Reorganise test fixtures

[lochhh]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
This PR closes #336 and #222.

What does this PR do?
This PR

• modularises fixtures in conftest.py by grouping these as either datasets.py, files.py, or helpers.py in tests/fixtures/; where datasets contains fixtures for valid and invalid movement datasets and arrays, dataframes; helpers contain the helper functions to count nans and the reused assert_valid_dataset()
• ensures file fixtures returning file paths are suffixed with "_file" to enable devs to easily identify file fixtures and search for existing ones
• prefixes VIA tracks-related file content fixtures with via_
• replaces the old and simpler valid_poses_dataset, valid_poses_dataset_with_nan, valid_position_array fixtures with the newer uniform_linear_motion fixtures and updates the affected tests
• updates poses_with_nan fixture to match that of bboxes (i.e. both centroids have nans at the same time points)
• ensures data fixtures containing nans are consistently suffixed with _with_nan (before we had a mix of _with_nans and _with_nan)
• groups tests using the same "parametrize" into Classes, e.g. TestComputeKinematics, TestFilteringValidDataset
• removes unused fixtures
• standardises the "individuals" IDs across fixtures to start from id_0 (before, poses ids start from id_1); semi-related note: movement by default sets "individuals" names to begin with "individual_0" if none are provided upon import.
• renames compute_time_derivative test to match new function name and parametrise expectations

I haven't changed the vector-related tests in test_kinematics.py as there is ongoing work in PR #385.

References

#336 #222

How has this PR been tested?

Tests passing

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.80%. Comparing base (84b245c) to head (8bd6ef1).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #380   +/-   ##
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  Coverage   99.80%   99.80%           
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  Files          15       15           
  Lines        1048     1048           
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  Hits         1046     1046           
  Misses          2        2           

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[niksirbi]

FYI @lochhh, @sfmig has arrived at a nice structure in ethology, by storing fixtures in separate files, see this PR.

I don't know of you were planning to go this deep into reorganising, leaving this reference here just in case its useful.

[sfmig]

thanks @lochhh it looks fantastic!

I really like the consistency (such as the _file endings, the via_ prefixes, with_nan suffixes etc), it makes a lot of it much more readable. I followed some of these ideas and suggested a few invalid_ prefixes for some dataset-related fixtures.

The only larger thing is that I had a go at moving the movement_dataset_asserts fixture to be under the helpers fixtures, since the class that wrapped it only had that one method - it's here, but you can revert if you disagree.

Re PR #385, since that is now merged, if you want to deal with that in this PR I am happy to review any additions. Otherwise we can deal with it separately in another PR/issue.

[niksirbi]

Re PR #385, since that is now merged, if you want to deal with that in this PR I am happy to review any additions. Otherwise we can deal with it separately in another PR/issue.

Oops sorry, we merged it without looking here.
Whatever scheme you agree on should be also applied to the kinematics tests (after merging/rebasing from main).

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[lochhh]

thanks @lochhh it looks fantastic!

I really like the consistency (such as the _file endings, the via_ prefixes, with_nan suffixes etc), it makes a lot of it much more readable. I followed some of these ideas and suggested a few invalid_ prefixes for some dataset-related fixtures.

The only larger thing is that I had a go at moving the movement_dataset_asserts fixture to be under the helpers fixtures, since the class that wrapped it only had that one method - it's here, but you can revert if you disagree.

Re PR #385, since that is now merged, if you want to deal with that in this PR I am happy to review any additions. Otherwise we can deal with it separately in another PR/issue.

Thanks for the thorough review and suggestions @sfmig ! I've adopted most suggestions and explained those that weren't. I also added your suggestion related to the renamed compute_time_derivative in this PR.

I briefly looked into PR #385 and there isn't any new additions to conf.py, meaning there aren't "shared fixtures" to be reorganised, so nothing within the scope of this PR.