Metadata-Version: 2.4
Name: omero-rdf
Version: 0.7.2
Summary: A plugin for exporting RDF from OMERO
Author: The Open Microscopy Team
Project-URL: Repository, https://github.com/German-BioImaging/omero-rdf
Project-URL: Changelog, https://github.com/German-BioImaging/omero-rdf/blob/master/CHANGES.txt
Keywords: OMERO.cli,plugin
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Plugins
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
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: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: <3.13,>=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE.txt
Requires-Dist: omero-py>=5.8
Requires-Dist: importlib-metadata
Requires-Dist: future
Requires-Dist: rdflib
Requires-Dist: pyld
Requires-Dist: rdflib-pyld-compat
Requires-Dist: omero-marshal
Requires-Dist: packaging
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Requires-Dist: restview; extra == "tests"
Requires-Dist: mox3; extra == "tests"
Provides-Extra: dev
Requires-Dist: ruff; extra == "dev"
Dynamic: license-file

.. image:: https://github.com/German-BioImaging/omero-rdf/workflows/OMERO/badge.svg
    :target: https://github.com/german-bioimaging/omero-rdf/actions

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

omero-rdf
=========

A plugin for exporting RDF from OMERO


Requirements
============

* OMERO 5.6.0 or newer
* Python 3.10, 3.11, or 3.12 (only versions with ``zeroc-ice`` binary wheels are supported; newer versions will be added when wheels are available)


Installing from PyPI
====================

This section assumes that an `OMERO.py <https://github.com/ome/omero-py>`_ is already installed and zeroc-ice is configured.

Install the command-line tool using `pip <https://pip.pypa.io/en/stable/>`_:

::

    $ pip install -U omero-rdf


Developer guidelines
====================

Using `uv` (recommended):

1. Fork/clone the repository (e.g. ``gh repo fork https://github.com/German-BioImaging/omero-rdf``).
2. Create a virtualenv and activate it:

   ::

       uv venv .venv
       source .venv/bin/activate

   (or prefix commands with ``uv run`` instead of activating).

3. Install in editable mode with test dependencies:

   ::
       uv pip install -r zeroc-ice-requirements.txt
       uv pip install -e ".[tests,dev]"

4. Run the test suite:

   ::

       pytest test/unit
       pytest test/integration/test_idr

5. Lint and format:

   ::

       ruff check
       ruff format --check
       ruff format

To run pre-commit hooks:

::

   uv tool install pre-commit
   pre-commit run --all-files


Quick check against IDR
-----------------------

Assuming you have the `uv` environment active (`source .venv/bin/activate`), use
the public IDR server to confirm the CLI works (public credentials):

1. Log in once to create a session:

   ::

       omero login -s idr.openmicroscopy.org -u [PUBLIC USER] -w [PUBLIC PASSWORD]

2. Export RDF for a project on IDR (2902) and inspect the first triples:

   ::

       omero rdf -F=turtle Project:2902 -S=flat | head  -n 10

Mocking GitHub Actions checks

1. If you have gh installed, you can run the checks locally:

   ::

       gh act push

Release process
---------------

This repository uses `versioneer <https://pypi.org/project/versioneer/>`_
to manage version numbers. A tag prefixed with `v` will be detected by
the library and used as the current version at runtime.

Remember to ``git push`` all commits and tags.

Funding
-------

Funded by the `Delta Tissue <https://wellcomeleap.org/delta-tissue/>`_
Program of `Wellcome Leap <https://wellcomeleap.org/>`_.

License
-------

This project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.

Copyright
---------

2022-2026, German BioImaging
