| State Transition model checkpoints are meant to be used with the [Arc State](https://pypi.org/project/arc-state/) package. | |
| State is distributed via [`uv`](https://docs.astral.sh/uv). To train models on your own AnnDatas, please see the [repository](https://github.com/ArcInstitute/state) README. | |
| ## Running inference from pypi | |
| ```bash | |
| uv tool install arc-state | |
| ``` | |
| To generate predictions: | |
| ```code | |
| state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR> | |
| ``` | |
| This will group the cells in your input AnnData by the specified `pert_col` and run inference with a pretrained ST checkpoint. | |
| ## 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 predictions: | |
| ```code | |
| state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR> | |
| ``` | |
| For model licenses please see `MODEL_ACCEPTABLE_USE_POLICY.md`, `MODEL_LICENSE.md`, and `LICENSE.md`. |