Dependencies: Add compatibility for pymatgen>=v2023.9.2 (#6109)

As of v2023.9.2, the ``properties`` argument of the `Specie` class is
removed and the ``spin`` argument should be used instead. See:
materialsproject/pymatgen@118c245

The ``spin`` argument was introduced in v2023.6.28. See:
materialsproject/pymatgen@9f2b393

Instead of removing support for versions older than v2023.6.28 the code
is updated to be able to deal with the new version where `properties` is
no longer supported.

Cherry-pick: 4e0e7d8

aiida/orm/nodes/data/structure.py

@@ -834,7 +834,17 @@ def build_kind_name(species_and_occu):
             species = list(species_and_occu.keys())
             occupations = list(species_and_occu.values())
 
-            has_spin = any(specie.as_dict().get('properties', {}).get('spin', 0) != 0 for specie in species)
+            # As of v2023.9.2, the ``properties`` argument is removed and the ``spin`` argument should be used.
+            # See: https://github.com/materialsproject/pymatgen/commit/118c245d6082fe0b13e19d348fc1db9c0d512019
+            # The ``spin`` argument was introduced in v2023.6.28.
+            # See: https://github.com/materialsproject/pymatgen/commit/9f2b3939af45d5129e0778d371d814811924aeb6
+            has_spin_attribute = hasattr(species[0], '_spin')
+
+            if has_spin_attribute:
+                has_spin = any(specie.spin != 0 for specie in species)
+            else:
+                has_spin = any(specie.as_dict().get('properties', {}).get('spin', 0) != 0 for specie in species)
+
             has_partial_occupancies = (len(occupations) != 1 or occupations[0] != 1.0)
 
             if has_partial_occupancies and has_spin:
@@ -847,7 +857,10 @@ def build_kind_name(species_and_occu):
 
                 # If there is spin, we can only have a single specie, otherwise we would have raised above
                 specie = species[0]
-                spin = specie.as_dict().get('properties', {}).get('spin', 0)
+                if has_spin_attribute:
+                    spin = specie.spin
+                else:
+                    spin = specie.as_dict().get('properties', {}).get('spin', 0)
 
                 if spin < 0:
                     kind_name += '1'
@@ -1846,13 +1859,16 @@ def _get_object_pymatgen_structure(self, **kwargs):
                 kind = self.get_kind(site.kind_name)
                 if len(kind.symbols) != 1 or (len(kind.weights) != 1 or sum(kind.weights) < 1.):
                     raise ValueError('Cannot set partial occupancies and spins at the same time')
-                species.append(
-                    Specie(
-                        kind.symbols[0],
-                        oxidation_state,
-                        properties={'spin': -1 if kind.name.endswith('1') else 1 if kind.name.endswith('2') else 0}
-                    )
-                )
+                spin = -1 if kind.name.endswith('1') else 1 if kind.name.endswith('2') else 0
+                try:
+                    specie = Specie(kind.symbols[0], oxidation_state, properties={'spin': spin})  # pylint: disable=unexpected-keyword-arg
+                except TypeError:
+                    # As of v2023.9.2, the ``properties`` argument is removed and the ``spin`` argument should be used.
+                    # See: https://github.com/materialsproject/pymatgen/commit/118c245d6082fe0b13e19d348fc1db9c0d512019
+                    # The ``spin`` argument was introduced in v2023.6.28.
+                    # See: https://github.com/materialsproject/pymatgen/commit/9f2b3939af45d5129e0778d371d814811924aeb6
+                    specie = Specie(kind.symbols[0], oxidation_state, spin=spin)  # pylint: disable=unexpected-keyword-arg
+                species.append(specie)
         else:
             # case when no spin are defined
             for site in self.sites:

requirements/requirements-py-3.11.txt

@@ -133,7 +133,7 @@ pycparser==2.21
 pydantic==1.10.9
 pydata-sphinx-theme==0.8.1
 pygments==2.15.1
-pymatgen==2023.5.31
+pymatgen==2023.9.2
 pympler==0.9
 pymysql==0.9.3
 pynacl==1.5.0

tests/test_dataclasses.py

@@ -2247,10 +2247,16 @@ def test_partial_occ_and_spin(self):
         from pymatgen.core.periodic_table import Specie
         from pymatgen.core.structure import Structure
 
-        Fe_spin_up = Specie('Fe', 0, properties={'spin': 1})
-        Mn_spin_up = Specie('Mn', 0, properties={'spin': 1})
-        Fe_spin_down = Specie('Fe', 0, properties={'spin': -1})
-        Mn_spin_down = Specie('Mn', 0, properties={'spin': -1})
+        try:
+            Fe_spin_up = Specie('Fe', 0, spin=1)  # pylint: disable=unexpected-keyword-arg
+            Mn_spin_up = Specie('Mn', 0, spin=1)  # pylint: disable=unexpected-keyword-arg
+            Fe_spin_down = Specie('Fe', 0, spin=-1)  # pylint: disable=unexpected-keyword-arg
+            Mn_spin_down = Specie('Mn', 0, spin=-1)  # pylint: disable=unexpected-keyword-arg
+        except TypeError:
+            Fe_spin_up = Specie('Fe', 0, properties={'spin': 1})  # pylint: disable=unexpected-keyword-arg
+            Mn_spin_up = Specie('Mn', 0, properties={'spin': 1})  # pylint: disable=unexpected-keyword-arg
+            Fe_spin_down = Specie('Fe', 0, properties={'spin': -1})  # pylint: disable=unexpected-keyword-arg
+            Mn_spin_down = Specie('Mn', 0, properties={'spin': -1})  # pylint: disable=unexpected-keyword-arg
         FeMn1 = Composition({Fe_spin_up: 0.5, Mn_spin_up: 0.5})
         FeMn2 = Composition({Fe_spin_down: 0.5, Mn_spin_down: 0.5})
         a = Structure(
@@ -2440,7 +2446,10 @@ def test_roundtrip_spins(self):
 
         b = a.get_pymatgen(add_spin=True)
         # check the spins
-        assert [s.as_dict()['properties']['spin'] for s in b.species] == [-1, -1, -1, -1, 1, 1, 1, 1]
+        try:
+            assert [s.as_dict()['spin'] for s in b.species] == [-1, -1, -1, -1, 1, 1, 1, 1]
+        except KeyError:
+            assert [s.as_dict()['properties']['spin'] for s in b.species] == [-1, -1, -1, -1, 1, 1, 1, 1]
         # back to StructureData
         c = StructureData(pymatgen=b)
         assert c.get_site_kindnames() == ['Mn1', 'Mn1', 'Mn1', 'Mn1', 'Mn2', 'Mn2', 'Mn2', 'Mn2']