Hey folks,
I've been searching all morning, but coming up empty. The question is this:
Is there a way to using the nbconvert python API with a kernel installed in
a conda environment?
Background:
I'm trying to write a documentation build script for a module that converts
notebooks to RST, and then compiles HTML docs with Sphinx.
I have installed the module I'm documenting into an isolated conda
environment called "probscale".
So with this trivial notebook (note the kernelspec):
a_test.ipynb:
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[-0.04809765 -0.65510951 -0.06389409 -0.78956431 1.12613107]\n"
]
}
],
"source": [
"import numpy\n",
"print(numpy.random.normal(size=5))"
]
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [conda env:probscale]",
"language": "python",
"name": "conda-env-probscale-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
When I run:
if 1:
import nbformat
from nbconvert import preprocessors
nbfile = 'a_test.ipynb'
meta = {
'metadata': {
'path': '.',
}
}
with open(nbfile, 'r') as nbf:
nbook = nbformat.read(nbf, as_version=4)
runner = preprocessors.ExecutePreprocessor()
runner.preprocess(nbook, meta)
with open(nbfile, 'w') as nbf:
nbformat.write(nbook, nbf)
I get a KeyError and a NoSuchKernal error
---------------------------------------------------------------------------KeyError
Traceback (most recent call
last)C:\Users\phobson\Miniconda3\envs\probscale\lib\site-packages\jupyter_client\kernelspec.py
in get_kernel_spec(self, kernel_name) 172 try:--> 173
resource_dir = d[kernel_name.lower()] 174 except KeyError:
KeyError: 'conda-env-probscale-py'
[snip]
C:\Users\phobson\Miniconda3\envs\probscale\lib\site-packages\jupyter_client\kernelspec.py
in get_kernel_spec(self, kernel_name) 173 resource_dir =
d[kernel_name.lower()] 174 except KeyError:--> 175 raise
NoSuchKernel(kernel_name) 176 177 return
self._get_kernel_spec_by_name(kernel_name, resource_dir)
NoSuchKernel: No such kernel named conda-env-probscale-py
I tried adding the kernel spec from the notebook to metadata passed to
runner.preprocess(nbook, meta), but that produced the same result.
Any thoughts or guidance would be much appreciated.
Cheers,
-Paul
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