Add SC2Spa

[linbuliao]

Mandatory
Name of the tool: SC2Spa

Short description: SC2Spa is a deep learning-based tool to predict the spatial coordinates of single cells.

How does the package use scverse data structures (please describe in a few sentences): scanpy and anndata are used for preprocessing for SC2Spa. SquidPy is used to calculate Moran's I in the downstream analysis of SC2Spa.

The code is publicly available under an OSI-approved license
Yes, SC2Spa is under BSD 3-Clause license

The package provides versioned releases
Yes

The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda) Yes, SC2Spa can be installed from PyPI

The package uses automated software tests and runs them via continuous integration (CI)
Yes

The package provides API documentation via a website or README
Yes

The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
Yes, SC2Spa uses AnnData, SCANPY and SquidPy

I am the author or maintainer of the tool and agree on listing the package on the scverse website
Yes

Recommended
I would like this package to be announced on scverse channels (zulip, discourse, twitter) [Include twitter handles you want us to tag]:
Yes, I would recommend these handles: SC2Spa, Spatial Inference, scRNA-seq, spatial transcriptomics, predict spatial coordinates, cell communication.

The package provides tutorials (or "vignettes") that help getting users started quickly
Yes, SC2Spa provides readthedocs tutorials.

The package uses the scverse cookiecutter template.
No, but I will consider adding this feature in the future

[grst]

Hi @linbuliao,

thans for submitting the package!

Overall, this looks good, but there are a few points to address to be fully compliant with our requirements:

• In addition to uploading releases on PyPI, the respective version should be tagged in git, either using git tag or using GitHub's release feature. You don't need this for all past version but you should update this for the current version and stick to it for all future releases.
• There's no API documentation. With that we mean a list of all public functions of the package with a link to the function documentations. In Sphinx, you can achieve this using the autodoc module. You can refer to our cookiecutter template for an example.

Minor comment (unrelated to the review checklist):

• you may want to update your .gitignore file... dist, __pycache__, .ipynb_checkpoints, *.egg-info, etc. should not be in a git repository.

[linbuliao]

Hi @grst,

Thank you for your comments! I just updated my repository according to your comemnts:

Release tags and an API documentation are added.
Irrelavant files are removed.

Best,
Linbu

[grst]

Thanks, LGTM now!