auxiliary.py

src/vame/util/auxiliary.py

@@ -18,7 +18,8 @@
 Licensed under GNU Lesser General Public License v3.0
 """
 
-import os, yaml
+import os
+import yaml
 from pathlib import Path
 import ruamel.yaml
 from typing import Tuple
@@ -28,8 +29,10 @@ def create_config_template() -> Tuple[dict, ruamel.yaml.YAML]:
     """
     Creates a template for the config.yaml file.
 
-    Returns:
-        Tuple[dict, ruamel.yaml.YAML]: A tuple containing the template dictionary and the Ruamel YAML instance.
+    Returns
+    -------
+    Tuple[dict, ruamel.yaml.YAML]
+        A tuple containing the template dictionary and the Ruamel YAML instance.
     """
     yaml_str = """\
 # Project configurations
@@ -120,21 +123,25 @@ def create_config_template() -> Tuple[dict, ruamel.yaml.YAML]:
     anneal_function:
     kl_start:
     annealtime:
-    """
+"""
     ruamelFile = ruamel.yaml.YAML()
     cfg_file = ruamelFile.load(yaml_str)
-    return(cfg_file,ruamelFile)
+    return (cfg_file, ruamelFile)
 
 
 def read_config(configname: str) -> dict:
     """
     Reads structured config file defining a project.
 
-    Args:
-        configname (str): Path to the config file.
+    Parameters
+    ----------
+    configname : str
+        Path to the config file.
 
-    Returns:
-        dict: The contents of the config file as a dictionary.
+    Returns
+    -------
+    dict
+        The contents of the config file as a dictionary.
     """
     ruamelFile = ruamel.yaml.YAML()
     path = Path(configname)
@@ -157,26 +164,30 @@ def read_config(configname: str) -> dict:
                         write_config(configname, cfg)
                 else:
                     raise
-
     else:
         raise FileNotFoundError(
             "Config file is not found. Please make sure that the file exists and/or that you passed the path of the config file correctly!"
         )
     return cfg
 
 
-def write_config(configname: str, cfg: dict) -> None:
+def write_config(
+    configname: str,
+    cfg: dict,
+) -> None:
     """
     Write structured config file.
 
-    Args:
-        configname (str): Path to the config file.
-        cfg (dict): Dictionary containing the config data.
+    Parameters
+    ----------
+    configname : str
+        Path to the config file.
+    cfg : dict
+        Dictionary containing the config data.
     """
-    with open(configname, 'w') as cf:
+    with open(configname, "w") as cf:
         ruamelFile = ruamel.yaml.YAML()
-        cfg_file,ruamelFile = create_config_template()
+        cfg_file, ruamelFile = create_config_template()
         for key in cfg.keys():
-            cfg_file[key]=cfg[key]
-
+            cfg_file[key] = cfg[key]
         ruamelFile.dump(cfg_file, cf)