update default config overwrite mechanism

cobrawap/__main__.py

@@ -192,10 +192,10 @@ def initialize(output_path=None, config_path=None, **kwargs):
 
     # populate config_path with template config files
     if any(config_path.iterdir()):
-        overwrite = (input(f"The config direcotry {config_path} already exists "\
+        overwrite = (input(f"The config directory {config_path} already exists "\
                             "and is not empty. Create template config files "\
-                            "anyway? [Y/n]").lower() == 'y'
-                     or True)
+                            "anyway? [y/N]").lower() == 'y'
+                     or False)
     else:
         overwrite = True
     if overwrite:
@@ -232,8 +232,10 @@ def create(profile=None, parent_profile=None, data_path=None,
                               profile=config_name,
                               parent=parent_profile)
 
-    setup_entry_stage(profile=profile, parent_profile=parent_profile,
-                  data_path=data_path, loading_script_name=loading_script_name)
+    setup_entry_stage(profile=profile, 
+                      parent_profile=parent_profile,
+                      data_path=data_path, 
+                      loading_script_name=loading_script_name)
     return None
 
 
@@ -303,7 +305,7 @@ def run_stage(profile=None, stage=None, extra_args=None, **kwargs):
 
     # select stage
     while stage not in stages.keys():
-        stage = input("Which stage should be executed?\n"
+        stage = input("Which stage should be executed?\n    "
             +"\n    ".join(f"{k} {v}" for k,v in get_setting('stages').items())
             +"\nSelect the stage index: ")
     stage = stages[stage]

cobrawap/cmd_utils.py

@@ -34,13 +34,24 @@ def create_new_configfile(profile, stage=None, stage_number=None, parent=None):
     config_path = Path(get_setting('config_path'))
 
     parent = f'_{parent}' if parent else ''
-    template_config_path = config_path / stage / 'configs' \
-                                       / f'config{parent}.yaml'
-    new_config_path = config_path / stage / 'configs' \
-                                  / f'config_{profile}.yaml'
+    config_dir = config_path / stage / 'configs'
+    template_config_path = config_dir / f'config{parent}.yaml'
+    new_config_path = config_dir / f'config_{profile}.yaml'
+
     if new_config_path.exists():
         log.debug(f"config file `{new_config_path}` already exists. Skip.")
         return None
+
+    if not template_config_path.exists():
+        log.debug(f"parent config file `{template_config_path}` doesn't exist.")
+        potential_parents = [f.name for f in config_dir.iterdir() \
+                                    if f.name.startswith(f'config{parent}')]
+        if potential_parents:
+            log.debug(f"Using `{potential_parents[0]}` instead.")
+            template_config_path = config_dir / potential_parents[0]
+        else:
+            raise FileNotFoundError("No parent config file fitting the name "
+                                   f"`{parent.strip('_')}` found!")
 
     shutil.copy(template_config_path, new_config_path)
     update_configfile(new_config_path, {'PROFILE':profile})
@@ -113,12 +124,12 @@ def setup_entry_stage(profile, parent_profile=None,
 
     stages = get_setting('stages')
     loading_script_path = config_path / stages['1'] / 'scripts' \
-                                        / f'{loading_script_name}'
+                                      / f'{loading_script_name}'
     if loading_script_path.exists():
         log.info(f"`{loading_script_name}` already exists. Skip.")
     else:
         shutil.copy(config_path / stages['1'] / 'scripts' \
-                                                / 'enter_data_template.py',
+                                              / 'enter_data_template.py',
                     loading_script_path)
 
     # update stage 01 config

pipeline/utils/snakefile.py

@@ -45,10 +45,10 @@ def set_setting(setting: dict) -> None:
     key_overlap = [k for k in setting.keys() if k in settings.keys()]
     if key_overlap:
         overwrite = (input(f"There are already settings for {key_overlap}! "\
-                            "Overwrite? [Y/n]").lower() == 'y'
-                    or True)
+                            "Overwrite? [y/N]").lower() == 'y'
+                    or False)
         if not overwrite:
-            setting.pop[key_overlap, None]
+            _ = [setting.pop(k, None) for k in key_overlap]
 
     settings.update(setting)
     with open(SETTINGS_PATH, 'w') as f: