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
- future
- numpy
- Pillow
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 ome python=3.6 zeroc-ice36-python omero-py conda activate myenv
Alternatively 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.
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.
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 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.
Unit tests are located under the test directory and can be run with pytest.
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 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 needs to be opened against conda-omero-py to update the official OMERO.py Conda package.
OMERO.py is released under the GPL v2.
2009-2020, The Open Microscopy Environment, Glencoe Software, Inc.