can't pickle PDBReader on python 3

[kain88-de]

Expected behaviour

I'm able to pickle PDBReader under python 3

Actual behaviour

I'm getting an error that TextIOWrapper cannot be pickled.

Code to reproduce the behaviour

import MDAnalysis as mda
from MDAnalysisTests.datafiles import PDB
import pickle

u = mda.Universe(PDB, PDB)
pickle.dumps(u.trajectory)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-7-d286063031e3> in <module>()
----> 1 pickle.dumps(u.trajectory)

TypeError: cannot serialize '_io.TextIOWrapper' object

....

Currently version of MDAnalysis:

(run python -c "import MDAnalysis as mda; print(mda.__version__)")
0.18.0

[orbeckst]

See #1940 – this issue is part of the problem.

[orbeckst]

I am labeling this as a defect because this is supposed to work (and will actually break code that tries to parallelize anything that reads a PDB!)

[kain88-de]

the chainreader problem seems to be a different one. I actually wanted to see where it uses generators and then came across this problem.

I should note that it works to pickle with cloudpickle

[orbeckst]

I should note that it works to pickle with cloudpickle

Can you please be more precise? What works with cloudpickle?

[orbeckst]

The generator is MDAnalysis/pmda#44 (comment)

ChainReader__chained_trajectories_iter': <generator object ChainReader._chained_iterator at 0x7f1c19716468>

the chainreader problem seems to be a different one

I said it is part of the problem because I am pretty sure that as soon as we solve the generator problem, we run into the issue described by you.

[kain88-de]

You can pickle the PDB reader with the cloudpickle library. It’s a drop in replacement for pickle.

[orbeckst]

closed with PR #2723