Fix other deprecation warnings

abipy/core/kpoints.py

@@ -1043,7 +1043,7 @@ def find_closest(self, obj):
 
         dist = np.empty(len(self))
         for i, kpt in enumerate(self):
-            dist[i] = kpt.lattice.norm(kpt.frac_coords - frac_coords)
+            dist[i] = float(kpt.lattice.norm(kpt.frac_coords - frac_coords))
 
         ind = dist.argmin()
         return ind, self[ind], np.copy(dist[ind])
@@ -1915,7 +1915,7 @@ def __init__(self, structure, mesh, is_shift, has_timrev):
         for ik_bz, ir_gp_id in enumerate(mapping):
             inds = np.where(uniq == ir_gp_id)
             assert len(inds) == 1
-            self.bz2ibz[ik_bz] = inds[0]
+            self.bz2ibz[ik_bz] = int(inds[0])
 
     def __str__(self):
         return self.to_string()

abipy/core/skw.py

@@ -88,7 +88,7 @@ def get_sampling(self, mesh, is_shift):
             inds = np.where(uniq == ir_gp_id)
             #print("inds", inds, "inds[0]", inds[0])
             assert len(inds) == 1
-            bz2ibz[i] = inds[0]
+            bz2ibz[i] = int(inds[0])
             #print("%3d ->%3d %s" % (i, ir_gp_id, (gp + [0.5, 0.5, 0.5]) / mesh))
             #print("%3d ->%3d %s" % (i, ir_gp_id, (gp + kshift) / mesh))
 

abipy/core/structure.py

@@ -391,6 +391,13 @@ def from_ase_atoms(cls, atoms) -> Structure:
         import pymatgen.io.ase as aio
         return aio.AseAtomsAdaptor.get_structure(atoms, cls=cls)
 
+    # FIXME: Temporary workaround to maintain compatbility with old pymatgen versions.
+    # m_elems was added in v2024.7.18
+    @property
+    def n_elems(self) -> int:
+        """Number of types of atoms."""
+
+        return len(self.types_of_species)
     def to_ase_atoms(self, calc=None):
         """
         Returns ASE Atoms object from structure and attach calculator calc.

abipy/iotools/tests/test_xsf.py

@@ -105,7 +105,7 @@ def test_bxsf_write(self):
         tmp_file = tempfile.TemporaryFile(mode="w+")
 
         nsppol, nband, ndivs, fermie = 1, 2, (2,2,2), 0.0
-        energies = np.arange(nsppol * nband * np.product(ndivs))
+        energies = np.arange(nsppol * nband * np.prod(ndivs))
         bxsf_write(tmp_file, self.mgb2, nsppol, nband, ndivs, energies, fermie, unit="Ha")
 
         xsf_string = \

abipy/iotools/xsf.py

@@ -142,7 +142,7 @@ def xsf_write_data(file, structure, data, add_replicas=True, cplx_mode=None,
     fdata = transpose_last3dims(data)
     fgrid = fdata.shape[-3:]
 
-    cell = structure.lattice_vectors(space="r")
+    cell = structure.lattice.matrix
     origin = np.zeros(3)
 
     fwrite('BEGIN_BLOCK_DATAGRID_3D\n')
@@ -227,7 +227,7 @@ def bxsf_write(file, structure, nsppol, nband, ndivs, ucdata_sbk, fermie, unit="
     fw("0 0 0\n")                   # Unshifted meshes are not supported.
 
     # Reciprocal lattice vectors in Ang^{-1}
-    gcell = structure.lattice_vectors("g")
+    gcell = structure.lattice.reciprocal_lattice.matrix
     for i in range(3):
         fw('%f %f %f\n' % tuple(gcell[i]))
 

abipy/lumi/deltaSCF.py

@@ -433,7 +433,7 @@ def lineshape_1D_zero_temp(self,energy_range=[0.5,5],max_m=25,phonon_width=0.01,
             A=A*E_x**3
 
         if normalized=="Area":
-            C = 1 / (simps(A, E_x))
+            C = 1 / (simps(A, x=E_x))
         if normalized=="Sum":
             C=1/(max(A))
 

abipy/panels/core.py

@@ -342,9 +342,9 @@ def ply(fig, sizing_mode='stretch_both', with_chart_studio=False, with_help=Fals
         showLink=True,
         plotlyServerURL="https://chart-studio.plotly.com",
     )
-    
+
     plotly_fig = mpl_to_ply(fig)
-    
+
     plotly_pane = pn.pane.Plotly(plotly_fig, config=config)
     ca(plotly_pane)
 
@@ -1566,7 +1566,7 @@ class BaseRobotPanel(AbipyParameterized):
     def __init__(self, robot, **params):
         self.robot = robot
         self.compare_params_btn = pnw.Button(name="Compare structures", button_type='primary')
-        self.transpose_params = pnw.Checkbox(name='Transpose table', default=True)
+        self.transpose_params = pnw.Checkbox(name='Transpose table', value=True)
 
         super().__init__(**params)