Get started

This page is the shortest path from a fresh clone to a working local example.

Install

Install the package in editable mode:

pip install -e .[io,bench,dev,docs]

Or create an environment from the repository file:

conda env create -f environment.yml

Download the public demo assets

Run:

python scripts/setup_demo_assets.py

This downloads the public SCimilarity tutorial dataset and the model assets used throughout the documentation.

First files to inspect

Start with these files before you dive into the code:

• configs/wetlab_metadata_template.csv

• notebooks/wet_lab_walkthrough.ipynb

• artifacts/wetlab_examples/

First search

An example CLI invocation looks like this:

tca search \
  --embeddings data/reference.npy \
  --metadata data/reference.jsonl \
  --query data/query.npy \
  --output artifacts/results.json

What to read next

• Wet-lab guide

• Rare-state retrieval

• What you need before using TurboCell Atlas