Merge branch 'v0.10.6' into 'master'

Hotfix for v0.10.6: broken provider specific optimade properties

See merge request !380

nomad/app/optimade/common.py

@@ -15,14 +15,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from typing import Tuple, Generator
+from typing import Tuple, Generator, cast
 
+from nomad.metainfo.metainfo import Quantity, Reference
 from nomad.metainfo.search_extension import Search
 from nomad.search import search_quantities
 
 
 def provider_specific_fields() -> Generator[Tuple[str, Search], None, None]:
     for search_quantity in search_quantities.values():
+        quantity = cast(Quantity, search_quantity.definition)
+        if isinstance(quantity.type, Reference):
+            # we can't yet support those
+            continue
+
         nmd_name = search_quantity.qualified_name
         nmd_name_split = nmd_name.split('.')
 

nomad/normalizing/encyclopedia/material.py

@@ -414,12 +414,12 @@ class MaterialBulkNormalizer(MaterialNormalizer):
         self.crystal_system(bulk, sec_symmetry)
         self.lattice_vectors_primitive(ideal, prim_atoms)
         self.formula(material, names, counts)
-        self.formula_reduced(material, names, reduced_counts)
+        self.formula_reduced(material, names, reduced_counts)  # type: ignore
         self.species(material, names)
-        self.species_and_counts(material, names, reduced_counts)
+        self.species_and_counts(material, names, reduced_counts)  # type: ignore
         self.has_free_wyckoff_parameters(bulk, symmetry_analyzer)
         self.lattice_parameters(ideal, std_atoms)
-        self.material_name(material, names, reduced_counts)
+        self.material_name(material, names, reduced_counts)  # type: ignore
         self.material_classification(material, sec_system)
         self.periodicity(ideal)
         self.point_group(bulk, sec_symmetry)
@@ -538,9 +538,9 @@ class Material2DNormalizer(MaterialNormalizer):
         self.lattice_vectors(ideal, std_atoms)
         self.lattice_vectors_primitive(ideal, prim_atoms)
         self.formula(material, names, counts)
-        self.formula_reduced(material, names, reduced_counts)
+        self.formula_reduced(material, names, reduced_counts)  # type: ignore
         self.species(material, names)
-        self.species_and_counts(material, names, reduced_counts)
+        self.species_and_counts(material, names, reduced_counts)  # type: ignore
         self.lattice_parameters(ideal, std_atoms, ideal.periodicity)
 
 
@@ -755,8 +755,8 @@ class Material1DNormalizer(MaterialNormalizer):
         self.atom_positions(ideal, std_atoms)
         self.lattice_vectors(ideal, std_atoms)
         self.formula(material, names, counts)
-        self.formula_reduced(material, names, reduced_counts)
+        self.formula_reduced(material, names, reduced_counts)  # type: ignore
         self.species(material, names)
-        self.species_and_counts(material, names, reduced_counts)
+        self.species_and_counts(material, names, reduced_counts)  # type: ignore
         self.material_id_1d(material, std_atoms)
         self.lattice_parameters(ideal, std_atoms, ideal.periodicity)

nomad/normalizing/encyclopedia/method.py

@@ -127,12 +127,12 @@ class MethodNormalizer():
         atom_positions = sec_sys['atom_positions']
         geom_dict['atom_positions'] = np.array2string(
             atom_positions.to(ureg.angstrom).magnitude,  # convert to Angstrom
-            formatter={'float_kind': lambda x: "%.6f" % x},
+            formatter={'float_kind': lambda x: "%.6f" % x},  # type: ignore
         ).replace('\n', '')
         cell = sec_sys['lattice_vectors']
         geom_dict['simulation_cell'] = np.array2string(
             cell.to(ureg.angstrom).magnitude,  # convert to Angstrom
-            formatter={'float_kind': lambda x: "%.6f" % x},
+            formatter={'float_kind': lambda x: "%.6f" % x},  # type: ignore
         ).replace('\n', '')
         param_dict['settings_geometry'] = geom_dict