rename recipes now that approved (#483)

docs/source/api/snapred.backend.recipe.rst

@@ -20,18 +20,18 @@ snapred.backend.recipe.CrystallographicInfoRecipe module
    :undoc-members:
    :show-inheritance:
 
-snapred.backend.recipe.algorithm.PixelDiffractionCalibration module
+snapred.backend.recipe.PixelDiffCalRecipe module
 ---------------------------------------------------------------------
 
-.. automodule:: snapred.backend.recipe.algorithm.PixelDiffractionCalibration
+.. automodule:: snapred.backend.recipe.PixelDiffCalRecipe
    :members:
    :undoc-members:
    :show-inheritance:
 
-snapred.backend.recipe.algorithm.GroupDiffractionCalibration module
+snapred.backend.recipe.algorithm.GroupDiffCalRecipe module
 ---------------------------------------------------------------------
 
-.. automodule:: snapred.backend.recipe.algorithm.GroupDiffractionCalibration
+.. automodule:: snapred.backend.recipe.GroupDiffCalRecipe
    :members:
    :undoc-members:
    :show-inheritance:

src/snapred/backend/recipe/DiffractionCalibrationRecipe.py

@@ -2,8 +2,8 @@
 
 from snapred.backend.dao.ingredients import DiffractionCalibrationIngredients as Ingredients
 from snapred.backend.log.logger import snapredLogger
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe
 from snapred.meta.decorators.Singleton import Singleton
 
 logger = snapredLogger.getLogger(__name__)

src/snapred/backend/recipe/algorithm/GroupDiffractionCalibration.py → src/snapred/backend/recipe/GroupDiffCalRecipe.py

@@ -13,14 +13,6 @@
 logger = snapredLogger.getLogger(__name__)
 
 
-"""
-NOTE this file in fact defines a RECIPE.  It needs to be renamed to GroupDiffCalRecipe.py
-and moved into the recipe folder as soon as it has been reviewed.  It is being temporarily
-stored in the wrong location to make reviewing this story easier, to ensure nothing is
-missing from the former algorithm implementation.
-"""
-
-
 class GroupDiffCalServing(BaseModel):
     result: bool
     diagnosticWorkspace: str

src/snapred/backend/recipe/algorithm/PixelDiffractionCalibration.py → src/snapred/backend/recipe/PixelDiffCalRecipe.py

@@ -13,14 +13,6 @@
 logger = snapredLogger.getLogger(__name__)
 
 
-"""
-NOTE this file in fact defines a RECIPE.  It needs to be renamed to PixelDiffCalRecipe.py
-and moved into the recipe folder as soon as it has been reviewed.  It is being temporarily
-stored in the wrong location to make reviewing this story easier, to ensure nothing is
-missing from the former algorithm implementation.
-"""
-
-
 class PixelDiffCalServing(BaseModel):
     result: bool
     medianOffsets: List[float]

src/snapred/backend/recipe/algorithm/__init__.py

@@ -44,16 +44,6 @@ def loadModule(x):
         # but it also is dead code and never used
         continue
 
-    if x == "PixelDiffractionCalibration":
-        # this is actually a recipe being temporarily stored here
-        # move it to recipe folder and delete this once review passes
-        continue
-
-    if x == "GroupDiffractionCalibration":
-        # this is actually a recipe being temporarily stored here
-        # move it to recipe folder and delete this once review passes
-        continue
-
     loadModule(x)
 
 # cleanup

tests/cis_tests/artificial_norm_script.py

@@ -16,8 +16,8 @@
 from snapred.backend.data.GroceryService import GroceryService
 
 ## the code to test
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as PixelRx
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe as GroupRx
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as PixelRx
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe as GroupRx
 from snapred.backend.recipe.algorithm.CreateArtificialNormalizationAlgo import CreateArtificialNormalizationAlgo as FakeNormAlgo
 from snapred.backend.recipe.DiffractionCalibrationRecipe import DiffractionCalibrationRecipe as Recipe
 

tests/cis_tests/diffcal_integration_test_script.py

@@ -23,8 +23,8 @@
 from snapred.backend.data.GroceryService import GroceryService
 
 ## the code to test
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as PixelDiffCalRx
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe as GroupDiffCalRx
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as PixelDiffCalRx
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe as GroupDiffCalRx
 from snapred.backend.recipe.DiffractionCalibrationRecipe import DiffractionCalibrationRecipe as Recipe
 
 # for running through service layer

tests/cis_tests/diffcal_masking_script.py

@@ -14,8 +14,8 @@
 SNAPRed_module_root = Path(snapred.__file__).parent.parent
 
 
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as PixelRx
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe as GroupRx
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as PixelRx
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe as GroupRx
 from snapred.backend.recipe.DiffractionCalibrationRecipe import DiffractionCalibrationRecipe as Recipe
 from snapred.backend.dao.ingredients import DiffractionCalibrationIngredients
 from snapred.backend.service.CalibrationService import CalibrationService

tests/cis_tests/diffcal_pixel_diffraction_background_subtraction_script.py

@@ -15,7 +15,7 @@
 from snapred.backend.data.GroceryService import GroceryService
 
 ## the code to test
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as PixelRx
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as PixelRx
 from snapred.backend.recipe.DiffractionCalibrationRecipe import DiffractionCalibrationRecipe as Recipe
 
 # for running through service layer

tests/cis_tests/lazy_rebin_ragged.py

@@ -10,7 +10,7 @@
 from snapred.backend.dao.DetectorPeak import DetectorPeak
 from snapred.backend.dao.GroupPeakList import GroupPeakList
 from snapred.backend.dao.ingredients import DiffractionCalibrationIngredients
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe as GroupRx
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe as GroupRx
 
 # needed to make mocked ingredients
 from snapred.backend.dao.RunConfig import RunConfig

tests/cis_tests/new_diffcal_script.py

@@ -15,8 +15,8 @@
 from snapred.backend.data.GroceryService import GroceryService
 
 ## the code to test
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as PixelDiffCalRx
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import GroupDiffCalRecipe as GroupDiffCalRx
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as PixelDiffCalRx
+from snapred.backend.recipe.GroupDiffCalRecipe import GroupDiffCalRecipe as GroupDiffCalRx
 from snapred.backend.recipe.DiffractionCalibrationRecipe import DiffractionCalibrationRecipe as Recipe
 
 # for running through service layer

tests/unit/backend/recipe/algorithm/test_GroupDiffractionCalibration.py → tests/unit/backend/recipe/test_GroupDiffCalRecipe.py

@@ -9,7 +9,7 @@
 from snapred.backend.log.logger import snapredLogger
 
 # the algorithm to test
-from snapred.backend.recipe.algorithm.GroupDiffractionCalibration import (
+from snapred.backend.recipe.GroupDiffCalRecipe import (
     GroupDiffCalRecipe as Recipe,  # noqa: E402
 )
 from util.diffraction_calibration_synthetic_data import SyntheticData

tests/unit/backend/recipe/algorithm/test_PixelDiffractionCalibration.py → tests/unit/backend/recipe/test_PixelDiffCalRecipe.py

@@ -8,7 +8,7 @@
 
 # needed to make mocked ingredients
 # the algorithm to test
-from snapred.backend.recipe.algorithm.PixelDiffractionCalibration import PixelDiffCalRecipe as Recipe
+from snapred.backend.recipe.PixelDiffCalRecipe import PixelDiffCalRecipe as Recipe
 from snapred.meta.Config import Config
 from util.diffraction_calibration_synthetic_data import SyntheticData
 from util.helpers import maskSpectra, setSpectraToZero
@@ -22,7 +22,7 @@
 """
 
 
-class TestPixelDiffractionCalibration(unittest.TestCase):
+class TestPixelDiffCalRecipe(unittest.TestCase):
     def setUp(self):
         """Create a set of mocked ingredients for calculating DIFC corrected by offsets"""
         inputs = SyntheticData()