Add DepWarnings to X3DNA code and docs

[hmacdope]

Fixes #3788

Changes made in this Pull Request:

• Adds deprecation warnings to X3DNA as slated for removal in 3.0

PR Checklist

• [ X] Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4333.org.readthedocs.build/en/4333/

[pep8speaks]

Hello @hmacdope! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/analysis/legacy/x3dna.py:

Line 143:72: W291 trailing whitespace
Line 171:80: E501 line too long (125 > 79 characters)
Line 491:12: E128 continuation line under-indented for visual indent
Line 491:72: W291 trailing whitespace
Line 740:12: E128 continuation line under-indented for visual indent
Line 740:72: W291 trailing whitespace

Comment last updated at 2023-11-05 08:51:21 UTC

[github-actions]

Linter Bot Results:

Hi @hmacdope! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	✅ Passed

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/6760288579/job/18373890117

---

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[IAlibay]

Thanks for testing this locally, that's probably good enough.

[IAlibay]

Thanks @hmacdope - I've got two comments here:

1. I believe someone at some point mentioned this code wasn't even usable - can you actually get these warnings if you try to use the method / class locally?
2. Please use the relevant decorator for the method.

[IAlibay]

we have a decorator for this - please see

mdanalysis/package/MDAnalysis/analysis/hole2/hole.py

Lines 50 to 52 in 5fa0d27

	@deprecate(release="2.6.0", remove="3.0.0",
	message=("This method has been moved to the MDAKit hole2-mdakit: "
	"https://github.com/MDAnalysis/hole2-mdakit"))

for an example

[hmacdope]

ah ta.

[hmacdope]

RE: 1 if the code is not usable and we are removing it i don't really want to invest any energy in finding out why / how. Is it okay just to put the warnings in as is? Let me know wither way.

[IAlibay]

@hmacdope - my point here is "what's the point in putting in a warning if it won't even work locally". If you can get the warnings locally then it's fine, otherwise I'd just add in the docstring changes and call it a day.

[hmacdope]

@IAlibay Okay you can get the warnings on before whatever is broken, at least it may warn the (possibly 0) people that have a niche setup that this works for this that it will be removed.

[IAlibay]

Thanks for testing this locally, that's probably good enough.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (5fa0d27) 93.37% compared to head (a7615ce) 93.37%.

Additional details and impacted files

@@            Coverage Diff             @@
##           develop    #4333     +/-   ##
==========================================
  Coverage    93.37%   93.37%             
==========================================
  Files          170      184     +14     
  Lines        22295    23403   +1108     
  Branches      4075     4075             
==========================================
+ Hits         20818    21853   +1035     
- Misses         962     1035     +73     
  Partials       515      515             

see 14 files with indirect coverage changes

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[IAlibay]

thanks @hmacdope !