Migration to Python 3¶
Warning
This is still a pre-release of OMERO 5.6. The instructions below are intended to help plan a migration path from your current OMERO installation. Do not perform the migration on your production systems until the 5.6.0 release is ready.
Basic steps¶
- 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.
- 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.
- 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, CentOS 7 and Ubuntu 18.04, have Python 3.6 as default installation and have therefore received the most testing which is why Python 3.6 is the preferred version of Python.
Both Python 3.5 and 3.7 should work and are slated to have support added, but Python 3.6 has been the focus of testing during the migration.
Similarly, other operating systems are slated for having support added, but help from the community would be very welcome! Obvious next candidates are CentOS 8 and Ubuntu 20.04.
Debian 9 is still on Python 3.5 and Debian 10 has moved to Ice 3.7 so neither is supported at the moment. We are working on a suitable set of installation guides.
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 1.14 or higher
- PostgreSQL 11
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 …
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 pre-released to PyPI. This means that their versions end in “.devX” and will only be installed by pip install if you add a version specifier:
pip install 'omero-iviewer>=0.9.0.dev1'
You can also get pre-releases by adding –pre, but this may introduce unintended pre-release versions of upstream requirements.
# Beaware of the implications of this usage!
pip install --pre omero-iviewer
We will be releasing full versions of each of the plugins over the next month.
