Patch lint (#197)

* test lint

* test lint

* test lint

.pre-commit-config.yaml

@@ -1,5 +1,3 @@
-exclude: ^(tests)
-
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.

tests/conftest.py

@@ -131,9 +131,7 @@ def v_N_GaN(test_dir):
 
 
 @pytest.fixture(scope="session")
-def basic_fed(
-    data_Mg_Ga, defect_entries_and_plot_data_Mg_Ga, stable_entries_Mg_Ga_N
-):
+def basic_fed(data_Mg_Ga, defect_entries_and_plot_data_Mg_Ga, stable_entries_Mg_Ga_N):
     bulk_vasprun = data_Mg_Ga["bulk_sc"]["vasprun"]
     bulk_bs = bulk_vasprun.get_band_structure()
     vbm = bulk_bs.get_vbm()["energy"]

tests/plotting/test_thermo.py

@@ -1,13 +1,14 @@
-import pytest
-from pymatgen.analysis.defects.plotting.thermo import plot_formation_energy_diagrams, plot_chempot_2d
+from pymatgen.analysis.defects.plotting.thermo import (
+    plot_chempot_2d,
+    plot_formation_energy_diagrams,
+)
 from pymatgen.core import Element
 
-def test_fed_plot(basic_fed):
-    fig = plot_formation_energy_diagrams([basic_fed])
-    assert {d_.name for d_ in fig.data} == {'Mg_Ga', 'Mg_Ga:slope'}
-
-def test_chempot_plot(basic_fed):
-    plot_chempot_2d(basic_fed, x_element=Element("Mg"), y_element=Element("Ga"))
 
+def test_fed_plot(basic_fed) -> None:
+    fig = plot_formation_energy_diagrams([basic_fed])
+    assert {d_.name for d_ in fig.data} == {"Mg_Ga", "Mg_Ga:slope"}
 
 
+def test_chempot_plot(basic_fed) -> None:
+    plot_chempot_2d(basic_fed, x_element=Element("Mg"), y_element=Element("Ga"))

tests/pyproject.toml

@@ -0,0 +1,12 @@
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"

tests/test_ccd.py

@@ -44,7 +44,8 @@ def hd1(v_ga):
     assert pytest.approx(hd1.omega_eV) == 0.03341323356861477
     return hd1
 
-def test_defect_band_raises(v_ga):
+
+def test_defect_band_raises(v_ga) -> None:
     vaspruns = v_ga[(0, -1)]["vaspruns"]
     procar = v_ga[(0, -1)]["procar"]
     hd0 = HarmonicDefect.from_vaspruns(
@@ -55,15 +56,16 @@ def test_defect_band_raises(v_ga):
     )
     # mis-matched defect band
     hd0.defect_band = [(138, 0, 1), (139, 1, 1)]
-    with pytest.raises(ValueError) as e:
+    with pytest.raises(ValueError):
         assert hd0.defect_band_index
-    
+
     # mis-matched defect spin
     hd0.defect_band = [(138, 0, 1), (138, 1, 0)]
-    with pytest.raises(ValueError) as e:
+    with pytest.raises(ValueError):
         assert hd0.spin_index == 1
 
-def test_HarmonicDefect(hd0, v_ga, test_dir):
+
+def test_HarmonicDefect(hd0, v_ga, test_dir) -> None:
     # test other basic reading functions for HarmonicDefect
     vaspruns = v_ga[(0, -1)]["vaspruns"]
     procar = v_ga[(0, -1)]["procar"]
@@ -100,7 +102,7 @@ def test_HarmonicDefect(hd0, v_ga, test_dir):
     assert "Spin index" in str(e.value)
 
 
-def test_wswq(hd0, test_dir):
+def test_wswq(hd0, test_dir) -> None:
     wswq_dir = test_dir / "v_Ga" / "ccd_0_-1" / "wswqs"
 
     # check for ValueError when you have mis-matched distortions and wswqs
@@ -119,7 +121,7 @@ def test_wswq(hd0, test_dir):
     assert np.linalg.norm(elph_me[..., 139]) > 0
 
 
-def test_wswq_slope():
+def test_wswq_slope() -> None:
     # Make sure the the slope is automatically defined as the sign of the distoration changes.
     mats = [np.ones((3, 5)), np.zeros((3, 5)), np.ones((3, 5))]
     FakeWSWQ = namedtuple("FakeWSWQ", ["data"])
@@ -132,7 +134,7 @@ def test_wswq_slope():
     assert np.allclose(res, np.ones((3, 5)) * 1)
 
 
-def test_SRHCapture(hd0, hd1, test_dir):
+def test_SRHCapture(hd0, hd1, test_dir) -> None:
     from pymatgen.analysis.defects.ccd import get_SRH_coefficient
 
     hd0.read_wswqs(test_dir / "v_Ga" / "ccd_0_-1" / "wswqs")
@@ -159,7 +161,7 @@ def test_SRHCapture(hd0, hd1, test_dir):
     assert "WSWQ" in str(e.value)
 
 
-def test_dielectric_func(test_dir):
+def test_dielectric_func(test_dir) -> None:
     dir0_opt = test_dir / "v_Ga" / "ccd_0_-1" / "optics"
     hd0 = HarmonicDefect.from_directories(
         directories=[dir0_opt],
@@ -187,5 +189,5 @@ def test_dielectric_func(test_dir):
     assert df.iloc[5]["jb"] == 100
 
 
-def test_plot_pes(hd0):
+def test_plot_pes(hd0) -> None:
     plot_pes(hd0)

tests/test_core.py

@@ -13,7 +13,7 @@
 from pymatgen.core.periodic_table import Element, Specie
 
 
-def test_vacancy(gan_struct):
+def test_vacancy(gan_struct) -> None:
     s = gan_struct.copy()
     vac = Vacancy(s, s.sites[0])
     vac2 = Vacancy(s, s.sites[1])
@@ -29,7 +29,7 @@ def test_vacancy(gan_struct):
     assert vac.latex_name == r"v$_{\rm Ga}$"
 
 
-def test_substitution(gan_struct):
+def test_substitution(gan_struct) -> None:
     s = gan_struct.copy()
     n_site = s.sites[3]
     assert n_site.specie.symbol == "N"
@@ -114,7 +114,7 @@ def test_substitution(gan_struct):
     assert n_ga.get_charge_states() == [-100, 102]
 
 
-def test_interstitial(gan_struct):
+def test_interstitial(gan_struct) -> None:
     s = gan_struct.copy()
     inter_fpos = [0, 0, 0.75]
     n_site = PeriodicSite(Specie("N"), inter_fpos, s.lattice)
@@ -143,7 +143,7 @@ def test_interstitial(gan_struct):
     assert inter2.get_charge_states() == [-100, 102]
 
 
-def test_adsorbate(gan_struct):
+def test_adsorbate(gan_struct) -> None:
     s = gan_struct.copy()
     ads_fpos = [0, 0, 0.75]
     n_site = PeriodicSite(Specie("N"), ads_fpos, s.lattice)
@@ -152,7 +152,7 @@ def test_adsorbate(gan_struct):
     assert str(ads) == "N adsorbate site at [0.00,0.00,0.75]"
 
 
-def test_complex(gan_struct):
+def test_complex(gan_struct) -> None:
     s = gan_struct.copy()
     o_site = PeriodicSite(Specie("O"), s[3].frac_coords, s.lattice)
     sub = Substitution(s, o_site)  # O substituted on N site
@@ -177,7 +177,7 @@ def test_complex(gan_struct):
     assert dc2 != dc
 
 
-def test_parsing_and_grouping_NamedDefects(test_dir):
+def test_parsing_and_grouping_NamedDefects(test_dir) -> None:
     bulk_dir = test_dir / "Mg_Ga" / "bulk_sc"
     defect_dir = test_dir / "Mg_Ga" / "q=0"
     bulk_struct = Structure.from_file(bulk_dir / "CONTCAR.gz")

tests/test_corrections.py

@@ -5,7 +5,7 @@
 )
 
 
-def test_freysoldt(data_Mg_Ga):
+def test_freysoldt(data_Mg_Ga) -> None:
     """Older basic test for Freysoldt correction."""
     bulk_locpot = data_Mg_Ga["bulk_sc"]["locpot"]
     defect_locpot = data_Mg_Ga["q=0"]["locpot"]
@@ -44,7 +44,7 @@ def test_freysoldt(data_Mg_Ga):
     )
 
 
-def test_freysoldt_sxdefect_compare(v_N_GaN):
+def test_freysoldt_sxdefect_compare(v_N_GaN) -> None:
     """More detailed test for Freysoldt correction.
 
     Compare against results from the sxdefectalign tool from SPHInX.

tests/test_finder.py

@@ -1,4 +1,4 @@
-def test_defect_finder(test_dir):
+def test_defect_finder(test_dir) -> None:
     from pymatgen.analysis.defects.finder import DefectSiteFinder
     from pymatgen.core import IStructure
 

tests/test_generators.py

@@ -11,7 +11,7 @@
 )
 
 
-def test_vacancy_generators(gan_struct):
+def test_vacancy_generators(gan_struct) -> None:
     vacancy_generator = VacancyGenerator().get_defects(gan_struct)
     for defect in vacancy_generator:
         assert isinstance(defect, Vacancy)
@@ -29,7 +29,7 @@ def test_vacancy_generators(gan_struct):
         )
 
 
-def test_substitution_generators(gan_struct):
+def test_substitution_generators(gan_struct) -> None:
     sub_generator = SubstitutionGenerator().get_defects(
         gan_struct, {"Ga": ["Mg", "Ca"]}
     )
@@ -49,13 +49,13 @@ def test_substitution_generators(gan_struct):
     }
 
 
-def test_antisite_generator(gan_struct):
+def test_antisite_generator(gan_struct) -> None:
     anti_gen = AntiSiteGenerator().get_defects(gan_struct)
     def_names = [defect.name for defect in anti_gen]
     assert sorted(def_names) == ["Ga_N", "N_Ga"]
 
 
-def test_interstitial_generator(gan_struct):
+def test_interstitial_generator(gan_struct) -> None:
     gen = InterstitialGenerator().get_defects(
         gan_struct, insertions={"Mg": [[0, 0, 0]]}
     )
@@ -71,7 +71,7 @@ def test_interstitial_generator(gan_struct):
     assert len(l_gen) == 1
 
 
-def test_charge_interstitial_generator(chgcar_fe3o4):
+def test_charge_interstitial_generator(chgcar_fe3o4) -> None:
     gen = ChargeInterstitialGenerator().get_defects(chgcar_fe3o4, {"Ga"})
     cnt = 0
     for defect in gen:
@@ -81,7 +81,7 @@ def test_charge_interstitial_generator(chgcar_fe3o4):
     assert cnt == 2
 
 
-def test_voronoi_interstitial_generator(chgcar_fe3o4):
+def test_voronoi_interstitial_generator(chgcar_fe3o4) -> None:
     gen = VoronoiInterstitialGenerator().get_defects(chgcar_fe3o4.structure, {"Li"})
     cnt = 0
     for defect in gen:
@@ -91,7 +91,7 @@ def test_voronoi_interstitial_generator(chgcar_fe3o4):
     assert cnt == 4
 
 
-def test_generate_all_native_defects(chgcar_fe3o4):
+def test_generate_all_native_defects(chgcar_fe3o4) -> None:
     gen = generate_all_native_defects(chgcar_fe3o4)
     assert len(list(gen)) == 14
 

tests/test_recombination.py

@@ -12,7 +12,7 @@
 )
 
 
-def test_boltzmann():
+def test_boltzmann() -> None:
     ref_results = [
         0.9791034813819097,
         0.020459854127734073,
@@ -27,7 +27,7 @@ def test_boltzmann():
     assert np.allclose(results2[:, 1], ref_results, rtol=1e-3)
 
 
-def test_get_vibronic_matrix_elements():
+def test_get_vibronic_matrix_elements() -> None:
     # precompute values of the overlap
     dQ, omega_i, omega_f = 0, 0.2, 0.2
     Ni, Nf = 5, 5
@@ -42,7 +42,7 @@ def test_get_vibronic_matrix_elements():
     assert np.allclose(matel, ref_result)
 
 
-def test_pchip_eval():
+def test_pchip_eval() -> None:
     x_c = np.linspace(0, 2, 5)
     y_c = np.sin(x_c) + 1
     xx = np.linspace(-3, 3, 1000)
@@ -52,7 +52,7 @@ def test_pchip_eval():
     assert int_val == pytest.approx(int_ref, rel=1e-3)
 
 
-def test_get_SRH_coef():
+def test_get_SRH_coef() -> None:
     ref_res = [4.64530153e-14, 4.64752885e-14, 4.75265302e-14]
     res = get_SRH_coef(
         T=[100, 200, 300],
@@ -67,8 +67,8 @@ def test_get_SRH_coef():
     assert np.allclose(res, ref_res)
 
 
-def test_get_Rad_coef():
-    res = get_Rad_coef(
+def test_get_Rad_coef() -> None:
+    get_Rad_coef(
         T=[100, 200, 300],
         dQ=1.0,
         dE=1.0,

tests/test_supercells.py

@@ -1,16 +1,16 @@
 import numpy as np
+import pytest
 from monty.serialization import loadfn
 from pymatgen.analysis.defects.generators import VacancyGenerator
 from pymatgen.analysis.defects.supercells import (
     _ase_cubic,
+    get_closest_sc_mat,
     get_matched_structure_mapping,
     get_sc_fromstruct,
-    get_closest_sc_mat
 )
-import pytest
 
 
-def test_supercells(gan_struct):
+def test_supercells(gan_struct) -> None:
     uc = gan_struct.copy()
     sc_mat = get_sc_fromstruct(uc)
     sc = uc * sc_mat
@@ -24,7 +24,7 @@ def test_supercells(gan_struct):
     )  # the sc_mat can be reconstructed from the sc
 
 
-def test_ase_supercells(gan_struct):
+def test_ase_supercells(gan_struct) -> None:
     sc_mat = _ase_cubic(gan_struct, min_atoms=4, max_atoms=8, min_length=1.0)
     sc = gan_struct * sc_mat
     assert 4 <= sc.num_sites <= 8
@@ -34,27 +34,28 @@ def test_ase_supercells(gan_struct):
         _ase_cubic(gan_struct, min_atoms=4, max_atoms=8, min_length=10)
 
 
-def test_closest_sc_mat(test_dir):
+def test_closest_sc_mat(test_dir) -> None:
     si_o_structs = loadfn(test_dir / "Si-O_structs.json")
-    ref_sc_mat = [[2,1,2], [2,0,3], [2,1,1]]
-    
+    ref_sc_mat = [[2, 1, 2], [2, 0, 3], [2, 1, 1]]
+
     vg = VacancyGenerator()
+
     def get_vac(s, sc_mat):
         vac = next(vg.generate(s, rm_species=["O"]))
         return vac.get_supercell_structure(sc_mat=sc_mat)
-    
-    def check_uc(uc_struct, sc_mat):
+
+    def check_uc(uc_struct, sc_mat) -> None:
         vac_sc = get_vac(uc_struct, sc_mat)
         sorted_results = get_closest_sc_mat(uc_struct, vac_sc, debug=True)
         min_dist = sorted_results[0][0]
-        close_mats = [r[2] for r in sorted_results if r[0] < min_dist*1.1]
+        close_mats = [r[2] for r in sorted_results if r[0] < min_dist * 1.1]
         is_matched = [np.allclose(ref_sc_mat, x) for x in close_mats]
         assert any(is_matched)
-    
+
     for s in si_o_structs:
         check_uc(s, ref_sc_mat)
 
     uc_struct = si_o_structs[0]
     vac_struct = get_vac(uc_struct, ref_sc_mat)
     res = get_closest_sc_mat(uc_struct=uc_struct, sc_struct=vac_struct, debug=False)
-    assert np.allclose(res, ref_sc_mat)
+    assert np.allclose(res, ref_sc_mat)