wip fix: basedpyright errors

.gitea/workflows/ci.yml

@@ -17,11 +17,18 @@ jobs:
         with:
           python_version: "3.12"
 
-      - name: Format
+      - name: Activate environment
         run: |
           source .venv/bin/activate
+
+      - name: Format
+        run: |
           ruff format --check
 
+      - name: Type checking
+        run: |
+          basedpyright .
+
   test:
     runs-on: ubuntu-latest
     needs: "lint"

src/aarecommon/config/logger.py

@@ -3,6 +3,7 @@ import logging.config
 import os
 from pathlib import Path
 
+from aarecommon.types import JsonableDict
 import yaml
 
 
@@ -33,7 +34,7 @@ class IgnoreSuccessfulStatusAccessFilter(logging.Filter):
         )
 
 
-def get_uvicorn_logging_config() -> dict:
+def get_uvicorn_logging_config() -> JsonableDict:
     return {
         "version": 1,
         "disable_existing_loggers": False,
@@ -80,10 +81,12 @@ def get_config_path(env: str = "dev") -> Path:
     return config_path
 
 
-# TODO fix logging.
+_FALLBACK_BASE_DIR = "~/tmp/mxlogs/"
 def setup_logger(
-    name="aareDAQ", base_dir: str | None = f"~/tmp/mxlogs/", config_path: str | None = None
+    name="aareDAQ", base_dir: str | None = _FALLBACK_BASE_DIR, config_path: str | None = None
 ):
+    if base_dir is None:
+        base_dir = _FALLBACK_BASE_DIR
     # switch to production mode using: $ APP_ENV=prod python main.py
     env = os.getenv("APP_ENV", "dev")  # default: dev
 
@@ -139,7 +142,7 @@ def find_existing_formatter(
     return logging.Formatter(default_fmt, datefmt=default_datefmt)
 
 
-def attach_to_logger(logger_name: str = "", handler: logging.Handler = None):
+def attach_to_logger(logger_name: str, handler: logging.Handler):
     logging.getLogger(logger_name).addHandler(handler)
 
 

src/aarecommon/errors/exception_handler.py

@@ -10,19 +10,12 @@ logger = setup_logger("aareDAQ")
 
 
 class AareException(Exception):
-    """Root of the aare exception hierarchy.
+    """Root of the aare exception hierarchy."""
 
-    Class-level ``critical`` is the default; pass ``critical=...`` to the
-    constructor of an "optionally critical" subclass to override on a single
-    raise site.
-    """
-
-    critical: ClassVar[bool] = False
-
-    def __init__(self, *args, critical: bool | None = None, **kwargs):
-        super().__init__(*args, **kwargs)
-        if critical is not None:
-            self.critical = critical
+    def __init__(self, message: str, *args, critical: bool = False, **kwargs):
+        super().__init__(message, *args, **kwargs)
+        self.message=message
+        self.critical = critical
 
 
 class AutomationError(AareException):
@@ -76,23 +69,18 @@ class BeamlineStateException(AutomationError):
 
 
 class TransformationInvalidException(AutomationError):
-    critical: ClassVar[bool] = True
-
     def __init__(
-        self, message: str = "Transformation is not implemented", *, critical: bool | None = None
+        self, message: str = "Transformation is not implemented", *, critical: bool = True
     ):
         super().__init__(message, critical=critical)
-        self.message = message
 
     def __str__(self) -> str:
         return self.message
 
 
 class StateTransitionFailed(BeamlineStateException):
-    critical: ClassVar[bool] = True
-
     def __init__(
-        self, message: str = "Beamline state transition failed", *, critical: bool | None = None
+        self, message: str = "Beamline state transition failed", *, critical: bool=True
     ):
         super().__init__(message, critical=critical)
         self.message = message
@@ -102,13 +90,10 @@ class StateTransitionFailed(BeamlineStateException):
 
 
 class MaintenanceStateException(BeamlineStateException):
-    critical: ClassVar[bool] = True
-
     def __init__(
-        self, message: str = "Beamline is in Maintenance state", *, critical: bool | None = None
+        self, message: str = "Beamline is in Maintenance state", *, critical: bool = True
     ):
         super().__init__(message, critical=critical)
-        self.message = message
 
     def __str__(self) -> str:
         return self.message
@@ -209,13 +194,10 @@ class DoorSafetyError(AutomationError):
     critical so automation halts and the GUI shows a pop-up.
     """
 
-    critical: ClassVar[bool] = True
-
     def __init__(
-        self, message: str = "Door safety could not be activated", *, critical: bool | None = None
+        self, message: str = "Door safety could not be activated", *, critical: bool = True
     ):
         super().__init__(message, critical=critical)
-        self.message = message
 
     def __str__(self) -> str:
         return self.message
@@ -519,13 +501,10 @@ class AerotechCommunicationError(AerotechException):
 
 
 class MagnetPositionSensorErorr(AutomationError):
-    critical: ClassVar[bool] = True
-
     def __init__(
-        self, message: str = "Magnet position sensor error", *, critical: bool | None = None
+        self, message: str = "Magnet position sensor error", *, critical: bool = True
     ):
         super().__init__(message, critical=critical)
-        self.message = message
 
     def __str__(self) -> str:
         return self.message

src/aarecommon/math/find_xtal.py

@@ -540,7 +540,7 @@ def crystal_mask_kmeans(arr: np.ndarray, n_clusters: int = 3) -> tuple[np.ndarra
     return mask, threshold
 
 
-CRYSTAL_METHOD_MAP: dict = {
+CRYSTAL_METHOD_MAP: dict[str, tuple[str, Callable]] = {
     "corner": ("Corner background", crystal_mask_corner_background),
     "otsu": ("Otsu (nonzero)", crystal_mask_otsu_nonzero),
     "mean_sigma": ("Mean + 0.5σ", lambda arr: crystal_mask_mean_sigma(arr, n_sigma=0.5)),

tests/test_data_collection_parameters.py

@@ -50,7 +50,9 @@ def test_processingpipeline_accepts_unknown_value_after_refactor():
 
 def test_datacollectionparameters_accepts_legacy_aliases():
     params = DataCollectionParameters(
-        totalrange=180, cellparameters="10 20 30 90 90 120", userresolution=1.4
+        totalrange=180,
+        cellparameters="10 20 30 90 90 120",
+        userresolution=1.4,  # type: ignore # legacy
     )
     assert params.totalangle == 180
     assert params.unitcell == "10 20 30 90 90 120"

tests/test_find_xtal.py

@@ -102,6 +102,7 @@ def test_raster_centre_of_mass(mock_raster_results):
     arr = np.zeros((3, 3))
     arr[1, 1] = 10.0
     com = raster_centre_of_mass(arr, mock_raster_results)
+    assert com is not None
     assert com.n_x == 1.0
     assert com.n_y == 1.0
 
@@ -110,7 +111,7 @@ def test_has_sufficient_low_res_spots():
     arr = np.array([[1, 2], [3, 4]])
     assert has_sufficient_low_res_spots(arr, 3.0) is True
     assert has_sufficient_low_res_spots(arr, 5.0) is False
-    assert has_sufficient_low_res_spots(None, 1.0) is False
+    assert has_sufficient_low_res_spots(None, 1.0) is False  # type: ignore # expected wrong type
 
 
 @pytest.fixture
@@ -161,6 +162,7 @@ def test_compute_crystal_score_array_weights():
 
 def test_raster_highest_score(mock_score_results):
     com = raster_highest_score(mock_score_results)
+    assert com is not None
     assert com.n_x == 1.0
     assert com.n_y == 1.0
     assert com.max_image == 3

tests/test_models_extra.py

@@ -53,6 +53,7 @@ def test_sample_short_info_methods():
     }
     info2 = SampleShortInfo.from_dict(data)
     assert info2.db_id == 2
+    assert info2.location is not None
     assert info2.location.segment == "B"
     assert info2.aaredb_params is not None
     assert info2.aaredb_params.totalangle == 120
@@ -72,6 +73,7 @@ def test_ml_output_model_extra_methods():
     key = model.add_box(MLBoxType.CRYSTAL, (1, 2, 3, 4), 0.8)
 
     box_model = model.get_box_model(key)
+    assert box_model is not None
     assert box_model.conf == 0.8
 
     assert model.get_box_tuple(key) == (1, 2, 3, 4)
@@ -94,10 +96,10 @@ def test_ml_output_model_extra_methods():
     assert MLOutputModel.get_class_str(MLBoxType.LOOP_FACE) == "Loop_face"
     assert MLOutputModel.get_class_str(MLBoxType.ICE) == "Ice"
     assert MLOutputModel.get_class_str(MLBoxType.NEEDLE) == "Needle"
-    assert MLOutputModel.get_class_str(100) == "Unknown"
+    assert MLOutputModel.get_class_str(100) == "Unknown"  # type: ignore # Should be an unknown argument
 
 
 def test_beamline_state_enum_display_name():
     assert BeamlineStateEnum.SampleExchange.display_name() == "Sample exchange"
     assert BeamlineStateEnum.Moving.display_name() == "Moving"
-    assert BeamlineStateEnum.display_name(None) == "-"
+    assert BeamlineStateEnum.display_name(None) == "-"  # type: ignore # Should be an unknown argument