f-string path construction everywhere, no need for os.path.join(...) (

#3229)

* simplify: f-string path construction everywhere, no need for os.path.join(...)

* fix _get_oxid_state_guesses doc str

* rename to _get_oxi_state_guesses

dev_scripts/regen_libxcfunc.py

@@ -88,7 +88,7 @@ def main():
 
     # Generate new json file in pycore
     pmg_core = os.path.abspath("../pymatgen/core/")
-    json_path = os.path.join(pmg_core, "libxc_docs.json")
+    json_path = f"{pmg_core}/libxc_docs.json"
     write_libxc_docs_json(xc_funcs, json_path)
 
     # Build new enum list.
@@ -101,7 +101,7 @@ def main():
 
     # Re-generate enumerations.
     # [0] read py module.
-    xc_funcpy_path = os.path.join(pmg_core, "libxcfunc.py")
+    xc_funcpy_path = f"{pmg_core}/libxcfunc.py"
     with open(xc_funcpy_path) as fh:
         lines = fh.readlines()
 

pymatgen/alchemy/materials.py

@@ -8,7 +8,6 @@
 
 import datetime
 import json
-import os
 import re
 from typing import TYPE_CHECKING, Any
 from warnings import warn
@@ -217,7 +216,7 @@ def write_vasp_input(
             **kwargs: All keyword args supported by the VASP input set.
         """
         vasp_input_set(self.final_structure, **kwargs).write_input(output_dir, make_dir_if_not_present=create_directory)
-        with open(os.path.join(output_dir, "transformations.json"), "w") as fp:
+        with open(f"{output_dir}/transformations.json", "w") as fp:
             json.dump(self.as_dict(), fp)
 
     def __str__(self) -> str:

pymatgen/analysis/bond_valence.py

@@ -26,11 +26,11 @@
 
 # Read in BV parameters.
 BV_PARAMS = {}
-for key, val in loadfn(os.path.join(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(os.path.join(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()}
 

pymatgen/analysis/cost.py

@@ -123,7 +123,7 @@ class CostDBElements(CostDBCSV):
 
     def __init__(self):
         """Init."""
-        CostDBCSV.__init__(self, os.path.join(module_dir, "costdb_elements.csv"))
+        CostDBCSV.__init__(self, f"{module_dir}/costdb_elements.csv")
 
 
 class CostAnalyzer:

pymatgen/analysis/local_env.py

@@ -51,13 +51,13 @@
 _directory = os.path.join(os.path.dirname(__file__))
 yaml = YAML()
 
-with open(os.path.join(_directory, "op_params.yaml")) as f:
+with open(f"{_directory}/op_params.yaml") as f:
     default_op_params = yaml.load(f)
 
-with open(os.path.join(_directory, "cn_opt_params.yaml")) as f:
+with open(f"{_directory}/cn_opt_params.yaml") as f:
     cn_opt_params = yaml.load(f)
 
-with open(os.path.join(_directory, "ionic_radii.json")) as fp:
+with open(f"{_directory}/ionic_radii.json") as fp:
     _ion_radii = json.load(fp)
 
 
@@ -4218,7 +4218,7 @@ def from_preset(preset):
             A CutOffDictNN using the preset cut-off dictionary.
         """
         if preset == "vesta_2019":
-            cut_offs = loadfn(os.path.join(_directory, "vesta_cutoffs.yaml"))
+            cut_offs = loadfn(f"{_directory}/vesta_cutoffs.yaml")
             return CutOffDictNN(cut_off_dict=cut_offs)
 
         raise ValueError(f"Unknown {preset=}")

pymatgen/analysis/magnetism/analyzer.py

@@ -39,10 +39,10 @@
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
 try:
-    DEFAULT_MAGMOMS = loadfn(os.path.join(MODULE_DIR, "default_magmoms.yaml"))
+    DEFAULT_MAGMOMS = loadfn(f"{MODULE_DIR}/default_magmoms.yaml")
 except Exception:
     warnings.warn("Could not load default_magmoms.yaml, falling back to VASPIncarBase.yaml")
-    DEFAULT_MAGMOMS = loadfn(os.path.join(MODULE_DIR, "../../io/vasp/VASPIncarBase.yaml"))
+    DEFAULT_MAGMOMS = loadfn(f"{MODULE_DIR}/../../io/vasp/VASPIncarBase.yaml")
     DEFAULT_MAGMOMS = DEFAULT_MAGMOMS["MAGMOM"]
 
 

pymatgen/analysis/structure_prediction/substitution_probability.py

@@ -57,7 +57,7 @@ def __init__(self, lambda_table=None, alpha=-5):
             self._lambda_table = lambda_table
         else:
             module_dir = os.path.dirname(__file__)
-            json_file = os.path.join(module_dir, "data", "lambda.json")
+            json_file = f"{module_dir}/data/lambda.json"
             with open(json_file) as f:
                 self._lambda_table = json.load(f)
 

pymatgen/analysis/structure_prediction/volume_predictor.py

@@ -13,7 +13,7 @@
 from pymatgen.core import Structure
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
-bond_params = loadfn(os.path.join(MODULE_DIR, "DLS_bond_params.yaml"))
+bond_params = loadfn(f"{MODULE_DIR}/DLS_bond_params.yaml")
 
 
 def _is_ox(structure):

pymatgen/analysis/transition_state.py

@@ -252,14 +252,14 @@ def from_dir(cls, root_dir, relaxation_dirs=None, **kwargs):
         terminal_dirs.append([os.path.join(root_dir, d) for d in ["initial", "final"]])
 
         for i, d in neb_dirs:
-            outcar = glob(os.path.join(d, "OUTCAR*"))
-            contcar = glob(os.path.join(d, "CONTCAR*"))
-            poscar = glob(os.path.join(d, "POSCAR*"))
+            outcar = glob(f"{d}/OUTCAR*")
+            contcar = glob(f"{d}/CONTCAR*")
+            poscar = glob(f"{d}/POSCAR*")
             terminal = i in [0, neb_dirs[-1][0]]
             if terminal:
                 for ds in terminal_dirs:
                     od = ds[0] if i == 0 else ds[1]
-                    outcar = glob(os.path.join(od, "OUTCAR*"))
+                    outcar = glob(f"{od}/OUTCAR*")
                     if outcar:
                         outcar = sorted(outcar)
                         outcars.append(Outcar(outcar[-1]))

pymatgen/apps/borg/hive.py

@@ -117,9 +117,9 @@ def assimilate(self, path):
         """
         files = os.listdir(path)
         if "relax1" in files and "relax2" in files:
-            filepath = glob(os.path.join(path, "relax2", "vasprun.xml*"))[0]
+            filepath = glob(f"{path}/relax2/vasprun.xml*")[0]
         else:
-            vasprun_files = glob(os.path.join(path, "vasprun.xml*"))
+            vasprun_files = glob(f"{path}/vasprun.xml*")
             filepath = None
             if len(vasprun_files) == 1:
                 filepath = vasprun_files[0]
@@ -157,8 +157,8 @@ def get_valid_paths(self, path):
             (not parent.endswith("/relax1"))
             and (not parent.endswith("/relax2"))
             and (
-                len(glob(os.path.join(parent, "vasprun.xml*"))) > 0
-                or (len(glob(os.path.join(parent, "POSCAR*"))) > 0 and len(glob(os.path.join(parent, "OSZICAR*"))) > 0)
+                len(glob(f"{parent}/vasprun.xml*")) > 0
+                or (len(glob(f"{parent}/POSCAR*")) > 0 and len(glob(f"{parent}/OSZICAR*")) > 0)
             )
         ):
             return [parent]
@@ -225,10 +225,10 @@ def assimilate(self, path):
             filenames = {"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"}
             if "relax1" in files and "relax2" in files:
                 for filename in ("INCAR", "POTCAR", "POSCAR"):
-                    search_str = os.path.join(path, "relax1", filename + "*")
+                    search_str = f"{path}/relax1", filename + "*"
                     files_to_parse[filename] = glob(search_str)[0]
                 for filename in ("CONTCAR", "OSZICAR"):
-                    search_str = os.path.join(path, "relax2", filename + "*")
+                    search_str = f"{path}/relax2", filename + "*"
                     files_to_parse[filename] = glob(search_str)[-1]
             else:
                 for filename in filenames:
@@ -427,7 +427,7 @@ def from_dict(cls, dct):
 
 def _get_transformation_history(path):
     """Checks for a transformations.json* file and returns the history."""
-    trans_json = glob(os.path.join(path, "transformations.json*"))
+    trans_json = glob(f"{path}/transformations.json*")
     if trans_json:
         try:
             with zopen(trans_json[0]) as f:

pymatgen/cli/pmg_config.py

@@ -38,8 +38,8 @@ def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None:
     from pymatgen.io.cp2k.inputs import GaussianTypeOrbitalBasisSet, GthPotential
     from pymatgen.io.cp2k.utils import chunk
 
-    basis_files = glob(os.path.join(data_dir, "*BASIS*"))
-    potential_files = glob(os.path.join(data_dir, "*POTENTIAL*"))
+    basis_files = glob(f"{data_dir}/*BASIS*")
+    potential_files = glob(f"{data_dir}/*POTENTIAL*")
 
     settings: dict[str, dict] = {str(el): {"potentials": {}, "basis_sets": {}} for el in Element}
 
@@ -158,7 +158,7 @@ def setup_potcars(potcar_dirs: list[str]):
                     if subdir == "Osmium":
                         subdir = "Os"
                     dest = os.path.join(base_dir, f"POTCAR.{subdir}")
-                    shutil.move(os.path.join(base_dir, "POTCAR"), dest)
+                    shutil.move(f"{base_dir}/POTCAR", dest)
                     with subprocess.Popen(["gzip", "-f", dest]) as p:
                         p.communicate()
                 except Exception as exc:
@@ -181,10 +181,10 @@ def build_enum(fortran_command: str = "gfortran") -> bool:
     state = True
     try:
         subprocess.call(["git", "clone", "--recursive", "https://github.com/msg-byu/enumlib.git"])
-        os.chdir(os.path.join(cwd, "enumlib", "symlib", "src"))
+        os.chdir(f"{cwd}/enumlib/symlib/src")
         os.environ["F90"] = fortran_command
         subprocess.call(["make"])
-        enumpath = os.path.join(cwd, "enumlib", "src")
+        enumpath = f"{cwd}/enumlib/src"
         os.chdir(enumpath)
         subprocess.call(["make"])
         subprocess.call(["make", "enum.x"])

pymatgen/cli/pmg_potcar.py

@@ -39,7 +39,7 @@ def gen_potcar(dirname, filename):
             elements = f.readlines()
         symbols = [el.strip() for el in elements if el.strip() != ""]
         potcar = Potcar(symbols)
-        potcar.write_file(os.path.join(dirname, "POTCAR"))
+        potcar.write_file(f"{dirname}/POTCAR")
 
 
 def generate_potcar(args):

pymatgen/command_line/bader_caller.py

@@ -490,17 +490,17 @@ def bader_analysis_from_objects(chgcar, potcar=None, aeccar0=None, aeccar2=None)
             if aeccar0 and aeccar2:
                 # construct reference file
                 chgref = aeccar0.linear_add(aeccar2)
-                chgref_path = os.path.join(tmp_dir, "CHGCAR_ref")
+                chgref_path = f"{tmp_dir}/CHGCAR_ref"
                 chgref.write_file(chgref_path)
             else:
                 chgref_path = None
 
             chgcar.write_file("CHGCAR")
-            chgcar_path = os.path.join(tmp_dir, "CHGCAR")
+            chgcar_path = f"{tmp_dir}/CHGCAR"
 
             if potcar:
                 potcar.write_file("POTCAR")
-                potcar_path = os.path.join(tmp_dir, "POTCAR")
+                potcar_path = f"{tmp_dir}/POTCAR"
             else:
                 potcar_path = None
 
@@ -530,7 +530,7 @@ def bader_analysis_from_objects(chgcar, potcar=None, aeccar0=None, aeccar2=None)
                 chgcar.is_spin_polarized = False
                 chgcar.write_file("CHGCAR_mag")
 
-                chgcar_mag_path = os.path.join(tmp_dir, "CHGCAR_mag")
+                chgcar_mag_path = f"{tmp_dir}/CHGCAR_mag"
                 ba = BaderAnalysis(
                     chgcar_filename=chgcar_mag_path,
                     potcar_filename=potcar_path,

pymatgen/command_line/chargemol_caller.py

@@ -219,42 +219,42 @@ def _from_data_dir(self, chargemol_output_path=None):
         if chargemol_output_path is None:
             chargemol_output_path = ""
 
-        charge_path = os.path.join(chargemol_output_path, "DDEC6_even_tempered_net_atomic_charges.xyz")
+        charge_path = f"{chargemol_output_path}/DDEC6_even_tempered_net_atomic_charges.xyz"
         self.ddec_charges = self._get_data_from_xyz(charge_path)
         self.dipoles = self._get_dipole_info(charge_path)
 
-        bond_order_path = os.path.join(chargemol_output_path, "DDEC6_even_tempered_bond_orders.xyz")
+        bond_order_path = f"{chargemol_output_path}/DDEC6_even_tempered_bond_orders.xyz"
         if os.path.exists(bond_order_path):
             self.bond_order_sums = self._get_data_from_xyz(bond_order_path)
             self.bond_order_dict = self._get_bond_order_info(bond_order_path)
         else:
             self.bond_order_sums = self.bond_order_dict = None
 
-        spin_moment_path = os.path.join(chargemol_output_path, "DDEC6_even_tempered_atomic_spin_moments.xyz")
+        spin_moment_path = f"{chargemol_output_path}/DDEC6_even_tempered_atomic_spin_moments.xyz"
         if os.path.exists(spin_moment_path):
             self.ddec_spin_moments = self._get_data_from_xyz(spin_moment_path)
         else:
             self.ddec_spin_moments = None
 
-        rsquared_path = os.path.join(chargemol_output_path, "DDEC_atomic_Rsquared_moments.xyz")
+        rsquared_path = f"{chargemol_output_path}/DDEC_atomic_Rsquared_moments.xyz"
         if os.path.exists(rsquared_path):
             self.ddec_rsquared_moments = self._get_data_from_xyz(rsquared_path)
         else:
             self.ddec_rsquared_moments = None
 
-        rcubed_path = os.path.join(chargemol_output_path, "DDEC_atomic_Rcubed_moments.xyz")
+        rcubed_path = f"{chargemol_output_path}/DDEC_atomic_Rcubed_moments.xyz"
         if os.path.exists(rcubed_path):
             self.ddec_rcubed_moments = self._get_data_from_xyz(rcubed_path)
         else:
             self.ddec_rcubed_moments = None
 
-        rfourth_path = os.path.join(chargemol_output_path, "DDEC_atomic_Rfourth_moments.xyz")
+        rfourth_path = f"{chargemol_output_path}/DDEC_atomic_Rfourth_moments.xyz"
         if os.path.exists(rfourth_path):
             self.ddec_rfourth_moments = self._get_data_from_xyz(rfourth_path)
         else:
             self.ddec_rfourth_moments = None
 
-        ddec_analysis_path = os.path.join(chargemol_output_path, "VASP_DDEC_analysis.output")
+        ddec_analysis_path = f"{chargemol_output_path}/VASP_DDEC_analysis.output"
         if os.path.exists(ddec_analysis_path):
             self.cm5_charges = self._get_cm5_data_from_output(ddec_analysis_path)
         else:

pymatgen/command_line/gulp_caller.py

@@ -881,7 +881,7 @@ class TersoffPotential:
     def __init__(self):
         """Init TersoffPotential."""
         module_dir = os.path.dirname(os.path.abspath(__file__))
-        with open(os.path.join(module_dir, "OxideTersoffPotentials")) as f:
+        with open(f"{module_dir}/OxideTersoffPotentials") as f:
             data = {}
             for row in f:
                 metaloxi = row.split()[0]

pymatgen/core/composition.py

@@ -751,7 +751,7 @@ def oxi_state_guesses(
                 oxidation state across all sites in that composition. If the
                 composition is not charge balanced, an empty list is returned.
         """
-        return self._get_oxid_state_guesses(all_oxi_states, max_sites, oxi_states_override, target_charge)[0]
+        return self._get_oxi_state_guesses(all_oxi_states, max_sites, oxi_states_override, target_charge)[0]
 
     def replace(self, elem_map: dict[str, str | dict[str, int | float]]) -> Composition:
         """
@@ -843,9 +843,7 @@ def add_charges_from_oxi_state_guesses(
             on the results form guessing oxidation states. If no oxidation state
             is possible, returns a Composition where all oxidation states are 0.
         """
-        _, oxidation_states = self._get_oxid_state_guesses(
-            all_oxi_states, max_sites, oxi_states_override, target_charge
-        )
+        _, oxidation_states = self._get_oxi_state_guesses(all_oxi_states, max_sites, oxi_states_override, target_charge)
 
         # Special case: No charged compound is possible
         if not oxidation_states:
@@ -872,7 +870,7 @@ def remove_charges(self) -> Composition:
             dct[Element(specie.symbol)] += amt
         return Composition(dct)
 
-    def _get_oxid_state_guesses(self, all_oxi_states, max_sites, oxi_states_override, target_charge):
+    def _get_oxi_state_guesses(self, all_oxi_states, max_sites, oxi_states_override, target_charge):
         """
         Utility operation for guessing oxidation states.
 
@@ -898,13 +896,10 @@ def _get_oxid_state_guesses(self, all_oxi_states, max_sites, oxi_states_override
                 formula is greater than abs(max_sites).
 
         Returns:
-            A list of dicts - each dict reports an element symbol and average
-                oxidation state across all sites in that composition. If the
-                composition is not charge balanced, an empty list is returned.
-            A list of dicts - each dict maps the element symbol to a list of
+            list[dict]: Each dict maps the element symbol to a list of
                 oxidation states for each site of that element. For example, Fe3O4 could
-                return a list of [2,2,2,3,3,3] for the oxidation states of If the composition
-                is
+                return a list of [2,2,2,3,3,3] for the oxidation states of the 6 Fe sites.
+                If the composition is not charge balanced, an empty list is returned.
         """
         comp = self.copy()
         # reduce Composition if necessary
@@ -925,7 +920,7 @@ def _get_oxid_state_guesses(self, all_oxi_states, max_sites, oxi_states_override
         # Load prior probabilities of oxidation states, used to rank solutions
         if not Composition.oxi_prob:
             module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
-            all_data = loadfn(os.path.join(module_dir, "..", "analysis", "icsd_bv.yaml"))
+            all_data = loadfn(f"{module_dir}/../analysis/icsd_bv.yaml")
             Composition.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

pymatgen/core/ion.py

@@ -274,7 +274,7 @@ def oxi_state_guesses(  # type: ignore
                 oxidation state across all sites in that composition. If the
                 composition is not charge balanced, an empty list is returned.
         """
-        return self._get_oxid_state_guesses(all_oxi_states, max_sites, oxi_states_override, self.charge)[0]
+        return self._get_oxi_state_guesses(all_oxi_states, max_sites, oxi_states_override, self.charge)[0]
 
     def __eq__(self, other: object) -> bool:
         if not isinstance(other, Ion):

pymatgen/core/surface.py

@@ -1327,7 +1327,7 @@ def nonstoichiometric_symmetrized_slab(self, init_slab):
 
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
-with open(os.path.join(module_dir, "reconstructions_archive.json")) as data_file:
+with open(f"{module_dir}/reconstructions_archive.json") as data_file:
     reconstructions_archive = json.load(data_file)