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♻️ Refactor prepro #3

Merged
merged 14 commits into from
Sep 27, 2021
Merged

♻️ Refactor prepro #3

merged 14 commits into from
Sep 27, 2021

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dyollb
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@dyollb dyollb commented Sep 24, 2021

What do these changes do?

  • add gh action to install and test the package
  • add unit tests
  • refactor code in prepro, load/save_tissue_list now use same Dict[str,int] and check for duplicate labels

Related issue/s

How to test

  • run the tests with pytest tests from inside the folder
  • check the gh action log (and badge)

Checklist

  • Unit tests for the changes exist

@dyollb dyollb self-assigned this Sep 24, 2021
tests/test_prepro_labels.py Outdated Show resolved Hide resolved
tests/test_prepro_labels.py Outdated Show resolved Hide resolved
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@dyollb
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dyollb commented Sep 24, 2021

@pcrespov pip (via setup.py) install currently checks for cuda 11, and installs one or the other requirements. For this reason I would not use dev.txt with -r generic.txt.

  • we should be able to install optional stuff (like pytest) for flavors of the package
  • make dev should use that mechanism to do the same, not something independent

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👍

@dyollb dyollb merged commit c8d71b3 into main Sep 27, 2021
@dyollb dyollb deleted the refactor_prepro branch September 27, 2021 07:59
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2 participants