Closed CodyCBakerPhD closed 11 months ago
@weiglszonja Should be easy, instead of that stuff in run_conversion
here just define mapping protocol in add_to_nwbfile
Also if you could triple check that a unified (all data streams) conversion runs in the fresh environment, that would be awesome
@laurelrr I apologise for this oversight! I opened #34 that should fix this.
@laurelrr OK can you try to pull the latest changes and let us know of any further issues?
I pulled in your changes with
git pull
Then attempted to convert the same subject file using:
python src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_all_sessions.py
Did I miss a step?
I immediately got this error:
(tye_lab_to_nwb_env) lkeyes@node32:/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb$ python src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_al l_sessions.py
Traceback (most recent call last):
File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_all_sessions.py", line 13, in <module>
from tye_lab_to_nwb.neurotensin_valence.neurotensin_valence_convert_session import session_to_nwb
File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py", line 16, in <modu le>
from nwbinspector import inspect_nwbfile
ImportError: cannot import name 'inspect_nwbfile' from 'nwbinspector' (/home/lkeyes/anaconda3/envs/tye_lab_to_nwb_env/lib/python3.11/site-packages/nwbinspector /__init__.py)
@laurelrr Might be worth trying @weiglszonja's steps in https://github.com/catalystneuro/tye-lab-to-nwb/pull/34#issuecomment-1740606634 to create a new fresh environment; it looks like external packages might have gotten a little out of sync otherwise
Thanks, I'll try that on Monday.
I got an error while trying @weiglszonja's steps in https://github.com/catalystneuro/tye-lab-to-nwb/pull/34#issuecomment-1740606634 to create a new fresh environment:
conda create --name tyenwb39 python=3.9
conda activate tyenwb39
pip install -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt
gave this error:
(tyenwb39) lkeyes@node32:/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb$ pip install -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt
Obtaining neuroconv from git+https://github.com/catalystneuro/neuroconv@add_ignore_timestamps_errors_to_interface#egg=neuroconv (from -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt (line 1))
Updating ./src/neuroconv clone (to revision add_ignore_timestamps_errors_to_interface)
Running command git fetch -q --tags
fatal: pack has 5 unresolved deltas
fatal: index-pack failed
error: subprocess-exited-with-error
× git fetch -q --tags did not run successfully.
│ exit code: 128
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× git fetch -q --tags did not run successfully.
│ exit code: 128
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
I attempted to pip uninstall neuroconv
but it is not installed in this environment.
Thanks
This is what is in my current neurotensin_valence_requirements.txt:
-e git+https://github.com/catalystneuro/neuroconv@add_ignore_timestamps_errors_to_interface#egg=neuroconv
neuroconv[openephys,plexon,video]
git+https://github.com/neuralensemble/python-neo@master
ndx_pose>=0.1.1
oiffile==2022.9.29
easydict>=1.10
openpyxl>=3.1.2
Originally posted by @laurelrr in https://github.com/catalystneuro/tye-lab-to-nwb/issues/29#issuecomment-1739987761