Metadata-Version: 2.4
Name: scsketch
Version: 0.0.3
Summary: Interactive exploration of single-cell embeddings with directional analysis
Project-URL: Homepage, https://github.com/colabobio/scsketch
Project-URL: Repository, https://github.com/colabobio/scsketch
Project-URL: Bug Tracker, https://github.com/colabobio/scsketch/issues
Author-email: Askar Temirbek <askar.temirbek@umassmed.edu>, Andres Colubri <andres.colubri@umassmed.edu>, Fritz Lekschas <code@lekschas.de>, Kris Sankaran <ksankaran@wisc.edu>
Keywords: bioinformatics,jupyter,single-cell,visualization,widget
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.12
Requires-Dist: anywidget>=0.9.0
Requires-Dist: ipywidgets>=8.0.0
Requires-Dist: jupyter-scatter>=0.21.0
Requires-Dist: llvmlite>=0.44.0
Requires-Dist: matplotlib>=3.7.0
Requires-Dist: numpy>=1.26.0
Requires-Dist: pandas>=2.0.0
Requires-Dist: requests>=2.31.0
Requires-Dist: scanpy>=1.9.0
Requires-Dist: scipy>=1.11.0
Requires-Dist: umap-learn>=0.5.7
Provides-Extra: dev
Requires-Dist: jupyterlab>=4.0.0; extra == 'dev'
Requires-Dist: llvmlite>=0.44.0; extra == 'dev'
Requires-Dist: torch>=2.2.0; extra == 'dev'
Requires-Dist: watchfiles>=0.20.0; extra == 'dev'
Provides-Extra: lab
Requires-Dist: jupyterlab>=4.0.0; extra == 'lab'
Description-Content-Type: text/markdown

# scSketch

Interactive tooling for exploring single-cell embeddings in Jupyter (built on top of `jupyter-scatter` + `anywidget`).

## Install (Pip)

If you already have JupyterLab installed, this is all you need:

```sh
pip install scsketch
```

If you do not have JupyterLab yet, install it (or use the convenience extra):

```sh
pip install jupyterlab
# or: pip install "scsketch[lab]"
```

## Run

- Launch JupyterLab: `jupyter lab`
- Open `demo.ipynb` for an end-to-end example (it downloads example data from the internet).

## Install (Conda / Fallback)

If `pip install` fails on your system (common with scientific packages), use conda:

```sh
git clone https://github.com/colabobio/scsketch.git
cd scsketch

conda env create -f environment.yml
conda activate scsketch

jupyter lab demo.ipynb
```

## Troubleshooting

- Widgets don’t show up in JupyterLab:
  - Make sure `ipywidgets` and `jupyterlab_widgets` are installed in the same environment as `jupyter lab`.
  - Restart JupyterLab after installing dependencies.
  - If you’re on JupyterLab 3, you may need to run `jupyter lab build` once.

## Development

With [uv](https://github.com/astral-sh/uv):

```sh
uv run jupyter lab demo.ipynb
```

Or with editable installs:

```sh
python -m venv .venv
source .venv/bin/activate
python -m pip install -e ".[dev]"
jupyter lab demo.ipynb
```
