jupyter
16 posts
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Do you need JupyterHub for your workshop? JupyterLite runs Python in the browser
You're organizing a Python workshop or teaching a class that uses Jupyter notebooks. The first question that comes up is almost always the same: how do I get everyone running notebooks without spending an hour on installation?
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Keep Jupyter notebooks clean in git, but rendered with outputs in Sphinx
A small Sphinx extension that fetches an executed notebook from a Gist or raw URL, verifies the sources still match, and replaces the local notebook during the docs build.
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Jupyter Notebook frontmatter for Quarto to download source notebook
Quarto is one of the best platforms to create statically generated blogs with Markdown and Jupyter Notebooks. I switched zonca.dev to Quarto back in 2022.
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Run PyTorch with GPU support on Expanse
In this tutorial we will create a Python environment with PyTorch and see how to get Jupyterlab running on a GPU node. First of all we want to create an isolated Python environment, I generally favor micromamba, see the documentation on how to install it
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Remove unique cell id from Jupyter Notebooks
I know! Jupyter is littering your git diff with randomly generated cell ids and nbstripout doesn't remove them, (I'm sure they are useful for some reason).
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Workflow for Jupyter Notebooks under version control
I'll present here my strategy for keeping Jupyter Notebooks under version control. TLDR:
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How to share Jupyter Notebooks
I tend to preserve and post online all the work I do for later reference and sharing. Jupyter Notebooks are a bit more complex than standard source code because they are natively in a format (JSON) that needs to be rendered to be readable.
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Kill Jupyter Notebook servers
Just today I learned how to properly stop previously running Jupyter Notebook servers, here for future reference: jupyter notebook stop
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Execute Jupyter Notebooks not interactively
Over the years, I have explored how to scale up easily computation through Jupyter Notebooks by executing them not-interactively, possibily parametrized and remotely. This is mostly for reference.
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Advanced pandas with astrophysics example notebook
Taught a lesson today on advanced python and pandas based on an example application in Astrophysics with simulations of data from the Planck Satellite), features also a Binder button to run it yourself. Jupyter Notebook available at: under CC-BY
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Use the distributed file format Zarr on Jetstream Swift object storage
Use the distributed file format Zarr on Jetstream Swift object storage
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Use the distributed file format Zarr on Jetstream Swift object storage
Zarr is a pretty new file format designed for cloud computing, see documentation and a webinar for more details. Zarr is also supported by dask, the parallel computing framework for Dask, and the Dask team implemented storage backends for Google Cloud Storage and Amazon S3.
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Store a conda environment inside a Notebook
Last August, during the Container Analysis Environments Workshop held at Urbana-Champaign, we had discussion about reproducibility in the Jupyter Notebooks. There came out the idea of storing all the details about the Python environment inside the Notebook, in the metadata.
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IPython/Jupyter notebook setup on NERSC Edison
This tutorial explains the setup to run an IPython Notebook on a computing node on the supercomputer Edison at NERSC and forward its port encrypted with SSH to the browser on a local laptop. This setup is a bit more complicated than other supercomputers, i.e. see my tutorial for Comet for 2 reasons:
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IPython/Jupyter notebook setup on SDSC Comet
This tutorial explains the setup to run an IPython Notebook on a computing node on the supercomputer Comet at the San Diego Supercomputer Center and forward the port encrypted with SSH to the browser on a local laptop.