Use pre-commit for CI linting and update to latest tool versions

Author: francois-drielsma

.github/workflows/ci.yml

@@ -284,27 +284,14 @@ jobs:
       with:
         python-version: '3.10'
 
-    - name: Install quality tools
+    - name: Install pre-commit
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 black==25.9.0 isort mypy
+        pip install pre-commit
         pip install -e .
 
-    - name: Run Black
-      run: black --check --diff src/spine/
-
-    - name: Run isort
-      run: isort --check-only --diff src/spine/
-
-    - name: Run flake8
-      run: |
-        # Configure flake8 to focus on critical issues while allowing common library patterns
-        # Ignoring: F401/F403/F405 (import patterns), F841 (unused vars), E501 (line length handled by Black)
-        # E711/E712/E713 (comparison style), W391/W291/W293 (whitespace), E221/E265/E266 (spacing/comments)
-        # F822/F601/F823 (name issues), E722 (bare except), others (library-specific patterns)
-        flake8 src/spine/ \
-          --max-line-length=88 \
-          --extend-ignore=E203,W503,F401,F403,F405,W605,E731,E741,F811,F821,F541,F841,E501,W391,W291,W293,E221,E265,E266,F822,F601,F823,E722,E711,E712,E713
+    - name: Run pre-commit checks
+      run: pre-commit run --all-files --show-diff-on-failure
 
     - name: Run mypy on critical modules
       run: |

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0  # Updated to latest
+    rev: v6.0.0  # Updated to latest
     hooks:
       - id: trailing-whitespace
         exclude: '\.md$'  # Allow trailing spaces in Markdown
@@ -19,20 +19,20 @@ repos:
       - id: requirements-txt-fixer
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0  # Updated to latest
+    rev: 26.1.0  # Updated to latest
     hooks:
       - id: black
         language_version: python3
         args: [--line-length=88]  # Explicit line length
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2  # Updated to latest
+    rev: 7.0.0  # Updated to latest
     hooks:
       - id: isort
         args: [--profile=black, --line-length=88]  # Match Black config
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1  # Updated to latest
+    rev: 7.3.0  # Updated to latest
     hooks:
       - id: flake8
         # Use same ignore list as CI for consistency

src/spine/model/experimental/layer/pointnet.py

@@ -57,21 +57,17 @@ def __init__(self, cfg, name="pointnet"):
         elif isinstance(self.sampling_ratio, list):
             assert len(self.sampling_ratio) == self.depth
         else:
-            raise ValueError(
-                "Sampling ratio must either be given as \
-                             float or list of floats."
-            )
+            raise ValueError("Sampling ratio must either be given as \
+                             float or list of floats.")
 
         self.neighbor_radius = self.model_config.get("neighbor_radius", 3.0)
         if isinstance(self.neighbor_radius, float):
             self.neighbor_radius = [self.neighbor_radius] * self.depth
         elif isinstance(self.neighbor_radius, list):
             assert len(self.neighbor_radius) == self.depth
         else:
-            raise ValueError(
-                "Neighbor aggregation radius must either \
-                             be given as float or list of floats."
-            )
+            raise ValueError("Neighbor aggregation radius must either \
+                             be given as float or list of floats.")
 
         self.mlp_specs = []
         self.sa_modules = nn.ModuleList()

src/spine/model/full_chain.py

@@ -711,7 +711,7 @@ def run_part_aggregation(self, data, clust_label=None, coord_label=None):
                 # Use GraPA to aggregate instances
                 prefix = f"{name}_fragment" if name != "particle" else "fragment"
                 model = getattr(self, f"grappa_{name}")
-                (groups, group_shapes, group_primaries, shape_index) = self.run_grappa(
+                groups, group_shapes, group_primaries, shape_index = self.run_grappa(
                     prefix,
                     model,
                     data,
@@ -738,16 +738,14 @@ def run_part_aggregation(self, data, clust_label=None, coord_label=None):
 
             elif switch == "label":
                 # Use cluster labels to aggregate instances
-                (groups, group_shapes, group_primaries, shape_index) = (
-                    self.group_labels(
-                        shapes[name],
-                        data,
-                        fragments,
-                        fragment_shapes,
-                        aggregate_shapes=True,
-                        shape_use_primary=use_primary[name],
-                        retain_primaries=use_primary[name],
-                    )
+                groups, group_shapes, group_primaries, shape_index = self.group_labels(
+                    shapes[name],
+                    data,
+                    fragments,
+                    fragment_shapes,
+                    aggregate_shapes=True,
+                    shape_use_primary=use_primary[name],
+                    retain_primaries=use_primary[name],
                 )
 
             elif switch == "skip":

src/spine/model/layer/cnn/blocks.py

@@ -568,10 +568,8 @@ def __init__(
         elif mode == "sum":
             self.pool_fn = ME.MinkowskiSumPooling
         else:
-            raise ValueError(
-                "Invalid pooling mode, must be one of \
-                'sum', 'max' or 'average'"
-            )
+            raise ValueError("Invalid pooling mode, must be one of \
+                'sum', 'max' or 'average'")
 
         self.unpool_fn = ME.MinkowskiPoolingTranspose