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This directory contains OMERO scripts which use the
OMERO.scripts API. All scripts (e.g. *.py
) present in the
directory will be automatically distributed with all binary
builds. Which file-endings will be detected and how they
will be launched are both configured centrally in the server.
.py
, .jy
, and .m
(MATLAB) files should all be detected
by default starting with OMERO 5.
Scripts are separated into several categories, one per directory.
+------------------------+-------------------------------------------------------------------------------+
| Directory | Description |
+========================+===============================================================================+
| analysis_scripts | crunch images to produce numerical results and similar tasks |
+------------------------+-------------------------------------------------------------------------------+
| export_scripts | take one or more images as an input, and produce a representation for exchange|
+------------------------+-------------------------------------------------------------------------------+
| figure_scripts | take one or more images as an input, and produce a summary representation |
+------------------------+-------------------------------------------------------------------------------+
| import_scripts | are run on images after import for extra processing |
+------------------------+-------------------------------------------------------------------------------+
| util_scripts | perform other miscellaneous tasks like cleaning up or optimizing OMERO itself |
+------------------------+-------------------------------------------------------------------------------+
Scripts which would like to rely on other scripts can use::
import omero.<sub_dir>.<script_name>
For this to work, the official script in question must be properly importable, i.e.::
def run():
client = omero.scripts.client(...)
if __name__ == "__main__":
run()
If you would like to provide your own scripts for others to install into their OMERO installations, please see https://openmicroscopy.org/info/scripts
Integration tests under test/
require an OMERO server with scripts installed.
The tests are run by Travis for open PRs using omero-test-infra to deploy OMERO
via Docker containers.
To run tests locally::
# All tests
$ python setup.py test
# Single test in a single file
$ python setup.py test -t test/integration/test_util_scripts.py -k test_dataset_to_plate
See https://omero-scripts.readthedocs.io/en/stable/
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.
2010-2024, The Open Microscopy Environment