Update readthedocs, wiki, and READMEs

[sdhutchins]

We need to update the readthedocs and wiki with our current documentation (mainly the tutorial).

I'm considering changing the style of the readthedocs page.

As it stands, we are in a fairly stable place #36 #33 #66 and others have all given our project a well-defined shape and functionality.

We need to add documentation to the Classes and modules that we've created.

• Mini Tutorial (Readme in OrthoEvol directory)
• Main README file
• Tools
• Cookies (custom cookiecutter templates)
• Manager
• Orthologs

[grabear]

Can you link to a guide for that. I haven't ever done any of that. I know all of our docs are in the Docs folder, but thats about it..

[sdhutchins]

There's more to it than this, but it may take me a while to document what I did.

[sdhutchins]

I'll take this on for this evening or in the morning.

[sdhutchins]

@grabear http://datasnakes-scripts.readthedocs.io/en/docs-patch/index.html Those are the docs using the docs-path.

Much improved from http://datasnakes-scripts.readthedocs.io/en/master/

I'm still working on how to link to .rst files from within .rst files.

[sdhutchins]

#123

[sdhutchins]

Going to use https://github.com/kennethreitz/python-guide/tree/master/docs as a reference.

[sdhutchins]

Still issues generating sphinx api docs, but docs are updated via #132

[sdhutchins]

• Remove all Tools documentation from package