docrev 0.9.3 → 0.9.4

package/dist/lib/journals.js

@@ -233,6 +233,19 @@ export const JOURNAL_PROFILES = {
             sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
         },
     },
+    'methods-ecology-evolution': {
+        name: 'Methods in Ecology and Evolution',
+        url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/author-guidelines',
+        requirements: {
+            wordLimit: { main: 7000, abstract: 350 },
+            references: { doiRequired: true },
+            sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+        },
+        formatting: {
+            csl: 'methods-in-ecology-and-evolution',
+            pdf: { fontsize: '12pt', geometry: 'margin=2.5cm', linestretch: 2 },
+        },
+    },
 };
 /**
  * Get all profiles (built-in + custom)

package/dist/lib/journals.js.map

@@ -1 +1 @@
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package/dist/lib/types.d.ts

@@ -36,6 +36,8 @@ export interface CommentFilterOptions {
 export interface Author {
     name: string;
     affiliation?: string;
+    affiliations?: string[];
+    corresponding?: boolean;
     email?: string;
     orcid?: string;
 }

package/dist/lib/types.d.ts.map

@@ -1 +1 @@
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package/lib/build.ts

@@ -13,7 +13,7 @@ import * as path from 'path';
 import { execSync, spawn, ChildProcess } from 'child_process';
 import YAML from 'yaml';
 import { stripAnnotations } from './annotations.js';
-import { buildRegistry, labelToDisplay, detectDynamicRefs, resolveForwardRefs } from './crossref.js';
+import { buildRegistry, labelToDisplay, detectDynamicRefs, resolveForwardRefs, resolveSupplementaryRefs } from './crossref.js';
 import { processVariables, hasVariables } from './variables.js';
 import { processSlideMarkdown, hasSlideSyntax } from './slides.js';
 import { generatePptxTemplate, templateNeedsRegeneration, injectMediaIntoPptx, injectSlideNumbers, applyThemeFonts, applyCentering, applyBuildupColors } from './pptx-template.js';
@@ -50,6 +50,7 @@ export interface CrossrefConfig {
 
 export interface PdfConfig {
   template?: string | null;
+  headerIncludes?: string | null;
   documentclass?: string;
   fontsize?: string;
   geometry?: string;
@@ -111,6 +112,7 @@ export interface PostprocessConfig {
 export interface BuildConfig {
   title: string;
   authors: (string | Author)[];
+  affiliations: Record<string, string>;
   sections: string[];
   bibliography: string | null;
   csl: string | null;
@@ -189,6 +191,7 @@ interface Registry {
 export const DEFAULT_CONFIG: BuildConfig = {
   title: 'Untitled Document',
   authors: [],
+  affiliations: {},
   sections: [],
   bibliography: null,
   csl: null,
@@ -507,6 +510,15 @@ export function combineSections(directory: string, config: BuildConfig, options:
       // Store resolved count for optional reporting
       options._forwardRefsResolved = resolved.length;
     }
+
+    // Resolve supplementary references and strip their anchors.
+    // pandoc-crossref cannot produce "Figure S1" numbering — it numbers all
+    // figures sequentially. We resolve supplementary refs to plain text and
+    // remove the {#fig:...} attributes so crossref ignores them.
+    const supp = resolveSupplementaryRefs(paperContent, registry);
+    if (supp.resolved.length > 0) {
+      paperContent = supp.text;
+    }
   }
 
   const paperPath = path.join(directory, 'paper.md');
@@ -524,7 +536,9 @@ function buildFrontmatter(config: BuildConfig): Record<string, unknown> {
 
   if (config.title) fm.title = config.title;
 
-  if (config.authors && config.authors.length > 0) {
+  // Skip author in frontmatter when using numbered affiliations —
+  // the author block is injected separately per format
+  if (config.authors && config.authors.length > 0 && !hasNumberedAffiliations(config)) {
     fm.author = config.authors;
   }
 
@@ -550,6 +564,114 @@ function stripFrontmatter(content: string): string {
   return content;
 }
 
+/**
+ * Check if config uses numbered affiliation mode
+ * (authors have `affiliations` arrays and an affiliations map is defined)
+ */
+function hasNumberedAffiliations(config: BuildConfig): boolean {
+  if (!config.affiliations || Object.keys(config.affiliations).length === 0) return false;
+  return config.authors.some(a => typeof a !== 'string' && a.affiliations && a.affiliations.length > 0);
+}
+
+/**
+ * Generate LaTeX author block using authblk package for numbered superscript affiliations.
+ * Returns LaTeX code to be injected via header-includes.
+ */
+function generateLatexAuthorBlock(config: BuildConfig): string {
+  const lines: string[] = [];
+  lines.push('\\usepackage{authblk}');
+  lines.push('\\renewcommand\\Authfont{\\normalsize}');
+  lines.push('\\renewcommand\\Affilfont{\\small}');
+  lines.push('');
+
+  // Map affiliation keys to numbers
+  const affiliationKeys = Object.keys(config.affiliations);
+  const keyToNum = new Map<string, number>();
+  affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+
+  // Authors
+  for (const author of config.authors) {
+    if (typeof author === 'string') {
+      lines.push(`\\author{${author}}`);
+      continue;
+    }
+    const marks = (author.affiliations || [])
+      .map(k => keyToNum.get(k))
+      .filter((n): n is number => n !== undefined);
+
+    const markStr = marks.length > 0 ? `[${marks.join(',')}]` : '';
+    let nameStr = author.name;
+    if (author.corresponding && author.email) {
+      nameStr += `\\thanks{Corresponding author: ${author.email}}`;
+    } else if (author.corresponding) {
+      nameStr += '\\thanks{Corresponding author}';
+    }
+    lines.push(`\\author${markStr}{${nameStr}}`);
+  }
+
+  // Affiliations
+  for (const [key, text] of Object.entries(config.affiliations)) {
+    const num = keyToNum.get(key);
+    if (num !== undefined) {
+      lines.push(`\\affil[${num}]{${text}}`);
+    }
+  }
+
+  return lines.join('\n');
+}
+
+/**
+ * Generate markdown author block for DOCX output with superscript affiliations.
+ * Returns markdown text to insert after the YAML frontmatter.
+ */
+function generateMarkdownAuthorBlock(config: BuildConfig): string {
+  const lines: string[] = [];
+
+  // Map affiliation keys to numbers
+  const affiliationKeys = Object.keys(config.affiliations);
+  const keyToNum = new Map<string, number>();
+  affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+
+  // Author line: Name^1,2^, Name^3^, ...
+  const authorParts: string[] = [];
+  for (const author of config.authors) {
+    if (typeof author === 'string') {
+      authorParts.push(author);
+      continue;
+    }
+    const marks = (author.affiliations || [])
+      .map(k => keyToNum.get(k))
+      .filter((n): n is number => n !== undefined);
+    let entry = author.name;
+    const superParts = marks.map(String);
+    if (author.corresponding) superParts.push('\\*');
+    if (superParts.length > 0) {
+      entry += `^${superParts.join(',')}^`;
+    }
+    authorParts.push(entry);
+  }
+  lines.push(authorParts.join(', '));
+  lines.push('');
+
+  // Affiliation lines: ^1^ Department of ...
+  for (const [key, text] of Object.entries(config.affiliations)) {
+    const num = keyToNum.get(key);
+    if (num !== undefined) {
+      lines.push(`^${num}^ ${text}`);
+    }
+  }
+
+  // Corresponding author footnote
+  const corresponding = config.authors.find(a => typeof a !== 'string' && a.corresponding) as Author | undefined;
+  if (corresponding?.email) {
+    lines.push('');
+    lines.push(`^\\*^ Corresponding author: ${corresponding.email}`);
+  }
+
+  lines.push('');
+  return lines.join('\n');
+}
+
 /**
  * Process markdown tables to apply nowrap formatting to specified columns.
  * Converts distribution notation (Normal, Student-t, Gamma) to LaTeX math.
@@ -672,12 +794,28 @@ export function prepareForFormat(
 
     // Process tables for nowrap columns (convert Normal() → $\mathcal{N}()$ etc.)
     content = processTablesForFormat(content, config.tables, format);
+
+    // Inject LaTeX author block with numbered affiliations
+    if (hasNumberedAffiliations(config)) {
+      const latexBlock = generateLatexAuthorBlock(config);
+      // Inject as header-includes in the YAML frontmatter
+      content = content.replace(/^(---\r?\n[\s\S]*?)(---\r?\n)/, (match, yamlContent, closing) => {
+        return `${yamlContent}header-includes: |\n${latexBlock.split('\n').map(l => '  ' + l).join('\n')}\n${closing}`;
+      });
+    }
   } else if (format === 'docx') {
     // Strip track changes, optionally keep comments
     content = stripAnnotations(content, { keepComments: config.docx.keepComments });
 
     // Convert @fig:label to "Figure 1" for Word readers
     content = convertDynamicRefsToDisplay(content, registry);
+
+    // Inject markdown author block with superscript affiliations
+    if (hasNumberedAffiliations(config)) {
+      const mdBlock = generateMarkdownAuthorBlock(config);
+      // Insert after YAML frontmatter, before body content
+      content = content.replace(/^(---\r?\n[\s\S]*?---\r?\n)/, `$1\n${mdBlock}\n`);
+    }
   } else if (format === 'beamer' || format === 'pptx') {
     // Strip annotations for slide output
     content = stripAnnotations(content);
@@ -759,6 +897,9 @@ export function buildPandocArgs(format: string, config: BuildConfig, outputPath:
     args.push('-V', `documentclass=${config.pdf.documentclass}`);
     args.push('-V', `fontsize=${config.pdf.fontsize}`);
     args.push('-V', `geometry:${config.pdf.geometry}`);
+    if (config.pdf.headerIncludes) {
+      args.push('-H', config.pdf.headerIncludes);
+    }
     if (config.pdf.linestretch !== 1) {
       args.push('-V', `linestretch=${config.pdf.linestretch}`);
     }

package/lib/crossref.ts

@@ -157,7 +157,7 @@ const EXCLUSION_PATTERNS = [
 /**
  * Pattern for extracting anchors from markdown: {#fig:label}, {#tbl:label}
  */
-const ANCHOR_PATTERN = /\{#(fig|tbl|eq):([^}]+)\}/gi;
+const ANCHOR_PATTERN = /\{#(fig|tbl|eq):([a-zA-Z0-9_-]+)/gi;
 
 /**
  * Pattern for @-style references: @fig:label, @tbl:label
@@ -681,6 +681,67 @@ export function resolveForwardRefs(
   return { text: result, resolved, unresolved };
 }
 
+/**
+ * Resolve ALL supplementary references and strip supplementary anchor labels.
+ *
+ * pandoc-crossref cannot produce "Figure S1" numbering — it numbers all figures
+ * sequentially. This function resolves every @fig:label / @tbl:label that points
+ * to a supplementary item to plain text ("Figure S1", "Table S1") and removes
+ * the {#fig:label} / {#tbl:label} attributes so pandoc-crossref ignores them.
+ */
+export function resolveSupplementaryRefs(
+  text: string,
+  registry: Registry
+): {
+  text: string;
+  resolved: Array<{ from: string; to: string }>;
+} {
+  const resolved: Array<{ from: string; to: string }> = [];
+  let result = text;
+
+  // Collect supplementary labels
+  const suppLabels = new Set<string>();
+  for (const [label, info] of registry.figures) {
+    if (info.isSupp) suppLabels.add(`fig:${label}`);
+  }
+  for (const [label, info] of registry.tables) {
+    if (info.isSupp) suppLabels.add(`tbl:${label}`);
+  }
+
+  if (suppLabels.size === 0) return { text: result, resolved };
+
+  // 1. Replace all @fig:label / @tbl:label references to supplementary items
+  const refs = detectDynamicRefs(result);
+  // Process in reverse to preserve positions
+  for (let i = refs.length - 1; i >= 0; i--) {
+    const ref = refs[i];
+    if (!ref) continue;
+    const key = `${ref.type}:${ref.label}`;
+    if (!suppLabels.has(key)) continue;
+
+    const display = labelToDisplay(ref.type as 'fig' | 'tbl' | 'eq', ref.label, registry);
+    if (display) {
+      result =
+        result.slice(0, ref.position) + display + result.slice(ref.position + ref.match.length);
+      resolved.push({ from: ref.match, to: display });
+    }
+  }
+
+  // 2. Strip {#fig:label} and {#tbl:label} attributes from supplementary anchors
+  //    so pandoc-crossref does not re-number them
+  for (const key of suppLabels) {
+    // Match {#fig:label ...} or just {#fig:label}
+    const escaped = key.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+    const pattern = new RegExp(`\\{#${escaped}(?:\\s[^}]*)?\\}`, 'g');
+    result = result.replace(pattern, (match) => {
+      resolved.push({ from: match, to: '(stripped)' });
+      return '';
+    });
+  }
+
+  return { text: result, resolved };
+}
+
 /**
  * Format registry for display
  */

package/lib/journals.ts

@@ -257,6 +257,20 @@ export const JOURNAL_PROFILES: Record<string, JournalProfile> = {
       sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
     },
   },
+
+  'methods-ecology-evolution': {
+    name: 'Methods in Ecology and Evolution',
+    url: 'https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/author-guidelines',
+    requirements: {
+      wordLimit: { main: 7000, abstract: 350 },
+      references: { doiRequired: true },
+      sections: ['Abstract', 'Introduction', 'Methods', 'Results', 'Discussion'],
+    },
+    formatting: {
+      csl: 'methods-in-ecology-and-evolution',
+      pdf: { fontsize: '12pt', geometry: 'margin=2.5cm', linestretch: 2 },
+    },
+  },
 };
 
 /**

package/lib/types.ts

@@ -50,6 +50,8 @@ export interface CommentFilterOptions {
 export interface Author {
   name: string;
   affiliation?: string;
+  affiliations?: string[];
+  corresponding?: boolean;
   email?: string;
   orcid?: string;
 }

package/package.json

@@ -1,77 +1,77 @@
 {
   "name": "docrev",
-  "version": "0.9.3",
+  "version": "0.9.4",
   "description": "Academic paper revision workflow: Word ↔ Markdown round-trips, DOI validation, reviewer comments",
   "type": "module",
-  "types": "types/index.d.ts",
+  "types": "dist/lib/types.d.ts",
   "exports": {
     ".": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/annotations.js"
+      "types": "./dist/lib/annotations.d.ts",
+      "import": "./dist/lib/annotations.js"
     },
     "./annotations": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/annotations.js"
+      "types": "./dist/lib/annotations.d.ts",
+      "import": "./dist/lib/annotations.js"
     },
     "./build": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/build.js"
+      "types": "./dist/lib/build.d.ts",
+      "import": "./dist/lib/build.js"
     },
     "./citations": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/citations.js"
+      "types": "./dist/lib/citations.d.ts",
+      "import": "./dist/lib/citations.js"
     },
     "./crossref": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/crossref.js"
+      "types": "./dist/lib/crossref.d.ts",
+      "import": "./dist/lib/crossref.js"
     },
     "./doi": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/doi.js"
+      "types": "./dist/lib/doi.d.ts",
+      "import": "./dist/lib/doi.js"
     },
     "./equations": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/equations.js"
+      "types": "./dist/lib/equations.d.ts",
+      "import": "./dist/lib/equations.js"
     },
     "./git": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/git.js"
+      "types": "./dist/lib/git.d.ts",
+      "import": "./dist/lib/git.js"
     },
     "./journals": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/journals.js"
+      "types": "./dist/lib/journals.d.ts",
+      "import": "./dist/lib/journals.js"
     },
     "./merge": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/merge.js"
+      "types": "./dist/lib/merge.d.ts",
+      "import": "./dist/lib/merge.js"
     },
     "./sections": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/sections.js"
+      "types": "./dist/lib/sections.d.ts",
+      "import": "./dist/lib/sections.js"
     },
     "./word": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/word.js"
+      "types": "./dist/lib/word.d.ts",
+      "import": "./dist/lib/word.js"
     },
     "./variables": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/variables.js"
+      "types": "./dist/lib/variables.d.ts",
+      "import": "./dist/lib/variables.js"
     },
     "./grammar": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/grammar.js"
+      "types": "./dist/lib/grammar.d.ts",
+      "import": "./dist/lib/grammar.js"
     },
     "./trackchanges": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/trackchanges.js"
+      "types": "./dist/lib/trackchanges.d.ts",
+      "import": "./dist/lib/trackchanges.js"
     },
     "./spelling": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/spelling.js"
+      "types": "./dist/lib/spelling.d.ts",
+      "import": "./dist/lib/spelling.js"
     },
     "./wordcomments": {
-      "types": "./types/index.d.ts",
-      "import": "./lib/wordcomments.js"
+      "types": "./dist/lib/wordcomments.d.ts",
+      "import": "./dist/lib/wordcomments.js"
     }
   },
   "engines": {
@@ -81,7 +81,7 @@
     "rev": "bin/rev.js"
   },
   "scripts": {
-    "build": "tsc",
+    "build": "tsc && node scripts/postbuild.js",
     "build:watch": "tsc --watch",
     "dev": "tsx bin/rev.ts",
     "test": "tsx --test test/*.test.js",

package/scripts/postbuild.js

@@ -0,0 +1,28 @@
+#!/usr/bin/env node
+
+/**
+ * Post-build fixups for compiled TypeScript output.
+ *
+ * tsc compiles bin/rev.ts → dist/bin/rev.js but:
+ *   1. Preserves the #!/usr/bin/env tsx shebang (needs to be node)
+ *   2. Relative paths like '../package.json' break (bin/ → dist/bin/ adds a level)
+ */
+
+import { readFileSync, writeFileSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const revPath = join(__dirname, '..', 'dist', 'bin', 'rev.js');
+
+let content = readFileSync(revPath, 'utf-8');
+
+// Fix shebang: tsx → node
+content = content.replace('#!/usr/bin/env tsx', '#!/usr/bin/env node');
+
+// Fix package.json path: ../package.json → ../../package.json
+// (bin/rev.ts uses ../package.json which is correct from bin/, but from dist/bin/ needs one more level)
+content = content.replace("'../package.json'", "'../../package.json'");
+
+writeFileSync(revPath, content, 'utf-8');
+console.log('postbuild: fixed dist/bin/rev.js (shebang + paths)');

package/skill/REFERENCE.md

@@ -185,7 +185,7 @@ Built-in scientific vocabulary reduces false positives. Possible author names ar
 Check against journal requirements.
 ```bash
 rev validate --journal nature
-rev validate --list          # List 21 available journals
+rev validate --list          # List 22 available journals
 ```
 
 ### rev citations

package/skill/SKILL.md

@@ -151,7 +151,7 @@ rev doi add 10.1234/example          # Add citation from DOI
 
 ```bash
 rev validate --journal nature        # Check journal requirements
-rev validate --list                  # List 21 available journal profiles
+rev validate --list                  # List 22 available journal profiles
 rev lint                             # Check broken refs, missing citations
 ```