Deprecate encore

[fiona-naughton]

Add deprecation messages/warnings for encore referencing the MDAKit mdaencore, per #4274

(The code itself is left for now, but could be replaced (prior to deprecation in 3.0) with the MDAKit later, as for hole2/waterdynamics/psa)

PR Checklist

• Tests?
• 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--4737.org.readthedocs.build/en/4737/

[pep8speaks]

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

• In the file package/MDAnalysis/analysis/encore/bootstrap.py:

Line 36:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py:

Line 35:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py:

Line 36:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/clustering/cluster.py:

Line 35:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/confdistmatrix.py:

Line 38:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/covariance.py:

Line 35:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py:

Line 36:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py:

Line 35:46: W291 trailing whitespace

• In the file package/MDAnalysis/analysis/encore/similarity.py:

Line 33:46: W291 trailing whitespace

Comment last updated at 2024-10-18 15:57:40 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.27%. Comparing base (48e9e01) to head (669f6b6).
Report is 2 commits behind head on develop.

❗ There is a different number of reports uploaded between BASE (48e9e01) and HEAD (669f6b6). Click for more details.

HEAD has 5 uploads less than BASE

Flag	BASE (48e9e01)	HEAD (669f6b6)
	10	5

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4737      +/-   ##
===========================================
- Coverage    93.60%   86.27%   -7.33%     
===========================================
  Files          173      185      +12     
  Lines        21464    22533    +1069     
  Branches      2993     2993              
===========================================
- Hits         20091    19440     -651     
- Misses         929     2664    +1735     
+ Partials       444      429      -15     

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[orbeckst]

LGTM.

The distopia-related failures need to be fixed elsewhere (#4739 or PR #4734 ).

[orbeckst]

I'd like to have merged develop into this branch but GH did not provide a convenient button to do so. Because I am too lazy to do this locally and because I know that "it will work"™ now that PR #4740 has been merged I am going to merge as is.

EDIT: I'll wait with merging in case anyone else wants to review. @fiona-naughton please merge when you think it's ready and got enough scrutiny.

[IAlibay]

lgtm thanks!