OMERO.py

Introduction

OMERO.py provides Python bindings to the OMERO.blitz server as well as a pluggable command-line interface.

Dependencies

Direct dependencies of OMERO.py are:

ZeroC IcePy 3.6
future
numpy
Pillow

Installation

We recommend installing omero-py in a Python virtual environment. You can create one using either venv or conda (preferred). If you opt for Conda, you will need to install it first, see miniconda for more details.

To install omero-py using venv:

python3.6 -m venv myenv
. myenv/bin/activate
pip install omero-py

You may need to replace python3.6 with python or python3 depending on your Python distribution.

To install omero-py using conda (preferred):

conda create -n myenv -c ome python=3.6 zeroc-ice36-python omero-py
conda activate myenv

Setting of the environment variable OMERODIR is required for some functionality. $OMERODIR/var/log/ directory will contain log files. $OMERODIR/etc/grid/config.xml is used to store config.

If OMERODIR is set to an OMERO.server directory, the import and admin commands will be enabled:

# If you need import or admin commands:
export OMERODIR=/path/to/OMERO.server/

# otherwise, can choose any location.
export OMERODIR=$(pwd)

See: OMERO documentation for more details.

Usage

For OMERO python language bindings, see OMERO.py.
For Command Line usage, see OMERO.CLI.

Contributing

See: OMERO documentation

Developer installation

OMERO.py currently depends on an externally built artifact which is automatically bundled in the PyPI package.

For a development installation we recommend creating a virtualenv with the following setup (example assumes python3.6 but you can create and activate the virtualenv using any compatible Python):

To install using venv:

python3.6 -mvenv myenv
. myenv/bin/activate
git clone https://github.com/ome/omero-py
cd omero-py
python setup.py devtarget
pip install -e .

To install omero-py using conda (preferred):

conda create -n myenv -c ome python=3.6 zeroc-ice36-python
conda activate myenv
git clone https://github.com/ome/omero-py
cd omero-py
python setup.py devtarget
pip install -e .

This will install omero-py into your virtualenv as an editable package, so any edits to src files should be reflected in your installation. Note that if you add or remove files you must rerun the last two steps.

Running tests

Unit tests are located under the test directory and can be run with pytest.

Integration tests

Integration tests are stored in the main repository (ome/openmicroscopy) and depend on the OMERO integration testing framework. Reading about Running and writing tests in the OMERO documentation is essential.

License

OMERO.py is released under the GPL v2.

Copyright

2009-2020, The Open Microscopy Environment, Glencoe Software, Inc.

chris-allan/omero-py