Show FutureWarning and DeprecationWarning for pytest

pyproject.toml

@@ -57,7 +57,7 @@ dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
     "monty>=2024.7.29",
-    "networkx>=3",  # PR #4116
+    "networkx>=3",  # PR4116
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",
@@ -252,7 +252,17 @@ docstring-code-format = true
 "dev_scripts/*" = ["D"]
 
 [tool.pytest.ini_options]
-addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mode=importlib"
+addopts = "--durations=30 --quiet -r xXs --color=yes --import-mode=importlib"
+filterwarnings = [
+    # NOTE: the last matching option is used
+    "ignore::Warning",               # Ignore all Warning
+    "default::FutureWarning",        # Show FutureWarnings
+    "default::DeprecationWarning",   # Show DeprecationWarnings
+    # TODO: pybtex (perhaps some others) emits the following warnings
+    'ignore:pkg_resources is deprecated as an API:DeprecationWarning',
+    'ignore:distutils Version classes are deprecated:DeprecationWarning',
+    'ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning',
+]
 
 [tool.coverage.run]
 parallel = true

src/pymatgen/alchemy/materials.py

@@ -192,7 +192,7 @@ def get_vasp_input(self, vasp_input_set: type[VaspInputSet] = MPRelaxSet, **kwar
                 to create VASP input files from structures
             **kwargs: All keyword args supported by the VASP input set.
         """
-        dct = vasp_input_set(self.final_structure, **kwargs).get_vasp_input()
+        dct = vasp_input_set(self.final_structure, **kwargs).get_input_set()
         dct["transformations.json"] = json.dumps(self.as_dict())
         return dct
 

src/pymatgen/analysis/magnetism/heisenberg.py

@@ -320,6 +320,8 @@ def _get_exchange_df(self):
 
                 # Ignore the row if it is a duplicate to avoid singular matrix
                 # Create a temporary DataFrame with the new row
+                ex_mat = ex_mat.dropna(how="all", axis=1)
+                ex_row = ex_row.dropna(how="all", axis=1)
                 temp_df = pd.concat([ex_mat, ex_row], ignore_index=True)
                 if temp_df[j_columns].equals(temp_df[j_columns].drop_duplicates(keep="first")):
                     e_index = self.ordered_structures.index(sgraph.structure)

src/pymatgen/analysis/piezo_sensitivity.py

@@ -620,17 +620,17 @@ def get_rand_FCM(self, asum=15, force=10):
             for n in range(n_sites):
                 dyn_mass[m][n] = dyn[m][n] * np.sqrt(masses[m]) * np.sqrt(masses[n])
 
-        supercell = pn_struct.get_supercell()
-        primitive = pn_struct.get_primitive()
+        supercell = pn_struct.supercell
+        primitive = pn_struct.primitive
 
         converter = dyntofc.DynmatToForceConstants(primitive, supercell)
 
         dyn = np.reshape(np.swapaxes(dyn_mass, 1, 2), (n_sites * 3, n_sites * 3))
 
-        converter.set_dynamical_matrices(dynmat=[dyn])
+        converter.dynamical_matrices = [dyn]
 
         converter.run()
-        return converter.get_force_constants()
+        return converter.force_constants
 
 
 def get_piezo(BEC, IST, FCM, rcond=0.0001):

src/pymatgen/analysis/quasiharmonic.py

@@ -16,7 +16,7 @@
 import numpy as np
 from monty.dev import deprecated
 from scipy.constants import physical_constants
-from scipy.integrate import quadrature
+from scipy.integrate import quad
 from scipy.misc import derivative
 from scipy.optimize import minimize
 
@@ -261,7 +261,7 @@ def debye_integral(y):
         # 6.4939394 (from wolfram alpha).
         factor = 3.0 / y**3
         if y < 155:
-            integral = quadrature(lambda x: x**3 / (np.exp(x) - 1.0), 0, y)
+            integral = quad(lambda x: x**3 / (np.exp(x) - 1.0), 0, y)
             return next(iter(integral)) * factor
         return 6.493939 * factor
 
@@ -299,6 +299,11 @@ def gruneisen_parameter(self, temperature, volume):
             d3EdV3 = np.polyder(p, 3)(volume)
         else:
             func = self.ev_eos_fit.func
+
+            # TODO: scipy.misc.derivative is deprecated in SciPy v1.10.0;
+            # and will be completely removed in SciPy v1.12.0.
+            # You may consider using findiff: https://github.com/maroba/findiff
+            # or numdifftools: https://github.com/pbrod/numdifftools
             dEdV = derivative(func, volume, dx=1e-3)
             d2EdV2 = derivative(func, volume, dx=1e-3, n=2, order=5)
             d3EdV3 = derivative(func, volume, dx=1e-3, n=3, order=7)

src/pymatgen/analysis/wulff.py

@@ -578,7 +578,7 @@ def get_plotly(
             x=[0],
             y=[0],
             z=[0],
-            colorbar=go.ColorBar(
+            colorbar=go.mesh3d.ColorBar(
                 title={
                     "text": f"Surface energy {units}",
                     "side": "right",

src/pymatgen/io/lammps/inputs.py

@@ -913,14 +913,18 @@ def write_inputs(self, output_dir: str, **kwargs) -> None:
             output_dir (str): Directory to output the input files.
             **kwargs: kwargs supported by LammpsData.write_file.
         """
-        write_lammps_inputs(
-            output_dir=output_dir,
-            script_template=self.script_template,
-            settings=self.settings,
-            data=self.data,
-            script_filename=self.script_filename,
-            **kwargs,
-        )
+        # TODO: write_lammps_inputs is deprecated
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", message="write_lammps_inputs is deprecated")
+
+            write_lammps_inputs(
+                output_dir=output_dir,
+                script_template=self.script_template,
+                settings=self.settings,
+                data=self.data,
+                script_filename=self.script_filename,
+                **kwargs,
+            )
 
     @classmethod
     def md(

src/pymatgen/io/lammps/outputs.py

@@ -81,9 +81,8 @@ def from_dict(cls, dct: dict) -> Self:
         Returns:
             LammpsDump
         """
-        items = {"timestep": dct["timestep"], "natoms": dct["natoms"]}
-        items["box"] = LammpsBox.from_dict(dct["box"])
-        items["data"] = pd.read_json(dct["data"], orient="split")
+        items = {"timestep": dct["timestep"], "natoms": dct["natoms"], "box": LammpsBox.from_dict(dct["box"])}
+        items["data"] = pd.read_json(StringIO(dct["data"]), orient="split")
         return cls(**items)
 
     def as_dict(self) -> dict[str, Any]:

src/pymatgen/io/lobster/lobsterenv.py

@@ -190,16 +190,16 @@ def __init__(
             if valences_from_charges and filename_charge is not None:
                 chg = Charge(filename=filename_charge)
                 if which_charge == "Mulliken":
-                    self.valences = chg.Mulliken
+                    self.valences = chg.mulliken
                 elif which_charge == "Loewdin":
-                    self.valences = chg.Loewdin
+                    self.valences = chg.loewdin
 
             elif valences_from_charges and obj_charge is not None:
                 chg = obj_charge
                 if which_charge == "Mulliken":
-                    self.valences = chg.Mulliken
+                    self.valences = chg.mulliken
                 elif which_charge == "Loewdin":
-                    self.valences = chg.Loewdin
+                    self.valences = chg.loewdin
 
             else:
                 bv_analyzer = BVAnalyzer()

src/pymatgen/io/lobster/outputs.py

@@ -1677,7 +1677,7 @@ def _read(self, lines: list[str], spin_numbers: list[int]) -> None:
                         _lines.append(float(el))
                 overlaps.append(_lines)
                 if len(overlaps) == len(_lines):
-                    self.band_overlaps_dict[spin]["matrices"].append(np.matrix(overlaps))
+                    self.band_overlaps_dict[spin]["matrices"].append(np.array(overlaps))
 
     def has_good_quality_maxDeviation(self, limit_maxDeviation: float = 0.1) -> bool:
         """Check if the maxDeviation from the ideal bandoverlap is smaller

src/pymatgen/io/openff.py

@@ -85,7 +85,7 @@ def mol_graph_from_openff_mol(molecule: tk.Molecule) -> MoleculeGraph:
     Returns:
         MoleculeGraph: The converted MoleculeGraph.
     """
-    mol_graph = MoleculeGraph.with_empty_graph(Molecule([], []), name="none")
+    mol_graph = MoleculeGraph.from_empty_graph(Molecule([], []), name="none")
     p_table = {el.Z: str(el) for el in Element}
     total_charge = cum_atoms = 0
 
@@ -173,7 +173,7 @@ def infer_openff_mol(
     Returns:
         tk.Molecule: The inferred OpenFF Molecule.
     """
-    mol_graph = MoleculeGraph.with_local_env_strategy(mol_geometry, OpenBabelNN())
+    mol_graph = MoleculeGraph.from_local_env_strategy(mol_geometry, OpenBabelNN())
     mol_graph = metal_edge_extender(mol_graph)
     return mol_graph_to_openff_mol(mol_graph)
 

src/pymatgen/io/phonopy.py

@@ -266,17 +266,17 @@ def get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=Non
     )
 
     if yaml_fname is not None:
-        displacements = phonon.get_displacements()
+        displacements = phonon.displacements
         write_disp_yaml(
             displacements=displacements,
-            supercell=phonon.get_supercell(),
+            supercell=phonon.supercell,
             filename=yaml_fname,
         )
 
     # Supercell structures with displacement
-    disp_supercells = phonon.get_supercells_with_displacements()
+    disp_supercells = phonon.supercells_with_displacements
     # Perfect supercell structure
-    init_supercell = phonon.get_supercell()
+    init_supercell = phonon.supercell
     # Structure list to be returned
     structure_list = [get_pmg_structure(init_supercell)]
 
@@ -313,7 +313,7 @@ def get_phonon_dos_from_fc(
     """
     structure_phonopy = get_phonopy_structure(structure)
     phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
-    phonon.set_force_constants(force_constants)
+    phonon.force_constants = force_constants
     phonon.run_mesh(
         mesh_density,
         is_mesh_symmetry=False,
@@ -329,7 +329,7 @@ def get_phonon_dos_from_fc(
 
     phonon.run_projected_dos(freq_min=freq_min, freq_max=freq_max, freq_pitch=freq_pitch)
 
-    dos_raw = phonon.projected_dos.get_partial_dos()
+    dos_raw = (phonon.projected_dos.frequency_points, phonon.projected_dos.projected_dos)
     p_doses = dict(zip(structure, dos_raw[1], strict=True))
 
     total_dos = PhononDos(dos_raw[0], dos_raw[1].sum(axis=0))
@@ -360,7 +360,7 @@ def get_phonon_band_structure_from_fc(
     """
     structure_phonopy = get_phonopy_structure(structure)
     phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
-    phonon.set_force_constants(force_constants)
+    phonon.force_constants = force_constants
     phonon.run_mesh(mesh_density, is_mesh_symmetry=False, is_gamma_center=True)
     mesh = phonon.get_mesh_dict()
 
@@ -394,14 +394,14 @@ def get_phonon_band_structure_symm_line_from_fc(
     """
     structure_phonopy = get_phonopy_structure(structure)
     phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, symprec=symprec, **kwargs)
-    phonon.set_force_constants(force_constants)
+    phonon.force_constants = force_constants
 
     k_path = HighSymmKpath(structure, symprec=symprec)
 
     kpoints, labels = k_path.get_kpoints(line_density=line_density, coords_are_cartesian=False)
 
     phonon.run_qpoints(kpoints)
-    frequencies = phonon.qpoints.get_frequencies().T
+    frequencies = phonon.qpoints.frequencies.T
 
     labels_dict = {a: k for a, k in zip(labels, kpoints, strict=True) if a != ""}
 

src/pymatgen/io/vasp/outputs.py

@@ -1523,7 +1523,7 @@ def _parse_structure(self, elem: XML_Element) -> Structure:
     @staticmethod
     def _parse_diel(elem: XML_Element) -> tuple[list, list, list]:
         """Parse dielectric properties."""
-        if elem.find("real") and elem.find("imag"):
+        if elem.find("real") is not None and elem.find("imag") is not None:
             imag = [
                 [_vasprun_float(line) for line in r.text.split()]  # type: ignore[union-attr]
                 for r in elem.find("imag").find("array").find("set").findall("r")  # type: ignore[union-attr]

src/pymatgen/io/vasp/sets.py

@@ -2676,7 +2676,7 @@ def incar_updates(self) -> dict[str, Any]:
         updates = {
             "ALGO": "Fast",
             "ISIF": 3,
-            "LANGEVIN_GAMMA": [10] * self.structure.ntypesp,
+            "LANGEVIN_GAMMA": [10] * self.structure.n_elems,
             "LANGEVIN_GAMMA_L": 1,
             "MDALGO": 3,
             "PMASS": 10,
@@ -2707,7 +2707,7 @@ def incar_updates(self) -> dict[str, Any]:
             "LDAU": False,
         }
         # Set NPT-AIMD ENCUT = 1.5 * VASP_default
-        enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.ntypesp)]
+        enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.n_elems)]
         updates["ENCUT"] = max(enmax) * 1.5
         return updates
 

src/pymatgen/symmetry/analyzer.py

@@ -274,7 +274,11 @@ def _get_symmetry(self) -> tuple[NDArray, NDArray]:
             "translations" gives the numpy float64 array of the translation
             vectors in scaled positions.
         """
-        dct = spglib.get_symmetry(self._cell, symprec=self._symprec, angle_tolerance=self._angle_tol)
+        with warnings.catch_warnings():
+            # TODO: DeprecationWarning: Use get_magnetic_symmetry() for cell with magnetic moments.
+            warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry", category=DeprecationWarning)
+            dct = spglib.get_symmetry(self._cell, symprec=self._symprec, angle_tolerance=self._angle_tol)
+
         if dct is None:
             symprec = self._symprec
             raise ValueError(

src/pymatgen/transformations/advanced_transformations.py

@@ -21,13 +21,13 @@
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.energy_models import SymmetryModel
 from pymatgen.analysis.ewald import EwaldSummation
-from pymatgen.analysis.gb.grain import GrainBoundaryGenerator
 from pymatgen.analysis.local_env import MinimumDistanceNN
 from pymatgen.analysis.structure_matcher import SpinComparator, StructureMatcher
 from pymatgen.analysis.structure_prediction.substitution_probability import SubstitutionPredictor
 from pymatgen.command_line.enumlib_caller import EnumError, EnumlibAdaptor
 from pymatgen.command_line.mcsqs_caller import run_mcsqs
 from pymatgen.core import DummySpecies, Element, Species, Structure, get_el_sp
+from pymatgen.core.interface import GrainBoundaryGenerator
 from pymatgen.core.surface import SlabGenerator
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.io.ase import AseAtomsAdaptor

tests/analysis/elasticity/test_elastic.py

@@ -465,6 +465,10 @@ def test_get_diff_coeff(self):
             backward_26,
             [137 / 180, -27 / 5, 33 / 2, -254 / 9, 117 / 4, -87 / 5, 203 / 45],
         )
+        # TODO: scipy.misc.central_diff_weights is deprecated in SciPy v1.10.0;
+        # and will be completely removed in SciPy v1.12.0.
+        # You may consider using findiff: https://github.com/maroba/findiff
+        # or numdifftools: https://github.com/pbrod/numdifftools
         assert_allclose(central_29, central_diff_weights(9, 2))
 
     def test_generate_pseudo(self):

tests/analysis/test_piezo_sensitivity.py

@@ -220,7 +220,7 @@ def test_rand_fcm(self):
         structure = get_phonopy_structure(self.piezo_struct)
         pn_struct = Phonopy(structure, np.eye(3), np.eye(3))
 
-        pn_struct.set_force_constants(rand_FCM)
+        pn_struct.force_constants = rand_FCM
         dyn = pn_struct.get_dynamical_matrix_at_q([0, 0, 0])
         dyn = np.reshape(dyn, (10, 3, 10, 3)).swapaxes(1, 2)
         dyn = np.real(dyn)
@@ -296,7 +296,7 @@ def test_rand_piezo(self):
         structure = get_phonopy_structure(self.piezo_struct)
         pn_struct = Phonopy(structure, np.eye(3), np.eye(3))
 
-        pn_struct.set_force_constants(rand_FCM)
+        pn_struct.force_constants = rand_FCM
         dyn = pn_struct.get_dynamical_matrix_at_q([0, 0, 0])
         dyn = np.reshape(dyn, (10, 3, 10, 3)).swapaxes(1, 2)
         dyn = np.real(dyn)

tests/command_line/test_bader_caller.py

@@ -116,7 +116,9 @@ def test_bader_analysis_from_path(self):
         assert summary["reference_used"]
         assert sum(summary["magmom"]) == approx(28, abs=1e-1)
 
+    @pytest.mark.filterwarnings("ignore:_parse_atomic_densities is deprecated")
     def test_atom_parsing(self):
+        """TODO: Deprecated, remove after 2025-2-26, see PR3652."""
         # test with reference file
         analysis = BaderAnalysis(
             chgcar_filename=f"{VASP_OUT_DIR}/CHGCAR.Fe3O4.gz",

tests/entries/test_compatibility.py

@@ -42,6 +42,7 @@
 PMG_ENTRIES_DIR = os.path.dirname(os.path.abspath(pymatgen.entries.__file__))
 
 
+@pytest.mark.filterwarnings("ignore:MaterialsProjectCompatibility is deprecated")
 class TestCorrectionSpecificity(TestCase):
     """Make sure corrections are only applied to GGA or GGA+U entries."""
 
@@ -202,6 +203,7 @@ def test_overlapping_adjustments():
     assert len(processed) == 0
 
 
+@pytest.mark.filterwarnings("ignore:MaterialsProjectCompatibility is deprecated")
 class TestMaterialsProjectCompatibility(TestCase):
     def setUp(self):
         self.entry1 = ComputedEntry(
@@ -592,6 +594,9 @@ def test_process_entries(self):
         assert len(entries) == 2
 
     def test_parallel_process_entries(self):
+        # TODO: DeprecationWarning: This process (pid=xxxx) is multi-threaded,
+        # use of fork() may lead to deadlocks in the child.
+        # pid = os.fork()
         with pytest.raises(
             ValueError,
             match="Parallel processing is not possible with for 'inplace=True'",
@@ -1132,6 +1137,7 @@ def test_element_processing(self):
         assert entry.energy == approx(-1)
         assert self.gga_compat.process_entry(entry).energy == approx(-1)
 
+    @pytest.mark.filterwarnings("ignore:MaterialsProjectCompatibility is deprecated")
     def test_get_explanation_dict(self):
         compat = MaterialsProjectCompatibility(check_potcar_hash=False)
         entry = ComputedEntry(