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OMERO.web provides a web based client and plugin infrastructure.
Direct dependencies of OMERO.web are:
OMERO.py
_ZeroC IcePy
_Pillow
_NumPy
_We recommend installing omero-web in a Python virtual environment.
Here we show the install using Conda
. For more details and
other options, please see OMERO.py
.
::
conda create -n myenv python=3.9 conda-forge::zeroc-ice==3.6.5 omero-py
conda activate myenv
pip install omero-web
Setting of the environment variable OMERODIR
is required.
$OMERODIR/var/log/
directory will contain log files.
$OMERODIR/etc/grid/config.xml
is used to store config::
export OMERODIR=$(pwd)
For running omero-web in production with NGINX, see See: OMERO.web install
_ documentation.
To run in development mode, see below.
See: OMERO
_ documentation
For a development installation we recommend creating a virtual environment as described above. Then install OMERO.web into your virtual environment as an editable package, so that any edits to source files will be reflected in your installation.
::
git clone https://github.com/ome/omero-web
cd omero-web
pip install -e .
Note some omero-web tests may not run when this module and/or omero-py are installed in editable mode.
Configuration for developer usage::
omero config set omero.web.debug True
omero config set omero.web.application_server development
# If you want to connect to OMERO.server other than 'localhost'
omero config append omero.web.server_list '["demo.openmicroscopy.org", 4064, "demo"]'
Then run omero-web in the foreground with::
omero web start
...
Starting development server at http://127.0.0.1:4080/
Or, run Django directly::
cd omero-web
python omeroweb/manage.py runserver 4080
...
Starting development server at http://127.0.0.1:4080/
Plugin developers should review the Upgrading <UPGRADING.md>
_
document highlighting steps that may need to be taken
when upgrading OMERO.web to ensure plugins or other customizations
continue to function as expected.
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
is essential.
This repository uses bump2version <https://pypi.org/project/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 patch
NB: this assumes next release will be a patch
(see below).
To complete the release, push the master branch and the release tag to origin::
$ git push origin master v5.8.0
If any PRs are merged that would require the next release to be a major
or minor
version
(see semver.org <https://semver.org/>
_) then that PR can include a version bump created via::
$ bumpversion --no-tag minor|major
If this hasn't been performed prior to release and you wish to specify the next version number directly when creating the release, this can be achieved with::
$ bumpversion --new-version 5.9.0 release
omero-web-docker ^^^^^^^^^^^^^^^^
Following omero-web
release, need to update and release omero-web-docker
.
OMERO.web is released under the AGPL.
2009-2024, The Open Microscopy Environment, Glencoe Software, Inc.
.. _OMERO: https://www.openmicroscopy.org/omero .. _OMERO.web install: https://docs.openmicroscopy.org/latest/omero/sysadmins/unix/install-web/web-deployment.html .. _OMERO.py: https://pypi.python.org/pypi/omero-py .. _ZeroC IcePy: https://zeroc.com/ .. _Pillow: https://python-pillow.org/ .. _NumPy: http://matplotlib.org/ .. _Running and writing tests: https://docs.openmicroscopy.org/latest/omero/developers/testing.html .. _Conda: https://docs.conda.io/en/latest/