ezomero 3.0.0

A suite of convenience functions for working with OMERO. Written and maintained by the Research IT team at The Jackson Laboratory.

ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

Installation

Just pip install ezomero and you should be good to go! The repo contains the specific package versions we test ezomero with in setup.py, but any Python>=3.8 and latest omero-py and numpy should work - note that this package is in active development!

If you want to use get_table and post_table to/from Pandas dataframes, you need to install ezomero[tables] - that install an optional pandas dependency. Installing ezomero without this will default get_table and post_table to use lists of row lists as their default.

Usage

In general, you will need to create a BlitzGateway object using ezomero.connect(), then pass the conn object to most of these helper functions along with function-specific parameters.

Documentation

Documentation is available at https://thejacksonlaboratory.github.io/ezomero/

Development

You will need Docker installed and running to run the tests.

Setup your "omero" python environment with a local ezomero and pytest:

> conda activate omero  # Activate your omero environment with conda or pip
(omero) > cd /your_local_clone/ezomero
(omero) > pip install -e .
(omero) > pip install pytest

To run the tests, startup the test OMERO server with Docker and run pytest

> cd /your_local_clone/ezomero
> docker-compose -f tests/docker-compose.yml up -d
> conda activate omero
(omero) > python -m pytest .\tests