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[REF] Move PETLinear pipeline to new clinica.pipelines.pet module #1224

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NicolasGensollen
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Following #1223, this PR is a portion of #1122 focusing on the PETLinear pipeline.

More precisely, it does the following:

  • Create module clinica.pipelines.pet.linear
  • Move previous clinica.pipelines.pet_linear module to this new module
  • Use the classical structure in the new module:
    • cli.py: Contains the CLI
    • pipeline.py: Contains the pipeline definition
    • utils.py: Contains the utility functions used by the PETLinear pipeline only
    • tasks.py: Contains the adapters for Nipype function interfaces built around utility functions
  • Use better variable names
  • Use type hints everywhere with better types (Path vs str mainly)
  • Update tests and some imports in the Pydra module

Note: Needs to be tested against regression test suite to make sure I didn't break anything.

@NicolasGensollen NicolasGensollen self-assigned this Jul 8, 2024
@NicolasGensollen NicolasGensollen marked this pull request as ready for review July 8, 2024 13:46
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@AliceJoubert AliceJoubert left a comment

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Looks good, @NicolasGensollen !

@NicolasGensollen NicolasGensollen merged commit 68364a5 into aramis-lab:dev Jul 9, 2024
14 of 15 checks passed
@NicolasGensollen NicolasGensollen deleted the refactor-pet-pipelines-new-2 branch July 9, 2024 06:00
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2 participants