feat(cli): add --debug flag for verbose logging in serve mode (#141)

* feat(cli): add --debug flag for verbose logging in serve mode

* feat(cli): add log_level config field with priority over env var

Replace dead `debug` parameter in `main()` with a proper `log_level`
config field in EvoScientistConfig. Enables `EvoSci config set log_level
debug` with priority: config file > EVOSCIENTIST_LOG_LEVEL env var.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

EvoScientist/cli/__init__.py

@@ -26,13 +26,18 @@ from .tui_runtime import (  # noqa: F401
 
 def main():
     """CLI entry point."""
+    import os
     import warnings
 
     warnings.filterwarnings("ignore", message=".*not known to support tools.*")
     warnings.filterwarnings(
         "ignore", message=".*type is unknown and inference may fail.*"
     )
+    from ..config import load_config
     from .commands import _configure_logging
 
-    _configure_logging()
+    # Priority: env var > config file > default (WARNING)
+    config = load_config()
+    _log_level = os.environ.get("EVOSCIENTIST_LOG_LEVEL", "") or config.log_level
+    _configure_logging(debug=_log_level.upper() == "DEBUG")
     app()

EvoScientist/cli/commands.py

@@ -498,6 +498,11 @@ def serve(
         "--ask-user",
         help="Enable agent to ask clarifying questions about your research preferences",
     ),
+    debug: bool = typer.Option(
+        False,
+        "--debug",
+        help="Enable debug logging (shows all log levels including DEBUG)",
+    ),
 ):
     """Run EvoScientist in headless mode -- channels only, no interactive prompt.
 
@@ -514,6 +519,10 @@ def serve(
     config = get_effective_config(cli_overrides)
     apply_config_to_env(config)
 
+    # Enable verbose logging when debug flag is set
+    if debug:
+        _configure_logging(debug=True)
+
     # Auto-start ccproxy if any provider uses OAuth mode
     _ccproxy_proc_serve = None
     if config.anthropic_auth_mode == "oauth" or config.openai_auth_mode == "oauth":
@@ -1166,10 +1175,12 @@ def _main_callback(
         )
 
 
-def _configure_logging():
+def _configure_logging(debug: bool = False):
     """Configure logging with warning symbols for better visibility."""
     from rich.logging import RichHandler
 
+    log_level = logging.DEBUG if debug else logging.WARNING
+
     class DimWarningHandler(RichHandler):
         """Custom handler that renders warnings in dim style."""
 
@@ -1185,9 +1196,9 @@ def _configure_logging():
 
     # Configure root logger to use our handler for WARNING and above
     handler = DimWarningHandler(
-        console=console, show_time=False, show_path=False, show_level=False
+        console=console, show_time=debug, show_path=debug, show_level=debug
     )
-    handler.setLevel(logging.WARNING)
+    handler.setLevel(log_level)
 
     # Apply to root logger (catches all loggers including deepagents)
     root_logger = logging.getLogger()
@@ -1195,7 +1206,7 @@ def _configure_logging():
     for h in root_logger.handlers[:]:
         root_logger.removeHandler(h)
     root_logger.addHandler(handler)
-    root_logger.setLevel(logging.WARNING)
+    root_logger.setLevel(log_level)
 
     # Suppress noisy schema warnings from langchain_google_genai
     # (e.g. "Key '$schema' is not supported in schema, ignoring")

EvoScientist/config/settings.py

@@ -92,6 +92,9 @@ class EvoScientistConfig:
     # UI Settings
     show_thinking: bool = True
     ui_backend: Literal["cli", "tui"] = "tui"
+    log_level: str = (
+        ""  # "DEBUG" | "WARNING" | "" (empty = check env var EVOSCIENTIST_LOG_LEVEL)
+    )
 
     # Channel Settings
     channel_enabled: str = ""  # "imessage" | "telegram" | "discord" | "slack" | "wechat" | "dingtalk" | "feishu" | "email" | "qq" | "signal" | "" (comma-separated for multiple)

tests/test_config.py

@@ -30,6 +30,11 @@ def temp_config_dir(tmp_path, monkeypatch):
     """Use a temporary directory for config during tests."""
     config_dir = tmp_path / "evoscientist"
     monkeypatch.setenv("XDG_CONFIG_HOME", str(tmp_path))
+    # Prevent load_dotenv from loading the project's real .env file
+    monkeypatch.setattr(
+        "EvoScientist.config.settings.find_dotenv",
+        lambda *a, **k: str(tmp_path / ".env"),
+    )
     # Also clear any API keys from environment
     for key in [
         "ANTHROPIC_API_KEY",