paper2code

name	paper2code
description	Converts an arxiv paper into a minimal, citation-anchored Python implementation. Trigger when user runs /paper2code with an arxiv URL or paper ID, says "implement this paper", or pastes an arxiv link asking for implementation. Flags all ambiguities honestly. Never invents implementation details not stated in the paper.

paper2code — Orchestration

You are executing the paper2code skill. This file governs the high-level flow. Each stage dispatches to a detailed reasoning protocol in pipeline/. Do NOT skip stages. Do NOT combine stages. Execute them in order.

Parse arguments

Extract from the user's input:

• ARXIV_ID: the arxiv paper ID (e.g., 2106.09685). Strip any URL prefix.
• MODE: one of minimal (default), full, educational.
• FRAMEWORK: one of pytorch (default), jax, numpy.

If the user provided a full URL like https://arxiv.org/abs/2106.09685, extract the ID 2106.09685. If the user provided a versioned ID like 2106.09685v2, keep the version.

Set up working directory

Create a temporary working directory: .paper2code_work/{ARXIV_ID}/ This is where intermediate artifacts go. The final output goes in the current directory under {paper_slug}/.

Install dependencies

Run via Bash:

pip install pymupdf4llm pdfplumber requests pyyaml

Execute pipeline

Stage 1 — Paper Acquisition and Parsing

Read and follow: pipeline/01_paper_acquisition.md

Run the helper script to fetch and parse the paper:

python skills/paper2code/scripts/fetch_paper.py {ARXIV_ID} .paper2code_work/{ARXIV_ID}/

Then run structure extraction:

python skills/paper2code/scripts/extract_structure.py .paper2code_work/{ARXIV_ID}/paper_text.md .paper2code_work/{ARXIV_ID}/

Verify the outputs exist before proceeding. If extraction failed, follow the fallback protocol in pipeline/01_paper_acquisition.md.

The script also searches for official code repositories (in the paper text and on the arxiv page) and saves any found links to paper_metadata.json under the official_code key. Verify these links before relying on them — see Step 8 in pipeline/01_paper_acquisition.md.

Optional but recommended: run a paperclip pass before Stage 2 to surface comparable implementations the paper itself omits. A quick paperclip search "{paper_title} {core_method}" -s arxiv followed by grep "github\.com" --from <handle> reveals prior art and design decisions that comparable repos already settled. See skills/paperclip/SKILL.md recipe 6.

Stage 2 — Contribution Identification

Read and follow: pipeline/02_contribution_identification.md

Read the parsed paper sections. Identify the single core contribution. Classify the paper type. Write the contribution statement. Save it to .paper2code_work/{ARXIV_ID}/contribution.md.

Stage 3 — Ambiguity Audit

Read and follow: pipeline/03_ambiguity_audit.md

Before reading this stage, also read: guardrails/hallucination_prevention.md

Go through every implementation-relevant detail. Classify each as SPECIFIED, PARTIALLY_SPECIFIED, or UNSPECIFIED. Save the audit to .paper2code_work/{ARXIV_ID}/ambiguity_audit.md.

Stage 4 — Code Generation

Read and follow: pipeline/04_code_generation.md

Before writing code, read:

• guardrails/scope_enforcement.md — to determine what's in and out of scope
• guardrails/badly_written_papers.md — if the paper is vague or inconsistent
• The relevant knowledge files in knowledge/ for the paper's domain
• The scaffold templates in scaffolds/ for the expected file structure

Determine the paper_slug from the paper title (lowercase, underscores, no special chars). Generate all files under {paper_slug}/ in the current working directory.

Stage 5 — Walkthrough Notebook

Read and follow: pipeline/05_walkthrough_notebook.md

Generate the walkthrough notebook that connects paper sections to code with runnable sanity checks. Save to {paper_slug}/notebooks/walkthrough.ipynb.

Cleanup

Remove the .paper2code_work/ directory after successful completion.

Final output

Print a summary:

✓ paper2code complete for: {paper_title}
  Output directory: {paper_slug}/
  Files generated: {list of files}
  Unspecified choices: {count} (see REPRODUCTION_NOTES.md)
  Mode: {MODE} | Framework: {FRAMEWORK}

Mode-specific behavior

• minimal (default): Core contribution only. Training loop only if contribution involves training. No data pipeline beyond Dataset skeleton.
• full: Core contribution + full training loop + data pipeline + evaluation pipeline. More code, same citation rigor.
• educational: Same as minimal but with extra inline comments explaining ML concepts, expanded walkthrough notebook with theory sections, and a PAPER_GUIDE.md that walks through the paper section by section.

Guardrails — always active

These apply at ALL stages. Read them if you haven't already:

• guardrails/hallucination_prevention.md — the most important file in this skill
• guardrails/scope_enforcement.md — what to implement and what to skip
• guardrails/badly_written_papers.md — what to do when the paper is unclear

Knowledge base — consult as needed

Before implementing any of these components, read the corresponding knowledge file:

• Transformer layers, attention, positional encoding → knowledge/transformer_components.md
• Optimizers, LR schedules, batch size semantics → knowledge/training_recipes.md
• Cross-entropy, contrastive loss, diffusion loss, ELBO → knowledge/loss_functions.md
• Framework-specific pitfalls, notation mismatches → knowledge/paper_to_code_mistakes.md