Finalizing #2537

[wvdtoorn]

Fixes #2502

Changes made in this Pull Request:

• [DOC] add sphinx deprecated paragraph to density/BFactor2RMSF docstring
• [TEST] decrease precision in assert_almost_equal test_density/test_density_from_PDB
• [TEST] Bring back TestGridImport class in test_density

PR Checklist

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

[wvdtoorn]

I see my editor had a go at some trailing white spaces in the CHANGELOG, let me know if that's a problem for you.

[codecov]

Codecov Report

Merging #2616 into densityanalysis-2502 will increase coverage by 0.66%.
The diff coverage is n/a.

@@                   Coverage Diff                    @@
##           densityanalysis-2502    #2616      +/-   ##
========================================================
+ Coverage                 91.01%   91.68%   +0.66%     
========================================================
  Files                       170       15     -155     
  Lines                     23192     2008   -21184     
  Branches                   2946        0    -2946     
========================================================
- Hits                      21108     1841   -19267     
+ Misses                     1495      167    -1328     
+ Partials                    589        0     -589     

Impacted Files	Coverage Δ
__init__.py	91.89% <0.00%> (-2.34%)	⬇️
coordinates/__init__.py	100.00% <0.00%> (ø)
package/MDAnalysis/coordinates/DLPoly.py
package/MDAnalysis/coordinates/TRJ.py
package/MDAnalysis/topology/tpr/obj.py
package/MDAnalysis/analysis/pca.py
package/MDAnalysis/selections/base.py
package/MDAnalysis/topology/ParmEdParser.py
package/MDAnalysis/analysis/encore/utils.py
...ge/MDAnalysis/transformations/positionaveraging.py
... and 148 more

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[IAlibay]

@orbeckst do you prefer this be a two stage PR (i.e. PR into your branch, and then we close your PR), or for @wvandertoorn's PR to directly go into develop?

[orbeckst]

Merge into my original PR.

[IAlibay]

Thanks for picking this up :)

Remember to add yourself to AUTHORS too.

Main change required here is to add a bit more details to the .. deprecated docs. Could you also add details for the .. deprecated in notwithin_coordinates_factory? Saying that it will be removed in 2.0.0 with density_from_Universe?

[IAlibay]

One new change, one info request on a previously requested change.

[IAlibay]

lgtm thanks for your work @wvandertoorn

I'm still not 100% sure this will end up fixing all the Travis failures we were seeing in #2537, but unfortunately it looks like we can't test this until this gets pushed to @orbeckst's PR.

I'll wait for appveyor to return green here and then squash-merge. If the issues with Travis continue, I might ping you for another PR if that's ok with you?