murfey 0.23.1

Client-Server architecture hauling Cryo-EM data

Murfey

A transporter for data from Diamond eBIC microscope and detector machines onto the Diamond network.

Who is Murfey?

Murfey, the package, is named after Eliza Murfey, the inventor:

Focusing on the mechanics of the railroad, inventor Eliza Murfey created devices designed to improve the bearings on rail wheels. With sixteen patents for her lubrication system, it was Murfey who designed the packings that would lubricate the axles with oil, aiding in the reduction of derailments caused by seized axles and bearings.

How do I set up a development environment?

We suggest you start with your favourite virtual environment (mamba/conda/python virtualenv/...), then install using the following command.

$ git clone [e-mail]:DiamondLightSource/python-murfey.git
$ cd python-murfey
$ pip install -e .[server,developer]

The packages included under the [developer] installation key contain some helpful tools to aid you with developing Murfey further:

• bump-my-version - Simplifies version control.
• ipykernel - Enables interactive code development via Jupyter Notebooks.
• pre-commit - Allows for the installation and running of hooks to help with linting, formatting, and type checking your code.
• pytest - Used in conjunction with test functions to evaluate the reliability of your code.

Instructions for setting up the database for Murfey to register files to can be found here.

Finally, you may want to set up an ISPyB mock database server and a Zocalo development environment. The instructions for this are out of scope here.

You can then start the Murfey server with

$ murfey.server

and connect the client with

$ murfey.instrument_server --port 8000

You can also install a client on a remote machine. This machine only needs to have a minimum Python installation and curl. Open the murfey server website in a browser on the client, and navigate to the bootstrap page. Then copy the displayed commands into a command line terminal.