Restructure Documentation

[isaacgsmith]

This is part 1 of a series of PRs restructuring the documentation. Please view the built documentation here.

Description

There are a lot of changes made. The overarching themes of these changes are as follows:

• Removes "using TARDIS" section
• Creates "I/O" section which is differently organized
• Splits the configuration documentation into many different pages, and incorporates the atomic and models sections in it
• Creates "outdated" section
• Reorganizes physics to be a walkthrough of the code (more changes to come regarding that)
• Hyperlink and referencing fixes

Motivation and context

This is part of an ongoing project to make the documentation as interactive and easy-to-understand as possible.

How has this been tested?

• Testing pipeline.
• Other.
  Documentation has been built.

Examples

See the top of this PR for the link to the built documentation.

Type of change

• Bug fix.
• New feature.
• Breaking change.
• None of the above.

Checklist

• My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • (optional) I have built the documentation on my fork following the instructions.
• I have assigned and requested two reviewers for this pull request.

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[tardis-bot]

Before a pull request is accepted, it must meet the following criteria:

• Is the necessary information provided?
• Is this a duplicate PR?
  • If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
  • If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
• Does it pass existing tests and are new tests provided if required?
  • The test coverage should not decrease, and for new features should be close to 100%.
• Is the code tidy?
  • No unnecessary print lines or code comments.

[andrewfullard]

Generally good. Left a few comments. I hope you've tested all the new links to make sure nothing is broken.

[andrewfullard]

Please fix the test failures caused by the relocation/rename/editing of some csvy configuration files

[codecov]

Codecov Report

Merging #1643 (c8d96aa) into master (8ceacc0) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1643   +/-   ##
=======================================
  Coverage   67.13%   67.13%           
=======================================
  Files          73       73           
  Lines        6100     6100           
=======================================
  Hits         4095     4095           
  Misses       2005     2005           

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[tardis-bot]

Before a pull request is accepted, it must meet the following criteria:

• Is the necessary information provided?
• Is this a duplicate PR?
  • If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
  • If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
• Does it pass existing tests and are new tests provided if required?
  • The test coverage should not decrease, and for new features should be close to 100%.
• Is the code tidy?
  • No unnecessary print lines or code comments.