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 --upgrade

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 --upgrade 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
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