Merge remote-tracking branch 'trunk/master'

src/pymatgen/analysis/graphs.py

@@ -808,8 +808,7 @@ def get_coordination_of_site(self, n: int) -> int:
         Returns:
             int: number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,
@@ -2478,8 +2477,7 @@ def get_coordination_of_site(self, n) -> int:
         Returns:
             int: the number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,

src/pymatgen/core/composition.py

@@ -487,7 +487,7 @@ def chemical_system(self) -> str:
         sorted alphabetically and joined by dashes, by convention for use
         in database keys.
         """
-        return "-".join(sorted(el.symbol for el in self.elements))
+        return "-".join(sorted(self.chemical_system_set))
 
     @property
     def num_atoms(self) -> float:

tests/analysis/test_graphs.py

@@ -409,7 +409,7 @@ def test_from_local_env_and_equality_and_diff(self):
         diff = struct_graph.diff(sg2)
         assert diff["dist"] == 0
 
-        assert self.square_sg.get_coordination_of_site(0) == 2
+        assert self.square_sg.get_coordination_of_site(0) == 4
 
     def test_from_edges(self):
         edges = {

tests/core/test_composition.py

@@ -701,6 +701,7 @@ def test_elements(self):
     def test_chemical_system(self):
         assert Composition({"Na": 1, "Cl": 1}).chemical_system == "Cl-Na"
         assert Composition({"Na+": 1, "Cl-": 1}).chemical_system == "Cl-Na"
+        assert Composition({"Na+": 1, "Na2+": 1, "Cl-": 1}).chemical_system == "Cl-Na"
 
     def test_chemical_system_set(self):
         assert Composition({"Na": 1, "Cl": 1}).chemical_system_set == {"Cl", "Na"}

tests/io/abinit/test_netcdf.py

@@ -1,7 +1,11 @@
 from __future__ import annotations
 
+import os
+import tarfile
+
 import numpy as np
 import pytest
+from monty.tempfile import ScratchDir
 from numpy.testing import assert_allclose, assert_array_equal
 from pymatgen.core.structure import Structure
 from pymatgen.io.abinit import EtsfReader
@@ -81,19 +85,24 @@ def test_read_si2(self):
 
     @pytest.mark.skipif(netCDF4 is None, reason="Requires Netcdf4")
     def test_read_fe(self):
-        path = self.GSR_paths["Fe_magmoms_collinear"]
-        ref_magmom_collinear = [-0.5069359730980665]
-
-        with EtsfReader(path) as data:
-            structure = data.read_structure()
-            assert structure.site_properties["magmom"] == ref_magmom_collinear
-
-        path = self.GSR_paths["Fe_magmoms_noncollinear"]
-        ref_magmom_noncollinear = [[0.357939487, 0.357939487, 0]]
-
-        with EtsfReader(path) as data:
-            structure = data.read_structure()
-            assert structure.site_properties["magmom"] == ref_magmom_noncollinear
+        with ScratchDir(".") as tmp_dir:
+            with tarfile.open(f"{TEST_DIR}/Fe_magmoms_collinear_GSR.tar.xz", mode="r:xz") as t:
+                t.extractall(tmp_dir)
+                ref_magmom_collinear = [-0.5069359730980665]
+                path = os.path.join(tmp_dir, "Fe_magmoms_collinear_GSR.nc")
+
+                with EtsfReader(path) as data:
+                    structure = data.read_structure()
+                    assert structure.site_properties["magmom"] == ref_magmom_collinear
+
+            with tarfile.open(f"{TEST_DIR}/Fe_magmoms_noncollinear_GSR.tar.xz", mode="r:xz") as t:
+                t.extractall(tmp_dir)
+                ref_magmom_noncollinear = [[0.357939487, 0.357939487, 0]]
+                path = os.path.join(tmp_dir, "Fe_magmoms_noncollinear_GSR.nc")
+
+                with EtsfReader(path) as data:
+                    structure = data.read_structure()
+                    assert structure.site_properties["magmom"] == ref_magmom_noncollinear
 
 
 class TestAbinitHeader(PymatgenTest):

tests/io/abinit/test_pseudos.py

@@ -1,9 +1,11 @@
 from __future__ import annotations
 
 import os.path
+import tarfile
 from collections import defaultdict
 
 import pytest
+from monty.tempfile import ScratchDir
 from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 from pytest import approx
@@ -110,28 +112,32 @@ def test_nc_pseudos(self):
 
     def test_paw_pseudos(self):
         """Test 28ni.paw."""
-        for symbol, pseudos in self.paw_pseudos.items():
-            for pseudo in pseudos:
-                assert repr(pseudo)
-                assert str(pseudo)
-                assert not pseudo.isnc
-                assert pseudo.ispaw
-                assert pseudo.Z == 28
-                assert pseudo.symbol == symbol
-                assert pseudo.Z_val == 18
-                assert pseudo.paw_radius >= 0.0
-
-                # Test pickle
-                self.serialize_with_pickle(pseudo)
-
-                # Test MSONable
-                self.assert_msonable(pseudo)
-
-        pseudo = self.Ni_paw
-        assert pseudo.l_max == 2
-        assert pseudo.l_local == 0
-        assert pseudo.supports_soc
-        assert pseudo.md5 is not None
+        file_name = f"{TEST_DIR}/28ni.paw.tar.xz"
+        symbol = "Ni"
+        with ScratchDir(".") as tmp_dir, tarfile.open(file_name, mode="r:xz") as t:
+            t.extractall(tmp_dir)
+            path = os.path.join(tmp_dir, "28ni.paw")
+            pseudo = Pseudo.from_file(path)
+
+            assert repr(pseudo)
+            assert str(pseudo)
+            assert not pseudo.isnc
+            assert pseudo.ispaw
+            assert pseudo.Z == 28
+            assert pseudo.symbol == symbol
+            assert pseudo.Z_val == 18
+            assert pseudo.paw_radius >= 0.0
+
+            assert pseudo.l_max == 2
+            assert pseudo.l_local == 0
+            assert pseudo.supports_soc
+            assert pseudo.md5 is not None
+
+            # Test pickle
+            self.serialize_with_pickle(pseudo)
+
+            # Test MSONable
+            self.assert_msonable(pseudo)
 
     def test_pawxml_pseudos(self):
         """Test O.GGA_PBE-JTH-paw.xml."""