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New lint test: schema param description #1017

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ewels opened this issue Apr 14, 2021 · 4 comments · Fixed by #1049
Closed

New lint test: schema param description #1017

ewels opened this issue Apr 14, 2021 · 4 comments · Fixed by #1049
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@ewels
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ewels commented Apr 14, 2021

I can't think of a time when it's ok for a parameter in a schema to not have a description. So we should probably lint for that and throw a warning.

Also warn if there are any ungrouped parameters.

@ewels ewels added the linting label Apr 14, 2021
@ewels ewels added this to the 1.14 milestone Apr 25, 2021
@KevinMenden KevinMenden self-assigned this May 3, 2021
@KevinMenden
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Looking into this, I realized that the lint tests are not self-contained. Meaning one only runs when the other has been run before.
That's pretty dangerous, and in fact you can easily break it when running only nf-core lint <pipeline> -k schema_params

So we should probably make that more robust/ the tests self-contained.

@ewels
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ewels commented May 3, 2021

Yes, good point with the -k. You mean stuff like getting the pipeline config?

@KevinMenden
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KevinMenden commented May 3, 2021

Yeah creating the schema object, the error was easy to catch because we basically have a comment saying that:

# First, get the top-level config options for the pipeline
# Schema object already created in the `schema_lint` test
self.schema_obj.get_schema_path(self.wf_path)
self.schema_obj.get_wf_params()
self.schema_obj.no_prompts = True

@KevinMenden
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Remnants of the old code structure I guess

@KevinMenden KevinMenden linked a pull request May 3, 2021 that will close this issue
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@ewels ewels closed this as completed May 9, 2021
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