docrev 0.3.0 → 0.5.0

package/completions/rev.bash

@@ -0,0 +1,127 @@
+# Bash completion for rev (docrev)
+# Install: source this file or add to ~/.bashrc:
+#   eval "$(rev completions bash)"
+
+_rev_completions() {
+    local cur prev words cword
+    _init_completion || return
+
+    local commands="build new import sections extract review status comments resolve reply strip refs migrate config install doi citations equations figures response anonymize validate merge diff history help init split word-count wc stats search backup export preview watch lint grammar annotate apply comment completions"
+    local build_formats="pdf docx tex all"
+    local doi_actions="check lookup fetch add"
+    local eq_actions="list extract convert from-word"
+    local help_topics="workflow syntax commands"
+    local preview_formats="pdf docx"
+
+    case "${prev}" in
+        rev)
+            COMPREPLY=($(compgen -W "${commands} --help --version" -- "${cur}"))
+            return
+            ;;
+        build)
+            COMPREPLY=($(compgen -W "${build_formats} --toc --show-changes --clean" -- "${cur}"))
+            return
+            ;;
+        new)
+            COMPREPLY=($(compgen -W "--list --template" -- "${cur}"))
+            return
+            ;;
+        --template)
+            COMPREPLY=($(compgen -W "paper minimal thesis proposal" -- "${cur}"))
+            return
+            ;;
+        doi)
+            COMPREPLY=($(compgen -W "${doi_actions}" -- "${cur}"))
+            return
+            ;;
+        equations|eq)
+            COMPREPLY=($(compgen -W "${eq_actions}" -- "${cur}"))
+            return
+            ;;
+        validate)
+            COMPREPLY=($(compgen -W "--journal --list" -- "${cur}"))
+            return
+            ;;
+        --journal)
+            COMPREPLY=($(compgen -W "nature science plos cell ecology custom" -- "${cur}"))
+            return
+            ;;
+        help)
+            COMPREPLY=($(compgen -W "${help_topics}" -- "${cur}"))
+            return
+            ;;
+        config)
+            COMPREPLY=($(compgen -W "user" -- "${cur}"))
+            return
+            ;;
+        word-count|wc)
+            COMPREPLY=($(compgen -W "--limit --journal" -- "${cur}"))
+            return
+            ;;
+        preview)
+            COMPREPLY=($(compgen -W "${preview_formats}" -- "${cur}"))
+            return
+            ;;
+        watch)
+            COMPREPLY=($(compgen -W "pdf docx all --no-open" -- "${cur}"))
+            return
+            ;;
+        lint)
+            COMPREPLY=($(compgen -W "--fix" -- "${cur}"))
+            return
+            ;;
+        grammar)
+            COMPREPLY=($(compgen -W "--learn --forget --list --rules --no-scientific --severity" -- "${cur}"))
+            return
+            ;;
+        annotate)
+            COMPREPLY=($(compgen -f -X '!*.docx' -- "${cur}"))
+            return
+            ;;
+        apply)
+            COMPREPLY=($(compgen -f -X '!*.md' -- "${cur}"))
+            return
+            ;;
+        comment)
+            COMPREPLY=($(compgen -f -X '!*.docx' -- "${cur}"))
+            return
+            ;;
+        completions)
+            COMPREPLY=($(compgen -W "bash zsh" -- "${cur}"))
+            return
+            ;;
+        import|sections|extract|review|status|comments|strip|refs|migrate|figures|response|anonymize|split)
+            # Complete with .md and .docx files
+            COMPREPLY=($(compgen -f -X '!*.@(md|docx)' -- "${cur}"))
+            return
+            ;;
+        resolve|reply)
+            # Complete with -n option or .md files
+            if [[ "${cur}" == -* ]]; then
+                COMPREPLY=($(compgen -W "-n -m" -- "${cur}"))
+            else
+                COMPREPLY=($(compgen -f -X '!*.md' -- "${cur}"))
+            fi
+            return
+            ;;
+        check|lookup|add|fetch)
+            # DOI subcommands - complete with .bib files
+            COMPREPLY=($(compgen -f -X '!*.bib' -- "${cur}"))
+            return
+            ;;
+        citations)
+            COMPREPLY=($(compgen -f -X '!*.bib' -- "${cur}"))
+            return
+            ;;
+        merge)
+            # Complete with .md and .docx files
+            COMPREPLY=($(compgen -f -X '!*.@(md|docx)' -- "${cur}"))
+            return
+            ;;
+    esac
+
+    # Default: complete with files
+    COMPREPLY=($(compgen -f -- "${cur}"))
+}
+
+complete -F _rev_completions rev

package/completions/rev.zsh

@@ -0,0 +1,207 @@
+#compdef rev
+
+# Zsh completion for rev (docrev)
+# Install: add to fpath or run:
+#   eval "$(rev completions zsh)"
+
+_rev() {
+    local -a commands build_formats doi_actions eq_actions help_topics journals preview_formats
+
+    commands=(
+        'build:Build PDF/DOCX/TEX from sections'
+        'new:Create new project from template'
+        'import:Import Word document'
+        'sections:Import to section files'
+        'extract:Extract text from Word'
+        'review:Interactive review TUI'
+        'status:Show annotation counts'
+        'comments:List comments'
+        'resolve:Mark comment as resolved'
+        'reply:Reply to comments'
+        'strip:Output clean markdown'
+        'refs:Show reference status'
+        'migrate:Convert hardcoded refs'
+        'config:Configure settings'
+        'install:Check dependencies'
+        'doi:DOI validation'
+        'citations:Validate citations'
+        'equations:Extract equations'
+        'figures:List figures'
+        'response:Generate response letter'
+        'anonymize:Prepare for blind review'
+        'validate:Check journal requirements'
+        'merge:Merge reviewer feedback'
+        'diff:Compare against git history'
+        'history:Show revision history'
+        'help:Show help'
+        'init:Initialize project'
+        'split:Split paper.md to sections'
+        'word-count:Show word counts per section'
+        'wc:Show word counts (alias)'
+        'stats:Show project statistics'
+        'search:Search across files'
+        'backup:Create timestamped backup'
+        'export:Export project as zip'
+        'preview:Build and open document'
+        'watch:Watch and auto-rebuild'
+        'lint:Check for issues'
+        'grammar:Check grammar and style'
+        'annotate:Add comments to DOCX'
+        'apply:Apply annotations as track changes'
+        'comment:Interactive comment mode'
+        'completions:Generate shell completions'
+    )
+
+    preview_formats=(
+        'pdf:Preview PDF'
+        'docx:Preview Word document'
+    )
+
+    build_formats=(
+        'pdf:Build PDF'
+        'docx:Build Word document'
+        'tex:Build LaTeX'
+        'all:Build all formats'
+    )
+
+    doi_actions=(
+        'check:Validate DOIs'
+        'lookup:Find missing DOIs'
+        'fetch:Get BibTeX from DOI'
+        'add:Add citation by DOI'
+    )
+
+    eq_actions=(
+        'list:List equations'
+        'extract:Extract to file'
+        'convert:Convert to Word'
+        'from-word:Extract from Word'
+    )
+
+    help_topics=(
+        'workflow:Review workflow'
+        'syntax:CriticMarkup syntax'
+        'commands:All commands'
+    )
+
+    journals=(
+        'nature:Nature journal'
+        'science:Science journal'
+        'plos:PLOS ONE'
+        'cell:Cell journal'
+        'ecology:Ecology journals'
+        'custom:Custom profile'
+    )
+
+    case "$words[2]" in
+        build)
+            _describe -t formats 'format' build_formats
+            _arguments \
+                '--toc[Include table of contents]' \
+                '--show-changes[Show track changes in DOCX]' \
+                '--clean[Clean build files]'
+            ;;
+        new)
+            _arguments \
+                '--list[List templates]' \
+                '--template[Template name]:template:(paper minimal thesis proposal)'
+            ;;
+        doi)
+            _describe -t actions 'action' doi_actions
+            ;;
+        equations|eq)
+            _describe -t actions 'action' eq_actions
+            ;;
+        validate)
+            _arguments \
+                '--list[List journals]' \
+                '--journal[Journal name]:journal:($journals)'
+            ;;
+        help)
+            _describe -t topics 'topic' help_topics
+            ;;
+        config)
+            _values 'setting' 'user[Set user name]'
+            ;;
+        word-count|wc)
+            _arguments \
+                '--limit[Word limit]:number:' \
+                '--journal[Use journal word limit]:journal:'
+            ;;
+        preview)
+            _describe -t formats 'format' preview_formats
+            ;;
+        watch)
+            _arguments \
+                '--no-open[Do not open after build]'
+            _values 'format' 'pdf' 'docx' 'all'
+            ;;
+        lint)
+            _arguments \
+                '--fix[Auto-fix issues]'
+            ;;
+        grammar)
+            _arguments \
+                '--learn[Add word to dictionary]:word:' \
+                '--forget[Remove from dictionary]:word:' \
+                '--list[List dictionary words]' \
+                '--rules[List grammar rules]' \
+                '--no-scientific[Disable science rules]' \
+                '--severity[Minimum severity]:level:(error warning info)'
+            _files -g '*.md'
+            ;;
+        annotate)
+            _arguments \
+                '-m[Comment message]:text:' \
+                '-s[Search text]:text:' \
+                '-a[Author name]:name:'
+            _files -g '*.docx'
+            ;;
+        apply)
+            _arguments \
+                '-a[Author name]:name:'
+            _files -g '*.md'
+            ;;
+        comment)
+            _arguments \
+                '-a[Author name]:name:'
+            _files -g '*.docx'
+            ;;
+        completions)
+            _values 'shell' 'bash' 'zsh'
+            ;;
+        import|sections|extract|review|status|comments|strip|refs|migrate|figures|response|anonymize|split|search|stats)
+            _files -g '*.md' -g '*.docx'
+            ;;
+        resolve|reply)
+            _arguments \
+                '-n[Comment number]:number:' \
+                '-m[Reply message]:message:'
+            _files -g '*.md'
+            ;;
+        check|lookup|add|citations)
+            _files -g '*.bib'
+            ;;
+        merge)
+            _files -g '*.md' -g '*.docx'
+            ;;
+        backup)
+            _arguments \
+                '--name[Custom backup name]:name:' \
+                '--output[Output directory]:dir:_files -/'
+            ;;
+        export)
+            _arguments \
+                '--output[Output filename]:file:' \
+                '--include-output[Include built files]'
+            ;;
+        *)
+            _describe -t commands 'command' commands
+            _arguments \
+                '--help[Show help]' \
+                '--version[Show version]'
+            ;;
+    esac
+}
+
+_rev "$@"

package/lib/build.js

@@ -14,6 +14,7 @@ import { execSync, spawn } from 'child_process';
 import yaml from 'js-yaml';
 import { stripAnnotations } from './annotations.js';
 import { buildRegistry, labelToDisplay, detectDynamicRefs } from './crossref.js';
+import { processVariables, hasVariables } from './variables.js';
 
 /**
  * Default rev.yaml configuration
@@ -156,6 +157,9 @@ export function combineSections(directory, config, options = {}) {
   parts.push('---');
   parts.push('');
 
+  // Read all section contents for variable processing
+  const sectionContents = [];
+
   // Combine sections
   for (const section of sections) {
     const filePath = path.join(directory, section);
@@ -163,13 +167,20 @@ export function combineSections(directory, config, options = {}) {
 
     // Remove any existing frontmatter from section files
     content = stripFrontmatter(content);
+    sectionContents.push(content);
 
     parts.push(content.trim());
     parts.push('');
     parts.push(''); // Double newline between sections
   }
 
-  const paperContent = parts.join('\n');
+  let paperContent = parts.join('\n');
+
+  // Process template variables if any exist
+  if (hasVariables(paperContent)) {
+    paperContent = processVariables(paperContent, config, { sectionContents });
+  }
+
   const paperPath = path.join(directory, 'paper.md');
 
   fs.writeFileSync(paperPath, paperContent, 'utf-8');

package/lib/doi.js

@@ -105,9 +105,13 @@ export function parseBibEntries(bibPath) {
     const skipMatch = entryContent.match(/\bnodoi\s*=\s*[{"]?(true|yes|1)[}""]?/i);
     const skip = !!skipMatch;
 
-    // Check for comment marker before entry: % no-doi
+    // Check for comment marker immediately before entry: % no-doi
+    // Only look at the text between the last entry end (or start) and this entry
     const linesBefore = content.slice(Math.max(0, startPos - 200), startPos);
-    const commentSkip = /% *no-?doi/i.test(linesBefore);
+    // Find the last closing brace or start of file to avoid matching comments for previous entries
+    const lastEntryEnd = linesBefore.lastIndexOf('}');
+    const relevantBefore = lastEntryEnd >= 0 ? linesBefore.slice(lastEntryEnd + 1) : linesBefore;
+    const commentSkip = /% *no-?doi/i.test(relevantBefore);
 
     entries.push({
       key,

package/lib/equations.js

@@ -52,12 +52,30 @@ export function extractEquations(text, file = '') {
     // Skip code blocks
     if (line.trim().startsWith('```')) continue;
 
+    // Handle inline math ($...$) in a segment of text
+    // Careful not to match $$ or escaped \$
+    const inlinePattern = /(?<![\$\\])\$(?!\$)([^$\n]+)\$(?!\$)/g;
+    const extractInline = (segment) => {
+      let match;
+      inlinePattern.lastIndex = 0;
+      while ((match = inlinePattern.exec(segment)) !== null) {
+        equations.push({
+          type: 'inline',
+          content: match[1].trim(),
+          line: lineNum + 1,
+          file,
+        });
+      }
+    };
+
     // Handle display math blocks ($$...$$)
     if (line.includes('$$')) {
       const parts = line.split('$$');
 
       if (!inDisplayMath && parts.length >= 3) {
         // Single-line display math: $$content$$
+        // Also extract inline math from surrounding text
+        extractInline(parts[0]); // Text before $$
         for (let i = 1; i < parts.length; i += 2) {
           if (parts[i].trim()) {
             equations.push({
@@ -68,8 +86,13 @@ export function extractEquations(text, file = '') {
             });
           }
         }
+        // Extract inline from text after the last $$
+        if (parts.length % 2 === 1 && parts[parts.length - 1]) {
+          extractInline(parts[parts.length - 1]);
+        }
       } else if (!inDisplayMath) {
         // Start of multi-line display math
+        extractInline(parts[0]); // Text before $$
         inDisplayMath = true;
         displayMathStart = lineNum + 1;
         displayMathContent = parts[1] || '';
@@ -86,6 +109,10 @@ export function extractEquations(text, file = '') {
           });
         }
         displayMathContent = '';
+        // Text after $$ on closing line
+        if (parts[1]) {
+          extractInline(parts[1]);
+        }
       }
       continue;
     }
@@ -95,18 +122,8 @@ export function extractEquations(text, file = '') {
       continue;
     }
 
-    // Handle inline math ($...$)
-    // Careful not to match $$ or escaped \$
-    const inlinePattern = /(?<!\$)\$(?!\$)([^$\n]+)\$(?!\$)/g;
-    let match;
-    while ((match = inlinePattern.exec(line)) !== null) {
-      equations.push({
-        type: 'inline',
-        content: match[1].trim(),
-        line: lineNum + 1,
-        file,
-      });
-    }
+    // No display math on this line - extract inline math
+    extractInline(line);
   }
 
   return equations;