review-paper-code

Review Paper Code

Review a research project's paper and code for reproducibility, code quality, and paper-code alignment. Be constructive, concrete, and calibrated. Treat gaps as items to verify, not accusations.

Scope

This skill supports:

• LaTeX papers
• Stata (.do), R (.R, .r), and Python (.py) code

Default review depth:

• main: prioritize the main paper, main scripts, and core outputs
• full: inspect all detected code files in scope

If no depth is provided, default to main.

Phase 1: Discover the Project

First parse $ARGUMENTS:

• If one argument looks like a .tex path, use it as PAPER_FILE.
• If one argument looks like a directory path, use it as CODE_DIR.
• If one argument is main or full, use it as REVIEW_DEPTH.

If any of the above are missing, auto-detect them.

1. Find the paper

Use Glob to search for **/*.tex, excluding obvious build folders such as _minted-*, build/, output/, .git/, node_modules/.

Identify the main paper file as the best candidate containing \documentclass or \begin{document}.

If multiple candidates exist, first discard files whose document class is beamer (slides) and files whose name or folder suggests an old draft or a response letter (response*, letter*, slides*, old*, archive/, etc.). Then prefer:

1. A path explicitly provided in $ARGUMENTS
2. A file in Writing/, writing/, Paper/, paper/, Draft/, or the repo root
3. The file that appears to include the most component files via \input{} / \include{}

Record the result as PAPER_FILE.

2. Find the code

If CODE_DIR was not provided, look for likely code roots in this order:

• Code/
• Analysis/
• code/
• analysis/
• scripts/
• src/
• programs/
• replication/

If no single directory is clearly best, use the repo root and limit later discovery to likely code files.

Record the result as CODE_DIR.

3. Find code files

Within CODE_DIR and subdirectories, find:

• **/*.do
• **/*.R
• **/*.r
• **/*.py