replace tests 'str(x) is not None' with actual expected value (#3472)

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -1191,8 +1191,7 @@ def get_coordination_symmetry_measures(self, only_minimum=True, all_csms=True, o
     def _update_results_all_csms(self, result_dict, permutations, imin, geometry):
         permutation = permutations[imin]
         # Without central site, centered on the centroid (centroid does not include the central site)
-        # result_dict[geometry.mp_symbol]['csm_wocs_ctwocc'] = \
-        # result[imin]
+        # result_dict[geometry.mp_symbol]['csm_wocs_ctwocc'] = result[imin]
         pdist = self.local_geometry.points_wocs_ctwocc(permutation=permutation)
         pperf = self.perfect_geometry.points_wocs_ctwocc()
         sm_info = symmetry_measure(points_distorted=pdist, points_perfect=pperf)

pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -205,23 +205,23 @@ def diamond_functions(xx, yy, y_x0, x_y0):
     Returns:
         A dictionary with the lower and upper diamond functions.
     """
-    npxx = np.array(xx)
-    npyy = np.array(yy)
-    if np.any(npxx == npyy):
+    np_xx = np.array(xx)
+    np_yy = np.array(yy)
+    if np.any(np_xx == np_yy):
         raise RuntimeError("Invalid points for diamond_functions")
-    if np.all(npxx < npyy) or np.all(npxx > npyy):
-        if npxx[0] < npyy[0]:
-            p1 = npxx
-            p2 = npyy
+    if np.all(np_xx < np_yy) or np.all(np_xx > np_yy):
+        if np_xx[0] < np_yy[0]:
+            p1 = np_xx
+            p2 = np_yy
         else:
-            p1 = npyy
-            p2 = npxx
-    elif npxx[0] < npyy[0]:
-        p1 = npxx
-        p2 = npyy
+            p1 = np_yy
+            p2 = np_xx
+    elif np_xx[0] < np_yy[0]:
+        p1 = np_xx
+        p2 = np_yy
     else:
-        p1 = npyy
-        p2 = npxx
+        p1 = np_yy
+        p2 = np_xx
     slope = (p2[1] - p1[1]) / (p2[0] - p1[0])
     if slope > 0.0:
         x_bpoint = p1[0] + x_y0

pymatgen/analysis/elasticity/stress.py

@@ -81,10 +81,7 @@ def piola_kirchoff_1(self, def_grad):
             def_grad (3x3 array-like): deformation gradient tensor
         """
         if not self.is_symmetric:
-            raise ValueError(
-                "The stress tensor is not symmetric, \
-                             PK stress is based on a symmetric stress tensor."
-            )
+            raise ValueError("The stress tensor is not symmetric, PK stress is based on a symmetric stress tensor.")
         def_grad = SquareTensor(def_grad)
         return def_grad.det * np.dot(self, def_grad.inv.trans)
 
@@ -97,8 +94,5 @@ def piola_kirchoff_2(self, def_grad):
         """
         def_grad = SquareTensor(def_grad)
         if not self.is_symmetric:
-            raise ValueError(
-                "The stress tensor is not symmetric, \
-                             PK stress is based on a symmetric stress tensor."
-            )
+            raise ValueError("The stress tensor is not symmetric, PK stress is based on a symmetric stress tensor.")
         return def_grad.det * np.dot(np.dot(def_grad.inv, self), def_grad.inv.trans)

pymatgen/analysis/local_env.py

@@ -4204,8 +4204,7 @@ def from_preset(cls, preset) -> CutOffDictNN:
 
         Args:
             preset (str): A preset name. The list of supported presets are:
-                - "vesta_2019": The distance cutoffs used by the VESTA
-                  visualisation program.
+                - "vesta_2019": The distance cutoffs used by the VESTA visualisation program.
 
         Returns:
             A CutOffDictNN using the preset cut-off dictionary.

pymatgen/analysis/structure_analyzer.py

@@ -40,13 +40,13 @@ def average_coordination_number(structures, freq=10):
     for spec in structures[0].composition.as_dict():
         coordination_numbers[spec] = 0.0
     count = 0
-    for i, s in enumerate(structures):
-        if i % freq != 0:
+    for idx, site in enumerate(structures):
+        if idx % freq != 0:
             continue
         count += 1
         vnn = VoronoiNN()
-        for j, atom in enumerate(s):
-            cn = vnn.get_cn(s, j, use_weights=True)
+        for j, atom in enumerate(site):
+            cn = vnn.get_cn(site, j, use_weights=True)
             coordination_numbers[atom.species_string] += cn
     elements = structures[0].composition.as_dict()
     return {el: v / elements[el] / count for el, v in coordination_numbers.items()}

pymatgen/analysis/surface_analysis.py

@@ -1008,7 +1008,7 @@ def monolayer_vs_BE(self, plot_eads=False):
 
         Args:
             plot_eads (bool): Option to plot the adsorption energy (binding
-                 energy multiplied by number of adsorbates) instead.
+                energy multiplied by number of adsorbates) instead.
 
         Returns:
             Plot: Plot of binding energy vs monolayer for all facets.

pymatgen/core/lattice.py

@@ -1315,7 +1315,7 @@ def get_points_in_sphere(
             center: Cartesian coordinates of center of sphere.
             r: radius of sphere.
             zip_results (bool): Whether to zip the results together to group by
-                 point, or return the raw fcoord, dist, index arrays
+                point, or return the raw fcoord, dist, index arrays
 
         Returns:
             if zip_results:
@@ -1389,7 +1389,7 @@ def get_points_in_sphere_py(
             center: Cartesian coordinates of center of sphere.
             r: radius of sphere.
             zip_results (bool): Whether to zip the results together to group by
-                 point, or return the raw fcoord, dist, index arrays
+                point, or return the raw fcoord, dist, index arrays
 
         Returns:
             if zip_results:
@@ -1446,7 +1446,7 @@ def get_points_in_sphere_old(
             center: Cartesian coordinates of center of sphere.
             r: radius of sphere.
             zip_results (bool): Whether to zip the results together to group by
-                 point, or return the raw fcoord, dist, index arrays
+                point, or return the raw fcoord, dist, index arrays
 
         Returns:
             if zip_results:

pymatgen/electronic_structure/boltztrap2.py

@@ -253,10 +253,10 @@ def get_lattvec(self):
 
     def bandana(self, emin=-np.inf, emax=np.inf):
         """Cut out bands outside the range (emin,emax)."""
-        bandmin = np.min(self.ebands_all, axis=1)
-        bandmax = np.max(self.ebands_all, axis=1)
-        ntoolow = np.count_nonzero(bandmax <= emin)
-        accepted = np.logical_and(bandmin < emax, bandmax > emin)
+        band_min = np.min(self.ebands_all, axis=1)
+        band_max = np.max(self.ebands_all, axis=1)
+        n_too_low = np.count_nonzero(band_max <= emin)
+        accepted = np.logical_and(band_min < emax, band_max > emin)
         # self.data_bkp = np.copy(self.data.ebands)
         self.ebands = self.ebands_all[accepted]
 
@@ -273,7 +273,7 @@ def bandana(self, emin=-np.inf, emax=np.inf):
             self.mommat = self.mommat[:, accepted, :]
         # Removing bands may change the number of valence electrons
         if self.nelect_all:
-            self.nelect = self.nelect_all - self.dosweight * ntoolow
+            self.nelect = self.nelect_all - self.dosweight * n_too_low
 
         return accepted
 
@@ -282,8 +282,7 @@ def set_upper_lower_bands(self, e_lower, e_upper):
         range in the spin up/down bands when calculating the DOS.
         """
         warnings.warn(
-            "This method does not work anymore in case of spin \
-        polarized case due to the concatenation of bands !"
+            "This method does not work anymore in case of spin polarized case due to the concatenation of bands !"
         )
 
         lower_band = e_lower * np.ones((1, self.ebands.shape[1]))
@@ -1166,10 +1165,7 @@ def merge_up_down_doses(dos_up, dos_dn):
     Return:
     CompleteDos object
     """
-    warnings.warn(
-        "This function is not useful anymore. VasprunBSLoader deals \
-                   with spin case."
-    )
+    warnings.warn("This function is not useful anymore. VasprunBSLoader deals with spin case.")
     cdos = Dos(
         dos_up.efermi,
         dos_up.energies,

pymatgen/electronic_structure/plotter.py

@@ -1524,9 +1524,9 @@ def get_projected_plots_dots_patom_pmorb(
                 result, correct index numbers of atoms.
             sum_atoms: Sum projection of the similar atoms together (e.g.: Cu
                 on site-1 and Cu on site-5). The format is {Element: [Site numbers]}, for instance:
-                 {'Cu': [1,5], 'O': [3,4]} means summing projections over Cu on site-1 and Cu on
-                 site-5 and O on site-3 and on site-4. If you do not want to use this functional,
-                 just turn it off by setting sum_atoms = None.
+                {'Cu': [1,5], 'O': [3,4]} means summing projections over Cu on site-1 and Cu on
+                site-5 and O on site-3 and on site-4. If you do not want to use this functional,
+                just turn it off by setting sum_atoms = None.
             sum_morbs: Sum projections of individual orbitals of similar atoms
                 together (e.g.: 'dxy' and 'dxz'). The format is {Element: [individual orbitals]},
                 for instance: {'Cu': ['dxy', 'dxz'], 'O': ['px', 'py']} means summing projections

pymatgen/io/abinit/abiobjects.py

@@ -689,8 +689,8 @@ def __init__(
                 Number of division for the sampling of the smallest segment if mode is "path".
                 Not used for the other modes
             kpts: Number of divisions. Even when only a single specification is
-                  required, e.g. in the automatic scheme, the kpts should still
-                  be specified as a 2D array. e.g., [[20]] or [[2,2,2]].
+                required, e.g. in the automatic scheme, the kpts should still
+                be specified as a 2D array. e.g., [[20]] or [[2,2,2]].
             kpt_shifts: Shifts for Kpoints.
             use_symmetries: False if spatial symmetries should not be used
                 to reduce the number of independent k-points.

pymatgen/io/exciting/inputs.py

@@ -247,10 +247,7 @@ def write_etree(self, celltype, cartesian=False, bandstr=False, symprec: float =
                         symbol = "GAMMA"
                     _ = ET.SubElement(path, "point", coord=coord, label=symbol)
         elif bandstr and celltype != "primitive":
-            raise ValueError(
-                "Bandstructure is only implemented for the \
-                              standard primitive unit cell!"
-            )
+            raise ValueError("Bandstructure is only implemented for the standard primitive unit cell!")
 
         # write extra parameters from kwargs if provided
         self._dicttoxml(kwargs, root)

pymatgen/io/feff/sets.py

@@ -244,10 +244,7 @@ def tags(self) -> Tags:
                     mult = (self.nkpts * abc[0] * abc[1] * abc[2]) ** (1 / 3)
                     self.config_dict["KMESH"] = [int(round(mult / length)) for length in abc]
             else:
-                logger.warning(
-                    "Large system(>=14 atoms) or EXAFS calculation, \
-                                removing K-space settings"
-                )
+                logger.warning("Large system(>=14 atoms) or EXAFS calculation, removing K-space settings")
                 del self.config_dict["RECIPROCAL"]
                 self.config_dict.pop("CIF", None)
                 self.config_dict.pop("TARGET", None)

pymatgen/io/lammps/data.py

@@ -1245,7 +1245,7 @@ def __init__(
         """
         Args:
             list_of_molecules: A list of LammpsData objects of a chemical cluster.
-                 Each LammpsData object (cluster) may contain one or more molecule ID.
+                Each LammpsData object (cluster) may contain one or more molecule ID.
             list_of_names: A list of name (string) for each cluster. The characters in each name are
                 restricted to word characters ([a-zA-Z0-9_]). If names with any non-word characters
                 are passed in, the special characters will be substituted by '_'.

pymatgen/io/lammps/sets.py

@@ -52,10 +52,10 @@ def __init__(
     ) -> None:
         """
         Args:
-            inputfile: The input file containing settings.
-                       It can be a LammpsInputFile object or a string representation.
+            inputfile: The input file containing settings. It can be a LammpsInputFile object
+                or a string representation.
             data: The data file containing structure and topology information.
-                  It can be a LammpsData or a CombinedData object.
+                It can be a LammpsData or a CombinedData object.
             calc_type: Human-readable string used to briefly describe the type of computations performed by LAMMPS.
             template_file: Path (string) to the template file used to create the input file for LAMMPS.
             keep_stages: Whether to keep the stage structure of the LammpsInputFile or not.

pymatgen/io/qchem/inputs.py

@@ -615,8 +615,8 @@ def svp_template(svp: dict) -> str:
 
         Returns:
             str: the $svp section. Note that all parameters will be concatenated onto
-                 a single line formatted as a FORTRAN namelist. This is necessary
-                 because the isodensity SS(V)PE model in Q-Chem calls a secondary code.
+                a single line formatted as a FORTRAN namelist. This is necessary
+                because the isodensity SS(V)PE model in Q-Chem calls a secondary code.
         """
         svp_list = []
         svp_list.append("$svp")

pymatgen/io/shengbte.py

@@ -90,13 +90,11 @@ def __init__(self, ngrid: list[int] | None = None, temperature: float | dict[str
                 for ShengBTE to run - we have listed these parameters below:
                 - nelements (int): number of different elements in the compound
                 - natoms (int): number of atoms in the unit cell
-                - lattvec (size 3x3 array): real-space lattice vectors, in units
-                  of lfactor
+                - lattvec (size 3x3 array): real-space lattice vectors, in units of lfactor
                 - lfactor (float): unit of measurement for lattice vectors (nm).
                     I.e., set to 0.1 if lattvec given in Angstrom.
                 - types (size natom list): a vector of natom integers, ranging
-                  from 1 to nelements, assigning an element to each atom in the
-                  system
+                  from 1 to nelements, assigning an element to each atom in the system
                 - elements (size natom list): a vector of element names
                 - positions (size natomx3 array): atomic positions in lattice
                   coordinates

pymatgen/io/vasp/outputs.py

@@ -241,7 +241,7 @@ def __init__(
                 where no hashes will be determined and the potcar_spec dictionaries
                 will read {"symbol": ElSymbol, "hash": None}. By Default, looks in
                 the same directory as the vasprun.xml, with same extensions as
-                 Vasprun.xml. If a string is provided, looks at that filepath.
+                Vasprun.xml. If a string is provided, looks at that filepath.
             occu_tol (float): Sets the minimum tol for the determination of the
                 vbm and cbm. Usually the default of 1e-8 works well enough,
                 but there may be pathological cases.
@@ -1443,7 +1443,7 @@ def __init__(
                 where no hashes will be determined and the potcar_spec dictionaries
                 will read {"symbol": ElSymbol, "hash": None}. By Default, looks in
                 the same directory as the vasprun.xml, with same extensions as
-                 Vasprun.xml. If a string is provided, looks at that filepath.
+                Vasprun.xml. If a string is provided, looks at that filepath.
             occu_tol: Sets the minimum tol for the determination of the
                 vbm and cbm. Usually the default of 1e-8 works well enough,
                 but there may be pathological cases.

pymatgen/io/vasp/sets.py

@@ -3072,16 +3072,16 @@ def batch_write_input(
             in addition to structure.
     """
     output_dir = Path(output_dir)
-    for i, s in enumerate(structures):
-        formula = re.sub(r"\s+", "", s.formula)
+    for idx, site in enumerate(structures):
+        formula = re.sub(r"\s+", "", site.formula)
         if subfolder is not None:
-            subdir = subfolder(s)
+            subdir = subfolder(site)
             d = output_dir / subdir
         else:
-            d = output_dir / f"{formula}_{i}"
+            d = output_dir / f"{formula}_{idx}"
         if sanitize:
-            s = s.copy(sanitize=True)
-        v = vasp_input_set(s, **kwargs)
+            site = site.copy(sanitize=True)
+        v = vasp_input_set(site, **kwargs)
         v.write_input(
             str(d),
             make_dir_if_not_present=make_dir_if_not_present,
@@ -3195,7 +3195,7 @@ def __init__(
                 Need to be tested for convergence.
             reciprocal_density: the k-points density
             nkred: the reduced number of kpoints to calculate, equal to the k-mesh. Only applies in "RPA" mode
-                  because of the q->0 limit.
+                because of the q->0 limit.
             nedos: the density of DOS, default: 2001.
             **kwargs: All kwargs supported by DictSet. Typically, user_incar_settings is a commonly used option.
         """

pymatgen/io/zeopp.py

@@ -336,13 +336,12 @@ def get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1):
             for el in rad_dict:
                 print(f"{el} {rad_dict[el].real}", file=fp)
 
-        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
-        # vornet, vor_edge_centers, vor_face_centers = \
-        #        atmnet.perform_voronoi_decomposition()
-        red_ha_vornet = prune_voronoi_network_close_node(atmnet)
-        # generate_simplified_highaccuracy_voronoi_network(atmnet)
-        # get_nearest_largest_diameter_highaccuracy_vornode(atmnet)
-        red_ha_vornet.analyze_writeto_XYZ(name, probe_rad, atmnet)
+        atom_net = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
+        # vornet, vor_edge_centers, vor_face_centers = atom_net.perform_voronoi_decomposition()
+        red_ha_vornet = prune_voronoi_network_close_node(atom_net)
+        # generate_simplified_highaccuracy_voronoi_network(atom_net)
+        # get_nearest_largest_diameter_highaccuracy_vornode(atom_net)
+        red_ha_vornet.analyze_writeto_XYZ(name, probe_rad, atom_net)
         voro_out_filename = name + "_voro.xyz"
         voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule
 
@@ -403,9 +402,9 @@ def get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1):
                 for el in rad_dict:
                     fp.write(f"{el} {rad_dict[el].real}\n")
 
-        atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
+        atom_net = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
         out_file = "temp.res"
-        atmnet.calculate_free_sphere_parameters(out_file)
+        atom_net.calculate_free_sphere_parameters(out_file)
         if os.path.isfile(out_file) and os.path.getsize(out_file) > 0:
             with open(out_file) as fp:
                 output = fp.readline()

pymatgen/symmetry/kpath.py

@@ -160,8 +160,7 @@ def __init__(self, structure: Structure, symprec: float = 0.01, angle_tolerance=
         """
         if "magmom" in structure.site_properties:
             warn(
-                "'magmom' entry found in site properties but will be ignored \
-                  for the Setyawan and Curtarolo convention."
+                "'magmom' entry found in site properties but will be ignored for the Setyawan and Curtarolo convention."
             )
 
         super().__init__(structure, symprec=symprec, angle_tolerance=angle_tolerance, atol=atol)