Fix PDF documentation build configuration

[sonu-saini19]

This PR fixes the PDF documentation build configuration for the project. The Sphinx documentation setup was updated to ensure that the LaTeX and PDF build process runs successfully without errors.

Changes

• Updated the Sphinx configuration to support proper PDF generation.
• Fixed documentation structure issues related to the Sphinx source directory.
• Resolved LaTeX build configuration problems.
• Ensured that the documentation build process completes successfully.

Testing

• Ran the documentation build locally using the Sphinx build command.
• Verified that the LaTeX files are generated correctly.
• Confirmed that the PDF documentation build completes without blocking errors.

Additional Notes

Some warnings related to deprecated modules or optional dependencies may still appear during the build, but they do not prevent the successful generation of the PDF documentation.

---

📚 Documentation preview 📚: https://mdanalysis--5310.org.readthedocs.build/en/5310/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.83%. Comparing base (50dc512) to head (40b912c).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5310   +/-   ##
========================================
  Coverage    93.82%   93.83%           
========================================
  Files          182      182           
  Lines        22487    22487           
  Branches      3196     3196           
========================================
+ Hits         21099    21100    +1     
+ Misses         925      924    -1     
  Partials       463      463           

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[jeremyleung521]

Hi, welcome. Though, please restore the PR template and answer the sections. While you're at it, please add yourself into the the AUTHORS list and update the CHANGELOG. We will not be reviewing the code changes unless the PR template is restored and filled. Thanks.

[sonu-saini19]

Description

Fix dependency configuration for FULL tests.

Changes Made

Adjusted dependency configuration used in FULL test environment.

Related Issue

Fixes #

Checklist

• Tests pass locally
• Code follows project guidelines

[jeremyleung521]

@sonu-saini19 , you're still missing certain sections. I also just noticed that there are 177 file changes, but the diff basically shows no changes for a majority of them. Would be good to explain why those files are labeled changed (and why they need to be changed in the first place). Is it a black formatting thing or a dos2unix thing?

Full PR Template:

<!-- 
Insert issue number that this PR fixes (if any) just after 'Fixes #'.
If this PR does not fix an existing issue, consider opening one or remove 'Fixes #' from the PR description.
-->
Fixes #

Changes made in this Pull Request:
<!-- Describe the changes that this PR makes. If applicable, use the following bullet list. --> 
-

## LLM / AI generated code disclosure
<!-- Please update this disclosure to reflect if you did or did not use LLMs / AI to generate code -->
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no

## PR Checklist
<!-- Please use the following checklist to ensure the PR is ready to be reviewed/merged. -->
 - [ ] Issue raised/referenced?
 - [ ] Tests updated/added?
 - [ ] Documentation updated/added?
 - [ ] `package/CHANGELOG` file updated?
 - [ ] Is your name in `package/AUTHORS`? (If it is not, add it!)
 - [ ] LLM/AI disclosure was updated.

## Developers Certificate of Origin
<!-- 
In order for this PR to be merged you **must certify that you are able to submit your code to be included in MDAnalysis**.
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I certify that I can submit this code contribution as described in the [**Developer Certificate of Origin**](https://developercertificate.org/), under the MDAnalysis [LICENSE](https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE).

[sonu-saini19]

@jeremyleung521 Thanks for pointing this out. The large number of changed files is not due to functional modifications.

These changes are primarily caused by normalization of line endings (CRLF to LF) and minor formatting adjustments, which made many files appear as modified even though their actual content remains the same.

No unintended logic or behavioral changes were introduced in those files.

[sonu-saini19]

Fixes #5821

Changes made in this Pull Request:

• Fixed dependency list for FULL TestPyPI tests
• Ensured compatibility handling for macOS with Python 3.13

LLM / AI generated code disclosure

LLMs or other AI-powered tools were used in this contribution: yes

PR Checklist

• [✔] Issue raised/referenced?
• [❌ ] Tests updated/added?
• [❌ ] Documentation updated/added?
• [✔] package/CHANGELOG file updated?
• [✔] Is your name in package/AUTHORS?
• [✔] LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE

[jeremyleung521]

Since you answered 'yes' to the AI section, I'll be closing this, per the AI policy.

Next time, I would also suggest not committing unnecessary changes, which clogs up git history. A LF => CR-LF swap is not useful at all ("not [...] functional modifications", as you say) and completely obfuscate what important changes actually are. Looking at the github diff, if I didn't know beforehand that sphinx options are in conf.py, I wouldn't even know what was changed for PDF building (the GitHub UI keeps jumping up and down around the specific file when I scroll)!

Also, for future reference, you would want to include the CHANGELOG/author changes directly within in the PR, not pushed directly to your fork.