omero-py

Python project containing Ice remoting code for OMERO

https://github.com/ome/omero-py

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
26 of 48 committers (54.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary

Keywords

component lib omero omero-py python

Keywords from Contributors

napari closember software-carpentry training imaging-solutions omero-api omero-server napari-plugin ngff zarr

Last synced: 6 months ago · JSON representation

Repository

Python project containing Ice remoting code for OMERO

Basic Info

Host: GitHub
Owner: ome
License: gpl-2.0
Language: Python
Default Branch: master
Homepage: https://www.openmicroscopy.org/omero
Size: 11.4 MB

Statistics

Stars: 24
Watchers: 11
Forks: 35
Open Issues: 67
Releases: 42

Topics

component lib omero omero-py python

Created over 6 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License

README.rst

OMERO.py
========

.. image:: https://github.com/ome/omero-py/workflows/Build/badge.svg
:target: https://github.com/ome/omero-py/actions

.. image:: https://badge.fury.io/py/omero-py.svg
:target: https://badge.fury.io/py/omero-py

Introduction
------------

OMERO.py provides Python bindings to the OMERO.blitz server
as well as a pluggable command-line interface.

Dependencies
------------

Direct dependencies of OMERO.py are:

- `ZeroC IcePy 3.6`_
- numpy
- Pillow >= 10.0.0

Installation
------------

We recommend installing omero-py in a Python virtual environment.
You can create one using for example ``venv``, ``conda`` or ``mamba``.

Before installing ``omero-py``, we recommend to install the `ZeroC IcePy 3.6`_ Python bindings.
Our commercial partner `Glencoe Software `_ has produced several Python wheels to install the Ice-Python bindings depending on the desired Python version and the operating system. Please visit `OMERO.py`_ for a list of supported platforms and Python versions.

When the wheel is installed, activate the virtual environment and install ``omero-py`` from `PyPI `_::

$ pip install -U omero-py

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)

Since version 5.13.0, the use of ``omero certificates`` is required to ensure that an OMERO server installation has, at minimum, a self-signed certificate.

See: `OMERO`_ documentation for more details and
`OMERO server certificate management plugin `_

Usage
-----

- For Command Line usage, see `OMERO.CLI`_.
- For API documentation, see https://omero-py.readthedocs.io/

Contributing
------------

See: `OMERO`_ documentation

Developer installation
----------------------

OMERO.py currently depends on an externally built artifact which is automatically bundled in the PyPI package.

For a development installation, we recommend to create a virtual environment with the Ice-Python binding matching your Python version and your operating system, see `OMERO.py`_.

Activate the virtual environment and clone this repository::

$ 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.

Running tests
-------------

Unit tests are located under the `test` directory and can be run with pytest.

Integration tests
^^^^^^^^^^^^^^^^^

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

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. Once released,
a Pull Request will be automatically opened against
`conda-omero-py `_ to update the
official `OMERO.py Conda package `_.

Documentation
-------------

The API documentation is generated using Sphinx.
To generate it:

- Install `Sphinx `_.
- Set the environment variable ``NO_TEMP_MANAGER`` to ``true``.
- In the ``docs`` directory, run ``make clean html``.

License
-------

OMERO.py is released under the GPL v2.

2009-2024, The Open Microscopy Environment, Glencoe Software, Inc.

.. _ZeroC IcePy 3.6: https://zeroc.com/downloads/ice/3.6
.. _OMERO.py: https://omero.readthedocs.io/en/stable/developers/Python.html
.. _OMERO.CLI: https://omero.readthedocs.io/en/stable/users/cli/index.html
.. _OMERO: https://omero.readthedocs.io/en/stable/index.html
.. _Running and writing tests: https://omero.readthedocs.io/en/stable/developers/testing.html

Owner

Name: Open Microscopy Environment
Login: ome
Kind: organization
Email: ome-users@lists.openmicroscopy.org.uk

Website: https://www.openmicroscopy.org/
Twitter: openmicroscopy
Repositories: 337
Profile: https://github.com/ome

Software and data format standards for management of microscopy image data. Joint project between international private and public research

GitHub Events

Total

Create event: 3
Release event: 25
Issues event: 36
Watch event: 1
Issue comment event: 123
Push event: 22
Pull request review comment event: 11
Pull request review event: 33
Pull request event: 60
Fork event: 3

Last Year

Create event: 3
Release event: 25
Issues event: 36
Watch event: 1
Issue comment event: 123
Push event: 22
Pull request review comment event: 11
Pull request review event: 33
Pull request event: 60
Fork event: 3

Committers

Last synced: 8 months ago

All Time

Total Commits: 6,181
Total Committers: 48
Avg Commits per committer: 128.771
Development Distribution Score (DDS): 0.726

Past Year

Commits: 82
Committers: 11
Avg Commits per committer: 7.455
Development Distribution Score (DDS): 0.378

Top Committers

Name	Email	Commits
Josh Moore	j**h@o**g	1,696
Will Moore	w**e@d**k	1,019
Sébastien Besson	s**n@g**m	933
Simon Li	s**i@d**k	427
Jean-Marie Burel	j**l@d**k	401
Aleksandra Tarkowska	a**a@d**k	334
Colin Blackburn	c**n@d**k	300
Carlos Neves	c**s@g**m	261
Mark Carroll	m**l@d**k	183
Chris Allan	c**n@g**m	155
Donald MacDonald	d**d@l**k	102
Blazej Pindelski	b**i@d**k	63
Dominik Lindner	d**r@d**k	55
Snoopy Crime Cop	s**p@g**m	49
Emil Rozbicki	e**l@g**m	29
Andreas Knab	a**s@g**m	22
Roger Leigh	r**h@d**k	15
Petr Walczysko	p**o@d**k	13
Kevin Kozlowski	k**n@g**m	13
Simone Leo	s**o@d**k	12
Sam Hart	s**m@g**m	11
Guillaume Gay	g**e@d**m	8
Harald Waxenegger	h**r@d**k	7
Douglas Russell	d**l@b**k	7
Rémy Dornier	r**r@e**h	6
barrettMCW	1****W	5
Talley Lambert	t**t@g**m	5
Josh Ballanco	j**c@g**m	5
Johannes Müller	3****r	5
Helen Flynn	h**n@d**k	5
and 18 more...

Committer Domains (Top 20 + Academic)

dundee.ac.uk: 15 glencoesoftware.com: 12 lifesci.dundee.ac.uk: 3 epfl.ch: 2 bioch.ox.ac.uk: 2 hhu.de: 1 lin-magdeburg.de: 1 sussex.ac.uk: 1 hms.harvard.edu: 1 pasteur.fr: 1 wisc.edu: 1 damcb.com: 1 openmicroscopy.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 62
Total pull requests: 183
Average time to close issues: almost 2 years
Average time to close pull requests: 5 months
Total issue authors: 35
Total pull request authors: 22
Average comments per issue: 2.53
Average comments per pull request: 3.29
Merged pull requests: 140
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 14
Pull requests: 47
Average time to close issues: 26 days
Average time to close pull requests: 21 days
Issue authors: 11
Pull request authors: 9
Average comments per issue: 1.0
Average comments per pull request: 2.43
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

joshmoore (7)
will-moore (5)
manics (4)
multimeric (3)
dominikl (3)
pwalczysko (3)
barrettMCW (2)
jburel (2)
lldelisle (2)
ArtemLogachov (2)
jo-mueller (2)
drjrkuhn (2)
glyg (2)
Tom-TBT (2)
Rdornier (2)

Pull Request Authors

jburel (71)
sbesson (55)
will-moore (17)
joshmoore (12)
manics (8)
chris-allan (7)
multimeric (5)
dominikl (4)
Tom-TBT (4)
barrettMCW (3)
jmuhlich (3)
jo-mueller (3)
DavidStirling (2)
ehrenfeu (2)
muhanadz (2)

Top Labels

Issue Labels

bug (1) enhancement (1)

Pull Request Labels

include (6) exclude (1)

Packages

Total packages: 2
Total downloads:
- pypi 5,006 last-month
Total docker downloads: 395,223

Total dependent packages: 22
(may contain duplicates)
Total dependent repositories: 39
(may contain duplicates)
Total versions: 59
Total maintainers: 4

pypi.org: omero-py

Python bindings to the OMERO.blitz server

Homepage: https://github.com/ome/omero-py
Documentation: https://docs.openmicroscopy.org/omero/latest/developers/Python.html
License: GNU General Public License v2 or later (GPLv2+)
Latest release: 5.21.0
published 8 months ago

Versions: 54
Dependent Packages: 20
Dependent Repositories: 32
Downloads: 5,006 Last month
Docker Downloads: 395,223

Rankings

Dependent packages count: 0.6%

Docker downloads count: 0.9%

Dependent repos count: 2.6%

Downloads: 3.0%

Average: 4.8%

Forks count: 7.3%

Stargazers count: 14.5%

Maintainers (4)

jburel joshmoore sbesson ome

Last synced: 6 months ago

conda-forge.org: omero-py

Homepage: https://www.openmicroscopy.org/
License: GPL-2.0-or-later
Latest release: 5.12.1
published over 3 years ago

Versions: 5
Dependent Packages: 2
Dependent Repositories: 7

Rankings

Dependent repos count: 12.9%

Dependent packages count: 19.6%

Average: 29.3%

Forks count: 32.4%

Stargazers count: 52.4%

Last synced: 6 months ago

Dependencies

setup.py pypi

Pillow *
PyYAML *
appdirs *
future *
numpy *
pywin32 *
requests *
zeroc-ice >=3.6.4,<3.7

.github/workflows/workflow.yml actions

actions/checkout v2 composite
actions/setup-python v4 composite
actions/setup-python v2 composite
pypa/gh-action-pypi-publish v1.3.0 composite

Dockerfile docker

centos centos7 build