libertem-jupyter-proxy 0.1

Run LiberTEM via JupyterLab/JupyterHub

Run the LiberTEM GUI in JupyterLab / JupyterHub

See the LiberTEM docs for more details!

Requirements

• Python 3.6+
• Jupyter Notebook 6.0+
• JupyterLab 2.1+
• LiberTEM 0.8.0+ (currently requires unreleased changes only available in the master branch!)

LiberTEM

LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets and live data streams using a modified MapReduce programming model. The current focus is pixelated scanning transmission electron microscopy (STEM) and scanning electron beam diffraction data.

Install

1. Clone this repo

   $ git clone https://github.com/LiberTEM/LiberTEM-jupyter-proxy

2. Install dependencies and LiberTEM master:

   $ pip install -e .

   $ pip install -e "git+https://github.com/liberTEM/LiberTEM/#egg=libertem"

3. enable jupyter-server-proxy extension

For Jupyter Classic, activate the jupyter-server-proxy extension:

jupyter serverextension enable --sys-prefix jupyter_server_proxy

For Jupyter Lab, install the @jupyterlab/server-proxy extension:

jupyter labextension install @jupyterlab/server-proxy
jupyter lab build

4. Start jupyter-lab or jupyter-notebook

   $ jupyter-lab

or

$ jupyter notebook

Now LiberTEM should be available as an icon in JupyterLab, or in the "New" dropdown in the classical notebook interface / JupyterHub.

Deployment notes

When deploying behind a reverse proxy, make sure websocket requests are proxied for all URLs, not just for specifically matching ones. Otherwise, something like connecting to wss://<hostname>/user/<username>/libertem/events/ will fail with 400 bad request, as Upgrade: websocket is not supported.

If you want to customize the startup of LiberTEM, you can drop a JSON file into $PREFIX/etc/libertem_jupyter_proxy.json, with contents like this:

{"libertem_server_path": "/path/to/a/venv/bin/libertem-server"}

One use case is to install LiberTEM itself into a different Python environment than Jupyter, as in the example above. Another is to write a wrapper script to customize the environment setup, as in the example script libertem_jupyter_proxy/share/launch_juwels.sh

Without configuration, libertem-server is expected to be found in $PATH.

Try it (WIP)

Thanks

Mostly stolen from https://github.com/betatim/vscode-binder