imio will be merging into
imio package will be absorbed into
brainglobe-utils as a submodule, so will no longer be receiving standalone updates.
This decision was made because:
brainglobe-utilsas a direct dependency as it stands anyway, so users are already installing
There was a circular dependency between the two packages. Whilst not a circular import, this behaviour is undesirable going forward.
It reduces the number of repositories that have to be maintained.
imio’s functionality will be available under the new
brainglobe_utils.image_io submodule, and can otherwise be interacted with in the same way as the old
In terms of your source code, the only necessary changes should be to:
brainglobe_utilsto at least version 0.4.0, which provides the
Remove any dependencies on
from imio import Xwith
from brainglobe_utils.image_io import Xeverywhere in your source code.
What do I need to do?#
Users who installed BrainGlobe through it’s single (“meta”) package install with
pip install brainglobe will just need to update the package by running
pip install brainglobe --update
in your environment, which will fetch the new version of all the affected packages.
You can use
pip show brainglobe to check your version has updated - you should find you now have
brainglobe version as 1.0.2 or higher.
If you are manually managing your BrainGlobe tools, you will need to uninstall
imio and update
brainglobe-utils to at least version 0.4.0, through
pip uninstall imio
pip install --update brainglobe-utils
You’ll also need to update the following packages, which now depend on at least
brainglobe-utils version 0.4.0 instead of
brainglobe-segment, version 1.2.2 or newer.
brainreg, version 1.0.5 or newer.