rename single-letter variables f->file

Author: janosh

pymatgen/alchemy/materials.py

@@ -206,8 +206,8 @@ 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", mode="w") as fp:
-            json.dump(self.as_dict(), fp)
+        with open(f"{output_dir}/transformations.json", mode="w") as file:
+            json.dump(self.as_dict(), file)
 
     def __str__(self) -> str:
         output = ["Current structure", "------------", str(self.final_structure), "\nHistory", "------------"]

pymatgen/alchemy/transmuters.py

@@ -268,8 +268,8 @@ def from_filenames(cls, filenames, transformations=None, primitive=True, extend_
             extend_collection: Same meaning as in __init__.
         """
         cif_files = []
-        for fname in filenames:
-            with open(fname) as file:
+        for filename in filenames:
+            with open(filename) as file:
                 cif_files.append(file.read())
         return cls(
             "\n".join(cif_files),

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -165,8 +165,8 @@ def auto_load(cls, root_dir=None):
             root_dir = f"{home}/.chemenv"
         config_file = f"{root_dir}/config.json"
         try:
-            with open(config_file) as f:
-                config_dict = json.load(f)
+            with open(config_file) as file:
+                config_dict = json.load(file)
             return ChemEnvConfig(package_options=config_dict["package_options"])
 
         except OSError:

pymatgen/analysis/hhi.py

@@ -37,8 +37,8 @@ def __init__(self):
         """Init for HHIModel."""
         self.symbol_hhip_hhir = {}  # symbol->(HHI_production, HHI reserve)
 
-        with open(csv_path) as f:
-            for line in f:
+        with open(csv_path) as file:
+            for line in file:
                 if line[0] != "#":
                     symbol, hhi_production, hhi_reserve = line.split(",")
                     self.symbol_hhip_hhir[symbol] = float(hhi_production), float(hhi_reserve)

pymatgen/analysis/structure_prediction/substitution_probability.py

@@ -58,8 +58,8 @@ def __init__(self, lambda_table=None, alpha=-5):
         else:
             module_dir = os.path.dirname(__file__)
             json_file = f"{module_dir}/data/lambda.json"
-            with open(json_file) as f:
-                self._lambda_table = json.load(f)
+            with open(json_file) as file:
+                self._lambda_table = json.load(file)
 
         # build map of specie pairs to lambdas
         self.alpha = alpha

pymatgen/cli/pmg_potcar.py

@@ -33,8 +33,8 @@ def gen_potcar(dirname, filename):
     """
     if filename == "POTCAR.spec":
         fullpath = os.path.join(dirname, filename)
-        with open(fullpath) as f:
-            elements = f.readlines()
+        with open(fullpath) as file:
+            elements = file.readlines()
         symbols = [el.strip() for el in elements if el.strip() != ""]
         potcar = Potcar(symbols)
         potcar.write_file(f"{dirname}/POTCAR")

pymatgen/command_line/enumlib_caller.py

@@ -353,8 +353,8 @@ def _get_structures(self, num_structs):
             inv_org_latt = None
 
         for file in glob("vasp.*"):
-            with open(file) as f:
-                data = f.read()
+            with open(file) as file:
+                data = file.read()
                 data = re.sub(r"scale factor", "1", data)
                 data = re.sub(r"(\d+)-(\d+)", r"\1 -\2", data)
                 poscar = Poscar.from_str(data, self.index_species)

pymatgen/command_line/mcsqs_caller.py

@@ -234,8 +234,8 @@ def _parse_clusters(filename):
                 num_possible_species: int
                 cluster_function: float
     """
-    with open(filename) as f:
-        lines = f.readlines()
+    with open(filename) as file:
+        lines = file.readlines()
 
     clusters = []
     cluster_block = []

pymatgen/command_line/vampire_caller.py

@@ -296,8 +296,8 @@ def _create_input(self):
 
         input_script = "\n".join(input_script)
 
-        with open("input", mode="w") as f:
-            f.write(input_script)
+        with open("input", mode="w") as file:
+            file.write(input_script)
 
     def _create_ucf(self):
         structure = self.structure

pymatgen/core/structure.py

@@ -2887,8 +2887,8 @@ def from_file(  # type: ignore[override]
         from pymatgen.io.vasp import Chgcar, Vasprun
 
         fname = os.path.basename(filename)
-        with zopen(filename, mode="rt", errors="replace") as f:
-            contents = f.read()
+        with zopen(filename, mode="rt", errors="replace") as file:
+            contents = file.read()
         if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
             return cls.from_str(contents, fmt="cif", primitive=primitive, sort=sort, merge_tol=merge_tol, **kwargs)
         if fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):