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Add more ruff rules (B, PTH, RSE, SIM, C4, BLE, A)#4034

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mashehu merged 59 commits intonf-core:devfrom
mashehu:new-ruff-rules
Apr 14, 2026
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Add more ruff rules (B, PTH, RSE, SIM, C4, BLE, A)#4034
mashehu merged 59 commits intonf-core:devfrom
mashehu:new-ruff-rules

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@mashehu mashehu commented Feb 11, 2026 •
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Additional rules we could add:

  • "C4", # flake8-comprehensions - better list/dict/set comprehensions
    - [ ] "RUF", # Ruff-specific rules - includes RUF103/104 for validating suppressions
  • "SIM", # flake8-simplify - simplifies code patterns
    - [ ] "PIE", # flake8-pie - misc lints for common issues
  • "RSE", # flake8-raise - unnecessary parentheses on raised exceptions
    - [ ] "RET", # flake8-return - unnecessary variable assignments before return
    - [ ] "ARG", # flake8-unused-arguments - finds unused function arguments
  • "BLE", # flake8-blind-except - catches blind except clauses
  • "A", # flake8-builtins - catches shadowing of Python builtins
    - [ ] "TRY", # tryceratops - exception handling best practices

Update:
Rest of the rules would need too many exceptions etc. to be applicable for our code

@mashehu mashehu requested a review from a team February 11, 2026 10:14
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codecov Bot commented Feb 11, 2026 •
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Codecov Report

❌ Patch coverage is 69.81567% with 131 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.09%. Comparing base (3d5d0e8) to head (65d05f6).
⚠️ Report is 1 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/pipelines/schema.py 48.48% 17 Missing ⚠️
nf_core/synced_repo.py 31.25% 11 Missing ⚠️
nf_core/components/update.py 65.21% 8 Missing ⚠️
nf_core/pipelines/create/githubrepo.py 30.00% 7 Missing ⚠️
nf_core/pipelines/refgenie.py 0.00% 7 Missing ⚠️
nf_core/pipelines/rocrate.py 66.66% 6 Missing ⚠️
nf_core/modules/modules_json.py 77.27% 5 Missing ⚠️
nf_core/modules/modules_repo.py 16.66% 5 Missing ⚠️
nf_core/pipelines/create/create.py 55.55% 4 Missing ⚠️
nf_core/pipelines/launch.py 77.77% 4 Missing ⚠️
... and 32 more

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@mashehu mashehu changed the title Add more ruff rules (B, PTH) Add more ruff rules (B, PTH, RSE) Feb 11, 2026
@mashehu mashehu changed the title Add more ruff rules (B, PTH, RSE) Add more ruff rules (B, PTH, RSE, SIM) Feb 12, 2026
@mashehu mashehu changed the title Add more ruff rules (B, PTH, RSE, SIM) Add more ruff rules (B, PTH, RSE, SIM, C4) Feb 16, 2026
@mashehu mashehu changed the title Add more ruff rules (B, PTH, RSE, SIM, C4) Add more ruff rules (B, PTH, RSE, SIM, C4, BLE) Feb 16, 2026
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mashehu commented Feb 20, 2026

hah, looks like most of these new rules are anyway part of an upcoming set of default ruff rules: astral-sh/ruff#23203

@mashehu mashehu force-pushed the new-ruff-rules branch 3 times, most recently from b2cd1b3 to dada220 Compare February 26, 2026 20:22
@mashehu mashehu changed the title Add more ruff rules (B, PTH, RSE, SIM, C4, BLE) Add more ruff rules (B, PTH, RSE, SIM, C4, BLE, A) Feb 27, 2026
@mashehu mashehu mentioned this pull request Mar 6, 2026
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fabianegli
fabianegli reviewed Mar 9, 2026
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Comment thread nf_core/synced_repo.py Outdated
fabianegli
fabianegli reviewed Mar 9, 2026
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Comment thread nf_core/modules/modules_utils.py Outdated
@mashehu mashehu added this to the 4.0.0 milestone Mar 31, 2026
ningyuxin1999
ningyuxin1999 reviewed Mar 31, 2026
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Comment thread nf_core/modules/lint/main_nf.py
ningyuxin1999
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Will continue with reviewing tomorrow :))

mashehu and others added 28 commits April 14, 2026 15:31
@mashehu
fix PTH103
ff37f6b
@mashehu
fix PTH112
d7f5e01
@mashehu
fix PTH113
4aeca76
@mashehu
fix PTH116
9f06afb
@mashehu
fix PTH202
b0e8411
@mashehu
fix missing import
1768792
@mashehu
fix outdated log.warn
be8f70f
@nf-core-bot @mashehu
[automated] Update CHANGELOG.md
18a3536 
# Conflicts:
#	CHANGELOG.md

# Conflicts:
#	CHANGELOG.md

# Conflicts:
#	CHANGELOG.md
@mashehu
fix tests by creating the dummy files instead of mocking
7934381
@mashehu
add RSE and run --fix
ed69982
@mashehu
add "SIM" rules and apply automated fixes
0178a8d
@mashehu
fix SIM115
90fb654
@mashehu
fix SIM102
08b25fd
@mashehu
fix SIM113
6be0821
@mashehu
fix SIM117
35e6fcf
@mashehu
fix SIM108
bf0c6f0
@mashehu
fix SIM105
c9a4fdc
@mashehu
fix SIM115
6fe884e
@mashehu
add C4 and run --fix
b59e942
@mashehu
add BLE and fix errors
b829aef
@mashehu
fix F401
3aa18af
@mashehu
fix C419
50f25a4
@mashehu
add "E902" and "W" from upcoming default set
1fef36f
@mashehu
add "A" and fix errors
90f0cf9
@mashehu
add PIE and fix errors
d96287e
@mashehu
don't reassign variable
42525c1
@mashehu
use cast instead of assert
ece5755
@mashehu
fix ruff errors after rebase
65d05f6
@mashehu mashehu merged commit dd201a7 into nf-core:dev Apr 14, 2026
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