Run jupyter notebooks from the command line

jupyter_nbconvert_execute.sh

# Run Jupyter notebooks via the console
# Here: TeachOpenCADD talktorials on https://github.com/volkamerlab/TeachOpenCADD

# Change to TeachOpenCADD directory
#cd /path/to/TeachOpenCADD

# Activate TeachOpenCADD conda environment
#conda activate teachopencadd

# Install kernelspec teachopencadd
#python -m ipykernel install --user --name teachopencadd


##########################################################
# Example talktorial
##########################################################

# Run Jupyter notebook
jupyter nbconvert --execute talktorials/1_ChEMBL/T1_ChEMBL.ipynb

# Will generate an html file (T1_ChEMBL.html) showing the executed Jupyter notebook


##########################################################
# Iterate all talktorials
##########################################################

# Run iteratively all Jupyter notebooks in directory
for i in talktorials/*/*.ipynb; do echo; echo $i; jupyter nbconvert --execute --ExecutePreprocessor.kernel_name=teachopencadd --ExecutePreprocessor.timeout=300 $i; done