migrate alchemy and command_line

tests/alchemy/test_filters.py

@@ -14,7 +14,7 @@
 from pymatgen.alchemy.transmuters import StandardTransmuter
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Lattice, Species, Structure
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
 
 class TestContainsSpecieFilter:
@@ -52,7 +52,7 @@ def test_as_from_dict(self):
         assert isinstance(ContainsSpecieFilter.from_dict(dct), ContainsSpecieFilter)
 
 
-class TestSpecieProximityFilter:
+class TestSpecieProximityFilter(PymatgenTest):
     def test_filter(self):
         struct = self.get_structure("Li10GeP2S12")
         sf = SpecieProximityFilter({"Li": 1})
@@ -70,8 +70,8 @@ def test_as_from_dict(self):
         assert isinstance(SpecieProximityFilter.from_dict(dct), SpecieProximityFilter)
 
 
-class TestRemoveDuplicatesFilter(TestCase):
-    def setUp(self):
+class TestRemoveDuplicatesFilter:
+    def setup_method(self):
         with open(f"{TEST_FILES_DIR}/entries/TiO2_entries.json") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [entry.structure for entry in entries]

tests/alchemy/test_materials.py

@@ -22,7 +22,7 @@
 
 
 class TestTransformedStructure:
-    def setUp(self):
+    def setup_method(self):
         structure = PymatgenTest.get_structure("LiFePO4")
         self.structure = structure
         trafos = [SubstitutionTransformation({"Li": "Na"})]

tests/command_line/test_bader_caller.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import warnings
 from shutil import which
 
 import numpy as np
@@ -10,16 +9,13 @@
 from pytest import approx
 
 from pymatgen.command_line.bader_caller import BaderAnalysis, bader_analysis_from_path
-from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
 TEST_DIR = f"{TEST_FILES_DIR}/command_line/bader"
 
 
 @pytest.mark.skipif(not which("bader"), reason="bader executable not present")
-class TestBaderAnalysis:
-    def setUp(self):
-        warnings.catch_warnings()
-
+class TestBaderAnalysis(PymatgenTest):
     def test_init(self):
         # test with reference file
         analysis = BaderAnalysis(

tests/command_line/test_critic2_caller.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from shutil import which
-from unittest import TestCase
 
 import pytest
 from pytest import approx
@@ -75,8 +74,8 @@ def test_from_structure(self):
         assert "ERROR : load int.CHGCAR id chg_int zpsp Mo 6 S 6" in c2c._input_script
 
 
-class TestCritic2Analysis(TestCase):
-    def setUp(self):
+class TestCritic2Analysis:
+    def setup_method(self):
         stdout_file = f"{TEST_DIR}/MoS2_critic2_stdout.txt"
         stdout_file_new_format = f"{TEST_DIR}/MoS2_critic2_stdout_new_format.txt"
         with open(stdout_file) as file:

tests/command_line/test_enumlib_caller.py

@@ -11,14 +11,14 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.transformations.site_transformations import RemoveSitesTransformation
 from pymatgen.transformations.standard_transformations import SubstitutionTransformation
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
 ENUM_CMD = which("enum.x") or which("multienum.x")
 MAKESTR_CMD = which("makestr.x") or which("makeStr.x") or which("makeStr.py")
 
 
 @pytest.mark.skipif(not (ENUM_CMD and MAKESTR_CMD), reason="enumlib not present.")
-class TestEnumlibAdaptor:
+class TestEnumlibAdaptor(PymatgenTest):
     def test_init(self):
         struct = self.get_structure("LiFePO4")
         sub_trans = SubstitutionTransformation({"Li": {"Li": 0.5}})

tests/command_line/test_gulp_caller.py

@@ -9,7 +9,6 @@
 import os
 import sys
 from shutil import which
-from unittest import TestCase
 
 import numpy as np
 import pytest
@@ -106,8 +105,8 @@ def test_decimal(self):
         caller.run(buckingham_input)
 
 
-class TestGulpIO(TestCase):
-    def setUp(self):
+class TestGulpIO:
+    def setup_method(self):
         self.structure = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Al12O18")
         self.gio = GulpIO()
 
@@ -276,8 +275,8 @@ def test_tersoff_input(self):
         self.gio.tersoff_input(self.structure)
 
 
-class TestGlobalFunctions(TestCase):
-    def setUp(self):
+class TestGlobalFunctions:
+    def setup_method(self):
         mgo_latt = np.eye(3) * 4.212
         mgo_specie = ["Mg", "O"] * 4
         mgo_frac_cord = [
@@ -327,8 +326,8 @@ def test_get_energy_relax_structure_buckingham(self):
         assert site_len == len(self.mgo_uc)
 
 
-class TestBuckinghamPotentialLewis(TestCase):
-    def setUp(self):
+class TestBuckinghamPotentialLewis:
+    def setup_method(self):
         self.bpl = BuckinghamPotential("lewis")
 
     def test_existing_element(self):
@@ -354,8 +353,8 @@ def test_spring(self):
         assert self.bpl.spring_dict["O"] != ""
 
 
-class TestBuckinghamPotentialBush(TestCase):
-    def setUp(self):
+class TestBuckinghamPotentialBush:
+    def setup_method(self):
         self.bpb = BuckinghamPotential("bush")
 
     def test_existing_element(self):

tests/command_line/test_mcsqs_caller.py

@@ -7,7 +7,7 @@
 
 from pymatgen.command_line.mcsqs_caller import run_mcsqs
 from pymatgen.core.structure import Structure
-from pymatgen.util.testing import TEST_FILES_DIR
+from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
 __author__ = "Handong Ling, Rachel Woods-Robinson"
 __maintainer__ = "Handong Ling, Rachel Woods-Robinson"
@@ -18,7 +18,7 @@
 
 
 @pytest.mark.skipif(not (which("mcsqs") and which("str2cif")), reason="mcsqs executable not present")
-class TestMcsqsCaller:
+class TestMcsqsCaller(PymatgenTest):
     def setUp(self):
         self.pzt_structs = loadfn(f"{TEST_DIR}/pzt-structs.json")
         self.pzt_structs2 = loadfn(f"{TEST_DIR}/pzt-structs-2.json")
@@ -103,5 +103,5 @@ def test_mcsqs_caller_runtime_error(self):
         struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
         struct.replace_species({"Pb": {"Ti": 0.2, "Pb": 0.8}})
         struct.replace_species({"O": {"F": 0.8, "O": 0.2}})
-        with pytest.raises(RuntimeError, match="mcsqs exited before timeout reached"):
+        with pytest.raises(RuntimeError, match="mcsqs did not generate output files"):
             run_mcsqs(struct, {2: 6, 3: 4}, 10, 0.000001)

tests/command_line/test_vampire_caller.py

@@ -16,7 +16,7 @@
 @pytest.mark.skipif(not which("vampire-serial"), reason="vampire executable not present")
 class TestVampireCaller:
     @classmethod
-    def setUpClass(cls):
+    def setup_class(cls):
         cls.Mn3Al = pd.read_json(f"{TEST_DIR}/Mn3Al.json")
 
         cls.compounds = [cls.Mn3Al]