OMERO.py

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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_
• numpy
• Pillow >= 10.0.0

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 conda (preferred)::

conda create -n myenv python=3.9 conda-forge::zeroc-ice==3.6.5 omero-py
conda activate myenv

Alternatively install omero-py using venv::

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

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

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)

Since version 5.13.0, the use of omero certificates is required to ensure that an OMERO server installation has, at minimum, a self-signed certificate.

See: OMERO_ documentation for more details and OMERO server certificate management plugin <https://pypi.org/project/omero-certificates/>_

Usage

• For OMERO python language bindings, see OMERO.py_.
• For Command Line usage, see OMERO.CLI_.
• For API documentation, see https://omero-py.readthedocs.io/

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 python3.9 but you can create and activate the virtualenv using any compatible Python):

To install using venv::

python3 -mvenv myenv
. myenv/bin/activate
git clone https://github.com/ome/omero-py
cd omero-py
# Install zeroc Ice Python corresponding to your operation system see tox.ini for example
python setup.py devtarget
pip install -e .

To install omero-py using conda (preferred)::

conda create -n myenv python=3.9 conda-forge::zeroc-ice==3.6.5
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

Release process

This repository uses bump2version <https://pypi.org/project/bump2version/>_ to manage version numbers. To tag a release run::

$ bumpversion release

This will remove the .dev0 suffix from the current version, commit, and tag the release.

To switch back to a development version run::

$ bumpversion --no-tag [major|minor|patch]

specifying major, minor or patch depending on whether the development branch will be a major, minor or patch release <https://semver.org/>_. This will also add the .dev0 suffix.

Remember to git push all commits and tags.s essential.

The CI pipeline will automatically deploy the tag onto PyPI. Once released, a Pull Request needs to be opened against conda-omero-py <https://github.com/ome/conda-omero-py>_ to update the official OMERO.py Conda package <https://anaconda.org/ome/omero-py>_.

Documentation

The API documentation is generated using Sphinx. To generate it:

• Install Sphinx <https://www.sphinx-doc.org/en/master/>_.
• Set the environment variable NO_TEMP_MANAGER to true.
• In the docs directory, run make clean html.

License

OMERO.py is released under the GPL v2.

Copyright

2009-2024, The Open Microscopy Environment, Glencoe Software, Inc.

.. _ZeroC IcePy 3.6: https://zeroc.com/downloads/ice/3.6 .. _OMERO.py: https://docs.openmicroscopy.org/omero/5.6/developers/Python.html .. _OMERO.CLI: https://docs.openmicroscopy.org/omero/5.6/users/cli/index.html .. _OMERO: https://docs.openmicroscopy.org/omero/5.6/index.html .. _Running and writing tests: https://docs.openmicroscopy.org/latest/omero/developers/testing.html .. _Conda: https://docs.conda.io/en/latest/ .. _miniconda: https://docs.conda.io/en/latest/miniconda.html