Release of OMERO 5.6.0 with Python 3

Dear all,

Today we are very excited (also proud, delighted and relieved) to announce the release of OMERO 5.6.0, the first Python3-based release of the OMERO server and web components. This release of OMERO also upgrades the version of Bio-Formats to 6.3.1.

All Python code can and must now be installed separately from the OMERO.server.zip, meaning that fixes can be released more quickly. This version does not require a database upgrade but only supports Python 3. We strongly encourage an immediate upgrade since maintenance of Python 2.7 ended promptly on New Year’s Day and all future OMERO security patches will only be available for OMERO 5.6 and greater.

Deployment environments:

The current list of supported platforms is:

  • CentOS 7
  • Ubuntu 18.04
  • Debian 10*

* Note that Ice 3.6 is the only version of Ice that we support. On Debian 10, the default is Ice 3.7 requiring extra installation steps. There are no plans to add support for Ice 3.7.

Additionally, we have installation guides for Debian 9 and Ubuntu 16.04. In both cases, Python 3.5 will be installed. Not all functionality has been tested with Python 3.5 but we do not expect major issues. If you choose to install OMERO on these environments, we’d welcome feedback and comments.

For all other platforms, we recommend using conda. An ome channel is available on anaconda.org while we investigate moving to conda-forge.

Getting Started:

Documentation for this release is available under https://docs.openmicroscopy.org/omero/5.6.0/ with the Python 3 Migration page being a good place for developers and system administrators to start.

OMERO.server.zip is available at https//downloads.openmicroscopy.org/omero/5.6.0/. The OMERO.py.zip has been dropped in favor of PyPI.

Clients are available on GitHub. The updated OMERO.insight 5.5.8 is available at https://github.com/ome/omero-insight/releases/tag/v5.5.8, which supports connections to both 5.5 and 5.6 servers.

Official Docker images are available as usual on Docker Hub with either the latest or the 5.6 tag:

And the PyPI-released components include:


A huge thanks to several beta testers for all the help in making this release possible!

All the best with your upgrades,

The @OMETeam

6 Likes

Thank you for this release! It must have been a lot of work!

I was wondering something though: is it expected behaviour that OMERO.web does not set the path for gunicorn?
If I use this systemd service, no PID file is created.
But if I add this:

Environment="PATH=/opt/omero/web/venv3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin"

then, it works.

That looks like a bug, I’ve opened an issue:

In the previous release announcements, I failed to point out that any OMERO.scripts that you may have uploaded to your OMERO installation may need modifications, e.g. a script with print 100 will fail with a message of the form:

---------------------------------
  File "./script", line 7
    print 100
            ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(100)?

---------------------------------

and must be updated to print(100). Notes from our migration work are available under https://docs.openmicroscopy.org/omero/5.6/developers/python3-migration.html

With thanks to @T-Zobel for the heads up,
~Josh

1 Like