Docstring tweaks for io.vasp.inputs and format tweaks for some othe…

…r parts (#3996)

* docstring tweaks

* fix typo

* reduce indentation level

* fix vasp case to VASP

* use walrus operator

* revert overlapping functional changes from #3994

* my bad, I get confused hopping between two PRs

* remove debug code from vasp.help

* fix `use-named-expression` with sourcery

* clean up Vasprun.as_dict

* simplify dict generation

* re-raise and update -> |=

* simplify logic conditions

* remove unused logger

* remove a lot of unused logger, wondering if they exist for a reason?

* remove some unused module_dir, they must have gone stranded

* CAPS LOCK ENGAGED: Go up! module level variables!

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/bond_dissociation.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import logging
 import warnings
 from typing import cast
 
@@ -23,8 +22,6 @@
 __status__ = "Alpha"
 __date__ = "7/26/18"
 
-logger = logging.getLogger(__name__)
-
 
 class BondDissociationEnergies(MSONable):
     """

src/pymatgen/analysis/bond_valence.py

@@ -22,15 +22,15 @@
 # JACS, 1991, 113(9), 3226-3229. doi:10.1021/ja00009a002.
 ELECTRONEG = [Element(sym) for sym in "H B C Si N P As Sb O S Se Te F Cl Br I".split()]
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 # Read in BV parameters.
 BV_PARAMS = {}
-for key, val in loadfn(f"{module_dir}/bvparam_1991.yaml").items():
+for key, val in loadfn(f"{MODULE_DIR}/bvparam_1991.yaml").items():
     BV_PARAMS[Element(key)] = val
 
 # Read in YAML containing data-mined ICSD BV data.
-all_data = loadfn(f"{module_dir}/icsd_bv.yaml")
+all_data = loadfn(f"{MODULE_DIR}/icsd_bv.yaml")
 ICSD_BV_DATA = {Species.from_str(sp): data for sp, data in all_data["bvsum"].items()}
 PRIOR_PROB = {Species.from_str(sp): data for sp, data in all_data["occurrence"].items()}
 

src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -8,7 +8,6 @@
 from __future__ import annotations
 
 import abc
-import os
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -43,8 +42,6 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
-
 MPSYMBOL_TO_CN = AllCoordinationGeometries().get_symbol_cn_mapping()
 ALLCG = AllCoordinationGeometries()
 

src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -32,7 +32,7 @@
 __email__ = "david.waroquiers@gmail.com"
 __date__ = "Feb 20, 2016"
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 UNKNOWN_ENVIRONMENT_SYMBOL = "UNKNOWN"
 UNCLEAR_ENVIRONMENT_SYMBOL = "UNCLEAR"
@@ -850,17 +850,17 @@ def __init__(self, permutations_safe_override=False, only_symbols=None):
         dict.__init__(self)
         self.cg_list: list[CoordinationGeometry] = []
         if only_symbols is None:
-            with open(f"{module_dir}/coordination_geometries_files/allcg.txt") as file:
+            with open(f"{MODULE_DIR}/coordination_geometries_files/allcg.txt") as file:
                 data = file.readlines()
             for line in data:
-                cg_file = f"{module_dir}/{line.strip()}"
+                cg_file = f"{MODULE_DIR}/{line.strip()}"
                 with open(cg_file) as file:
                     dd = json.load(file)
                 self.cg_list.append(CoordinationGeometry.from_dict(dd))
         else:
             for symbol in only_symbols:
                 fsymbol = symbol.replace(":", "#")
-                cg_file = f"{module_dir}/coordination_geometries_files/{fsymbol}.json"
+                cg_file = f"{MODULE_DIR}/coordination_geometries_files/{fsymbol}.json"
                 with open(cg_file) as file:
                     dd = json.load(file)
                 self.cg_list.append(CoordinationGeometry.from_dict(dd))

src/pymatgen/analysis/cost.py

@@ -32,7 +32,7 @@
 __email__ = "ajain@lbl.gov"
 __date__ = "Aug 27, 2013"
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 
 class CostEntry(PDEntry):
@@ -112,7 +112,7 @@ class CostDBElements(CostDBCSV):
     """Singleton that provides the cost data for elements."""
 
     def __init__(self):
-        CostDBCSV.__init__(self, f"{module_dir}/costdb_elements.csv")
+        CostDBCSV.__init__(self, f"{MODULE_DIR}/costdb_elements.csv")
 
 
 class CostAnalyzer:

src/pymatgen/analysis/diffraction/tem.py

@@ -30,8 +30,8 @@
 __date__ = "03/31/2020"
 
 
-module_dir = os.path.dirname(__file__)
-with open(f"{module_dir}/atomic_scattering_params.json", encoding="utf-8") as file:
+MODULE_DIR = os.path.dirname(__file__)
+with open(f"{MODULE_DIR}/atomic_scattering_params.json", encoding="utf-8") as file:
     ATOMIC_SCATTERING_PARAMS = json.load(file)
 
 

src/pymatgen/analysis/fragmenter.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import copy
-import logging
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
@@ -23,8 +22,6 @@
 __status__ = "Beta"
 __date__ = "8/21/19"
 
-logger = logging.getLogger(__name__)
-
 
 class Fragmenter(MSONable):
     """Molecule fragmenter class."""

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/hhi.py

@@ -25,8 +25,8 @@
 __date__ = "Oct 27, 2014"
 
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
-csv_path = f"{module_dir}/hhi_data.csv"
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
+HHI_CSV_PATH = f"{MODULE_DIR}/hhi_data.csv"
 
 
 @singleton
@@ -37,7 +37,7 @@ def __init__(self):
         """Init for HHIModel."""
         self.symbol_hhip_hhir = {}  # symbol->(HHI_production, HHI reserve)
 
-        with open(csv_path) as file:
+        with open(HHI_CSV_PATH) as file:
             for line in file:
                 if line[0] != "#":
                     symbol, hhi_production, hhi_reserve = line.split(",")

src/pymatgen/analysis/local_env.py

@@ -50,16 +50,16 @@
 __status__ = "Production"
 __date__ = "August 17, 2017"
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 yaml = YAML()
 
-with open(f"{module_dir}/op_params.yaml") as file:
+with open(f"{MODULE_DIR}/op_params.yaml") as file:
     default_op_params = yaml.load(file)
 
-with open(f"{module_dir}/cn_opt_params.yaml") as file:
+with open(f"{MODULE_DIR}/cn_opt_params.yaml") as file:
     cn_opt_params = yaml.load(file)
 
-with open(f"{module_dir}/ionic_radii.json") as file:
+with open(f"{MODULE_DIR}/ionic_radii.json") as file:
     _ion_radii = json.load(file)
 
 
@@ -1211,7 +1211,7 @@ def __init__(
         self.min_bond_distance = min_bond_distance
 
         # Load elemental radii table
-        bonds_file = f"{module_dir}/bonds_jmol_ob.yaml"
+        bonds_file = f"{MODULE_DIR}/bonds_jmol_ob.yaml"
         with open(bonds_file) as file:
             yaml = YAML()
             self.el_radius = yaml.load(file)
@@ -4226,7 +4226,7 @@ def from_preset(cls, preset) -> Self:
             A CutOffDictNN using the preset cut-off dictionary.
         """
         if preset == "vesta_2019":
-            cut_offs = loadfn(f"{module_dir}/vesta_cutoffs.yaml")
+            cut_offs = loadfn(f"{MODULE_DIR}/vesta_cutoffs.yaml")
             return cls(cut_off_dict=cut_offs)
 
         raise ValueError(f"Unknown {preset=}")

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/prototypes.py

@@ -24,8 +24,8 @@
 if TYPE_CHECKING:
     from pymatgen.core import Structure
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
-AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{module_dir}/aflow_prototypes.json")
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
+AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
 
 
 @due.dcite(

src/pymatgen/analysis/reaction_calculator.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import logging
 import re
 from itertools import chain, combinations
 from typing import TYPE_CHECKING, no_type_check, overload
@@ -32,9 +31,6 @@
 __date__ = "Jul 11 2012"
 
 
-logger = logging.getLogger(__name__)
-
-
 class BalancedReaction(MSONable):
     """Represent a complete chemical reaction."""
 

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/command_line/gulp_caller.py

@@ -23,7 +23,7 @@
 __status__ = "Production"
 __date__ = "Jun 22, 2013M"
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 _anions = set(map(Element, ["O", "S", "F", "Cl", "Br", "N", "P"]))
 _cations = set(
@@ -868,7 +868,7 @@ class TersoffPotential:
 
     def __init__(self):
         """Init TersoffPotential."""
-        with open(f"{module_dir}/OxideTersoffPotentials") as file:
+        with open(f"{MODULE_DIR}/OxideTersoffPotentials") as file:
             data = {}
             for row in file:
                 metaloxi = row.split()[0]

src/pymatgen/core/composition.py

@@ -31,7 +31,7 @@
 
     from pymatgen.util.typing import SpeciesLike
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 
 @total_ordering
@@ -959,7 +959,7 @@ def _get_oxi_state_guesses(
 
         # Load prior probabilities of oxidation states, used to rank solutions
         if not type(self).oxi_prob:
-            all_data = loadfn(f"{module_dir}/../analysis/icsd_bv.yaml")
+            all_data = loadfn(f"{MODULE_DIR}/../analysis/icsd_bv.yaml")
             type(self).oxi_prob = {Species.from_str(sp): data for sp, data in all_data["occurrence"].items()}
         oxi_states_override = oxi_states_override or {}
         # Assert Composition only has integer amounts