test error messages

pymatgen/analysis/xas/tests/test_spectrum.py

@@ -126,5 +126,5 @@ def test_site_weighted_spectrum(self):
         assert weighted_spectrum.y[0] == approx((4 * self.site1_xanes.y[0] + 2 * self.site2_xanes.y[0]) / 6, abs=1e-2)
         assert min(weighted_spectrum.x) == max(min(self.site1_xanes.x), min(self.site2_xanes.x))
         self.site2_xanes.absorbing_index = self.site1_xanes.absorbing_index
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match="Need at least two site-wise spectra to perform site-weighting"):
             site_weighted_spectrum([self.site1_xanes, self.site2_xanes])

pymatgen/command_line/enumlib_caller.py

@@ -266,7 +266,7 @@ def get_sg_info(ss):
         # enumeration. See Cu7Te5.cif test file.
         base *= 10
 
-        # base = ndisordered # 10 ** int(math.ceil(math.log10(ndisordered)))
+        # base = n_disordered # 10 ** int(math.ceil(math.log10(n_disordered)))
         # To get a reasonable number of structures, we fix concentrations to the
         # range expected in the original structure.
         total_amounts = sum(index_amounts)
@@ -298,7 +298,7 @@ def _run_multienum(self):
                     timer.cancel()
 
                 if timed_out:
-                    raise TimeoutError("Enumeration took too long.")
+                    raise TimeoutError("Enumeration took too long")
 
             else:
                 output = p.communicate()[0].decode("utf-8")

pymatgen/command_line/tests/test_enumlib_caller.py

@@ -128,5 +128,5 @@ def test_timeout(self):
         SpacegroupAnalyzer(struct, 0.1)
         struct["Al3+"] = {"Al3+": 0.5, "Ga3+": 0.5}
         adaptor = EnumlibAdaptor(struct, 1, 1, enum_precision_parameter=0.01, timeout=0.0000000000001)
-        with pytest.raises(TimeoutError):
+        with pytest.raises(TimeoutError, match="Enumeration took too long"):
             adaptor._run_multienum()

pymatgen/command_line/tests/test_mcsqs_caller.py

@@ -33,7 +33,7 @@ def test_mcsqs_caller_supercell(self):
         sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=[2, 1, 1], search_time=0.01, instances=1)
 
         matches = [sqs.bestsqs.matches(s) for s in self.pzt_structs]
-        assert True in matches
+        assert any(matches)
 
         assert isinstance(sqs.bestsqs, Structure)
 
@@ -52,15 +52,15 @@ def test_mcsqs_caller_total_atoms(self):
         sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=1)
 
         matches = [sqs.bestsqs.matches(s) for s in self.pzt_structs2]
-        assert True in matches
+        assert any(matches)
 
     def test_mcsqs_caller_total_atoms_auto_instances(self):
         struct = self.struct.copy()
         struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
         sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=None)
 
         matches = [sqs.bestsqs.matches(s) for s in self.pzt_structs2]
-        assert True in matches
+        assert any(matches)
 
     def test_mcsqs_caller_parallel(self):
         # explicitly test with four instances
@@ -70,7 +70,7 @@ def test_mcsqs_caller_parallel(self):
         sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=4)
 
         matches = [sqs.bestsqs.matches(s) for s in self.pzt_structs2]
-        assert True in matches
+        assert any(matches)
 
     def test_mcsqs_perfect_match_error(self):
         scale = 32 / self.perfect_match_zzn_rs.num_sites
@@ -101,5 +101,5 @@ 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):
+        with pytest.raises(RuntimeError, match="mcsqs exited before timeout reached"):
             run_mcsqs(struct, {2: 6, 3: 4}, 10, 0.000001)

pymatgen/core/tests/test_periodic_table.py

@@ -545,8 +545,12 @@ def test_sort(self):
 
     def test_immutable(self):
         sp = Species("Fe", 2, spin=5)
-        with pytest.raises(AttributeError, match="property 'spin' of 'Species' object has no setter"):
+        with pytest.raises(AttributeError) as exc:
             sp.spin = 6
+
+        assert "can't set attribute" in str(exc.value) or "property 'spin' of 'Species' object has no setter" in str(
+            exc.value
+        )  # 'can't set attribute' on Linux, for some reason different message on Windows and Mac
         sp.properties["spin"] = 7
         assert sp.spin == 5
 

pymatgen/electronic_structure/tests/test_core.py

@@ -28,7 +28,7 @@ class OrbitalTest(unittest.TestCase):
     def test_init(self):
         for orb in Orbital:
             assert Orbital(orb.value) == orb
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match="100 is not a valid Orbital"):
             Orbital(100)
 
     def test_cached(self):

pymatgen/ext/tests/test_matproj.py

@@ -169,11 +169,15 @@ def test_get_structure_by_material_id(self):
         assert s1.formula == "Cs1"
 
         # requesting via task-id instead of mp-id
-        with pytest.warns(Warning):
+        with pytest.warns(
+            Warning,
+            match="calculation task mp-698856 is mapped to canonical mp-id mp-1394, so structure for mp-1394 returned",
+        ):
             self.rester.get_structure_by_material_id("mp-698856")
 
         # requesting unknown mp-id
-        with pytest.raises(MPRestError):
+        # TODO (janosh) this seems like the wrong error message for this case
+        with pytest.raises(MPRestError, match="'id' is not a valid Element"):
             self.rester.get_structure_by_material_id("id-does-not-exist")
 
     def test_get_entry_by_material_id(self):

pymatgen/io/babel.py

@@ -15,8 +15,7 @@
 from pymatgen.core.structure import IMolecule, Molecule
 
 try:
-    from openbabel import openbabel
-    from openbabel import pybel as pb
+    from openbabel import openbabel, pybel
 except Exception:
     openbabel = None
 
@@ -75,7 +74,7 @@ def __init__(self, mol):
             self._obmol = ob_mol
         elif isinstance(mol, openbabel.OBMol):
             self._obmol = mol
-        elif isinstance(mol, pb.Molecule):
+        elif isinstance(mol, pybel.Molecule):
             self._obmol = mol.OBMol
 
     @property
@@ -102,9 +101,9 @@ def localopt(self, forcefield="mmff94", steps=500):
                 'mmff94', 'mmff94s', and 'uff'.
             steps: Default is 500.
         """
-        pbmol = pb.Molecule(self._obmol)
-        pbmol.localopt(forcefield=forcefield, steps=steps)
-        self._obmol = pbmol.OBMol
+        pybelmol = pybel.Molecule(self._obmol)
+        pybelmol.localopt(forcefield=forcefield, steps=steps)
+        self._obmol = pybelmol.OBMol
 
     def make3d(self, forcefield="mmff94", steps=50):
         """
@@ -125,9 +124,9 @@ def make3d(self, forcefield="mmff94", steps=50):
                 'mmff94', 'mmff94s', and 'uff'.
             steps: Default is 50.
         """
-        pbmol = pb.Molecule(self._obmol)
-        pbmol.make3D(forcefield=forcefield, steps=steps)
-        self._obmol = pbmol.OBMol
+        pybelmol = pybel.Molecule(self._obmol)
+        pybelmol.make3D(forcefield=forcefield, steps=steps)
+        self._obmol = pybelmol.OBMol
 
     def add_hydrogen(self):
         """Add hydrogens (make all hydrogen explicit)."""
@@ -288,7 +287,7 @@ def confab_conformers(
     @property
     def pybel_mol(self):
         """Returns Pybel's Molecule object."""
-        return pb.Molecule(self._obmol)
+        return pybel.Molecule(self._obmol)
 
     def write_file(self, filename, file_format="xyz"):
         """
@@ -298,7 +297,7 @@ def write_file(self, filename, file_format="xyz"):
             filename: Filename of file to output
             file_format: String specifying any OpenBabel supported formats.
         """
-        mol = pb.Molecule(self._obmol)
+        mol = pybel.Molecule(self._obmol)
         return mol.write(file_format, filename, overwrite=True)
 
     @staticmethod
@@ -316,7 +315,7 @@ def from_file(filename, file_format="xyz", return_all_molecules=False):
         Returns:
             BabelMolAdaptor object or list thereof
         """
-        mols = pb.readfile(str(file_format), str(filename))
+        mols = pybel.readfile(str(file_format), str(filename))
         if return_all_molecules:
             return [BabelMolAdaptor(mol.OBMol) for mol in mols]
 
@@ -348,5 +347,5 @@ def from_string(string_data, file_format="xyz"):
         Returns:
             BabelMolAdaptor object
         """
-        mols = pb.readstring(str(file_format), str(string_data))
+        mols = pybel.readstring(str(file_format), str(string_data))
         return BabelMolAdaptor(mols.OBMol)

pymatgen/io/lammps/utils.py

@@ -18,9 +18,9 @@
 from pymatgen.util.coord import get_angle
 
 try:
-    from openbabel import pybel as pb
+    from openbabel import pybel
 except ImportError:
-    pb = None
+    pybel = None
 
 __author__ = "Kiran Mathew, Brandon Wood, Michael Humbert"
 __email__ = "kmathew@lbl.gov"
@@ -276,7 +276,7 @@ def _write_input(self, input_dir="."):
                 # all other filetypes
                 else:
                     a = BabelMolAdaptor(mol)
-                    pm = pb.Molecule(a.openbabel_mol)
+                    pm = pybel.Molecule(a.openbabel_mol)
                     pm.write(
                         self.control_params["filetype"],
                         filename=filename,
@@ -330,7 +330,7 @@ def write_pdb(mol, filename, name=None, num=None):
         name = name or f"ml{num}"
 
         # bma = BabelMolAdaptor(mol)
-        pbm = pb.Molecule(bma._obmol)
+        pbm = pybel.Molecule(bma._obmol)
         for x in pbm.residues:
             x.OBResidue.SetName(name)
             x.OBResidue.SetNum(num)
@@ -353,7 +353,7 @@ def convert_obatoms_to_molecule(self, atoms, residue_name=None, site_property="f
 
         Args:
             atoms ([OBAtom]): list of OBAtom objects
-            residue_name (str): the key in self.map_residue_to_mol. Usec to
+            residue_name (str): the key in self.map_residue_to_mol. Used to
                 restore the site properties in the final packed molecule.
             site_property (str): the site property to be restored.
 
@@ -407,7 +407,7 @@ def restore_site_properties(self, site_property="ff_map", filename=None):
 
         filename = filename or self.control_params["output"]
         bma = BabelMolAdaptor.from_file(filename, "pdb")
-        pbm = pb.Molecule(bma._obmol)
+        pbm = pybel.Molecule(bma._obmol)
 
         assert len(pbm.residues) == sum(x["number"] for x in self.param_list)
 

pymatgen/io/tests/test_babel.py

@@ -15,7 +15,7 @@
 from pymatgen.io.xyz import XYZ
 from pymatgen.util.testing import PymatgenTest
 
-pytest.importorskip("openbabel")
+pybel = pytest.importorskip("openbabel.pybel")
 
 
 class BabelMolAdaptorTest(unittest.TestCase):
@@ -81,18 +81,14 @@ def test_localopt(self):
             assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
 
     def test_make3d(self):
-        from openbabel import pybel as pb
-
-        mol_0d = pb.readstring("smi", "CCCC").OBMol
+        mol_0d = pybel.readstring("smi", "CCCC").OBMol
         adaptor = BabelMolAdaptor(mol_0d)
         adaptor.make3d()
         assert mol_0d.GetDimension() == 3
 
     def add_hydrogen(self):
-        from openbabel import pybel as pb
-
-        mol_0d = pb.readstring("smi", "CCCC").OBMol
-        assert len(pb.Molecule(mol_0d).atoms) == 2
+        mol_0d = pybel.readstring("smi", "CCCC").OBMol
+        assert len(pybel.Molecule(mol_0d).atoms) == 2
         adaptor = BabelMolAdaptor(mol_0d)
         adaptor.add_hydrogen()
         assert len(adaptor.pymatgen_mol) == 14
@@ -126,9 +122,7 @@ def test_rotor_search_rrs(self):
             assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
 
     def test_confab_conformers(self):
-        from openbabel import pybel as pb
-
-        mol = pb.readstring("smi", "CCCC").OBMol
+        mol = pybel.readstring("smi", "CCCC").OBMol
         adaptor = BabelMolAdaptor(mol)
         adaptor.make3d()
         conformers = adaptor.confab_conformers()

pymatgen/io/vasp/tests/test_outputs.py

@@ -11,6 +11,7 @@
 
 import numpy as np
 import pytest
+from numpy.testing import assert_allclose
 from pytest import approx
 
 from pymatgen.core import Element
@@ -368,7 +369,7 @@ def test_dielectric_vasp608(self):
 
     def test_indirect_vasprun(self):
         vasp_run = Vasprun(self.TEST_FILES_DIR / "vasprun.xml.indirect.gz")
-        (gap, cbm, vbm, direct) = vasp_run.eigenvalue_band_properties
+        _gap, _cbm, _vbm, direct = vasp_run.eigenvalue_band_properties
         assert not direct
 
     def test_optical_vasprun(self):
@@ -392,16 +393,12 @@ def test_optical_vasprun(self):
     def test_force_constants(self):
         vasprun_fc = Vasprun(self.TEST_FILES_DIR / "vasprun.xml.dfpt.phonon", parse_potcar_file=False)
         assert vasprun_fc.force_constants.shape == (16, 16, 3, 3)
-        assert np.allclose(
+        assert_allclose(
             vasprun_fc.force_constants[8, 9],
-            [
-                [-0.00184451, -0.0, -0.0],
-                [-0.0, -0.00933824, -0.03021279],
-                [-0.0, -0.03021279, 0.01202547],
-            ],
+            [[-0.00184451, 0, 0], [0, -0.00933824, -0.03021279], [0, -0.03021279, 0.01202547]],
         )
         assert vasprun_fc.normalmode_eigenvals.size == 48
-        assert np.allclose(
+        assert_allclose(
             vasprun_fc.normalmode_eigenvals[17:29],
             [
                 -0.59067079,
@@ -419,7 +416,7 @@ def test_force_constants(self):
             ],
         )
         assert vasprun_fc.normalmode_eigenvecs.shape == (48, 16, 3)
-        assert np.allclose(
+        assert_allclose(
             vasprun_fc.normalmode_eigenvecs[33],
             [
                 [0.0884346, -0.08837289, -0.24995639],
@@ -1168,8 +1165,8 @@ def test_drift(self):
     def test_electrostatic_potential(self):
         outcar = Outcar(self.TEST_FILES_DIR / "OUTCAR")
         assert outcar.ngf == [54, 30, 54]
-        assert np.allclose(outcar.sampling_radii, [0.9748, 0.9791, 0.7215])
-        assert np.allclose(
+        assert_allclose(outcar.sampling_radii, [0.9748, 0.9791, 0.7215])
+        assert_allclose(
             outcar.electrostatic_potential,
             [-26.0704, -45.5046, -45.5046, -72.9539, -73.0621, -72.9539, -73.0621],
         )
@@ -1467,7 +1464,7 @@ def test_init(self):
 
         ans = [1.56472768, 3.25985108, 3.49205728, 3.66275028, 3.8045896, 5.10813352]
         myans = self.chgcar_fe3o4.get_integrated_diff(0, 3, 6)
-        assert np.allclose(myans[:, 1], ans)
+        assert_allclose(myans[:, 1], ans)
 
     def test_write(self):
         self.chgcar_spin.write_file("CHGCAR_pmg")
@@ -1657,11 +1654,11 @@ def test_init(self):
         assert d.nspecs == 2
         assert d.natoms == 6
         assert d.ndisps == 3
-        assert np.allclose(d.masses, [63.546, 196.966])
+        assert_allclose(d.masses, [63.546, 196.966])
         assert 4 in d.data
         assert 2 in d.data[4]
-        assert np.allclose(d.data[4][2]["dispvec"], [0.0, 0.05, 0.0])
-        assert np.allclose(d.data[4][2]["dynmat"][3], [0.055046, -0.298080, 0.0])
+        assert_allclose(d.data[4][2]["dispvec"], [0.0, 0.05, 0.0])
+        assert_allclose(d.data[4][2]["dynmat"][3], [0.055046, -0.298080, 0.0])
         # TODO: test get_phonon_frequencies once cross-checked
 
 
@@ -1698,8 +1695,8 @@ def test_standard(self):
         assert w.encut == 25.0
         assert w.nb == 9
         assert w.nk == 1
-        assert np.allclose(w.a, a)
-        assert np.allclose(w.b, b)
+        assert_allclose(w.a, a)
+        assert_allclose(w.b, b)
         assert w.vol == approx(vol)
         assert len(w.kpoints) == w.nk
         assert len(w.coeffs) == w.nk
@@ -1746,8 +1743,8 @@ def test_n2_45210(self):
         assert w.encut == 25.0
         assert w.nb == 9
         assert w.nk == 1
-        assert np.allclose(w.a, self.a)
-        assert np.allclose(w.b, self.b)
+        assert_allclose(w.a, self.a)
+        assert_allclose(w.b, self.b)
         assert w.vol == approx(self.vol)
         assert len(w.kpoints) == w.nk
         assert len(w.coeffs) == w.nk
@@ -1912,7 +1909,7 @@ def test_get_parchg(self):
         assert "total" in c.data
         assert "diff" not in c.data
         assert np.prod(c.data["total"].shape) == np.prod(w.ng * 2)
-        assert np.allclose(c.data["total"], 0.0)
+        assert_allclose(c.data["total"], 0.0)
 
     def test_write_unks(self):
         unk_std = Unk.from_file(self.TEST_FILES_DIR / "UNK.N2.std")