Include a link in PyNEST examples to run them as notebooks #2605
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jessica-mitchell
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The documentation builds for me locally, and everything looks the same as in your example, and the links to the ebrains notebooks work. The user guide looks great.
I'm getting a few warnings when building the documentation that are not present when I build from the master branch:
/home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/compartmental_model/receptors_and_current.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/compartmental_model/two_comps.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/pong/generate_gif.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/pong/networks.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/pong/pong.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/pong/run_simulations.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/sudoku/plot_progress.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/auto_examples/sudoku/sudoku_net.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/janeirik/nest_repository/2605/nest-simulator-build/doc/htmldoc/faqs
I'm also getting some warnings that are also present when building it from the master branch, mostly related to HillTononiModels.ipynb and hl_api_*.py.
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@janskaar Thanks for the review, I addressed your comments. As for the sphinx warnings you see at build time, we are aware of them and you can ignore them as they need to be dealt with in separate issues. |
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@med-ayssar @janskaar Can you please take another look? thanks! |
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@med-ayssar I made the changes you suggested |
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Could you post the new |
I get the following error: |
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@med-ayssar I fixed the link by adding https://nest-test.readthedocs.io/en/add-link-examples/auto_examples/balancedneuron.html |
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@med-ayssar @janskaar Could you please resolve all conversations that you opened so that we can merge? Our general policy is that the person who started a conversation should mark it as resolved. |
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Done! |
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I can't find any resolve button for my conversations. Is there a special
permission or something needed that I don't have?
…On Tue, 21 Mar 2023, 09:25 Hans Ekkehard Plesser, ***@***.***> wrote:
@med-ayssar <https://github.com/med-ayssar> @janskaar
<https://github.com/janskaar> Could you please resolve all conversations
that you opened so that we can merge? Our general policy is that the person
who started a conversation should mark it as resolved.
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Just go back to your comments, and you will see the resolve button.
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This is what it looks like for me:
…On Tue, 21 Mar 2023, 12:53 med-ayssar, ***@***.***> wrote:
I can't find any resolve button for my conversations. Is there a special
permission or something needed that I don't have?
… <#m_-6056052959423086475_>
On Tue, 21 Mar 2023, 09:25 Hans Ekkehard Plesser, *@*.*> wrote:
@med-ayssar <https://github.com/med-ayssar> https://github.com/med-ayssar
<https://github.com/med-ayssar> @janskaar <https://github.com/janskaar>
https://github.com/janskaar <https://github.com/janskaar> Could you please
resolve all conversations that you opened so that we can merge? Our general
policy is that the person who started a conversation should mark it as
resolved. — Reply to this email directly, view it on GitHub <#2605
(comment)
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[image: Screenshot from 2023-03-21 12-52-55]
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@janskaar I think you forgot to post the photo, but if you don't mind, I can resolve your threads instead. |
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Yes, please do!
…On Tue, 21 Mar 2023, 14:16 med-ayssar, ***@***.***> wrote:
@janskaar <https://github.com/janskaar> I think you forgot to post the
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This PR adds a link (see nbgitpuller) to the PyNEST examples so they can run as a notebook - using the EBRAINS JupyterHub as service.
The link is added at build time so it is not in the source repository.
It is added to the reStructuredText files in
auto_examplesgenerated by sphinx_gallery.The notebooks are located in nest/nest-simulator-examples/ repository.
This PR also includes a file that explains how to run the notebooks and some basic troubleshooting.
The Python download button generated by sphinx_gallery remains but the notebook button is removed.
This PR only deals with the sphinx-build of the link.
The notebooks are already available but the automated generation/maintenance of the notebooks will be dealt with in another PR.
See sample: https://nest-test.readthedocs.io/en/add-link-examples/auto_examples/one_neuron.html