Remove properties from abivars dict as this breaks the interface with… (

#3642) * Remove properties from abivars dict as this breaks the interface with Abinit * Fix test_to_from_abivars * Fix typo * tweak comments --------- Co-authored-by: Janosh Riebesell <[email protected]>
materialsproject · Feb 23, 2024 · daf42d2 · daf42d2
1 parent 5ce2ae1
commit daf42d2
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Showing 5 changed files with 14 additions and 4 deletions.
diff --git a/pymatgen/io/abinit/abiobjects.py b/pymatgen/io/abinit/abiobjects.py
@@ -158,7 +158,6 @@ def structure_from_abivars(cls=None, *args, **kwargs) -> Structure:
         validate_proximity=False,
         to_unit_cell=False,
         coords_are_cartesian=coords_are_cartesian,
-        properties=kwargs.get("properties"),
     )
 
 
@@ -251,7 +250,6 @@ def structure_to_abivars(
         "typat": typat,
         "znucl": znucl_type,
         "xred": x_red,
-        "properties": structure.properties,
     }
 
     # Add info on the lattice.

diff --git a/pymatgen/io/abinit/netcdf.py b/pymatgen/io/abinit/netcdf.py
@@ -471,3 +471,7 @@ def to_str(self, verbose=0, title=None, **kwargs):
         if title is not None:
             return "\n".join([marquee(title, mark="="), header_str])
         return header_str
+
+    # to_string alias required for backwards compatibility
+    # PLEASE DO NOT REMOVE THIS LINE AS THIS API HAS BEEN AROUND FOR SEVERAL YEARS
+    to_string = to_str
diff --git a/tests/core/test_structure.py b/tests/core/test_structure.py
@@ -1307,9 +1307,14 @@ def test_default_dict_attrs(self):
 
     def test_to_from_abivars(self):
         """Test as_dict, from_dict with fmt == abivars."""
-        dct = self.struct.as_dict(fmt="abivars")
+        # Properties are not supported if fmt="abivars" as its not a serialization protocol
+        # but a format that allows one to get a dict with the abinit variables defining the structure.
+        struct = self.struct.copy()
+        struct.properties = {}
+        dct = struct.as_dict(fmt="abivars")
+        assert "properties" not in dct
         s2 = Structure.from_dict(dct, fmt="abivars")
-        assert s2 == self.struct
+        assert s2 == struct
         assert isinstance(s2, Structure)
 
     def test_to_from_file_str(self):

diff --git a/tests/io/abinit/test_abiobjects.py b/tests/io/abinit/test_abiobjects.py
@@ -97,6 +97,7 @@ def test_znucl_typat(self):
         assert_array_equal(enf_vars["znucl"], enforce_znucl)
         assert_array_equal(enf_vars["typat"], enforce_typat)
         assert_array_equal(def_vars["xred"], enf_vars["xred"])
+        assert "properties" not in enf_vars
 
         assert [s.symbol for s in species_by_znucl(gan)] == ["Ga", "N"]
 

diff --git a/tests/io/abinit/test_netcdf.py b/tests/io/abinit/test_netcdf.py
@@ -93,3 +93,5 @@ def test_api(self):
         assert head.foo == 1
         assert str(head)
         assert head.to_str(verbose=2, title="title")
+        # PLEASE DO NOT REMOVE THIS LINE AS THIS API HAS BEEN AROUND FOR SEVERAL YEARS,
+        assert head.to_string(verbose=2, title="title")