Deprecate PymatgenTest, migrate pymatgen tests to pytest from unittest

tests/command_line/test_enumlib_caller.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import unittest
 from shutil import which
 
 import numpy as np
@@ -14,12 +13,11 @@
 from pymatgen.transformations.standard_transformations import SubstitutionTransformation
 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")
-enumlib_present = enum_cmd and makestr_cmd
+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 enumlib_present, reason="enum_lib not present.")
+@pytest.mark.skipif(not (ENUM_CMD and MAKESTR_CMD), reason="enumlib not present.")
 class TestEnumlibAdaptor(PymatgenTest):
     def test_init(self):
         struct = self.get_structure("LiFePO4")
@@ -119,7 +117,7 @@ def test_partial_disorder(self):
         for struct in structures:
             assert struct.formula == "Ca12 Al8 Si4 Ge8 O48"
 
-    @unittest.skip("Fails seemingly at random.")
+    @pytest.mark.skip("Fails seemingly at random.")
     def test_timeout(self):
         struct = Structure.from_file(filename=f"{TEST_FILES_DIR}/cif/garnet.cif")
         SpacegroupAnalyzer(struct, 0.1)

tests/command_line/test_gulp_caller.py

@@ -8,7 +8,6 @@
 
 import os
 import sys
-import unittest
 from shutil import which
 from unittest import TestCase
 
@@ -30,13 +29,15 @@
 
 TEST_DIR = f"{TEST_FILES_DIR}/command_line/gulp"
 
-gulp_present = which("gulp") and os.getenv("GULP_LIB") and ("win" not in sys.platform)
-# disable gulp tests for now. Right now, it is compiled against libgfortran3, which is no longer supported in the new
-# Ubuntu 20.04.
-gulp_present = False
+GULP_PRESENT = which("gulp") and os.getenv("GULP_LIB") and ("win" not in sys.platform)
+# Disable GULP tests for now: it is compiled against `libgfortran3``,
+# which is no longer supported in Ubuntu 20.04 and onwards.
+GULP_PRESENT = False
+
+if not GULP_PRESENT:
+    pytest.skip(reason="GULP not available", allow_module_level=True)
 
 
-@pytest.mark.skipif(not gulp_present, reason="gulp not present.")
 class TestGulpCaller:
     def test_run(self):
         mgo_lattice = np.eye(3) * 4.212
@@ -105,7 +106,6 @@ def test_decimal(self):
         caller.run(buckingham_input)
 
 
-@pytest.mark.skipif(not gulp_present, reason="gulp not present.")
 class TestGulpIO(TestCase):
     def setUp(self):
         self.structure = Structure.from_file(f"{VASP_IN_DIR}/POSCAR_Al12O18")
@@ -132,15 +132,6 @@ def test_structure_lines_no_frac_coords(self):
         assert "cell" not in inp_str
         assert "cart" in inp_str
 
-    @unittest.skip("Not Implemented yet")
-    def test_specie_potential(self):
-        pass
-
-    @unittest.expectedFailure
-    def test_library_line_explicit_path(self):
-        gin = self.gio.library_line("/Users/mbkumar/Research/Defects/GulpExe/Libraries/catlow.lib")
-        assert "lib" in gin
-
     def test_library_line_wrong_file(self):
         with pytest.raises(GulpError, match="GULP library not found"):
             self.gio.library_line("temp_to_fail.lib")
@@ -280,12 +271,11 @@ def test_get_relaxed_structure(self):
         assert struct.lattice.a == 4.212
         assert struct.lattice.alpha == 90
 
-    @unittest.skip("Test later")
+    @pytest.mark.skip("Test later")
     def test_tersoff_input(self):
         self.gio.tersoff_input(self.structure)
 
 
-@pytest.mark.skipif(not gulp_present, reason="gulp not present.")
 class TestGlobalFunctions(TestCase):
     def setUp(self):
         mgo_latt = np.eye(3) * 4.212
@@ -337,7 +327,6 @@ def test_get_energy_relax_structure_buckingham(self):
         assert site_len == len(self.mgo_uc)
 
 
-@pytest.mark.skipif(not gulp_present, reason="gulp not present.")
 class TestBuckinghamPotentialLewis(TestCase):
     def setUp(self):
         self.bpl = BuckinghamPotential("lewis")
@@ -365,7 +354,6 @@ def test_spring(self):
         assert self.bpl.spring_dict["O"] != ""
 
 
-@pytest.mark.skipif(not gulp_present, reason="gulp not present.")
 class TestBuckinghamPotentialBush(TestCase):
     def setUp(self):
         self.bpb = BuckinghamPotential("bush")

tests/core/test_surface.py

@@ -2,9 +2,9 @@
 
 import json
 import os
-import unittest
 
 import numpy as np
+import pytest
 from numpy.testing import assert_allclose
 from pytest import approx
 
@@ -697,7 +697,7 @@ def test_get_d(self):
         s2 = recon2.get_unreconstructed_slabs()[0]
         assert get_d(s1) == approx(get_d(s2))
 
-    @unittest.skip("This test relies on neighbor orders and is hard coded. Disable temporarily")
+    @pytest.mark.skip("This test relies on neighbor orders and is hard coded. Disable temporarily")
     def test_previous_reconstructions(self):
         # Test to see if we generated all reconstruction types correctly and nothing changes
 

tests/io/test_zeopp.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import unittest
 from unittest import TestCase
 
 import pytest
@@ -167,7 +166,7 @@ def test_get_voronoi_nodes(self):
         assert isinstance(vor_face_center_struct, Structure)
 
 
-@unittest.skip("TODO: file free_sph.cif not present")
+@pytest.mark.skip("TODO: file free_sph.cif not present")
 class TestGetFreeSphereParams(TestCase):
     def setUp(self):
         filepath = f"{TEST_FILES_DIR}/cif/free_sph.cif"

tests/io/vasp/test_sets.py

@@ -2,7 +2,6 @@
 
 import hashlib
 import os
-import unittest
 from glob import glob
 from zipfile import ZipFile
 
@@ -1607,7 +1606,7 @@ def test_user_incar_settings(self):
         assert not vis.incar["LASPH"], "LASPH user setting not applied"
         assert vis.incar["VDW_SR"] == 1.5, "VDW_SR user setting not applied"
 
-    @unittest.skipIf(not os.path.exists(TEST_DIR), "Test files are not present.")
+    @pytest.mark.skipif(not os.path.exists(TEST_DIR), reason="Test files are not present.")
     def test_from_prev_calc(self):
         prev_run = os.path.join(TEST_DIR, "fixtures", "relaxation")
 
@@ -1624,7 +1623,7 @@ def test_from_prev_calc(self):
         assert "VDW_A2" in vis_bj.incar
         assert "VDW_S8" in vis_bj.incar
 
-    @unittest.skipIf(not os.path.exists(TEST_DIR), "Test files are not present.")
+    @pytest.mark.skipif(not os.path.exists(TEST_DIR), reason="Test files are not present.")
     def test_override_from_prev_calc(self):
         prev_run = os.path.join(TEST_DIR, "fixtures", "relaxation")