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added check for parameter description #1049

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Merged
ewels merged 9 commits into from
May 5, 2021
Merged

added check for parameter description #1049

ewels merged 9 commits into from
May 5, 2021

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@KevinMenden
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@KevinMenden KevinMenden commented May 3, 2021 •
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Adding a lint check to look missing parameter descriptions in the schema and warn about parameters outside of groups.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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KevinMenden commented May 3, 2021

closes #1017

@KevinMenden KevinMenden linked an issue May 3, 2021 that may be closed by this pull request
New lint test: schema param description #1017
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codecov bot commented May 3, 2021 •
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Codecov Report

Merging #1049 (4f75b6a) into dev (5dd3fc6) will decrease coverage by 0.00%.
The diff coverage is 71.87%.

❗ Current head 4f75b6a differs from pull request most recent head 819f018. Consider uploading reports for the commit 819f018 to get more accurate results
Impacted file tree graph

@@            Coverage Diff             @@
##              dev    #1049      +/-   ##
==========================================
- Coverage   73.51%   73.50%   -0.01%     
==========================================
  Files          35       36       +1     
  Lines        4364     4397      +33     
==========================================
+ Hits         3208     3232      +24     
- Misses       1156     1165       +9
Impacted Files Coverage Δ
nf_core/lint/schema_description.py 68.96% <68.96%> (ø)
nf_core/lint/__init__.py 76.89% <100.00%> (+0.09%) ⬆️
nf_core/lint/schema_params.py 80.95% <100.00%> (+2.00%) ⬆️
nf_core/download.py 64.87% <0.00%> (+0.09%) ⬆️

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ewels
ewels requested changes May 3, 2021
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Looks good, but please add some code so that params can be ignored using the lint config file.

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KevinMenden commented May 4, 2021

Ah sure, sorry! Will add that.
Thanks for the review! 👍

ewels
ewels requested changes May 5, 2021
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Need to report the ignored tests, then looks good 👍🏻

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KevinMenden commented May 5, 2021

🤦

ewels
ewels approved these changes May 5, 2021
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LGTM 🚀

@ewels ewels enabled auto-merge May 5, 2021 22:54
@ewels ewels merged commit da71010 into nf-core:dev May 5, 2021
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New lint test: schema param description

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@KevinMenden @ewels