Fix errors and warnings at compile time, pin versions, add readme

[aofarrel]

General improvements to the documentation website. No actual docs content has been changed, this is just for devs.

Input needed The link to find sister clades results in a 403.

Overview

• Add readme with info on how to compile + common issues
• Add requirements.txt
• Pin a certain version of attrs (trust me on this one), sphinx, and the rtd theme
• Explicitly call the RTD theme, since that's clearly what the website is using
• Add support for excluding certain URLs from linkcheck, ie that dodgy wustl.edu link
• Minor updates to Sphinx's template files

Warnings/Errors fixed

• Lots of duplicate target name issues
• Underlines too short
• Probable typo in code-block (was code-black, but probably wasn't intended to be this)
• Several broken links

Will be done in another PR

• Add the presentations to a "presentations" folder and mark that as a template folder
  • Doing this will allow us to render the three presentation RSTs without including them in the toctree
  • Will require rearranging lots of files, hence why that'll be a fresh PR
• Change SPHINXOPTS to -W --keep-going in order to escalate warnings into errors
  • Will require the presentations fix mentioned above

[AngieHinrichs]

@yatisht do you have permissions to accept pull requests in this repo?

[AngieHinrichs]

Thanks @bpt26! Didn't know if you were still on here. 🙂