EvoScientist Ai4Sci

EvoScientist/EvoScientist.py

@@ -641,9 +641,13 @@ def _get_default_middleware(
     *,
     for_async_subagent: bool = False,
     workspace_dir: str | Path | None = None,
+    memory_dir: str | Path | None = None,
     cfg=None,
     chat_model=None,
     memory_source_agent: str = "EvoScientist",
+    tool_selector_threshold: int | None = None,
+    memory_max_inline_profile_chars: int | None = None,
+    enable_background_execution: bool = True,
 ):
     """Build the default middleware list.
 
@@ -684,7 +688,7 @@ def _get_default_middleware(
     if cfg.model_fallbacks:
         load_fallback_chain(cfg.model_fallbacks)
     model = chat_model if chat_model is not None else _ensure_chat_model()
-    memory_dir = str(_paths_mod.MEMORIES_DIR)
+    memory_dir = str(memory_dir or _paths_mod.MEMORIES_DIR)
     source_type = (
         MemorySourceType.SUBAGENT if for_async_subagent else MemorySourceType.TURN
     )
@@ -699,18 +703,20 @@ def _get_default_middleware(
     # ``ModelFallbackMiddleware``: a configurable.model override sets the
     # PRIMARY model only, leaving the fallback chain free to try its own
     # alternatives instead of re-overriding every retry to the same model.
-    memory_middleware = create_memory_middleware(
+    memory_kwargs = {
-        memory_dir,
+        "workspace_dir": workspace_dir,
-        workspace_dir=workspace_dir,
+        "source_type": source_type,
-        source_type=source_type,
+        "source_agent": memory_source_agent,
-        source_agent=memory_source_agent,
+        "enable_profile_memory": memory_controls.profile_enabled,
-        enable_profile_memory=memory_controls.profile_enabled,
+        "enable_observation_memory": memory_controls.observations_enabled,
-        enable_observation_memory=memory_controls.observations_enabled,
+        "enable_observation_tool": memory_controls.observation_tool_enabled(
-        enable_observation_tool=memory_controls.observation_tool_enabled(
             MemoryObservationTarget.AGENT
         ),
-        memory_scheduler=memory_scheduler,
+        "memory_scheduler": memory_scheduler,
-    )
+    }
+    if memory_max_inline_profile_chars is not None:
+        memory_kwargs["max_inline_profile_chars"] = memory_max_inline_profile_chars
+    memory_middleware = create_memory_middleware(memory_dir, **memory_kwargs)
     # Main-agent tool selection may use the auxiliary model; async sub-agents
     # keep the main model (they do real work, not a one-off helper call).
     # context_editing stays on the main model — its model only sizes the
@@ -735,6 +741,11 @@ def _get_default_middleware(
         ContextOverflowMapperMiddleware(),
         ToolErrorHandlerMiddleware(),
         *create_tool_selector_middleware(
+            **(
+                {"threshold": tool_selector_threshold}
+                if tool_selector_threshold is not None
+                else {}
+            ),
             model=tool_selector_model,
             track_stream_selection=not for_async_subagent,
         ),
@@ -770,7 +781,7 @@ def _get_default_middleware(
     # Background-process tools (run_in_background / check_process / stop_process /
     # list_processes) — main agent only. Async sub-agents run on langgraph-dev and
     # must not spawn local OS processes.
-    if not for_async_subagent:
+    if not for_async_subagent and enable_background_execution:
         from .middleware.background import BackgroundExecutionMiddleware
 
         mw.append(BackgroundExecutionMiddleware())
@@ -868,6 +879,12 @@ def create_cli_agent(
     chat_model=None,
     *,
     on_mcp_progress=None,
+    workspace_backend=None,
+    memory_dir: str | Path | None = None,
+    tool_selector_threshold: int | None = None,
+    memory_max_inline_profile_chars: int | None = None,
+    enable_subagents: bool = True,
+    enable_background_execution: bool = True,
 ) -> "CompiledStateGraph":
     """Create agent with checkpointer for CLI multi-turn support.
 
@@ -894,6 +911,16 @@ def create_cli_agent(
         chat_model: Optional pre-built chat model.  Only triggers the pure
             path when ``config`` is also explicit; otherwise it is ignored in
             favor of the ``_ensure_chat_model()`` fallback.
+        workspace_backend: Optional host-provided backend for the workspace
+            route. The default remains ``CustomSandboxBackend``.
+        memory_dir: Optional memory root used by both the backend route and
+            memory middleware.
+        tool_selector_threshold: Optional adaptive tool-selection threshold.
+        memory_max_inline_profile_chars: Optional memory profile injection cap.
+        enable_subagents: Whether configured subagents are available to the agent.
+        enable_background_execution: Whether local background-process tools are
+            installed. Embedding hosts should disable this when process execution
+            is provided by an external backend.
     """
     import os as _os
 
@@ -935,19 +962,21 @@ def create_cli_agent(
         workspace_dir = str(_paths.WORKSPACE_ROOT)
 
     # Read paths dynamically so runtime set_workspace_root() changes are picked up
-    _mem_dir = str(_paths.MEMORIES_DIR)
+    _mem_dir = str(memory_dir or _paths.MEMORIES_DIR)
     _usr_skills_dir = str(_paths.USER_SKILLS_DIR)
     _global_skills_dir = str(_paths.GLOBAL_SKILLS_DIR)
 
     # Always construct fresh backends from current paths (avoids stale
     # module-level backend when workspace root changed at runtime).
     set_active_workspace(workspace_dir)
-    ws_backend = CustomSandboxBackend(
+    ws_backend = workspace_backend
-        root_dir=workspace_dir,
+    if ws_backend is None:
-        virtual_mode=True,
+        ws_backend = CustomSandboxBackend(
-        timeout=cfg.sandbox_execute_timeout,
+            root_dir=workspace_dir,
-        dangerous=cfg.dangerous_mode,
+            virtual_mode=True,
-    )
+            timeout=cfg.sandbox_execute_timeout,
+            dangerous=cfg.dangerous_mode,
+        )
     sk_backend = MergedSkillsBackend(
         primary_dir=_usr_skills_dir,
         global_dir=_global_skills_dir,
@@ -969,7 +998,13 @@ def create_cli_agent(
     # CLI agent never drifts from the default chain. Anything CLI-specific
     # (e.g. ``HumanInTheLoopMiddleware``) is appended below.
     mw: list[AgentMiddleware] = _get_default_middleware(
-        workspace_dir=workspace_dir, cfg=cfg, chat_model=chat_model
+        workspace_dir=workspace_dir,
+        memory_dir=_mem_dir,
+        cfg=cfg,
+        chat_model=chat_model,
+        tool_selector_threshold=tool_selector_threshold,
+        memory_max_inline_profile_chars=memory_max_inline_profile_chars,
+        enable_background_execution=enable_background_execution,
     )
 
     # HITL on main agent only — passing `interrupt_on=` to create_deep_agent
@@ -995,6 +1030,8 @@ def create_cli_agent(
         chat_model=chat_model,
         workspace_dir=workspace_dir,
     )
+    if not enable_subagents:
+        kwargs = {**kwargs, "subagents": []}
 
     return create_deep_agent(
         **kwargs,

EvoScientist/__init__.py

@@ -9,6 +9,8 @@ from __future__ import annotations
 
 from importlib import import_module
 
+__version__ = "0.2.2"
+
 _EXPORTS: dict[str, tuple[str, str]] = {
     # Agent graph (lazy to avoid expensive initialization at import time)
     "EvoScientist_agent": (".EvoScientist", "EvoScientist_agent"),

EvoScientist/config/settings.py

@@ -106,11 +106,23 @@ def _normalize_hhmm(value: Any) -> str | None:
 def get_config_dir() -> Path:
     """Get the configuration directory path.
 
-    Uses XDG_CONFIG_HOME if set, otherwise ~/.config/evoscientist/
+    Priority:
+        1. EVOSCIENTIST_CONFIG_DIR
+        2. EVOSCIENTIST_HOME/config
+        3. XDG_CONFIG_HOME/evoscientist
+        4. ~/.config/evoscientist
     """
+    configured = os.environ.get("EVOSCIENTIST_CONFIG_DIR")
+    if configured:
+        return Path(configured).expanduser().resolve()
+
+    home = os.environ.get("EVOSCIENTIST_HOME")
+    if home:
+        return Path(home).expanduser().resolve() / "config"
+
     xdg_config = os.environ.get("XDG_CONFIG_HOME")
     if xdg_config:
-        return Path(xdg_config) / "evoscientist"
+        return Path(xdg_config).expanduser() / "evoscientist"
     return Path.home() / ".config" / "evoscientist"
 
 

EvoScientist/llm/models.py

@@ -68,6 +68,11 @@ _THINKING_CAPABLE_PROVIDERS: set[str] = {"minimax"}
 _TRUTHY_ENV_VALUES = {"1", "true", "yes", "on"}
 _FALSEY_ENV_VALUES = {"0", "false", "no", "off"}
 
+# Legacy/provider-specific options that are not accepted by the installed
+# LangChain chat model constructors. Leaving them at the top level makes
+# LangChain move them into model_kwargs and can later leak them into SDK calls.
+_UNSUPPORTED_CHAT_MODEL_KWARGS = frozenset({"sanitize_openai_sdk_headers"})
+
 # Model registry: list of (short_name, model_id, provider)
 # Allows same short_name across different providers.
 _MODEL_ENTRIES: list[tuple[str, str, str]] = [
@@ -264,6 +269,15 @@ def _env_flag_disabled(name: str) -> bool:
     return value is not None and value.strip().lower() in _FALSEY_ENV_VALUES
 
 
+def _drop_unsupported_chat_model_kwargs(kwargs: dict[str, Any]) -> None:
+    for key in _UNSUPPORTED_CHAT_MODEL_KWARGS:
+        kwargs.pop(key, None)
+    model_kwargs = kwargs.get("model_kwargs")
+    if isinstance(model_kwargs, dict):
+        for key in _UNSUPPORTED_CHAT_MODEL_KWARGS:
+            model_kwargs.pop(key, None)
+
+
 def _supports_openrouter_anthropic_prompt_cache(provider: str, model_id: str) -> bool:
     """Return whether EvoScientist should declare OpenRouter Claude caching."""
     return provider == "openrouter" and model_id.startswith(
@@ -321,8 +335,16 @@ def _apply_auto_config(
     Mutates *kwargs* in place.  Only sets keys that the caller hasn't already
     provided, so explicit user settings are never overridden.
     """
+    disable_reasoning = bool(kwargs.pop("_disable_reasoning", False))
+    disable_thinking = bool(kwargs.pop("_disable_thinking", False))
+    if disable_reasoning:
+        kwargs.pop("reasoning", None)
+        kwargs.pop("include_thoughts", None)
+    if disable_thinking:
+        kwargs.pop("thinking", None)
+
     # Anthropic: extended thinking
-    if provider == "anthropic" and "thinking" not in kwargs:
+    if provider == "anthropic" and not disable_thinking and "thinking" not in kwargs:
         _supports_thinking = original_provider in _THINKING_CAPABLE_PROVIDERS
         # Detect local proxy (e.g. ccproxy): thinking blocks in conversation
         # history cause 422 errors because the proxy doesn't accept 'thinking'
@@ -341,8 +363,13 @@ def _apply_auto_config(
             kwargs["thinking"] = {"type": "enabled", "budget_tokens": 10000}
 
     # OpenAI (native, not third-party routed): reasoning
-    if provider == "openai" and not is_third_party and "reasoning" not in kwargs:
+    if (
-        if _is_ccproxy_codex():
+        provider == "openai"
+        and not is_third_party
+        and not disable_reasoning
+        and "reasoning" not in kwargs
+    ):
+        if _is_ccproxy_codex(kwargs.get("base_url"), kwargs.get("api_key")):
             # ccproxy uses Chat Completions which doesn't support reasoning.
             pass
         else:
@@ -354,11 +381,11 @@ def _apply_auto_config(
             kwargs["reasoning"] = {"effort": _eff, "summary": "auto"}
 
     # Google GenAI: surface thinking traces
-    if provider == "google-genai":
+    if provider == "google-genai" and not disable_reasoning:
         kwargs.setdefault("include_thoughts", True)
 
     # Ollama: separate reasoning content from response for thinking models
-    if provider == "ollama" and "reasoning" not in kwargs:
+    if provider == "ollama" and not disable_reasoning and "reasoning" not in kwargs:
         kwargs["reasoning"] = True
 
 
@@ -385,7 +412,46 @@ def get_chat_model(
         >>> model = get_chat_model("gpt-4o")  # OpenAI model
         >>> model = get_chat_model("claude-3-opus-20240229", provider="anthropic")  # Full ID
     """
-    model = model or DEFAULT_MODEL
+    skip_runtime_resolver = bool(kwargs.pop("_skip_runtime_model_resolver", False))
+    runtime_provider_name: str | None = None
+    runtime_supports_reasoning: bool | None = None
+    runtime_resolved = None
+    if not skip_runtime_resolver:
+        from EvoScientist.runtime_integrations import resolve_runtime_model
+
+        runtime_resolved = resolve_runtime_model(model, provider)
+
+    if runtime_resolved is not None:
+        resolved_params = dict(getattr(runtime_resolved, "params", {}) or {})
+        extra_body = resolved_params.pop("_extra_body", None)
+        default_headers = resolved_params.pop("_default_headers", None)
+        if extra_body:
+            resolved_params["extra_body"] = extra_body
+        if default_headers:
+            resolved_params["default_headers"] = default_headers
+        resolved_params.update(kwargs)
+        kwargs = resolved_params
+
+        resolved_api_key = str(getattr(runtime_resolved, "api_key", "") or "")
+        resolved_base_url = str(getattr(runtime_resolved, "base_url", "") or "")
+        if resolved_api_key:
+            kwargs.setdefault("api_key", resolved_api_key)
+        if resolved_base_url:
+            kwargs.setdefault("base_url", resolved_base_url.rstrip("/"))
+
+        runtime_provider_name = str(
+            getattr(runtime_resolved, "provider_name", "") or ""
+        )
+        runtime_supports_reasoning = bool(
+            getattr(runtime_resolved, "supports_reasoning", False)
+        )
+        if not runtime_supports_reasoning:
+            kwargs.setdefault("_disable_reasoning", True)
+            kwargs.setdefault("_disable_thinking", True)
+        model = str(runtime_resolved.model_id)
+        provider = str(runtime_resolved.protocol)
+    else:
+        model = model or DEFAULT_MODEL
 
     # Look up short name in registry (provider-aware)
     model_id = None
@@ -420,22 +486,35 @@ def get_chat_model(
     _is_third_party = (
         provider in _OPENAI_ROUTED_PROVIDERS or provider in _ANTHROPIC_ROUTED_PROVIDERS
     )
+    if runtime_provider_name and runtime_provider_name != provider:
+        _is_third_party = True
+    if (
+        runtime_resolved is not None
+        and provider == "openai"
+        and resolved_base_url
+        and "api.openai.com" not in resolved_base_url.lower()
+    ):
+        _is_third_party = True
     _is_openai_proxy = False
-    _original_provider: str | None = None
+    _original_provider: str | None = (
+        runtime_provider_name if runtime_provider_name != provider else None
+    )
     if provider == "anthropic":
         base_url = os.environ.get("ANTHROPIC_BASE_URL", "")
         if base_url:
-            kwargs["base_url"] = base_url
+            kwargs.setdefault("base_url", base_url)
         api_key = os.environ.get("ANTHROPIC_API_KEY", "")
         if api_key:
-            kwargs["api_key"] = api_key
+            kwargs.setdefault("api_key", api_key)
 
     # Native OpenAI base_url override (e.g. ccproxy Codex at localhost:8000/codex/v1)
     elif provider == "openai":
         base_url = os.environ.get("OPENAI_BASE_URL", "")
         if base_url:
-            kwargs["base_url"] = base_url
+            kwargs.setdefault("base_url", base_url)
-            _is_openai_proxy = _is_ccproxy_codex()
+            _is_openai_proxy = _is_ccproxy_codex(
+                kwargs.get("base_url"), kwargs.get("api_key")
+            )
             if _is_openai_proxy:
                 # Use Responses API for ccproxy: bypasses the format chain
                 # converter (Chat→Responses→Chat) which returns 502 on
@@ -450,7 +529,7 @@ def get_chat_model(
                 kwargs.pop("streaming", None)  # remove if set elsewhere
         api_key = os.environ.get("OPENAI_API_KEY", "")
         if api_key:
-            kwargs["api_key"] = api_key
+            kwargs.setdefault("api_key", api_key)
 
     # OpenAI-routed providers → route through OpenAI provider with base_url
     elif provider in _OPENAI_ROUTED_PROVIDERS:
@@ -468,10 +547,10 @@ def get_chat_model(
         else:
             base_url = base_url_default
         if base_url:
-            kwargs["base_url"] = base_url
+            kwargs.setdefault("base_url", base_url)
         api_key = os.environ.get(api_key_env, "")
         if api_key:
-            kwargs["api_key"] = api_key
+            kwargs.setdefault("api_key", api_key)
         # SiliconFlow: disable thinking — LangChain drops reasoning_content
         # from history, causing error 20015 on multi-turn requests.
         if provider == "siliconflow":
@@ -488,7 +567,7 @@ def get_chat_model(
         _is_third_party = True
         api_key = os.environ.get("OPENROUTER_API_KEY", "")
         if api_key:
-            kwargs["api_key"] = api_key
+            kwargs.setdefault("api_key", api_key)
         # Reasoning via `effort` + `summary: "auto"` so a readable reasoning
         # summary is returned for display. OpenAI-Responses also emits encrypted
         # reasoning items (`rs_*` id) that can't be replayed on multi-turn
@@ -517,10 +596,10 @@ def get_chat_model(
         else:
             base_url = base_url_default
         if base_url:
-            kwargs["base_url"] = base_url
+            kwargs.setdefault("base_url", base_url)
         api_key = os.environ.get(api_key_env, "")
         if api_key:
-            kwargs["api_key"] = api_key
+            kwargs.setdefault("api_key", api_key)
         # Kimi Coding Plan requires claude-code User-Agent header
         if provider == "kimi-coding":
             kwargs.setdefault("default_headers", {})["User-Agent"] = "claude-code/0.1.0"
@@ -529,8 +608,9 @@ def get_chat_model(
     elif provider == "ollama":
         base_url = os.environ.get("OLLAMA_BASE_URL", "")
         if base_url:
-            kwargs["base_url"] = base_url
+            kwargs.setdefault("base_url", base_url)
 
+    _drop_unsupported_chat_model_kwargs(kwargs)
     _apply_auto_config(provider, model_id, _is_third_party, kwargs, _original_provider)
     _apply_openrouter_anthropic_prompt_cache(provider, model_id, kwargs)
 
@@ -547,7 +627,14 @@ def get_chat_model(
         elif _responses_api_setting == "true":
             kwargs["use_responses_api"] = True
 
-    chat_model = init_chat_model(model=model_id, model_provider=provider, **kwargs)
+    anthropic_auth_token = None
+    if provider == "anthropic" and kwargs.get("api_key"):
+        anthropic_auth_token = os.environ.pop("ANTHROPIC_AUTH_TOKEN", None)
+    try:
+        chat_model = init_chat_model(model=model_id, model_provider=provider, **kwargs)
+    finally:
+        if anthropic_auth_token is not None:
+            os.environ["ANTHROPIC_AUTH_TOKEN"] = anthropic_auth_token
 
     # Flatten list content to strings for strict OpenAI-compatible providers
     # (DeepSeek, SiliconFlow, OpenRouter, custom-openai, etc.) and

EvoScientist/llm/patches.py

@@ -25,6 +25,7 @@ Utilities:
 
 from __future__ import annotations
 
+import hashlib
 import os
 from typing import Any
 
@@ -178,15 +179,20 @@ _patch_ccproxy_codex_compat()
 # ---------------------------------------------------------------------------
 # Utility: detect ccproxy's Codex adapter (as opposed to generic localhost).
 # ---------------------------------------------------------------------------
-def _is_ccproxy_codex() -> bool:
+def _is_ccproxy_codex(
+    base_url: str | None = None,
+    api_key: str | None = None,
+) -> bool:
     """Return True if the OpenAI endpoint is ccproxy's Codex adapter.
 
     Checks for the ccproxy-specific markers set by ``setup_codex_env()``
     in ``ccproxy_manager.py``: the sentinel API key and the ``/codex/v1``
     path.  Plain localhost endpoints (vLLM, Ollama, etc.) are not affected.
     """
-    base_url = os.environ.get("OPENAI_BASE_URL", "")
+    if base_url is None:
-    api_key = os.environ.get("OPENAI_API_KEY", "")
+        base_url = os.environ.get("OPENAI_BASE_URL", "")
+    if api_key is None:
+        api_key = os.environ.get("OPENAI_API_KEY", "")
     return (
         ("127.0.0.1" in base_url or "localhost" in base_url)
         and api_key == "ccproxy-oauth"
@@ -267,6 +273,82 @@ def _flatten_message_content(content: Any) -> str | list[Any] | Any:
     return "\n\n".join(parts) if parts else ""
 
 
+def _stable_tool_call_id(message: Any, message_index: int, call_index: int) -> str:
+    seed = ":".join(
+        (
+            str(getattr(message, "id", "") or "message"),
+            str(message_index),
+            str(call_index),
+        )
+    )
+    return "call_" + hashlib.sha256(seed.encode("utf-8")).hexdigest()[:24]
+
+
+def _ensure_openai_tool_call_ids(messages: list[Any]) -> list[Any]:
+    """Copy messages and repair missing AI/ToolMessage call identifiers."""
+    import copy
+    from collections import deque
+
+    pending_call_ids: deque[str] = deque()
+    normalized: list[Any] = []
+
+    for message_index, message in enumerate(messages):
+        message_type = getattr(message, "type", None)
+        if message_type == "ai":
+            tool_calls = list(getattr(message, "tool_calls", None) or [])
+            if not tool_calls:
+                normalized.append(message)
+                continue
+
+            copied = copy.copy(message)
+            normalized_calls: list[dict[str, Any]] = []
+            for call_index, original_call in enumerate(tool_calls):
+                call = dict(original_call)
+                call_id = str(call.get("id") or "") or _stable_tool_call_id(
+                    message, message_index, call_index
+                )
+                call["id"] = call_id
+                normalized_calls.append(call)
+                pending_call_ids.append(call_id)
+            copied.tool_calls = normalized_calls
+
+            if isinstance(copied.content, list):
+                call_index = 0
+                blocks: list[Any] = []
+                for original_block in copied.content:
+                    if not isinstance(original_block, dict):
+                        blocks.append(original_block)
+                        continue
+                    block = dict(original_block)
+                    if block.get("type") in {"tool_call", "function_call"}:
+                        if call_index < len(normalized_calls):
+                            block["id"] = normalized_calls[call_index]["id"]
+                        call_index += 1
+                    blocks.append(block)
+                copied.content = blocks
+            normalized.append(copied)
+            continue
+
+        if message_type == "tool":
+            tool_call_id = str(getattr(message, "tool_call_id", "") or "")
+            if tool_call_id:
+                try:
+                    pending_call_ids.remove(tool_call_id)
+                except ValueError:
+                    pass
+                normalized.append(message)
+                continue
+            if pending_call_ids:
+                copied = copy.copy(message)
+                copied.tool_call_id = pending_call_ids.popleft()
+                normalized.append(copied)
+                continue
+
+        normalized.append(message)
+
+    return normalized
+
+
 def _sanitize_messages(messages: list[Any], hoist_tool_media: bool = True) -> list[Any]:
     """Flatten list content for OpenAI-compatible APIs, preserving media.
 
@@ -282,6 +364,7 @@ def _sanitize_messages(messages: list[Any], hoist_tool_media: bool = True) -> li
 
     from langchain_core.messages import HumanMessage
 
+    messages = _ensure_openai_tool_call_ids(messages)
     out: list[Any] = []
     pending_media: list[Any] = []  # media hoisted out of a run of tool messages
 

EvoScientist/logging_config.py

@@ -0,0 +1,302 @@
+"""Shared logging configuration helpers."""
+
+from __future__ import annotations
+
+import logging
+import os
+import sys
+from datetime import UTC, datetime
+from pathlib import Path
+from typing import Any, TextIO
+
+DEFAULT_LOG_RETENTION_DAYS = 30
+DEFAULT_LOG_FORMAT = "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
+DEFAULT_LOG_DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
+MANAGED_HANDLER_ATTR = "_evoscientist_managed_handler"
+
+
+def resolve_log_level(level: int | str | None, default: int = logging.INFO) -> int:
+    """Resolve a logging level from config or environment input."""
+    if isinstance(level, int):
+        return level
+    raw = str(level or "").strip()
+    if not raw:
+        return default
+    if raw.isdigit():
+        return int(raw)
+    normalized = raw.upper()
+    if normalized == "WARN":
+        normalized = "WARNING"
+    resolved = logging.getLevelNamesMapping().get(normalized)
+    return resolved if isinstance(resolved, int) else default
+
+
+def _mark_managed(handler: logging.Handler, kind: str) -> logging.Handler:
+    setattr(handler, MANAGED_HANDLER_ATTR, kind)
+    return handler
+
+
+def _managed_kind(handler: logging.Handler) -> str | None:
+    kind = getattr(handler, MANAGED_HANDLER_ATTR, None)
+    return kind if isinstance(kind, str) else None
+
+
+def remove_managed_handlers(
+    logger: logging.Logger | None = None,
+    *,
+    kinds: set[str] | None = None,
+) -> None:
+    """Remove handlers installed by this module without touching external ones."""
+    target = logger or logging.getLogger()
+    for handler in target.handlers[:]:
+        kind = _managed_kind(handler)
+        if kind and (kinds is None or kind in kinds):
+            target.removeHandler(handler)
+            handler.close()
+
+
+def _standard_formatter() -> logging.Formatter:
+    return logging.Formatter(DEFAULT_LOG_FORMAT, datefmt=DEFAULT_LOG_DATE_FORMAT)
+
+
+class DailyLogFileHandler(logging.FileHandler):
+    """File handler that writes the active log to a date-based filename."""
+
+    def __init__(
+        self,
+        log_dir: str | Path,
+        *,
+        prefix: str = "evoscientist",
+        retention_days: int = DEFAULT_LOG_RETENTION_DAYS,
+        encoding: str = "utf-8",
+        utc: bool = False,
+    ) -> None:
+        self.log_dir = Path(log_dir).expanduser()
+        self.prefix = prefix
+        self.retention_days = max(1, retention_days)
+        self.utc = utc
+        self.log_dir.mkdir(parents=True, exist_ok=True)
+        super().__init__(self._dated_log_path(), encoding=encoding, delay=True)
+
+    @property
+    def active_log_path(self) -> Path:
+        """Return the active log path for the current date."""
+        return self._dated_log_path()
+
+    def _dated_log_path(self) -> Path:
+        now = datetime.now(UTC if self.utc else None)
+        return self.log_dir / f"{self.prefix}-{now:%Y-%m-%d}.log"
+
+    def emit(self, record: logging.LogRecord) -> None:
+        try:
+            expected = str(self.active_log_path)
+            if self.baseFilename != expected:
+                if self.stream:
+                    self.stream.close()
+                    self.stream = None
+                self.baseFilename = expected
+            self._delete_expired_logs()
+            super().emit(record)
+        except OSError:
+            self.handleError(record)
+
+    def getFilesToDelete(self) -> list[str]:
+        candidates = sorted(self.log_dir.glob(f"{self.prefix}-????-??-??.log"))
+        if len(candidates) <= self.retention_days:
+            return []
+        return [str(path) for path in candidates[: -self.retention_days]]
+
+    def _delete_expired_logs(self) -> None:
+        for path in self.getFilesToDelete():
+            try:
+                os.remove(path)
+            except OSError:
+                pass
+
+
+def default_log_dir() -> Path:
+    """Return the default runtime log directory."""
+    env_dir = os.environ.get("EVOSCIENTIST_LOG_DIR")
+    if env_dir:
+        return Path(env_dir).expanduser()
+
+    from EvoScientist.paths import DATA_DIR
+
+    return DATA_DIR / "logs"
+
+
+def configure_daily_file_logging(
+    logger: logging.Logger | None = None,
+    *,
+    log_dir: str | Path | None = None,
+    prefix: str = "evoscientist",
+    level: int | str = logging.INFO,
+    retention_days: int = DEFAULT_LOG_RETENTION_DAYS,
+) -> DailyLogFileHandler:
+    """Attach a daily file handler, replacing older matching handlers."""
+    target = logger or logging.getLogger()
+    resolved_level = resolve_log_level(level, default=logging.INFO)
+    retention_days = max(1, int(retention_days))
+    resolved_dir = Path(log_dir).expanduser() if log_dir else default_log_dir()
+
+    for handler in target.handlers[:]:
+        if (
+            isinstance(handler, DailyLogFileHandler)
+            and handler.prefix == prefix
+            and handler.log_dir == resolved_dir
+        ):
+            target.removeHandler(handler)
+            handler.close()
+
+    handler = DailyLogFileHandler(
+        resolved_dir,
+        prefix=prefix,
+        retention_days=retention_days,
+    )
+    _mark_managed(handler, "file")
+    handler.setLevel(resolved_level)
+    handler.setFormatter(_standard_formatter())
+    target.addHandler(handler)
+    if target.level == logging.NOTSET or target.level > resolved_level:
+        target.setLevel(resolved_level)
+    return handler
+
+
+def configure_console_logging(
+    logger: logging.Logger | None = None,
+    *,
+    level: int | str | None = logging.INFO,
+    stream: TextIO | None = None,
+    replace: bool = True,
+) -> logging.StreamHandler:
+    """Attach a standard console handler for non-interactive entry points."""
+    target = logger or logging.getLogger()
+    resolved_level = resolve_log_level(level, default=logging.INFO)
+    if replace:
+        remove_managed_handlers(target, kinds={"console", "rich"})
+
+    handler = logging.StreamHandler(stream or sys.stderr)
+    _mark_managed(handler, "console")
+    handler.setLevel(resolved_level)
+    handler.setFormatter(_standard_formatter())
+    target.addHandler(handler)
+    target.setLevel(resolved_level)
+    return handler
+
+
+def configure_rich_console_logging(
+    logger: logging.Logger | None = None,
+    *,
+    level: int | str | None = logging.INFO,
+    console: Any = None,
+    replace: bool = True,
+    dim_warnings: bool = False,
+    show_time: bool | None = None,
+    show_path: bool | None = None,
+    show_level: bool | None = None,
+) -> logging.Handler:
+    """Attach a Rich console handler for interactive CLI output."""
+    from rich.logging import RichHandler
+    from rich.markup import escape
+
+    target = logger or logging.getLogger()
+    resolved_level = resolve_log_level(level, default=logging.INFO)
+    verbose = resolved_level <= logging.DEBUG
+    if replace:
+        remove_managed_handlers(target, kinds={"console", "rich"})
+
+    class DimWarningHandler(RichHandler):
+        def emit(self, record: logging.LogRecord) -> None:
+            if dim_warnings and record.levelno == logging.WARNING and console is not None:
+                console.print(
+                    "[dim yellow]\u26a0\ufe0f  Warning:[/dim yellow] "
+                    f"[dim]{escape(record.getMessage())}[/dim]"
+                )
+                return
+            super().emit(record)
+
+    handler = DimWarningHandler(
+        console=console,
+        show_time=verbose if show_time is None else show_time,
+        show_path=verbose if show_path is None else show_path,
+        show_level=verbose if show_level is None else show_level,
+    )
+    _mark_managed(handler, "rich")
+    handler.setLevel(resolved_level)
+    target.addHandler(handler)
+    target.setLevel(resolved_level)
+    return handler
+
+
+def configure_logging(
+    logger: logging.Logger | None = None,
+    *,
+    level: int | str | None = logging.INFO,
+    log_dir: str | Path | None = None,
+    retention_days: int = DEFAULT_LOG_RETENTION_DAYS,
+    prefix: str = "evoscientist",
+    console: bool = True,
+    file: bool = True,
+    replace_managed: bool = True,
+) -> list[logging.Handler]:
+    """Configure standard EvoScientist console and daily file logging."""
+    target = logger or logging.getLogger()
+    resolved_level = resolve_log_level(level, default=logging.INFO)
+    if replace_managed:
+        remove_managed_handlers(target, kinds={"console", "rich", "file"})
+
+    handlers: list[logging.Handler] = []
+    if console:
+        handlers.append(
+            configure_console_logging(target, level=resolved_level, replace=False)
+        )
+    if file:
+        handlers.append(
+            configure_daily_file_logging(
+                target,
+                log_dir=log_dir,
+                prefix=prefix,
+                level=resolved_level,
+                retention_days=retention_days,
+            )
+        )
+    target.setLevel(resolved_level)
+    return handlers
+
+
+def configure_logging_from_settings(
+    logger: logging.Logger | None = None,
+    *,
+    default_level: int = logging.INFO,
+    prefix: str = "evoscientist",
+    console: bool = True,
+    file: bool = True,
+) -> list[logging.Handler]:
+    """Configure logging from EvoScientist settings and environment overrides."""
+    level: int | str | None = os.environ.get("EVOSCIENTIST_LOG_LEVEL")
+    log_dir: str | Path | None = os.environ.get("EVOSCIENTIST_LOG_DIR") or None
+    retention_days = int(
+        os.environ.get("EVOSCIENTIST_LOG_RETENTION_DAYS", DEFAULT_LOG_RETENTION_DAYS)
+    )
+
+    try:
+        from EvoScientist.config import get_effective_config
+
+        cfg = get_effective_config()
+        level = level or getattr(cfg, "log_level", None)
+        log_dir = log_dir or getattr(cfg, "log_dir", None) or None
+        retention_days = int(
+            getattr(cfg, "log_retention_days", DEFAULT_LOG_RETENTION_DAYS)
+        )
+    except Exception:
+        level = level or default_level
+
+    return configure_logging(
+        logger,
+        level=resolve_log_level(level, default=default_level),
+        log_dir=log_dir,
+        retention_days=retention_days,
+        prefix=prefix,
+        console=console,
+        file=file,
+    )

EvoScientist/mcp/__init__.py

@@ -10,6 +10,7 @@ from .client import (
     build_mcp_add_kwargs,
     build_mcp_edit_fields,
     edit_mcp_server,
+    get_mcp_server_errors,
     load_mcp_config,
     load_mcp_tools,
     parse_mcp_add_args,
@@ -38,6 +39,7 @@ __all__ = [
     "find_server_by_name",
     "get_all_tags",
     "get_installed_names",
+    "get_mcp_server_errors",
     "install_mcp_server",
     "install_mcp_servers",
     "load_mcp_config",

EvoScientist/mcp/client.py

@@ -114,6 +114,10 @@ _URL_TRANSPORTS = {"http", "streamable_http", "sse", "websocket"}
 # still parallelizing the common 3–7 server case to completion.
 _MAX_CONCURRENT_CONNECTIONS = 8
 
+# Last connection error per configured server. This is process-local runtime
+# diagnostics for the Web/CLI status surfaces, not persisted configuration.
+_MCP_SERVER_ERRORS: dict[str, str] = {}
+
 # Env vars forwarded to stdio MCP subprocesses on top of the MCP SDK's
 # minimal default set (HOME/PATH/USER/…). Without this, servers behind
 # a proxy or with a custom CA bundle silently fail with long timeouts.
@@ -764,6 +768,9 @@ async def _load_tools(
     if not connections:
         return {}
 
+    for stale_name in set(_MCP_SERVER_ERRORS) - set(connections):
+        _MCP_SERVER_ERRORS.pop(stale_name, None)
+
     client = MultiServerMCPClient(connections)  # type: ignore[invalid-argument-type]
 
     def _report(event: str, name: str, detail: str = "") -> None:
@@ -787,10 +794,13 @@ async def _load_tools(
             _report("start", name)
             try:
                 tools = await client.get_tools(server_name=name)
+                _MCP_SERVER_ERRORS.pop(name, None)
                 logger.info("MCP server %r: loaded %d tool(s)", name, len(tools))
                 _report("success", name, str(len(tools)))
                 return name, tools
             except Exception as exc:
+                detail = str(exc) or type(exc).__name__
+                _MCP_SERVER_ERRORS[name] = detail
                 # When the caller wired up ``on_progress`` they own the
                 # user-facing display; downgrade the logger so we don't
                 # double-print.
@@ -798,7 +808,7 @@ async def _load_tools(
                     logger.warning("MCP server %r: failed to load tools: %s", name, exc)
                 else:
                     logger.debug("MCP server %r: failed to load tools: %s", name, exc)
-                _report("error", name, str(exc))
+                _report("error", name, detail)
                 return name, []
 
     # ``return_exceptions=False`` is fine because ``_fetch`` already
@@ -807,6 +817,11 @@ async def _load_tools(
     return dict(results)
 
 
+def get_mcp_server_errors() -> dict[str, str]:
+    """Return a snapshot of the most recent per-server connection errors."""
+    return dict(_MCP_SERVER_ERRORS)
+
+
 async def aload_mcp_tools(
     config: dict[str, Any] | None = None,
     *,

EvoScientist/paths.py

@@ -5,6 +5,7 @@ from __future__ import annotations
 import logging
 import os
 import shutil
+from collections.abc import Iterator
 from datetime import datetime
 from pathlib import Path
 
@@ -215,3 +216,65 @@ def resolve_virtual_path(virtual_path: str) -> Path:
     """Resolve a virtual workspace path (e.g. /image.png) to a real filesystem path."""
     vpath = virtual_path if virtual_path.startswith("/") else "/" + virtual_path
     return (_active_workspace / vpath.lstrip("/")).resolve()
+
+
+def evoscientist_root() -> Path:
+    """Return the application root used by Gateway-managed runtime data."""
+    env_root = os.environ.get("EVOSCIENTIST_HOME")
+    if env_root:
+        return Path(env_root).expanduser().resolve()
+    return DATA_DIR.expanduser().resolve()
+
+
+_EVOSCIENTIST_DATA_ROOT: Path | None = None
+
+
+def _data_root() -> Path:
+    """Return the root directory for isolated Web user workspaces."""
+    global _EVOSCIENTIST_DATA_ROOT
+    if _EVOSCIENTIST_DATA_ROOT is not None:
+        return _EVOSCIENTIST_DATA_ROOT
+
+    env_root = os.environ.get("EVOSCIENTIST_DATA_ROOT")
+    if env_root:
+        root = Path(env_root).expanduser().resolve()
+    else:
+        root = evoscientist_root() / "data"
+    _EVOSCIENTIST_DATA_ROOT = root
+    return root
+
+
+def user_data_dir(user_id: str) -> Path:
+    """Return and create the isolated data directory for a Web user."""
+    path = _data_root() / user_id
+    path.mkdir(parents=True, exist_ok=True)
+    return path
+
+
+def iter_user_data_dirs() -> Iterator[Path]:
+    """Yield existing Web user directories without creating the data root."""
+    root = _data_root()
+    if not root.exists():
+        return
+    for path in root.iterdir():
+        if path.is_dir():
+            yield path
+
+
+def thread_data_dir(user_id: str, thread_id: str) -> Path:
+    """Return and create a user's isolated thread workspace."""
+    path = user_data_dir(user_id) / thread_id
+    path.mkdir(parents=True, exist_ok=True)
+    return path
+
+
+def global_data_dir(user_id: str) -> Path:
+    """Return and create a user's directory shared across all threads."""
+    path = user_data_dir(user_id) / "__global__"
+    path.mkdir(parents=True, exist_ok=True)
+    return path
+
+
+def uploads_dir() -> Path:
+    """Return the Gateway upload staging directory."""
+    return evoscientist_root() / "uploads"

EvoScientist/runtime_integrations.py

@@ -0,0 +1,116 @@
+"""Optional runtime services supplied by an application embedding EvoScientist.
+
+The CLI package must not import a concrete web gateway. Applications such as
+Ai4Sci-Web can register their database, storage, metering, and media services
+at process startup through this module.
+"""
+
+from __future__ import annotations
+
+from collections.abc import Awaitable, Callable
+from dataclasses import dataclass, replace
+from datetime import date
+from pathlib import Path
+from typing import Any
+
+AsyncProvider = Callable[[], Awaitable[Any]]
+AsyncFileHandler = Callable[[Path], Awaitable[Any]]
+AsyncUsageRecorder = Callable[[str, str], Awaitable[Any]]
+ModelResolver = Callable[[str | None, str | None], Any | None]
+
+
+class RuntimeIntegrationUnavailable(RuntimeError):
+    """Raised when an optional host-provided service is not configured."""
+
+
+@dataclass(frozen=True)
+class RuntimeIntegrations:
+    app_connection_provider: AsyncProvider | None = None
+    session_connection_provider: AsyncProvider | None = None
+    session_dsn_provider: Callable[[], str | None] | None = None
+    current_date_provider: Callable[[], date] | None = None
+    user_storage_root_provider: Callable[[str], Path] | None = None
+    knowledge_file_handler: AsyncFileHandler | None = None
+    usage_recorder: AsyncUsageRecorder | None = None
+    image_backend_factory: Callable[[], Any] | None = None
+    model_resolver: ModelResolver | None = None
+
+
+_integrations = RuntimeIntegrations()
+
+
+def configure_runtime_integrations(**services: Any) -> RuntimeIntegrations:
+    """Register host-provided services and return the resulting configuration."""
+    global _integrations
+    _integrations = replace(_integrations, **services)
+    return _integrations
+
+
+def reset_runtime_integrations() -> None:
+    """Clear all host-provided services, primarily for tests."""
+    global _integrations
+    _integrations = RuntimeIntegrations()
+
+
+def has_session_connection_provider() -> bool:
+    return _integrations.session_connection_provider is not None
+
+
+def get_session_dsn() -> str | None:
+    provider = _integrations.session_dsn_provider
+    return provider() if provider is not None else None
+
+
+async def get_session_connection() -> Any:
+    provider = _integrations.session_connection_provider
+    if provider is None:
+        raise RuntimeIntegrationUnavailable(
+            "No session connection provider is configured"
+        )
+    return await provider()
+
+
+async def get_app_connection() -> Any:
+    provider = _integrations.app_connection_provider
+    if provider is None:
+        raise RuntimeIntegrationUnavailable(
+            "No application connection provider is configured"
+        )
+    return await provider()
+
+
+def current_date() -> date:
+    provider = _integrations.current_date_provider
+    return provider() if provider is not None else date.today()
+
+
+def resolve_user_storage_root(user_id: str) -> Path | None:
+    provider = _integrations.user_storage_root_provider
+    return provider(user_id) if provider is not None else None
+
+
+def resolve_runtime_model(model: str | None, provider: str | None = None) -> Any | None:
+    """Resolve a host-managed model configuration when one is registered."""
+    resolver = _integrations.model_resolver
+    return resolver(model, provider) if resolver is not None else None
+
+
+async def handle_knowledge_file(path: Path) -> None:
+    handler = _integrations.knowledge_file_handler
+    if handler is not None:
+        await handler(path)
+
+
+async def record_service_usage(service: str, action: str) -> None:
+    recorder = _integrations.usage_recorder
+    if recorder is not None:
+        await recorder(service, action)
+
+
+def get_image_backend() -> Any:
+    factory = _integrations.image_backend_factory
+    if factory is None:
+        raise RuntimeIntegrationUnavailable(
+            "Image generation is unavailable in this runtime. Configure an image backend first."
+        )
+    return factory()

EvoScientist/stream/events.py

@@ -8,10 +8,12 @@ import base64
 import inspect
 import mimetypes
 import os
+import warnings
 from collections.abc import AsyncGenerator, AsyncIterator, Mapping
 from dataclasses import dataclass
 from typing import Any, TypeAlias
 
+from langchain_core._api import LangChainBetaWarning
 from langchain_core.messages import AIMessage, AIMessageChunk, BaseMessage, ToolMessage
 from langgraph.graph import END
 from langgraph.types import Command, Interrupt
@@ -43,6 +45,12 @@ GraphRunInput: TypeAlias = str | Command
 LangGraphStreamInput: TypeAlias = dict[str, list[dict[str, object]]] | Command
 _ValueMessageKey: TypeAlias = tuple[str, ...]
 
+warnings.filterwarnings(
+    "ignore",
+    message=r"The v3 streaming protocol on Pregel is experimental\.",
+    category=LangChainBetaWarning,
+)
+
 
 @dataclass(frozen=True, slots=True)
 class _AssistantValueMessage:

tests/test_agent_factory_extensions.py

@@ -0,0 +1,71 @@
+def test_create_cli_agent_accepts_host_backend_and_memory_options(
+    monkeypatch, tmp_path
+):
+    import EvoScientist.EvoScientist as agent_module
+    from EvoScientist.config.settings import EvoScientistConfig
+
+    calls = {}
+    workspace_backend = object()
+    chat_model = object()
+
+    class _CompositeBackend:
+        def __init__(self, *, default, routes):
+            calls["default_backend"] = default
+            calls["routes"] = routes
+
+    class _MemoryBackend:
+        def __init__(self, **kwargs):
+            calls["memory_backend_kwargs"] = kwargs
+
+    class _SkillsBackend:
+        def __init__(self, **kwargs):
+            calls["skills_backend_kwargs"] = kwargs
+
+    class _Agent:
+        def with_config(self, config):
+            calls["agent_config"] = config
+            return self
+
+    cfg = EvoScientistConfig(auto_approve=True, recursion_limit=321)
+
+    monkeypatch.setattr("deepagents.backends.CompositeBackend", _CompositeBackend)
+    monkeypatch.setattr("deepagents.create_deep_agent", lambda **kwargs: _Agent())
+    monkeypatch.setattr("EvoScientist.backends.MemoryFilesystemBackend", _MemoryBackend)
+    monkeypatch.setattr("EvoScientist.backends.MergedSkillsBackend", _SkillsBackend)
+    monkeypatch.setattr(agent_module, "set_active_workspace", lambda path: None)
+    monkeypatch.setattr(
+        agent_module,
+        "_get_default_middleware",
+        lambda **kwargs: calls.setdefault("middleware_kwargs", kwargs) or [],
+    )
+    monkeypatch.setattr(
+        agent_module,
+        "load_mcp_and_build_kwargs",
+        lambda *args, **kwargs: {"subagents": [{"name": "research"}]},
+    )
+
+    memory_dir = tmp_path / "memory"
+    result = agent_module.create_cli_agent(
+        workspace_dir=str(tmp_path / "workspace"),
+        checkpointer=object(),
+        config=cfg,
+        chat_model=chat_model,
+        workspace_backend=workspace_backend,
+        memory_dir=memory_dir,
+        tool_selector_threshold=8,
+        memory_max_inline_profile_chars=1000,
+        enable_subagents=False,
+        enable_background_execution=False,
+    )
+
+    assert isinstance(result, _Agent)
+    assert calls["default_backend"] is workspace_backend
+    assert calls["memory_backend_kwargs"] == {
+        "root_dir": str(memory_dir),
+        "virtual_mode": True,
+    }
+    assert calls["middleware_kwargs"]["memory_dir"] == str(memory_dir)
+    assert calls["middleware_kwargs"]["tool_selector_threshold"] == 8
+    assert calls["middleware_kwargs"]["memory_max_inline_profile_chars"] == 1000
+    assert calls["middleware_kwargs"]["enable_background_execution"] is False
+    assert calls["agent_config"] == {"recursion_limit": 321}

tests/test_config.py

@@ -52,6 +52,8 @@ def _restore_dangerous_env():
 def temp_config_dir(tmp_path, monkeypatch):
     """Use a temporary directory for config during tests."""
     config_dir = tmp_path / "evoscientist"
+    monkeypatch.delenv("EVOSCIENTIST_CONFIG_DIR", raising=False)
+    monkeypatch.delenv("EVOSCIENTIST_HOME", raising=False)
     monkeypatch.setenv("XDG_CONFIG_HOME", str(tmp_path))
     # Prevent load_dotenv from loading the project's real .env file
     monkeypatch.setattr(
@@ -199,14 +201,34 @@ class TestEvoScientistConfig:
 
 
 class TestConfigPaths:
+    def test_get_config_dir_with_explicit_override(self, monkeypatch, tmp_path):
+        """An explicit config directory has the highest priority."""
+        config_dir = tmp_path / "gateway-config"
+        monkeypatch.setenv("EVOSCIENTIST_CONFIG_DIR", str(config_dir))
+        monkeypatch.setenv("EVOSCIENTIST_HOME", str(tmp_path / "runtime-home"))
+
+        assert get_config_dir() == config_dir.resolve()
+
+    def test_get_config_dir_with_evoscientist_home(self, monkeypatch, tmp_path):
+        """Runtime home keeps configuration and data under one root."""
+        home = tmp_path / "runtime-home"
+        monkeypatch.delenv("EVOSCIENTIST_CONFIG_DIR", raising=False)
+        monkeypatch.setenv("EVOSCIENTIST_HOME", str(home))
+
+        assert get_config_dir() == home.resolve() / "config"
+
     def test_get_config_dir_with_xdg(self, monkeypatch, tmp_path):
         """Test config dir uses XDG_CONFIG_HOME when set."""
+        monkeypatch.delenv("EVOSCIENTIST_CONFIG_DIR", raising=False)
+        monkeypatch.delenv("EVOSCIENTIST_HOME", raising=False)
         monkeypatch.setenv("XDG_CONFIG_HOME", str(tmp_path))
         config_dir = get_config_dir()
         assert config_dir == tmp_path / "evoscientist"
 
     def test_get_config_dir_default(self, monkeypatch):
         """Test config dir defaults to ~/.config/evoscientist."""
+        monkeypatch.delenv("EVOSCIENTIST_CONFIG_DIR", raising=False)
+        monkeypatch.delenv("EVOSCIENTIST_HOME", raising=False)
         monkeypatch.delenv("XDG_CONFIG_HOME", raising=False)
         config_dir = get_config_dir()
         assert config_dir == Path.home() / ".config" / "evoscientist"

tests/test_llm.py

@@ -1,5 +1,6 @@
 """Tests for EvoScientist LLM module."""
 
+from types import SimpleNamespace
 from unittest.mock import patch
 
 import pytest
@@ -160,6 +161,68 @@ class TestGetModelInfo:
 
 
 class TestGetChatModel:
+    @patch("EvoScientist.llm.models.init_chat_model")
+    def test_uses_host_model_resolver(self, mock_init):
+        """An embedding host can provide model routing without a core dependency."""
+        from EvoScientist.runtime_integrations import (
+            configure_runtime_integrations,
+            reset_runtime_integrations,
+        )
+
+        mock_init.return_value = "mock_model"
+        resolved = SimpleNamespace(
+            provider_name="relay-a",
+            model_id="model-a",
+            protocol="openai",
+            api_key="sk-host",
+            base_url="https://relay.example/v1/",
+            params={"max_tokens": 8192, "_default_headers": {"X-Relay": "a"}},
+            supports_reasoning=False,
+        )
+        configure_runtime_integrations(model_resolver=lambda model, provider: resolved)
+        try:
+            assert get_chat_model("alias-a") == "mock_model"
+        finally:
+            reset_runtime_integrations()
+
+        call_kwargs = mock_init.call_args.kwargs
+        assert call_kwargs["model"] == "model-a"
+        assert call_kwargs["model_provider"] == "openai"
+        assert call_kwargs["api_key"] == "sk-host"
+        assert call_kwargs["base_url"] == "https://relay.example/v1"
+        assert call_kwargs["max_tokens"] == 8192
+        assert call_kwargs["default_headers"] == {"X-Relay": "a"}
+        assert "reasoning" not in call_kwargs
+
+    @patch("EvoScientist.llm.models._patch_openai_compat_content")
+    @patch("EvoScientist.llm.models.init_chat_model")
+    def test_host_openai_provider_with_custom_base_uses_compat_patch(
+        self, mock_init, mock_compat
+    ):
+        from EvoScientist.runtime_integrations import (
+            configure_runtime_integrations,
+            reset_runtime_integrations,
+        )
+
+        model_instance = object()
+        mock_init.return_value = model_instance
+        resolved = SimpleNamespace(
+            provider_name="openai",
+            model_id="gpt-5.5",
+            protocol="openai",
+            api_key="sk-host",
+            base_url="https://relay.example/v1",
+            params={},
+            supports_reasoning=True,
+        )
+        configure_runtime_integrations(model_resolver=lambda model, provider: resolved)
+        try:
+            get_chat_model("gpt-5.5", provider="openai")
+        finally:
+            reset_runtime_integrations()
+
+        mock_compat.assert_called_once_with(model_instance, hoist_tool_media=True)
+
     @patch("EvoScientist.llm.models.init_chat_model")
     def test_uses_default_model_when_none(self, mock_init):
         """Test that get_chat_model uses default model when model=None."""
@@ -229,6 +292,39 @@ class TestGetChatModel:
         assert call_kwargs["temperature"] == 0.7
         assert call_kwargs["max_tokens"] == 1000
 
+    @patch("EvoScientist.llm.models.init_chat_model")
+    def test_drops_unsupported_legacy_model_kwargs(self, mock_init):
+        mock_init.return_value = "mock_model"
+
+        get_chat_model(
+            "gpt-5-nano",
+            provider="openai",
+            sanitize_openai_sdk_headers=True,
+            model_kwargs={"sanitize_openai_sdk_headers": False, "custom": "value"},
+        )
+
+        call_kwargs = mock_init.call_args.kwargs
+        assert "sanitize_openai_sdk_headers" not in call_kwargs
+        assert call_kwargs["model_kwargs"] == {"custom": "value"}
+
+    @patch("EvoScientist.llm.models.init_chat_model")
+    def test_explicit_credentials_override_environment(self, mock_init, monkeypatch):
+        """Host-provided credentials take precedence over process defaults."""
+        mock_init.return_value = "mock_model"
+        monkeypatch.setenv("OPENAI_API_KEY", "sk-environment")
+        monkeypatch.setenv("OPENAI_BASE_URL", "https://environment.example/v1")
+
+        get_chat_model(
+            "gpt-5-nano",
+            provider="openai",
+            api_key="sk-explicit",
+            base_url="https://explicit.example/v1",
+        )
+
+        call_kwargs = mock_init.call_args.kwargs
+        assert call_kwargs["api_key"] == "sk-explicit"
+        assert call_kwargs["base_url"] == "https://explicit.example/v1"
+
     @patch("EvoScientist.llm.models.init_chat_model")
     def test_infers_openai_from_gpt_prefix(self, mock_init):
         """Test that OpenAI is inferred from gpt- prefix."""
@@ -957,6 +1053,52 @@ class TestPatchOpenAICompatContent:
         model._astream = AsyncMock()
         return model
 
+    def test_missing_tool_call_ids_are_repaired_without_mutating_history(self):
+        from langchain_core.messages import AIMessage, ToolMessage
+
+        from EvoScientist.llm.patches import _ensure_openai_tool_call_ids
+
+        ai = AIMessage(
+            content=[{"type": "tool_call", "id": "", "name": "execute", "args": {}}],
+            tool_calls=[{"id": "", "name": "execute", "args": {}}],
+        )
+        tool = ToolMessage(content="ok", tool_call_id="")
+
+        normalized = _ensure_openai_tool_call_ids([ai, tool])
+
+        call_id = normalized[0].tool_calls[0]["id"]
+        assert call_id.startswith("call_")
+        assert normalized[0].content[0]["id"] == call_id
+        assert normalized[1].tool_call_id == call_id
+        assert ai.tool_calls[0]["id"] == ""
+        assert tool.tool_call_id == ""
+
+    def test_missing_parallel_tool_call_ids_are_stable_and_ordered(self):
+        from langchain_core.messages import AIMessage, ToolMessage
+
+        from EvoScientist.llm.patches import _ensure_openai_tool_call_ids
+
+        messages = [
+            AIMessage(
+                id="assistant-1",
+                content="",
+                tool_calls=[
+                    {"id": "", "name": "read_file", "args": {}},
+                    {"id": "", "name": "execute", "args": {}},
+                ],
+            ),
+            ToolMessage(content="file", tool_call_id=""),
+            ToolMessage(content="command", tool_call_id=""),
+        ]
+
+        first = _ensure_openai_tool_call_ids(messages)
+        second = _ensure_openai_tool_call_ids(messages)
+        call_ids = [call["id"] for call in first[0].tool_calls]
+
+        assert call_ids == [call["id"] for call in second[0].tool_calls]
+        assert len(set(call_ids)) == 2
+        assert [message.tool_call_id for message in first[1:]] == call_ids
+
     def test_generate_flattened(self):
         from langchain_core.messages import HumanMessage
 
@@ -2238,6 +2380,33 @@ class TestPatchOpenrouterStripResponsesReasoning:
 
 
 class TestAutoConfig:
+    @patch("EvoScientist.llm.models.init_chat_model")
+    def test_internal_sentinels_disable_auto_reasoning(self, mock_init, monkeypatch):
+        """Internal callers can disable reasoning without leaking sentinels."""
+        mock_init.return_value = "mock_model"
+        monkeypatch.delenv("ANTHROPIC_BASE_URL", raising=False)
+        monkeypatch.delenv("OPENAI_BASE_URL", raising=False)
+
+        for model, provider in (
+            ("claude-sonnet-4-6", "anthropic"),
+            ("gpt-5-nano", "openai"),
+            ("gemini-2.5-flash", "google-genai"),
+            ("llama3.1:8b", "ollama"),
+        ):
+            mock_init.reset_mock()
+            get_chat_model(
+                model,
+                provider=provider,
+                _disable_reasoning=True,
+                _disable_thinking=True,
+            )
+            call_kwargs = mock_init.call_args.kwargs
+            assert "_disable_reasoning" not in call_kwargs
+            assert "_disable_thinking" not in call_kwargs
+            assert "reasoning" not in call_kwargs
+            assert "thinking" not in call_kwargs
+            assert "include_thoughts" not in call_kwargs
+
     @patch("EvoScientist.llm.models.init_chat_model")
     def test_anthropic_4_5_thinking(self, mock_init, monkeypatch):
         """Anthropic 4-5 models get enabled thinking with budget."""

tests/test_logging_config.py

@@ -0,0 +1,129 @@
+import logging
+from datetime import UTC, datetime
+from io import StringIO
+
+from EvoScientist.logging_config import (
+    DailyLogFileHandler,
+    configure_console_logging,
+    configure_daily_file_logging,
+    configure_logging,
+    default_log_dir,
+    resolve_log_level,
+)
+
+
+def test_daily_log_file_handler_uses_dated_active_file(tmp_path):
+    handler = DailyLogFileHandler(tmp_path, prefix="evoscientist", retention_days=30)
+    logger = logging.getLogger("tests.daily_log_file_handler")
+    logger.handlers.clear()
+    logger.propagate = False
+    logger.setLevel(logging.INFO)
+    logger.addHandler(handler)
+
+    logger.info("hello")
+    handler.close()
+
+    today = datetime.now().strftime("%Y-%m-%d")
+    assert (tmp_path / f"evoscientist-{today}.log").read_text(encoding="utf-8").strip()
+
+
+def test_daily_log_file_handler_keeps_latest_retention_days(tmp_path):
+    for day in range(1, 33):
+        (tmp_path / f"evoscientist-2026-01-{day:02d}.log").write_text(
+            "x", encoding="utf-8"
+        )
+
+    handler = DailyLogFileHandler(tmp_path, prefix="evoscientist", retention_days=30)
+    handler._delete_expired_logs()
+    handler.close()
+
+    remaining = sorted(path.name for path in tmp_path.glob("evoscientist-*.log"))
+    assert len(remaining) == 30
+    assert remaining[0] == "evoscientist-2026-01-03.log"
+
+
+def test_configure_daily_file_logging_replaces_matching_handler(tmp_path):
+    logger = logging.getLogger("tests.configure_daily_file_logging")
+    logger.handlers.clear()
+    logger.propagate = False
+
+    first = configure_daily_file_logging(logger, log_dir=tmp_path)
+    second = configure_daily_file_logging(logger, log_dir=tmp_path)
+
+    try:
+        handlers = [h for h in logger.handlers if isinstance(h, DailyLogFileHandler)]
+        assert handlers == [second]
+        assert first.stream is None
+    finally:
+        for handler in logger.handlers[:]:
+            logger.removeHandler(handler)
+            handler.close()
+
+
+def test_configure_logging_replaces_only_managed_handlers(tmp_path):
+    logger = logging.getLogger("tests.configure_logging")
+    logger.handlers.clear()
+    logger.propagate = False
+    external = logging.NullHandler()
+    logger.addHandler(external)
+
+    configure_logging(logger, log_dir=tmp_path, level="debug")
+    configure_logging(logger, log_dir=tmp_path, level="info")
+
+    try:
+        daily_handlers = [h for h in logger.handlers if isinstance(h, DailyLogFileHandler)]
+        stream_handlers = [
+            h
+            for h in logger.handlers
+            if isinstance(h, logging.StreamHandler)
+            and not isinstance(h, DailyLogFileHandler)
+        ]
+        assert external in logger.handlers
+        assert len(daily_handlers) == 1
+        assert len(stream_handlers) == 1
+        assert logger.level == logging.INFO
+    finally:
+        for handler in logger.handlers[:]:
+            logger.removeHandler(handler)
+            handler.close()
+
+
+def test_configure_console_logging_emits_to_stream():
+    logger = logging.getLogger("tests.configure_console_logging")
+    logger.handlers.clear()
+    logger.propagate = False
+    stream = StringIO()
+
+    configure_console_logging(logger, level="INFO", stream=stream)
+    try:
+        logger.info("hello")
+        assert "tests.configure_console_logging: hello" in stream.getvalue()
+    finally:
+        for handler in logger.handlers[:]:
+            logger.removeHandler(handler)
+            handler.close()
+
+
+def test_resolve_log_level_accepts_alias_numeric_and_fallback():
+    assert resolve_log_level("warn") == logging.WARNING
+    assert resolve_log_level("10") == logging.DEBUG
+    assert resolve_log_level("", default=logging.ERROR) == logging.ERROR
+    assert resolve_log_level("not-a-level", default=logging.CRITICAL) == logging.CRITICAL
+
+
+def test_daily_log_file_handler_supports_utc(tmp_path):
+    handler = DailyLogFileHandler(tmp_path, utc=True)
+    try:
+        today_utc = datetime.now(UTC).strftime("%Y-%m-%d")
+        assert handler.active_log_path.name == f"evoscientist-{today_utc}.log"
+    finally:
+        handler.close()
+
+
+def test_default_log_dir_uses_current_data_dir(monkeypatch, tmp_path):
+    import EvoScientist.paths as paths
+
+    monkeypatch.delenv("EVOSCIENTIST_LOG_DIR", raising=False)
+    monkeypatch.setattr(paths, "DATA_DIR", tmp_path / "data")
+
+    assert default_log_dir() == tmp_path / "data" / "logs"

tests/test_mcp_client.py

@@ -1421,22 +1421,35 @@ class TestLoadToolsProgressCallback:
         ]
 
     async def test_failure_emits_start_then_error_with_detail(self, monkeypatch):
-        from EvoScientist.mcp.client import _load_tools
+        from EvoScientist.mcp import client as mcp_client
 
         events: list[tuple[str, str, str]] = []
         self._patch_client(monkeypatch, {"srv": RuntimeError("boom")})
+        monkeypatch.setattr(mcp_client, "_MCP_SERVER_ERRORS", {})
 
         config = {"srv": {"transport": "stdio", "command": "demo"}}
 
         def record(event, name, detail):
             events.append((event, name, detail))
 
-        await _load_tools(config, on_progress=record)
+        await mcp_client._load_tools(config, on_progress=record)
 
         assert events == [
             ("start", "srv", ""),
             ("error", "srv", "boom"),
         ]
+        assert mcp_client.get_mcp_server_errors() == {"srv": "boom"}
+
+    async def test_success_clears_previous_server_error(self, monkeypatch):
+        from EvoScientist.mcp import client as mcp_client
+
+        self._patch_client(monkeypatch, {"srv": ["tool1"]})
+        monkeypatch.setattr(mcp_client, "_MCP_SERVER_ERRORS", {"srv": "old error"})
+
+        config = {"srv": {"transport": "stdio", "command": "demo"}}
+        await mcp_client._load_tools(config)
+
+        assert mcp_client.get_mcp_server_errors() == {}
 
     async def test_mixed_fleet_reports_each_server_independently(self, monkeypatch):
         from EvoScientist.mcp.client import _load_tools

tests/test_paths.py

@@ -21,6 +21,7 @@ def _restore_paths():
         "GLOBAL_MEMORIES_DIR": paths.GLOBAL_MEMORIES_DIR,
         "USER_SKILLS_DIR": paths.USER_SKILLS_DIR,
         "_active_workspace": paths._active_workspace,
+        "_EVOSCIENTIST_DATA_ROOT": paths._EVOSCIENTIST_DATA_ROOT,
     }
     yield
     paths.WORKSPACE_ROOT = orig["WORKSPACE_ROOT"]
@@ -32,6 +33,7 @@ def _restore_paths():
     paths.GLOBAL_MEMORIES_DIR = orig["GLOBAL_MEMORIES_DIR"]
     paths.USER_SKILLS_DIR = orig["USER_SKILLS_DIR"]
     paths._active_workspace = orig["_active_workspace"]
+    paths._EVOSCIENTIST_DATA_ROOT = orig["_EVOSCIENTIST_DATA_ROOT"]
 
 
 class TestSetWorkspaceRoot:
@@ -140,6 +142,63 @@ class TestDataDir:
         assert paths.GLOBAL_MEMORIES_DIR == paths.DATA_DIR / "memories"
 
 
+class TestGatewayDataDirs:
+    def test_evoscientist_root_prefers_home_override(self, tmp_path, monkeypatch):
+        home = tmp_path / "runtime-home"
+        monkeypatch.setenv("EVOSCIENTIST_HOME", str(home))
+
+        assert paths.evoscientist_root() == home.resolve()
+
+    def test_evoscientist_root_falls_back_to_data_dir(self, tmp_path, monkeypatch):
+        data_dir = tmp_path / "app-data"
+        monkeypatch.delenv("EVOSCIENTIST_HOME", raising=False)
+        monkeypatch.setattr(paths, "DATA_DIR", data_dir)
+
+        assert paths.evoscientist_root() == data_dir.resolve()
+
+    def test_data_root_respects_environment_override(self, tmp_path, monkeypatch):
+        data_root = tmp_path / "web-data"
+        monkeypatch.setenv("EVOSCIENTIST_DATA_ROOT", str(data_root))
+        paths._EVOSCIENTIST_DATA_ROOT = None
+
+        assert paths._data_root() == data_root.resolve()
+
+    def test_user_thread_and_global_dirs_are_created(self, tmp_path, monkeypatch):
+        data_root = tmp_path / "web-data"
+        monkeypatch.setenv("EVOSCIENTIST_DATA_ROOT", str(data_root))
+        paths._EVOSCIENTIST_DATA_ROOT = None
+
+        user_dir = paths.user_data_dir("user-a")
+        thread_dir = paths.thread_data_dir("user-a", "thread-1")
+        shared_dir = paths.global_data_dir("user-a")
+
+        assert user_dir == data_root / "user-a"
+        assert thread_dir == user_dir / "thread-1"
+        assert shared_dir == user_dir / "__global__"
+        assert user_dir.is_dir()
+        assert thread_dir.is_dir()
+        assert shared_dir.is_dir()
+
+    def test_iter_user_data_dirs_yields_directories_only(self, tmp_path, monkeypatch):
+        data_root = tmp_path / "web-data"
+        monkeypatch.setenv("EVOSCIENTIST_DATA_ROOT", str(data_root))
+        paths._EVOSCIENTIST_DATA_ROOT = None
+        paths.user_data_dir("user-a")
+        paths.user_data_dir("user-b")
+        (data_root / "metadata.json").write_text("{}", encoding="utf-8")
+
+        assert {path.name for path in paths.iter_user_data_dirs()} == {
+            "user-a",
+            "user-b",
+        }
+
+    def test_uploads_dir_uses_evoscientist_root(self, tmp_path, monkeypatch):
+        home = tmp_path / "runtime-home"
+        monkeypatch.setenv("EVOSCIENTIST_HOME", str(home))
+
+        assert paths.uploads_dir() == home.resolve() / "uploads"
+
+
 class TestLegacySessionsDbMigration:
     """Tests for migrate_legacy_sessions_db() — transitional helper.
 

tests/test_runtime_integrations.py

@@ -0,0 +1,117 @@
+from __future__ import annotations
+
+import ast
+from pathlib import Path
+
+import pytest
+
+from EvoScientist.runtime_integrations import (
+    RuntimeIntegrationUnavailable,
+    configure_runtime_integrations,
+    get_app_connection,
+    get_image_backend,
+    get_session_connection,
+    get_session_dsn,
+    handle_knowledge_file,
+    record_service_usage,
+    reset_runtime_integrations,
+    resolve_runtime_model,
+)
+
+
+@pytest.fixture(autouse=True)
+def reset_integrations():
+    reset_runtime_integrations()
+    yield
+    reset_runtime_integrations()
+
+
+def test_core_package_does_not_import_gateway():
+    package_root = Path(__file__).resolve().parents[1] / "EvoScientist"
+    violations = []
+    for source_file in package_root.rglob("*.py"):
+        tree = ast.parse(
+            source_file.read_text(encoding="utf-8"), filename=str(source_file)
+        )
+        for node in ast.walk(tree):
+            if isinstance(node, ast.Import):
+                names = [alias.name for alias in node.names]
+            elif isinstance(node, ast.ImportFrom):
+                if node.level:
+                    continue
+                names = [node.module or ""]
+            else:
+                continue
+            if any(name == "gateway" or name.startswith("gateway.") for name in names):
+                violations.append(
+                    f"{source_file.relative_to(package_root)}:{node.lineno}"
+                )
+    assert violations == []
+
+
+@pytest.mark.anyio
+async def test_optional_integrations_are_safe_without_web_runtime(tmp_path):
+    assert get_session_dsn() is None
+    await handle_knowledge_file(tmp_path / "result.md")
+    await record_service_usage("search", "query")
+    with pytest.raises(RuntimeIntegrationUnavailable):
+        await get_app_connection()
+    with pytest.raises(RuntimeIntegrationUnavailable):
+        await get_session_connection()
+    with pytest.raises(RuntimeIntegrationUnavailable):
+        get_image_backend()
+
+
+@pytest.mark.anyio
+async def test_host_can_register_runtime_integrations(tmp_path):
+    app_connection = object()
+    session_connection = object()
+    knowledge_paths = []
+    usage = []
+    image_backend = object()
+
+    async def provide_app_connection():
+        return app_connection
+
+    async def provide_session_connection():
+        return session_connection
+
+    async def handle_file(path):
+        knowledge_paths.append(path)
+
+    async def record_usage(service, action):
+        usage.append((service, action))
+
+    configure_runtime_integrations(
+        app_connection_provider=provide_app_connection,
+        session_connection_provider=provide_session_connection,
+        session_dsn_provider=lambda: "postgresql://example/session",
+        knowledge_file_handler=handle_file,
+        usage_recorder=record_usage,
+        image_backend_factory=lambda: image_backend,
+    )
+
+    path = tmp_path / "result.md"
+    await handle_knowledge_file(path)
+    await record_service_usage("mineru", "parse")
+
+    assert await get_app_connection() is app_connection
+    assert await get_session_connection() is session_connection
+    assert get_session_dsn() == "postgresql://example/session"
+    assert get_image_backend() is image_backend
+    assert knowledge_paths == [path]
+    assert usage == [("mineru", "parse")]
+
+
+def test_host_can_register_model_resolver():
+    resolved = object()
+    calls = []
+
+    def resolve_model(model, provider):
+        calls.append((model, provider))
+        return resolved
+
+    configure_runtime_integrations(model_resolver=resolve_model)
+
+    assert resolve_runtime_model("model-a", "provider-a") is resolved
+    assert calls == [("model-a", "provider-a")]

uv.lock

@@ -944,7 +944,7 @@ wheels = [
 
 [[package]]
 name = "evoscientist"
-version = "0.2.1"
+version = "0.2.2"
 source = { editable = "." }
 dependencies = [
     { name = "deepagents", extra = ["quickjs"] },