Pandas 0.24 incompatibility - module 'pandas' has no attribute 'lib'

[blakecaldwell]

I received an AttributeError("module 'pandas' has no attribute 'lib'") when running the NetPyNE tutorials. Full output below:

Microsoft Windows [Version 10.0.17134.523]
(c) 2018 Microsoft Corporation. All rights reserved.

C:\Users\caldw>activate netpyne

(netpyne) C:\Users\caldw>cd repos\netpyne\examples\HHTut

(netpyne) C:\Users\caldw\repos\netpyne\examples\HHTut>nrniv -python tut2.py
NEURON -- VERSION 7.6.5 master (f3dad62b) 2019-01-11
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018
See http://neuron.yale.edu/neuron/credits

Note: NeuroML import failed; import/export functions for NeuroML will not be available.
  To install the pyNeuroML & libNeuroML Python packages visit: https://www.neuroml.org/getneuroml

Creating network of 2 cell populations on 1 hosts...
  Number of cells on node 0: 40
  Done; cell creation time = 0.01 s.
Making connections...
  Number of connections on node 0: 203
  Done; cell connection time = 0.01 s.
Adding stims...
  Number of stims on node 0: 40
  Done; cell stims creation time = 0.01 s.
Recording 1 traces of 1 types on node 0

Running simulation for 1000.0 ms...
  Done; run time = 0.64 s; real-time ratio: 1.57.

Gathering data...
  Done; gather time = 0.01 s.

Analyzing...
  Cells: 40
  Connections: 243 (6.08 per cell)
  Spikes: 932 (23.30 Hz)
  Simulated time: 1.0 s; 1 workers
  Run time: 0.64 s
fatal: not a git repository (or any of the parent directories): .git
  Done; saving time = 0.05 s.
Plotting raster...
(<class 'AttributeError'>, AttributeError("module 'pandas' has no attribute 'lib'"), <traceback object at 0x000000000E9BEE48>)
No spikes available to plot raster
Plotting recorded cell traces ...
Plotting 2D representation of network cell locations and connections...
  Done; plotting time = 0.83 s

Total time = 1.56 s

This was initially with a Windows 10 system using miniconda3 (Python 3.7) and NetPyNE installed with "pip install netpyne". The same result occurred with virtualenv. Uninstalling pandas 0.24 and building pandas 0.23 solved the issue.

The change is mentioned in the pandas release notes:
https://pandas.pydata.org/pandas-docs/stable/whatsnew/v0.24.0.html#removal-of-prior-version-deprecations-changes

The specific issue regarding the deprecation of pandas.lib:
pandas-dev/pandas#15537

I hope this helps. For now, using pandas 0.23 is acceptable to me.

Packages installed:

(netpyne) C:\Users\caldw\repos\netpyne\examples\HHTut>conda list
# packages in environment at C:\Users\caldw\Miniconda3\envs\netpyne:
#
# Name                    Version                   Build  Channel
ca-certificates           2018.12.5                     0
certifi                   2018.11.29               py37_0
cycler                    0.10.0                    <pip>
Cython                    0.29.3                    <pip>
future                    0.17.1                    <pip>
kiwisolver                1.0.1                     <pip>
matplotlib                3.0.2                     <pip>
matplotlib-scalebar       0.5.1                     <pip>
netpyne                   0.9.1.1                   <pip>
numpy                     1.16.1                    <pip>
openssl                   1.1.1a               he774522_0
pandas                    0.24.0                    <pip>
pip                       18.1                     py37_0
pyparsing                 2.3.1                     <pip>
python                    3.7.2                h8c8aaf0_0
python-dateutil           2.7.5                     <pip>
pytz                      2018.9                    <pip>
scipy                     1.2.0                     <pip>
setuptools                40.6.3                   py37_0
six                       1.12.0                    <pip>
sqlite                    3.26.0               he774522_0
vc                        14.1                 h0510ff6_4
vs2015_runtime            14.15.26706          h3a45250_0
wheel                     0.32.3                   py37_0
wincertstore              0.2                      py37_0

[cliffckerr]

Confirm this is an issue for me too, with the same solution.

[salvadord]

Thank so much Avrama for pointing this out (sorry for the delay), and cliff for providing a fix -- we'll include it in the next release.