clean up warning filters

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/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", "Mean of empty slice", 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", r"No (default )?ionic radius for .+", UserWarning)
                 sp = Species(sym, oxidation_state)
                 radius = sp.ionic_radius
                 if radius is not None:

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/core/test_units.py

@@ -117,7 +117,7 @@ def test_deprecated_memory(self):
 
         with warnings.catch_warnings():
             for unit in ("KB", "MB", "GB", "TB"):
-                warnings.filterwarnings("error", message=f"Unit {unit} is deprecated", category=DeprecationWarning)
+                warnings.filterwarnings("error", f"Unit {unit} is deprecated", DeprecationWarning)
                 Memory(1, unit)
 
     def test_unitized(self):