format codes

Author: hsulab

src/gdpx/utils/command.py

@@ -12,20 +12,18 @@
 import json
 import yaml
 
-import numpy as np
 
-
-def dict2str(d: dict, indent: int=2):
+def dict2str(d: dict, indent: int = 2):
     """Convert a nested dict to str."""
 
     def _dict2str(d_: dict, indent_: int):
         """Recursive function."""
         content = ""
         for k, v in d_.items():
             if isinstance(v, dict):
-                content += f"{k}:\n" + _dict2str(v, indent_+indent)
+                content += f"{k}:\n" + _dict2str(v, indent_ + indent)
             else:
-                content += " "*indent_ + f"{k}: {v}\n"
+                content += " " * indent_ + f"{k}: {v}\n"
 
         return content
 
@@ -34,49 +32,57 @@ def _dict2str(d_: dict, indent_: int):
     return content
 
 
-class CustomTimer():
+class CustomTimer:
 
     def __init__(self, name="code", func=print):
         """"""
         self.name = name
         self._print = func
 
         return
-    
+
     def __call__(self, func) -> Any:
         """"""
 
         def func_timer(*args, **kwargs):
             st = time.time()
             ret = func(*args, **kwargs)
             et = time.time()
-            content = "*** "+self.name+" time: "+"{:>8.4f}".format(et-st)+" ***"
+            content = (
+                "*** " + self.name + " time: " + "{:>8.4f}".format(et - st) + " ***"
+            )
             self._print(content)
 
             return ret
 
         return func_timer
 
-
     def __enter__(self):
         """"""
-        self.st = time.time() # start time
+        self.st = time.time()  # start time
 
         return self
-    
+
     def __exit__(self, *args):
         """"""
-        self.et = time.time() # end time
-
-        content = "*** "+self.name+" time: "+"{:>8.4f}".format(self.et-self.st)+" ***"
+        self.et = time.time()  # end time
+
+        content = (
+            "*** "
+            + self.name
+            + " time: "
+            + "{:>8.4f}".format(self.et - self.st)
+            + " ***"
+        )
         self._print(content)
 
         return
 
+
 def check_path(target_dir: Union[str, Path]) -> bool:
-    """ check path existence, if so skip the following
-        TODO: add output option
-        make this into a context?
+    """check path existence, if so skip the following
+    TODO: add output option
+    make this into a context?
     """
     target_dir = Path(target_dir)
     if not target_dir.exists():
@@ -86,26 +92,31 @@ def check_path(target_dir: Union[str, Path]) -> bool:
 
     return
 
+
 def find_backups(dpath, fname, prefix="bak"):
-    """ find a series of files in a dir
-        such as fname, bak.0.fname, bak.1.fname
+    """find a series of files in a dir
+    such as fname, bak.0.fname, bak.1.fname
     """
     dpath = Path(dpath)
     fpath = dpath / fname
     if not fpath.exists():
         raise FileNotFoundError(f"fpath does not exist.")
 
-    backups = list(dpath.glob(prefix+".[0-9]*."+fname))
+    backups = list(dpath.glob(prefix + ".[0-9]*." + fname))
     backups = sorted(backups, key=lambda x: int(x.name.split(".")[1]))
     backups.append(fpath)
 
     return backups
 
+
 def run_command(directory, command, comment="", timeout=None):
     proc = subprocess.Popen(
-        command, shell=True, cwd=directory, 
-        stdout=subprocess.PIPE, stderr=subprocess.PIPE,
-        encoding = "utf-8"
+        command,
+        shell=True,
+        cwd=directory,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        encoding="utf-8",
     )
     if timeout is None:
         errorcode = proc.wait()
@@ -115,20 +126,21 @@ def run_command(directory, command, comment="", timeout=None):
     msg = "Message: " + "".join(proc.stdout.readlines())
     print(msg)
     if errorcode:
-        raise RuntimeError("Error in %s at %s." %(comment, directory))
-    
+        raise RuntimeError("Error in %s at %s." % (comment, directory))
+
     return msg
 
-def convert_indices(indices: Union[str,List[int]], index_convention="lmp"):
-    """ parse indices for reading xyz by ase, get start for counting
-        constrained indices followed by lammps convention
-        "2:4 3:8"
-        convert [1,2,3,6,7,8] to "1:3 6:8"
-        lammps convention starts from 1 and includes end
-        ---
-        input can be either py or lmp
-        output for indices is in py since it can be used to access atoms
-        output for text is in lmp since it can be used in lammps or sth
+
+def convert_indices(indices: Union[str, List[int]], index_convention="lmp"):
+    """parse indices for reading xyz by ase, get start for counting
+    constrained indices followed by lammps convention
+    "2:4 3:8"
+    convert [1,2,3,6,7,8] to "1:3 6:8"
+    lammps convention starts from 1 and includes end
+    ---
+    input can be either py or lmp
+    output for indices is in py since it can be used to access atoms
+    output for text is in lmp since it can be used in lammps or sth
     """
     ret = []
     if isinstance(indices, str):
@@ -140,9 +152,9 @@ def convert_indices(indices: Union[str,List[int]], index_convention="lmp"):
             else:
                 start, end = cur_range
             if index_convention == "lmp":
-                ret.extend([i-1 for i in list(range(start,end+1))])
+                ret.extend([i - 1 for i in list(range(start, end + 1))])
             elif index_convention == "py":
-                ret.extend(list(range(start,end)))
+                ret.extend(list(range(start, end)))
             else:
                 pass
     elif isinstance(indices, list):
@@ -151,17 +163,17 @@ def convert_indices(indices: Union[str,List[int]], index_convention="lmp"):
         if index_convention == "lmp":
             pass
         elif index_convention == "py":
-            indices = [i+1 for i in indices]
+            indices = [i + 1 for i in indices]
         ret = []
-        #ranges = []
-        for k, g in groupby(enumerate(indices),lambda x:x[0]-x[1]):
-            group = (map(itemgetter(1),g))
-            group = list(map(int,group))
-            #ranges.append((group[0],group[-1]))
+        # ranges = []
+        for k, g in groupby(enumerate(indices), lambda x: x[0] - x[1]):
+            group = map(itemgetter(1), g)
+            group = list(map(int, group))
+            # ranges.append((group[0],group[-1]))
             if group[0] == group[-1]:
                 ret.append(str(group[0]))
             else:
-                ret.append("{}:{}".format(group[0],group[-1]))
+                ret.append("{}:{}".format(group[0], group[-1]))
         ret = " ".join(ret)
     else:
         pass
@@ -171,11 +183,11 @@ def convert_indices(indices: Union[str,List[int]], index_convention="lmp"):
 
 def parse_input_file(
     input_fpath: Union[str, Path],
-    write_json: bool = False # write readin dict to check if alright
+    write_json: bool = False,  # write readin dict to check if alright
 ):
     """"""
     input_dict = None
-    
+
     # - parse input type
     if isinstance(input_fpath, dict):
         input_dict = input_fpath
@@ -203,7 +215,7 @@ def parse_input_file(
         except FileNotFoundError as e:
             # NOTE: There is json or yaml in the string but it is not a file though.
             input_dict = None
-    
+
     # NOTE: recursive read internal json or yaml files
     if input_dict is not None:
         for key, value in input_dict.items():
@@ -212,11 +224,12 @@ def parse_input_file(
                 input_dict[key] = key_dict
 
     if input_dict and write_json:
-        with open(json_path/"params.json", "w") as fopen:
+        with open(json_path / "params.json", "w") as fopen:
             json.dump(input_dict, fopen, indent=4)
         print("See params.json for values of all parameters...")
 
     return input_dict
 
+
 if __name__ == "__main__":
     ...