Add Novae

[quentinblampey]

Hi!
I added novae, and updated the YAML file associated to Sopa (replace the preprint DOI by the publication DOI).

Checklist for adding packages

Mandatory

Name of the tool: novae

Short description: Novae is a deep learning model for spatial domain assignments of spatial transcriptomics data (at both single-cell or spot resolution). It works across multiple gene panels, tissues, and technologies. Novae offers several additional features, including: (i) native batch-effect correction, (ii) analysis of spatially variable genes and pathways, and (iii) architecture analysis of tissue slides.

How does the package use scverse data structures (please describe in a few sentences): it uses AnnData as a data structure, and some plots are based on scanpy. In terms of training, it also looks similar to scvi-tools (as it uses PyTorch Lightning for model training).

• The code is publicly available under an OSI-approved license
• The package provides versioned releases
• The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
• Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
• Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
• The package provides API documentation via a website or README[^3]
• The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
• I am an author or maintainer of the tool and agree on listing the package on the scverse website

Recommended

• Please announce this package on scverse communication channels (zulip, discourse, twitter)
• Please tag the author(s) these announcements.
• The package provides tutorials (or "vignettes") that help getting users started quickly
• The package uses the scverse cookiecutter template.