Installation
CellType-Refinery can be installed from source using pip.
Requirements
- Python >= 3.10
- pip
From Source
Clone the repository and install in editable mode:
git clone https://github.com/kimpenn/CellType-Refinery.git
cd CellType-Refinery
pip install -e .
Optional Dependencies
Visualization Support
For generating plots and figures:
pip install -e ".[viz]"
This includes matplotlib and seaborn.
GPU Acceleration
For RAPIDS/cuGraph-accelerated Leiden clustering:
pip install -e ".[gpu]"
This includes rapids-singlecell and cupy-cuda12x.
Development Tools
For testing and code quality:
pip install -e ".[dev]"
This includes pytest, pytest-cov, ruff, and mypy.
All Dependencies
Install everything:
pip install -e ".[all]"
Verify Installation
After installation, verify CellType-Refinery is working:
# Check CLI is available
celltype-refinery --help
# Check Python import
python -c "from celltype_refinery.core.annotation import AnnotationEngine; print('OK')"
Dependencies
Core Dependencies
| Package | Version | Purpose |
|---|---|---|
| numpy | >= 1.24 | Numerical computing |
| pandas | >= 2.0 | Data manipulation |
| scipy | >= 1.10 | Statistical functions |
| scikit-learn | >= 1.2 | Machine learning utilities |
| anndata | >= 0.10 | AnnData objects |
| scanpy | >= 1.9 | Single-cell analysis |
| leidenalg | >= 0.10 | Leiden clustering |
| pyyaml | >= 6.0 | Configuration files |
| click | >= 8.0 | CLI framework |
| tqdm | >= 4.65 | Progress bars |
| statsmodels | >= 0.14 | Statistical models |
Optional Dependencies
| Extra | Packages | Purpose |
|---|---|---|
viz | matplotlib, seaborn | Visualization |
gpu | rapids-singlecell, cupy | GPU acceleration |
dev | pytest, ruff, mypy | Development tools |