Docstring tweaks for io.vasp.inputs and format tweaks for some other parts

src/pymatgen/alchemy/filters.py

@@ -132,8 +132,7 @@ def test(self, structure: Structure):
         all_species = set(self.specie_and_min_dist)
         for site in structure:
             species = set(site.species)
-            sp_to_test = species.intersection(all_species)
-            if sp_to_test:
+            if sp_to_test := species.intersection(all_species):
                 max_r = max(self.specie_and_min_dist[sp] for sp in sp_to_test)
                 neighbors = structure.get_neighbors(site, max_r)
                 for sp in sp_to_test:

src/pymatgen/analysis/graphs.py

@@ -429,8 +429,7 @@ def add_edge(
         # there should only ever be at most one edge
         # between a given (site, jimage) pair and another
         # (site, jimage) pair
-        existing_edge_data = self.graph.get_edge_data(from_index, to_index)
-        if existing_edge_data:
+        if existing_edge_data := self.graph.get_edge_data(from_index, to_index):
             for d in existing_edge_data.values():
                 if d["to_jimage"] == to_jimage:
                     if warn_duplicates:
@@ -1287,12 +1286,10 @@ def __rmul__(self, other):
     def _edges_to_str(cls, g) -> str:
         header = "from    to  to_image    "
         header_line = "----  ----  ------------"
-        edge_weight_name = g.graph["edge_weight_name"]
-        if edge_weight_name:
+        if g.graph["edge_weight_name"]:
             print_weights = True
             edge_label = g.graph["edge_weight_name"]
-            edge_weight_units = g.graph["edge_weight_units"]
-            if edge_weight_units:
+            if edge_weight_units := g.graph["edge_weight_units"]:
                 edge_label += f" ({edge_weight_units})"
             header += f"  {edge_label}"
             header_line += f"  {'-' * max([18, len(edge_label)])}"
@@ -2673,12 +2670,10 @@ def from_dict(cls, dct: dict) -> Self:
     def _edges_to_str(cls, g):
         header = "from    to  to_image    "
         header_line = "----  ----  ------------"
-        edge_weight_name = g.graph["edge_weight_name"]
-        if edge_weight_name:
+        if g.graph["edge_weight_name"]:
             print_weights = ["weight"]
             edge_label = g.graph["edge_weight_name"]
-            edge_weight_units = g.graph["edge_weight_units"]
-            if edge_weight_units:
+            if edge_weight_units := g.graph["edge_weight_units"]:
                 edge_label += f" ({edge_weight_units})"
             header += f"  {edge_label}"
             header_line += f"  {'-' * max([18, len(edge_label)])}"

src/pymatgen/analysis/pourbaix_diagram.py

@@ -604,8 +604,7 @@ def _preprocess_pourbaix_entries(self, entries, nproc=None):
         else:
             # Serial processing of multi-entry generation
             for combo in all_combos:
-                multi_entry = self.process_multientry(combo, prod_comp=tot_comp)
-                if multi_entry:
+                if multi_entry := self.process_multientry(combo, prod_comp=tot_comp):
                     multi_entries.append(multi_entry)
 
         return multi_entries

src/pymatgen/analysis/structure_matcher.py

@@ -968,8 +968,7 @@ def get_rms_anonymous(self, struct1, struct2):
         struct1, struct2 = self._process_species([struct1, struct2])
         struct1, struct2, fu, s1_supercell = self._preprocess(struct1, struct2)
 
-        matches = self._anonymous_match(struct1, struct2, fu, s1_supercell, use_rms=True, break_on_match=False)
-        if matches:
+        if matches := self._anonymous_match(struct1, struct2, fu, s1_supercell, use_rms=True, break_on_match=False):
             best = min(matches, key=lambda x: x[1][0])
             return best[1][0], best[0]
 
@@ -993,9 +992,7 @@ def get_best_electronegativity_anonymous_mapping(self, struct1: Structure, struc
         struct1, struct2 = self._process_species([struct1, struct2])
         struct1, struct2, fu, s1_supercell = self._preprocess(struct1, struct2)
 
-        matches = self._anonymous_match(struct1, struct2, fu, s1_supercell, use_rms=True, break_on_match=True)
-
-        if matches:
+        if matches := self._anonymous_match(struct1, struct2, fu, s1_supercell, use_rms=True, break_on_match=True):
             min_X_diff = np.inf
             best = None
             for match in matches:
@@ -1027,8 +1024,7 @@ def get_all_anonymous_mappings(self, struct1, struct2, niggli=True, include_dist
         struct1, struct2 = self._process_species([struct1, struct2])
         struct1, struct2, fu, s1_supercell = self._preprocess(struct1, struct2, niggli)
 
-        matches = self._anonymous_match(struct1, struct2, fu, s1_supercell, break_on_match=not include_dist)
-        if matches:
+        if matches := self._anonymous_match(struct1, struct2, fu, s1_supercell, break_on_match=not include_dist):
             if include_dist:
                 return [(m[0], m[1][0]) for m in matches]
 

src/pymatgen/analysis/transition_state.py

@@ -248,8 +248,7 @@ def from_dir(cls, root_dir, relaxation_dirs=None, **kwargs) -> Self:
             if terminal:
                 for ds in terminal_dirs:
                     od = ds[0] if idx == 0 else ds[1]
-                    outcar = glob(f"{od}/OUTCAR*")
-                    if outcar:
+                    if outcar := glob(f"{od}/OUTCAR*"):
                         outcar = sorted(outcar)
                         outcars.append(Outcar(outcar[-1]))
                         break

src/pymatgen/apps/borg/hive.py

@@ -418,8 +418,7 @@ def from_dict(cls, dct: dict) -> Self:
 
 def _get_transformation_history(path):
     """Check for a transformations.json* file and returns the history."""
-    trans_json = glob(f"{path}/transformations.json*")
-    if trans_json:
+    if trans_json := glob(f"{path}/transformations.json*"):
         try:
             with zopen(trans_json[0]) as file:
                 return json.load(file)["history"]

src/pymatgen/apps/borg/queen.py

@@ -110,8 +110,7 @@ def load_data(self, filename):
 def order_assimilation(args):
     """Internal helper method for BorgQueen to process assimilation."""
     path, drone, data, status = args
-    new_data = drone.assimilate(path)
-    if new_data:
+    if new_data := drone.assimilate(path):
         data.append(json.dumps(new_data, cls=MontyEncoder))
     status["count"] += 1
     count = status["count"]

src/pymatgen/command_line/critic2_caller.py

@@ -277,17 +277,16 @@ def from_path(cls, path, suffix="", zpsp=None) -> Self:
         chgcar = Chgcar.from_file(chgcar_path)
         chgcar_ref = None
 
-        if not zpsp:
-            potcar_path = get_filepath(
+        if not zpsp and (
+            potcar_path := get_filepath(
                 "POTCAR",
                 "Could not find POTCAR, will not be able to calculate charge transfer.",
                 path,
                 suffix,
             )
-
-            if potcar_path:
-                potcar = Potcar.from_file(potcar_path)
-                zpsp = {p.element: p.zval for p in potcar}
+        ):
+            potcar = Potcar.from_file(potcar_path)
+            zpsp = {p.element: p.zval for p in potcar}
 
         if not zpsp:
             # try and get reference "all-electron-like" charge density if zpsp not present

src/pymatgen/core/periodic_table.py

@@ -380,10 +380,8 @@ def average_cationic_radius(self) -> FloatWithUnit:
         taken over all positive oxidation states of the element for which
         data is present.
         """
-        if "Ionic radii" in self._data:
-            radii = [v for k, v in self._data["Ionic radii"].items() if int(k) > 0]
-            if radii:
-                return FloatWithUnit(sum(radii) / len(radii), "ang")
+        if "Ionic radii" in self._data and (radii := [v for k, v in self._data["Ionic radii"].items() if int(k) > 0]):
+            return FloatWithUnit(sum(radii) / len(radii), "ang")
         return FloatWithUnit(0.0, "ang")
 
     @property
@@ -392,10 +390,8 @@ def average_anionic_radius(self) -> FloatWithUnit:
         taken over all negative oxidation states of the element for which
         data is present.
         """
-        if "Ionic radii" in self._data:
-            radii = [v for k, v in self._data["Ionic radii"].items() if int(k) < 0]
-            if radii:
-                return FloatWithUnit(sum(radii) / len(radii), "ang")
+        if "Ionic radii" in self._data and (radii := [v for k, v in self._data["Ionic radii"].items() if int(k) < 0]):
+            return FloatWithUnit(sum(radii) / len(radii), "ang")
         return FloatWithUnit(0.0, "ang")
 
     @property

src/pymatgen/io/abinit/inputs.py

@@ -1059,8 +1059,7 @@ def __init__(self, structure: Structure | Sequence[Structure], pseudos, pseudo_d
             pseudo_dir = os.path.abspath(pseudo_dir)
             pseudo_paths = [os.path.join(pseudo_dir, p) for p in pseudos]
 
-            missing = [p for p in pseudo_paths if not os.path.isfile(p)]
-            if missing:
+            if missing := [p for p in pseudo_paths if not os.path.isfile(p)]:
                 raise self.Error(f"Cannot find the following pseudopotential files:\n{missing}")
 
             pseudos = PseudoTable(pseudo_paths)

src/pymatgen/io/abinit/pseudos.py

@@ -1540,8 +1540,7 @@ def from_dir(cls, top, exts=None, exclude_dirs="_*") -> Self | None:
             for filepath in [os.path.join(top, fn) for fn in os.listdir(top)]:
                 if os.path.isfile(filepath):
                     try:
-                        pseudo = Pseudo.from_file(filepath)
-                        if pseudo:
+                        if pseudo := Pseudo.from_file(filepath):
                             pseudos.append(pseudo)
                         else:
                             logger.info(f"Skipping file {filepath}")

src/pymatgen/io/cp2k/outputs.py

@@ -932,13 +932,12 @@ def parse_mulliken(self):
         pattern = r"\s+(\d)\s+(\w+)\s+(\d+)\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)"
         footer = r".+Total charge"
 
-        d = self.read_table_pattern(
+        if self.read_table_pattern(
             header_pattern=header,
             row_pattern=pattern,
             footer_pattern=footer,
             last_one_only=False,
-        )
-        if d:
+        ):
             print("Found data, but not yet implemented!")
 
     def parse_hirshfeld(self):

src/pymatgen/io/feff/outputs.py

@@ -122,12 +122,11 @@ def from_file(cls, feff_inp_file: str = "feff.inp", ldos_file: str = "ldos") ->
             all_pdos.append(defaultdict(dict))
             for k, v in vorb.items():
                 density = [ldos[pot_index][j][forb[k] + 1] for j in range(d_length)]
-                updos = density
-                downdos = None
-                if downdos:
-                    all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
+                up_dos = density
+                if down_dos := None:
+                    all_pdos[-1][v] = {Spin.up: up_dos, Spin.down: down_dos}
                 else:
-                    all_pdos[-1][v] = {Spin.up: updos}
+                    all_pdos[-1][v] = {Spin.up: up_dos}
 
         pdos = all_pdos
         vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}

src/pymatgen/io/optimade.py

@@ -175,8 +175,7 @@ def get_structure(resource: dict) -> Structure:
         properties: dict[str, Any] = {"optimade_id": _id}
 
         # Take any prefixed attributes and save them as properties
-        custom_properties = {k: v for k, v in attributes.items() if k.startswith("_")}
-        if custom_properties:
+        if custom_properties := {k: v for k, v in attributes.items() if k.startswith("_")}:
             properties["optimade_attributes"] = custom_properties
 
         return Structure(

src/pymatgen/io/vasp/help.py

@@ -62,11 +62,9 @@ def get_help(cls, tag: str, fmt: str = "text") -> str:
         main_doc = soup.find(id="mw-content-text")
         if fmt == "text":
             output = main_doc.text
-            output = re.sub("\n{2,}", "\n\n", output)
-        else:
-            output = str(main_doc)
+            return re.sub("\n{2,}", "\n\n", output)
 
-        return output
+        return str(main_doc)
 
     @classmethod
     def get_incar_tags(cls) -> list[str]:
@@ -83,9 +81,3 @@ def get_incar_tags(cls) -> list[str]:
                 for child in children:
                     tags.append(child.text.strip())
         return tags
-
-
-if __name__ == "__main__":
-    doc = VaspDoc()
-    doc.print_help("ISYM")
-    print(doc.get_incar_tags())