Metadata-Version: 2.1
Name: omero-scripts
Version: 5.7.1
Summary: OMERO scripts
Home-page: https://github.com/ome/omero-scripts/
Download-URL: https://github.com/ome/omero-scripts/
Author: The Open Microscopy Team
Author-email: ome-devel@lists.openmicroscopy.org.uk
License: GPL-2.0+
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Plugins
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3

.. image:: https://github.com/ome/omero-scripts/workflows/OMERO/badge.svg
    :target: https://github.com/ome/omero-scripts/actions

.. 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.

| In the directory       | should be scripts which ...                                                   |
| ----------------       | ---------------------                                                         |
| **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     |
| **hcs_scripts**        | work with screens/plates/wells rather than just images                        |
| **import_scripts**     | are run on images after import for extra processing                           |
| **processing_scripts** | create new images from existing images or other data                          |
| **setup_scripts**      | are executed once, often by administrators, to configure OMERO itself         |
| **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 http://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

Copyright
---------

2010-2020, The Open Microscopy Environment
