MemoryReader copy creates new Timestep object

[richardjgowers]

Expected behavior

MemoryReader.copy should return a working-as-intended MemoryReader

Actual behavior

The Timestep attached to the MemoryReader is disjointed from the stored arrays on MemoryReader. Modifying the Timestep then doesn't update the underlying arrays

Code to reproduce the behavior

from MDAnalysis.coordinates.memory import MemoryReader
import numpy as np

coords = np.arange(60).reshape(2, 10, 3).astype(np.float32)
mr = MemoryReader(coords)
mr.coordinate_array
mr2 = mr.copy()

# assign value to positions
# as this is a  memoryreader, this change should be permanent
mr2.ts.positions = -1

mr2[0]

assert mr2.ts.positions == -1  # will fail

# not saved to master array
mr2.coordinate_array

Currently version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
• Which version of Python (python -V)?
• Which operating system?

0.18.0