Skip to main content

OMERO scripts

Project description

https://github.com/ome/omero-scripts/workflows/OMERO/badge.svg https://readthedocs.org/projects/omero-scripts/badge/?version=stable https://badge.fury.io/py/omero-scripts.svg

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 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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

omero_scripts-5.9.1.tar.gz (102.0 kB view details)

Uploaded Source

Built Distribution

omero_scripts-5.9.1-py3-none-any.whl (136.7 kB view details)

Uploaded Python 3

File details

Details for the file omero_scripts-5.9.1.tar.gz.

File metadata

  • Download URL: omero_scripts-5.9.1.tar.gz
  • Upload date:
  • Size: 102.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.8.20

File hashes

Hashes for omero_scripts-5.9.1.tar.gz
Algorithm Hash digest
SHA256 8ad83d9c8950f05871ab8e95258f11be80eded18bdc10f64beac530558313271
MD5 67f5c49a0fe421a87956f147c575003e
BLAKE2b-256 ea0f019d83776791c0af54c373b9eb32bebaf6857b7556e1060e4dba3de03441

See more details on using hashes here.

File details

Details for the file omero_scripts-5.9.1-py3-none-any.whl.

File metadata

  • Download URL: omero_scripts-5.9.1-py3-none-any.whl
  • Upload date:
  • Size: 136.7 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.8.20

File hashes

Hashes for omero_scripts-5.9.1-py3-none-any.whl
Algorithm Hash digest
SHA256 e1a6063b8b732c500eac708f15ed48eedcd174eaa25179ecf111e79bc98f280e
MD5 d1cded58674f558f3070e1fcf4d7e69e
BLAKE2b-256 08ccc9408f400f3f373777548715224e259bc80d9877cdd2beb81aaed632fd3e

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page