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OMERO.py provides Python bindings to the OMERO.blitz server as well as a pluggable command-line interface.
Direct dependencies of OMERO.py are:
ZeroC IcePy 3.6
_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 <https://www.glencoesoftware.com/blog/2023/12/08/ice-binaries-for-omero.html>
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 <https://pypi.org/>
_::
$ 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 <https://pypi.org/project/omero-certificates/>
OMERO.CLI
_.See: OMERO
_ documentation
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.
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
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 will be automatically 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>
.
The API documentation is generated using Sphinx. To generate it:
Sphinx <https://www.sphinx-doc.org/en/master/>
_.NO_TEMP_MANAGER
to true
.docs
directory, run make clean html
.OMERO.py is released under the GPL v2.
2009-2024, The Open Microscopy Environment, Glencoe Software, Inc.
.. _ZeroC IcePy 3.6: https://zeroc.com/downloads/ice/3.6 .. _OMERO.py: https://omero.readthedocs.io/en/stable/developers/Python.html .. _OMERO.CLI: https://omero.readthedocs.io/en/stable/users/cli/index.html .. _OMERO: https://omero.readthedocs.io/en/stable/index.html .. _Running and writing tests: https://omero.readthedocs.io/en/stable/developers/testing.html