OMERO.py
========
.. image:: https://github.com/ome/omero-py/workflows/Build/badge.svg
:target: https://github.com/ome/omero-py/actions
.. image:: https://badge.fury.io/py/omero-py.svg
:target: https://badge.fury.io/py/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 (deprecated)
- 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 -c conda-forge python=3.8 omero-py
conda activate myenv
Alternatively install ``omero-py`` using venv::
python3.8 -m venv myenv
. myenv/bin/activate
pip install omero-py
You may need to replace ``python3.8`` with ``python`` or ``python3`` 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 ``python3.8`` but you can create and activate the virtualenv using any compatible Python):
To install using venv::
python3.8 -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=3.8 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
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
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