SpaceGroup.__repr__

.github/workflows/test.yml

@@ -23,7 +23,7 @@ permissions:
 jobs:
   pytest:
     # prevent this action from running on forks
-    if: github.repository == 'materialsproject/pymatgen'
+    if: ${{ !github.event.pull_request.head.repo.fork }}
     strategy:
       fail-fast: false
       matrix:

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ ci:
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.0.275
     hooks:
       - id: ruff

pymatgen/analysis/elasticity/tests/test_elastic.py

@@ -233,11 +233,7 @@ def test_energy_density(self):
                 [
                     [0.99774738, 0.11520994, -0],
                     [-0.11520994, 0.99774738, 0],
-                    [
-                        -0,
-                        -0,
-                        1,
-                    ],
+                    [-0, -0, 1],
                 ]
             )
         )
@@ -268,9 +264,9 @@ def tearDown(self):
         warnings.simplefilter("default")
 
     def test_init(self):
-        cijkl = Tensor.from_voigt(self.c2)
-        cijklmn = Tensor.from_voigt(self.c3)
-        exp = ElasticTensorExpansion([cijkl, cijklmn])
+        c_ijkl = Tensor.from_voigt(self.c2)
+        c_ijklmn = Tensor.from_voigt(self.c3)
+        exp = ElasticTensorExpansion([c_ijkl, c_ijklmn])
         ElasticTensorExpansion.from_voigt([self.c2, self.c3])
         assert exp.order == 3
 

pymatgen/analysis/tests/test_surface_analysis.py

@@ -2,7 +2,6 @@
 
 import json
 import os
-import warnings
 
 from pytest import approx
 from sympy import Number, Symbol
@@ -25,9 +24,6 @@ def get_path(path_str):
 
 class SlabEntryTest(PymatgenTest):
     def setUp(self):
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")
-
         with open(os.path.join(get_path(""), "ucell_entries.txt")) as ucell_entries:
             ucell_entries = json.loads(ucell_entries.read())
         self.ucell_entries = ucell_entries

pymatgen/apps/borg/tests/test_hive.py

@@ -26,20 +26,18 @@ def test_get_valid_paths(self):
                 assert len(self.drone.get_valid_paths(path)) > 0
 
     def test_assimilate(self):
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")
-            entry = self.drone.assimilate(PymatgenTest.TEST_FILES_DIR)
-            for p in ["hubbards", "is_hubbard", "potcar_spec", "run_type"]:
-                assert p in entry.parameters
-            assert entry.data["efermi"] == approx(-6.62148548)
-            assert entry.composition.reduced_formula == "Xe"
-            assert entry.energy == approx(0.5559329)
-            entry = self.structure_drone.assimilate(PymatgenTest.TEST_FILES_DIR)
-            assert entry.composition.reduced_formula == "Xe"
-            assert entry.energy == approx(0.5559329)
-            assert isinstance(entry, ComputedStructureEntry)
-            assert entry.structure is not None
-            # assert len(entry.parameters["history"]) == 2
+        entry = self.drone.assimilate(PymatgenTest.TEST_FILES_DIR)
+        for p in ["hubbards", "is_hubbard", "potcar_spec", "run_type"]:
+            assert p in entry.parameters
+        assert entry.data["efermi"] == approx(-6.62148548)
+        assert entry.composition.reduced_formula == "Xe"
+        assert entry.energy == approx(0.5559329)
+        entry = self.structure_drone.assimilate(PymatgenTest.TEST_FILES_DIR)
+        assert entry.composition.reduced_formula == "Xe"
+        assert entry.energy == approx(0.5559329)
+        assert isinstance(entry, ComputedStructureEntry)
+        assert entry.structure is not None
+        # assert len(entry.parameters["history"]) == 2
 
     def tearDown(self):
         warnings.simplefilter("default")

pymatgen/command_line/mcsqs_caller.py

@@ -209,9 +209,7 @@ def _parse_sqs_path(path) -> Sqs:
         corr_out = f"bestcorr{i + 1}.out"
         with Popen(f"str2cif < {sqs_out} > {sqs_cif}", shell=True, cwd=path) as p:
             p.communicate()
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")
-            sqs = Structure.from_file(path / sqs_out)
+        sqs = Structure.from_file(path / sqs_out)
         with open(path / corr_out) as f:
             lines = f.readlines()
 

pymatgen/command_line/tests/test_enumlib_caller.py

@@ -2,7 +2,6 @@
 
 import os
 import unittest
-import warnings
 from shutil import which
 
 import pytest
@@ -26,62 +25,60 @@ class EnumlibAdaptorTest(PymatgenTest):
     _multiprocess_shared_ = True
 
     def test_init(self):
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")
-            struct = self.get_structure("LiFePO4")
-            subtrans = SubstitutionTransformation({"Li": {"Li": 0.5}})
-            adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 86
-            for s in structures:
-                assert s.composition.get_atomic_fraction(Element("Li")) == approx(0.5 / 6.5)
-            adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2, refine_structure=True)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 52
+        struct = self.get_structure("LiFePO4")
+        subtrans = SubstitutionTransformation({"Li": {"Li": 0.5}})
+        adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 86
+        for s in structures:
+            assert s.composition.get_atomic_fraction(Element("Li")) == approx(0.5 / 6.5)
+        adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 2, refine_structure=True)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 52
 
-            subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
-            adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 1, refine_structure=True)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 1
-            for s in structures:
-                assert s.composition.get_atomic_fraction(Element("Li")) == approx(0.25 / 6.25)
-
-            # Make sure it works for completely disordered structures.
-            struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{"Fe": 0.5}], [[0, 0, 0]])
-            adaptor = EnumlibAdaptor(struct, 1, 2)
-            adaptor.run()
-            assert len(adaptor.structures) == 3
-
-            # Make sure it works properly when symmetry is broken by ordered sites.
-            struct = self.get_structure("LiFePO4")
-            subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
-            s = subtrans.apply_transformation(struct)
-            # REmove some ordered sites to break symmetry.
-            removetrans = RemoveSitesTransformation([4, 7])
-            s = removetrans.apply_transformation(s)
-            adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 4
-
-            struct = Structure(
-                [[3, 0, 0], [0, 3, 0], [0, 0, 3]],
-                [{"Si": 0.5}] * 2,
-                [[0, 0, 0], [0.5, 0.5, 0.5]],
-            )
-            adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 10
+        subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
+        adaptor = EnumlibAdaptor(subtrans.apply_transformation(struct), 1, 1, refine_structure=True)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 1
+        for s in structures:
+            assert s.composition.get_atomic_fraction(Element("Li")) == approx(0.25 / 6.25)
 
-            struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "EnumerateTest.json"))
-            adaptor = EnumlibAdaptor(struct, 1, 1)
-            adaptor.run()
-            structures = adaptor.structures
-            assert len(structures) == 2
+        # Make sure it works for completely disordered structures.
+        struct = Structure([[10, 0, 0], [0, 10, 0], [0, 0, 10]], [{"Fe": 0.5}], [[0, 0, 0]])
+        adaptor = EnumlibAdaptor(struct, 1, 2)
+        adaptor.run()
+        assert len(adaptor.structures) == 3
+
+        # Make sure it works properly when symmetry is broken by ordered sites.
+        struct = self.get_structure("LiFePO4")
+        subtrans = SubstitutionTransformation({"Li": {"Li": 0.25}})
+        s = subtrans.apply_transformation(struct)
+        # REmove some ordered sites to break symmetry.
+        removetrans = RemoveSitesTransformation([4, 7])
+        s = removetrans.apply_transformation(s)
+        adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 4
+
+        struct = Structure(
+            [[3, 0, 0], [0, 3, 0], [0, 0, 3]],
+            [{"Si": 0.5}] * 2,
+            [[0, 0, 0], [0.5, 0.5, 0.5]],
+        )
+        adaptor = EnumlibAdaptor(struct, 1, 3, enum_precision_parameter=0.01)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 10
+
+        struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "EnumerateTest.json"))
+        adaptor = EnumlibAdaptor(struct, 1, 1)
+        adaptor.run()
+        structures = adaptor.structures
+        assert len(structures) == 2
 
     def test_rounding_errors(self):
         # It used to be that a rounding issue would result in this structure

pymatgen/core/structure.py

@@ -1013,8 +1013,8 @@ def from_spacegroup(
         from pymatgen.symmetry.groups import SpaceGroup
 
         try:
-            i = int(sg)
-            spg = SpaceGroup.from_int_number(i)
+            num = int(sg)
+            spg = SpaceGroup.from_int_number(num)
         except ValueError:
             spg = SpaceGroup(sg)  # type: ignore
 
@@ -1038,12 +1038,12 @@ def from_spacegroup(
         all_sp: list[str | Element | Species | DummySpecies | Composition] = []
         all_coords: list[list[float]] = []
         all_site_properties: dict[str, list] = collections.defaultdict(list)
-        for i, (sp, c) in enumerate(zip(species, frac_coords)):
+        for idx, (sp, c) in enumerate(zip(species, frac_coords)):
             cc = spg.get_orbit(c, tol=tol)
             all_sp.extend([sp] * len(cc))
             all_coords.extend(cc)  # type: ignore
             for k, v in props.items():
-                all_site_properties[k].extend([v[i]] * len(cc))
+                all_site_properties[k].extend([v[idx]] * len(cc))
 
         return cls(latt, all_sp, all_coords, site_properties=all_site_properties)