Merge pull request #143 from Exabyte-io/feature/SOF-7266-1-round-coordinates

feature/SOF-7266-1-round-coordinates

Author: timurbazhirov

express/__init__.py

@@ -1,5 +1,6 @@
 import warnings
 import importlib
+import numpy as np
 
 try:
     from ._version import version as __version__

express/mixins.py

@@ -0,0 +1,7 @@
+import numpy as np
+from express import settings
+
+
+class RoundNumericValuesMixin(object):
+    def _round(self, array):
+        return np.round(array, settings.PRECISION).tolist()

express/parsers/__init__.py

@@ -1,7 +1,9 @@
 import os
 
+from express.mixins import RoundNumericValuesMixin
 
-class BaseParser(object):
+
+class BaseParser(RoundNumericValuesMixin):
     """
     Base Parser class.
     """

express/parsers/structure.py

@@ -77,12 +77,12 @@ def lattice_bravais(self):
         """
         return {
             "type": self._lattice_type(),
-            "a": self.structure.lattice.a,
-            "b": self.structure.lattice.b,
-            "c": self.structure.lattice.c,
-            "alpha": self.structure.lattice.alpha,
-            "beta": self.structure.lattice.beta,
-            "gamma": self.structure.lattice.gamma,
+            "a": self._round(self.structure.lattice.a),
+            "b": self._round(self.structure.lattice.b),
+            "c": self._round(self.structure.lattice.c),
+            "alpha": self._round(self.structure.lattice.alpha),
+            "beta": self._round(self.structure.lattice.beta),
+            "gamma": self._round(self.structure.lattice.gamma),
             "units": {"length": "angstrom", "angle": "degree"},
         }
 
@@ -159,7 +159,9 @@ def basis(self):
         return {
             "units": "crystal",
             "elements": [{"id": i, "value": v.species_string} for i, v in enumerate(self.structure.sites)],
-            "coordinates": [{"id": i, "value": v.frac_coords.tolist()} for i, v in enumerate(self.structure.sites)],
+            "coordinates": [
+                {"id": i, "value": self._round(v.frac_coords.tolist())} for i, v in enumerate(self.structure.sites)
+            ],
         }
 
     def space_group_symbol(self):

express/properties/__init__.py

@@ -1,8 +1,10 @@
 from mat3ra.esse import ESSE
 from abc import abstractmethod
 
+from express.mixins import RoundNumericValuesMixin
 
-class BaseProperty(object):
+
+class BaseProperty(RoundNumericValuesMixin):
     """
     Base Property class.
 
@@ -35,6 +37,7 @@ def serialize_and_validate(self):
             dict
         """
         instance = self._serialize()
+        # TODO: consider rounding all numbers at this stage
         self.esse.validate(instance, self.schema)
         return instance
 

express/properties/non_scalar/bandgaps.py

@@ -1,7 +1,6 @@
 import numpy as np
 from typing import Tuple
 from copy import deepcopy
-from express import settings
 from express.properties.utils import eigenvalues
 from express.properties.non_scalar import NonScalarProperty
 
@@ -184,6 +183,3 @@ def _eigenvalues(self) -> list:
                 eigens_at_spin["energies"] = eigens_at_spin["energies"][start:end]
                 eigens_at_spin["occupations"] = eigens_at_spin["occupations"][start:end]
         return eigens_at_kpoints
-
-    def _round(self, array):
-        return np.round(array, settings.PRECISION).tolist()