Code Refactoring for scPortrait Release

[sophiamaedler]

This is an issue to track major code changes that need to be implemented before we publish the package (this issue focuses not on new features but on cleaning up currently implemented features to make the code base more robust and better maintainable).

• segmentation workflows code refactoring: segmentation workflows #7
• classification workflows code refactoring: modulare classification/inference code #22
• downsampling/upsampling functions code refactoring: downsampling upsampling workflows #8
• switch to using spatial data for saving intermediate results utilize spatialdata format to save sparcspy results #40
• ensure all example datasets work with the new spatial data implementation
• implementing tests for continuous integration testing: implement full pipeline test with an example datasets #9
• Adopt scverse cookiecutter template Adopt the scverse cookiecutter template #17
• implement coding best practices Coding best practices #43

Furthermore the following features should be implemented:

• new features Features to implement for spatialdata #47