Metadata-Version: 2.1
Name: revise-svc
Version: 0.0.4
Summary: Spatial transcriptomics benchmarking and annotation toolkit.
Author: Yushuai Wu and Yifeng Jiao
License: MIT License
        
        Copyright (c) 2025 Yushuai Wu
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
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Project-URL: Homepage, https://github.com/wuys13/REVISE
Project-URL: Repository, https://github.com/wuys13/REVISE
Project-URL: Issues, https://github.com/wuys13/REVISE/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata>=0.9
Requires-Dist: matplotlib>=3.6
Requires-Dist: numba>=0.57
Requires-Dist: numpy>=1.22
Requires-Dist: pandas>=1.5
Requires-Dist: POT==0.9.5
Requires-Dist: scanpy>=1.9
Requires-Dist: scikit-image>=0.20
Requires-Dist: scikit-learn>=1.2
Requires-Dist: scipy>=1.9
Requires-Dist: seaborn>=0.12
Requires-Dist: squidpy>=1.2
Requires-Dist: tqdm>=4.64
Provides-Extra: annotation
Requires-Dist: tacco>=0.2; extra == "annotation"
Provides-Extra: dev
Requires-Dist: black; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"

# REVISE

REVISE is a Python toolkit for reconstruct and analyse spatial transcriptomics (ST) data at single-cell resolution across diverse ST platforms.

Visit our [documentation](https://revise-svc.readthedocs.io/en/latest/) for installation, tutorials, examples and more.

## Highlights
- **Benchmark module**: Reproducible evaluation pipelines for simulated or public datasets, enabling method-to-method comparisons.
- **Application module**: Annotation, reconstruction, and downstream analyses for real ST data.

## Quick Start
If you just need the published Python package:
```bash
pip install revise-svc
```

## Example
```python
import anndata as ad
from revise.application import SpSvc

st = ad.read_h5ad("data/spatial.h5ad")
sc = ad.read_h5ad("data/single_cell_reference.h5ad")
config = ...

svc = SpSvc(st, sc, config=config, logger=None)
svc.annotate()
svc.reconstruct()
```

## Repository Layout
- `revise/application`: SVC workflows for real datasets.
- `revise/benchmark`: SVC variants for benchmarking studies.
- `revise/methods`: Algorithm implementations and model components.
- `revise/tools`: Distance metrics, logging helpers, and general utilities.
- `conf`: Example configurations and experiment parameters.

## License
REVISE is released under the MIT License (see `LICENSE`).
