FIX: Addresses an issue where badger was resetting some config settings

src/badger/actions/config.py

@@ -31,8 +31,14 @@ def config_settings(args):
 
 def _config_path_var(var_name):
     config_singleton = init_settings()
-    display_name = config_singleton[var_name]['display name']
-    desc = config_singleton[var_name]['description']
+
+    is_path = config_singleton.read_is_path(var_name)    
+
+    if not is_path:
+        raise KeyError
+
+    display_name = config_singleton.read_display_name(var_name)
+    desc = config_singleton.read_description(var_name)
 
     print(f'=== Configure {display_name} ===')
     print(f'*** {desc} ***\n')

src/badger/actions/doctor.py

@@ -3,7 +3,6 @@
 
 
 def self_check(args):
-
     config = init_settings()
     # Reset Badger
     if args.reset:
@@ -37,17 +36,14 @@ def check_n_config_paths():
     issue_list = []
 
     for pname in config._config.dict(by_alias=True):
-        if not config.read_value(pname):
+        if config.read_value(pname) == None:
             good = False
-            # dname = BADGER_PATH_DICT[pname]['display name']
-            # print(f'\n{dname} needs to be configured!')
-
             issue_list.append(pname)
 
     if not good:
         # Initial setup
         init = True
-        while False:
+        while True:
             _res = input(
                 'If this is your first time launching Badger, you should initialize it now.\n'
                 'Proceed ([y]/n)? ')

src/badger/settings.py

@@ -24,6 +24,7 @@ class Setting(BaseModel):
     display_name: str 
     description: str
     value: Optional[Union[str, int, bool, None]] = Field(None, description="The value of the setting which can be of different types.")
+    is_path: bool
 
 class BadgerConfig(BaseModel):
     """
@@ -50,41 +51,49 @@ class BadgerConfig(BaseModel):
         display_name="plugin root",
         description="This setting (BADGER_PLUGIN_ROOT) tells Badger where to look for the plugins",
         value=None,
+        is_path=True
     )
     BADGER_DB_ROOT: Setting = Setting(
         display_name="database root",
         description="This setting (BADGER_DB_ROOT) tells Badger where to store the routine database",
         value=None,
+        is_path=True
     )
     BADGER_LOGBOOK_ROOT: Setting = Setting(
         display_name="logbook root",
         description="This setting (BADGER_LOGBOOK_ROOT) tells Badger where to send the logs (GUI mode)",
         value=None,
+        is_path=True
     )
     BADGER_ARCHIVE_ROOT: Setting = Setting(
         display_name="archive root",
         description="This setting (BADGER_ARCHIVE_ROOT) tells Badger where to archive the historical optimization runs",
         value=None,
+        is_path=True
     )
     BADGER_DATA_DUMP_PERIOD: Setting = Setting(
         display_name="data dump period",
         description="Minimum time interval between data dumps, unit is second",
         value=1,
+        is_path=False
     )
     BADGER_THEME: Setting = Setting(
         display_name="theme",
         description="Theme for the Badger GUI",
         value="dark",
+        is_path=False
     )
     BADGER_ENABLE_ADVANCED: Setting = Setting(
         display_name="enable advanced features",
         description="Enable advanced features on the GUI",
         value=False,
+        is_path=False
     )
     AUTO_REFRESH: Setting = Setting(
         display_name="Auto-refresh",
         description="Permits each run to start from the initial points calculated based on the current values and the rules",
-        value=False
+        value=False,
+        is_path=False
     )
 
 class ConfigSingleton:
@@ -120,19 +129,21 @@ def load_or_create_config(config_path: str) -> BadgerConfig:
 
             # Convert each entry in config_data to an instance of Setting
             for key, value in config_data.items():
-                if isinstance(value, dict) and 'value' in value:                    
+                if isinstance(value, dict) and 'value' in value:
                     # Convert to Setting instance
                     config_data[key] = Setting(
                         display_name=value.get('display_name', key),
                         description=value.get('description', f"Setting for {key.replace('_', ' ').lower()}"),
-                        value=value['value']
+                        value=value['value'],
+                        is_path=value.get('is_path', key)
                     )
                 else:
                     # If it's a direct value, wrap it in a Setting
                     config_data[key] = Setting(
                         display_name=key,
                         description=f"Setting for {key.replace('_', ' ').lower()}",
-                        value=value
+                        value=value,
+                        is_path=False
                     )
 
             try:
@@ -216,6 +227,84 @@ def read_value(self, key: str, return_value_field: bool = True) -> Any:
             return data[key]['value'] if return_value_field else data[key]
         raise KeyError(f"Key '{key}' not found in the configuration.")
 
+    def read_description(self, key: str, return_description_field: bool = True) -> Any:
+        """
+        Searches for the key in all sections of the configuration.
+
+        Parameters
+        ----------
+        key: str
+            The key to search for.
+        return_description_field: bool
+            If True, returns the 'description' field of the setting; otherwise, returns the entire setting.
+
+        Returns
+        -------
+        str
+            The description associated with the provided key.
+
+        Raises
+        ------
+        KeyError
+            If the key is not found in the configuration.
+        """
+        data = self._config.dict(by_alias=True)
+        if key in data:
+            return data[key]['description'] if return_description_field else data[key]
+        raise KeyError(f"Key '{key}' not found in the configuration.") 
+
+    def read_display_name(self, key: str, return_display_name_field: bool = True) -> Any:
+        """
+        Searches for the key in all sections of the configuration.
+
+        Parameters
+        ----------
+        key: str
+            The key to search for.
+        return_display_name_field: bool
+            If True, returns the 'display_name' field of the setting; otherwise, returns the entire setting.
+
+        Returns
+        -------
+        str
+            The display_name associated with the provided key.
+
+        Raises
+        ------
+        KeyError
+            If the key is not found in the configuration.
+        """
+        data = self._config.dict(by_alias=True)
+        if key in data:
+            return data[key]['display_name'] if return_display_name_field else data[key]
+        raise KeyError(f"Key '{key}' not found in the configuration.") 
+
+    def read_is_path(self, key: str, return_is_path_field: bool = True) -> Any:
+        """
+        Searches for the key in all sections of the configuration.
+
+        Parameters
+        ----------
+        key: str
+            The key to search for.
+        return_is_path_field: bool
+            If True, returns the 'is_path' field of the setting; otherwise, returns the entire setting.
+
+        Returns
+        -------
+        bool
+            The is_path associated with the provided key.
+
+        Raises
+        ------
+        KeyError
+            If the key is not found in the configuration.
+        """
+        data = self._config.dict(by_alias=True)
+        if key in data:
+            return data[key]['is_path'] if return_is_path_field else data[key]
+        raise KeyError(f"Key '{key}' not found in the configuration.") 
+
     def write_value(self, key: str, value: Any) -> None:
         """A method for setting a new value to the config.
 

src/badger/tests/test_settings.py

@@ -10,13 +10,13 @@ class TestBadgerConfig:
 
     def setup_method(self, method):
         self.mock_badger_config = BadgerConfig(
-            BADGER_PLUGIN_ROOT=Setting(display_name="plugin root", description="Mock plugin root", value="/mock/plugin/root"),
-            BADGER_DB_ROOT=Setting(display_name="database root", description="Mock database root", value="/mock/db/root"),
-            BADGER_LOGBOOK_ROOT=Setting(display_name="logbook root", description="Mock logbook root", value="/mock/logbook/root"),
-            BADGER_ARCHIVE_ROOT=Setting(display_name="archive root", description="Mock archive root", value="/mock/archive/root"),
-            BADGER_DATA_DUMP_PERIOD=Setting(display_name="data dump period", description="Mock data dump period", value=5),
-            BADGER_THEME=Setting(display_name="theme", description="Mock theme", value="light"),
-            BADGER_ENABLE_ADVANCED=Setting(display_name="enable advanced", description="Mock enable advanced", value=True),
+            BADGER_PLUGIN_ROOT=Setting(display_name="plugin root", description="Mock plugin root", value="/mock/plugin/root", is_path=True),
+            BADGER_DB_ROOT=Setting(display_name="database root", description="Mock database root", value="/mock/db/root", is_path=True),
+            BADGER_LOGBOOK_ROOT=Setting(display_name="logbook root", description="Mock logbook root", value="/mock/logbook/root", is_path=True),
+            BADGER_ARCHIVE_ROOT=Setting(display_name="archive root", description="Mock archive root", value="/mock/archive/root", is_path=True),
+            BADGER_DATA_DUMP_PERIOD=Setting(display_name="data dump period", description="Mock data dump period", value=5, is_path=False),
+            BADGER_THEME=Setting(display_name="theme", description="Mock theme", value="light", is_path=False),
+            BADGER_ENABLE_ADVANCED=Setting(display_name="enable advanced", description="Mock enable advanced", value=True, is_path=False),
         )
 
     def teardown_method(self, method):
@@ -98,6 +98,27 @@ def test_read_value(self):
                 value = config_singleton.read_value('BADGER_PLUGIN_ROOT')
                 assert value == '/mock/plugin/root'
 
+    def test_read_display_name(self):
+        with patch('os.path.exists', return_value=True):
+            with patch("builtins.open", mock_open(read_data=yaml.dump(self.mock_badger_config.dict(by_alias=True)))):
+                config_singleton = ConfigSingleton(self.config_file)
+                display_name = config_singleton.read_display_name('BADGER_PLUGIN_ROOT')
+                assert display_name == 'plugin root'
+
+    def test_read_description(self):
+        with patch('os.path.exists', return_value=True):
+            with patch("builtins.open", mock_open(read_data=yaml.dump(self.mock_badger_config.dict(by_alias=True)))):
+                config_singleton = ConfigSingleton(self.config_file)
+                description = config_singleton.read_description('BADGER_PLUGIN_ROOT')
+                assert description == 'Mock plugin root'
+
+    def test_read_is_path(self):
+        with patch('os.path.exists', return_value=True):
+            with patch("builtins.open", mock_open(read_data=yaml.dump(self.mock_badger_config.dict(by_alias=True)))):
+                config_singleton = ConfigSingleton(self.config_file)
+                is_path = config_singleton.read_is_path('BADGER_PLUGIN_ROOT')
+                assert is_path == True
+
     def test_write_value(self):
         with patch('os.path.exists', return_value=True):
             with patch("builtins.open", mock_open(read_data=yaml.dump(self.mock_badger_config.dict(by_alias=True)))):