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Linting error if quay.io found in biocontainer name #2278

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Merged
adamrtalbot merged 8 commits into from
May 9, 2023
Merged

Linting error if quay.io found in biocontainer name #2278

adamrtalbot merged 8 commits into from
May 9, 2023

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@adamrtalbot adamrtalbot commented May 4, 2023

Changes:

  • Linting error if container starts with quay.io/biocontainers but not quay.io/biocontainers/mulled

Fixes #2276

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

@adamrtalbot
error if quay.io found in docker container name
4bad234 
Changes:
 - Linting error if container starts with quay.io/biocontainers but not
   quay.io/biocontainers/mulled

Fixes nf-core#2276
ewels
ewels approved these changes May 5, 2023
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LGTM 👍🏻

For a separate issue / PR - this file really needs breaking into many smaller ones with different tests. Also the docs are severely lacking.. 😞

ewels
ewels requested changes May 5, 2023
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Wait, need to add a self.passed when the test is passing..

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adamrtalbot commented May 5, 2023 •
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Wait, need to add a self.passed when the test is passing..

Do we want one for the general container? E.g. if docker image name looks valid ✅

adamrtalbot added 2 commits May 5, 2023 10:45
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Add passed test if quay.io is correct
86aee0c
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Container status check only occurs once
4351a34 
Puts container status check into a single if statement
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adamrtalbot commented May 5, 2023

Wait, need to add a self.passed when the test is passing..

Do we want one for the general container? E.g. if docker image name looks valid ✅

Nevermind, I've copied the existing format. Also updated one of the checks to occur once.

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adamrtalbot commented May 9, 2023

@drpatelh This PR now changes if you are removing quay.io/ from mulled containers as well. Shall we drop it?

@adamrtalbot adamrtalbot requested a review from ewels May 9, 2023 13:51
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codecov bot commented May 9, 2023 •
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Codecov Report

Merging #2278 (00bd8ef) into dev (12404d2) will increase coverage by 0.07%.
The diff coverage is 57.14%.

@@            Coverage Diff             @@
##              dev    #2278      +/-   ##
==========================================
+ Coverage   73.05%   73.12%   +0.07%     
==========================================
  Files          77       77              
  Lines        8424     8433       +9     
==========================================
+ Hits         6154     6167      +13     
+ Misses       2270     2266       -4
Impacted Files Coverage Δ
nf_core/modules/lint/main_nf.py 68.19% <57.14%> (+0.10%) ⬆️

... and 9 files with indirect coverage changes

@adamrtalbot adamrtalbot merged commit 14b0736 into nf-core:dev May 9, 2023
@adamrtalbot adamrtalbot deleted the catch_modules_with_quay.io branch May 9, 2023 14:51
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@mashehu mashehu mashehu approved these changes

@ewels ewels Awaiting requested review from ewels

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@adamrtalbot @ewels @mashehu @mirpedrol