Merge branch 'master' of https://github.com/materialsproject/pymatgen

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.253
+    rev: v0.0.254
     hooks:
       - id: ruff
         args: [--fix, --ignore, 'D,SIM']
@@ -38,7 +38,7 @@ repos:
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.12.4
+    rev: v0.12.5
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]

dev_scripts/regen_libxcfunc.py

@@ -22,10 +22,9 @@ def parse_libxc_docs(path):
 
     def parse_section(section):
         d = {}
-        for l in section:
-            key, value = l.split(":")
-            key = key.strip()
-            d[key] = value.strip()
+        for line in section:
+            key, value = line.split(":")
+            d[key.strip()] = value.strip()
 
         return int(d["Number"]), d
 

docs_rst/installation.rst

@@ -29,6 +29,12 @@ Optional libraries that are required if you need certain features.
 5. networkx: For graph analysis associated with critic2 topological analysis
    of electron charge densities, pygraphviz is also required for visualization.
 6. pytest - For unittesting. Not optional for developers.
+7. numba: Optionally can be installed for faster evaluation of certain 
+   functionality, such as the SubstrateAnalyzer. It incurrs an initial 
+   slowdown the first time the relevant function is called, as it is 
+   compiled, for dramatically faster subsequent evaluations. Note that 
+   numba places additional constraints on the versions of numpy and 
+   Python that may be used.
 
 Optional non-Python programs
 ----------------------------

docs_rst/team.rst

@@ -43,8 +43,8 @@ Lead Maintainers
    :alt: ORCID profile for 0000-0001-5726-2587
 
 | **Matthew Horton** |mkhorton| |0000-0001-7777-8871|
-| Materials Project Staff, Persson Group Member
-| Lawrence Berkeley National Laboratory
+| Senior Research Software Engineer
+| Microsoft Research
 
 .. |mkhorton| image:: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg
    :target: https://github.com/mkhorton
@@ -58,11 +58,6 @@ Lead Maintainers
    :height: 16
    :alt: ORCID profile for 0000-0001-7777-8871
 
-Pull Request Review
--------------------
-
-Additional support for reviewing pull requests from:
-
 | **Janosh Riebesell** |janosh|
 | University of Cambridge
 .. |janosh| image:: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg

pymatgen/alchemy/materials.py

@@ -75,10 +75,10 @@ def undo_last_change(self) -> None:
             raise IndexError("Can't undo. Latest history has no input_structure")
         h = self.history.pop()
         self._undone.append((h, self.final_structure))
-        s = h["input_structure"]
-        if isinstance(s, dict):
-            s = Structure.from_dict(s)
-        self.final_structure = s
+        struct = h["input_structure"]
+        if isinstance(struct, dict):
+            struct = Structure.from_dict(struct)
+        self.final_structure = struct
 
     def redo_next_change(self) -> None:
         """
@@ -347,8 +347,8 @@ def from_dict(cls, d) -> TransformedStructure:
         """
         Creates a TransformedStructure from a dict.
         """
-        s = Structure.from_dict(d)
-        return cls(s, history=d["history"], other_parameters=d.get("other_parameters", None))
+        struct = Structure.from_dict(d)
+        return cls(struct, history=d["history"], other_parameters=d.get("other_parameters", None))
 
     def to_snl(self, authors, **kwargs) -> StructureNL:
         """

pymatgen/alchemy/tests/test_filters.py

@@ -28,38 +28,29 @@ class ContainsSpecieFilterTest(PymatgenTest):
     def test_filtering(self):
         coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5], [0.25, 0.25, 0.25]]
         lattice = Lattice([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00], [0.00, -2.0, 3.0]])
-        s = Structure(
-            lattice,
-            [
-                {"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
-                {"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
-                {"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
-                {"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
-            ],
-            coords,
-        )
+        struct = Structure(lattice, [{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25}] * 4, coords)
 
         species1 = [Species("Si", 5), Species("Mg", 2)]
         f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
-        assert not f1.test(s), "Incorrect filter"
+        assert not f1.test(struct), "Incorrect filter"
         f2 = ContainsSpecieFilter(species1, strict_compare=False, AND=False)
-        assert f2.test(s), "Incorrect filter"
+        assert f2.test(struct), "Incorrect filter"
         species2 = [Species("Si", 4), Species("Mg", 2)]
         f3 = ContainsSpecieFilter(species2, strict_compare=True, AND=False)
-        assert f3.test(s), "Incorrect filter"
+        assert f3.test(struct), "Incorrect filter"
         f4 = ContainsSpecieFilter(species2, strict_compare=False, AND=False)
-        assert f4.test(s), "Incorrect filter"
+        assert f4.test(struct), "Incorrect filter"
 
         species3 = [Species("Si", 5), Species("O", -2)]
         f5 = ContainsSpecieFilter(species3, strict_compare=True, AND=True)
-        assert not f5.test(s), "Incorrect filter"
+        assert not f5.test(struct), "Incorrect filter"
         f6 = ContainsSpecieFilter(species3, strict_compare=False, AND=True)
-        assert f6.test(s), "Incorrect filter"
+        assert f6.test(struct), "Incorrect filter"
         species4 = [Species("Si", 4), Species("Mg", 2)]
         f7 = ContainsSpecieFilter(species4, strict_compare=True, AND=True)
-        assert not f7.test(s), "Incorrect filter"
+        assert not f7.test(struct), "Incorrect filter"
         f8 = ContainsSpecieFilter(species4, strict_compare=False, AND=True)
-        assert not f8.test(s), "Incorrect filter"
+        assert not f8.test(struct), "Incorrect filter"
 
     def test_to_from_dict(self):
         species1 = ["Si5+", "Mg2+"]

pymatgen/analysis/bond_valence.py

@@ -475,14 +475,14 @@ def get_oxi_state_decorated_structure(self, structure):
         Raises:
             ValueError if the valences cannot be determined.
         """
-        s = structure.copy()
-        if s.is_ordered:
-            valences = self.get_valences(s)
-            s.add_oxidation_state_by_site(valences)
+        struct = structure.copy()
+        if struct.is_ordered:
+            valences = self.get_valences(struct)
+            struct.add_oxidation_state_by_site(valences)
         else:
-            valences = self.get_valences(s)
-            s = add_oxidation_state_by_site_fraction(s, valences)
-        return s
+            valences = self.get_valences(struct)
+            struct = add_oxidation_state_by_site_fraction(struct, valences)
+        return struct
 
 
 def get_z_ordered_elmap(comp):

pymatgen/analysis/chemenv/utils/math_utils.py

@@ -46,18 +46,18 @@ def _cartesian_product(lists):
     return reduce(_append_es2sequences, lists, [])
 
 
-def prime_factors(n):
+def prime_factors(n: int) -> list[int]:
     """Lists prime factors of a given natural integer, from greatest to smallest
     :param n: Natural integer
     :rtype : list of all prime factors of the given natural n
     """
-    i = 2
-    while i <= sqrt(n):
-        if n % i == 0:
-            l = prime_factors(n / i)
-            l.append(i)
-            return l
-        i += 1
+    idx = 2
+    while idx <= sqrt(n):
+        if n % idx == 0:
+            lst = prime_factors(n // idx)
+            lst.append(idx)
+            return lst
+        idx += 1
     return [n]  # n is prime
 
 

pymatgen/analysis/diffraction/tests/test_xrd.py

@@ -32,9 +32,9 @@ def test_type_wavelength(self):
             XRDCalculator(wavelength)
 
     def test_get_pattern(self):
-        s = self.get_structure("CsCl")
+        struct = self.get_structure("CsCl")
         c = XRDCalculator()
-        xrd = c.get_pattern(s, two_theta_range=(0, 90))
+        xrd = c.get_pattern(struct, two_theta_range=(0, 90))
         assert xrd.to_json()  # Test MSONAble property
         # Check the first two peaks
         assert xrd.x[0] == pytest.approx(21.107738329639844)
@@ -46,20 +46,20 @@ def test_get_pattern(self):
         assert xrd.hkls[1] == [{"hkl": (1, 1, 0), "multiplicity": 12}]
         assert xrd.d_hkls[1] == pytest.approx(2.976212442014178)
 
-        s = self.get_structure("LiFePO4")
-        xrd = c.get_pattern(s, two_theta_range=(0, 90))
+        struct = self.get_structure("LiFePO4")
+        xrd = c.get_pattern(struct, two_theta_range=(0, 90))
         assert xrd.x[1] == pytest.approx(17.03504233621785)
         assert xrd.y[1] == pytest.approx(50.400928948337075)
 
-        s = self.get_structure("Li10GeP2S12")
-        xrd = c.get_pattern(s, two_theta_range=(0, 90))
+        struct = self.get_structure("Li10GeP2S12")
+        xrd = c.get_pattern(struct, two_theta_range=(0, 90))
         assert xrd.x[1] == pytest.approx(14.058274883353876)
         assert xrd.y[1] == pytest.approx(4.4111123641667671)
 
         # Test a hexagonal structure.
-        s = self.get_structure("Graphite")
+        struct = self.get_structure("Graphite")
 
-        xrd = c.get_pattern(s, two_theta_range=(0, 90))
+        xrd = c.get_pattern(struct, two_theta_range=(0, 90))
         assert xrd.x[0] == pytest.approx(26.21057350859598)
         assert xrd.y[0] == pytest.approx(100)
         assert len(xrd.hkls[0][0]["hkl"]) == pytest.approx(4)
@@ -75,13 +75,13 @@ def test_get_pattern(self):
             [0.75, 0.75, 0.324],
         ]
         sp = ["Si", "Si", "Ru", "Ru", "Pr", "Pr"]
-        s = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
-        xrd = c.get_pattern(s)
+        struct = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
+        xrd = c.get_pattern(struct)
         assert xrd.x[0] == pytest.approx(12.86727341476735)
         assert xrd.y[0] == pytest.approx(31.448239816769796)
         assert xrd.d_hkls[0] == pytest.approx(6.88)
         assert len(xrd) == 42
-        xrd = c.get_pattern(s, two_theta_range=[0, 60])
+        xrd = c.get_pattern(struct, two_theta_range=[0, 60])
         assert len(xrd) == 18
 
         # Test with and without Debye-Waller factor

pymatgen/analysis/dimensionality.py

@@ -540,13 +540,13 @@ def get_dimensionality_gorai(
         bonds = get_max_bond_lengths(structure, el_radius_updates)
 
     num_surfaces = 0
-    for h in range(max_hkl):
-        for k in range(max_hkl):
-            for l in range(max_hkl):
-                if max([h, k, l]) > 0 and num_surfaces < 2:
+    for hh in range(max_hkl):
+        for kk in range(max_hkl):
+            for ll in range(max_hkl):
+                if max([hh, kk, ll]) > 0 and num_surfaces < 2:
                     sg = SlabGenerator(
                         structure,
-                        (h, k, l),
+                        (hh, kk, ll),
                         min_slab_size=min_slab_size,
                         min_vacuum_size=min_vacuum_size,
                     )

pymatgen/analysis/ferroelectricity/polarization.py

@@ -351,7 +351,7 @@ def get_lattice_quanta(self, convert_to_muC_per_cm2=True, all_in_polar=True):
                 lattice = lattices[-1]
                 lattices[i] = Lattice.from_parameters(*(np.array(lattice.lengths) * units.ravel()[-1]), *lattice.angles)
 
-        quanta = np.array([np.array(l.lengths) for l in lattices])
+        quanta = np.array([np.array(latt.lengths) for latt in lattices])
 
         return quanta