Merge pull request #419 from nipreps/chore/ruff

effigies · web-flow · commit 4b6d38d66caa · 2024-03-07T14:46:28.000-05:00
CHORE: Update ruff, ignore certain rules
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,3 +1,5 @@
+# 2024-03-07 - mathiasg@stanford.edu - STY: ruff format smriprep [git-blame-ignore-rev]
+83a50d465145c6e8176c3f13d4673ed4e0bdb26f
 # 2023-11-21 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]
 3a586cf46cb1bb963b93d9546f20273194d15de5
 # 2023-11-20 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
@@ -119,5 +119,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run ruff smriprep
+    - run: pipx run ruff check smriprep
     - run: pipx run ruff format --diff smriprep
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       - id: check-toml
       - id: check-json
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.3.1
     hooks:
       - id: ruff
       - id: ruff-format
diff --git a/pyproject.toml b/pyproject.toml
@@ -163,6 +163,11 @@ extend-select = [
   "PT",
   "Q",
 ]
+extend-ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
+]
 
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
diff --git a/smriprep/__init__.py b/smriprep/__init__.py
@@ -8,6 +8,7 @@
 
 
 """
+
 from .__about__ import (
     __copyright__,
     __credits__,
diff --git a/smriprep/conf/__init__.py b/smriprep/conf/__init__.py
@@ -1,4 +1,5 @@
 """sMRIPrep settings."""
+
 from templateflow.api import templates as _get_templates
 
 TF_TEMPLATES = tuple(_get_templates())
diff --git a/smriprep/interfaces/freesurfer.py b/smriprep/interfaces/freesurfer.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Nipype's recon-all replacement."""
+
 import os
 
 from looseversion import LooseVersion
diff --git a/smriprep/interfaces/gifti.py b/smriprep/interfaces/gifti.py
@@ -1,4 +1,5 @@
 """Interfaces for manipulating GIFTI files."""
+
 import os
 
 import nibabel as nb
diff --git a/smriprep/interfaces/surf.py b/smriprep/interfaces/surf.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Handling surfaces."""
+
 import os
 from pathlib import Path
 
diff --git a/smriprep/interfaces/templateflow.py b/smriprep/interfaces/templateflow.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Interfaces to get templates from TemplateFlow."""
+
 import logging
 
 from nipype.interfaces.base import (
diff --git a/smriprep/utils/bids.py b/smriprep/utils/bids.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities to handle BIDS inputs."""
+
 from json import loads
 from pathlib import Path
 
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Anatomical reference preprocessing workflows."""
+
 import typing as ty
 
 from nipype import logging
diff --git a/smriprep/workflows/base.py b/smriprep/workflows/base.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """*sMRIPrep* base processing workflows."""
+
 import os
 import sys
 from copy import deepcopy
diff --git a/smriprep/workflows/fit/registration.py b/smriprep/workflows/fit/registration.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Spatial normalization workflows."""
+
 from collections import defaultdict
 
 from nipype.interfaces import ants
diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Writing outputs."""
+
 import typing as ty
 
 from nipype.interfaces import utility as niu
diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py
@@ -27,6 +27,7 @@
 structural images.
 
 """
+
 import typing as ty
 
 from nipype.interfaces import freesurfer as fs

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# 2024-03-07 - [email protected] - STY: ruff format smriprep [git-blame-ignore-rev]`
	`2`	`+83a50d465145c6e8176c3f13d4673ed4e0bdb26f`
`1`	`3`	`# 2023-11-21 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]`
`2`	`4`	`3a586cf46cb1bb963b93d9546f20273194d15de5`
`3`	`5`	`# 2023-11-20 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""sMRIPrep settings."""`
	`2`	`+`
`2`	`3`	`from templateflow.api import templates as _get_templates`
`3`	`4`
`4`	`5`	`TF_TEMPLATES = tuple(_get_templates())`
Original file line number	Diff line number	Diff line change
`@@ -21,6 +21,7 @@`
`21`	`21`	`# https://www.nipreps.org/community/licensing/`
`22`	`22`	`#`
`23`	`23`	`"""Nipype's recon-all replacement."""`
	`24`	`+`
`24`	`25`	`import os`
`25`	`26`
`26`	`27`	`from looseversion import LooseVersion`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Interfaces for manipulating GIFTI files."""`
	`2`	`+`
`2`	`3`	`import os`
`3`	`4`
`4`	`5`	`import nibabel as nb`