More test coverage and other cleanup

[bhazelton]

Description

I thought I'd added coverage for all the easy to cover lines in #449 but after it was merged I found that there were still some lines missing in simsetup.py. This PR does several things (sorry!):

• Adds coverage for some missing lines
• Updates the badges on the readme and other things throughout the repo to point to the main branch rather than master.
• Adds some text about pyradiosky in the tutorial and a link to the pyradiosky docs.
• Changes the RTD sphinx theme to match the one we use on other RASG repos.
• Runs one CI job on pip rather than conda. This has exposed some weirdnesses in the past on pyradiosky, so I wanted to do it here. I used the min_deps run because it's hard to get mpi4py to install via pip.
• Explicitly test against both Open MPI and MPICH implementations to ensure they both work and to avoid picking up the Intel MPI implementation (impi), which was breaking our tests.

Motivation and Context

closes #319

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Reference simulation update or replacement
• Documentation change (documentation changes only)
• Version change
• Build or continuous integration change

Checklist:

For all pull requests:

• I have read the contribution guide.
• My code follows the code style of this project.

Build or continuous integration change checklist:

• If required or optional dependencies have changed (including version numbers), I have updated the readme to reflect this.
• If this is a new CI setup, I have added the associated badge to the readme and to references/make_index.py (if appropriate).

Documentation change checklist:

• Any updated docstrings use the numpy docstring format.
• If this is a significant change to the readme or other docs, I have checked that they are rendered properly on ReadTheDocs. (you may need help to get this branch to build on RTD, just ask!)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.86%. Comparing base (80b9f6a) to head (7d989d8).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #450      +/-   ##
==========================================
+ Coverage   99.68%   99.86%   +0.17%     
==========================================
  Files          12       12              
  Lines        2235     2235              
==========================================
+ Hits         2228     2232       +4     
+ Misses          7        3       -4     

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[mkolopanis]

Just one question!

[mkolopanis]

yeah this works for me thanks!