| State Embedding model checkpoints are meant to be used with the [Arc State](https://pypi.org/project/arc-state/) repository. | |
| State is distributed via [`uv`](https://docs.astral.sh/uv). | |
| ## Running from pypi | |
| ```bash | |
| uv tool install arc-state | |
| ``` | |
| To generate embeddings given an AnnData: | |
| ```code | |
| state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad | |
| ``` | |
| ## Running from source | |
| ```bash | |
| # Clone repo | |
| git clone github.com:arcinstitute/state | |
| cd state | |
| # Initialize venv | |
| uv venv | |
| # Install | |
| uv tool install -e . | |
| ``` | |
| To generate embeddings given an AnnData: | |
| ```code | |
| state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad | |
| ``` | |
| For model licenses please see `MODEL_ACCEPTABLE_USE_POLICY.md`, `MODEL_LICENSE.md`, and `LICENSE.md`. |