msm.its UnicodeDecodeError

[and-tos]

Hi,

I am running into a UnicodeDecodeError when running pyemma.msm.its.

UnicodeDecodeError: 'ascii' codec can't decode byte 0x9a in position 0: ordinal not in range(128)

The discrete trajectories I pass to its seem OK. I would really appreciate any hint on what is happening.

import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import os
import seaborn as sns
from pymol import cmd
import pyemma

...
cluster = pyemma.coordinates.cluster_mini_batch_kmeans(tica_output, k=n_clusters)
dtrajs=cluster.dtrajs
its = pyemma.msm.its(dtrajs, lags=50, errors='bayes')

[and-tos]

The error appears only when running from pymol import cmd

[marscher]

That's strange. How did you manage to pin this down? Are you still on Python 2.7?

Am 22. Juni 2019 14:36:06 MESZ schrieb andt88 notifications@github.com:

The error appears only when running from pymol import cmd

[and-tos]

No I'm running python 3.6. It was the last thing I added to the script before the error started appearing. I just separated the tasks in two different scripts. Not really elegant though.

[marscher]

Could you also please add the list of installed packages (e.g. conda list > pkg.txt or pip list > pkg.txt)?

[and-tos]

Please find attached the requested file. pkg.txt

[marscher]

Thank you. Does upgrading pathos resolve the issue? If not, I would be glad, if you could post the exact stack trace or even better a minimal example producing the error.

[and-tos]

Upgrading did not work. Here's the stack trace: I will make a minimal example later

Traceback (most recent call last):
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/threading.py", line 917, in _bootstrap_inner
    self.run()
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/threading.py", line 865, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/site-packages/multiprocess/pool.py", line 470, in _handle_results
    task = get()
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/site-packages/multiprocess/connection.py", line 254, in recv
    return _ForkingPickler.loads(buf.getbuffer())
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/site-packages/dill/_dill.py", line 317, in loads
    return load(file, ignore)
  File "/Users/andy/.conda/envs/plot.py/lib/python3.7/site-packages/dill/_dill.py", line 305, in load
    obj = pik.load()
UnicodeDecodeError: 'ascii' codec can't decode byte 0x81 in position 6: ordinal not in range(128)

[marscher]

Thanks. Did the update process also drag in dill-0.3.0?