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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

@@ -8,10 +8,10 @@
 # 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.ArtificialNormalizationIngredients import ArtificialNormalizationIngredients
+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
 
 
@@ -64,12 +64,10 @@ 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/data/LocalDataService.py

@@ -644,14 +644,14 @@ def writeReductionData(self, record: ReductionRecord):
         Persists the reduction data associated with a `ReductionRecord`
         -- `writeReductionRecord` must have been called prior to this method.
         """
-        
+
         # Implementation notes:
         #
         # 1) For SNAPRed's current reduction-workflow output implementation:
         #
-        #      *`SaveNexusESS` _must_ be used, `SaveNexus` by itself won't work; 
+        #      *`SaveNexusESS` _must_ be used, `SaveNexus` by itself won't work;
         #
-        #      * ONLY a simplified instrument geometry can be saved, 
+        #      * ONLY a simplified instrument geometry can be saved,
         #        for example, as produced by `EditInstrumentGeometry`:
         #          this geometry includes no monitors, only a single non-nested detector bank, and no parameter map.
         #
@@ -660,7 +660,7 @@ def writeReductionData(self, record: ReductionRecord):
         #    Hopefully this will eventually be fixed, but right now this is a limitation of Mantid's
         #    instrument-I/O implementation (for non XML-based instruments).
         #
-        # 2) For SNAPRed internal use: 
+        # 2) For SNAPRed internal use:
         #        if `reduction.output.useEffectiveInstrument` is set to false in "application.yml",
         #    output workspaces will be saved without converting their instruments to the reduced form.
         #    This case is retained to allow some flexibility in what specifically is saved with the reduction data.
@@ -677,26 +677,25 @@ def writeReductionData(self, record: ReductionRecord):
             raise RuntimeError(f"reduction version directories {filePath.parent} do not exist")
 
         useEffectiveInstrument = Config["reduction.output.useEffectiveInstrument"]
-        
+
         for ws in record.workspaceNames:
             # Append workspaces to hdf5 file, in order of the `workspaces` list
-            
+
             if ws.tokens("workspaceType") == wngt.REDUCTION_PIXEL_MASK:
-
                 # The mask workspace always uses the non-reduced instrument.
                 self.mantidSnapper.SaveNexus(
                     f"Append workspace '{ws}' to reduction output",
                     InputWorkspace=ws,
                     Filename=str(filePath),
                     Append=True,
-                )                
+                )
                 self.mantidSnapper.executeQueue()
-                
+
                 # Write an additional copy of the combined pixel mask as a separate `SaveDiffCal`-format file
                 maskFilename = ws + ".h5"
                 self.writePixelMask(filePath.parent, Path(maskFilename), ws)
             else:
-                if useEffectiveInstrument:            
+                if useEffectiveInstrument:
                     self.mantidSnapper.SaveNexusESS(
                         f"Append workspace '{ws}' to reduction output",
                         InputWorkspace=ws,
@@ -709,9 +708,9 @@ def writeReductionData(self, record: ReductionRecord):
                         InputWorkspace=ws,
                         Filename=str(filePath),
                         Append=True,
-                    )            
+                    )
                 self.mantidSnapper.executeQueue()
-            
+
         # Append the "metadata" group, containing the `ReductionRecord` metadata
         with h5py.File(filePath, "a") as h5:
             n5m.insertMetadataGroup(h5, record.dict(), "/metadata")

src/snapred/backend/error/ContinueWarning.py

@@ -30,7 +30,7 @@ def flags(self):
         return self.model.flags
 
     def __init__(self, message: str, flags: "Type" = 0):
-        ContinueWarning.Model.model_rebuild(force=True) # replaces: `update_forward_refs` method
+        ContinueWarning.Model.model_rebuild(force=True)  # replaces: `update_forward_refs` method
         self.model = ContinueWarning.Model(message=message, flags=flags)
         super().__init__(message)
 

src/snapred/backend/error/RecoverableException.py

@@ -37,7 +37,7 @@ def data(self):
         return self.model.data
 
     def __init__(self, message: str, flags: "Type" = 0, data: Optional[Any] = None):
-        RecoverableException.Model.model_rebuild(force=True) # replaces: `update_forward_refs` method
+        RecoverableException.Model.model_rebuild(force=True)  # replaces: `update_forward_refs` method
         self.model = RecoverableException.Model(message=message, flags=flags, data=data)
         logger.error(f"{extractTrueStacktrace()}")
         super().__init__(message)

src/snapred/backend/recipe/EffectiveInstrumentRecipe.py

@@ -1,4 +1,5 @@
 from typing import Any, Dict, List, Tuple
+
 import numpy as np
 
 from snapred.backend.dao.ingredients import EffectiveInstrumentIngredients as Ingredients
@@ -11,14 +12,14 @@
 logger = snapredLogger.getLogger(__name__)
 
 Pallet = Tuple[Ingredients, Dict[str, str]]
-
+
+
 @Singleton
 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
 
@@ -30,9 +31,7 @@ def queueAlgos(self):
         # `EditInstrumentGeometry` modifies in-place, so we need to clone if a distinct output workspace is required.
         if self.outputWS != self.inputWS:
             self.mantidSnapper.CloneWorkspace(
-                "Clone workspace for reduced instrument",
-                OutputWorkspace=self.outputWS,
-                InputWorkspace=self.inputWS
+                "Clone workspace for reduced instrument", OutputWorkspace=self.outputWS, InputWorkspace=self.inputWS
             )
         self.mantidSnapper.EditInstrumentGeometry(
             f"Editing instrument geometry for grouping '{self.unmaskedPixelGroup.focusGroup.name}'",
@@ -42,7 +41,7 @@ def queueAlgos(self):
             Polar=np.rad2deg(self.unmaskedPixelGroup.twoTheta),
             Azimuthal=np.rad2deg(self.unmaskedPixelGroup.azimuth),
             #
-            InstrumentName=f"SNAP_{self.unmaskedPixelGroup.focusGroup.name}"
+            InstrumentName=f"SNAP_{self.unmaskedPixelGroup.focusGroup.name}",
         )
 
     def validateInputs(self, ingredients: Ingredients, groceries: Dict[str, WorkspaceName]):

src/snapred/backend/recipe/ReductionRecipe.py

@@ -3,15 +3,15 @@
 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.GenericRecipe import ArtificialNormalizationRecipe
 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.Config import Config
 from snapred.meta.mantid.WorkspaceNameGenerator import ValueFormatter as wnvf
 from snapred.meta.mantid.WorkspaceNameGenerator import WorkspaceNameGenerator as wng
-from snapred.meta.Config import Config
 
 logger = snapredLogger.getLogger(__name__)
 
@@ -283,7 +283,7 @@ 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 (
     ArtificialNormalizationIngredients,
@@ -308,7 +308,9 @@ 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:
@@ -387,7 +389,7 @@ def fetchReductionGroceries(self, request: ReductionRequest) -> Dict[str, Any]:
                         raise RuntimeError(
                             f"reduction pixel mask '{mask}' has unexpected workspace-type '{mask.tokens('workspaceType')}'"  # noqa: E501
                         )
-            if calVersion is not None: # WARNING: version may be _zero_!
+            if calVersion is not None:  # WARNING: version may be _zero_!
                 self.groceryClerk.name("diffcalMaskWorkspace").diffcal_mask(request.runNumber, calVersion).useLiteMode(
                     request.useLiteMode
                 ).add()
@@ -409,7 +411,7 @@ def fetchReductionGroceries(self, request: ReductionRequest) -> Dict[str, Any]:
                 request.useLiteMode
             ).add()
 
-        if normVersion is not None: # WARNING: version may be _zero_!
+        if normVersion is not None:  # WARNING: version may be _zero_!
             self.groceryClerk.name("normalizationWorkspace").normalization(request.runNumber, normVersion).useLiteMode(
                 request.useLiteMode
             ).add()

src/snapred/backend/service/SousChef.py

@@ -1,7 +1,7 @@
-from typing import Dict, List, Optional, Tuple
 import os
 from copy import deepcopy
 from pathlib import Path
+from typing import Dict, List, Optional, Tuple
 
 import pydantic
 
@@ -29,9 +29,9 @@
 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__)
 
@@ -95,7 +95,9 @@ 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:
@@ -108,10 +110,7 @@ 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(
@@ -122,7 +121,9 @@ def prepPixelGroup(self, ingredients: FarmFreshIngredients, pixelMask: Optional[
             )
         return deepcopy(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:
@@ -248,7 +249,9 @@ def _pullNormalizationRecordFFI(
         # TODO: Should smoothing parameter be an ingredient?
         return ingredients, smoothingParameter, calibrantSamplePath
 
-    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_)

src/snapred/resources/application.yml

@@ -101,7 +101,7 @@ reduction:
     extension: .nxs
     # convert the instrument for the output workspaces into the reduced form
     useEffectiveInstrument: true
-    
+
 mantid:
   workspace:
     nameTemplate:

tests/resources/application.yml

@@ -108,7 +108,7 @@ reduction:
     extension: .nxs
     # convert the instrument for the output workspaces into the reduced form
     useEffectiveInstrument: true
-    
+
 mantid:
     workspace:
       nameTemplate:

tests/unit/backend/data/test_DataFactoryService.py

@@ -1,7 +1,9 @@
 import hashlib
+import time
+import unittest
+import unittest.mock as mock
 from pathlib import Path
 from random import randint
-import time
 
 from mantid.simpleapi import CreateSingleValuedWorkspace, DeleteWorkspace, mtd
 from snapred.backend.dao.calibration import Calibration
@@ -13,8 +15,6 @@
 from snapred.backend.data.DataFactoryService import DataFactoryService
 from snapred.backend.data.LocalDataService import LocalDataService
 
-import unittest
-import unittest.mock as mock
 
 class TestDataFactoryService(unittest.TestCase):
     def expected(cls, *args):