cellshape-cluster 0.0.1

Cell shape analysis using deep embedded clustering

cellshape-cluster

---

Cellshape-cluster is an easy-to-use tool to analyse the cluster cells by their shape using deep learning and, in particular, deep-embedded-clustering. The tool provides the ability to train popular graph-based or convolutional autoencoders on point cloud or voxel data of 3D single cell masks as well as providing pre-trained networks for inference.

To install

pip install cellshape-cluster

For developers

• Fork the repository
• Clone your fork

git clone https://github.com/USERNAME/cellshape-cluster 

• Install an editable version (-e) with the development requirements (dev)

cd cellshape-cluster
pip install -e .[dev] 

• To install pre-commit hooks to ensure formatting is correct:

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:

git push --follow-tags

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

bump2version release