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Add sample SLEAP data containing mixed (user/predicted) labels #85

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merged 3 commits into from
Nov 14, 2023

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lochhh
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@lochhh lochhh commented Nov 14, 2023

Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?
This PR is needed to provide test cases when SLEAP labels contain a mix of user-labelled and predicted instances.

What does this PR do?

  • This PR adds a .slp multi-animal SLEAP dataset containing a mix of user and predicted labels and a corresponding .h5 file (exported from SLEAP).
  • The sleap_file fixture has also been moved to the conftest.py as it is reusable across several test files.
  • This PR configures the run_stale_examples option in conf.py such that sphinx-gallery examples are re-run upon each build

References

This PR resolves the first task in #84

How has this PR been tested?

The new files can be fetched successfully.

Does this PR require an update to the documentation?

The example output on the website will be updated on the next deployment with run_stale_examples configured.

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

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codecov bot commented Nov 14, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (e5ccc83) 98.05% compared to head (78705f3) 98.05%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #85   +/-   ##
=======================================
  Coverage   98.05%   98.05%           
=======================================
  Files           8        8           
  Lines         308      308           
=======================================
  Hits          302      302           
  Misses          6        6           

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@lochhh lochhh linked an issue Nov 14, 2023 that may be closed by this pull request
@lochhh lochhh requested a review from niksirbi November 14, 2023 12:24
@niksirbi niksirbi marked this pull request as ready for review November 14, 2023 12:51
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Hey, looks good!

Need to check if the example output on the website is updated.

By the way, you can do that by forcing sphinx-gallery to rebuild the examples locally.
In conf.py:

sphinx_gallery_conf = = {
    ...
    'run_stale_examples': True,
}

Next time you will sphinx-build the examples will be updated, including the outputs. I did this locally and verified it works. I also successfully fetched the two new files.

Feel free to merge this whenever you deem appropriate.

@lochhh
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lochhh commented Nov 14, 2023

Hey, looks good!

Need to check if the example output on the website is updated.

By the way, you can do that by forcing sphinx-gallery to rebuild the examples locally. In conf.py:

sphinx_gallery_conf = = {
    ...
    'run_stale_examples': True,
}

Next time you will sphinx-build the examples will be updated, including the outputs. I did this locally and verified it works. I also successfully fetched the two new files.

Feel free to merge this whenever you deem appropriate.

Thanks, good to know!

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@lochhh lochhh merged commit 73858ad into main Nov 14, 2023
24 checks passed
@lochhh lochhh deleted the add-sample-data branch November 15, 2023 11:40
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Handle SLEAP data with mixed (user/predicted) labels
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