Set up Squidpy as a remote tool

Sharing this model for a user, not developing it? Follow the tooluniverse-share-computer guide; no ToolUniverse source checkout is needed. The model runs in its own Python environment, with its dependencies:

~/.local/bin/uv venv --python 3.12 ~/.tooluniverse/envs/squidpy
curl -fsSL -o ~/.tooluniverse/envs/squidpy-tooluniverse.txt https://connect.aiscientist.tools/install-requirements.txt
curl -fsSL -o ~/.tooluniverse/envs/squidpy-requirements.txt https://raw.githubusercontent.com/mims-harvard/ToolUniverse/main/src/tooluniverse/remote/squidpy/requirements.txt
~/.local/bin/uv pip install --python ~/.tooluniverse/envs/squidpy/bin/python -r ~/.tooluniverse/envs/squidpy-tooluniverse.txt -r ~/.tooluniverse/envs/squidpy-requirements.txt
~/.local/bin/tu remote check squidpy --python ~/.tooluniverse/envs/squidpy/bin/python   # lists anything still missing
~/.local/bin/tu serve --allow squidpy --python ~/.tooluniverse/envs/squidpy/bin/python --share --detach --name "<computer name>" --service https://tooluniverse-backend.onrender.com

If the check reports a missing environment variable (a data folder, a model cache, a provider key), set it in the same shell before tu serve; "Obtain credentials, data, and model weights" below says what each one is. The model reads only the variables it declares.

The rest of this guide is for developers working from the ToolUniverse source, and for diagnosing problems with this model.

Validation status (2026-08-16): Squidpy dependencies, loopback discovery, and a bounded 72-spot neighborhood-enrichment call passed with a finite 3 x 3 z-score matrix. Public publication, cross-user isolation, representative spatial biology, broad concurrency, and recovery remain incomplete. Authenticated private Platform import and owner testing passed on 2026-08-16; public publication and independent-caller authorization/isolation remain untested.