Residue.mass and Residue.charge use deprecated numpy indexing

[jbarnoud]

Running the tests throws a warning about MDAnalysis using a behaviour of numpy that is subject to change:

MDAnalysisTests/core/test_accumulate.py::TestTotals::test_total_charge_duplicates[residues]
  /home/jon/dev/mdanalysis/package/MDAnalysis/core/topologyattrs.py:1540: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    charges = self.values[resatoms].sum()

MDAnalysisTests/core/test_accumulate.py::TestTotals::test_total_mass_duplicates[residues]
  /home/jon/dev/mdanalysis/package/MDAnalysis/core/topologyattrs.py:1119: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    masses = self.values[resatoms].sum()

The warnings are thrown for core/test_accumulate.py::TestTotals::test_total_charge (and its mass equivalent):

mdanalysis/testsuite/MDAnalysisTests/core/test_accumulate.py

Line 121 in 2ee4e9d

ref = group.total_charge() + group[0].charge

The problematic call is a call to Residue.charge or Residue.mass (note the singular group name). This calls topologyattrs.Charges.get_residues which makes a problematic array indexing on line

mdanalysis/package/MDAnalysis/core/topologyattrs.py

Line 1540 in 2ee4e9d

charges = self.values[resatoms].sum()

or topologyattrs.Masses.get_residues on line

mdanalysis/package/MDAnalysis/core/topologyattrs.py

Line 1119 in 2ee4e9d

masses = self.values[resatoms].sum()

Here, an array is indexed with a list of arrays, hence the warning.

The get_segments counterpart are fixed and convert the list of arrays into a tuple of arrays, not triggering the warning.

Code to reproduce the behavior

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import XTC, TRR

u = mda.Universe(TRR, XTC)
u.residues[0].mass  # or u.residues[0].charge

or

pytest core/test_accumulate.py::TestTotals

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") 2.0.0-dev0 64a7c05
• Which version of Python (python -V)? Python 3.8.5
• Which operating system? Ubuntu 20.04 on WSL