- Apply ruff format .:

-- affected: testers + phonopy/calculator.py
-- local tests all pass

tests/conftest.py

@@ -18,8 +18,9 @@
 #
 import os
 import pytest
+
 # Set up pytest to pass control to the debugger on an exception.
-if os.getenv('_PYTEST_RAISE', "0") != "0":
+if os.getenv("_PYTEST_RAISE", "0") != "0":
 
     @pytest.hookimpl(tryfirst=True)
     def pytest_exception_interact(call):

tests/test_aflowparser.py

@@ -26,37 +26,41 @@ def approx(value, abs=0, rel=1e-6):
     return pytest.approx(value, abs=abs, rel=rel)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def parser():
     return AFLOWParser()
 
 
 def test_aflowlib(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/aflow/Ag1Co1O2_ICSD_246157/aflowlib.json', archive, None)
+    parser.parse("tests/data/aflow/Ag1Co1O2_ICSD_246157/aflowlib.json", archive, None)
 
     assert len(archive.run) == 3
 
-    assert archive.run[0].program.version == 'aflow30847'
-    assert archive.run[0].x_aflow_auid == 'aflow:fbc2cf03b9659c90'
+    assert archive.run[0].program.version == "aflow30847"
+    assert archive.run[0].x_aflow_auid == "aflow:fbc2cf03b9659c90"
     sec_system = archive.run[0].system[0]
     assert sec_system.atoms.lattice_vectors[1][0].magnitude == approx(-1.45323479e-10)
-    assert sec_system.x_aflow_Pearson_symbol_superlattice == 'hP8'
-    assert list(sec_system.x_aflow_Wyckoff_letters_orig) == [['c'], ['a'], ['f']]
+    assert sec_system.x_aflow_Pearson_symbol_superlattice == "hP8"
+    assert list(sec_system.x_aflow_Wyckoff_letters_orig) == [["c"], ["a"], ["f"]]
     sec_method = archive.run[0].method[0]
     assert sec_method.x_aflow_delta_electronic_energy_convergence == approx(3.06569e-05)
     sec_calculation = archive.run[0].calculation[0]
     assert sec_calculation.energy.total.value.magnitude == approx(-5.58872856e-18)
     assert sec_calculation.forces.total.value[0][1].magnitude == approx(-2.14691669e-13)
-    assert sec_calculation.thermodynamics[0].enthalpy.magnitude == approx(-5.58872856e-18)
+    assert sec_calculation.thermodynamics[0].enthalpy.magnitude == approx(
+        -5.58872856e-18
+    )
     assert sec_calculation.x_aflow_pressure_residual == approx(2.95)
 
     run = archive.run[1]
     assert len(run.system) == len(run.calculation) == 24
-    assert run.system[7].atoms.labels[6] == 'O'
-    assert run.system[21].atoms.lattice_vectors[0][1].magnitude == approx(-2.5241880209758e-10)
+    assert run.system[7].atoms.labels[6] == "O"
+    assert run.system[21].atoms.lattice_vectors[0][1].magnitude == approx(
+        -2.5241880209758e-10
+    )
     assert run.calculation[15].energy.total.value.magnitude == approx(-6.9854741e-19)
-    assert run.calculation[9].stress.total.value[2][2].magnitude == approx(-1.594e+08)
+    assert run.calculation[9].stress.total.value[2][2].magnitude == approx(-1.594e08)
     # TODO currently workflow is not a repeating section
     # assert archive.workflow.results.n_deformations == 3
     # assert archive.workflow.results.strain_maximum == pytest.approx(0.01)
@@ -68,7 +72,7 @@ def test_aflowlib(parser):
     run = archive.run[2]
     assert len(run.system) == len(run.calculation) == 28
     assert run.system[3].atoms.positions[3][2].magnitude == approx(5.53515521e-10)
-    assert run.calculation[19].thermodynamics[0].pressure.magnitude == (-1.6886e+09)
+    assert run.calculation[19].thermodynamics[0].pressure.magnitude == (-1.6886e09)
     sec_thermo = archive.workflow2.results
     assert sec_thermo.temperature[12].magnitude == 120
     # assert sec_thermo.thermal_conductivity[18].magnitude == approx(4.924586)
@@ -79,24 +83,30 @@ def test_aflowlib(parser):
 
 def test_aflowin(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/aflow/MgO/aflow.in', archive, None)
+    parser.parse("tests/data/aflow/MgO/aflow.in", archive, None)
 
     assert len(archive.run) == 2
 
-    assert archive.run[0].program.version == '3.2.1'
+    assert archive.run[0].program.version == "3.2.1"
     sec_system = archive.run[0].system[0]
     assert sec_system.atoms.lattice_vectors[1][2].magnitude == approx(2.1277509e-10)
     assert sec_system.atoms.positions[1][1].magnitude == approx(2.1277509e-10)
 
     sec_scc = archive.run[1].calculation[0]
     assert sec_scc.dos_phonon[0].energies[80].magnitude == approx(5.71011064e-22)
-    assert sec_scc.dos_phonon[0].total[0].value[1866].magnitude == approx(2.06688135e+20)
+    assert sec_scc.dos_phonon[0].total[0].value[1866].magnitude == approx(2.06688135e20)
     assert len(sec_scc.band_structure_phonon[0].segment) == 10
-    assert sec_scc.band_structure_phonon[0].segment[3].kpoints[7][1] == approx(1.02984830)
-    assert sec_scc.band_structure_phonon[0].segment[9].energies[0][10][3].magnitude == approx(1.92480691e-21)
+    assert sec_scc.band_structure_phonon[0].segment[3].kpoints[7][1] == approx(
+        1.02984830
+    )
+    assert sec_scc.band_structure_phonon[0].segment[9].energies[0][10][
+        3
+    ].magnitude == approx(1.92480691e-21)
 
     assert archive.workflow2.results.qpoints[9249][0] == approx(-4.7619047619e-02)
-    assert archive.workflow2.results.group_velocity[234][2][0].magnitude == approx(-133.348333)
+    assert archive.workflow2.results.group_velocity[234][2][0].magnitude == approx(
+        -133.348333
+    )
 
     # TODO currently workflow is not a repeating section
     # assert archive.workflow.results.temperature[161].magnitude == approx(1610)

tests/test_asrparser.py

@@ -28,7 +28,7 @@
 
 # TODO this does not work for the current version of ASR
 
-tests_path = 'tests/data/asr'
+tests_path = "tests/data/asr"
 
 
 def approx(value, abs=0, rel=1e-6):
@@ -37,21 +37,25 @@ def approx(value, abs=0, rel=1e-6):
 
 def clear_database():
     try:
-        subprocess.Popen('rm -rf %s/.asr' % tests_path)
+        subprocess.Popen("rm -rf %s/.asr" % tests_path)
     except Exception:
         pass
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def test_database():
     # TODO not sure how to do this properly
     cwd = os.getcwd()
     try:
         os.chdir(tests_path)
-        subprocess.Popen(['asr', 'init'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         subprocess.Popen(
-            ['asr', 'run', 'asr.c2db.relax -a Si.json -c {"name":"emt"}'],
-            stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            ["asr", "init"], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
+        subprocess.Popen(
+            ["asr", "run", 'asr.c2db.relax -a Si.json -c {"name":"emt"}'],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
     except Exception:
         pass
     finally:
@@ -60,7 +64,7 @@ def test_database():
 
 def test_parsing(test_database):
     asr_to_archives(tests_path)
-    archive_files = [f for f in os.listdir(tests_path) if f.startswith('archive_')]
+    archive_files = [f for f in os.listdir(tests_path) if f.startswith("archive_")]
     # assert len(archive_files) > 0
     for f in archive_files:
         data = json.load(open(os.path.join(tests_path, f)))

tests/test_atomateparser.py

@@ -27,27 +27,27 @@ def approx(value, abs=0, rel=1e-6):
     return pytest.approx(value, abs=abs, rel=rel)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def parser():
     return AtomateParser()
 
 
 def test_all(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/atomate/mp-149/mp-149_materials.json', archive, None)
+    parser.parse("tests/data/atomate/mp-149/mp-149_materials.json", archive, None)
 
     run = archive.run[0]
-    assert run.program.name == 'MaterialsProject'
+    assert run.program.name == "MaterialsProject"
 
     sec_system = run.system[0]
-    assert sec_system.atoms.labels == ['Si', 'Si']
+    assert sec_system.atoms.labels == ["Si", "Si"]
     assert sec_system.atoms.lattice_vectors[1][2].magnitude == approx(2.734364e-10)
     assert sec_system.atoms.positions[0][0].magnitude == approx(1.367182e-10)
     assert sec_system.x_mp_composition_reduced[0].x_mp_value == approx(1.0)
     assert sec_system.x_mp_symmetry[0].x_mp_symprec == approx(0.1)
-    assert sec_system.x_mp_elements[0] == 'Si'
+    assert sec_system.x_mp_elements[0] == "Si"
     assert sec_system.x_mp_volume == approx(40.88829284866483)
-    assert sec_system.x_mp_formula_anonymous == 'A'
+    assert sec_system.x_mp_formula_anonymous == "A"
 
     # TODO currently, workflow2 is not repeating
     # TODO error loading metainfo in github action

tests/test_elasticparser.py

@@ -27,14 +27,14 @@ def approx(value, abs=0, rel=1e-6):
     return pytest.approx(value, abs=abs, rel=rel)
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture(scope="module")
 def parser():
     return ElasticParser()
 
 
 def test_2nd(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/elastic/2nd/INFO_ElaStic', archive, None)
+    parser.parse("tests/data/elastic/2nd/INFO_ElaStic", archive, None)
 
     sec_system = archive.run[0].system[0]
     assert np.shape(sec_system.atoms.positions) == (8, 3)
@@ -46,34 +46,36 @@ def test_2nd(parser):
     sec_fit_parameters = sec_method.x_elastic_section_fitting_parameters[0]
     assert sec_fit_parameters.x_elastic_fitting_parameters_eta[0] == 0.05
 
-    assert archive.workflow2.method.energy_stress_calculator == 'exciting'
+    assert archive.workflow2.method.energy_stress_calculator == "exciting"
     results = archive.workflow2.results
-    assert results.deformation_types[2][5] == '2eta'
+    assert results.deformation_types[2][5] == "2eta"
     sec_strain = results.strain_diagrams
     assert len(sec_strain) == 7
     assert sec_strain[0].eta[1][3] == -0.02
     assert sec_strain[0].value[2][5] == approx(-3.30877062e-16)
-    assert sec_strain[3].type == 'cross-validation'
+    assert sec_strain[3].type == "cross-validation"
     assert sec_strain[2].eta[1][2] == 0.03
-    assert sec_strain[6].value[2][4] == approx(6.8708895e+12)
+    assert sec_strain[6].value[2][4] == approx(6.8708895e12)
     assert sec_strain[4].polynomial_fit_order == 6
 
-    assert results.elastic_constants_notation_matrix_second_order[1][2] == 'C12'
-    assert results.elastic_constants_matrix_second_order[0][2].magnitude == approx(1.008e+11)
+    assert results.elastic_constants_notation_matrix_second_order[1][2] == "C12"
+    assert results.elastic_constants_matrix_second_order[0][2].magnitude == approx(
+        1.008e11
+    )
     assert results.compliance_matrix_second_order[3][3].magnitude == approx(1.75e-12)
-    assert results.bulk_modulus_voigt.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_voigt.magnitude == approx(5.3074e+11)
-    assert results.bulk_modulus_reuss.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_reuss.magnitude == approx(5.2574e+11)
-    assert results.bulk_modulus_hill.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_hill.magnitude == approx(5.2824e+11)
-    assert results.young_modulus_voigt.magnitude == approx(1.14245e+12)
+    assert results.bulk_modulus_voigt.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_voigt.magnitude == approx(5.3074e11)
+    assert results.bulk_modulus_reuss.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_reuss.magnitude == approx(5.2574e11)
+    assert results.bulk_modulus_hill.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_hill.magnitude == approx(5.2824e11)
+    assert results.young_modulus_voigt.magnitude == approx(1.14245e12)
     assert results.poisson_ratio_voigt == 0.08
-    assert results.young_modulus_reuss.magnitude == approx(1.1347e+12)
+    assert results.young_modulus_reuss.magnitude == approx(1.1347e12)
     assert results.poisson_ratio_reuss == 0.08
-    assert results.young_modulus_hill.magnitude == approx(1.13858e+12)
+    assert results.young_modulus_hill.magnitude == approx(1.13858e12)
     assert results.poisson_ratio_hill == 0.08
-    assert results.eigenvalues_elastic[1].magnitude == approx(1.3481e+12)
+    assert results.eigenvalues_elastic[1].magnitude == approx(1.3481e12)
 
     sec_scc = archive.run[0].calculation[0]
     assert len(sec_scc.calculations_path) == 33
@@ -83,7 +85,7 @@ def test_2nd(parser):
 
 def test_3rd(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/elastic/3rd/INFO_ElaStic', archive, None)
+    parser.parse("tests/data/elastic/3rd/INFO_ElaStic", archive, None)
 
     # The strain diagram data cannot be parsed because of the inhomogeneous shape probably
     # due to error in output.
@@ -94,9 +96,15 @@ def test_3rd(parser):
     # assert sec_strain[3].value[8][7] == approx(2.06899957e-23)
 
     results = archive.workflow2.results
-    assert results.elastic_constants_matrix_third_order[3][1][3].magnitude == approx(1.274e+10)
-    assert results.elastic_constants_matrix_third_order[5][2][5].magnitude == approx(1.2825e+10)
-    assert results.elastic_constants_matrix_third_order[0][0][1].magnitude == approx(-1.18334e+12)
+    assert results.elastic_constants_matrix_third_order[3][1][3].magnitude == approx(
+        1.274e10
+    )
+    assert results.elastic_constants_matrix_third_order[5][2][5].magnitude == approx(
+        1.2825e10
+    )
+    assert results.elastic_constants_matrix_third_order[0][0][1].magnitude == approx(
+        -1.18334e12
+    )
 
 
 def test_stress(parser):