Added testing for PhysicalProperty

src/nomad_simulations/physical_property.py

@@ -16,8 +16,9 @@
 # limitations under the License.
 #
 
-from typing import Any
+from typing import Any, Optional
 
+from nomad import utils
 from nomad.datamodel.data import ArchiveSection
 from nomad.metainfo import (
     Quantity,
@@ -35,6 +36,10 @@
 from .numerical_settings import SelfConsistency
 
 
+# We add `logger` for the `PhysicalProperty.variables_shape` method
+logger = utils.get_logger(__name__)
+
+
 class PhysicalProperty(ArchiveSection):
     """
     A base section used to define the physical properties obtained in a simulation, experiment, or in a post-processing
@@ -133,7 +138,7 @@ class PhysicalProperty(ArchiveSection):
     )
 
     @property
-    def get_variables_shape(self) -> list:
+    def variables_shape(self) -> Optional[list]:
         """
         Shape of the variables over which the physical property varies. This is extracted from
         `Variables.n_grid_points` and appended in a list.
@@ -144,15 +149,17 @@ def get_variables_shape(self) -> list:
         Returns:
             (list): The shape of the variables over which the physical property varies.
         """
-        return [v.n_grid_points for v in self.variables]
+        if self.variables is not None:
+            return [v.get_n_grid_points(v.grid_points, logger) for v in self.variables]
+        return []
 
     @property
-    def get_full_shape(self) -> list:
+    def full_shape(self) -> list:
         """
         Full shape of the physical property. This quantity is calculated as:
             `full_shape = variables_shape + shape`
         where `shape` is passed as an attribute of the `PhysicalProperty` and is related with the order of
-        the tensor of `value`, and `variables_shape` is obtained from `get_variables_shape` and is
+        the tensor of `value`, and `variables_shape` is obtained from `variables_shape` and is
         related with the shapes of the `variables` over which the physical property varies.
 
         Example: a physical property which is a 3D vector and varies with `variables=[Temperature, ElectricField]`
@@ -162,7 +169,7 @@ def get_full_shape(self) -> list:
         Returns:
             (list): The full shape of the physical property.
         """
-        return self.get_variables_shape + self.shape
+        return self.variables_shape + self.shape
 
     def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
         super().__init__(m_def, m_context, **kwargs)
@@ -182,21 +189,18 @@ def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
     def __setattr__(self, name: str, val: Any) -> None:
         # For the special case of `value`, its `shape` needs to be defined from `_full_shape`
         if name == 'value':
-            # * This setattr logic for `value` only works if `variables` and `shape` have been stored BEFORE the `value` is set
-            _full_shape = self.get_full_shape
-
             # non-scalar or scalar `val`
             try:
                 value_shape = list(val.shape)
             except AttributeError:
                 value_shape = []
 
-            if value_shape != _full_shape:
+            if value_shape != self.full_shape:
                 raise ValueError(
-                    f'The shape of the stored `value` {value_shape} does not match the full shape {_full_shape} '
+                    f'The shape of the stored `value` {value_shape} does not match the full shape {self.full_shape} '
                     f'extracted from the variables `n_grid_points` and the `shape` defined in `PhysicalProperty`.'
                 )
-            self._new_value.shape = _full_shape
+            self._new_value.shape = self.full_shape
             self._new_value = val.magnitude * val.u
             return super().__setattr__(name, self._new_value)
         return super().__setattr__(name, val)

tests/conftest.py

@@ -1,3 +1,21 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 import os
 import pytest
 

tests/test_physical_properties.py

@@ -0,0 +1,143 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+import pytest
+
+from . import logger
+
+from nomad.units import ureg
+from nomad.metainfo import Quantity
+
+from nomad_simulations.variables import Variables
+from nomad_simulations.physical_property import PhysicalProperty
+
+
+class DummyPhysicalProperty(PhysicalProperty):
+    value = Quantity(
+        type=np.float64,
+        unit='eV',
+        description="""
+        This value is defined in order to test the `__setattr__` method in `PhysicalProperty`.
+        """,
+    )
+
+
+class TestPhysicalProperty:
+    """
+    Test the `PhysicalProperty` class defined in `physical_property.py`.
+    """
+
+    @pytest.mark.parametrize(
+        'shape, variables, result_variables_shape, result_full_shape',
+        [
+            ([], [], [], []),
+            ([3], [], [], [3]),
+            ([3, 3], [], [], [3, 3]),
+            ([], [Variables(n_grid_points=4)], [4], [4]),
+            ([3], [Variables(n_grid_points=4)], [4], [4, 3]),
+            ([3, 3], [Variables(n_grid_points=4)], [4], [4, 3, 3]),
+            (
+                [],
+                [Variables(n_grid_points=4), Variables(n_grid_points=10)],
+                [4, 10],
+                [4, 10],
+            ),
+            (
+                [3],
+                [Variables(n_grid_points=4), Variables(n_grid_points=10)],
+                [4, 10],
+                [4, 10, 3],
+            ),
+            (
+                [3, 3],
+                [Variables(n_grid_points=4), Variables(n_grid_points=10)],
+                [4, 10],
+                [4, 10, 3, 3],
+            ),
+        ],
+    )
+    def test_static_properties(
+        self,
+        shape: list,
+        variables: list,
+        result_variables_shape: list,
+        result_full_shape: list,
+    ):
+        """
+        Test the static properties of the `PhysicalProperty` class, `variables_shape` and `full_shape`.
+        """
+        physical_property = PhysicalProperty(
+            source='simulation',
+            shape=shape,
+            variables=variables,
+        )
+        assert physical_property.variables_shape == result_variables_shape
+        assert physical_property.full_shape == result_full_shape
+
+    def test_setattr_value(self):
+        """
+        Test the `__setattr__` method when setting the `value` quantity of a physical property.
+        """
+        physical_property = DummyPhysicalProperty(
+            source='simulation',
+            shape=[3, 3],
+            variables=[Variables(n_grid_points=4), Variables(n_grid_points=10)],
+        )
+        # `physical_property.value` must have full_shape=[4, 10, 3, 3]
+        value = np.ones((4, 10, 3, 3)) * ureg.eV
+        assert physical_property.full_shape == list(value.shape)
+        physical_property.value = value
+        assert np.all(physical_property.value == value)
+
+    def test_setattr_value_wrong_shape(self):
+        """
+        Test the `__setattr__` method when the `value` has a wrong shape.
+        """
+        physical_property = PhysicalProperty(
+            source='simulation',
+            shape=[],
+            variables=[],
+        )
+        # `physical_property.value` must have shape=[]
+        value = np.ones((3, 3))
+        wrong_shape = list(value.shape)
+        with pytest.raises(ValueError) as exc_info:
+            physical_property.value = value
+        assert (
+            str(exc_info.value)
+            == f'The shape of the stored `value` {wrong_shape} does not match the full shape {physical_property.full_shape} extracted from the variables `n_grid_points` and the `shape` defined in `PhysicalProperty`.'
+        )
+
+    def test_is_derived(self):
+        """
+        Test the `normalize` and `_is_derived` methods.
+        """
+        # Testing a directly parsed physical property
+        not_derived_physical_property = PhysicalProperty(source='simulation')
+        assert not_derived_physical_property._is_derived() is False
+        not_derived_physical_property.normalize(None, logger)
+        assert not_derived_physical_property.is_derived is False
+        # Testing a derived physical property
+        derived_physical_property = PhysicalProperty(
+            source='analysis',
+            physical_property_ref=not_derived_physical_property,
+        )
+        assert derived_physical_property._is_derived() is True
+        derived_physical_property.normalize(None, logger)
+        assert derived_physical_property.is_derived is True