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nb_conda_kernels not found when using nbconvert --execute

See original GitHub issue

I am trying to run a notebook that uses a kernel from an automatically registered environment like this:

jupyter nbconvert --to notebook --execute advanced_mapping.ipynb

I am getting:

[NbConvertApp] Converting notebook advanced_mapping.ipynb to notebook
[NbConvertApp] Executing notebook with kernel: testenv
Traceback (most recent call last):
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 201, in get_kernel_spec
    resource_dir = d[kernel_name.lower()]
KeyError: 'conda-env-testenv-py'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/croth1/miniconda2/envs/sci36/bin/jupyter-nbconvert", line 6, in <module>
    sys.exit(nbconvert.nbconvertapp.main())
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_core/application.py", line 267, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/nbconvertapp.py", line 305, in start
    self.convert_notebooks()
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/nbconvertapp.py", line 473, in convert_notebooks
    self.convert_single_notebook(notebook_filename)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/nbconvertapp.py", line 444, in convert_single_notebook
    output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/nbconvertapp.py", line 373, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/exporters/exporter.py", line 171, in from_filename
    return self.from_file(f, resources=resources, **kw)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/exporters/exporter.py", line 189, in from_file
    return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/exporters/notebook.py", line 31, in from_notebook_node
    nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/exporters/exporter.py", line 131, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/exporters/exporter.py", line 308, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__
    return self.preprocess(nb,resources)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py", line 207, in preprocess
    cwd=path)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py", line 188, in start_new_kernel
    km.start_kernel(**kwargs)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_client/manager.py", line 244, in start_kernel
    kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_client/manager.py", line 175, in format_kernel_cmd
    cmd = self.kernel_spec.argv + extra_arguments
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_client/manager.py", line 87, in kernel_spec
    self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
  File "/home/croth1/miniconda2/envs/sci36/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 203, in get_kernel_spec
    raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named conda-env-testenv-py

Issue Analytics

State:
Created 6 years ago
Comments:8 (1 by maintainers)

Top GitHub Comments

3reactions

mpacercommented, Feb 26, 2018

Note this issue discussing these problems on nbconvert: https://github.com/jupyter/nbconvert/issues/515

1reaction

mcg1969commented, May 30, 2018

It’s not clear to me that there is anything that can be done about this within nb_conda_kernels itself without monkeypatching the nbconvert package. That said, the work being done in Jupyter 6 to refactor the way kernels are discovered should benefit all Jupyter-based packages.

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