paper2code

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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.

3installs

Sourceprathamlearnstocode/paper2code

Added on2026-04-04

NPX Install

npx skill4agent add prathamlearnstocode/paper2code paper2code

SKILL.md Content

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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:

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:

bash

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

Then run structure extraction:

bash

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

.

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
```

paper2code

NPX Install

Tags

SKILL.md Content

paper2code — Orchestration

Parse arguments

Set up working directory

Install dependencies

Execute pipeline

Stage 1 — Paper Acquisition and Parsing

Stage 2 — Contribution Identification

Stage 3 — Ambiguity Audit

Stage 4 — Code Generation

Stage 5 — Walkthrough Notebook

Cleanup

Final output

Mode-specific behavior

Guardrails — always active

Knowledge base — consult as needed