Fixed PhysicalProperty when it does not have a magnitude or is a list

Added tests for SpectralProfile

src/nomad_simulations/physical_property.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 
+import numpy as np
 from typing import Any, Optional
 
 from nomad import utils
@@ -229,6 +230,11 @@ def __setattr__(self, name: str, val: Any) -> None:
                     f'The value of the physical property {self.name} is None. Please provide a finite valid value.'
                 )
             _new_value = self._new_value
+
+            # patch for when `val` does not have units and it is passed as a list (instead of np.array)
+            if isinstance(val, list):
+                val = np.array(val)
+
             # non-scalar or scalar `val`
             try:
                 value_shape = list(val.shape)
@@ -241,7 +247,10 @@ def __setattr__(self, name: str, val: Any) -> None:
                     f'extracted from the variables `n_grid_points` and the `shape` defined in `PhysicalProperty`.'
                 )
             _new_value.shape = self.full_shape
-            _new_value = val.magnitude * val.u
+            if hasattr(val, 'magnitude'):
+                _new_value = val.magnitude * val.u
+            else:
+                _new_value = val
             return super().__setattr__(name, _new_value)
         return super().__setattr__(name, val)
 

src/nomad_simulations/properties/spectral_profile.py

@@ -187,8 +187,12 @@ def _check_spin_polarized(self, logger: BoundLogger) -> bool:
             (bool): True if the simulation is spin-polarized, False otherwise.
         """
         # TODO use this in `ElectronicBandGap` too
+        outputs = self.m_parent
+        if outputs is None:
+            logger.warning('Could not resolve the parent `Outputs`.')
+            return False
         model_method = get_sibling_section(
-            section=self, sibling_section_name='model_method', logger=logger
+            section=outputs, sibling_section_name='model_method', logger=logger
         )
         return (
             True

tests/conftest.py

@@ -21,8 +21,9 @@
 
 from nomad.units import ureg
 
-from nomad_simulations.outputs import ElectronicBandGap, Outputs, SCFOutputs
+from nomad_simulations.outputs import Outputs, SCFOutputs
 from nomad_simulations.numerical_settings import SelfConsistency
+from nomad_simulations.properties import ElectronicBandGap
 
 if os.getenv('_PYTEST_RAISE', '0') != '0':
 

tests/test_spectral_profile.py

@@ -28,16 +28,25 @@
     ElectronicDensityOfStates,
     XASSpectra,
 )
-from nomad_simulations.variables import Temperature
+from nomad_simulations.variables import Temperature, Energy2 as Energy
 
 
 class TestSpectralProfile:
     """
     Test the `SpectralProfile` class defined in `properties/spectral_profile.py`.
     """
 
-    def test_negative_value(self):
-        spectral_profile = SpectralProfile()
+    def test_is_valid_spectral_profile(self):
+        """
+        Test the `is_valid_spectral_profile` method.
+        """
+        spectral_profile = SpectralProfile(
+            variables=[Energy(grid_points=[-3, -2, -1, 0, 1, 2, 3] * ureg.joule)]
+        )
+        spectral_profile.value = [1.5, 1.2, 0, 0, 0, 0.8, 1.3]
+        assert spectral_profile.is_valid_spectral_profile()
+        spectral_profile.value = [3, 2, 0, 0, 0, -4, 1]
+        assert not spectral_profile.is_valid_spectral_profile()
         # default value inherited in other SpectralProfile classes
         assert spectral_profile.rank == []
 
@@ -52,13 +61,28 @@ def test_default_quantities(self):
         """
         Test the default quantities assigned when creating an instance of the `ElectronicDensityOfStates` class.
         """
-        electronic_band_gap = ElectronicDensityOfStates()
+        electronic_dos = ElectronicDensityOfStates()
         assert (
-            electronic_band_gap.iri
+            electronic_dos.iri
             == 'http://fairmat-nfdi.eu/taxonomy/ElectronicDensityOfStates'
         )
-        assert electronic_band_gap.name == 'ElectronicDensityOfStates'
-        assert electronic_band_gap.rank == []
+        assert electronic_dos.name == 'ElectronicDensityOfStates'
+        assert electronic_dos.rank == []
+
+    def test_check_energy_variables(self):
+        """
+        Test the `_check_energy_variables` method.
+        """
+        electronic_dos = ElectronicDensityOfStates()
+        electronic_dos.variables = [
+            Temperature(grid_points=[-3, -2, -1, 0, 1, 2, 3] * ureg.kelvin)
+        ]
+        assert electronic_dos._check_energy_variables(logger) is None
+        electronic_dos.variables.append(
+            Energy(grid_points=[-3, -2, -1, 0, 1, 2, 3] * ureg.joule)
+        )
+        energies = electronic_dos._check_energy_variables(logger)
+        assert (energies.magnitude == np.array([-3, -2, -1, 0, 1, 2, 3])).all()
 
 
 class TestXASSpectra:
@@ -71,7 +95,7 @@ def test_default_quantities(self):
         """
         Test the default quantities assigned when creating an instance of the `XASSpectra` class.
         """
-        electronic_band_gap = XASSpectra()
-        assert electronic_band_gap.iri is None  # Add iri when available
-        assert electronic_band_gap.name == 'XASSpectra'
-        assert electronic_band_gap.rank == []
+        xas_spectra = XASSpectra()
+        assert xas_spectra.iri is None  # Add iri when available
+        assert xas_spectra.name == 'XASSpectra'
+        assert xas_spectra.rank == []