Expand training tests

[alessandrofelder]

Description

What is this PR

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

Why is this PR needed?

To increase test coverage ("Smoke tests") and add additional checks to the tests.

What does this PR do?

• Adds smoke tests to increase test coverage to 95%
• All files have coverage > 90% individually
• Some of the smoke tests are expanded to also include (some) checks
• Minor improvements:
  • fix default value of model depth in training to "50" (which is what it used to be before brainglobe/cellfinder-napari#41 changed it unintentionally!)
  • ensure file name and function names don't overlap (to avoid confusion when patching in tests)
  • add type hint to add_layers utility

References

Largely addresses brainglobe/cellfinder#317 Partially addresses brainglobe/cellfinder#338

How has this PR been tested?

No existing functionality has changed (apart from one default value that was wrong). The tests added as part of this PR increase the likelihood that current and future breakages will be picked up early, and tests pass.

Is this a breaking change?

No.

Does this PR require an update to the documentation?

If any features have changed, or have been added. Please explain how the documentation has been updated (and link to the associated PR). See here for details.

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

[deprecated-napari-hub-preview-bot[bot]]

Preview page for your plugin is ready here: https://preview.napari-hub.org/brainglobe/cellfinder-napari/128 Updated: 2022-06-28T16:34:50.479012

[codecov-commenter]

Codecov Report

Merging #128 (34dbb8a) into main (7d2495a) will increase coverage by 14.26%. The diff coverage is 98.18%.

@@             Coverage Diff             @@
##             main     brainglobe/cellfinder-napari#128       +/-   ##
===========================================
+ Coverage   81.20%   95.46%   +14.26%     
===========================================
  Files          15       17        +2     
  Lines         665      816      +151     
===========================================
+ Hits          540      779      +239     
+ Misses        125       37       -88     

Impacted Files	Coverage Δ
cellfinder_napari/train/train.py	92.10% <50.00%> (+35.69%)	:arrow_up:
cellfinder_napari/detect/__init__.py	100.00% <100.00%> (ø)
cellfinder_napari/detect/detect.py	93.44% <100.00%> (+44.26%)	:arrow_up:
cellfinder_napari/tests/test_curation.py	100.00% <100.00%> (ø)
cellfinder_napari/tests/test_detection.py	100.00% <100.00%> (ø)
cellfinder_napari/tests/test_train_containers.py	100.00% <100.00%> (ø)
cellfinder_napari/tests/test_training.py	100.00% <100.00%> (ø)
cellfinder_napari/tests/test_utils.py	100.00% <100.00%> (ø)
cellfinder_napari/train/__init__.py	100.00% <100.00%> (ø)
cellfinder_napari/train/train_containers.py	100.00% <100.00%> (+20.96%)	:arrow_up:
... and 7 more

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