Moving iri and rank to m_def

src/nomad_simulations/physical_property.py

@@ -54,18 +54,12 @@ class PhysicalProperty(ArchiveSection):
     # TODO add `errors`
     # TODO add `smearing`
 
+    m_def = Section()  # modify `m_def` adding `iri` and `rank`
+
     name = Quantity(
         type=str,
         description="""
-        Name of the physical property. Example: `'ElectronicBandGap'`.
-        """,
-    )
-
-    iri = Quantity(
-        type=URL,
-        description="""
-        Internationalized Resource Identifier (IRI) of the physical property defined in the FAIRmat
-        taxonomy, https://fairmat-nfdi.github.io/fairmat-taxonomy/.
+        Name of the physical property.
         """,
     )
 
@@ -96,20 +90,6 @@ class PhysicalProperty(ArchiveSection):
         # ! add more examples in the description to improve the understanding of this quantity
     )
 
-    rank = DirectQuantity(
-        type=Dimension,
-        shape=['0..*'],
-        default=[],
-        name='rank',
-        description="""
-        Rank of the tensor describing the physical property. This quantity is stored as a Dimension:
-            - scalars (tensor rank 0) have `rank=[]` (`len(rank) = 0`),
-            - vectors (tensor rank 1) have `rank=[a]` (`len(rank) = 1`),
-            - matrices (tensor rank 2), have `rank=[a, b]` (`len(rank) = 2`),
-            - etc.
-        """,
-    )
-
     variables = SubSection(sub_section=Variables.m_def, repeats=True)
 
     # * `value` must be overwritten in the derived classes defining its type, unit, and description
@@ -125,12 +105,13 @@ class PhysicalProperty(ArchiveSection):
         """,
     )
 
-    physical_property_ref = Quantity(
-        type=Reference(SectionProxy('PhysicalProperty')),
+    physical_property_ref = SubSection(
+        section_def=SectionProxy('PhysicalProperty'),
         description="""
         Reference to the `PhysicalProperty` section from which the physical property was derived. If `physical_property_ref`
         is populated, the quantity `is_derived` is set to True via normalization.
         """,
+        repeats=False,
     )
 
     is_derived = Quantity(
@@ -196,7 +177,7 @@ def full_shape(self) -> list:
         Returns:
             (list): The full shape of the physical property.
         """
-        return self.variables_shape + self.rank
+        return self.variables_shape + self.m_def.rank
 
     @property
     def _new_value(self) -> Quantity:
@@ -221,9 +202,10 @@ def __init__(
         self, m_def: Section = None, m_context: Context = None, **kwargs
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
-        if self.iri is None:
+        if self.m_def.iri is None:
             logger.warning(
-                'The used property is not defined in the FAIRmat taxonomy (https://fairmat-nfdi.github.io/fairmat-taxonomy/). You can contribute there if you want to extend the list of available materials properties.'
+                'The used property is not defined in the FAIRmat taxonomy (http://fairmat-nfdi.eu/taxonomy/). '
+                'You can contribute there if you want to extend the list of available materials properties.'
             )
 
     def __setattr__(self, name: str, val: Any) -> None:

src/nomad_simulations/properties/band_gap.py

@@ -31,9 +31,7 @@ class ElectronicBandGap(PhysicalProperty):
     Energy difference between the highest occupied electronic state and the lowest unoccupied electronic state.
     """
 
-    # ! implement `iri` and `rank` as part of `m_def = Section()`
-
-    iri = 'http://fairmat-nfdi.eu/taxonomy/ElectronicBandGap'
+    m_def = Section(iri='http://fairmat-nfdi.eu/taxonomy/ElectronicBandGap', rank=[])
 
     type = Quantity(
         type=MEnum('direct', 'indirect'),
@@ -80,8 +78,6 @@ def __init__(
         self, m_def: Section = None, m_context: Context = None, **kwargs
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
-        self.name = self.m_def.name
-        self.rank = []
 
     def _check_negative_values(self, logger: BoundLogger) -> Optional[pint.Quantity]:
         """

src/nomad_simulations/properties/energies.py

@@ -28,9 +28,7 @@ class FermiLevel(PhysicalProperty):
     Energy required to add or extract a charge from a material at zero temperature. It can be also defined as the chemical potential at zero temperature.
     """
 
-    # ! implement `iri` and `rank` as part of `m_def = Section()`
-
-    iri = 'http://fairmat-nfdi.eu/taxonomy/FermiLevel'
+    m_def = Section(iri='http://fairmat-nfdi.eu/taxonomy/FermiLevel', rank=[])
 
     value = Quantity(
         type=np.float64,
@@ -44,8 +42,6 @@ def __init__(
         self, m_def: Section = None, m_context: Context = None, **kwargs
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
-        self.rank = []
-        self.name = self.m_def.name
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
@@ -56,9 +52,7 @@ class ChemicalPotential(PhysicalProperty):
     Free energy cost of adding or extracting a particle from a thermodynamic system.
     """
 
-    # ! implement `iri` and `rank` as part of `m_def = Section()`
-
-    iri = 'http://fairmat-nfdi.eu/taxonomy/ChemicalPotential'
+    m_def = Section(iri='http://fairmat-nfdi.eu/taxonomy/ChemicalPotential', rank=[])
 
     value = Quantity(
         type=np.float64,
@@ -72,8 +66,6 @@ def __init__(
         self, m_def: Section = None, m_context: Context = None, **kwargs
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
-        self.rank = []
-        self.name = self.m_def.name
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)

src/nomad_simulations/properties/spectral_profile.py

@@ -36,6 +36,8 @@ class SpectralProfile(PhysicalProperty):
     A base section used to define the spectral profile.
     """
 
+    m_def = Section(rank=[])
+
     value = Quantity(
         type=np.float64,
         description="""
@@ -47,7 +49,6 @@ def __init__(
         self, m_def: Section = None, m_context: Context = None, **kwargs
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
-        self.rank = []
 
     def _get_energy_points(self, logger: BoundLogger) -> Optional[pint.Quantity]:
         """
@@ -145,8 +146,9 @@ class ElectronicDensityOfStates(DOSProfile):
     Number of electronic states accessible for the charges per energy and per volume.
     """
 
-    # ! implement `iri` and `rank` as part of `m_def = Section()`
-    iri = 'http://fairmat-nfdi.eu/taxonomy/ElectronicDensityOfStates'
+    m_def = Section(
+        iri='http://fairmat-nfdi.eu/taxonomy/ElectronicDensityOfStates', rank=[]
+    )
 
     spin_channel = Quantity(
         type=np.int32,
@@ -533,7 +535,7 @@ class XASSpectra(SpectralProfile):
     X-ray Absorption Spectra (XAS).
     """
 
-    # ! implement `iri` and `rank` as part of `m_def = Section()`
+    m_def = Section(rank=[])  # TODO add XASSpectra to taxonomy
 
     xanes_spectra = SubSection(
         sub_section=SpectralProfile.m_def,

tests/conftest.py

@@ -22,6 +22,8 @@
 
 from nomad.units import ureg
 from nomad.datamodel import EntryArchive
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, Section, Context, SubSection
 
 from . import logger
 
@@ -31,6 +33,7 @@
 from nomad_simulations.model_method import ModelMethod
 from nomad_simulations.numerical_settings import SelfConsistency
 from nomad_simulations.outputs import Outputs, SCFOutputs
+from nomad_simulations.physical_property import PhysicalProperty
 from nomad_simulations.variables import Energy2 as Energy
 from nomad_simulations.properties import (
     ElectronicBandGap,

tests/test_band_gap.py

@@ -41,11 +41,10 @@ def test_default_quantities(self):
         """
         electronic_band_gap = ElectronicBandGap()
         assert (
-            electronic_band_gap.iri
+            electronic_band_gap.m_def.iri
             == 'http://fairmat-nfdi.eu/taxonomy/ElectronicBandGap'
         )
-        assert electronic_band_gap.name == 'ElectronicBandGap'
-        assert electronic_band_gap.rank == []
+        assert electronic_band_gap.m_def.rank == []
 
     @pytest.mark.parametrize(
         'value, result',

tests/test_energies.py

@@ -30,9 +30,8 @@ def test_default_quantities(self):
         Test the default quantities assigned when creating an instance of the `FermiLevel` class.
         """
         fermi_level = FermiLevel()
-        assert fermi_level.iri == 'http://fairmat-nfdi.eu/taxonomy/FermiLevel'
-        assert fermi_level.name == 'FermiLevel'
-        assert fermi_level.rank == []
+        assert fermi_level.m_def.iri == 'http://fairmat-nfdi.eu/taxonomy/FermiLevel'
+        assert fermi_level.m_def.rank == []
 
 
 class TestChemicalPotential:
@@ -47,8 +46,7 @@ def test_default_quantities(self):
         """
         chemical_potential = ChemicalPotential()
         assert (
-            chemical_potential.iri
+            chemical_potential.m_def.iri
             == 'http://fairmat-nfdi.eu/taxonomy/ChemicalPotential'
         )
-        assert chemical_potential.name == 'ChemicalPotential'
-        assert chemical_potential.rank == []
+        assert chemical_potential.m_def.rank == []

tests/test_outputs.py

@@ -24,7 +24,8 @@
 from . import logger
 from .conftest import generate_scf_electronic_band_gap_template
 
-from nomad_simulations.outputs import Outputs, ElectronicBandGap
+from nomad_simulations.outputs import Outputs
+from nomad_simulations.properties import ElectronicBandGap
 
 
 class TestOutputs:

tests/test_physical_properties.py

@@ -21,7 +21,8 @@
 
 from nomad.units import ureg
 from nomad.datamodel import EntryArchive
-from nomad.metainfo import Quantity
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, Section, Context, SubSection
 
 from . import logger
 
@@ -30,6 +31,10 @@
 
 
 class DummyPhysicalProperty(PhysicalProperty):
+    m_def = Section(
+        iri='http://fairmat-nfdi.eu/taxonomy/DummyPhysicalProperty', rank=[3, 3]
+    )
+
     value = Quantity(
         type=np.float64,
         unit='eV',
@@ -38,6 +43,17 @@ class DummyPhysicalProperty(PhysicalProperty):
         """,
     )
 
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+
+
+class SectionWithProperties(ArchiveSection):
+    m_def = Section()
+
+    physical_property = SubSection(sub_section=PhysicalProperty.m_def, repeats=True)
+
 
 class TestPhysicalProperty:
     """
@@ -84,10 +100,12 @@ def test_static_properties(
         Test the static properties of the `PhysicalProperty` class, `variables_shape` and `full_shape`.
         """
         physical_property = PhysicalProperty(
-            source='simulation',
-            rank=rank,
-            variables=variables,
+            m_def=Section(
+                iri='http://fairmat-nfdi.eu/taxonomy/PhysicalProperty', rank=rank
+            )
         )
+        physical_property.source = 'simulation'
+        physical_property.variables = variables
         assert physical_property.variables_shape == result_variables_shape
         assert physical_property.full_shape == result_full_shape
 
@@ -97,8 +115,10 @@ def test_setattr_value(self):
         """
         physical_property = DummyPhysicalProperty(
             source='simulation',
-            rank=[3, 3],
-            variables=[Variables(n_grid_points=4), Variables(n_grid_points=10)],
+            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
@@ -111,10 +131,12 @@ def test_setattr_value_wrong_shape(self):
         Test the `__setattr__` method when the `value` has a wrong shape.
         """
         physical_property = PhysicalProperty(
-            source='simulation',
-            rank=[],
-            variables=[],
+            m_def=Section(
+                iri='http://fairmat-nfdi.eu/taxonomy/PhysicalProperty', rank=[]
+            )
         )
+        physical_property.source = 'simulation'
+        physical_property.variables = []
         # `physical_property.value` must have shape=[]
         value = np.ones((3, 3))
         wrong_shape = list(value.shape)
@@ -130,10 +152,12 @@ def test_setattr_none(self):
         Test the `__setattr__` method when setting the `value` to `None`.
         """
         physical_property = PhysicalProperty(
-            source='simulation',
-            rank=[],
-            variables=[],
+            m_def=Section(
+                iri='http://fairmat-nfdi.eu/taxonomy/PhysicalProperty', rank=[]
+            )
         )
+        physical_property.source = 'simulation'
+        physical_property.variables = []
         with pytest.raises(ValueError) as exc_info:
             physical_property.value = None
         assert (
@@ -145,16 +169,27 @@ def test_is_derived(self):
         """
         Test the `normalize` and `_is_derived` methods.
         """
+        section = SectionWithProperties()
         # 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(EntryArchive(), logger)
-        assert not_derived_physical_property.is_derived is False
+        not_derived_property = PhysicalProperty(
+            m_def=Section(
+                iri='http://fairmat-nfdi.eu/taxonomy/PhysicalProperty', rank=[]
+            )
+        )
+        not_derived_property.source = 'simulation'
+        section.physical_property.append(not_derived_property)
+        assert not_derived_property._is_derived() is False
+        not_derived_property.normalize(EntryArchive(), logger)
+        assert not_derived_property.is_derived is False
         # Testing a derived physical property
-        derived_physical_property = PhysicalProperty(
-            source='analysis',
-            physical_property_ref=not_derived_physical_property,
+        derived_property = PhysicalProperty(
+            m_def=Section(
+                iri='http://fairmat-nfdi.eu/taxonomy/PhysicalProperty', rank=[]
+            )
         )
-        assert derived_physical_property._is_derived() is True
-        derived_physical_property.normalize(EntryArchive(), logger)
-        assert derived_physical_property.is_derived is True
+        section.physical_property.append(derived_property)
+        derived_property.source = 'analysis'
+        derived_property.physical_property_ref = not_derived_property
+        assert derived_property._is_derived() is True
+        derived_property.normalize(EntryArchive(), logger)
+        assert derived_property.is_derived is True