jupyter-jsmol

This is JSmol viewer widget which can be used in Jupyter Notebooks and JupyterLab

Installation

You can install using pip:

pip install jupyter_jsmol

Or if you use jupyterlab:

pip install jupyter_jsmol
jupyter labextension install @jupyter-widgets/jupyterlab-manager

If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable the nbextension:

jupyter nbextension enable --py [--sys-prefix|--user|--system] jupyter_jsmol

Development Installation

Create a dev environment:

conda create -n jupyter-jsmol-dev -c conda-forge python pip nodejs yarn jupyter jupyterlab ipywidgets jupyter-packaging==0.7.9 ase pymatgen
conda activate jupyter-jsmol-dev

Install the python. This will also build the TS package.

# First install the python package. This will also build the JS packages.
pip install -e ".[test, examples]"

# Run the python tests. This should not give you a few successful example tests
py.test

When developing your extensions, you need to manually enable your extensions with the notebook / lab frontend. For lab, this is done by the command:

cd js
jupyter labextension develop --overwrite .
yarn run build

For classic notebook, you can run:

jupyter nbextension install --sys-prefix --symlink --overwrite --py jupyter_jsmol
jupyter nbextension enable --sys-prefix --py jupyter_jsmol

Note that the --symlink flag doesn't work on Windows, so you will here have to run the install command every time that you rebuild your extension. For certain installations you might also need another flag instead of --sys-prefix, but we won't cover the meaning of those flags here.

How to see your changes

JavaScript:

If you use JupyterLab to develop then you can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the widget.

# Watch the source directory in one terminal, automatically rebuilding when needed
yarn run watch
# Run JupyterLab in another terminal
jupyter lab

After a change wait for the build to finish and then refresh your browser and the changes should take effect.

Python:

If you make a change to the python code then you will need to restart the notebook kernel to have it take effect.