry?: string;
+  linestretch?: number;
+  toc?: boolean;
+  /**
+   * LaTeX engine to use for PDF output. One of `pdflatex` (default),
+   * `xelatex`, `lualatex`, `tectonic`, etc. xelatex/lualatex are required
+   * for native UTF-8 rendering of diacritics in author names, place
+   * names, and species epithets.
+   */
+  engine?: string;
+  /** Roman/serif main font (xelatex/lualatex only — uses fontspec). */
+  mainfont?: string;
+  /** Sans-serif font (xelatex/lualatex only). */
+  sansfont?: string;
+  /** Monospace font (xelatex/lualatex only). */
+  monofont?: string;
+  numbersections?: boolean;
+  template?: string;
+  headerIncludes?: string;
+}
+
+export interface DocxConfig {
+  reference?: string;
+  keepComments?: boolean;
+  toc?: boolean;
+}
+
+export interface BuildConfig {
+  title?: string;
+  authors?: Author[];
+  sections?: string[];
+  bibliography?: string;
+  csl?: string;
+  crossref?: CrossrefConfig;
+  pdf?: PdfConfig;
+  docx?: DocxConfig;
+  postprocess?: { [key: string]: string };
+  _configPath?: string;
+  [key: string]: unknown;
+}
+
+export interface BuildResult {
+  format: string;
+  output: string;
+  success: boolean;
+  error?: string;
+}
+
+// ============================================
+// Citations
+// ============================================
+
+export interface Citation {
+  key: string;
+  line: number;
+  file: string;
+}
+
+export interface CitationValidation {
+  valid: Citation[];
+  missing: Citation[];
+  unused: string[];
+  duplicates: Array<{ key: string; count: number; locations: Citation[] }>;
+}
+
+export interface CitationStats {
+  totalCitations: number;
+  uniqueCited: number;
+  valid: number;
+  missing: number;
+  missingKeys: string[];
+  bibEntries: number;
+  unused: number;
+  unusedKeys: string[];
+}
+
+// ============================================
+// Crossref
+// ============================================
+
+export interface RefNumber {
+  num: number;
+  isSupp: boolean;
+  suffix: string | null;
+}
+
+export interface HardcodedRef {
+  type: 'fig' | 'tbl' | 'eq';
+  match: string;
+  numbers: RefNumber[];
+  position: number;
+}
+
+export interface DynamicRef {
+  type: 'fig' | 'tbl' | 'eq';
+  label: string;
+  match: string;
+  position: number;
+}
+
+export interface FigureInfo {
+  label: string;
+  num: number;
+  isSupp: boolean;
+  file: string;
+}
+
+export interface Registry {
+  figures: Map<string, FigureInfo>;
+  tables: Map<string, FigureInfo>;
+  equations: Map<string, FigureInfo>;
+  byNumber: {
+    fig: Map<number, string>;
+    figS: Map<number, string>;
+    tbl: Map<number, string>;
+    tblS: Map<number, string>;
+    eq: Map<number, string>;
+  };
+}
+
+export interface RefStatus {
+  dynamic: DynamicRef[];
+  hardcoded: HardcodedRef[];
+  anchors: { figures: number; tables: number; equations: number };
+}
+
+export interface ConversionResult {
+  converted: string;
+  conversions: Array<{ from: string; to: string }>;
+  warnings: string[];
+}
+
+// ============================================
+// DOI
+// ============================================
+
+export interface BibEntry {
+  key: string;
+  type: string;
+  doi: string | null;
+  title: string;
+  authorRaw: string;
+  year: number | null;
+  journal: string;
+  skip: boolean;
+  expectDoi: boolean;
+  noDoi: boolean;
+  line: number;
+}
+
+export interface DoiCheckResult {
+  valid: boolean;
+  source?: 'crossref' | 'datacite';
+  metadata?: {
+    title: string;
+    authors: string[];
+    year: number;
+    journal: string;
+    type?: string;
+  };
+  error?: string;
+}
+
+export interface BibtexFetchResult {
+  success: boolean;
+  bibtex?: string;
+  error?: string;
+}
+
+export interface DoiLookupResult {
+  found: boolean;
+  doi?: string;
+  confidence?: 'low' | 'medium' | 'high';
+  score?: number;
+  metadata?: {
+    title: string;
+    authors: string[];
+    year: number;
+    journal: string;
+  };
+  alternatives?: Array<{
+    doi: string;
+    title: string;
+    score: number;
+  }>;
+  error?: string;
+}
+
+export interface BibCheckResult {
+  entries: Array<BibEntry & { status: string; message?: string; metadata?: object }>;
+  valid: number;
+  invalid: number;
+  missing: number;
+  skipped: number;
+}
+
+// ============================================
+// Equations
+// ============================================
+
+export interface Equation {
+  type: 'inline' | 'display';
+  content: string;
+  line: number;
+  file: string;
+}
+
+export interface EquationStats {
+  total: number;
+  display: number;
+  inline: number;
+  byFile: Array<{ file: string; display: number; inline: number }>;
+}
+
+export interface WordEquationResult {
+  success: boolean;
+  equations: Array<{
+    type: 'inline' | 'display' | 'unknown';
+    latex: string | null;
+    position: number;
+    line?: number;
+    raw?: string;
+    error?: string;
+  }>;
+  error?: string;
+}
+
+// ============================================
+// Git
+// ============================================
+
+export interface FileChange {
+  added: number;
+  removed: number;
+  changes: Array<{ added?: boolean; removed?: boolean; value: string }>;
+}
+
+export interface CommitInfo {
+  hash: string;
+  date: string;
+  author: string;
+  message: string;
+}
+
+export interface ChangedFile {
+  file: string;
+  status: 'added' | 'deleted' | 'modified';
+}
+
+export interface BlameEntry {
+  line: number;
+  author: string;
+  date: string;
+  hash: string;
+  content: string;
+}
+
+export interface AuthorStats {
+  lines: number;
+  percentage: number;
+}
+
+export interface ContributorStats {
+  lines: number;
+  files: number;
+}
+
+// ============================================
+// Journals
+// ============================================
+
+export interface JournalRequirements {
+  wordLimit?: { main?: number; abstract?: number };
+  references?: { max?: number; doiRequired?: boolean };
+  figures?: { max?: number };
+  tables?: { max?: number };
+  sections?: string[];
+}
+
+export interface JournalFormatting {
+  csl?: string;
+  pdf?: {
+    documentclass?: string;
+    fontsize?: string;
+    geometry?: string;
+    linestretch?: number;
+    template?: string;
+    numbersections?: boolean;
+    engine?: string;
+    mainfont?: string;
+    sansfont?: string;
+    monofont?: string;
+  };
+  docx?: {
+    reference?: string;
+  };
+  crossref?: {
+    figPrefix?: string | string[];
+    tblPrefix?: string | string[];
+  };
+}
+
+export interface JournalProfile {
+  name: string;
+  url: string;
+  requirements: JournalRequirements;
+  formatting?: JournalFormatting;
+}
+
+export interface ValidationResult {
+  journal: string;
+  valid: boolean;
+  wordCount: { main: number; abstract: number; limit: { main: number; abstract: number } };
+  figures: { count: number; max: number };
+  tables: { count: number; max: number };
+  references: { count: number; max: number };
+  sections: { found: string[]; missing: string[]; required: string[] };
+  errors: string[];
+  warnings: string[];
+}
+
+// ============================================
+// Merge
+// ============================================
+
+export interface ReviewerChange {
+  reviewer: string;
+  type: 'insert' | 'delete' | 'replace';
+  start: number;
+  end: number;
+  oldText: string;
+  newText: string;
+}
+
+export interface Conflict {
+  id: string;
+  start: number;
+  end: number;
+  original: string;
+  changes: ReviewerChange[];
+  section?: string;
+  line?: number;
+  resolved: string | null;
+}
+
+export interface MergeResult {
+  merged: string;
+  conflicts: Conflict[];
+  stats: {
+    reviewers: number;
+    totalChanges: number;
+    nonConflicting: number;
+    conflicts: number;
+    comments: number;
+  };
+  originalText: string;
+}
+
+// ============================================
+// Sections
+// ============================================
+
+export interface SectionConfig {
+  header: string;
+  aliases?: string[];
+  order?: number;
+}
+
+export interface SectionsConfig {
+  version: number;
+  description?: string;
+  sections: Record<string, SectionConfig>;
+}
+
+export interface ExtractedSection {
+  file: string;
+  header: string;
+  content: string;
+  matched: boolean;
+}
+
+// ============================================
+// Word
+// ============================================
+
+export interface WordComment {
+  id: string;
+  author: string;
+  date?: string;
+  text: string;
+}
+
+export interface WordMetadata {
+  title?: string;
+  author?: string;
+  created?: string;
+  modified?: string;
+}
+
+export interface CommentAnchor {
+  text: string;
+  context: string;
+}
+
+export interface WordContent {
+  text: string;
+  html: string;
+}
+
+export interface TrackChangesResult {
+  hasTrackChanges: boolean;
+  content: string | null;
+  stats: { insertions: number; deletions: number };
+}
+
+// ============================================
+// TrackChanges
+// ============================================
+
+export interface TrackChangeMarker {
+  id: number;
+  type: 'insert' | 'delete' | 'substitute' | 'comment';
+  content: string;
+  author: string;
+  replacement?: string;
+}
+
+// ============================================
+// Spelling
+// ============================================
+
+export interface SpellingIssue {
+  word: string;
+  line: number;
+  column: number;
+  file?: string;
+  suggestions?: string[];
+}
+
+export interface SpellingResult {
+  misspelled: SpellingIssue[];
+  possibleNames: SpellingIssue[];
+}
+
+// ============================================
+// Config
+// ============================================
+
+export interface UserConfig {
+  userName?: string;
+  defaultSections?: string[];
+}
+
+// ============================================
+// DOI Cache
+// ============================================
+
+export interface DoiCacheEntry {
+  result: DoiCheckResult | DoiLookupResult;
+  timestamp: number;
+}
+
+export interface DoiCache {
+  entries: Record<string, DoiCacheEntry>;
+  version: number;
+}
+
+export interface DoiCacheStats {
+  size: number;
+  path: string;
+}
+
+// ============================================
+// Errors
+// ============================================
+
+export interface ErrorInfo {
+  code: string;
+  message: string;
+  help?: string;
+  cause?: Error;
+}