Nuclinfo Major Pair and Minor Pair overhaul (#3735)

* add major pair and minor pair classes with optimized distance calculations to nucleicacids module
* partially completes #3720
* refactor to use new select_strand_atoms static method
* use typealias for union[residue, reiduegroup]
* deprecate  List[Residue] as input for WatsonCrickDist (remove in 3.0.0): use ResidueGroup
* refactor results dict and clarify result structure in docs:
  - use results.distances
  - deprecate results.pair_distances for WatsonCrickDist (remove in 3.0.0)
* add tests (match the old nuclinfo ones)
* refactor previous tests to use pytest approx
* update CHANGELOG

---------

Co-authored-by: Alia <[email protected]>
Co-authored-by: Oliver Beckstein <[email protected]>
Co-authored-by: Irfan Alibay <[email protected]>

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, 
-         richardjgowers, lilyminium
+         richardjgowers, lilyminium, ALescoulie
 
  * 2.7.0
 
@@ -29,6 +29,8 @@ Fixes
   * Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
 
 Enhancements
+  * Add faster nucleic acid Major and Minor pair distance calculators using
+    AnalysisBase for updated nucleicacids module (Issue #3720, PR #3735)
   * Adds external sidebar links (Issue #4296)
   * Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64
     inputs (PR #4273, part of #3927)
@@ -48,10 +50,18 @@ Changes
     replacing the now deprecated `xdrlib` core Python library
     (PR #4271)
   * ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404)
+  * Results for WatsonCrickDist nucleic acids analysis are now stored in 
+    `analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)
 
 Deprecations
   * coordinates.base.ConverterBase has been deprecated and will be removed in 3.0.0;
     use converters.base.ConvertBase instead (Issue #3404)
+  * In `nucleicacids.WatsonCrickDist`, accepting lists of `Residue` objects was deprecated
+    in favor of using `ResidueGroup`: using `List[Residue]` will be removed in release
+    3.0.0; instead use a `ResidueGroup` (Issue #3720, PR #3735)
+  * In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was
+    deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720, 
+    PR #3735)
 
 
 28/08/23 IAlibay, hmacdope, pillose, jaclark5, tylerjereddy