NWBWidget-demo.ipynb: ModuleNotFoundError: No module named 'hdmf.common'

[yarikoptic]

Discovered while #10

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_18732/3880075473.py in <module>
      1 import pynwb
      2 from pynwb import NWBHDF5IO
----> 3 from nwbwidgets import nwb2widget
      4 import requests
      5 

/opt/conda/lib/python3.9/site-packages/nwbwidgets/__init__.py in <module>
      1 import plotly.io as pio
      2 
----> 3 from .view import nwb2widget, default_neurodata_vis_spec
      4 
      5 # from .ephys_viz_interface import ephys_viz_neurodata_vis_spec

/opt/conda/lib/python3.9/site-packages/nwbwidgets/view.py in <module>
      7 import zarr
      8 from ipywidgets import widgets
----> 9 from ndx_icephys_meta.icephys import SweepSequences
     10 from ndx_spectrum import Spectrum
     11 

/opt/conda/lib/python3.9/site-packages/ndx_icephys_meta/__init__.py in <module>
     30 
     31 # Import the files
---> 32 from .icephys import ICEphysFile,  IntracellularRecordings, Sweeps, SweepSequences, Runs, Conditions # noqa E402, F401
     33 from . import io as __io  # noqa E402, F401

/opt/conda/lib/python3.9/site-packages/ndx_icephys_meta/icephys.py in <module>
      3 from pynwb.icephys import IntracellularElectrode
      4 from pynwb.base import TimeSeries
----> 5 from hdmf.common import DynamicTable, DynamicTableRegion
      6 from hdmf.utils import docval, popargs, getargs, call_docval_func, get_docval, fmt_docval_args
      7 import warnings

ModuleNotFoundError: No module named 'hdmf.common'

@bendichter - any immediate idea on how to mitigate?

[yarikoptic]

ha -- can't reproduce while trying "manually". May be it was a different environment in which the pytest was running it. will double check. BUT interestingly

io = NWBHDF5IO("~/Downloads/sub-anm324650_ses-20160422_behavior+icephys+ogen.nwb", mode='r', load_namespaces=True)

doesn't work due to not expanding ~! So the

import os.path as op
io = NWBHDF5IO(op.expanduser("~/Downloads/sub-anm324650_ses-20160422_behavior+icephys+ogen.nwb"), mode='r', load_namespaces=True)

works ... I will send a PR for that

[bendichter]

what is your environment? Are you in Allen-SDK?

[yarikoptic]

no... that was in the base. I guess indeed for this one to succeed I should have chosen another conda env. heh -- complicates providing automated solution for #10 ;)

Also strangely it succeeded later when I tried again -- I guess one of the notebooks does install allen-sdk via some pip install command it contains... uff. Anyways -- I will send a PR for the expanduser to close this issue