ModuleNotFoundError: No module named 'jupyter_bokeh'

[ryanschwark]

After launching the most up-to date version of the Keypoint MoSeq Analysis Visualization Notebook, we start with the "Set up notebook for interactive widgets" step. We launched the jupyter notebbok via the Anaconda navigator using the environment called keypoint_moseq. The cell we run has these lines:

Install and Enable widget extensions configurator

!jupyter nbextension install --py jupyter_nbextensions_configurator --sys-prefix !jupyter nbextension enable --py --sys-prefix widgetsnbextension !jupyter nbextension enable --py --sys-prefix --py qgrid

Install bokeh extensions

!jupyter nbextension install --sys-prefix --symlink --py jupyter_bokeh !jupyter nbextension enable jupyter_bokeh --py --sys-prefix

However, when we run this cell, we get the following error message:

Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE__main.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 702, in start self.install_extensions() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 675, in install_extensions full_dests = install(self.extra_args[0], File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 203, in install_nbextension_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import(parts[0]) ModuleNotFoundError: No module named 'jupyter_nbextensions_configurator' Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE__main__.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 882, in start self.toggle_nbextension_python(self.extra_args[0]) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 855, in toggle_nbextension_python return toggle(module, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 470, in enable_nbextension_python return _set_nbextension_state_python(True, module, user, sys_prefix, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 368, in _set_nbextension_state_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import(parts[0]) ModuleNotFoundError: No module named 'widgetsnbextension' Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE__main__.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 882, in start self.toggle_nbextension_python(self.extra_args[0]) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 855, in toggle_nbextension_python return toggle(module, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 470, in enable_nbextension_python return _set_nbextension_state_python(True, module, user, sys_prefix, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 368, in _set_nbextension_state_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import(parts[0]) ModuleNotFoundError: No module named 'qgrid' Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE__main.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 702, in start self.install_extensions() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 675, in install_extensions full_dests = install(self.extra_args[0], File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 203, in install_nbextension_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import(parts[0]) ModuleNotFoundError: No module named 'jupyter_bokeh' Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE\main__.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 882, in start self.toggle_nbextension_python(self.extra_args[0]) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 855, in toggle_nbextension_python return toggle(module, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 470, in enable_nbextension_python return _set_nbextension_state_python(True, module, user, sys_prefix, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 368, in _set_nbextension_state_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import__(parts[0]) ModuleNotFoundError: No module named 'jupyter_bokeh'

What might be causing this issue? Thanks!

[calebweinreb]

We are planning to change this step slightly. Try running those lines (without the exclamation marks) in a command terminal with the keypoint_moseq environment activated. Then after they run, start a jupyter notebook server. Once this notebook is open again, you can skip those lines.

[ryanschwark]

Thanks! I tried running the first line of code without the exclamation mark in the command terminal with the keypoint_moseq environment activated. I tried this both in the anaconda shell and in miniconda3. However, it looks like I get an error:

(keypoint_moseq) C:\Users\Abdus-saboor>jupyter nbextension install --py jupyter_nbextensions_configurator --sys-prefix Traceback (most recent call last): File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\Scripts\jupyter-nbextension.EXE__main.py", line 7, in File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\config\application.py", line 1043, in launch_instance app.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 972, in start super().start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\jupyter_core\application.py", line 266, in start self.subapp.start() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 702, in start self.install_extensions() File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 675, in install_extensions full_dests = install(self.extra_args[0], File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 203, in install_nbextension_python m, nbexts = _get_nbextension_metadata(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\notebook\nbextensions.py", line 1107, in _get_nbextension_metadata m = import_item(module) File "C:\Users\Abdus-saboor\miniconda3\envs\keypoint_moseq\lib\site-packages\traitlets\utils\importstring.py", line 38, in import_item return import__(parts[0]) ModuleNotFoundError: No module named 'jupyter_nbextensions_configurator'

[calebweinreb]

What steps did you take to install the branch with the analysis? I ask because jupyter_nbextensions_configurator is listed in the requirements, so it should have been installed. Just to be sure, these are the steps:

conda activate keypoint_moseq
pip install -U git+https://github.com/dattalab/keypoint-moseq@sherry_updates

[ryanschwark]

Thanks Caleb! It looks like for whatever reason I didn't have the jupyter_nbextensions_configurator installed. After installing by running the lines of code above, it fixed the issue!