ezomero

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

Installation

ezomero's dependencies are easily pip-installable from PyPI, except for zeroc-ice==3.6.5. For those, we recommend pip-installing using one of the wheels provided by Glencoe Software (use the one compatible with your OS/Python version - link provided is for Linux wheels, for more information see this Glencoe Software blog post).

In general, we strongly recommend starting from a clean virtual environment, pip installing zeroc-ice from a Glencoe wheel, and only then doing pip install ezomero.

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://erickmartins.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