Fixing various physics documentation issues

[isaacgsmith]

Description

• Fixed an error on the propagation page regarding the accumulation of optical depth after reaching a cell boundary.
• Added a figure to the discussion about the propagation direction in the initialization notebook.
• Explicitly mentioned the relationship between initialized packet frequency and the number of photons it represents.
• Added information about reference frames in the initialization and spectrum generation notebooks.
• Revised the treatment of the photospheric temperature in the initialization and spectrum generation notebooks.
• Removed an outdated note from the quickstart notebook.
• Other small notation and organizational changes to make the documentation more readable and consistent.

How has this been tested?

• Testing pipeline.
• Docs built locally and on GitHub.

Examples

Pages with significant changes:
https://smithis7.github.io/tardis/branch/physics_fix_doc/physics/setup/model.html
https://smithis7.github.io/tardis/branch/physics_fix_doc/physics/montecarlo/initialization.html
https://smithis7.github.io/tardis/branch/physics_fix_doc/physics/spectrum/basic.html

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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[wkerzendorf]

@smithis7 uuuh - tests fail - what have you done 🤣

[isaacgsmith]

@smithis7 uuuh - tests fail - what have you done 🤣

I’ll look into it. I only edited within the docs/ directory so I have no clue…

[isaacgsmith]

@smithis7 uuuh - tests fail - what have you done 🤣

I just rebased and it now passes.

[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.