[fmt] Format analysis module and tests

[RMeli]

Format most of the MDAnalysis/analysis module and corresponding test. Some files actives in current PRs are ignored and will be formatted once the corresponding PRs are merged (see #4815).

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📚 Documentation preview 📚: https://mdanalysis--4848.org.readthedocs.build/en/4848/

[codecov]

Codecov Report

Attention: Patch coverage is 93.60947% with 54 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (c08cb79) to head (56ea875).
Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
...ckage/MDAnalysis/analysis/encore/confdistmatrix.py	60.00%	9 Missing and 1 partial ⚠️
...nalysis/analysis/hydrogenbonds/wbridge_analysis.py	92.68%	2 Missing and 7 partials ⚠️
package/MDAnalysis/analysis/encore/similarity.py	88.88%	1 Missing and 7 partials ⚠️
package/MDAnalysis/analysis/encore/utils.py	62.50%	4 Missing and 2 partials ⚠️
package/MDAnalysis/analysis/nuclinfo.py	88.46%	2 Missing and 4 partials ⚠️
...nalysis/analysis/hydrogenbonds/hbond_autocorrel.py	90.00%	2 Missing and 2 partials ⚠️
package/MDAnalysis/analysis/bat.py	93.33%	2 Missing and 1 partial ⚠️
...e/MDAnalysis/analysis/encore/clustering/cluster.py	84.61%	1 Missing and 1 partial ⚠️
.../dimensionality_reduction/reduce_dimensionality.py	84.61%	1 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/rms.py	96.15%	2 Missing ⚠️
... and 2 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4848      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21779    22845    +1066     
  Branches      3064     3064              
===========================================
+ Hits         20398    21391     +993     
- Misses         929     1002      +73     
  Partials       452      452              

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[orbeckst]

blanket LGTM

🎄 🎁

[RMeli]

I turned off formatting for some ugly x3dna parts. I don't think it matters much, since the code will be removed for 3.0.0.

[RMeli]

@marinegor this should be good for a final review, I think.

[RMeli]

Merging to avoid other PRs getting in the way. @marinegor please review regardless. If you spot something off, we can fix it retrospectively.

[marinegor]

retrospective LGTM