Documentation and Package Restructure

JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.

https://doubletdetection.readthedocs.io/en/stable/

MIT License

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Documentation and Package Restructure #121

Closed adamgayoso closed 5 years ago

adamgayoso commented 5 years ago

Adds documentation for DoubletDetection via Readthedocs

Restructures package in a more sensible way

Moves requirements into setup.py so they get installed automatically
Unfortunately now phenograph has to be manually installed (it basically was before wrapped in requirements.txt)
If phenograph is not installed, an ImportError is raised with install instructions.

Note that phenograph will become optional in v3.0 so this is a fine temporary solution.

adamgayoso commented 5 years ago

The new package structure was tested. Everything imports fine.

JonathanShor commented 5 years ago

Why should this not go into 3.0?

adamgayoso commented 5 years ago

Why should this not go into 3.0?

This doesn't change the API, but really just adds documentation. The documentation is relevant now, as opposed to when 3.0 comes out.

adamgayoso commented 5 years ago

By the way, we can squash this into master.

adamgayoso commented 5 years ago

Also, I'm not familiar with sphinx, so I'm assuming your design is reasonable re: Makefile etc. Being self contained within the docs folder seems good.

Sphinx pretty much automates this.