Metadata-Version: 2.1
Name: cellshape-cloud
Version: 0.0.1
Summary: Cell shape analysis using graph neural networks
Home-page: https://github.com/DeVriesMatt/cellshape-cloud
Author: Matt DeVries, Adam Tyson
Author-email: matthew.devries.13@gmail.com
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/DeVriesMatt/cellshape-cloud/issues
Project-URL: Documentation, https://github.com/DeVriesMatt/cellshape-cloud#README.md
Project-URL: Source Code, https://github.com/DeVriesMatt/cellshape-cloud
Project-URL: User Support, https://github.com/DeVriesMatt/cellshape-cloud/issues
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: torch
Requires-Dist: torchvision
Requires-Dist: pyntcloud
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: Pillow
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: bump2version ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: flake8 ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
<img src="https://github.com/DeVriesMatt/cellshape-cloud/blob/main/img/cellshape_cloud.png" 
     alt="Cellshape logo by Matt De Vries">
___
Cellshape-cloud is an easy-to-use tool to analyse the shapes of cells using deep learning and, in particular, graph-neural networks. The tool provides the ability to train popular graph-based autoencoders on point cloud data of 2D and 3D single cell masks as well as providing pre-trained networks for inference.



### To install
```bash
pip install cellshape-cloud
```

### For developers
* Fork the repository
* Clone your fork
```bash
git clone https://github.com/USERNAME/cellshape-cloud 
```
* Install an editable version (`-e`) with the development requirements (`dev`)
```bash
cd cellshape-cloud
pip install -e .[dev] 
```
* To install pre-commit hooks to ensure formatting is correct:
```bash
pre-commit install
```

* To release a new version:

Firstly, update the version with bump2version (`bump2version patch`, 
`bump2version minor` or `bump2version major`). This will increment the 
package version (to a release candidate - e.g. `0.0.1rc0`) and tag the 
commit. Push this tag to GitHub to run the deployment workflow:

```bash
git push --follow-tags
```

Once the release candidate has been tested, the release version can be created with:

```bash
bump2version release
```


