linter workflow runs ruff fixing now

.github/workflows/linter.yml

@@ -6,19 +6,25 @@ on:
   pull_request:
     branches: [ main ]
 
+permissions:
+  contents: write
+
 jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.head_ref }}
+    - uses: actions/setup-python@v5
     - run: pip install ruff
-    - run: ruff check . #--fix
-    #- uses: chartboost/ruff-action@v1
-    #  with:
-    #    fix_args: --fix
-    #  with:
-    #    args: --check .
-    - uses: stefanzweifel/git-auto-commit-action@v4
+    - name: Apply ruff auto-fixes
+      run: |
+        ruff check . --fix
+        ruff format .
+    - name: Commit auto-fixes
+      uses: stefanzweifel/git-auto-commit-action@v5
       with:
         commit_message: 'style fixes by ruff'
+    - name: Gate on remaining lint errors
+      run: ruff check .

README.md

@@ -73,8 +73,8 @@ nii.get_array()  # get numpy array
 nii.affine  # Affine matrix
 nii.header  # NIFTY header
 nii.orientation  # Orientation in 3-Letters
-nii.zoom # Scale of the three image axis
-nii.shape #shape
+nii.zoom  # Scale of the three image axis
+nii.shape  # shape
 ```
 
 

TPTBox/core/README.md

@@ -38,7 +38,7 @@ Numpy functionalities that a lot of NII functions above utilize under the hood.
 ```python
 from TPTBox.core.np_utils import np_unique, np_center_of_mass
 
-a = np.array([0,1,2,3], [4,5,6,7], dtype=np.uint8)
+a = np.array([0, 1, 2, 3], [4, 5, 6, 7], dtype=np.uint8)
 
 label = np_unique(a)
 center_of_mass_of_label_four = np_center_of_mass(a)[4]
@@ -59,6 +59,7 @@ center_of_mass_of_label_four = np_center_of_mass(a)[4]
 
 ```python
 from TPTBox import NII, Location
+
 # Segmentation
 seg = NII.load("path/to/seg.nii.gz", seg=True)
 

TPTBox/core/README_BIDS.md

@@ -49,11 +49,7 @@ from TPTBox import BIDS_FILE
 root = Path("path/to/dataset-dsname")
 
 # Example BIDS-compliant input file
-example_file = (
-    root
-    / "rawdata/sub-Max-Mustermann/ses-01012026/anat/"
-      "sub-Max-Mustermann_ses-01012026_acq-sag_ce-GBCA_T1w.nii.gz"
-)
+example_file = root / "rawdata/sub-Max-Mustermann/ses-01012026/anat/sub-Max-Mustermann_ses-01012026_acq-sag_ce-GBCA_T1w.nii.gz"
 
 # Create a BIDS_FILE object
 bf_file = BIDS_FILE(example_file, root)
@@ -85,5 +81,4 @@ seg_path = bf_file.get_changed_path(
     # If True, disables strict validation against predefined key--value pairs
     non_strict_mode=False,
 )
-
 ```

TPTBox/core/README_NII.md

@@ -20,6 +20,7 @@ The `core` subpackage is the foundation of TPTBox. It provides the three primary
 
 ```python
 from TPTBox import NII
+
 # Image
 nii = NII.load("path/to/img.nii.gz", seg=False)
 # Segmentation

TPTBox/core/README_POI.md

@@ -32,15 +32,12 @@ Compute a full set of anatomical landmarks. The registry of supported non-centro
 from TPTBox.core.poi_fun.vertebra_pois_non_centroids import all_poi_functions
 
 poi_full = calc_poi_from_subreg_vert(
-    instance_nii, semantic_nii,
+    instance_nii,
+    semantic_nii,
     subreg_id=list(all_poi_functions.keys()),
 )
 # export as a 3D Slicer markup file
-poi_full.to_global().save_mrk(
-    "poi_as_markup.mrk.json",
-    split_by_region=True,
-    pointLabelsVisibility=True
-)
+poi_full.to_global().save_mrk("poi_as_markup.mrk.json", split_by_region=True, pointLabelsVisibility=True)
 ```
 
 
@@ -136,7 +133,4 @@ poi.save(poi_path)
 # Loading local/global Poi
 poi = POI.load(poi_path)
 poi = POI_Global.load(poi_path)
-
-
-
 ```

TPTBox/logger/README.md

@@ -38,7 +38,7 @@ from TPTBox import Logger, Print_Logger, No_Logger, String_Logger, Log_Type
 ## Example
 
 ```python
-logger.print() # logs/prints empty line
+logger.print()  # logs/prints empty line
 
 logger.print("Started logging to path: ./logs/test.log", lt.LOG)
 logger.print()
@@ -69,6 +69,7 @@ log.print("Missing T2w for sub-007", Log_Type.WARNING)
 
 # Suppress all output (e.g. in a library function)
 from TPTBox import No_Logger
+
 log = No_Logger()
 log.print("This is silently discarded")
 ```

TPTBox/registration/README.md

@@ -12,8 +12,8 @@ from TPTBox.registration import (
     ridged_points_from_subreg_vert,
     Deformable_Registration,
     Template_Registration,
-    General_Registration,          # requires hf-deepali
-    Rigid_Elements_Registration,   # requires hf-deepali
+    General_Registration,  # requires hf-deepali
+    Rigid_Elements_Registration,  # requires hf-deepali
 )
 ```
 
@@ -49,5 +49,4 @@ reg_obj = Point_Registration(poi_fixed, poi_moving)
 nii_moving = NII.load("path/to/moving_img.nii.gz", False)
 nii_moved = reg_obj.transform_nii(nii_moving)
 poi_moved = reg_obj.transform_poi(poi_moving)
-
 ```

TPTBox/spine/snapshot2D/README.md

@@ -43,38 +43,44 @@ poi = calc_poi_from_subreg_vert(vert, subreg)
 create_snapshot(
     out_path,
     [
-        Snapshot_Frame(img, vert, poi, sagittal=True, coronal=True,
-                    mode="CT"),
-        Snapshot_Frame(img, subreg, poi, sagittal=True, coronal=True,
-               axial=True, mode="CTs", axial_heights=[0.20, 0.4, 0.6, 0.8]),
+        Snapshot_Frame(img, vert, poi, sagittal=True, coronal=True, mode="CT"),
+        Snapshot_Frame(img, subreg, poi, sagittal=True, coronal=True, axial=True, mode="CTs", axial_heights=[0.20, 0.4, 0.6, 0.8]),
     ],
 )
 create_snapshot(
     out_path2,
     [
         Snapshot_Frame(
-            img, subreg, poi,
-            sagittal=True, coronal=True,
+            img,
+            subreg,
+            poi,
+            sagittal=True,
+            coronal=True,
             mode="MINMAX",
             only_mask_area=True,
             hide_segmentation=True,
         ),
         Snapshot_Frame(
-            img, subreg, poi,
-            sagittal=True, coronal=True,
+            img,
+            subreg,
+            poi,
+            sagittal=True,
+            coronal=True,
             mode="MINMAX",
             only_mask_area=True,
             visualization_type=Visualization_Type.Maximum_Intensity,
             hide_segmentation=True,
         ),
         Snapshot_Frame(
-            img, subreg, poi,
-            sagittal=True, coronal=True,
+            img,
+            subreg,
+            poi,
+            sagittal=True,
+            coronal=True,
             mode="MINMAX",
             visualization_type=Visualization_Type.Maximum_Intensity,
             hide_segmentation=True,
         ),
     ],
 )
-
 ```

TPTBox/spine/spinestats/README.md

@@ -350,9 +350,9 @@ collector = ExcelCollector(out_folder="/tmp/nako_summary")
 collector.start()
 for nako_id in ids:
     f = get_nako_paths(nako_id)
-    run_all(f)                       # writes the per-subject json
+    run_all(f)  # writes the per-subject json
     collector.submit(nako_id, _final_json_path(f))
-collector.close()                    # flushes and joins
+collector.close()  # flushes and joins
 ```
 
 The collector re-writes the Excel files every `flush_every` submissions

TPTBox/stitching/README.md

@@ -58,7 +58,11 @@ pip install TPTBox
 ```python
 from TPTBox.stitching import stitching
 
-list_of_files = ["File_A.nii.gz", "File_B.nii.gz", "File_C.nii.gz",]
+list_of_files = [
+    "File_A.nii.gz",
+    "File_B.nii.gz",
+    "File_C.nii.gz",
+]
 
 # Call the stitching function
 # This will combine your images into a single NIfTI file

docs/modules/stitching.md

@@ -58,15 +58,18 @@ pip install TPTBox
 ```python
 from TPTBox import NII
 from TPTBox.stitching import stitching
-out_nii,_ = stitching([NII.load("a.nii.gz",seg=False), NII.load("b.nii.gz",seg=False), NII.load("c.nii.gz",seg=False)], out="out.nii.gz")
 
+out_nii, _ = stitching(
+    [NII.load("a.nii.gz", seg=False), NII.load("b.nii.gz", seg=False), NII.load("c.nii.gz", seg=False)], out="out.nii.gz"
+)
 ```
 
 or
 
 
 ```python
 from TPTBox.stitching import stitching_raw
+
 stitching_raw(["a.nii.gz", "b.nii.gz", "c.nii.gz"], "out.nii.gz", is_segmentation=False)
 ```
 

unit_tests/test_compat.py

@@ -12,14 +12,14 @@
 class TestZipStrict(unittest.TestCase):
     def test_equal_length_lists(self):
         a = [1, 2, 3]
-        b = ['a', 'b', 'c']
-        expected = [(1, 'a'), (2, 'b'), (3, 'c')]
+        b = ["a", "b", "c"]
+        expected = [(1, "a"), (2, "b"), (3, "c")]
         result = list(zip_strict(a, b))
         self.assertEqual(result, expected)
 
     def test_unequal_length_lists(self):
         a = [1, 2, 3]
-        b = ['a', 'b']
+        b = ["a", "b"]
         with self.assertRaises(ValueError) as context:
             list(zip_strict(a, b))
         self.assertIn("Length mismatch", str(context.exception))
@@ -41,6 +41,6 @@ def test_multiple_iterables(self):
     def test_generator_iterables(self):
         a = (x for x in range(3))
         b = (chr(97 + x) for x in range(3))
-        expected = [(0, 'a'), (1, 'b'), (2, 'c')]
+        expected = [(0, "a"), (1, "b"), (2, "c")]
         result = list(zip_strict(a, b))
         self.assertEqual(result, expected)