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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

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998a22c
add ruff formatter and linter
mirpedrol Dec 22, 2023
9fdcf03
remove isort
mirpedrol Dec 22, 2023
418f0be
remove python black
mirpedrol Dec 22, 2023
2ca9b19
remove pyupgrade
mirpedrol Dec 22, 2023
c25c5be
update CONTRIBUTING.md
mirpedrol Dec 22, 2023
e40f7b9
select import sorting and run first linter and then formatter
mirpedrol Dec 22, 2023
df3d3a1
ignore import checks in __init__.py files
mirpedrol Dec 22, 2023
14ca618
run ruff check --fix
mirpedrol Dec 22, 2023
8cc98a2
manually fix other ruff errors
mirpedrol Dec 22, 2023
f2f3645
remove unused fullname from SyncedRepo and fix circular import
mirpedrol Dec 22, 2023
3579de6
locate ruff cache dir at ~/.cache/ruff
mirpedrol Dec 22, 2023
691e654
Apply suggestions from code review
mirpedrol Dec 22, 2023
aaa5166
use required to create params file
mirpedrol Dec 22, 2023
b430bbf
don't run prettier on things handled by ruff
mashehu Jan 2, 2024
4971496
Apply suggestions from code review
mirpedrol Jan 4, 2024
0c3c779
select E1, UP and N, don't ignore E501
mirpedrol Jan 4, 2024
4fc75f9
run ruff check --fix
mirpedrol Jan 4, 2024
d00c1b6
manually fix other ruff errors
mirpedrol Jan 4, 2024
5df6586
Update .github/CONTRIBUTING.md
mirpedrol Jan 4, 2024
74a262b
fix typo
mirpedrol Jan 4, 2024
9184c1d
Apply suggestions from code review
mirpedrol Jan 4, 2024
eb4b775
fix formatting
mirpedrol Jan 4, 2024
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4 changes: 4 additions & 0 deletions nf_core/params_file.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,6 +195,7 @@ def format_param(self, name, properties, required_properties=(), show_hidden=Fal
self.schema_obj.get_schema_defaults()
default = properties.get("default")
typ = properties.get("type")
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required = name in required_properties

out += _print_wrapped(name, "-", mode="both")

Expand All @@ -204,6 +205,9 @@ def format_param(self, name, properties, required_properties=(), show_hidden=Fal
if typ:
out += _print_wrapped(f"Type: {typ}", mode="none", indent=4)

if required:
out += _print_wrapped("Required", mode="none", indent=4)

out += _print_wrapped("\n", mode="end")
out += f"# {name} = {json.dumps(default)}\n"

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