Quickly parametrize Jupyter Notebooks and extract images and text outputs

example.py

# Add these lines to the first cell of Jupyter Notebook
# for argument support
try:
    from _run_extract_args import arg
except Exception as e:
    arg = [
        "0",  # nrefs
        "P1",  # udeg
        "P0",  # lamdeg
        "stab",  # "stab" enables stabilization
    ]
arg
# Call example:
#   sh run_extract.sh notebook_name 1 P1 P0 stab
# Do not include the extension .ipynb!

run_extract.sh

#!/bin/bash
mkdir -p output
ARGU=`echo "${@:2:99}" | tr " " "_"`
rm output/$1$ARGU.celltext* || true
rm output/$1$ARGU.cellimage* || true
echo "arg = '${@:2:99}'.split(' ')" > _run_extract_args.py
cat _run_extract_args.py
jupyter nbconvert --to notebook --ExecutePreprocessor.timeout=600 --execute $1.ipynb
jq -r '.cells[].outputs[].data."text/plain" | select( . != null) | to_entries[] | .value' $1.nbconvert.ipynb | grep . > output/$1$ARGU.alltexts
jq -r '.cells[].outputs[].data."image/png" | select( . != null)' $1.nbconvert.ipynb | grep . > output/$1$ARGU.allimages
split -l 1 output/$1$ARGU.alltexts output/$1$ARGU.celltext
split -l 1 output/$1$ARGU.allimages output/$1$ARGU.cellimage
find . | grep output/$1$ARGU.cellimage | xargs -I{} sh -c 'base64 -d "{}" > "{}.png"; rm "{}"'
rm output/$1$ARGU.alltexts || true
rm output/$1$ARGU.allimages || true
mv $1.nbconvert.ipynb output/$1$ARGU.nbconvert.ipynb
rm _run_extract_args.py