Dedup numpydependency in pyproject (#3970)

* dedup numpy dep as pointed out by @DanielYang59's 71f5245#r144995852

* fix some ruff PERF401

Author: janosh

pyproject.toml

@@ -59,8 +59,8 @@ dependencies = [
     "matplotlib>=3.8",
     "monty>=2024.7.29",
     "networkx>=2.2",
-    'numpy>=1.25.0,<2.0 ; platform_system == "Windows"',
-    'numpy>=1.25.0 ; platform_system != "Windows"',
+    "numpy>=1.25.0 ; platform_system != 'Windows'",
+    "numpy>=1.25.0,<2.0 ; platform_system == 'Windows'",
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",
@@ -73,8 +73,6 @@ dependencies = [
     "tabulate>=0.9",
     "tqdm>=4.60",
     "uncertainties>=3.1.4",
-    'numpy>=1.25.0 ; platform_system != "Windows"',
-    'numpy>=1.25.0,<2.0 ; platform_system == "Windows"',
 ]
 version = "2024.7.18"
 
@@ -217,7 +215,7 @@ ignore = [
     "PLR0912", # too many branches
     "PLR0913", # too many arguments
     "PLR0915", # too many statements
-    "PLR2004", # magic values in comparison
+    "PLR2004", # magic-value-comparison TODO fix these
     "PLW2901", # Outer for loop variable overwritten by inner assignment target
     "PT013",   # pytest-incorrect-pytest-import
     "SIM105",  # Use contextlib.suppress() instead of try-except-pass
@@ -235,7 +233,9 @@ docstring-code-format = true
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
-"tests/**" = ["ANN201", "D", "PLR0124"]
+# PLR2004: magic-value-comparison
+# PLR6301: no-self-use
+"tests/**" = ["ANN201", "D", "PLR0124", "PLR2004", "PLR6301"]
 "src/pymatgen/analysis/*" = ["D"]
 "src/pymatgen/io/*" = ["D"]
 "dev_scripts/*" = ["D"]

src/pymatgen/symmetry/analyzer.py

@@ -277,10 +277,9 @@ def _get_symmetry(self) -> tuple[NDArray, NDArray]:
         # [1e-4, 2e-4, 1e-4]
         # (these are in fractional coordinates, so should be small denominator
         # fractions)
-        _translations: list = []
-        for trans in dct["translations"]:
-            _translations.append([float(Fraction(c).limit_denominator(1000)) for c in trans])
-        translations: NDArray = np.array(_translations)
+        translations: NDArray = np.array(
+            [[float(Fraction(c).limit_denominator(1000)) for c in trans] for trans in dct["translations"]]
+        )
 
         # Fractional translations of 1 are more simply 0
         translations[np.abs(translations) == 1] = 0

src/pymatgen/symmetry/kpath.py

@@ -1343,11 +1343,7 @@ def _choose_path(
         # Choose remaining unconnected key points for k-path. The ones that remain are
         # those with inversion symmetry. Connect them to gamma.
 
-        unconnected = []
-
-        for idx in range(len(key_points_inds_orbits)):
-            if idx not in point_orbits_in_path:
-                unconnected.append(idx)
+        unconnected = [idx for idx in range(len(key_points_inds_orbits)) if idx not in point_orbits_in_path]
 
         for ind in unconnected:
             connect = False

src/pymatgen/symmetry/maggroups.py

@@ -237,19 +237,15 @@ def _parse_lattice(b):
                 return None
             raw_lattice = [b[i : i + 4] for i in range(0, len(b), 4)]
 
-            lattice = []
-
-            for r in raw_lattice:
-                lattice.append(
-                    {
-                        "vector": [r[0] / r[3], r[1] / r[3], r[2] / r[3]],
-                        "str": f"({Fraction(r[0] / r[3]).limit_denominator()},"
-                        f"{Fraction(r[1] / r[3]).limit_denominator()},"
-                        f"{Fraction(r[2] / r[3]).limit_denominator()})+",
-                    }
-                )
-
-            return lattice
+            return [
+                {
+                    "vector": [r[0] / r[3], r[1] / r[3], r[2] / r[3]],
+                    "str": f"({Fraction(r[0] / r[3]).limit_denominator()},"
+                    f"{Fraction(r[1] / r[3]).limit_denominator()},"
+                    f"{Fraction(r[2] / r[3]).limit_denominator()})+",
+                }
+                for r in raw_lattice
+            ]
 
         def _parse_transformation(b):
             """Parse compact binary representation into transformation between OG and BNS settings."""
@@ -559,9 +555,7 @@ def _write_all_magnetic_space_groups_to_file(filename):
         "http://stokes.byu.edu/iso/magnetic_data.txt\n"
         "Used with kind permission from Professor Branton Campbell, BYU\n\n"
     )
-    all_msgs = []
-    for i in range(1, 1652):
-        all_msgs.append(MagneticSpaceGroup(i))
+    all_msgs = list(map(MagneticSpaceGroup, range(1, 1652)))
     for msg in all_msgs:
         out += f"\n{msg.data_str()}\n\n--------\n"
     with open(filename, mode="w") as file:

src/pymatgen/symmetry/structure.py

@@ -118,8 +118,7 @@ def __str__(self) -> str:
             row = [str(idx), site.species_string]
             row.extend([f"{j:>10.6f}" for j in site.frac_coords])
             row.append(self.wyckoff_symbols[idx])
-            for key in keys:
-                row.append(props[key][idx])
+            row += [props[key][idx] for key in keys]
             data.append(row)
         outs.append(tabulate(data, headers=["#", "SP", "a", "b", "c", "Wyckoff", *keys]))
         return "\n".join(outs)

tests/analysis/test_local_env.py

@@ -1202,7 +1202,6 @@ def test_weighted_cn(self):
 
     def test_weighted_cn_no_oxid(self):
         cnn = CrystalNN(weighted_cn=True)
-        cn_array = []
         # fmt: off
         expected_array = [
             5.8962, 5.8996, 5.8962, 5.8996, 5.7195, 5.7195, 5.7202, 5.7194, 4.0012, 4.0012,
@@ -1211,8 +1210,7 @@ def test_weighted_cn_no_oxid(self):
         ]
         # fmt: on
         struct = self.lifepo4.copy().remove_oxidation_states()
-        for idx in range(len(struct)):
-            cn_array.append(cnn.get_cn(struct, idx, use_weights=True))
+        cn_array = [cnn.get_cn(struct, idx, use_weights=True) for idx in range(len(struct))]
 
         assert_allclose(expected_array, cn_array, 2)