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Migrating basicpy to nf-test #6929

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Migrating basicpy to nf-test #6929

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kbestak
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@kbestak kbestak commented Nov 4, 2024 •
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Migrated testing of BasicPy to nf-test instead of pytest.

PR checklist

Closes #6927

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements. --> not possible, conda not supported
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@kbestak kbestak requested a review from a team as a code owner November 4, 2024 13:14
@SPPearce
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SPPearce commented Nov 5, 2024

The tests are failing because the md5sums are not consistent, do they just need updating or do the files contain a datestamp or something?

SPPearce
SPPearce reviewed Nov 5, 2024
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modules/nf-core/basicpy/main.nf
@@ -36,13 +36,17 @@ process BASICPY {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
}
def args = task.ext.args ?: ''
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Suggested change
def args = task.ext.args ?: ''

modules/nf-core/basicpy/tests/nextflow.config
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Can delete this file.

@kbestak kbestak mentioned this pull request Nov 5, 2024
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@kbestak , are you able to continue here?

@kbestak kbestak mentioned this pull request Dec 16, 2024
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kbestak commented Dec 16, 2024

Hi @SPPearce , I've opened a new PR now because I decided it would be easier than resolving conflicts: #7228

@kbestak kbestak closed this Dec 16, 2024
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner automatically assigned from nf-core/a-team

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nf-test for Basicpy
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@kbestak @SPPearce