Revert "zopen: explicit binary/text mode , and explicit encoding as UTF…" (#4221)

This reverts commit b2a5e0f.

Author: shyuep

dev_scripts/potcar_scrambler.py

@@ -124,7 +124,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         return scrambled_potcar_str
 
     def to_file(self, filename: str) -> None:
-        with zopen(filename, mode="wt", encoding="utf-8") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod

src/pymatgen/apps/borg/hive.py

@@ -445,7 +445,7 @@ def _get_transformation_history(path: PathLike):
     """Check for a transformations.json* file and return the history."""
     if trans_json := glob(f"{path!s}/transformations.json*"):
         try:
-            with zopen(trans_json[0], mode="rt", encoding="utf-8") as file:
+            with zopen(trans_json[0]) as file:
                 return json.load(file)["history"]
         except Exception:
             return None

src/pymatgen/apps/borg/queen.py

@@ -103,12 +103,12 @@ def save_data(self, filename: PathLike) -> None:
                 that if the filename ends with gz or bz2, the relevant gzip
                 or bz2 compression will be applied.
         """
-        with zopen(filename, mode="wt", encoding="utf-8") as file:
+        with zopen(filename, mode="wt") as file:
             json.dump(list(self._data), file, cls=MontyEncoder)
 
     def load_data(self, filename: PathLike) -> None:
         """Load assimilated data from a file."""
-        with zopen(filename, mode="rt", encoding="utf-8") as file:
+        with zopen(filename, mode="rt") as file:
             self._data = json.load(file, cls=MontyDecoder)
 
 

src/pymatgen/core/structure.py

@@ -2953,15 +2953,15 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
         elif fmt == "json" or fnmatch(filename.lower(), "*.json*"):
             json_str = json.dumps(self.as_dict())
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt") as file:
                     file.write(json_str)
             return json_str
         elif fmt == "xsf" or fnmatch(filename.lower(), "*.xsf*"):
             from pymatgen.io.xcrysden import XSF
 
             res_str = XSF(self).to_str()
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt", encoding="utf8") as file:
                     file.write(res_str)
             return res_str
         elif (
@@ -2987,15 +2987,15 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
             yaml.dump(self.as_dict(), str_io)
             yaml_str = str_io.getvalue()
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt") as file:
                     file.write(yaml_str)
             return yaml_str
         elif fmt == "aims" or fnmatch(filename, "geometry.in"):
             from pymatgen.io.aims.inputs import AimsGeometryIn
 
             geom_in = AimsGeometryIn.from_structure(self)
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="w") as file:
                     file.write(geom_in.get_header(filename))
                     file.write(geom_in.content)
                     file.write("\n")
@@ -3010,7 +3010,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
 
             res_str = ResIO.structure_to_str(self)
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt", encoding="utf8") as file:
                     file.write(res_str)
             return res_str
         elif fmt == "pwmat" or fnmatch(filename.lower(), "*.pwmat") or fnmatch(filename.lower(), "*.config"):
@@ -3173,7 +3173,7 @@ def from_file(
             return struct
 
         fname = os.path.basename(filename)
-        with zopen(filename, mode="rt", errors="replace", encoding="utf-8") as file:
+        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(
@@ -3919,7 +3919,7 @@ def to(self, filename: str = "", fmt: str = "") -> str | None:
         elif fmt == "json" or fnmatch(filename, "*.json*") or fnmatch(filename, "*.mson*"):
             json_str = json.dumps(self.as_dict())
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt", encoding="utf8") as file:
                     file.write(json_str)
             return json_str
         elif fmt in {"yaml", "yml"} or fnmatch(filename, "*.yaml*") or fnmatch(filename, "*.yml*"):
@@ -3928,7 +3928,7 @@ def to(self, filename: str = "", fmt: str = "") -> str | None:
             yaml.dump(self.as_dict(), str_io)
             yaml_str = str_io.getvalue()
             if filename:
-                with zopen(filename, mode="wt", encoding="utf-8") as file:
+                with zopen(filename, mode="wt", encoding="utf8") as file:
                     file.write(yaml_str)
             return yaml_str
         else:
@@ -4010,7 +4010,7 @@ def from_file(cls, filename: PathLike) -> Self | None:
         """
         filename = str(filename)
 
-        with zopen(filename, mode="rt", encoding="utf-8") as file:
+        with zopen(filename) as file:
             contents = file.read()
         fname = filename.lower()
         if fnmatch(fname, "*.xyz*"):

src/pymatgen/core/trajectory.py

@@ -467,7 +467,7 @@ def write_Xdatcar(
 
         xdatcar_str = "\n".join(lines) + "\n"
 
-        with zopen(filename, mode="wt", encoding="utf-8") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(xdatcar_str)
 
     def as_dict(self) -> dict:

src/pymatgen/io/adf.py

@@ -645,7 +645,7 @@ def _parse_logfile(self, logfile):
         # The last non-empty line of the logfile must match the end pattern.
         # Otherwise the job has some internal failure. The TAPE13 part of the
         # ADF manual has a detailed explanation.
-        with zopen(logfile, mode="rt", encoding="utf-8") as file:
+        with zopen(logfile, mode="rt") as file:
             for line in reverse_readline(file):
                 if line == "":
                     continue

src/pymatgen/io/aims/inputs.py

@@ -133,7 +133,7 @@ def from_file(cls, filepath: str | Path) -> Self:
         Returns:
             AimsGeometryIn: The input object represented in the file
         """
-        with zopen(filepath, mode="rt", encoding="utf-8") as in_file:
+        with zopen(filepath, mode="rt") as in_file:
             content = in_file.read()
         return cls.from_str(content)
 
@@ -753,7 +753,7 @@ def from_file(cls, filename: str, label: str | None = None) -> Self:
         Returns:
             AimsSpeciesFile
         """
-        with zopen(filename, mode="rt", encoding="utf-8") as file:
+        with zopen(filename, mode="rt") as file:
             return cls(data=file.read(), label=label)
 
     @classmethod

src/pymatgen/io/cif.py

@@ -299,7 +299,7 @@ def from_file(cls, filename: PathLike) -> Self:
         Returns:
             CifFile
         """
-        with zopen(filename, mode="rt", errors="replace", encoding="utf-8") as file:
+        with zopen(filename, mode="rt", errors="replace") as file:
             return cls.from_str(file.read())
 
 
@@ -1760,9 +1760,9 @@ def cif_file(self) -> CifFile:
 
     def write_file(
         self,
-        filename: PathLike,
-        mode: Literal["wt", "at"] = "wt",
+        filename: str | Path,
+        mode: Literal["w", "a", "wt", "at"] = "w",
     ) -> None:
         """Write the CIF file."""
-        with zopen(filename, mode=mode, encoding="utf-8") as file:
+        with zopen(filename, mode=mode) as file:
             file.write(str(self))

src/pymatgen/io/common.py

@@ -354,7 +354,7 @@ def to_cube(self, filename, comment: str = ""):
             filename (str): Name of the cube file to be written.
             comment (str): If provided, this will be added to the second comment line
         """
-        with zopen(filename, mode="wt", encoding="utf-8") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(f"# Cube file for {self.structure.formula} generated by Pymatgen\n")
             file.write(f"# {comment}\n")
             file.write(f"\t {len(self.structure)} 0.000000 0.000000 0.000000\n")
@@ -386,7 +386,7 @@ def from_cube(cls, filename: str | Path) -> Self:
         Args:
             filename (str): of the cube to read
         """
-        file = zopen(filename, mode="rt", encoding="utf-8")
+        file = zopen(filename, mode="rt")
 
         # skip header lines
         file.readline()
@@ -529,7 +529,7 @@ def __getitem__(self, item):
             f"No parser defined for {item}. Contents are returned as a string.",
             stacklevel=2,
         )
-        with zopen(fpath, mode="rt", encoding="utf-8") as f:
+        with zopen(fpath, "rt") as f:
             return f.read()
 
     def get_files_by_name(self, name: str) -> dict[str, Any]:

src/pymatgen/io/core.py

@@ -74,7 +74,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename: The filename to output to, including path.
         """
-        with zopen(Path(filename), mode="wt", encoding="utf-8") as file:
+        with zopen(Path(filename), mode="wt") as file:
             file.write(self.get_str())
 
     @classmethod
@@ -102,7 +102,7 @@ def from_file(cls, path: PathLike) -> None:
         Returns:
             InputFile
         """
-        with zopen(Path(path), mode="rt", encoding="utf-8") as file:
+        with zopen(Path(path), mode="rt") as file:
             return cls.from_str(file.read())  # from_str not implemented
 
 
@@ -218,7 +218,7 @@ def write_input(
             if isinstance(contents, InputFile):
                 contents.write_file(file_path)
             else:
-                with zopen(file_path, mode="wt", encoding="utf-8") as file:
+                with zopen(file_path, mode="wt") as file:
                     file.write(str(contents))
 
         if zip_inputs: