Section Drafting Protocol

Inputs

• •Section Name: (e.g., "Methods", "Results", "Introduction") provided by the user or plan.
• •Context Files: The list of code/data files identified in manuscript/outline.md.

Workflow

1. •Read Outline: Read manuscript/outline.md to understand section requirements and evidence files.
2. •Load Context: Read the specified code/data files. DO NOT read unrelated files to save tokens.
3. •Load Citations: Read references.bib or manuscript/literature_citations.bib to find relevant citation keys.
4. •Drafting: Write the text in Markdown.
   • •Use LaTeX for math (e.g., $x^2$).
   • •Use [Key] format for citations (e.g., [smith2020]).
   • •Style: Formal academic prose. Passive voice for Methods; Active voice for Results.

Fact-Checking Requirement

CRITICAL: You must verify all numerical claims.

• •Before finalizing a sentence containing a number, locate that number in the source file (*.csv or *.log).
• •If the number involves a calculation (e.g., mean, p-value), generate a temporary Python script to compute it from the raw data and verify your claim.
• •Command: python scripts/rrwrite-verify-stats.py --file <PATH> --col [NAME] --op [mean/max/min]

Figure referencing

• •Ensure every Figure mentioned is referenced as "Figure X" (capitalized).
• •Describe the figure content based on the generating script's logic (e.g., "Figure 1 visualizes the t-SNE projection...").

Output and Naming (per schema: schemas/manuscript.yaml)

Write the section to manuscript/SECTIONNAME.md where SECTIONNAME is:

• •abstract.md for Abstract
• •introduction.md for Introduction
• •methods.md for Methods
• •results.md for Results
• •discussion.md for Discussion
• •conclusion.md for Conclusion

Validation

After drafting, validate the section:

python scripts/rrwrite-validate-manuscript.py --file manuscript/SECTIONNAME.md --type section

State Update

After successful validation, update workflow state:

import sys
from pathlib import Path
sys.path.insert(0, str(Path('scripts').resolve()))
from rrwrite_state_manager import StateManager

manager = StateManager()
manager.add_section_completed("SECTIONNAME")  # e.g., "methods", "results"

Display updated progress:

python scripts/rrwrite-status.py

Report validation status and updated workflow progress. If validation fails, fix issues and re-validate.