Pass file IO modes as kwarg (#3560)

* pass file IO mode as kwarg

* remove pointless Lattice() calls

* rename fh/fd -> file

Author: janosh

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