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src/snapred/backend/dao/ingredients/EffectiveInstrumentIngredients.py

@@ -4,7 +4,6 @@
 
 
 class EffectiveInstrumentIngredients(BaseModel):
-
     unmaskedPixelGroup: PixelGroup
 
     model_config = ConfigDict(

src/snapred/backend/dao/ingredients/ReductionIngredients.py

@@ -6,12 +6,11 @@
 
 # These are from the same `__init__` module, so for the moment, we require the full import specifications.
 # (That is, not just "from snapred.backend.dao.ingredients import ...".)
-
 from snapred.backend.dao.ingredients.ApplyNormalizationIngredients import ApplyNormalizationIngredients
+from snapred.backend.dao.ingredients.EffectiveInstrumentIngredients import EffectiveInstrumentIngredients
 from snapred.backend.dao.ingredients.GenerateFocussedVanadiumIngredients import GenerateFocussedVanadiumIngredients
 from snapred.backend.dao.ingredients.PreprocessReductionIngredients import PreprocessReductionIngredients
 from snapred.backend.dao.ingredients.ReductionGroupProcessingIngredients import ReductionGroupProcessingIngredients
-from snapred.backend.dao.ingredients.EffectiveInstrumentIngredients import EffectiveInstrumentIngredients
 from snapred.backend.dao.state.PixelGroup import PixelGroup
 
 
@@ -61,12 +60,10 @@ def applyNormalization(self, groupingIndex: int) -> ApplyNormalizationIngredient
         return ApplyNormalizationIngredients(
             pixelGroup=self.pixelGroups[groupingIndex],
         )
-    
+
     def effectiveInstrument(self, groupingIndex: int) -> EffectiveInstrumentIngredients:
-        return EffectiveInstrumentIngredients(
-            unmaskedPixelGroup=self.unmaskedPixelGroups[groupingIndex]
-        )
-
+        return EffectiveInstrumentIngredients(unmaskedPixelGroup=self.unmaskedPixelGroups[groupingIndex])
+
     model_config = ConfigDict(
         extra="forbid",
     )

src/snapred/backend/recipe/EffectiveInstrumentRecipe.py

@@ -17,7 +17,7 @@ class EffectiveInstrumentRecipe(Recipe[Ingredients]):
     def unbagGroceries(self, groceries: Dict[str, Any]):
         self.inputWS = groceries["inputWorkspace"]
         self.outputWS = groceries.get("outputWorkspace", groceries["inputWorkspace"])
- 
+
     def chopIngredients(self, ingredients):
         self.unmaskedPixelGroup = ingredients.unmaskedPixelGroup
 
@@ -32,7 +32,7 @@ def queueAlgos(self):
             L2=self.unmaskedPixelGroup.L2,
             Polar=self.unmaskedPixelGroup.twoTheta,
             Azimuthal=self.unmaskedPixelGroup.azimuth,
-            InstrumentName=f"SNAP_{self.unmaskedPixelGroup.focusGroup.name}"
+            InstrumentName=f"SNAP_{self.unmaskedPixelGroup.focusGroup.name}",
         )
         self.outputWS = self.inputWS
 

src/snapred/backend/recipe/ReductionRecipe.py

@@ -3,9 +3,9 @@
 from snapred.backend.dao.ingredients import ReductionIngredients as Ingredients
 from snapred.backend.log.logger import snapredLogger
 from snapred.backend.recipe.ApplyNormalizationRecipe import ApplyNormalizationRecipe
+from snapred.backend.recipe.EffectiveInstrumentRecipe import EffectiveInstrumentRecipe
 from snapred.backend.recipe.GenerateFocussedVanadiumRecipe import GenerateFocussedVanadiumRecipe
 from snapred.backend.recipe.PreprocessReductionRecipe import PreprocessReductionRecipe
-from snapred.backend.recipe.EffectiveInstrumentRecipe import EffectiveInstrumentRecipe
 from snapred.backend.recipe.Recipe import Recipe, WorkspaceName
 from snapred.backend.recipe.ReductionGroupProcessingRecipe import ReductionGroupProcessingRecipe
 from snapred.meta.mantid.WorkspaceNameGenerator import ValueFormatter as wnvf
@@ -213,7 +213,7 @@ def execute(self):
                 self.ingredients.effectiveInstrument(groupingIndex),
                 inputWorkspace=sampleClone,
             )
-            
+
             # Cleanup
             outputs.append(sampleClone)
 

src/snapred/backend/service/ReductionService.py

@@ -1,7 +1,7 @@
-from typing import Any, Dict, List, Optional
 import json
 from collections.abc import Iterable
 from pathlib import Path
+from typing import Any, Dict, List, Optional
 
 from snapred.backend.dao.ingredients import GroceryListItem, ReductionIngredients
 from snapred.backend.dao.reduction.ReductionRecord import ReductionRecord
@@ -257,7 +257,9 @@ def prepCombinedMask(
         return combinedMask
 
     @FromString
-    def prepReductionIngredients(self, request: ReductionRequest, combinedPixelMask: Optional[WorkspaceName] = None) -> ReductionIngredients:
+    def prepReductionIngredients(
+        self, request: ReductionRequest, combinedPixelMask: Optional[WorkspaceName] = None
+    ) -> ReductionIngredients:
         """
         Prepare the needed ingredients for calculating reduction.
         Requires:

src/snapred/backend/service/SousChef.py

@@ -1,6 +1,6 @@
-from typing import Dict, List, Optional, Tuple
 import os
 from pathlib import Path
+from typing import Dict, List, Optional, Tuple
 
 import pydantic
 
@@ -28,9 +28,9 @@
 from snapred.backend.recipe.PixelGroupingParametersCalculationRecipe import PixelGroupingParametersCalculationRecipe
 from snapred.backend.service.CrystallographicInfoService import CrystallographicInfoService
 from snapred.backend.service.Service import Service
-from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceName
 from snapred.meta.Config import Config
 from snapred.meta.decorators.Singleton import Singleton
+from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceName
 
 logger = snapredLogger.getLogger(__name__)
 
@@ -94,7 +94,9 @@ def prepFocusGroup(self, ingredients: FarmFreshIngredients) -> FocusGroup:
             groupingMap = self.dataFactoryService.getGroupingMap(ingredients.runNumber)
             return groupingMap.getMap(ingredients.useLiteMode)[ingredients.focusGroup.name]
 
-    def prepPixelGroup(self, ingredients: FarmFreshIngredients, pixelMask: Optional[WorkspaceName] = None) -> PixelGroup:
+    def prepPixelGroup(
+        self, ingredients: FarmFreshIngredients, pixelMask: Optional[WorkspaceName] = None
+    ) -> PixelGroup:
         groupingSchema = ingredients.focusGroup.name
         key = (ingredients.runNumber, ingredients.useLiteMode, groupingSchema, pixelMask)
         if key not in self._pixelGroupCache:
@@ -107,10 +109,7 @@ def prepPixelGroup(self, ingredients: FarmFreshIngredients, pixelMask: Optional[
             self.groceryClerk.name("groupingWorkspace").fromRun(ingredients.runNumber).grouping(
                 focusGroup.name
             ).useLiteMode(ingredients.useLiteMode).add()
-            groceries = self.groceryService.fetchGroceryDict(
-                self.groceryClerk.buildDict(),
-                maskWorkspace=pixelMask
-            )
+            groceries = self.groceryService.fetchGroceryDict(self.groceryClerk.buildDict(), maskWorkspace=pixelMask)
             data = PixelGroupingParametersCalculationRecipe().executeRecipe(pixelIngredients, groceries)
 
             self._pixelGroupCache[key] = PixelGroup(
@@ -121,7 +120,9 @@ def prepPixelGroup(self, ingredients: FarmFreshIngredients, pixelMask: Optional[
             )
         return self._pixelGroupCache[key]
 
-    def prepManyPixelGroups(self, ingredients: FarmFreshIngredients, pixelMask: Optional[WorkspaceName] = None) -> List[PixelGroup]:
+    def prepManyPixelGroups(
+        self, ingredients: FarmFreshIngredients, pixelMask: Optional[WorkspaceName] = None
+    ) -> List[PixelGroup]:
         pixelGroups = []
         ingredients_ = ingredients.model_copy()
         for focusGroup in ingredients.focusGroups:
@@ -242,7 +243,9 @@ def _pullNormalizationRecordFFI(
             smoothingParameter = normalizationRecord.smoothingParameter
         return ingredients, smoothingParameter
 
-    def prepReductionIngredients(self, ingredients: FarmFreshIngredients, combinedPixelMask: Optional[WorkspaceName] = None) -> ReductionIngredients:
+    def prepReductionIngredients(
+        self, ingredients: FarmFreshIngredients, combinedPixelMask: Optional[WorkspaceName] = None
+    ) -> ReductionIngredients:
         ingredients_ = ingredients.model_copy()
         # some of the reduction ingredients MUST match those used in the calibration/normalization processes
         ingredients_ = self._pullCalibrationRecordFFI(ingredients_)

tests/unit/backend/recipe/test_EffectiveInstrumentRecipe.py

@@ -1,13 +1,14 @@
-from snapred.backend.recipe.algorithm.Utensils import Utensils
-from snapred.backend.recipe.EffectiveInstrumentRecipe import EffectiveInstrumentRecipe
+from unittest import mock
+
+import pytest
 from snapred.backend.dao.ingredients import EffectiveInstrumentIngredients as Ingredients
 from snapred.backend.dao.state.FocusGroup import FocusGroup
 from snapred.backend.dao.state.PixelGroup import PixelGroup
+from snapred.backend.recipe.algorithm.Utensils import Utensils
+from snapred.backend.recipe.EffectiveInstrumentRecipe import EffectiveInstrumentRecipe
 from snapred.meta.Config import Resource
 from util.SculleryBoy import SculleryBoy
 
-from unittest import mock
-import pytest
 
 class TestEffectiveInstrumentRecipe:
     fakeInstrumentFilePath = Resource.getPath("inputs/testInstrument/fakeSNAP_Definition.xml")
@@ -22,11 +23,8 @@ def setup(self):
                 L2=mock.Mock(),
                 twoTheta=mock.Mock(),
                 azimuth=mock.Mock(),
-                focusGroup=FocusGroup(
-                    name="a_grouping",
-                    definition="a/grouping/path"
-                )
-            )
+                focusGroup=FocusGroup(name="a_grouping", definition="a/grouping/path"),
+            ),
         )
         self.ingredients1 = mock.Mock(
             spec=Ingredients,
@@ -35,20 +33,16 @@ def setup(self):
                 L2=mock.Mock(),
                 twoTheta=mock.Mock(),
                 azimuth=mock.Mock(),
-                focusGroup=FocusGroup(
-                    name="another_grouping",
-                    definition="another/grouping/path"
-                )
-            )
+                focusGroup=FocusGroup(name="another_grouping", definition="another/grouping/path"),
+            ),
         )
         self.ingredientss = [self.ingredients, self.ingredients1]
-
-
+
         yield
-        
+
         # teardown follows ...
         pass
-        
+
     def test_chopIngredients(self):
         recipe = EffectiveInstrumentRecipe()
         ingredients = self.ingredients
@@ -78,7 +72,7 @@ def test_queueAlgos(self):
 
         queuedAlgos = recipe.mantidSnapper._algorithmQueue
         editInstrumentGeometryTuple = queuedAlgos[0]
- 
+
         assert editInstrumentGeometryTuple[0] == "EditInstrumentGeometry"
         assert editInstrumentGeometryTuple[2]["Workspace"] == groceries["inputWorkspace"]
 
@@ -101,7 +95,7 @@ def test_cook(self):
             L2=ingredients.unmaskedPixelGroup.L2,
             Polar=ingredients.unmaskedPixelGroup.twoTheta,
             Azimuthal=ingredients.unmaskedPixelGroup.azimuth,
-            InstrumentName=f"SNAP_{ingredients.unmaskedPixelGroup.focusGroup.name}"
+            InstrumentName=f"SNAP_{ingredients.unmaskedPixelGroup.focusGroup.name}",
         )
 
     def test_cater(self):
@@ -110,7 +104,7 @@ def test_cater(self):
         untensils.mantidSnapper = mockSnapper
         recipe = EffectiveInstrumentRecipe(utensils=untensils)
         ingredientss = self.ingredientss
-        
+
         groceriess = [{"inputWorkspace": mock.Mock()}, {"inputWorkspace": mock.Mock()}]
 
         output = recipe.cater(zip(ingredientss, groceriess))
@@ -122,14 +116,13 @@ def test_cater(self):
             L2=ingredientss[0].unmaskedPixelGroup.L2,
             Polar=ingredientss[0].unmaskedPixelGroup.twoTheta,
             Azimuthal=ingredientss[0].unmaskedPixelGroup.azimuth,
-            InstrumentName=f"SNAP_{ingredientss[0].unmaskedPixelGroup.focusGroup.name}"
+            InstrumentName=f"SNAP_{ingredientss[0].unmaskedPixelGroup.focusGroup.name}",
         )
         mockSnapper.EditInstrumentGeometry.assert_any_call(
             f"Editing instrument geometry for grouping '{ingredientss[1].unmaskedPixelGroup.focusGroup.name}'",
             Workspace=groceriess[1]["inputWorkspace"],
             L2=ingredientss[1].unmaskedPixelGroup.L2,
             Polar=ingredientss[1].unmaskedPixelGroup.twoTheta,
             Azimuthal=ingredientss[1].unmaskedPixelGroup.azimuth,
-            InstrumentName=f"SNAP_{ingredientss[1].unmaskedPixelGroup.focusGroup.name}"
+            InstrumentName=f"SNAP_{ingredientss[1].unmaskedPixelGroup.focusGroup.name}",
         )
-

tests/unit/backend/recipe/test_PreprocessReductionRecipe.py

@@ -1,17 +1,18 @@
+import unittest
+
 from mantid.simpleapi import (
     CreateEmptyTableWorkspace,
     CreateSampleWorkspace,
     LoadInstrument,
     mtd,
 )
+from snapred.backend.dao.ingredients import PreprocessReductionIngredients as Ingredients
 from snapred.backend.recipe.algorithm.Utensils import Utensils
 from snapred.backend.recipe.PreprocessReductionRecipe import PreprocessReductionRecipe
-from snapred.backend.dao.ingredients import PreprocessReductionIngredients as Ingredients
 from snapred.meta.Config import Resource
 from util.helpers import createCompatibleMask
 from util.SculleryBoy import SculleryBoy
 
-import unittest
 
 class PreprocessReductionRecipeTest(unittest.TestCase):
     fakeInstrumentFilePath = Resource.getPath("inputs/testInstrument/fakeSNAP_Definition.xml")

tests/unit/backend/recipe/test_ReductionRecipe.py

@@ -1,5 +1,7 @@
 import time
+from unittest import TestCase, mock
 
+import pytest
 from mantid.simpleapi import CreateSingleValuedWorkspace, mtd
 from snapred.backend.dao.ingredients import ReductionIngredients
 from snapred.backend.recipe.ReductionRecipe import (
@@ -13,8 +15,6 @@
 from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceNameGenerator as wng
 from util.SculleryBoy import SculleryBoy
 
-from unittest import TestCase, mock
-import pytest
 
 class ReductionRecipeTest(TestCase):
     sculleryBoy = SculleryBoy()

tests/unit/backend/service/test_SousChef.py

@@ -194,7 +194,12 @@ def test_prepPixelGroup_nocache(
 
     @mock.patch(thisService + "PixelGroupingParametersCalculationRecipe")
     def test_prepPixelGroup_cache(self, PixelGroupingParametersCalculationRecipe):
-        key = (self.ingredients.runNumber, self.ingredients.useLiteMode, self.ingredients.focusGroup.name, self.pixelMask)
+        key = (
+            self.ingredients.runNumber,
+            self.ingredients.useLiteMode,
+            self.ingredients.focusGroup.name,
+            self.pixelMask,
+        )
         # ensure the cache is prepared
         self.instance._pixelGroupCache[key] = mock.Mock()
 
@@ -396,14 +401,14 @@ def test_prepReductionIngredients(self, ReductionIngredients):
         ingredients_.peakIntensityThreshold = self.instance._getThresholdFromCalibrantSample(
             "calibrationCalibrantSamplePath"
         )
-        
+
         combinedMask = mock.Mock()
         result = self.instance.prepReductionIngredients(ingredients_, combinedMask)
 
         assert self.instance.prepManyPixelGroups.call_count == 2
         self.instance.prepManyPixelGroups.assert_any_call(ingredients_)
         self.instance.prepManyPixelGroups.assert_any_call(ingredients_, combinedMask)
-        
+
         self.instance.dataFactoryService.getCifFilePath.assert_called_once_with("sample")
         ReductionIngredients.assert_called_once_with(
             runNumber=ingredients_.runNumber,

tests/util/SculleryBoy.py

@@ -15,8 +15,8 @@
 from snapred.backend.dao.state.PixelGroup import PixelGroup
 from snapred.backend.dao.state.PixelGroupingParameters import PixelGroupingParameters
 from snapred.backend.recipe.GenericRecipe import DetectorPeakPredictorRecipe
-from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceName
 from snapred.meta.Config import Resource
+from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceName
 from snapred.meta.redantic import parse_file_as
 from util.dao import DAOFactory
 
@@ -92,7 +92,9 @@ def prepDetectorPeaks(self, ingredients: FarmFreshIngredients, purgePeaks=False)
         except (TypeError, AttributeError):
             return [mock.Mock(spec_set=GroupPeakList)]
 
-    def prepReductionIngredients(self, ingredients: FarmFreshIngredients, combinedPixelMask: Optional[WorkspaceName] = None):  # noqa ARG002
+    def prepReductionIngredients(
+        self, ingredients: FarmFreshIngredients, combinedPixelMask: Optional[WorkspaceName] = None
+    ):  # noqa ARG002
         path = Resource.getPath("/inputs/calibration/ReductionIngredients.json")
         return parse_file_as(ReductionIngredients, path)