Great ! Sorry about the inconvenience. I'm not sure how things would interact, but if you install the spec with the right `--name` you might not have to switch each notebook.
Cheers, -- M On Tue, Feb 7, 2017 at 1:14 PM, Paul Hobson <[email protected]> wrote: > Matthias, > > Many thanks for the quick response and helpful solution. > > Indeed, running: > > $ # source activate <envname> # non-windows > $ activate <envname> # windows > (envname) $ python -m ipykernel install --name <envname> > > And then manually changing the kernel in each of the notebooks before > running my script solved it. > > > On Tue, Feb 7, 2017 at 1:05 PM, Matthias Bussonnier > <[email protected]> wrote: >> >> Hi Paul, >> >> As far as I can tell this is one of the limit of the conda extension >> shiped with conda that autolist the kernelspecs. It does not work with >> nbconvert. >> You need to activate the env and manually install the spec using >> `python -m ipykernel install <--options>`, and set the notebook to use >> this kernelspec using the notebook UI. >> Then, it should work. >> >> Cheers, >> -- >> M >> >> On Tue, Feb 7, 2017 at 12:58 PM, Paul Hobson <[email protected]> wrote: >> > 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 >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "Project Jupyter" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > To view this discussion on the web visit >> > >> > https://groups.google.com/d/msgid/jupyter/cbee4894-2f86-44f0-a130-2cf63081e47c%40googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "Project Jupyter" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/jupyter/CANJQusW2j%2B%3DSGrr%3DodjNEsXgTHwGHHNxQd0LCsksE2K8x4iqTw%40mail.gmail.com. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "Project Jupyter" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/jupyter/CADT3MECr_J1kgHaFBOdv22wrR44kzUDzSZzE2_H%3DOkMchzmWAA%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "Project Jupyter" group. 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