read-code

---

name: read-code description: Verify paper claims with evidence_type "code" against the actual codebase. Use after read-txt to check if code matches what the paper says. author: PaperDoctor Research license: MIT argument-hint: [paper.pdf] [codebase-path] allowed-tools: Read, Grep, Glob, Bash(python *)

Verify Code Claims

Check each claim tagged evidence_type: "code" from read-txt against the actual codebase.

Workflow

Verify Code:
- [ ] Step 1: Load claims
- [ ] Step 2: Read code index
- [ ] Step 3: Verify each code claim
- [ ] Step 4: Save report

Step 1: Load Claims

Read {paper_dir}/reports/check_claim.json

Filter to claims where evidence_type includes "code". These are the claims to verify.

Each claim's id, source, quote, claim, evidence_type fields should be copied as-is into the output — do not modify them.

Step 2: Read Code Index

Read {paper_dir}/metadata/code/index.json

This is the tree-sitter index from prepare-paper. Use it to locate relevant files, symbols, and config entries.

Step 3: Verify Each Code Claim

For each code claim, find the relevant code and judge whether it matches.

How to find code: Use Grep, Glob, and the code index. For hyperparameters, check config files first. For architecture claims, check class definitions and __init__ / forward methods.

For each claim, produce:

{
  "id": 7,
  "source": "experiments",
  "quote": "model/encoder.py:42 — num_layers=12, hidden_size=768\n\nWe use a 12-layer transformer with embedding dimension 768",
  "claim": "Model architecture is a 12-layer, 768-dim transformer",
  "evidence_type": ["code"],
  "status": "pass",
  "reason": ""
}

Field definitions (paper triple → fields):

Field	When	Purpose
quote	always	The Where evidence. Must start with path/to/file.ext:LINE (or :LINE-LINE) followed by — short note about what the code shows. If the issue is "feature X is missing from the repo", anchor to the most relevant file at line 0, e.g. src/trainer/fgt_prediction_trainer.py:0 — no margin-loss entry point present. After the file:line prefix you may include the original paper sentence on a new line so the reviewer sees both ends of the comparison. Downstream tooling extracts the path:LINE prefix to wire the code viewer.
reason	warning/error only	The Why. Explanation of the discrepancy.
suggest	warning/error only	The How. One-sentence concrete fix the author can apply.

Statuses:

Status	Meaning
pass	Code matches the claim
warning	Code is related but differs in detail (e.g., paper says Adam, code uses AdamW)
error	Code contradicts the claim, or no implementation found in the repo

When status is warning or error, reason should explain the discrepancy and suggest should propose a concrete fix (e.g., "Update the paper text to match the code, or change the code to AdamW to match the paper claim").

Step 4: Save Report

Output: {paper_dir}/reports/check_code.json

{
  "summary": {
    "total": 8,
    "pass": 5,
    "warning": 2,
    "error": 1
  },
  "results": [
    {
      "id": 9,
      "source": "experiments",
      "quote": "configs/train.yaml:14 — optimizer: Adam\n\nWe train all models using the AdamW optimizer",
      "claim": "Training optimizer is AdamW",
      "evidence_type": ["code"],
      "status": "warning",
      "reason": "Paper says AdamW but configs/train.yaml line 14 sets optimizer: Adam",
      "suggest": "Update the paper text to AdamW or change the config to match the paper claim."
    },
    {
      "id": 10,
      "source": "method",
      "quote": "src/trainer/fgt_prediction_trainer.py:0 — no margin-loss entry point present\n\nWe use a custom margin-loss training objective",
      "claim": "Margin loss is the training objective",
      "evidence_type": ["code"],
      "status": "error",
      "reason": "No margin-loss entry point in src/trainer/; the released default uses binary cross-entropy.",
      "suggest": "Add the margin-loss entry point to the released code, or remove the claim from the paper."
    }
  ]
}

Coverage Rule

Every claim with code in evidence_type MUST appear in results. No claim may be silently skipped. Valid statuses are pass / warning / error. If a claim cannot be verified at all from the codebase (no relevant file found, repo too incomplete), use status: "warning" with quote like path/to/expected/file.ext:0 — file not in repo so the reviewer can still see what was being checked.

Tips

• Check config files (.json, .yaml) first — most hyperparameters live there, not in Python code
• Map paper terms to code terms (e.g., "learning rate" → lr, "layers" → depth)
• If the index has config_entries, search those before grepping full files
• A paper saying "Adam" when code uses "AdamW" is a warning, not an error