CONTRIBUTIONS.md

We welcome community contributions to help make this package better!

Contributing

to be written

Testing

Improving test coverage and automating the process is high priority but not done yet. For now, to test:

0. Ensure you are testing in a clean environment - we use micromamba for this

micromamba create -n esm
micromamba activate esm
micromamba install -c conda-forge python=3.10

# in root level of repo
pip install -e .
pip install examples/requirements.txt
python -c 'from huggingface_hub import login; login()'

# Ensure package can correctly interact with forge.
# This will require an API key from forge.evolutionaryscale.ai
ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python examples/forge_generate.py

1. Ensure the following scripts run without errors. Most have a pip install command installing the published esm package - comment this out so your release candidate version is tested and not the already published version.

ESM_API_KEY=$ESM_API_KEY PYTHONPATH='.' python examples/forge_generate.py
pip install treon
treon examples/esmprotein.ipynb
treon examples/gfp_design.ipynb

# requires a GPU
treon examples/generate.ipynb
python examples/local_generate.py
python examples/raw_forwards.py

examples/esmprotein.ipynb works. Remember to skip running the first cell - it will reinstall stock esm instead of your deployed version.

3. Ensure examples/generate.ipynb works. Note this notebook will require a node with a GPU that can fit ESM3 small open.

4. Ensure