Migrate from warnings.catch_warnings(record=True) to pytest.warns() (#3125)

* add args missing from doc strings

* refactor warnings.catch_warnings(record=True) to pytest.warns()

* np.math deprecated in numpy 1.25, was just an alias to std lib math

* finish warnings.catch_warnings(record=True) to pytest.warns() migration

* rename single-letter vars

Author: janosh

pymatgen/alchemy/tests/test_materials.py

@@ -2,7 +2,6 @@
 
 import json
 import os
-import warnings
 
 import pytest
 
@@ -106,15 +105,15 @@ def test_as_dict(self):
 
     def test_snl(self):
         self.trans.set_parameter("author", "will")
-        with warnings.catch_warnings(record=True) as w:
-            warnings.simplefilter("always")
+        with pytest.warns(UserWarning) as warns:
             snl = self.trans.to_snl([("will", "[email protected]")])
-            assert len(w) == 1, "Warning not raised on type conversion with other_parameters"
+        assert len(warns) == 1, "Warning not raised on type conversion with other_parameters"
+
         ts = TransformedStructure.from_snl(snl)
         assert ts.history[-1]["@class"] == "SubstitutionTransformation"
 
-        h = ("testname", "testURL", {"test": "testing"})
-        snl = StructureNL(ts.final_structure, [("will", "[email protected]")], history=[h])
+        hist = ("testname", "testURL", {"test": "testing"})
+        snl = StructureNL(ts.final_structure, [("will", "[email protected]")], history=[hist])
         snl = TransformedStructure.from_snl(snl).to_snl([("notwill", "[email protected]")])
-        assert snl.history == [h]
+        assert snl.history == [hist]
         assert snl.authors == [("notwill", "[email protected]")]

pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -239,8 +239,8 @@ def compute_environments(chemenv_configuration):
         if source_type == "cif":
             if not found:
                 input_source = input("Enter path to cif file : ")
-            cp = CifParser(input_source)
-            structure = cp.get_structures()[0]
+            parser = CifParser(input_source)
+            structure = parser.get_structures()[0]
         elif source_type == "mp":
             if not found:
                 input_source = input('Enter materials project id (e.g. "mp-1902") : ')

pymatgen/analysis/elasticity/elastic.py

@@ -7,6 +7,7 @@
 from __future__ import annotations
 
 import itertools
+import math
 import warnings
 from typing import TYPE_CHECKING
 
@@ -443,7 +444,7 @@ def get_structure_property_dict(
     def from_pseudoinverse(cls, strains, stresses):
         """
         Class method to fit an elastic tensor from stress/strain
-        data. Method uses Moore-Penrose pseudoinverse to invert
+        data. Method uses Moore-Penrose pseudo-inverse to invert
         the s = C*e equation with elastic tensor, stress, and
         strain in voigt notation.
 
@@ -453,11 +454,11 @@ def from_pseudoinverse(cls, strains, stresses):
         """
         # convert the stress/strain to Nx6 arrays of voigt-notation
         warnings.warn(
-            "Pseudoinverse fitting of Strain/Stress lists may yield "
+            "Pseudo-inverse fitting of Strain/Stress lists may yield "
             "questionable results from vasp data, use with caution."
         )
         stresses = np.array([Stress(stress).voigt for stress in stresses])
-        with warnings.catch_warnings(record=True):
+        with warnings.catch_warnings():
             strains = np.array([Strain(strain).voigt for strain in strains])
 
         voigt_fit = np.transpose(np.dot(np.linalg.pinv(strains), stresses))
@@ -837,7 +838,7 @@ def diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10):
     3. Find first, second .. nth derivatives of each stress
        with respect to scalar variable corresponding to
        the smallest perturbation in the strain.
-    4. Use the pseudoinverse of a matrix-vector expression
+    4. Use the pseudo-inverse of a matrix-vector expression
        corresponding to the parameterized stress-strain
        relationship and multiply that matrix by the respective
        calculated first or second derivatives from the
@@ -969,13 +970,13 @@ def get_strain_state_dict(strains, stresses, eq_stress=None, tol: float = 1e-10,
 
 def generate_pseudo(strain_states, order=3):
     """
-    Generates the pseudoinverse for a given set of strains.
+    Generates the pseudo-inverse for a given set of strains.
 
     Args:
         strain_states (6xN array like): a list of voigt-notation
             "strain-states", i. e. perturbed indices of the strain
             as a function of the smallest strain e. g. (0, 1, 0, 0, 1, 0)
-        order (int): order of pseudoinverse to calculate
+        order (int): order of pseudo-inverse to calculate
 
     Returns:
         mis: pseudo inverses for each order tensor, these can
@@ -996,7 +997,7 @@ def generate_pseudo(strain_states, order=3):
             exps = carr.copy()
             for _ in range(degree - 1):
                 exps = np.dot(exps, strain_v)
-            exps /= np.math.factorial(degree - 1)
+            exps /= math.factorial(degree - 1)
             sarr[n] = [sp.diff(exp, s, degree - 1) for exp in exps]
         svec = sarr.ravel()
         present_syms = set.union(*(exp.atoms(sp.Symbol) for exp in svec))

pymatgen/analysis/elasticity/tests/test_elastic.py

@@ -169,9 +169,11 @@ def test_new(self):
         self.assert_all_close(self.elastic_tensor_1, ElasticTensor(self.ft))
         non_symm = self.ft
         non_symm[0, 1, 2, 2] += 1.0
-        with warnings.catch_warnings(record=True) as w:
+        with pytest.warns(
+            UserWarning, match="Input elastic tensor does not satisfy standard Voigt symmetries"
+        ) as warns:
             ElasticTensor(non_symm)
-            assert len(w) == 1
+        assert len(warns) == 1
         bad_tensor1 = np.zeros((3, 3, 3))
         bad_tensor2 = np.zeros((3, 3, 3, 2))
         with pytest.raises(ValueError, match="ElasticTensor input must be rank 4"):
@@ -185,7 +187,11 @@ def test_new(self):
     def test_from_pseudoinverse(self):
         strain_list = [Strain.from_deformation(def_matrix) for def_matrix in self.def_stress_dict["deformations"]]
         stress_list = list(self.def_stress_dict["stresses"])
-        with warnings.catch_warnings(record=True):
+        with pytest.warns(
+            UserWarning,
+            match="Pseudo-inverse fitting of Strain/Stress lists may yield questionable results from "
+            "vasp data, use with caution",
+        ):
             et_fl = -0.1 * ElasticTensor.from_pseudoinverse(strain_list, stress_list).voigt
             self.assert_all_close(
                 et_fl.round(2),
@@ -202,8 +208,9 @@ def test_from_pseudoinverse(self):
     def test_from_independent_strains(self):
         strains = self.toec_dict["strains"]
         stresses = self.toec_dict["stresses"]
-        with warnings.catch_warnings(record=True):
+        with pytest.warns(UserWarning, match="No eq state found, returning zero voigt stress") as warns:
             et = ElasticTensor.from_independent_strains(strains, stresses)
+        assert len(warns) == 2
         self.assert_all_close(et.voigt, self.toec_dict["C2_raw"], decimal=-1)
 
     def test_energy_density(self):
@@ -429,9 +436,8 @@ def test_get_strain_state_dict(self):
     def test_find_eq_stress(self):
         test_strains = deepcopy(self.strains)
         test_stresses = deepcopy(self.pk_stresses)
-        with warnings.catch_warnings(record=True):
-            no_eq = find_eq_stress(test_strains, test_stresses)
-            self.assert_all_close(no_eq, np.zeros((3, 3)))
+        no_eq = find_eq_stress(test_strains, test_stresses)
+        self.assert_all_close(no_eq, np.zeros((3, 3)))
         test_strains[3] = Strain.from_voigt(np.zeros(6))
         eq_stress = find_eq_stress(test_strains, test_stresses)
         self.assert_all_close(test_stresses[3], eq_stress)
@@ -445,15 +451,7 @@ def test_get_diff_coeff(self):
         self.assert_all_close(forward_13, [-11 / 6, 3, -3 / 2, 1 / 3])
         self.assert_all_close(
             backward_26,
-            [
-                137 / 180,
-                -27 / 5,
-                33 / 2,
-                -254 / 9,
-                117 / 4,
-                -87 / 5,
-                203 / 45,
-            ],
+            [137 / 180, -27 / 5, 33 / 2, -254 / 9, 117 / 4, -87 / 5, 203 / 45],
         )
         self.assert_all_close(central_29, central_diff_weights(9, 2))
 
@@ -468,12 +466,11 @@ def test_fit(self):
         reduced = [(e, pk) for e, pk in zip(self.strains, self.pk_stresses) if not (abs(abs(e) - 0.05) < 1e-10).any()]
         # Get reduced dataset
         r_strains, r_pk_stresses = zip(*reduced)
-        with warnings.catch_warnings(record=True):
-            c2 = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=2)
-            c2, c3, c4 = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=4)
-            c2, c3 = diff_fit(self.strains, self.pk_stresses, self.data_dict["eq_stress"], order=3)
-            c2_red, c3_red = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=3)
-            self.assert_all_close(c2.voigt, self.data_dict["C2_raw"])
-            self.assert_all_close(c3.voigt, self.data_dict["C3_raw"], decimal=5)
-            self.assert_all_close(c2, c2_red, decimal=0)
-            self.assert_all_close(c3, c3_red, decimal=-1)
+        c2 = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=2)
+        c2, c3, c4 = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=4)
+        c2, c3 = diff_fit(self.strains, self.pk_stresses, self.data_dict["eq_stress"], order=3)
+        c2_red, c3_red = diff_fit(r_strains, r_pk_stresses, self.data_dict["eq_stress"], order=3)
+        self.assert_all_close(c2.voigt, self.data_dict["C2_raw"])
+        self.assert_all_close(c3.voigt, self.data_dict["C3_raw"], decimal=5)
+        self.assert_all_close(c2, c2_red, decimal=0)
+        self.assert_all_close(c3, c3_red, decimal=-1)

pymatgen/analysis/elasticity/tests/test_strain.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import warnings
-
 import numpy as np
 import pytest
 
@@ -91,9 +89,7 @@ def setUp(self):
 
         self.non_ind_str = Strain.from_deformation([[1, 0.02, 0.02], [0, 1, 0], [0, 0, 1]])
 
-        with warnings.catch_warnings(record=True):
-            warnings.simplefilter("always")
-            self.no_dfm = Strain([[0, 0.01, 0], [0.01, 0.0002, 0], [0, 0, 0]])
+        self.no_dfm = Strain([[0, 0.01, 0], [0.01, 0.0002, 0], [0, 0, 0]])
 
     def test_new(self):
         test_strain = Strain([[0, 0.01, 0], [0.01, 0.0002, 0], [0, 0, 0]])

pymatgen/analysis/elasticity/tests/test_stress.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import numpy as np
+import pytest
 from pytest import approx
 
 from pymatgen.analysis.elasticity.strain import Deformation
@@ -45,6 +46,9 @@ def test_properties(self):
         )
         # voigt
         assert list(self.symm_stress.voigt) == [0.51, 5.14, 5.33, 5.07, 2.42, 2.29]
-        # with warnings.catch_warnings(record=True) as w:
-        #     self.non_symm.voigt
-        #     assert len(w) == 1
+
+        with pytest.warns(
+            UserWarning, match="Tensor is not symmetric, information may be lost in voigt conversion"
+        ) as warns:
+            _ = self.non_symm.voigt
+        assert len(warns) == 1

pymatgen/analysis/molecule_matcher.py

@@ -867,7 +867,7 @@ def match(self, mol: Molecule, ignore_warning: bool = False) -> tuple[np.ndarray
         _, count = np.unique(mol.atomic_numbers, return_counts=True)
         total_permutations = 1
         for c in count:
-            total_permutations *= np.math.factorial(c)  # type: ignore
+            total_permutations *= math.factorial(c)
 
         if not ignore_warning and total_permutations > 1_000_000:
             raise ValueError(

pymatgen/analysis/solar/slme.py

@@ -39,8 +39,8 @@
 
 def get_dir_indir_gap(run=""):
     """Get direct and indirect bandgaps for a vasprun.xml."""
-    v = Vasprun(run)
-    bandstructure = v.get_band_structure()
+    vasp_run = Vasprun(run)
+    bandstructure = vasp_run.get_band_structure()
     dir_gap = bandstructure.get_direct_band_gap()
     indir_gap = bandstructure.get_band_gap()["energy"]
     return dir_gap, indir_gap

pymatgen/analysis/tests/test_fragmenter.py

@@ -72,7 +72,7 @@ def test_babel_pc_frag1(self):
     def test_babel_pc_old_defaults(self):
         pytest.importorskip("openbabel")
         fragmenter = Fragmenter(molecule=self.pc, open_rings=True)
-        assert fragmenter.open_rings is True
+        assert fragmenter.open_rings
         assert fragmenter.opt_steps == 10000
         default_mol_graph = MoleculeGraph.with_local_env_strategy(self.pc, OpenBabelNN())
         assert fragmenter.mol_graph == default_mol_graph

pymatgen/analysis/tests/test_interface_reactions.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import unittest
-import warnings
 
 import numpy as np
 import pytest
@@ -163,15 +162,13 @@ def setUp(self):
 
     def test_get_entry_energy(self):
         comp = Composition("MnO3")
-        with warnings.catch_warnings(record=True) as record:
-            warnings.simplefilter("always")
+        with pytest.warns(
+            UserWarning,
+            match="The reactant MnO3 has no matching entry with negative formation energy, instead "
+            "convex hull energy for this composition will be used for reaction energy calculation.",
+        ) as warns:
             energy = InterfacialReactivity._get_entry_energy(self.pd, comp)
-            assert len(record) == 1
-            assert (
-                "The reactant MnO3 has no matching entry with negative formation energy, "
-                "instead convex hull energy for this composition will be used"
-                " for reaction energy calculation." in str(record[-1].message)
-            )
+        assert len(warns) == 1
         test1 = np.isclose(energy, -30, atol=1e-03)
         assert test1, f"_get_entry_energy: energy for {comp.reduced_formula} is wrong!"
         # Test normal functionality