Allowing inference on multiple videos via `sleap-track`

[emdavis02]

Description

Adding an option to add a directory to sleap-track to allow the command to iterate through the files in the directory and run inferences on all of them.

Types of changes

• [ ] Bugfix
• [x] New feature
• [ ] Refactor / Code style update (no logical changes)
• [ ] Build / CI changes
• [ ] Documentation Update
• [ ] Other (explain)

Does this address any currently open issues?

#1777

Outside contributors checklist

• [ ] Review the guidelines for contributing to this repository
• [ ] Read and sign the CLA and add yourself to the authors list
• [x] Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
• [ ] Add tests that prove your fix is effective or that your feature works
• [ ] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

• New Features

  • Added support for handling multiple video inputs, allowing users to run inference on multiple files simultaneously. This includes managing output paths and improving error handling.

• Bug Fixes

  • Enhanced error handling and provenance metadata management to ensure smoother operations when processing multiple inputs.

• Tests

  • Introduced new test scenarios for multiple input tracking to ensure robustness and correctness.

[coderabbitai[bot]]

Walkthrough

The recent updates to the sleap/nn/inference.py and corresponding test files enhance the software to handle multiple video inputs. The changes refactor the code to iterate over a list of file paths, create providers for each file, run the inference, and save the results. Enhancements include better error handling, improved metadata management, and robust testing for various scenarios.

Changes

File	Change Summary
sleap/nn/inference.py	Refactored logic to handle multiple video inputs, created a provider list, managed output paths, and added provenance metadata.
tests/nn/test_inference.py	Added fixtures and test functions for multiple inference scenarios, including parameterized tests and handling invalid inputs.

Poem

In the land of code where videos roam,
A rabbit worked to bring them home.
With paths aplenty and providers in tow,
Each file's secrets would soon show.
Tests were written, robust and clear,
Ensuring the code ran without fear.
🎥✨🐇 The rabbit's joy was quick to grow!

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[codecov[bot]]

Codecov Report

Attention: Patch coverage is 89.16667% with 13 lines in your changes missing coverage. Please review.

Project coverage is 74.19%. Comparing base (7ed1229) to head (fb587e5). Report is 21 commits behind head on develop.

Files	Patch %	Lines
sleap/nn/inference.py	89.16%	13 Missing :warning:

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1784      +/-   ##
===========================================
+ Coverage    73.30%   74.19%   +0.88%     
===========================================
  Files          134      135       +1     
  Lines        24087    24639     +552     
===========================================
+ Hits         17658    18280     +622     
+ Misses        6429     6359      -70     

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[talmo]

Review notes from subgroup:

• Remove duplicate files from fixtures and instead just copy them on the fly inside the test into a temp dir
• Update docs to reference the new functionality (at least add usage examples to the CLI doc page for sleap-track)

[talmo]

In addition to the changes above, another comment re: supporting inputs that are multiple SLP files:

• We do want to support having multiple SLP files that have predicted poses on all frames and that the user wants to retrack only.
• We do want to support having multiple SLP files that have suggestion frames and that the user wants to generate predicted poses for, but not track.
• We do not want to overwrite SLP files in any case.
• We really do not want to mess around with .pkg.slp files, particularly not overwrite them. When re-saving labels that had embedded images, they'll get saved without the embedded images and will restore the source videos. If the user had embedded images, it'd be a serious data loss event to have that file get re-saved without the images. In this case, saving to a separate SLP file is the best compromise.

@roomrys am I missing any other dangerzone cases?

[talmo]

In addition to the changes above, another comment re: supporting inputs that are multiple SLP files:

• We do want to support having multiple SLP files that have predicted poses on all frames and that the user wants to retrack only.
• We do want to support having multiple SLP files that have suggestion frames and that the user wants to generate predicted poses for, but not track.
• We do not want to overwrite SLP files in any case.
• We really do not want to mess around with .pkg.slp files, particularly not overwrite them. When re-saving labels that had embedded images, they'll get saved without the embedded images and will restore the source videos. If the user had embedded images, it'd be a serious data loss event to have that file get re-saved without the images. In this case, saving to a separate SLP file is the best compromise.

@roomrys am I missing any other dangerzone cases?

On further assessment during subgroup: let's actually just not do multiple SLP file support.