Pass file IO modes as kwarg

dev_scripts/chemenv/explicit_permutations.py

@@ -34,11 +34,11 @@ class Algo:
 
 if __name__ == "__main__":
     # Choose the geometry
-    allcg = AllCoordinationGeometries()
+    all_cg = AllCoordinationGeometries()
     while True:
         cg_symbol = input("Enter symbol of the geometry for which you want to get the explicit permutations : ")
         try:
-            cg = allcg[cg_symbol]
+            cg = all_cg[cg_symbol]
             break
         except LookupError:
             print("Wrong geometry, try again ...")
@@ -93,5 +93,5 @@ class Algo:
         cg._algorithms = [ExplicitPermutationsAlgorithm(permutations=explicit_permutations)]
         new_geom_dir = "new_geometry_files"
         os.makedirs(new_geom_dir, exist_ok=True)
-        with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as f:
-            json.dump(cg.as_dict(), f)
+        with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w") as file:
+            json.dump(cg.as_dict(), file)

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -144,5 +144,5 @@
     if test == "y":
         cg._algorithms = new_algos
         cg_dict = cg.as_dict()
-        with open(f"../coordination_geometries_files_new/{cg_symbol}.json", "w") as f:
-            json.dump(cg_dict, f)
+        with open(f"../coordination_geometries_files_new/{cg_symbol}.json", mode="w") as file:
+            json.dump(cg_dict, file)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -432,5 +432,5 @@ def random_permutations_iterator(initial_permutation, n_permutations):
         if test == "y":
             new_geom_dir = "new_geometry_files"
             os.makedirs(new_geom_dir, exist_ok=True)
-            with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as file:
+            with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w") as file:
                 json.dump(cg.as_dict(), file)

dev_scripts/potcar_scrambler.py

@@ -125,7 +125,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle):
         return scrambled_potcar_str
 
     def to_file(self, filename: str):
-        with zopen(filename, "wt") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod

dev_scripts/regen_libxcfunc.py

@@ -30,9 +30,9 @@ def parse_section(section):
         return int(dct["Number"]), dct
 
     dct = {}
-    with open(path) as fh:
+    with open(path) as file:
         section = []
-        for line in fh:
+        for line in file:
             if not line.startswith("-"):
                 section.append(line)
             else:
@@ -63,8 +63,8 @@ def write_libxc_docs_json(xcfuncs, jpath):
             if desc is not None:
                 xcfuncs[num][opt] = desc
 
-    with open(jpath, "w") as fh:
-        json.dump(xcfuncs, fh)
+    with open(jpath, mode="w") as file:
+        json.dump(xcfuncs, file)
 
     return xcfuncs
 
@@ -101,8 +101,8 @@ def main():
     # Re-generate enumerations.
     # [0] read py module.
     xc_funcpy_path = f"{pmg_core}/libxcfunc.py"
-    with open(xc_funcpy_path) as fh:
-        lines = fh.readlines()
+    with open(xc_funcpy_path) as file:
+        lines = file.readlines()
 
     # [1] insert new enum values in list
     start = lines.index("#begin_include_dont_touch\n")
@@ -111,8 +111,8 @@ def main():
     del lines[start + 1 : stop]
 
     # [2] write new py module
-    with open(xc_funcpy_path, "w") as fh:
-        fh.writelines(lines)
+    with open(xc_funcpy_path, mode="w") as file:
+        file.writelines(lines)
 
     print("Files have been regenerated")
     print("Remember to update libxc_version in libxcfuncs.py!")

dev_scripts/update_pt_data.py

@@ -56,7 +56,7 @@ def parse_oxi_state():
             data[el]["Common oxidation states"] = common_oxi
         else:
             print(el)
-    with open("periodic_table2.yaml", "w") as file:
+    with open("periodic_table2.yaml", mode="w") as file:
         yaml.dump(data, file)
 
 
@@ -87,7 +87,7 @@ def parse_ionic_radii():
                 data[el]["Ionic_radii"] = ionic_radii
         else:
             print(el)
-    with open("periodic_table2.yaml", "w") as file:
+    with open("periodic_table2.yaml", mode="w") as file:
         yaml.dump(data, file)
 
 
@@ -121,9 +121,9 @@ def parse_radii():
             data[el]["Van der waals radius"] = vdw_radii
         else:
             print(el)
-    with open("periodic_table2.yaml", "w") as file:
+    with open("periodic_table2.yaml", mode="w") as file:
         yaml.dump(data, file)
-    with open("../pymatgen/core/periodic_table.json", "w") as file:
+    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
 
 
@@ -140,9 +140,9 @@ def update_ionic_radii():
         if "Ionic_radii_ls" in d:
             d["Ionic radii ls"] = {k: v / 100 for k, v in d["Ionic_radii_ls"].items()}
             del d["Ionic_radii_ls"]
-    with open("periodic_table2.yaml", "w") as file:
+    with open("periodic_table2.yaml", mode="w") as file:
         yaml.dump(data, file)
-    with open("../pymatgen/core/periodic_table.json", "w") as file:
+    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
 
 
@@ -180,14 +180,14 @@ def parse_shannon_radii():
             data[el]["Shannon radii"] = dict(radii[el])
 
     dumpfn(data, ptable_yaml_path)
-    with open("../pymatgen/core/periodic_table.json", "w") as file:
+    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
 
 
 def gen_periodic_table():
     data = loadfn(ptable_yaml_path)
 
-    with open("../pymatgen/core/periodic_table.json", "w") as file:
+    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
 
 

pymatgen/alchemy/materials.py

@@ -207,7 +207,7 @@ 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(f"{output_dir}/transformations.json", "w") as fp:
+        with open(f"{output_dir}/transformations.json", mode="w") as fp:
             json.dump(self.as_dict(), fp)
 
     def __str__(self) -> str:

pymatgen/alchemy/transmuters.py

@@ -308,8 +308,8 @@ def from_filenames(poscar_filenames, transformations=None, extend_collection=Fal
         """
         trafo_structs = []
         for filename in poscar_filenames:
-            with open(filename) as f:
-                trafo_structs.append(TransformedStructure.from_poscar_string(f.read(), []))
+            with open(filename) as file:
+                trafo_structs.append(TransformedStructure.from_poscar_string(file.read(), []))
         return StandardTransmuter(trafo_structs, transformations, extend_collection=extend_collection)
 
 

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -149,8 +149,8 @@ def save(self, root_dir=None):
             if test != "Y":
                 print("Configuration not saved")
                 return config_file
-        with open(config_file, "w") as f:
-            json.dump(config_dict, f)
+        with open(config_file, mode="w") as file:
+            json.dump(config_dict, file)
         print("Configuration saved")
         return config_file
 

pymatgen/analysis/cost.py

@@ -91,8 +91,8 @@ def __init__(self, filename):
         # read in data from file
         self._chemsys_entries = defaultdict(list)
         filename = os.path.join(os.path.dirname(__file__), filename)
-        with open(filename) as f:
-            reader = csv.reader(f, quotechar="|")
+        with open(filename) as file:
+            reader = csv.reader(file, quotechar="|")
             for row in reader:
                 comp = Composition(row[0])
                 cost_per_mol = float(row[1]) * comp.weight.to("kg") * const.N_A

pymatgen/analysis/diffraction/neutron.py

@@ -26,9 +26,9 @@
 __email__ = "[email protected]"
 __date__ = "4/19/18"
 
-with open(os.path.join(os.path.dirname(__file__), "neutron_scattering_length.json")) as f:
+with open(os.path.join(os.path.dirname(__file__), "neutron_scattering_length.json")) as file:
     # This table was cited from "Neutron Data Booklet" 2nd ed (Old City 2003).
-    ATOMIC_SCATTERING_LEN = json.load(f)
+    ATOMIC_SCATTERING_LEN = json.load(file)
 
 
 class NDCalculator(AbstractDiffractionPatternCalculator):

pymatgen/analysis/diffraction/xrd.py

@@ -47,8 +47,8 @@
     "AgKb1": 0.497082,
 }
 
-with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as f:
-    ATOMIC_SCATTERING_PARAMS = json.load(f)
+with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as file:
+    ATOMIC_SCATTERING_PARAMS = json.load(file)
 
 
 class XRDCalculator(AbstractDiffractionPatternCalculator):

pymatgen/analysis/graphs.py

@@ -926,17 +926,17 @@ def draw_graph_to_file(
         basename, extension = os.path.splitext(filename)
         extension = extension[1:]
 
-        write_dot(g, basename + ".dot")
+        write_dot(g, f"{basename}.dot")
 
-        with open(filename, "w") as f:
-            args = [algo, "-T", extension, basename + ".dot"]
-            with subprocess.Popen(args, stdout=f, stdin=subprocess.PIPE, close_fds=True) as rs:
+        with open(filename, mode="w") as file:
+            args = [algo, "-T", extension, f"{basename}.dot"]
+            with subprocess.Popen(args, stdout=file, stdin=subprocess.PIPE, close_fds=True) as rs:
                 rs.communicate()
                 if rs.returncode != 0:
                     raise RuntimeError(f"{algo} exited with return code {rs.returncode}.")
 
         if not keep_dot:
-            os.remove(basename + ".dot")
+            os.remove(f"{basename}.dot")
 
     @property
     def types_and_weights_of_connections(self):
@@ -2574,17 +2574,17 @@ def draw_graph_to_file(
         basename, extension = os.path.splitext(filename)
         extension = extension[1:]
 
-        write_dot(g, basename + ".dot")
+        write_dot(g, f"{basename}.dot")
 
-        with open(filename, "w") as f:
-            args = [algo, "-T", extension, basename + ".dot"]
-            with subprocess.Popen(args, stdout=f, stdin=subprocess.PIPE, close_fds=True) as rs:
+        with open(filename, mode="w") as file:
+            args = [algo, "-T", extension, f"{basename}.dot"]
+            with subprocess.Popen(args, stdout=file, stdin=subprocess.PIPE, close_fds=True) as rs:
                 rs.communicate()
                 if rs.returncode != 0:
                     raise RuntimeError(f"{algo} exited with return code {rs.returncode}.")
 
         if not keep_dot:
-            os.remove(basename + ".dot")
+            os.remove(f"{basename}.dot")
 
     def as_dict(self):
         """

pymatgen/analysis/interface_reactions.py

@@ -28,8 +28,8 @@
 __email__ = "[email protected]"
 __date__ = "Sep 1, 2021"
 
-with open(os.path.join(os.path.dirname(__file__), "..", "util", "plotly_interface_rxn_layouts.json")) as f:
-    plotly_layouts = json.load(f)
+with open(os.path.join(os.path.dirname(__file__), "..", "util", "plotly_interface_rxn_layouts.json")) as file:
+    plotly_layouts = json.load(file)
 
 
 @due.dcite(

pymatgen/analysis/local_env.py

@@ -49,14 +49,14 @@
 module_dir = os.path.dirname(os.path.abspath(__file__))
 yaml = YAML()
 
-with open(f"{module_dir}/op_params.yaml") as f:
-    default_op_params = yaml.load(f)
+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 f:
-    cn_opt_params = yaml.load(f)
+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 fp:
-    _ion_radii = json.load(fp)
+with open(f"{module_dir}/ionic_radii.json") as file:
+    _ion_radii = json.load(file)
 
 
 class ValenceIonicRadiusEvaluator:

pymatgen/apps/borg/hive.py

@@ -417,8 +417,8 @@ def _get_transformation_history(path):
     trans_json = glob(f"{path}/transformations.json*")
     if trans_json:
         try:
-            with zopen(trans_json[0]) as f:
-                return json.load(f)["history"]
+            with zopen(trans_json[0]) as file:
+                return json.load(file)["history"]
         except Exception:
             return None
     return None

pymatgen/apps/borg/queen.py

@@ -77,12 +77,12 @@ def serial_assimilate(self, rootpath):
         count = 0
         total = len(valid_paths)
         for path in valid_paths:
-            newdata = self._drone.assimilate(path)
-            self._data.append(newdata)
+            new_data = self._drone.assimilate(path)
+            self._data.append(new_data)
             count += 1
             logger.info(f"{count}/{total} ({count / total:.2%}) done")
-        for d in data:
-            self._data.append(json.loads(d, cls=MontyDecoder))
+        for json_str in data:
+            self._data.append(json.loads(json_str, cls=MontyDecoder))
 
     def get_data(self):
         """Returns an list of assimilated objects."""
@@ -96,21 +96,21 @@ def save_data(self, filename):
                 that if the filename ends with gz or bz2, the relevant gzip
                 or bz2 compression will be applied.
         """
-        with zopen(filename, "wt") as f:
-            json.dump(list(self._data), f, cls=MontyEncoder)
+        with zopen(filename, mode="wt") as file:
+            json.dump(list(self._data), file, cls=MontyEncoder)
 
     def load_data(self, filename):
         """Load assimilated data from a file."""
-        with zopen(filename, "rt") as f:
-            self._data = json.load(f, cls=MontyDecoder)
+        with zopen(filename, mode="rt") as file:
+            self._data = json.load(file, cls=MontyDecoder)
 
 
 def order_assimilation(args):
     """Internal helper method for BorgQueen to process assimilation."""
     (path, drone, data, status) = args
-    newdata = drone.assimilate(path)
-    if newdata:
-        data.append(json.dumps(newdata, cls=MontyEncoder))
+    new_data = drone.assimilate(path)
+    if new_data:
+        data.append(json.dumps(new_data, cls=MontyEncoder))
     status["count"] += 1
     count = status["count"]
     total = status["total"]

pymatgen/cli/pmg_config.py

@@ -87,7 +87,7 @@ def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None:
 
     for el in settings:
         print(f"Writing {el} settings file")
-        with open(os.path.join(target_dir, el), "w") as file:
+        with open(os.path.join(target_dir, el), mode="w") as file:
             yaml.dump(settings.get(el), file, default_flow_style=False)
 
     print(

pymatgen/command_line/bader_caller.py

@@ -157,8 +157,8 @@ def __init__(
                 )
 
             data = []
-            with open("ACF.dat") as f:
-                lines = f.readlines()
+            with open("ACF.dat") as file:
+                lines = file.readlines()
                 headers = ("x", "y", "z", "charge", "min_dist", "atomic_vol")
                 lines.pop(0)
                 lines.pop(0)
@@ -184,11 +184,7 @@ def __init__(
 
                 atomic_densities = []
                 # For each atom in the structure
-                for _, loc, chg in zip(
-                    self.chgcar.structure,
-                    self.chgcar.structure.frac_coords,
-                    atom_chgcars,
-                ):
+                for _site, loc, chg in zip(self.chgcar.structure, self.chgcar.structure.frac_coords, atom_chgcars):
                     # Find the index of the atom in the charge density atom
                     index = np.round(np.multiply(loc, chg.dim))
 

pymatgen/command_line/chargemol_caller.py

@@ -395,8 +395,8 @@ def _write_jobscript_for_chargemol(
             bo = ".true." if compute_bond_orders else ".false."
             lines += f"\n<compute BOs>\n{bo}\n</compute BOs>\n"
 
-        with open("job_control.txt", "w") as fh:
-            fh.write(lines)
+        with open("job_control.txt", mode="w") as file:
+            file.write(lines)
 
     @staticmethod
     def _get_dipole_info(filepath):