Context menu to add additional references

[alessandrofelder]

Description

What is this PR

• [ ] Bug fix
• [x] Addition of a new feature
• [ ] Other

Why is this PR needed? The main components of atlases we'd like to add as layers include additional reference images.

What does this PR do? Adds functionality to add additional reference images to napari (if the atlas has them). This is achieved by a custom context menu which can be opened via a right-click on the atlas table view. In order to test this well, we now have the mpin_zfish_1um atlas as part of the downloaded test data (as it is the smallest atlas that has additional references, AFAIK).

(Some improving of testing docstrings and variable names are included in this PR)

References

Closes #6

How has this PR been tested?

• A new test for the napari atlas representation part of the new functionality is added.
• Emulating a right-click to open the context menu was tricky in qtbot and has therefore been kicked down the line.

Is this a breaking change?

Nope

Does this PR require an update to the documentation?

In the future, yes. No high-level documentation for this plugin exists yet.

Checklist:

• [x] The code has been tested locally
• [x] Tests have been added to cover all new functionality (unit & integration)
• [x] The documentation has been updated to reflect any changes
• [x] The code has been formatted with pre-commit

[adamltyson]

FYI for me the tests don't complete locally (python 3.10, ubuntu). The atlas widget is produced and this seems to block the tests from completing (happens in test_napari_atlas_representation.py).

[alessandrofelder]

right clicking on an atlas without any additional references raises an error:

Good catch! Should be fixed with 7006970 (#54)

Is it a bug in the atlas data that some atlas metadata has an empty list under the "additional_references" key and other atlas metadata doesn't have that key at all, @adamltyson ?

[adamltyson]

Is it a bug in the atlas data that some atlas metadata has an empty list under the "additional_references" key and other atlas metadata doesn't have that key at all, @adamltyson ?

Yeah. I think it's because some atlases were generated before we added the additional_references key.

[alessandrofelder]

Merging as tests pass on CI and locally for me.