STY: Adopt ruff for linting and formatting (#3206)

Follow-up to nipreps/smriprep#397. This should
replace #3185 and #3147.

I would review this commit-by-commit, and skip
c0f2183, which was a pretty safe run of
`ruff format` and `ruff --fix`. It's dominated by quote changes, so I
would ignore it. Everything else could stand a review.

Author: effigies

.git-blame-ignore-revs

@@ -1,6 +1,12 @@
-# 2022-09-22 - [email protected] - STY: black/isort the docker wrapper
+# 2024-01-16 - [email protected] - STY: ruff --fix --unsafe-fixes (with cleanup) [git-blame-ignore-rev]
+66734bd0164d1dae3cf299fa9d9d682c22eeda66
+# 2024-01-16 - [email protected] - STY: ruff format and ruff --fix [git-blame-ignore-rev]
+311686eb329d3594732429f7c3d50d212b8dc519
+# 2023-02-02 - [email protected] - STY: black [git-blame-ignore-rev]
+d3f380701b3953087475a18cf23c0fb388f7aed6
+# 2022-09-22 - [email protected] - STY: black/isort the docker wrapper
 9976458388f369cba4b7d81359acc40b52f6621c
-# 2022-09-22 - [email protected] - STY: Apply black/isort to codebase
+# 2022-09-22 - [email protected] - STY: Apply black/isort to codebase
 7eedab8b29497cee1d8dd540c2266e740f484a86
 # 2021-11-05 - [email protected] - STY: Update black config
 d2ad20301306f283d504ec7b5a1bd73ce58c2b11

.github/ISSUE_TEMPLATE/documentation.md

@@ -11,4 +11,4 @@ For the Documentation request, please include the following:
 ------------------------
 What would you like changed/added and why?
 Do you have any suggestions for the new documents?
--->
+-->

.github/workflows/contrib.yml

@@ -22,32 +22,13 @@ permissions:
   contents: read
 
 jobs:
-  stable:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: [3]
-
+  style:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Install black/isort
-        run: python -m pip install black isort[colors]
-      - name: Check fMRIPrep
-        run: |
-          python -m black --diff --color --check fmriprep
-          python -m isort --diff --color --check fmriprep
-      - name: Check wrapper
-        run: |
-          python -m black --diff --color --check wrapper
-          python -m isort --diff --color --check wrapper
-  
+      - run: pipx run ruff fmriprep
+      - run: pipx run ruff format --diff fmriprep
+
   codespell:
     name: Check for spelling errors
     runs-on: ubuntu-latest

.maint/ci/install_dependencies.sh

@@ -13,7 +13,7 @@ if [ "$OS_TYPE" = "ubuntu-latest" ]; then
 elif  [ "$OS_TYPE" = "macos-latest" ]; then
     brew install graphviz
 else
-    echo "Unknown OS_TYPE: $OS_TYPE"	
+    echo "Unknown OS_TYPE: $OS_TYPE"
 fi
 
 set +eux

.maint/former.json

@@ -2,4 +2,4 @@
   {
     "name": "Berleant, Shoshana"
   }
-]
+]

.maint/paper_author_list.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python3
 """Generate an author list for a new paper or abstract."""
+import json
 import sys
 from pathlib import Path
-import json
-from update_zenodo import get_git_lines, sort_contributors
 
+from update_zenodo import get_git_lines, sort_contributors
 
 # These authors should go last
 AUTHORS_LAST = ['Gorgolewski, Krzysztof J.', 'Poldrack, Russell A.', 'Esteban, Oscar']
@@ -21,9 +21,11 @@ def _aslist(inlist):
     contribs = json.loads(Path('.maint/contributors.json').read_text())
 
     author_matches, unmatched = sort_contributors(
-        devs + contribs, get_git_lines(),
+        devs + contribs,
+        get_git_lines(),
         exclude=json.loads(Path('.maint/former.json').read_text()),
-        last=AUTHORS_LAST)
+        last=AUTHORS_LAST,
+    )
     # Remove position
     affiliations = []
     for item in author_matches:
@@ -32,18 +34,34 @@ def _aslist(inlist):
             if a not in affiliations:
                 affiliations.append(a)
 
-    aff_indexes = [', '.join(['%d' % (affiliations.index(a) + 1)
-                              for a in _aslist(author.get('affiliation', 'Unaffiliated'))])
-                   for author in author_matches]
+    aff_indexes = [
+        ', '.join(
+            [
+                '%d' % (affiliations.index(a) + 1)
+                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
+            ]
+        )
+        for author in author_matches
+    ]
 
-    print("Some people made commits, but are missing in .maint/ "
-          "files: %s." % ', '.join(unmatched), file=sys.stderr)
+    print(
+        'Some people made commits, but are missing in .maint/ '
+        'files: %s.' % ', '.join(unmatched),
+        file=sys.stderr,
+    )
 
     print('Authors (%d):' % len(author_matches))
-    print("%s." % '; '.join([
-        '%s \\ :sup:`%s`\\ ' % (i['name'], idx)
-        for i, idx in zip(author_matches, aff_indexes)
-    ]))
+    print(
+        '%s.'
+        % '; '.join(
+            [
+                '{} \\ :sup:`{}`\\ '.format(i['name'], idx)
+                for i, idx in zip(author_matches, aff_indexes, strict=False)
+            ]
+        )
+    )
 
-    print('\n\nAffiliations:\n%s' % '\n'.join(['{0: >2}. {1}'.format(i + 1, a)
-                                               for i, a in enumerate(affiliations)]))
+    print(
+        '\n\nAffiliations:\n%s'
+        % '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+    )