Fixing Docs Warnings

[isaacgsmith]

📝 Description

Type: 📝 documentation

Fixes issues in the documentation to eliminate warnings and clean up the docs build:

• Fixed headers on gamma ray deposition docs and included it within the documentation. Also ran first cell so it is not run in docs builds.
• Fixed API documentation formatting issues in the formal integral and configuration validators.
• Fixed links.
• Fixed issues with .gitignore when building the arepo_to_tardis notebook.
• Closes Profiling pages not built in docs #2100. I ran the first cell in one of the notebooks and ran the entire notebook in the second one (since it produced useful output) so that these notebooks do not run, though if a user wants them to run in their docs build, these notebooks can be restarted prior to the build.

Also, link issues affected by this pull request by using the keywords: close, closes, closed, fix, fixes, fixed, resolve, resolves or resolved.

📌 Resources

See docs build: https://github.com/tardis-sn/tardis/actions/runs/2691656319

🚦 Testing

How did you test these changes?

• Testing pipeline
• Other method (describe)
• My changes can't be tested (explain why)

Docs built on GitHub with no warnings.

☑️ Checklist

• I requested two reviewers for this pull request
• I updated the documentation according to my changes
• I built the documentation by applying the build_docs label

Note: If you are not allowed to perform any of these actions, ping (@) a contributor.

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[codecov]

Codecov Report

Merging #2093 (12f6599) into master (a2ed8b5) will increase coverage by 3.32%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2093      +/-   ##
==========================================
+ Coverage   58.13%   61.46%   +3.32%     
==========================================
  Files          75       75              
  Lines        8602     8620      +18     
==========================================
+ Hits         5001     5298     +297     
+ Misses       3601     3322     -279     

Impacted Files	Coverage Δ
tardis/io/config_validator.py	90.47% <ø> (ø)
...dis/montecarlo/montecarlo_numba/formal_integral.py	53.87% <ø> (ø)
tardis/simulation/base.py	83.85% <0.00%> (+0.22%)	⬆️
tardis/montecarlo/montecarlo_numba/base.py	31.35% <0.00%> (+0.84%)	⬆️
tardis/io/logger/logger.py	75.86% <0.00%> (+5.17%)	⬆️
tardis/montecarlo/montecarlo_numba/r_packet.py	61.53% <0.00%> (+11.53%)	⬆️
tardis/visualization/widgets/custom_abundance.py	59.53% <0.00%> (+42.96%)	⬆️

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[tardis-bot]

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

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[andrewfullard]

Approved, pending @epassaro comments on the profiling page build.