.. image:: https://github.com/ome/omero-scripts/workflows/OMERO/badge.svg
:target: https://github.com/ome/omero-scripts/actions
.. image:: https://readthedocs.org/projects/omero-scripts/badge/?version=stable
:target: https://readthedocs.org/projects/omero-scripts/badge/?version=stable
.. image:: https://badge.fury.io/py/omero-scripts.svg
:target: https://badge.fury.io/py/omero-scripts
OMERO Core Scripts
==================
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.
Categories
==========
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()
OMERO User Scripts
==================
If you would like to provide your own scripts for others to install
into their OMERO installations, please see https://openmicroscopy.org/info/scripts
Testing
=======
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
Usage
=====
See https://omero-scripts.readthedocs.io/en/stable/
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.
Copyright
=========
2010-2021, The Open Microscopy Environment
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