Merge pull request #161 from naik-aakash/snake_case_bond_type

snakecase whichbonds arg and update tests

lobsterpy/cli.py

@@ -666,16 +666,16 @@ def run(args):
         "autoplotia",
     ]:
         if args.allbonds:
-            whichbonds = "all"
+            which_bonds = "all"
         else:
-            whichbonds = "cation-anion"
+            which_bonds = "cation-anion"
 
         analyse = Analysis(
             path_to_poscar=args.poscar,
             path_to_charge=args.charge,
             path_to_cohpcar=args.cohpcar,
             path_to_icohplist=args.icohplist,
-            whichbonds=whichbonds,
+            which_bonds=which_bonds,
             are_coops=args.coops,
             are_cobis=args.cobis,
             noise_cutoff=args.noisecutoff,

lobsterpy/cohp/analyze.py

@@ -51,7 +51,7 @@ class Analysis:
         spg: space group information
         structure: Structure object
         type_charge: which charges are considered here
-        whichbonds: which bonds will be considered in analysis
+        which_bonds: which bonds will be considered in analysis
 
     """
 
@@ -62,7 +62,7 @@ def __init__(
         path_to_cohpcar: str,
         path_to_charge: str | None = None,
         path_to_madelung: str | None = None,
-        whichbonds: str = "cation-anion",
+        which_bonds: str = "cation-anion",
         cutoff_icohp: float = 0.1,
         noise_cutoff: float = 0.1,
         summed_spins=True,
@@ -83,7 +83,7 @@ def __init__(
             are_cobis : bool indicating if file contains COBI/ICOBI data
             are_coops : bool indicating if file contains COOP/ICOOP data
             noise_cutoff : float that sets the lower limit of icohps or icoops or icobis considered
-            whichbonds: selects which kind of bonds are analyzed. "cation-anion" is the default
+            which_bonds: selects which kind of bonds are analyzed. "cation-anion" is the default
             cutoff_icohp: only bonds that are stronger than cutoff_icohp*strongest ICOHP will be considered
             summed_spins: if true, spins will be summed
             type_charge: If no path_to_charge is given, Valences will be used. Otherwise, Mulliken charges.
@@ -94,7 +94,7 @@ def __init__(
         self.path_to_poscar = path_to_poscar
         self.path_to_icohplist = path_to_icohplist
         self.path_to_cohpcar = path_to_cohpcar
-        self.whichbonds = whichbonds
+        self.which_bonds = which_bonds
         self.cutoff_icohp = cutoff_icohp
         self.path_to_charge = path_to_charge
         self.path_to_madelung = path_to_madelung
@@ -142,7 +142,7 @@ def setup_env(self):
         self.set_equivalent_sites = list(set(equivalent_sites))
         self.spg = symmetry_dataset["international"]
 
-        if self.whichbonds == "cation-anion":
+        if self.which_bonds == "cation-anion":
             try:
                 self.chemenv = LobsterNeighbors(
                     filename_ICOHP=self.path_to_icohplist,
@@ -167,7 +167,7 @@ def setup_env(self):
                         " It looks like no cations are detected."
                     )
                 raise err
-        elif self.whichbonds == "all":
+        elif self.which_bonds == "all":
             # raise ValueError("only cation anion bonds implemented so far")
             self.chemenv = LobsterNeighbors(
                 filename_ICOHP=self.path_to_icohplist,
@@ -187,11 +187,11 @@ def setup_env(self):
 
         # determine cations and anions
         try:
-            if self.whichbonds == "cation-anion":
+            if self.which_bonds == "cation-anion":
                 self.lse = self.chemenv.get_light_structure_environment(
                     only_cation_environments=True
                 )
-            elif self.whichbonds == "all":
+            elif self.which_bonds == "all":
                 self.lse = self.chemenv.get_light_structure_environment(
                     only_cation_environments=False
                 )
@@ -226,9 +226,9 @@ def __init__(self, chemenv, valences=None):
                                     [{"ce_symbol": None}]
                                 )
 
-            if self.whichbonds == "all":
+            if self.which_bonds == "all":
                 self.lse = Lse(self.chemenv.list_coords)
-            elif self.whichbonds == "cation-anion":
+            elif self.which_bonds == "cation-anion":
                 # make a new list
                 self.lse = Lse(self.chemenv.list_coords, self.chemenv.valences)
 
@@ -240,7 +240,7 @@ def get_information_all_bonds(self, summed_spins=True):
             None
 
         """
-        if self.whichbonds == "cation-anion":
+        if self.which_bonds == "cation-anion":
             # this will only analyze cation anion bonds which simplifies the analysis
             self.seq_ineq_ions = []
             self.seq_coord_ions = []
@@ -281,7 +281,7 @@ def get_information_all_bonds(self, summed_spins=True):
                     self.seq_labels_cohps.append(aniontype_labels)
                     self.seq_cohps.append(aniontype_cohps)
 
-        elif self.whichbonds == "all":
+        elif self.which_bonds == "all":
             # this will only analyze all bonds
 
             self.seq_ineq_ions = []
@@ -681,14 +681,14 @@ def set_condensed_bonding_analysis(self):
         """
         self.condensed_bonding_analysis = {}
         # which icohps are considered
-        if self.whichbonds == "cation-anion":
+        if self.which_bonds == "cation-anion":
             limit_icohps = self.chemenv._get_limit_from_extremum(
                 self.chemenv.Icohpcollection,
                 self.cutoff_icohp,
                 adapt_extremum_to_add_cond=True,
                 additional_condition=1,
             )
-        elif self.whichbonds == "all":
+        elif self.which_bonds == "all":
             limit_icohps = self.chemenv._get_limit_from_extremum(
                 self.chemenv.Icohpcollection,
                 self.cutoff_icohp,
@@ -700,9 +700,9 @@ def set_condensed_bonding_analysis(self):
         # set population type
         type_pop = self._get_pop_type()
         # how many inequivalent cations are in the structure
-        if self.whichbonds == "cation-anion":
+        if self.which_bonds == "cation-anion":
             number_considered_ions = len(self.seq_ineq_ions)
-        elif self.whichbonds == "all":
+        elif self.which_bonds == "all":
             number_considered_ions = len(self.seq_ineq_ions)
 
         # what was the maximum bond lengths that was considered
@@ -713,7 +713,7 @@ def set_condensed_bonding_analysis(self):
 
         # dictionary including bonding information for each site
         site_dict = {}
-        if self.whichbonds == "cation-anion":
+        if self.which_bonds == "cation-anion":
             for ication, ce, cation_anion_infos, labels, cohps in zip(
                 self.seq_ineq_ions,
                 self.seq_coord_ions,
@@ -755,7 +755,7 @@ def set_condensed_bonding_analysis(self):
                     "charge": charge_list[ication],
                     "relevant_bonds": cation_anion_infos[3],
                 }
-        elif self.whichbonds == "all":
+        elif self.which_bonds == "all":
             for iion, ce, bond_infos, labels, cohps in zip(
                 self.seq_ineq_ions,
                 self.seq_coord_ions,
@@ -798,7 +798,7 @@ def set_condensed_bonding_analysis(self):
                 }
 
         if self.path_to_madelung is None:
-            if self.whichbonds == "cation-anion":
+            if self.which_bonds == "cation-anion":
                 # This sets the dictionary including the most important information on the compound
                 self.condensed_bonding_analysis = {
                     "formula": formula,
@@ -808,7 +808,7 @@ def set_condensed_bonding_analysis(self):
                     "sites": site_dict,
                     "type_charges": self.type_charge,
                 }
-            elif self.whichbonds == "all":
+            elif self.which_bonds == "all":
                 self.condensed_bonding_analysis = {
                     "formula": formula,
                     "max_considered_bond_length": max_bond_lengths,
@@ -826,7 +826,7 @@ def set_condensed_bonding_analysis(self):
             elif self.type_charge == "Löwdin":
                 madelung_energy = madelung.madelungenergies_Loewdin
             # This sets the dictionary including the most important information on the compound
-            if self.whichbonds == "cation-anion":
+            if self.which_bonds == "cation-anion":
                 self.condensed_bonding_analysis = {
                     "formula": formula,
                     "max_considered_bond_length": max_bond_lengths,
@@ -836,7 +836,7 @@ def set_condensed_bonding_analysis(self):
                     "type_charges": self.type_charge,
                     "madelung_energy": madelung_energy,
                 }
-            elif self.whichbonds == "all":
+            elif self.which_bonds == "all":
                 self.condensed_bonding_analysis = {
                     "formula": formula,
                     "max_considered_bond_length": max_bond_lengths,

lobsterpy/cohp/describe.py

@@ -45,7 +45,7 @@ def set_description(self):
         type_pop = self.analysis_object._get_pop_type()
         # set units for populations
         units = " eV" if type_pop == "COHP" else ""
-        if self.analysis_object.whichbonds == "cation-anion":
+        if self.analysis_object.which_bonds == "cation-anion":
             relevant_cations = ", ".join(
                 [
                     str(site.specie) + str(isite + 1)
@@ -119,7 +119,7 @@ def set_description(self):
                         + str(bonds)
                         + " bonds."
                     )
-        elif self.analysis_object.whichbonds == "all":
+        elif self.analysis_object.which_bonds == "all":
             relevant_ions = ", ".join(
                 [
                     str(site.specie) + str(isite + 1)
@@ -236,9 +236,9 @@ def plot_cohps(
 
         """
         seq_cohps = self.analysis_object.seq_cohps
-        if self.analysis_object.whichbonds == "cation-anion":
+        if self.analysis_object.which_bonds == "cation-anion":
             seq_ineq_cations = self.analysis_object.seq_ineq_ions
-        elif self.analysis_object.whichbonds == "all":
+        elif self.analysis_object.which_bonds == "all":
             seq_ineq_cations = self.analysis_object.seq_ineq_ions
         seq_labels = self.analysis_object.seq_labels_cohps
         structure = self.analysis_object.structure