Metadata-Version: 2.4
Name: spagcn-modern
Version: 1.2.7.post1
Summary: Maintained Python fork of SpaGCN
Author-email: Jian Hu <jianhu@pennmedicine.upenn.edu>
Maintainer-email: Chen Yang <cafferychen777@tamu.edu>
License-Expression: MIT
Project-URL: Homepage, https://github.com/cafferychen777/SpaGCN
Project-URL: Repository, https://github.com/cafferychen777/SpaGCN
Project-URL: Original project, https://github.com/jianhuupenn/SpaGCN
Project-URL: Issues, https://github.com/cafferychen777/SpaGCN/issues
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: <3.14,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata>=0.10
Requires-Dist: igraph<2,>=0.11.9
Requires-Dist: matplotlib>=3.7
Requires-Dist: numba>=0.58
Requires-Dist: numpy>=1.24
Requires-Dist: pandas>=1.5
Requires-Dist: scanpy>=1.10
Requires-Dist: scikit-learn>=1.2
Requires-Dist: scipy>=1.10
Requires-Dist: torch>=2.1
Dynamic: license-file

# SpaGCN Modern

`spagcn-modern` is an independently maintained fork of
[SpaGCN](https://github.com/jianhuupenn/SpaGCN), a graph convolutional network
for identifying spatial domains and spatially variable genes from gene
expression, spatial coordinates, and histology.

The distribution keeps the original `SpaGCN` import package and numerical API
while supporting current Python, SciPy, Scanpy, and AnnData releases. Graph
initialization uses the maintained Leiden implementation built into igraph.

## Installation

```bash
pip install spagcn-modern
```

The import name remains unchanged:

```python
import SpaGCN
```

## Maintenance scope

This repository contains only the maintained Python distribution. Tutorials,
sample outputs, prebuilt distributions, and paper assets remain available in
the [original repository](https://github.com/jianhuupenn/SpaGCN) and are not
runtime dependencies.

Compatibility fixes in this fork include:

- current SciPy sparse-array conversion through `toarray()`;
- corrected `use_raw` behavior in `plot_log_exp`;
- minimal runtime dependency metadata derived from imports;
- maintained igraph Leiden initialization instead of the obsolete Louvain
  extension;
- isolated wheel builds and sparse-data smoke tests in CI.

## Citation

Please cite the original SpaGCN publication:

> Hu J, et al. SpaGCN: Integrating gene expression, spatial location and
> histology to identify spatial domains and spatially variable genes by graph
> convolutional network. *Nature Methods* (2021).

## Attribution and license

SpaGCN was created by Jian Hu and collaborators. This maintained fork preserves
the original MIT license and records its upstream base in
[`NOTICE.md`](NOTICE.md).
