ci: tighten test selection and fix ruff findings

Author: Sam Porter

.github/workflows/tests.yml

@@ -28,7 +28,7 @@ jobs:
           ruff format --check .
       - name: Run CI-friendly tests
         run: |
-          python -m pytest tests/ -v -m "not requires_sirf and not requires_simind and not ci_skip" --cov=sirf_simind_connection --cov-report=xml
+          python -m pytest tests/ -v -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not requires_setr and not ci_skip" --cov=sirf_simind_connection --cov-report=xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
@@ -54,4 +54,4 @@ jobs:
           python -m build
       - name: Check package
         run: |
-          twine check dist/*
+          twine check dist/*

examples/04_custom_config.py

@@ -216,15 +216,19 @@ def main():
         "--backend",
         type=str,
         choices=["sirf", "stir"],
-        help="Force a specific backend (sirf or stir). If not specified, auto-detection is used.",
+        help=(
+            "Force a specific backend (sirf or stir). "
+            "If not specified, auto-detection is used."
+        ),
     )
     args = parser.parse_args()
 
     # Set backend if specified and backend layer is available.
     if args.backend:
         if set_backend is None:
             print(
-                f"Backend '{args.backend}' requested, but backend libraries are not installed."
+                f"Backend '{args.backend}' requested, "
+                "but backend libraries are not installed."
             )
         else:
             set_backend(args.backend)

examples/06_schneider_density_conversion.py

@@ -303,14 +303,20 @@ def create_ct_image_example(output_dir):
         "--backend",
         type=str,
         choices=["sirf", "stir"],
-        help="Force a specific backend (sirf or stir). Note: This example doesn't use backends but the argument is provided for consistency.",
+        help=(
+            "Force a specific backend (sirf or stir). "
+            "Note: This example doesn't use backends, but the argument is "
+            "provided for consistency."
+        ),
     )
     args = parser.parse_args()
 
-    # Note: This example doesn't actually use the backend, but we accept the argument for consistency
+    # This example does not use backend implementations directly, but accepts
+    # the argument for consistency with the rest of the examples.
     if args.backend:
         print(
-            f"Note: Backend argument '{args.backend}' specified but not used in this example."
+            f"Note: Backend argument '{args.backend}' "
+            "specified but not used in this example."
         )
 
     main()

examples/_python_connector_helpers.py

@@ -14,7 +14,8 @@
 def require_simind() -> None:
     if shutil.which("simind") is None:
         raise RuntimeError(
-            "SIMIND executable not found in PATH. Install SIMIND before running this example."
+            "SIMIND executable not found in PATH. "
+            "Install SIMIND before running this example."
         )
 
 

pyproject.toml

@@ -77,3 +77,6 @@ select = ["F", "E", "W", "I"]  # Include import sorting (I)
 force-single-line = false
 lines-after-imports = 2
 known-first-party = ["sirf_simind_connection"]
+
+[tool.ruff.lint.per-file-ignores]
+"sirf_simind_connection/configs/get_sirf_sinos.ipynb" = ["E501", "E722"]

pytest-ci.ini

@@ -18,7 +18,7 @@ addopts =
     -v
     --tb=short
     --strict-markers
-    -m "not requires_sirf and not requires_simind and not ci_skip"
+    -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not requires_setr and not ci_skip"
     --durations=10
 
 # Output
@@ -29,4 +29,4 @@ junit_family = xunit2
 # --cov=sirf_simind_connection
 # --cov-report=xml
 # --cov-report=html
-# --cov-report=term-missing
+# --cov-report=term-missing

sirf_simind_connection/backends/__init__.py

@@ -17,6 +17,7 @@
     set_backend("stir")  # Force STIR Python
 """
 
+import importlib
 import logging
 from typing import TYPE_CHECKING, Any, Literal, Optional, Union
 
@@ -141,14 +142,14 @@ def get_backend() -> str:
 
     # Auto-detect
     try:
-        import sirf.STIR
+        importlib.import_module("sirf.STIR")
 
         _backend = "sirf"
         logger.info("Auto-detected SIRF backend")
     except ImportError:
         try:
-            import stir
-            import stirextra
+            importlib.import_module("stir")
+            importlib.import_module("stirextra")
 
             _backend = "stir"
             logger.info("Auto-detected STIR Python backend")
@@ -182,13 +183,13 @@ def set_backend(backend: Literal["sirf", "stir"]) -> None:
     # Verify the backend is available
     if backend == "sirf":
         try:
-            import sirf.STIR
+            importlib.import_module("sirf.STIR")
         except ImportError:
             raise ImportError("SIRF is not available")
     elif backend == "stir":
         try:
-            import stir
-            import stirextra
+            importlib.import_module("stir")
+            importlib.import_module("stirextra")
         except ImportError:
             raise ImportError("STIR Python is not available")
 
@@ -355,7 +356,8 @@ def create_acquisition_data(
         if filepath_or_object is None:
             raise NotImplementedError(
                 "Creating empty STIR ProjData requires exam_info and proj_data_info. "
-                "Please provide a filepath or use StirAcquisitionData.create_empty() directly."
+                "Please provide a filepath or use "
+                "StirAcquisitionData.create_empty() directly."
             )
         elif isinstance(filepath_or_object, str):
             return StirAcquisitionData.read_from_file(filepath_or_object)

sirf_simind_connection/backends/base.py

@@ -12,7 +12,10 @@
 
 
 class ImageDataInterface(ABC):
-    """Abstract interface for image data objects (ImageData or FloatVoxelsOnCartesianGrid)."""
+    """Abstract interface for image data objects.
+
+    Includes SIRF ``ImageData`` and STIR ``FloatVoxelsOnCartesianGrid`` types.
+    """
 
     @classmethod
     @abstractmethod
@@ -123,7 +126,11 @@ def maximum(self, value: float) -> None:
     @property
     @abstractmethod
     def native_object(self):
-        """Get the underlying native object (ImageData or FloatVoxelsOnCartesianGrid)."""
+        """Get the underlying native object.
+
+        Returns either SIRF ``ImageData`` or STIR
+        ``FloatVoxelsOnCartesianGrid``.
+        """
         pass
 
     # Arithmetic operations

sirf_simind_connection/backends/sirf_backend.py

@@ -11,10 +11,10 @@
 
 from sirf_simind_connection.utils.import_helpers import get_sirf_types
 
+from .base import AcquisitionDataInterface, ImageDataInterface
 
-ImageData, AcquisitionData, SIRF_AVAILABLE = get_sirf_types()
 
-from .base import AcquisitionDataInterface, ImageDataInterface
+ImageData, AcquisitionData, SIRF_AVAILABLE = get_sirf_types()
 
 
 class SirfImageData(ImageDataInterface):
@@ -230,7 +230,8 @@ def get_energy_window_bounds(self) -> Tuple[float, float]:
             Tuple[float, float]: (lower_threshold, upper_threshold) in keV
 
         Raises:
-            NotImplementedError: SIRF backend does not currently support accessing energy window bounds
+            NotImplementedError: SIRF backend does not currently support
+                accessing energy window bounds.
         """
         raise NotImplementedError(
             "SIRF backend does not currently support accessing energy window bounds. "

sirf_simind_connection/builders/acquisition_builder.py

@@ -7,17 +7,15 @@
 import numpy as np
 import pydicom
 
+from sirf_simind_connection.utils.backend_access import BACKEND_AVAILABLE, BACKENDS
+
 # Conditional import for SIRF types
 from sirf_simind_connection.utils.import_helpers import get_sirf_types
+from sirf_simind_connection.utils.io_utils import temporary_directory
 
 
 _, AcquisitionData, SIRF_AVAILABLE = get_sirf_types()
 
-# Import backend factory using centralized access
-from sirf_simind_connection.utils.backend_access import BACKEND_AVAILABLE, BACKENDS
-from sirf_simind_connection.utils.io_utils import temporary_directory
-
-
 # Unpack interfaces needed by builder
 create_acquisition_data = BACKENDS.factories.create_acquisition_data
 
@@ -168,7 +166,8 @@ def _load_acquisition(self, header_path: str):
             return AcquisitionData(header_path)
 
         raise ImportError(
-            "Unable to load acquisition data: neither SIRF nor STIR Python backends are available."
+            "Unable to load acquisition data: neither SIRF nor STIR Python "
+            "backends are available."
         )
 
     @staticmethod