Update indexing in Charges and Masses get_residues

[jbarnoud]

Fixes #2990

Avoid indexing a numpy array with a list of arrays, use a tuple of array
instead. Multidimensional indexing of arrays with a non-tuple argument
is deprecated.

PR Checklist

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

[pep8speaks]

Hello @jbarnoud! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file testsuite/MDAnalysisTests/core/test_accumulate.py:

Line 121:80: E501 line too long (81 > 79 characters)
Line 143:80: E501 line too long (81 > 79 characters)

Comment last updated at 2020-10-16 09:31:12 UTC

[codecov]

Codecov Report

Merging #2991 into develop will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #2991   +/-   ##
========================================
  Coverage    93.05%   93.05%           
========================================
  Files          186      186           
  Lines        24609    24609           
  Branches      3187     3187           
========================================
  Hits         22900    22900           
  Misses        1661     1661           
  Partials        48       48           

Impacted Files	Coverage Δ
package/MDAnalysis/core/topologyattrs.py	96.49% <100.00%> (ø)

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[orbeckst]

This seems non-controversial and easy to review: LGTM — and good idea to add the tests that now fail on the warning to avoid regression. We should follow the same pattern for future warning deprecation fixes (if we're not already doing it).