Reorganize repository based on current plans

[damonbayer]

There are a few issues with the current repo structure:

1. Our NSSP model started as a "demo," hence the nssp_demo folder, but it is now the main offering of the repo.
2. We are collecting a variety of other "demo" scripts, currently stored in the notebooks folder.

I would like to reorganize the repo to make things a bit more clear. I think I will have a better idea of how to do that once we have run things in azure.

[SamuelBrand1]

My 2p worth, and this might be better implemented over more than one repo:

Have a structure of:

• tools: thats pyrenew-hew etc which do the analysis. This should be callable from projects in this repo.
• projects: thats discrete projects we want to work on in the open e.g. nssp.
• demos -> docs as vignettes.

[damonbayer]

Current thinking:

• pyrenew-hew: setup as a python library that has the PyRenew model(s)
• utils_R: R utility scripts that can be sourced or could be set up as an R package
• utils_py: Python utility scripts that can be imported.
• pipeline: scripts related to running the pipeline
  • could be further separated into different pipeline folders if we have different pipelines
• demos: vignettes / docs

[dylanhmorris]

Largely agree, but I think we can and should avoid import-able/source-able middle ground between pipeline scripts and packaged code. So I'd suggest the above except:

• Bundle anything reused enough to be a utils_py into pyrenew-hew.utils
• Any utils_R that don't belong in pipeline could be a micro-package called hewR or something