Add tpr_resid_from_one keyword to TPRParser

[lilyminium]

Fixes #2364

Master version of #3152.

Changes made in this Pull Request:

• Add tpr_resid_from_one keyword to TPRParser
• Set default to False, keeping current status quo
• Emits a warning for tpr_resid_from_one=False indicating that default behaviour will change in 2.0

PR Checklist

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

[codecov]

Codecov Report

Merging #3153 (ee03c5b) into master (7ed893d) will increase coverage by 0.84%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #3153      +/-   ##
==========================================
+ Coverage   90.97%   91.81%   +0.84%     
==========================================
  Files         162      167       +5     
  Lines       22194    22703     +509     
  Branches     3198     3199       +1     
==========================================
+ Hits        20190    20845     +655     
- Misses       1381     1774     +393     
+ Partials      623       84     -539     

Impacted Files	Coverage Δ
package/MDAnalysis/topology/TPRParser.py	93.93% <100.00%> (+6.06%)	⬆️
package/MDAnalysis/topology/tpr/utils.py	80.97% <100.00%> (+6.61%)	⬆️
package/MDAnalysis/topology/tpr/obj.py	96.82% <0.00%> (-3.18%)	⬇️
...onality_reduction/DimensionalityReductionMethod.py	97.14% <0.00%> (-2.86%)	⬇️
package/MDAnalysis/due.py	56.09% <0.00%> (ø)
package/MDAnalysis/analysis/legacy/x3dna.py	0.00% <0.00%> (ø)
package/MDAnalysis/analysis/legacy/__init__.py	0.00% <0.00%> (ø)
package/MDAnalysis/tests/datafiles.py	31.25% <0.00%> (ø)
package/MDAnalysis/tests/__init__.py	100.00% <0.00%> (ø)
package/MDAnalysis/core/selection.py	99.52% <0.00%> (+<0.01%)	⬆️
... and 87 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 7ed893d...ee03c5b. Read the comment docs.

[orbeckst]

Thank you.

The CHANGELOG entries are in the wrong spot (1.0.0?).

The introduction of the tpr_resid_from_one keyword forces us to make this 1.1.0 according to https://semver.org/ (ping @IAlibay ).

[orbeckst]

In the wrong spot.

[orbeckst]

Becomes 1.1.0 ...

[lilyminium]

I thought we were going to leave 1.x at the 1.0.x states? It's becoming increasingly difficult to deal with Python 2.7, as evidenced by the recent issues with CI. What about putting the deprecation in 2.0 and then making the final change in a later release?

Tagging any interested @MDAnalysis/coredevs.