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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:

Installation

We recommend installing omero-py in a Python virtual environment. You can create one using for example venv, conda or mamba.

Before installing omero-py, we recommend to install the ZeroC IcePy 3.6 Python bindings. Our commercial partner Glencoe Software has produced several Python wheels to install the Ice-Python bindings depending on the desired Python version and the operating system. Please visit OMERO.py for a list of supported platforms and Python versions.

When the wheel is installed, activate the virtual environment and install omero-py from PyPI:

$ pip install -U omero-py

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

Usage

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 to create a virtual environment with the Ice-Python binding matching your Python version and your operating system, see OMERO.py.

Activate the virtual environment and clone this repository:

$ 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 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. 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 will be automatically opened against conda-omero-py to update the official OMERO.py Conda package.

Documentation

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

  • Install Sphinx.
  • 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.