chore: minor dirtree modifications

[AngryMaciek]

I would suggest a few changes to the repo structure to conform with what is usually available:

• create a top lvl dir resources and put go_annotations inside
• create a top lvl dir test
  • add a simple bash script under scripts; the script would download the h5ad files from zenodo automatically and put them under test/data.
  • is theta_annotation a resource or an example input? It should be put either under resources or under test. Should this go together with the go annotations(?)
• DeepCycle.py is a script so it should go under scripts too.
• a standard name for a conda env is environment.yml (instead of DeepCycle_env.yml). Then you can just run conda env create and the package manager automatically looks for environment.yml file. The env will still retain the name specified within the YAML file.

[AngryMaciek]

Also: people generally include their colorful GH shields on top of the README file, they are very attractive ;)
I would suggest to move the zenodo example data shield to the top and later in the text just use a link with a URL. Also, it would be nice to upload the repo itself to zenodo! Nothing wrong with having two zenodo shields on top.