Schedule PymatgenTest for migration from unittest to pytest

src/pymatgen/analysis/elasticity/elastic.py

@@ -479,8 +479,7 @@ def from_pseudoinverse(cls, strains, stresses) -> Self:
             "questionable results from vasp data, use with caution."
         )
         stresses = np.array([Stress(stress).voigt for stress in stresses])
-        with warnings.catch_warnings():
-            strains = np.array([Strain(strain).voigt for strain in strains])
+        strains = np.array([Strain(strain).voigt for strain in strains])
 
         voigt_fit = np.transpose(np.dot(np.linalg.pinv(strains), stresses))
         return cls.from_voigt(voigt_fit)

src/pymatgen/command_line/mcsqs_caller.py

@@ -6,7 +6,6 @@
 
 import os
 import tempfile
-import warnings
 from pathlib import Path
 from shutil import which
 from subprocess import Popen, TimeoutExpired
@@ -32,7 +31,7 @@ class Sqs(NamedTuple):
 
 @requires(
     which("mcsqs") and which("str2cif"),
-    "run_mcsqs requires first installing AT-AT, see https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/",
+    "run_mcsqs requires ATAT, see https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/",
 )
 def run_mcsqs(
     structure: Structure,
@@ -146,7 +145,7 @@ def run_mcsqs(
 
         raise RuntimeError("mcsqs exited before timeout reached")
 
-    except TimeoutExpired:
+    except TimeoutExpired as exc:
         for process in mcsqs_find_sqs_processes:
             process.kill()
             process.communicate()
@@ -157,7 +156,7 @@ def run_mcsqs(
                 raise RuntimeError(
                     "mcsqs did not generate output files, "
                     "is search_time sufficient or are number of instances too high?"
-                )
+                ) from exc
 
             process = Popen(["mcsqs", "-best"])
             process.communicate()
@@ -166,7 +165,7 @@ def run_mcsqs(
             return _parse_sqs_path(".")
 
         os.chdir(original_directory)
-        raise TimeoutError("Cluster expansion took too long.")
+        raise TimeoutError("Cluster expansion took too long.") from exc
 
 
 def _parse_sqs_path(path) -> Sqs:
@@ -191,9 +190,7 @@ def _parse_sqs_path(path) -> Sqs:
         process = Popen(["str2cif"], stdin=input_file, stdout=output_file, cwd=path)
         process.communicate()
 
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        best_sqs = Structure.from_file(path / "bestsqs.out")
+    best_sqs = Structure.from_file(path / "bestsqs.out")
 
     # Get best SQS objective function
     with open(path / "bestcorr.out") as file:

src/pymatgen/entries/correction_calculator.py

@@ -226,7 +226,7 @@ def compute_corrections(self, exp_entries: list, calc_entries: dict) -> dict:
 
         with warnings.catch_warnings():
             # numpy raises warning if the entire array is nan values
-            warnings.simplefilter("ignore", category=RuntimeWarning)
+            warnings.filterwarnings("ignore", message="Mean of empty slice", category=RuntimeWarning)
             mean_uncert = np.nanmean(sigma)
 
         sigma = np.where(np.isnan(sigma), mean_uncert, sigma)

src/pymatgen/transformations/advanced_transformations.py

@@ -923,7 +923,7 @@ def find_codopant(
     for sym in symbols:
         try:
             with warnings.catch_warnings():
-                warnings.simplefilter("ignore")
+                warnings.filterwarnings("ignore", message=r"No (default )?ionic radius for .+")
                 sp = Species(sym, oxidation_state)
                 radius = sp.ionic_radius
                 if radius is not None:

src/pymatgen/util/testing/__init__.py

@@ -12,13 +12,13 @@
 import string
 from pathlib import Path
 from typing import TYPE_CHECKING
-from unittest import TestCase
 
 import pytest
 from monty.json import MontyDecoder, MontyEncoder, MSONable
 from monty.serialization import loadfn
 
 from pymatgen.core import ROOT, SETTINGS, Structure
+from pymatgen.util.testing._temp_testcase import _TempTestCase4Migrate
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -35,7 +35,7 @@
 FAKE_POTCAR_DIR = f"{VASP_IN_DIR}/fake_potcars"
 
 
-class PymatgenTest(TestCase):
+class PymatgenTest(_TempTestCase4Migrate):
     """Extends unittest.TestCase with several assert methods for array and str comparison."""
 
     # dict of lazily-loaded test structures (initialized to None)

src/pymatgen/util/testing/_temp_testcase.py

@@ -0,0 +1,84 @@
+"""Temporary TestCase for migration to `pytest` framework,
+inserted FutureWarning for unittest.TestCase-specific methods.
+
+TODO: remove entire module after migration
+"""
+
+# ruff: noqa: PT009, PT027
+
+from __future__ import annotations
+
+import warnings
+from unittest import TestCase
+
+
+class _TempTestCase4Migrate(TestCase):
+    @staticmethod
+    def _issue_warning(method_name):
+        warnings.warn(
+            f"unittest {method_name=} will not be supported by pytest after migration by 2026-01-01, see PR4209.",
+            FutureWarning,
+            stacklevel=2,
+        )
+
+    def setUp(self, *args, **kwargs):
+        self._issue_warning("setUp")
+        super().setUp(*args, **kwargs)
+
+    def tearDown(self, *args, **kwargs):
+        self._issue_warning("tearDown")
+        super().tearDown(*args, **kwargs)
+
+    @classmethod
+    def setUpClass(cls, *args, **kwargs):
+        cls._issue_warning("setUpClass")
+        super().setUpClass(*args, **kwargs)
+
+    @classmethod
+    def tearDownClass(cls, *args, **kwargs):
+        cls._issue_warning("tearDownClass")
+        super().tearDownClass(*args, **kwargs)
+
+    def assertEqual(self, *args, **kwargs):
+        self._issue_warning("assertEqual")
+        return super().assertEqual(*args, **kwargs)
+
+    def assertNotEqual(self, *args, **kwargs):
+        self._issue_warning("assertNotEqual")
+        return super().assertNotEqual(*args, **kwargs)
+
+    def assertTrue(self, *args, **kwargs):
+        self._issue_warning("assertTrue")
+        return super().assertTrue(*args, **kwargs)
+
+    def assertFalse(self, *args, **kwargs):
+        self._issue_warning("assertFalse")
+        return super().assertFalse(*args, **kwargs)
+
+    def assertIsNone(self, *args, **kwargs):
+        self._issue_warning("assertIsNone")
+        return super().assertIsNone(*args, **kwargs)
+
+    def assertIsNotNone(self, *args, **kwargs):
+        self._issue_warning("assertIsNotNone")
+        return super().assertIsNotNone(*args, **kwargs)
+
+    def assertIn(self, *args, **kwargs):  # codespell:ignore
+        self._issue_warning("assertIn")  # codespell:ignore
+        return super().assertIn(*args, **kwargs)  # codespell:ignore
+
+    def assertNotIn(self, *args, **kwargs):
+        self._issue_warning("assertNotIn")
+        return super().assertNotIn(*args, **kwargs)
+
+    def assertIsInstance(self, *args, **kwargs):
+        self._issue_warning("assertIsInstance")
+        return super().assertIsInstance(*args, **kwargs)
+
+    def assertNotIsInstance(self, *args, **kwargs):
+        self._issue_warning("assertNotIsInstance")
+        return super().assertNotIsInstance(*args, **kwargs)
+
+    def assertRaises(self, *args, **kwargs):
+        self._issue_warning("assertRaises")
+        return super().assertRaises(*args, **kwargs)

tests/analysis/test_phase_diagram.py

@@ -2,7 +2,6 @@
 
 import collections
 import unittest
-import unittest.mock
 from itertools import combinations
 from numbers import Number
 from unittest import TestCase

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
@@ -17,9 +16,6 @@
 
 @pytest.mark.skipif(not which("bader"), reason="bader executable not present")
 class TestBaderAnalysis(PymatgenTest):
-    def setUp(self):
-        warnings.catch_warnings()
-
     def test_init(self):
         # test with reference file
         analysis = BaderAnalysis(

tests/command_line/test_mcsqs_caller.py

@@ -17,7 +17,7 @@
 TEST_DIR = f"{TEST_FILES_DIR}/io/atat/mcsqs"
 
 
-@pytest.mark.skipif(not (which("mcsqs") and which("str2cif")), reason="mcsqs executable not present")
+@pytest.mark.skipif(not (which("mcsqs") and which("str2cif")), reason="mcsqs or str2cif executable not present")
 class TestMcsqsCaller(PymatgenTest):
     def setUp(self):
         self.pzt_structs = loadfn(f"{TEST_DIR}/pzt-structs.json")
@@ -103,5 +103,6 @@ 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/core/test_units.py

@@ -110,14 +110,14 @@ def test_memory(self):
         assert mega_0 == mega_1 == mega_2 == mega_3
 
     def test_deprecated_memory(self):
-        # TODO: remove after 2025-01-01
+        """TODO: remove entire test method after 2025-01-01"""
         for unit in ("Kb", "kb", "Mb", "mb", "Gb", "gb", "Tb", "tb"):
             with pytest.warns(DeprecationWarning, match=f"Unit {unit} is deprecated"):
                 Memory(1, unit)
 
         with warnings.catch_warnings():
-            warnings.simplefilter("error")
             for unit in ("KB", "MB", "GB", "TB"):
+                warnings.filterwarnings("error", f"Unit {unit} is deprecated", DeprecationWarning)
                 Memory(1, unit)
 
     def test_unitized(self):

tests/io/vasp/test_inputs.py

@@ -208,9 +208,8 @@ def test_from_file_potcar_overwrite_elements(self):
         copyfile(f"{VASP_IN_DIR}/POSCAR_C2", tmp_poscar_path := f"{self.tmp_path}/POSCAR")
         copyfile(f"{VASP_IN_DIR}/POTCAR_C2.gz", f"{self.tmp_path}/POTCAR.gz")
 
-        with warnings.catch_warnings(record=True) as record:
-            _poscar = Poscar.from_file(tmp_poscar_path)
-        assert not any("Elements in POSCAR would be overwritten" in str(warning.message) for warning in record)
+        warnings.filterwarnings("error", message="Elements in POSCAR would be overwritten")
+        _poscar = Poscar.from_file(tmp_poscar_path)
 
     def test_from_str_default_names(self):
         """Similar to test_from_file_bad_potcar, ensure "default_names"
@@ -237,18 +236,19 @@ def test_from_str_default_names(self):
         assert poscar.site_symbols == ["Si", "O"]
 
         # Assert no warning if using the same elements (or superset)
-        with warnings.catch_warnings(record=True) as record:
+        with warnings.catch_warnings():
+            warnings.filterwarnings("error", message="Elements in POSCAR would be overwritten")
+
             poscar = Poscar.from_str(poscar_str, default_names=["Si", "F"])
             assert poscar.site_symbols == ["Si", "F"]
 
             poscar = Poscar.from_str(poscar_str, default_names=["Si", "F", "O"])
             assert poscar.site_symbols == ["Si", "F"]
-        assert not any("Elements in POSCAR would be overwritten" in str(warning.message) for warning in record)
 
         # Make sure it could be bypassed (by using None, when not check_for_potcar)
-        with warnings.catch_warnings(record=True) as record:
+        with warnings.catch_warnings():
+            warnings.filterwarnings("error", message="Elements in POSCAR would be overwritten")
             _poscar = Poscar.from_str(poscar_str, default_names=None)
-        assert not any("Elements in POSCAR would be overwritten" in str(warning.message) for warning in record)
 
     def test_from_str_default_names_vasp4(self):
         """Poscar.from_str with default_names given could also be used to

tests/util/test_testing_migrate.py

@@ -0,0 +1,82 @@
+"""This is not a functional test but a utility to verify behaviors specific to
+`unittest.TestCase`. It ensures we're aware the side effects from the migration.
+
+TODO: remove this test module after migration (2026-01-01), see PR 4209.
+"""
+
+# ruff: noqa: PT009, PT027, FBT003
+
+from __future__ import annotations
+
+import pytest
+
+from pymatgen.util.testing import PymatgenTest
+
+
+@pytest.mark.filterwarnings("ignore", message="will not be supported by pytest after migration", category=FutureWarning)
+class TestPymatgenTestTestCase(PymatgenTest):
+    """Baseline inspector for migration side effects."""
+
+    def test_unittest_testcase_specific_funcs(self):
+        """Make sure TestCase-specific methods are available until migration,
+        and FutureWarning is emitted.
+        """
+        msg = "will not be supported by pytest after migration"
+
+        # Testing setUp and tearDown methods
+        with pytest.warns(FutureWarning, match=msg):
+            self.setUp()
+        with pytest.warns(FutureWarning, match=msg):
+            self.tearDown()
+
+        # Testing class-level setUp and tearDown methods
+        with pytest.warns(FutureWarning, match=msg):
+            self.setUpClass()
+        with pytest.warns(FutureWarning, match=msg):
+            self.tearDownClass()
+
+        # Test the assertion methods
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertEqual(1, 1)
+
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertNotEqual(1, 2)
+
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertTrue(True)
+
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertFalse(False)
+
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertIsNone(None)
+
+        with pytest.warns(FutureWarning, match=msg):
+            self.assertIsNotNone("hello")
+
+        with pytest.warns(FutureWarning, match=msg), self.assertRaises(ValueError):
+            raise ValueError("hi")
+
+
+class TestPymatgenTestPytest:
+    def test_unittest_testcase_specific_funcs(self):
+        """Test unittest.TestCase-specific methods for migration to pytest."""
+        # Testing setUp and tearDown methods
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.setUp()
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.tearDown()
+
+        # Testing class-level setUp and tearDown methods
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.setUpClass()
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.tearDownClass()
+
+        # Test the assertion methods
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.assertTrue(True)
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.assertFalse(False)
+        with pytest.raises(AttributeError, match="'TestPymatgenTestPytest' object has no attribute"):
+            self.assertEqual(1, 1)