imio will be merging into brainglobe-utils

The imio package will be absorbed into brainglobe-utils as a submodule, so will no longer be receiving standalone updates. This decision was made because:

• imio only has brainglobe-utils as a direct dependency as it stands anyway, so users are already installing brainglobe_utils to get imio currently.

• 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 imio library. In terms of your source code, the only necessary changes should be to:

• Pin brainglobe_utils to at least version 0.4.0, which provides the image_io submodule.

• Remove any dependencies on imio.

• Replace from imio import X with from brainglobe_utils.image_io import X everywhere 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 imio:

• brainglobe-segment, version 1.2.2 or newer.

• brainreg, version 1.0.5 or newer.

bg-space has been renamed   bg-atlasapi and bg-atlasgen have merged under a new name