Migration to Python 3

Basic steps

  1. Choose a platform and a Python version. If your current installation platform does not match one of the recommended platforms, you may want to choose a new platform as your migration target. See Choosing a platform below.

  2. Install OMERO.server and OMERO.web separately. Though not necessary, all instructions like OMERO.server and OMERO.web below as well as the main server and web installation pages now assume that the two are in separate installations.

  3. Once both have been installed, perform a backup and restore procedure and test your installation against the copy of your data.

Choosing a platform

The two recommended platforms, Rocky Linux/RHEL 9 and Ubuntu 22.04, have Python 3.9 and 3.10 respectively as default installation.

All Python 3.8+ versions should work.

Other prerequisites

OMERO’s other prerequisites have not changed substantially but if you would like to take this opportunity to move to the recommended version for all requirements, the current choices are:

  • Ice 3.6 (non-optional)

  • Java 11

  • Nginx 1.24 or higher

  • PostgreSQL 13+

Other options

The installation walkthroughs provided in the documentation try to stick to a minimum installation. The only requirements are an understanding of the Unix shell, the standard package manager for your platform, and the regular Python distribution mechanisms.

However, more advanced installation mechanisms are available if you are interested and have familiarity with the given mechanism:

  • Ansible roles are available for most installation steps. The primary roles, omero-server and omero-web have not yet been released and will need to be installed from GitHub.

  • A conda channel provides pre-built packages needed by OMERO if you prefer to use Anaconda/Miniconda instead of the Python distribution provided by your platform.

  • Docker images are also available. Both the omero-server and omero-web images are considered production quality.

Please get in touch at https://forum.image.sc/c/data if you have any questions.

OMERO.server

The steps for an OMERO.server installation have not changed substantially.

Download the OMERO.server.zip as you would usually do, and unpack it under your installation directory. We suggest /opt/omero/server/ and symlink the unpacked directory to OMERO.server

We highly recommend a virtualenv-based installation for all of the Python dependencies. Follow the standard installation instructions for your platform. All instructions use a virtual environment.

Once you have your installation in place, you will need to follow the standard upgrade instructions, working from a copy of your data.

OMERO.web

Although it is possible to also follow the previous installation steps for OMERO.web, installation no longer requires downloading a package from https://downloads.openmicroscopy.org. If you choose to follow this newly introduced route, all requirements will be installed directly into the virtualenv for OMERO.web. Instructions are available under web-deployment.

Note that setting of OMERODIR variable is now required to specify where the OMERO installation lives. This defines where configuration files and log files will be stored. We suggest /opt/omero/web as the root for your installation.

The upgrade guide can help you to transfer your previous configuration. Moving forward, however, web upgrades should be much simpler under Python 3. Only a pip install -U of the appropriate libraries should be necessary.

Plugins

Core OMERO.web plugins have been updated for Python 3 and released to PyPI e.g.

pip install 'omero-iviewer>=0.9.0'