add the option to specify the configuration path

Author: alexevag

docs/local_conf.md

@@ -309,4 +309,17 @@ export ETHOPY_DB_PASSWORD="your_secret_password"
 Then in your config file, you can leave the password field empty - EthoPy will use the environment variable instead.
 
 ### Custom Configuration Locations
-By default, EthoPy looks for configuration in `~/.ethopy/local_conf.json`. If you need to use a different location, you can specify it when starting EthoPy (ask your technical support person for help with this).
+By default, EthoPy looks for configuration in `~/.ethopy/local_conf.json`. You can specify a different configuration file using the `--config` option:
+
+```bash
+# Use a custom configuration file
+ethopy --config /path/to/my_config.json
+
+# Or use the short form
+ethopy -c /path/to/my_config.json
+```
+
+This is useful when you want to:
+- Switch between different experimental setups
+- Test with different database configurations
+- Keep separate configurations for different projects

src/ethopy/cli.py

@@ -26,6 +26,12 @@
     type=int,
     help="Task ID from database",
 )
+@click.option(
+    "-c",
+    "--config",
+    type=click.Path(exists=True),
+    help="Path to configuration file (default: ~/.ethopy/local_conf.json)",
+)
 @click.option(
     "--log-console",
     is_flag=True,
@@ -38,11 +44,18 @@
 )
 @click.version_option()
 def main(
-    task_path: Path, task_id: int, log_console: bool, log_level: str = None
+    task_path: Path, task_id: int, config: str, log_console: bool, log_level: str = None
 ) -> None:
     """EthoPy - Behavioral Training Control System."""
-    # Load configuration
-    local_conf = ConfigurationManager()
+    # Load configuration (custom or default)
+    if config:
+        # Create configuration manager with custom config file
+        local_conf = ConfigurationManager(config_file=config)
+        # Update the global configuration with the custom settings
+        local_conf.update_global_config()
+    else:
+        # Use default configuration
+        local_conf = ConfigurationManager()
 
     # Set a configuration value
     if not log_level:

src/ethopy/config.py

@@ -197,3 +197,35 @@ def update(self, updates: Dict[str, Any]) -> None:
         """Update multiple configuration values at once."""
         for key, value in updates.items():
             self.set(key, value)
+
+    def update_global_config(self) -> None:
+        """Update the global EthoPy configuration with this instance's settings.
+
+        This method updates the global configuration state used throughout EthoPy,
+        including DataJoint settings, schema mappings, and plugin manager.
+        Useful for CLI applications that need to override global configuration.
+        """
+        try:
+            import ethopy
+            import datajoint as dj
+            from ethopy.plugin_manager import PluginManager
+
+            # Update the global configuration instance
+            ethopy.local_conf = self
+
+            # Update DataJoint configuration with this instance's settings
+            dj_config = self.get("dj_local_conf", {})
+            dj.config.update(dj_config)
+            dj.logger.setLevel(dj_config.get("datajoint.loglevel", "WARNING"))
+
+            # Update global schema mappings
+            ethopy.SCHEMATA = self.get("SCHEMATA", {})
+
+            # Update plugin manager with new plugin path
+            ethopy.plugin_manager = PluginManager(self.get("plugin_path"))
+
+            self.logging.info(f"Updated configuration from {self.config_file}")
+
+        except Exception as e:
+            self.logging.error(f"Error updating configuration: {e}")
+            raise