[Module] Recognize_Bundles and Clean_Bundles

[CHrlS98]

Describe your changes

Add Recognize_Bundles and Clean_Bundles from rbx_flow.

Say which test data are used by your module

Uses scilpy bundles.zip test data.

A config.json file required for scil_recognize_multi_bundles.py is missing from the available test data.

Checklist before requesting a review

• Create the tool:
  • Edit ./modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./modules/nf-scil/<category>/<tool>/meta.yml
• Generate the tests:
  • Edit ./tests/modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./tests/modules/nf-scil/<category>/<tool>/nextflow.config
  • Add test data locally for tests with the fork repository
  • Generate the test infrastructure and md5sum for all outputs
• Ensure the syntax is correct :
  • Check indentation abides with the rest of the library (don't hesitate to correct others !)
  • Lint everything. Ensure your variables have good names.

[CHrlS98]

@AlexVCaron merged with main. I add some conflicts in file pytest_modules.yml I had to manually solve. Also, a reminder:

Uses scilpy bundles.zip test data.

A config.json file required for scil_recognize_multi_bundles.py is missing from the available test data.

[AlexVCaron]

Hi Charles ! You can update your PR with the main branch. Also, for the missing test data, can you prepare an archive or upload the missing file(s) here ? I'll make them available for your test cases.

[AlexVCaron]

Hi @CHrlS98 ! Can we try solving this PR ? There are two checks that fail, they should be fixable quickly :

• Run prettier --write <module path>, it should fix the prettier check
• Supply the data for the test, there are still some files missing I think

@gagnonanthony and @ThoumyreStanislas are available for support if you need a hand !

[CHrlS98]

@AlexVCaron @gagnonanthony @ThoumyreStanislas

Sorry for the delay it'd seem I missed the notification. I'm getting back to it this week.

[CHrlS98]

config.json

@AlexVCaron @ThoumyreStanislas @gagnonanthony Here is the missing file for the tests. It should go in bundles.zip. This file is generated on the fly in the scilpy test (https://github.com/scilus/scilpy/blob/41078d0aa0aea4d71d5f5dcda514185754c53131/scripts/tests/test_tractogram_segment_bundles.py#L31).

[CHrlS98]

I fixed the linting and the test input. However I did not run the test locally as it is unclear where I should put the config.json file. I may need some help with that.

[AlexVCaron]

Hi @CHrlS98 ! I am uploading the archive and updating the main right now, so you should be able to run the tests locally once you rebase or merge on those changes, I'll give you a heads up when ready. If you want to test with local files still, you can refer to #118.

[AlexVCaron]

@CHrlS98 The package is uploaded and main is up-to-date !

[CHrlS98]

Alright everything passes, ready for review @ThoumyreStanislas @gagnonanthony !

[gagnonanthony]

Minor changes, but overall really nice! Thanks @CHrlS98!

[ThoumyreStanislas]

That's really good! Well done! Just a minor comment and that will be good for me.

[ThoumyreStanislas]

Can you create another test in which you also test your parameters with other values (minimal_vote_ratio, seed, outlier_alpha).

[CHrlS98]

Done in b331082 !

[gagnonanthony]

LGTM! 💯

[ThoumyreStanislas]

LGTM!