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Add ruff - Replace Black, isort and pyupgrade #2620

Merged
merged 22 commits into from
Jan 4, 2024
Merged

Add ruff - Replace Black, isort and pyupgrade #2620

merged 22 commits into from
Jan 4, 2024

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mirpedrol
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Replace PR #2174
Close #2533

Implement Ruff linter. In replacement of Black, isort and pyupgrade. It also includes Flake8.

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codecov bot commented Dec 22, 2023 •
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Codecov Report

Attention: 58 lines in your changes are missing coverage. Please review.

Comparison is base (7831f7a) 75.19% compared to head (eb4b775) 75.00%.
Report is 1 commits behind head on dev.

Files Patch % Lines
nf_core/sync.py 50.00% 11 Missing ⚠️
nf_core/download.py 50.00% 9 Missing ⚠️
nf_core/__main__.py 0.00% 8 Missing ⚠️
nf_core/modules/bump_versions.py 33.33% 8 Missing ⚠️
nf_core/modules/lint/main_nf.py 87.75% 6 Missing ⚠️
nf_core/modules/lint/__init__.py 33.33% 2 Missing ⚠️
nf_core/subworkflows/lint/__init__.py 33.33% 2 Missing ⚠️
nf_core/components/info.py 50.00% 1 Missing ⚠️
nf_core/components/lint/__init__.py 50.00% 1 Missing ⚠️
nf_core/launch.py 66.66% 1 Missing ⚠️
... and 9 more
Additional details and impacted files 
@@            Coverage Diff             @@
##              dev    #2620      +/-   ##
==========================================
- Coverage   75.19%   75.00%   -0.19%     
==========================================
  Files          85       85              
  Lines        9384     9363      -21     
==========================================
- Hits         7056     7023      -33     
- Misses       2328     2340      +12

☔ View full report in Codecov by Sentry.
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mirpedrol
mirpedrol commented Dec 22, 2023
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mashehu
mashehu reviewed Jan 2, 2024
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mashehu
mashehu approved these changes Jan 2, 2024
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mirpedrol and others added 6 commits January 4, 2024 09:50
@mirpedrol @mashehu
Apply suggestions from code review
4971496 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mirpedrol
select E1, UP and N, don't ignore E501
0c3c779
@mirpedrol
run ruff check --fix
4fc75f9
@mirpedrol
manually fix other ruff errors
d00c1b6
@mirpedrol @mashehu
Update .github/CONTRIBUTING.md
5df6586 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mirpedrol
fix typo
74a262b
@mashehu mashehu mentioned this pull request Jan 4, 2024
Closed
@mirpedrol mirpedrol merged commit d91a3bf into nf-core:dev Jan 4, 2024
19 of 20 checks passed
@mirpedrol mirpedrol deleted the add-ruff branch January 4, 2024 10:24
@mirpedrol mirpedrol mentioned this pull request Jan 5, 2024
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@mashehu mashehu mashehu approved these changes

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@mirpedrol @mashehu