pyLoopSage 1.0.20__tar.gz → 1.0.22__tar.gz

{pyloopsage-1.0.20/pyLoopSage.egg-info → pyloopsage-1.0.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.0.20
+Version: 1.0.22
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.20 → pyloopsage-1.0.22}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.20"
+__version__ = "1.0.22"

{pyloopsage-1.0.20 → pyloopsage-1.0.22}/loopsage/run.py

@@ -17,36 +17,48 @@ def my_config_parser(config_parser: configparser.ConfigParser) -> List[tuple[str
             args_cp.append((name, value))
     return args_cp
 
-def get_config() -> ListOfArgs:
-    """This function prepares the list of arguments.
-    At first List of args with defaults is read.
-    Then it's overwritten by args from config file (ini file).
-    In the end config is overwritten by argparse options."""
+def get_config():
+    """Prepare list of arguments.
+    First, defaults are set.
+    Then, optionally config file values.
+    Finally, CLI arguments overwrite everything."""
+    
+    print("Reading config...")
 
-    print(f"Reading config...")
+    # Step 1: Setup argparse
     arg_parser = argparse.ArgumentParser()
-
     arg_parser.add_argument('-c', '--config_file', help="Specify config file (ini format)", metavar="FILE")
+
     for arg in args:
         arg_parser.add_argument(f"--{arg.name.lower()}", help=arg.help)
-    args_ap = arg_parser.parse_args()  # args from argparse
-    config_parser = configparser.ConfigParser()
-    config_parser.read(args_ap.config_file)
-    args_cp = my_config_parser(config_parser)
-    # Override defaults args with values from config file
-    for cp_arg in args_cp:
-        name, value = cp_arg
-        arg = args.get_arg(name)
-        arg.val = value
-    # Now again override args with values from command line.
-    for ap_arg in args_ap.__dict__:
-        if ap_arg not in ['config_file']:
-            name, value = ap_arg, getattr(args_ap, ap_arg)
-            if value is not None:
-                arg = args.get_arg(name)
-                arg.val = value
+    
+    args_ap = arg_parser.parse_args()  # parse command-line arguments
+    args_dict = vars(args_ap)
+
+    # Step 2: If config file provided, parse it
+    if args_ap.config_file:
+        config_parser = configparser.ConfigParser()
+        config_parser.read(args_ap.config_file)
+        args_cp = my_config_parser(config_parser)
+
+        # Override default args with values from config file
+        for cp_arg in args_cp:
+            name, value = cp_arg
+            arg = args.get_arg(name)
+            arg.val = value
+
+    # Step 3: Override again with CLI arguments (if present)
+    for name, value in args_dict.items():
+        if name == "config_file":
+            continue
+        if value is not None:
+            arg = args.get_arg(name.upper())
+            arg.val = value
+
+    # Step 4: Finalize
     args.to_python()
     args.write_config_file()
+    
     return args
 
 def main():

{pyloopsage-1.0.20 → pyloopsage-1.0.22}/loopsage/stochastic_simulation.py

@@ -254,7 +254,7 @@ class StochasticSimulation:
 
         # Save simulation info
         if save:
-            save_dir = os.path.join(self.path, 'other')
+            save_dir = os.path.join(self.path, 'other') + '/'
             with open(save_dir + 'info.txt', "w") as f:
                 f.write(f'Number of beads {self.N_beads}.\n')
                 f.write(f'Number of cohesins {self.N_lef}. Number of cohesins in second family {self.N_lef2}. Number of CTCFs {self.N_CTCF}. \n')

{pyloopsage-1.0.20 → pyloopsage-1.0.22/pyLoopSage.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLoopSage
-Version: 1.0.20
+Version: 1.0.22
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.20 → pyloopsage-1.0.22}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.20',  # Version of the software
+    version='1.0.22',  # Version of the software
     description='An energy-based stochastic model of loop extrusion in chromatin.',
     long_description=long_description,
     long_description_content_type='text/markdown',