Expected output (terminal logs):
from hbp_nrp_cle.brainsim.BrainInterface import IFixedSpikeGenerator, \ File "/home/lguyot/Documents/NRP/CLE/hbp_nrp_cle/hbp_nrp_cle/brainsim/__init__.py", line 44, in <module> import pyNN.nest File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/nest/__init__.py", line 17, in <module> from . import simulator File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/nest/simulator.py", line 28, in <module> from pyNN import common File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/common/__init__.py", line 47, in <module> from .populations import IDMixin, BasePopulation, Population, PopulationView, Assembly, is_conductance File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/common/populations.py", line 22, in <module> from pyNN import random, recording, errors, standardmodels, core, space, descriptions File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/recording/__init__.py", line 19, in <module> import neo File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/__init__.py", line 12, in <module> from neo.io import * File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/io/__init__.py", line 115, in <module> from neo.io.klustakwikio import KlustaKwikIO File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/io/klustakwikio.py", line 25, in <module> import matplotlib.mlab as mlab File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1163, in <module> rcParams = rc_params() File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1007, in rc_params return rc_params_from_file(fname, fail_on_error) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1143, in rc_params_from_file if key not in _all_deprecated]) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 895, in __init__ self.update(*args, **kwargs) File "/home/lguyot/.opt/platform_venv/lib/python2.7/_abcoll.py", line 572, in update self[key] = value File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 922, in __setitem__ cval = self.validate[key](val) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/rcsetup.py", line 846, in validate_cycler cycler_inst.change_key(prop, norm_prop) AttributeError: 'Cycler' object has no attribute 'change_key' unable to load app 0 (mountpoint='') (callable not found or import error)
My understanding is that neo==0.5.2, which is PyNN==0.9.0 depency (required by NRP) does not use a compatible matplotlib version. By default, neo==0.5.2 will install matplotlib==1.5.1 but scikit-image>=0.13.1 uninstalls it and subsequently installs matplotlib==2.2.2.
Upgrading neo doesn't help. Downgrading matplotlib to 1.5.1 removes the error but could have side effects.
Here are the steps to reproduce the problem:
Expected output (terminal logs):
from hbp_nrp_cle.brainsim.BrainInterface import IFixedSpikeGenerator, \ File "/home/lguyot/Documents/NRP/CLE/hbp_nrp_cle/hbp_nrp_cle/brainsim/__init__.py", line 44, in <module> import pyNN.nest File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/nest/__init__.py", line 17, in <module> from . import simulator File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/nest/simulator.py", line 28, in <module> from pyNN import common File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/common/__init__.py", line 47, in <module> from .populations import IDMixin, BasePopulation, Population, PopulationView, Assembly, is_conductance File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/common/populations.py", line 22, in <module> from pyNN import random, recording, errors, standardmodels, core, space, descriptions File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/pyNN/recording/__init__.py", line 19, in <module> import neo File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/__init__.py", line 12, in <module> from neo.io import * File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/io/__init__.py", line 115, in <module> from neo.io.klustakwikio import KlustaKwikIO File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/neo/io/klustakwikio.py", line 25, in <module> import matplotlib.mlab as mlab File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1163, in <module> rcParams = rc_params() File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1007, in rc_params return rc_params_from_file(fname, fail_on_error) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 1143, in rc_params_from_file if key not in _all_deprecated]) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 895, in __init__ self.update(*args, **kwargs) File "/home/lguyot/.opt/platform_venv/lib/python2.7/_abcoll.py", line 572, in update self[key] = value File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/__init__.py", line 922, in __setitem__ cval = self.validate[key](val) File "/home/lguyot/.opt/platform_venv/lib/python2.7/site-packages/matplotlib/rcsetup.py", line 846, in validate_cycler cycler_inst.change_key(prop, norm_prop) AttributeError: 'Cycler' object has no attribute 'change_key' unable to load app 0 (mountpoint='') (callable not found or import error)My understanding is that neo==0.5.2, which is PyNN==0.9.0 depency (required by NRP) does not use a compatible matplotlib version. By default, neo==0.5.2 will install matplotlib==1.5.1 but scikit-image>=0.13.1 uninstalls it and subsequently installs matplotlib==2.2.2.Upgrading neo doesn't help. Downgrading matplotlib to 1.5.1 removes the error but could have side effects.