# Codonfm Setup

Set up the public CodonFM v1 repository and download public Encodon checkpoints.

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA/skills --skill codonfm-setup -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill codonfm-setup -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill codonfm-setup -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill codonfm-setup -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

Set up the public CodonFM v1 repository and download public Encodon checkpoints. Use for requests to build or launch the CodonFM development container, configure local data/checkpoint mounts, verify GPU access, or download public Encodon 80M, 600M, 1B, or Cdwt-1B weights. Do not use for Decodon, Encodon 5B/10B, missense-aggregation, or codon-optimization setup because those implementations are not in the public repository.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# CodonFM public setup

Operate from the public CodonFM repository root. Support only the checked-in
public v1 code and public Encodon checkpoints.

## Instructions

1. Determine whether the user wants instructions, a downloaded checkpoint, a
   working model environment, or a combination of these.
2. For setup instructions or runtime work, inspect the supplied files and
   configuration directly: the [runner](../../src/runner.py),
   [model configuration](../../src/config.py), [Dockerfile](../../Dockerfile),
   [launcher](../../run_dev.sh), and [requirements](../../requirements.txt).
   Runtime setup requires a checkout; a supplied source archive is sufficient
   for preparing instructions.
3. Check the [public-v1 boundaries](#public-v1-boundaries). For an unsupported
   request, inspect `MODEL_ARCHITECTURES` in `src/config.py`, the model modules,
   and any requested script before explaining the boundary and ending that
   path. Runner argument choices alone do not establish implementation support.
4. Reuse available environments and checkpoints, and choose explicit paths
   from the user's project.
5. Follow only the requested paths below. Environment setup alone does not
   require a checkpoint download; download weights only when the request needs
   them and a suitable local checkpoint is unavailable.

| Requested scope | Action and completion condition |
| --- | --- |
| Instructions only | Inspect the supplied source/configuration, provide the commands described under Reporting setup instructions, then stop. No installation or GPU verification is required. |
| Checkpoint only | Follow Download a checkpoint, check the downloaded files, report their paths, then stop. No Docker, GPU, or model runtime is required. |
| Working model environment | Follow Runtime preflight, choose the container or direct-host path, then Verify the runtime. Report the checks performed and any remaining limitations. |

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-codonfm-setup/SKILL.md