Address code issues raised by qlty

.github/workflows/check_pull_request_title.yml

@@ -1,8 +1,13 @@
-name: "Check PR title"
+name: Check PR title
+
 on:
   pull_request:
     types: [edited, opened, synchronize, reopened]
 
+permissions:
+  pull-requests: read
+  statuses: write         # Required to update commit status (e.g. pass/fail)
+
 jobs:
   pr-title-check:
     runs-on: ubuntu-latest
@@ -14,12 +19,22 @@ jobs:
 
       - uses: naveenk1223/action-pr-title@master
         with:
-          # Valid titles: "Do something"
+          # ^                       Start of string
+          # [A-Z]                   First character must be an uppercase ASCII letter
+          # [a-zA-Z]*               Followed by zero or more ASCII letters
+          # (?<![^s]s)              Negative lookbehind: disallow a single 's' at the end of the first word
+          # ( .+)+                  At least one space and one or more characters (requires more words)
+          # [^.]                    Final character must not be a period
+          # $                       End of string
+          regex: '^[A-Z][a-zA-Z]*(?<![^s]s)( .+)+[^.]$'
+          # Valid titles:
+          # - "Do something"
+          # - "Address something"
           # Invalid title:
           # - "do something"
           # - "Do something."
           # - "Does something"
           # - "Do"
-          regex: "^[A-Z][a-zA-Z]*(?<!s)( .+)+[^.]$" # Thanks, ChatGPT
+          # - "Addresses something"
           min_length: 10
           max_length: 72

.github/workflows/code_quality.yml

@@ -9,6 +9,10 @@ on:
   schedule:
     - cron: "0 4 * * *"
 
+permissions:
+  contents: read
+  statuses: write
+
 env:
   FORCE_COLOR: 1
 

.github/workflows/publish.yml

@@ -4,6 +4,9 @@ on:
   push:
   workflow_dispatch:
 
+permissions:
+  pull-requests: read
+
 jobs:
   build:
     name: Build the package

.github/workflows/tests.yml

@@ -9,6 +9,10 @@ on:
   schedule:
     - cron: "0 4 * * *"
 
+permissions:
+  contents: read
+  statuses: write
+
 env:
   FORCE_COLOR: 1
 

src/torchio/datasets/ixi.py

@@ -107,7 +107,7 @@ def _check_exists(root, modalities):
         return exists
 
     @staticmethod
-    def _get_subjects_list(root, modalities):
+    def _get_subjects_list(root: Path, modalities: Sequence[str]) -> list[Subject]:
         # The number of files for each modality is not the same
         # E.g. 581 for T1, 578 for T2
         # Let's just use the first modality as reference for now
@@ -137,7 +137,7 @@ def _get_subjects_list(root, modalities):
             subjects.append(Subject(**images_dict))
         return subjects
 
-    def _download(self, root, modalities):
+    def _download(self, root: Path, modalities: Sequence[str]) -> None:
         """Download the IXI data if it does not exist already."""
         for modality in modalities:
             modality_dir = root / modality
@@ -195,7 +195,7 @@ def __init__(
         super().__init__(subjects_list, transform=transform, **kwargs)
 
     @staticmethod
-    def _get_subjects_list(root):
+    def _get_subjects_list(root: Path) -> list[Subject]:
         image_paths = sglob(root / 'image', '*.nii.gz')
         label_paths = sglob(root / 'label', '*.nii.gz')
         if not (image_paths and label_paths):
@@ -214,7 +214,7 @@ def _get_subjects_list(root):
             subjects.append(Subject(**subject_dict))
         return subjects
 
-    def _download(self, root):
+    def _download(self, root: Path) -> None:
         """Download the tiny IXI data if it doesn't exist already."""
         if root.is_dir():  # assume it's been downloaded
             print('Root directory for IXITiny found:', root)  # noqa: T201
@@ -234,9 +234,9 @@ def _download(self, root):
         shutil.rmtree(ixi_tiny_dir)
 
 
-def sglob(directory, pattern):
-    return sorted(Path(directory).glob(pattern))
+def sglob(directory: Path, pattern: str) -> list[Path]:
+    return sorted(directory.glob(pattern))
 
 
-def get_subject_id(path):
+def get_subject_id(path: Path) -> str:
     return '-'.join(path.name.split('-')[:-1])

src/torchio/utils.py

@@ -25,6 +25,9 @@
 from .types import TypeNumber
 from .types import TypePath
 
+ITK_SNAP = 'ITK-SNAP'
+SLICER = 'Slicer'
+
 
 def to_tuple(
     value: Any,
@@ -344,44 +347,64 @@ def add_images_from_batch(
 def guess_external_viewer() -> Path | None:
     """Guess the path to an executable that could be used to visualize images.
 
-    Currently, it looks for 1) ITK-SNAP and 2) 3D Slicer. Implemented
-    for macOS and Windows.
+    It looks for 1) ITK-SNAP and 2) 3D Slicer.
     """
     if 'SITK_SHOW_COMMAND' in os.environ:
         return Path(os.environ['SITK_SHOW_COMMAND'])
-    platform = sys.platform
-    itk = 'ITK-SNAP'
-    slicer = 'Slicer'
-    if platform == 'darwin':
+
+    if (platform := sys.platform) == 'darwin':
+        return _guess_macos_viewer()
+    elif platform == 'win32':
+        return _guess_windows_viewer()
+    elif 'linux' in platform:
+        return _guess_linux_viewer()
+    else:
+        return None
+
+
+def _guess_macos_viewer() -> Path | None:
+    def _get_app_path(app_name: str) -> Path:
         app_path = '/Applications/{}.app/Contents/MacOS/{}'
-        itk_snap_path = Path(app_path.format(2 * (itk,)))
+        return Path(app_path.format(2 * (app_name,)))
+
+    if (itk_snap_path := _get_app_path(ITK_SNAP)).is_file():
+        return itk_snap_path
+    elif (slicer_path := _get_app_path(SLICER)).is_file():
+        return slicer_path
+    else:
+        return None
+
+
+def _guess_windows_viewer() -> Path | None:
+    def _get_app_path(app_dirs: list[Path], bin_name: str) -> Path:
+        app_dir = app_dirs[-1]
+        app_path = app_dir / bin_name
+        if app_path.is_file():
+            return app_path
+
+    program_files_dir = Path(os.environ['ProgramW6432'])
+    itk_snap_dirs = list(program_files_dir.glob(f'{ITK_SNAP}*'))
+    slicer_dirs = list(program_files_dir.glob(f'{SLICER}*'))
+
+    if itk_snap_dirs:
+        itk_snap_path = _get_app_path(itk_snap_dirs, 'bin/itk-snap.exe')
         if itk_snap_path.is_file():
             return itk_snap_path
-        slicer_path = Path(app_path.format(2 * (slicer,)))
+    elif slicer_dirs:
+        slicer_path = _get_app_path(slicer_dirs, 'slicer.exe')
         if slicer_path.is_file():
             return slicer_path
-    elif platform == 'win32':
-        program_files_dir = Path(os.environ['ProgramW6432'])
-        itk_snap_dirs = list(program_files_dir.glob('ITK-SNAP*'))
-        if itk_snap_dirs:
-            itk_snap_dir = itk_snap_dirs[-1]
-            itk_snap_path = itk_snap_dir / 'bin/itk-snap.exe'
-            if itk_snap_path.is_file():
-                return itk_snap_path
-        slicer_dirs = list(program_files_dir.glob('Slicer*'))
-        if slicer_dirs:
-            slicer_dir = slicer_dirs[-1]
-            slicer_path = slicer_dir / 'slicer.exe'
-            if slicer_path.is_file():
-                return slicer_path
-    elif 'linux' in platform:
-        itk_snap_which = shutil.which('itksnap')
-        if itk_snap_which is not None:
-            return Path(itk_snap_which)
-        slicer_which = shutil.which('Slicer')
-        if slicer_which is not None:
-            return Path(slicer_which)
-    return None  # for mypy
+    else:
+        return None
+
+
+def _guess_linux_viewer() -> Path | None:
+    if (itk_snap_which := shutil.which('itksnap')) is not None:
+        return Path(itk_snap_which)
+    elif (slicer_which := shutil.which('Slicer')) is not None:
+        return Path(slicer_which)
+    else:
+        return None
 
 
 def parse_spatial_shape(shape):