Remove save part2

[IAlibay]

Partly addresses #1745 (completes save() removal with #2487 and #2486 )

Also addresses #2491, since the deprecation was unclear and it seems like there were no releases between the announced deprecation of analysis/hbonds/hbond_analysis.py and now, the deprecation was set as effective v1.0 and set for removal in v2.0 (this is just a placeholder date).

Fixes #2492

Changes made in this Pull Request:

• Set deprecation date for analysis/hbonds/hbond_analysis.py.
• Removed save_table from :class:HydrogenBondAnalysis.
• Removed save_results from :class:HydrogenBondAutoCorrel.
• Removed filename, store and save_result from :class:PSAnalysis.
• Deprecation notice for :meth:HydrogenBondAnalysis._reformat_hb has been removed, entire class will be removed in 2.0 (Deprecation of _reformat_hb in hbonds/hbond_analysis.py for v1.0 #2492 )

Things left to do:

• Confirm the removal date for MDAnalysis/analysis/hbonds/hbond_analysis.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #2494 into develop will increase coverage by 0.03%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop    #2494      +/-   ##
===========================================
+ Coverage    90.25%   90.28%   +0.03%     
===========================================
  Files          169      169              
  Lines        23210    23175      -35     
  Branches      3008     3001       -7     
===========================================
- Hits         20948    20924      -24     
+ Misses        1655     1648       -7     
+ Partials       607      603       -4     

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/base.py	97.24% <0.00%> (ø)	⬆️
package/MDAnalysis/lib/mdamath.py	93.54% <0.00%> (ø)	⬆️
package/MDAnalysis/lib/util.py	88.56% <0.00%> (ø)	⬆️
package/MDAnalysis/coordinates/TRZ.py	83.64% <0.00%> (ø)	⬆️
package/MDAnalysis/analysis/psa.py	83.68% <0.00%> (+0.63%)	⬆️
package/MDAnalysis/analysis/lineardensity.py	63.30% <0.00%> (ø)	⬆️
package/MDAnalysis/analysis/gnm.py	96.06% <0.00%> (ø)	⬆️
package/MDAnalysis/coordinates/TRJ.py	94.81% <0.00%> (ø)	⬆️
package/MDAnalysis/lib/transformations.py	78.62% <0.00%> (ø)	⬆️
package/MDAnalysis/core/topologyobjects.py	97.87% <0.00%> (ø)	⬆️
... and 9 more

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[orbeckst]

Set removal date for hbonds to 2.0 — that’s the plan.

[orbeckst]

I didn’t check why CI fails. But ping me when you need a review.

[IAlibay]

@orbeckst this should be good for review now

[orbeckst]

Minor changes, please – see comments.

Thanks for the work!!

[orbeckst]

Yay, less code!