PLA-13739 Update Cake demo to not have dimensionless absolute quantities (#203)

Author: kroenlein

gemd/demo/cake.py

@@ -647,7 +647,7 @@ def _make_material(*, material_name, template, process_tmpl_name, process_kwargs
         material=eggs,
         labels=['wet'],
         process=wetmix.process,
-        absolute_quantity=NominalReal(nominal=4, units='')
+        absolute_quantity=NominalReal(nominal=4, units='count')
     )
 
     vanilla = _make_material(

gemd/entity/object/has_quantities.py

@@ -1,4 +1,6 @@
 """For entities that hve quantities."""
+from sys import float_info
+
 from gemd.entity.bounds.real_bounds import RealBounds
 from gemd.entity.value.continuous_value import ContinuousValue
 from gemd.entity.value.base_value import BaseValue
@@ -50,7 +52,7 @@ def _check(value: BaseValue):
         level = get_validation_level()
         accept = level == WarningLevel.IGNORE or fraction_bounds.contains(value)
         if not accept:
-            message = f"Value {value} is not between 0 and 1."
+            message = f"Value {value} is not a dimensionless value between 0 and 1."
             if level == WarningLevel.WARNING:
                 logger.warning(message)
             else:
@@ -110,7 +112,29 @@ def absolute_quantity(self) -> ContinuousValue:
     def absolute_quantity(self, absolute_quantity: ContinuousValue):
         if absolute_quantity is None:
             self._absolute_quantity = None
-        elif isinstance(absolute_quantity, ContinuousValue):
-            self._absolute_quantity = absolute_quantity
-        else:
+        elif not isinstance(absolute_quantity, ContinuousValue):
             raise TypeError("absolute_quantity was not given as a continuous value")
+        else:
+            max_bounds = RealBounds(
+                lower_bound=0.0,
+                upper_bound=float_info.max,
+                default_units=absolute_quantity.units
+            )
+            dimensionless = RealBounds(
+                lower_bound=0.0,
+                upper_bound=float_info.max,
+                default_units=''
+            )
+            level = get_validation_level()
+            if level != WarningLevel.IGNORE:
+                messages = []
+                if not max_bounds.contains(absolute_quantity):
+                    messages.append(f"Value {absolute_quantity} is less than 0.0.")
+                if dimensionless.contains(absolute_quantity):
+                    messages.append(f"Value {absolute_quantity} is dimensionless.")
+                if level == WarningLevel.WARNING:
+                    for message in messages:
+                        logger.warning(message)
+                else:
+                    raise ValueError("; ".join(messages))
+            self._absolute_quantity = absolute_quantity

setup.py

@@ -4,7 +4,7 @@
 packages.append("")
 
 setup(name='gemd',
-      version='1.16.9',
+      version='1.17.0',
       python_requires='>=3.8',
       url='http://github.com/CitrineInformatics/gemd-python',
       description="Python binding for Citrine's GEMD data model",

tests/entity/object/test_ingredient_spec.py

@@ -33,13 +33,30 @@ def test_ingredient_reassignment():
     assert set(frying.ingredients) == {oil, potatoes}
 
 
+VALID_FRACTIONS = [
+    NominalReal(1.0, ''),
+    UniformReal(0.5, 0.6, ''),
+    NormalReal(0.2, 0.3, '')
+]
+
+INVALID_FRACTIONS = [
+    NominalReal(1.0, 'm'),
+    UniformReal(0.7, 1.1, ''),
+    NormalReal(-0.2, 0.3, '')
+]
+
 VALID_QUANTITIES = [
-    NominalReal(14.0, ''),
-    UniformReal(0.5, 0.6, 'm'),
-    NormalReal(-0.3, 0.6, "kg")
+    NominalReal(14.0, 'g'),
+    UniformReal(0.5, 0.6, 'mol'),
+    NormalReal(0.3, 0.6, 'cc')
 ]
 
 INVALID_QUANTITIES = [
+    NominalReal(14.0, ''),
+    UniformReal(-0.1, 0.3, 'mol'),
+]
+
+INVALID_TYPES = [
     NominalCategorical("blue"),
     NominalInteger(5),
     EmpiricalFormula("CH4"),
@@ -48,55 +65,79 @@ def test_ingredient_reassignment():
 ]
 
 
+@pytest.mark.parametrize("valid_fraction", VALID_FRACTIONS)
+def test_valid_fractions(valid_fraction, caplog):
+    """
+    Check that all fractional quantities must be continuous values.
+    """
+    with validation_level(WarningLevel.WARNING):
+        ingred = IngredientSpec(name="name", mass_fraction=valid_fraction)
+        assert ingred.mass_fraction == valid_fraction
+        ingred = IngredientSpec(name="name", volume_fraction=valid_fraction)
+        assert ingred.volume_fraction == valid_fraction
+        ingred = IngredientSpec(name="name", number_fraction=valid_fraction)
+        assert ingred.number_fraction == valid_fraction
+        assert ingred.absolute_quantity is None
+    assert len(caplog.records) == 0, "Warned on valid values with WARNING."
+
+
 @pytest.mark.parametrize("valid_quantity", VALID_QUANTITIES)
 def test_valid_quantities(valid_quantity, caplog):
     """
     Check that all quantities must be continuous values.
-
-    There are no restrictions on the value or the units. Although a volume fraction of -5 kg
-    does not make physical sense, it will not throw an error.
     """
-    with validation_level(WarningLevel.IGNORE):
-        ingred = IngredientSpec(name="name", mass_fraction=valid_quantity)
-        assert ingred.mass_fraction == valid_quantity
-        ingred = IngredientSpec(name="name", volume_fraction=valid_quantity)
-        assert ingred.volume_fraction == valid_quantity
-        ingred = IngredientSpec(name="name", number_fraction=valid_quantity)
-        assert ingred.number_fraction == valid_quantity
+    with validation_level(WarningLevel.WARNING):
         ingred = IngredientSpec(name="name", absolute_quantity=valid_quantity)
         assert ingred.absolute_quantity == valid_quantity
-    assert len(caplog.records) == 0, "Warned when validation set to IGNORE."
+        assert ingred.mass_fraction is None
+        assert ingred.number_fraction is None
+        assert ingred.volume_fraction is None
+    assert len(caplog.records) == 0, "Warned on valid values with WARNING."
 
 
-def test_validation_control(caplog):
-    """Verify that when validation is requested, limits are enforced."""
+@pytest.mark.parametrize("invalid_fraction", INVALID_FRACTIONS)
+def test_invalid_fractions(invalid_fraction, caplog):
+    """
+    Verify that when validation is requested, limits are enforced for fractions.
+    """
+    with validation_level(WarningLevel.IGNORE):
+        IngredientSpec(name="name", mass_fraction=invalid_fraction)
+    assert len(caplog.records) == 0, f"Warned on invalid values with IGNORE: {invalid_fraction}"
     with validation_level(WarningLevel.WARNING):
-        IngredientSpec(name="name", mass_fraction=NominalReal(0.5, ''))
-        assert len(caplog.records) == 0, "Warned on valid values with WARNING."
-        IngredientSpec(name="name", mass_fraction=NominalReal(5, ''))
-        assert len(caplog.records) == 1, "Didn't warn on invalid values with WARNING."
-        IngredientSpec(name="name", mass_fraction=NominalReal(0.5, 'm'))
-        assert len(caplog.records) == 2, "Didn't warn on invalid units with WARNING."
+        IngredientSpec(name="name", mass_fraction=invalid_fraction)
+    assert len(caplog.records) == 1, f"Didn't warn on invalid values with IGNORE: {invalid_fraction}"
     with validation_level(WarningLevel.FATAL):
-        # The following should not raise an exception
-        IngredientSpec(name="name", mass_fraction=NominalReal(0.5, ''))
-        with pytest.raises(ValueError):
-            IngredientSpec(name="name", mass_fraction=NominalReal(5, ''))
         with pytest.raises(ValueError):
-            IngredientSpec(name="name", mass_fraction=NominalReal(0.5, 'm'))
+            IngredientSpec(name="name", mass_fraction=invalid_fraction)
 
 
 @pytest.mark.parametrize("invalid_quantity", INVALID_QUANTITIES)
-def test_invalid_quantities(invalid_quantity):
+def test_invalid_quantities(invalid_quantity, caplog):
+    """
+    Verify that when validation is requested, limits are enforced for fractions.
+    """
+    with validation_level(WarningLevel.IGNORE):
+        IngredientSpec(name="name", absolute_quantity=invalid_quantity)
+    assert len(caplog.records) == 0, f"Warned on invalid values with IGNORE: {invalid_quantity}"
+    with validation_level(WarningLevel.WARNING):
+        IngredientSpec(name="name", absolute_quantity=invalid_quantity)
+    assert len(caplog.records) == 1, f"Didn't warn on invalid values with IGNORE: {invalid_quantity}"
+    with validation_level(WarningLevel.FATAL):
+        with pytest.raises(ValueError):
+            IngredientSpec(name="name", absolute_quantity=invalid_quantity)
+
+
+@pytest.mark.parametrize("invalid_type", INVALID_TYPES)
+def test_invalid_types(invalid_type):
     """Check that any non-continuous value for a quantity throws a TypeError."""
     with pytest.raises(TypeError):
-        IngredientSpec(name="name", mass_fraction=invalid_quantity)
+        IngredientSpec(name="name", mass_fraction=invalid_type)
     with pytest.raises(TypeError):
-        IngredientSpec(name="name", volume_fraction=invalid_quantity)
+        IngredientSpec(name="name", volume_fraction=invalid_type)
     with pytest.raises(TypeError):
-        IngredientSpec(name="name", number_fraction=invalid_quantity)
+        IngredientSpec(name="name", number_fraction=invalid_type)
     with pytest.raises(TypeError):
-        IngredientSpec(name="name", absolute_quantity=invalid_quantity)
+        IngredientSpec(name="name", absolute_quantity=invalid_type)
 
 
 def test_invalid_assignment():