Rrwrite Assemble

Manuscript Assembly Protocol

Purpose

Combine all drafted manuscript sections into a complete manuscript file with validation, metadata generation, and quality checks.

Prerequisites

Required files in {target_dir}:

• abstract.md
• introduction.md
• methods.md
• results.md
• discussion.md
• availability.md (optional)

Recommended:

• literature_citations.bib - For citation validation
• outline.md - For structure verification

Workflow

Phase 1: Pre-Assembly Validation

1. Check Required Sections:

   cd {target_dir}
   
   required_sections=("abstract.md" "introduction.md" "results.md" "discussion.md" "methods.md")
   missing=()
   
   for section in "${required_sections[@]}"; do
       if [ ! -f "$section" ]; then
           missing+=("$section")
       fi
   done
   
   if [ ${#missing[@]} -gt 0 ]; then
       echo "Error: Missing required sections: ${missing[*]}"
       exit 1
   fi
   

2. Verify Section Completion: Check workflow state to ensure all sections are marked as completed:

   import json
   from pathlib import Path
   
   state_file = Path("{target_dir}/.rrwrite/state.json")
   if state_file.exists():
       with open(state_file) as f:
           state = json.load(f)
   
       sections = state.get("workflow_status", {}).get("drafting", {}).get("sections", {})
       incomplete = [s for s, data in sections.items() if data.get("status") != "completed"]
   
       if incomplete:
           print(f"Warning: Incomplete sections: {incomplete}")
   

Phase 2: Section Assembly

1. Combine Sections in Order:

   For Nature format: Abstract → Introduction → Results → Discussion → Methods → Availability

   cd {target_dir}
   
   # Clear or create output file
   > manuscript_full.md
   
   # Add header
   cat >> manuscript_full.md << 'EOF'
   # MicroGrowAgents Manuscript
   
   **Target Journal:** Nature
   **Date:** $(date +%Y-%m-%d)
   
   ---
   
   EOF
   
   # Combine sections
   echo "# Abstract" >> manuscript_full.md
   echo "" >> manuscript_full.md
   cat abstract.md >> manuscript_full.md
   echo -e "\n\n---\n" >> manuscript_full.md
   
   echo "# Introduction" >> manuscript_full.md
   echo "" >> manuscript_full.md
   cat introduction.md >> manuscript_full.md
   echo -e "\n\n---\n" >> manuscript_full.md
   
   echo "# Results" >> manuscript_full.md
   echo "" >> manuscript_full.md
   cat results.md >> manuscript_full.md
   echo -e "\n\n---\n" >> manuscript_full.md
   
   echo "# Discussion" >> manuscript_full.md
   echo "" >> manuscript_full.md
   cat discussion.md >> manuscript_full.md
   echo -e "\n\n---\n" >> manuscript_full.md
   
   echo "# Methods" >> manuscript_full.md
   echo "" >> manuscript_full.md
   cat methods.md >> manuscript_full.md
   echo -e "\n\n---\n" >> manuscript_full.md
   
   if [ -f "availability.md" ]; then
       echo "# Data and Code Availability" >> manuscript_full.md
       echo "" >> manuscript_full.md
       cat availability.md >> manuscript_full.md
       echo -e "\n\n---\n" >> manuscript_full.md
   fi
   
   # Add references section placeholder
   echo "# References" >> manuscript_full.md
   echo "" >> manuscript_full.md
   echo "[References will be generated from literature_citations.bib]" >> manuscript_full.md
   
   echo "✓ Manuscript assembled: manuscript_full.md"
   

Phase 3: Metadata Generation

1. Calculate Statistics:

   import re
   from pathlib import Path
   from datetime import datetime
   import json
   
   target_dir = Path("{target_dir}")
   manuscript_file = target_dir / "manuscript_full.md"
   
   # Read manuscript
   with open(manuscript_file) as f:
       content = f.read()
   
   # Count words (exclude markdown headers, code blocks)
   text_only = re.sub(r'```.*?```', '', content, flags=re.DOTALL)
   text_only = re.sub(r'^#.*$', '', text_only, flags=re.MULTILINE)
   text_only = re.sub(r'\[.*?\]', '', text_only)
   words = len(text_only.split())
   
   # Count citations
   citations = re.findall(r'\[([a-zA-Z0-9,\s]+)\]', content)
   unique_citations = set()
   for cite_group in citations:
       for cite in cite_group.split(','):
           cite = cite.strip()
           if cite and cite[0].islower():  # Citation keys start with lowercase
               unique_citations.add(cite)
   
   # Count sections
   sections = re.findall(r'^# (.+)$', content, flags=re.MULTILINE)
   
   # Section word counts
   section_words = {}
   current_section = None
   current_text = []
   
   for line in content.split('\n'):
       if line.startswith('# '):
           if current_section:
               section_text = ' '.join(current_text)
               section_text = re.sub(r'\[.*?\]', '', section_text)
               section_words[current_section] = len(section_text.split())
           current_section = line[2:].strip()
           current_text = []
       else:
           current_text.append(line)
   
   if current_section:
       section_text = ' '.join(current_text)
       section_text = re.sub(r'\[.*?\]', '', section_text)
       section_words[current_section] = len(section_text.split())
   
   # Generate manifest
   manifest = {
       "version": "1.0",
       "generated": datetime.now().isoformat(),
       "manuscript_file": "manuscript_full.md",
       "statistics": {
           "total_words": words,
           "total_sections": len(sections),
           "unique_citations": len(unique_citations),
           "section_breakdown": section_words
       },
       "sections_included": sections,
       "validation": {
           "all_required_sections": True,
           "word_count_target": 3000,  # Nature
           "within_limit": words <= 3500
       }
   }
   
   # Save manifest
   manifest_file = target_dir / "manifest.json"
   with open(manifest_file, 'w') as f:
       json.dump(manifest, f, indent=2)
   
   print(f"✓ Generated manifest: {manifest_file}")
   print(f"  Total words: {words}")
   print(f"  Citations: {len(unique_citations)}")
   print(f"  Sections: {len(sections)}")
   

Phase 4: Quality Checks

1. Check Citation Validity:

   import re
   from pathlib import Path
   
   target_dir = Path("{target_dir}")
   manuscript_file = target_dir / "manuscript_full.md"
   bib_file = target_dir / "literature_citations.bib"
   
   # Extract citations from manuscript
   with open(manuscript_file) as f:
       content = f.read()
   
   cited_keys = set()
   for cite_group in re.findall(r'\[([a-zA-Z0-9,\s]+)\]', content):
       for cite in cite_group.split(','):
           cite = cite.strip()
           if cite and cite[0].islower():
               cited_keys.add(cite)
   
   # Extract citation keys from .bib file
   if bib_file.exists():
       with open(bib_file) as f:
           bib_content = f.read()
   
       bib_keys = set(re.findall(r'@\w+\{([^,]+),', bib_content))
   
       # Check for missing citations
       missing = cited_keys - bib_keys
       if missing:
           print(f"⚠ Warning: Citations not in .bib file: {missing}")
       else:
           print(f"✓ All {len(cited_keys)} citations found in .bib file")
   else:
       print("⚠ Warning: No literature_citations.bib file found")
   

2. Check Word Count Compliance:

   import json
   from pathlib import Path
   
   target_dir = Path("{target_dir}")
   manifest_file = target_dir / "manifest.json"
   
   with open(manifest_file) as f:
       manifest = json.load(f)
   
   total_words = manifest["statistics"]["total_words"]
   target = manifest["validation"]["word_count_target"]
   
   if total_words > target * 1.2:  # 20% over
       print(f"⚠ Warning: Manuscript is {total_words - target} words over target ({total_words}/{target})")
       print(f"  Recommendation: Trim {total_words - target} words before submission")
   elif total_words < target * 0.8:  # 20% under
       print(f"⚠ Warning: Manuscript is {target - total_words} words under target ({total_words}/{target})")
   else:
       print(f"✓ Word count within acceptable range: {total_words}/{target}")
   

Phase 5: State Update

1. Update Workflow State:

   import sys
   from pathlib import Path
   sys.path.insert(0, str(Path('scripts').resolve()))
   from rrwrite_state_manager import StateManager
   import json
   
   target_dir = "{target_dir}"
   manager = StateManager(output_dir=target_dir, enable_git=False)
   
   # Load manifest for statistics
   manifest_file = Path(target_dir) / "manifest.json"
   with open(manifest_file) as f:
       manifest = json.load(f)
   
   # Update assembly stage
   manager.update_workflow_stage(
       "assembly",
       status="completed",
       file=f"{target_dir}/manuscript_full.md",
       manifest_file=f"{target_dir}/manifest.json",
       sections_included=manifest["statistics"]["total_sections"],
       total_word_count=manifest["statistics"]["total_words"],
       validation_warnings=0  # TODO: count actual warnings
   )
   
   print("✓ Workflow state updated")
   

Output Files

The assembly process generates:

1. {target_dir}/manuscript_full.md

   • Complete manuscript with all sections
   • Section headers and separators
   • References placeholder

2. {target_dir}/manifest.json

   • Assembly metadata
   • Word counts per section
   • Citation statistics
   • Validation results

Validation Criteria

The manuscript is considered successfully assembled if:

✅ All required sections present and combined ✅ Word count statistics calculated ✅ Citations extracted and validated against .bib file ✅ Manifest generated with complete metadata ✅ Workflow state updated to mark assembly as completed

Display Summary

After successful assembly, display:

============================================================
MANUSCRIPT ASSEMBLY COMPLETE
============================================================

Output: {target_dir}/manuscript_full.md

Statistics:
  • Total words: [X]
  • Target: [Y] (Nature: 3000 words)
  • Status: [Within limit / Over by X words]
  • Citations: [N] unique citations
  • Sections: [M] sections included

Section Breakdown:
  • Abstract: [X] words
  • Introduction: [X] words
  • Results: [X] words
  • Discussion: [X] words
  • Methods: [X] words
  • Availability: [X] words

Next Steps:
  1. Review manuscript_full.md
  2. Run critique:
     /rrwrite-critique-manuscript --target-dir {target_dir} --file manuscript_full.md
  3. Address critique feedback
  4. Trim to target word count if needed

============================================================

Error Handling

Missing sections:

Error: Missing required sections: [list]
Please draft all sections before assembly:
  /rrwrite-draft-section --target-dir {target_dir} --section [name]

No sections found:

Error: No manuscript sections found in {target_dir}
Expected files: abstract.md, introduction.md, results.md, discussion.md, methods.md

Invalid target directory:

Error: Target directory not found: {target_dir}
Please specify a valid manuscript directory

Notes

• Assembly does NOT modify individual section files
• Original sections remain unchanged in {target_dir}
• Manifest can be regenerated by re-running assembly
• Word counts exclude markdown formatting and citations
• Nature format uses Abstract → Intro → Results → Discussion → Methods order
• For other journals (PLOS, Bioinformatics), adjust section order as needed

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