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Jupyter Notebook Tips and Tricks

A few (hopefully) useful tips and tricks to using the Jupyter Notebook with an eye to pragmatic usage. This is not, in any way, an exhaustive demonstration of the features of the Jupyter notebook. Further, you can go through these notebooks on your own, but I usually demonstrate using them and give lots of information verbally.

If you have any suggestions, edits, or corrections, please open an issue or let me know some other way. Best of luck!

Assuming you are on a Mac

Install Miniconda (if you haven't already)

cd ~/Downloads
# go through the licensing and accept the defaults
source ~/.bashrc
conda update conda

Create a new conda environments

The following commands are how I set up both my conda config and the enviroments that I use.

Add conda-forge to your automatic channels, and the second line makes it so that you don't have to confirm that you want to install when you do things like

conda install numpy
conda config --add channels conda-forge
conda config --set always_yes yes

This following block is bash -- I recommend pasting in the commands one at a time to see what's happening.

# set the environment name here


packages=' altair anaconda-client black bqplot ipyvolume ipywebrtc ipywidgets jupyter jupyter_contrib_nbextensions jupyterlab matplotlib mkl mpld3 notebook numpy pandas pip pivottablejs pyparsing pyscaffold qgrid scikit-learn scipy seaborn sphinx statsmodels vaex vega vega_datasets xlrd yapf '

conda create -n $envname python=3.8 $packages conda activate $envname

Pause here, double check that this pip is the correct one

type pip

the correct one will say something like...

$ type pip

pip is /Users/jonathan/miniconda3/envs/dspy3/bin/pip

python -m pip install pyhive sql_magic SQLAlchemy nbdime papermill nbdev

lets the notebook extension (like ToC2) be enabled.

Might not be needed!

jupyter nbextension enable --py --sys-prefix widgetsnbextension

This sets the name of the kernel that you want to select from the Kernel menu

python -m ipykernel install --user --name $envname --display-name "$envname"

jupyterlab widgets

conda install -c conda-forge nodejs

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter labextension install ipyvolume jupyter-threejs @jupyterlab/toc jupyter labextension install jupyter-threejs bqplot nbgather qgrid


If you see an error message that says something about the iopubdatarate_limit when you're trying to plot, try starting the notebook/lab with the following modified commands:

# Run to get a notebook
jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000

Run to get lab

jupyter lab --NotebookApp.iopub_data_rate_limit=10000000

Extra ideas

# create environment
conda env export -n dspy3 -f environment.lock.yaml
# load
conda env update --file environment.yaml

to create new python package I did this from root directory of this repo

putup insight cd insight/ python develop

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