docrev 0.9.0 → 0.9.4

package/README.md

@@ -42,7 +42,7 @@ Three reviewers send back three Word files. You manually compare changes, copy-p
 npm install -g docrev
 ```
 
-Requires [Node.js](https://nodejs.org) 18+, [Pandoc](https://pandoc.org) 2.11+, and [LaTeX](#installing-dependencies) for PDF output.
+Requires [Node.js](https://nodejs.org) 18+. [Pandoc](https://pandoc.org) is needed for building DOCX/PDF output. [LaTeX](#installing-dependencies) is additionally needed for PDF.
 
 ## Quick Example
 
@@ -248,6 +248,30 @@ Use `--verbose` to see script output:
 rev build pdf --verbose
 ```
 
+### Journal Profiles
+
+Journal profiles provide both validation rules and build formatting defaults. Set in `rev.yaml`:
+
+```yaml
+journal: nature
+```
+
+Or pass on the command line:
+
+```bash
+rev build pdf -j nature     # applies Nature's CSL style + PDF settings
+```
+
+When a journal is set, its formatting defaults (CSL citation style, font size, margins, line spacing) are applied automatically. Your explicit `rev.yaml` settings always take priority.
+
+Six profiles include formatting: `nature`, `science`, `cell`, `pnas`, `plos-one`, `elife`. All 21 profiles support validation. Custom profiles can include formatting too — see [docs/configuration.md](docs/configuration.md).
+
+```bash
+rev validate --list          # see all profiles ([formatting] tag = build support)
+rev profiles --fetch-csl apa # download a CSL style to cache
+rev profiles --list-csl      # list cached CSL styles
+```
+
 ## Annotation Syntax
 
 Track changes from Word appear as [CriticMarkup](http://criticmarkup.com/):

package/bin/rev.js

@@ -1,19 +1,12 @@
 #!/usr/bin/env node
 
-// Wrapper to run the TypeScript entry point via tsx
-// This allows `rev` command to work after npm link / npm install
+// Run the compiled TypeScript entry point directly (no tsx needed)
 
-import { spawnSync } from 'child_process';
-import { fileURLToPath } from 'url';
+import { pathToFileURL, fileURLToPath } from 'url';
 import { dirname, join } from 'path';
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
-const tsEntry = join(__dirname, 'rev.ts');
+const compiled = join(__dirname, '..', 'dist', 'bin', 'rev.js');
 
-// Run tsx with the TypeScript entry point
-const result = spawnSync('npx', ['tsx', tsEntry, ...process.argv.slice(2)], {
-  stdio: 'inherit',
-  shell: true
-});
-
-process.exit(result.status ?? 0);
+// Windows requires file:// URLs for dynamic ESM imports
+await import(pathToFileURL(compiled).href);

package/dist/bin/rev.js

@@ -1,4 +1,4 @@
-#!/usr/bin/env tsx
+#!/usr/bin/env node
 /**
  * rev - Revision workflow for Word ↔ Markdown round-trips
  *
@@ -39,7 +39,7 @@ function suggestCommand(input, commands) {
     return suggestions;
 }
 // Read version from package.json
-const pkgPath = new URL('../package.json', import.meta.url);
+const pkgPath = new URL('../../package.json', import.meta.url);
 const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
 program
     .name('rev')

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

@@ -1 +1 @@
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+{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../lib/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,YAAY,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAC;AAmHnG;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CA6G3D;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,MAAM,CA+EjF;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAqDvD;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAUpD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAiD3F;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CAG1D;AAED;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,UAAU,EAAE,CAyB1F;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,GAAG,MAAM,CAmB7F;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,gBAAgB,CAwB/D;AAED;;;;;;GAMG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CA6C3D"}

package/dist/lib/annotations.js

@@ -246,6 +246,8 @@ export function stripAnnotations(text, options = {}) {
         if (!keepComments) {
             text = text.replace(PATTERNS.comment, '');
         }
+        // Strip pandoc highlight spans: [text]{.mark} → text
+        text = text.replace(/\[([^\]]*)\]\{\.mark\}/g, '$1');
         // Clean up partial/orphaned markers within the loop
         // This handles cases where nested annotations leave behind fragments
         // Empty annotations (from nested stripping)
@@ -277,6 +279,10 @@ export function stripAnnotations(text, options = {}) {
     text = text.replace(/\{\+\+/g, '');
     text = text.replace(/\{~~/g, '');
     text = text.replace(/~>/g, '');
+    // Remove orphan [ from stripped {.mark} spans where the closing ]{.mark}
+    // was inside a comment. A [ is orphan if no matching ] follows before
+    // the next [ or end of line.
+    text = text.replace(/\[(?![^\[\]]*\])/g, '');
     return text;
 }
 /**

package/dist/lib/annotations.js.map

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package/dist/lib/build.d.ts

@@ -7,7 +7,7 @@
  * - Strips annotations appropriately per output format
  * - Runs pandoc with crossref filter
  */
-import type { Author } from './types.js';
+import type { Author, JournalFormatting } from './types.js';
 export interface CrossrefConfig {
     figureTitle?: string;
     tableTitle?: string;
@@ -18,6 +18,7 @@ export interface CrossrefConfig {
 }
 export interface PdfConfig {
     template?: string | null;
+    headerIncludes?: string | null;
     documentclass?: string;
     fontsize?: string;
     geometry?: string;
@@ -72,6 +73,7 @@ export interface PostprocessConfig {
 export interface BuildConfig {
     title: string;
     authors: (string | Author)[];
+    affiliations: Record<string, string>;
     sections: string[];
     bibliography: string | null;
     csl: string | null;
@@ -118,6 +120,11 @@ interface FullBuildResult {
  * Default rev.yaml configuration
  */
 export declare const DEFAULT_CONFIG: BuildConfig;
+/**
+ * Merge journal formatting defaults into a config.
+ * Priority: DEFAULT_CONFIG < journal formatting < rev.yaml explicit settings
+ */
+export declare function mergeJournalFormatting(config: BuildConfig, formatting: JournalFormatting, directory: string): BuildConfig;
 /**
  * Load rev.yaml config from directory
  * @param directory - Project directory path

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

@@ -1 +1 @@
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package/dist/lib/build.js

@@ -12,7 +12,7 @@ import * as path from 'path';
 import { spawn } 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 { injectMediaIntoPptx, injectSlideNumbers, applyBuildupColors } from './pptx-template.js';
@@ -20,6 +20,8 @@ import { getThemePath } from './pptx-themes.js';
 import { runPostprocess } from './postprocess.js';
 import { hasPandoc, hasPandocCrossref, hasLatex } from './dependencies.js';
 import { buildImageRegistry, writeImageRegistry } from './image-registry.js';
+import { getJournalProfile } from './journals.js';
+import { resolveCSL } from './csl.js';
 // =============================================================================
 // Constants
 // =============================================================================
@@ -33,6 +35,7 @@ const MAX_TITLE_FILENAME_LENGTH = 50;
 export const DEFAULT_CONFIG = {
     title: 'Untitled Document',
     authors: [],
+    affiliations: {},
     sections: [],
     bibliography: null,
     csl: null,
@@ -94,6 +97,63 @@ export const DEFAULT_CONFIG = {
 // =============================================================================
 // Public API
 // =============================================================================
+/**
+ * Merge journal formatting defaults into a config.
+ * Priority: DEFAULT_CONFIG < journal formatting < rev.yaml explicit settings
+ */
+export function mergeJournalFormatting(config, formatting, directory) {
+    const merged = { ...config };
+    // CSL: only apply if user hasn't set one
+    if (formatting.csl && !config.csl) {
+        const resolved = resolveCSL(formatting.csl, directory);
+        if (resolved) {
+            merged.csl = resolved;
+        }
+        // If not resolved locally, store the name — pandoc --citeproc
+        // can sometimes resolve it, and the user can fetch with rev profiles --fetch-csl
+        if (!resolved) {
+            merged.csl = formatting.csl;
+        }
+    }
+    // PDF settings: merge only unset fields
+    if (formatting.pdf) {
+        const userPdf = config.pdf || {};
+        const defaults = DEFAULT_CONFIG.pdf;
+        merged.pdf = { ...config.pdf };
+        for (const [key, value] of Object.entries(formatting.pdf)) {
+            const k = key;
+            // Apply journal value only if user config matches the default (i.e., wasn't explicitly set)
+            if (value !== undefined && JSON.stringify(userPdf[k]) === JSON.stringify(defaults[k])) {
+                merged.pdf[k] = value;
+            }
+        }
+    }
+    // DOCX settings: merge only unset fields
+    if (formatting.docx) {
+        const userDocx = config.docx || {};
+        const defaults = DEFAULT_CONFIG.docx;
+        merged.docx = { ...config.docx };
+        for (const [key, value] of Object.entries(formatting.docx)) {
+            const k = key;
+            if (value !== undefined && JSON.stringify(userDocx[k]) === JSON.stringify(defaults[k])) {
+                merged.docx[k] = value;
+            }
+        }
+    }
+    // Crossref settings: merge only unset fields
+    if (formatting.crossref) {
+        const userCrossref = config.crossref || {};
+        const defaults = DEFAULT_CONFIG.crossref;
+        merged.crossref = { ...config.crossref };
+        for (const [key, value] of Object.entries(formatting.crossref)) {
+            const k = key;
+            if (value !== undefined && JSON.stringify(userCrossref[k]) === JSON.stringify(defaults[k])) {
+                merged.crossref[k] = value;
+            }
+        }
+    }
+    return merged;
+}
 /**
  * Load rev.yaml config from directory
  * @param directory - Project directory path
@@ -113,7 +173,7 @@ export function loadConfig(directory) {
         const content = fs.readFileSync(configPath, 'utf-8');
         const userConfig = YAML.parse(content) || {};
         // Deep merge with defaults
-        const config = {
+        let config = {
             ...DEFAULT_CONFIG,
             ...userConfig,
             crossref: { ...DEFAULT_CONFIG.crossref, ...userConfig.crossref },
@@ -126,6 +186,13 @@ export function loadConfig(directory) {
             postprocess: { ...DEFAULT_CONFIG.postprocess, ...userConfig.postprocess },
             _configPath: configPath,
         };
+        // Apply journal formatting defaults (between DEFAULT_CONFIG and user settings)
+        if (userConfig.journal) {
+            const profile = getJournalProfile(userConfig.journal);
+            if (profile?.formatting) {
+                config = mergeJournalFormatting(config, profile.formatting, directory);
+            }
+        }
         return config;
     }
     catch (err) {
@@ -255,6 +322,14 @@ export function combineSections(directory, config, 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');
     fs.writeFileSync(paperPath, paperContent, 'utf-8');
@@ -267,7 +342,9 @@ function buildFrontmatter(config) {
     const fm = {};
     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;
     }
     if (config.bibliography) {
@@ -288,6 +365,104 @@ function stripFrontmatter(content) {
     }
     return content;
 }
+/**
+ * Check if config uses numbered affiliation mode
+ * (authors have `affiliations` arrays and an affiliations map is defined)
+ */
+function hasNumberedAffiliations(config) {
+    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) {
+    const lines = [];
+    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();
+    affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+    // Authors
+    for (const author of config.authors) {
+        if (typeof author === 'string') {
+            lines.push(`\\author{${author}}`);
+            continue;
+        }
+        const marks = (author.affiliations || [])
+            .map(k => keyToNum.get(k))
+            .filter((n) => n !== undefined);
+        const markStr = marks.length > 0 ? `[${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}]{${text}}`);
+        }
+    }
+    return lines.join('\n');
+}
+/**
+ * Generate markdown author block for DOCX output with superscript affiliations.
+ * Returns markdown text to insert after the YAML frontmatter.
+ */
+function generateMarkdownAuthorBlock(config) {
+    const lines = [];
+    // Map affiliation keys to numbers
+    const affiliationKeys = Object.keys(config.affiliations);
+    const keyToNum = new Map();
+    affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+    // Author line: Name^1,2^, Name^3^, ...
+    const authorParts = [];
+    for (const author of config.authors) {
+        if (typeof author === 'string') {
+            authorParts.push(author);
+            continue;
+        }
+        const marks = (author.affiliations || [])
+            .map(k => keyToNum.get(k))
+            .filter((n) => n !== undefined);
+        let entry = author.name;
+        const superParts = marks.map(String);
+        if (author.corresponding)
+            superParts.push('\\*');
+        if (superParts.length > 0) {
+            entry += `^${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);
+    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.
@@ -382,12 +557,26 @@ export function prepareForFormat(paperPath, format, config, options = {}) {
         content = stripAnnotations(content);
         // 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
@@ -462,6 +651,9 @@ export function buildPandocArgs(format, config, 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}`);
         }