Improving Software Sustainability of brainglobe-utils

[willGraham01]

brainglobe-utils was designed to be our package that contains a wide range of general-purpose functionality that can be re-used across all brainglobe tools. However, it currently suffers from a number of problems from a software sustainability standpoint that we should address.

Preliminaries for new developers

A new developer tackling this issue should first head over to our developer documentation (site, repo) and familiarise themselves with the content.

The content itself is fairly new - if during tackling this issue, or even after reading through it, there are clarifications that need to be made, please raise issues on the documentation site and propose solutions! 🙂

Improving brainglobe-utils

Once familiar with our developer docs; the following topics need to be addressed in brainglobe-utils.

Where there's already an issue tracking one of these tasks, it's linked to below. However feel free to edit the content of these issues with updated task lists etc.

Documentation

• A lack of docstrings Add docstrings brainglobe-utils#19. If we don't have proper docstrings, it is not clear to us as developers what functionality has actually been pulled into this repository.
• The imio package was recently merged into brainglobe_utils as the image_io submodule. However, imio itself was never properly documented, and so we should make amends and document image_io: Add documentation brainglobe-utils#34

Testing

• We also want to improve our test coverage to ~90% on brainglobe-utils. There is currently no issue to track this, but it might be worth opening them on a per-submodule basis.
• Improve napari-related test infrastructure and share it across BrainGlobe
  • Automatically Mock user data for local test runs thoughout brainglobe #68
  • Use fixture to test for leaky Qt Widgets #69
• [Feature] Run CI on ARM runners too #63

Refactoring

• There are several refactor-ings that can be done to bring additional functionality across the brainglobe tool-suite into utils. Some that spring to mind:
  • Unify BrainGlobe Modal dialogs brainglobe-utils#3
  • [FEATURE] Refactor LoadFileException into brainglobe-utils brainreg#180
  • Remove all test data from repositories #5

[alessandrofelder]

Re-using utils code elsewhere

• Import HTML headers from brainglobe-utils cellfinder#327 (comment)