Metadata-Version: 2.1
Name: revise-svc
Version: 0.0.2
Summary: Spatial transcriptomics benchmarking and annotation toolkit.
Author: Yushuai Wu
License: MIT License
        
        Copyright (c) 2025 Yushuai Wu
        
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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: mkl>=2023.2
Requires-Dist: numba>=0.57
Requires-Dist: numpy>=1.22
Requires-Dist: pandas>=1.5
Requires-Dist: POT>=0.9
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: sparse-dot-mkl>=0.9
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 (Regenerative Evaluation of VIable Spatial Expression) is a Python toolkit for benchmarking and annotating spatial transcriptomics (ST) data. It bundles standardized benchmarking workflows and application-ready SVC (Spatial transcriptomics Variational Comparison) pipelines so that researchers can compare algorithms, reproduce analyses, and build their own reference pipelines with minimal friction.

## 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 with built-in ST/SC preprocessing.
- **Utility tools**: Ready-to-use helpers such as efficient similarity metrics in `revise.tools.distance`, simplifying scripting.
- **Extensible architecture**: Layered `BaseSvc` / `ApplicationSvc` classes make it straightforward to plug in new tasks or methods.

## Quick Start
```bash
git clone https://github.com/wuys13/REVISE.git
cd REVISE
python -m venv .venv && source .venv/bin/activate
pip install -e ".[annotation]"
```

## Minimal 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()
```

Explore the full set of benchmark/application services in `revise/application` and `revise/benchmark`. To extend the framework, inherit from the relevant base class and override preprocessing, optimization, or evaluation hooks.

## 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.

## Contributing
Issues and pull requests are welcome-especially bug reports, documentation improvements, and new method implementations. Install the dev extras via `pip install -e ".[dev]"` to run `ruff` and `pytest` before submitting changes.

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