EvoScientist 0.0.1__tar.gz

evoscientist-0.0.1/EvoScientist/EvoScientist.py

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+"""EvoScientist Agent graph construction.
+
+This module defines the agent graph and its factory functions.  All heavy
+initialization (deepagents, backends, LLM, middleware) is deferred to first
+use so that importing this module is fast and non-agent CLI commands
+(``EvoSci config list``, ``EvoSci onboard``) never pay the cost.
+
+Usage:
+    from EvoScientist import EvoScientist_agent
+
+    # Notebook / programmatic usage
+    for state in EvoScientist_agent.stream(
+        {"messages": [HumanMessage(content="your question")]},
+        config={"configurable": {"thread_id": "1"}},
+        stream_mode="values",
+    ):
+        ...
+"""
+
+import json
+import logging
+from datetime import datetime
+from pathlib import Path
+
+from .config import get_effective_config, apply_config_to_env
+from .prompts import RESEARCHER_INSTRUCTIONS, get_system_prompt
+from . import paths as _paths_mod
+from .paths import set_active_workspace, set_workspace_root
+
+# Suppress noisy warnings from deepagents skill loader (non-string frontmatter fields, etc.)
+logging.getLogger("deepagents.middleware.skills").setLevel(logging.ERROR)
+
+# =============================================================================
+# Constants
+# =============================================================================
+
+SUBAGENTS_CONFIG = Path(__file__).parent / "subagent.yaml"
+SKILLS_DIR = str(Path(__file__).parent / "skills")
+
+# =============================================================================
+# Lazy state — initialized on first use, not at import time
+# =============================================================================
+
+_config = None
+_chat_model = None
+_system_prompt = None
+
+# Cache MCP tools by the effective config signature to avoid reconnecting
+# to MCP servers on every `/new` when config is unchanged.
+_MCP_TOOLS_CACHE_KEY: str | None = None
+_MCP_TOOLS_CACHE_VALUE: dict[str, list] | None = None
+
+# Default agent (no checkpointer) — used by langgraph dev / LangSmith / notebooks.
+# Lazily constructed on first access so MCP tools are included without
+# spawning subprocesses at import time.
+_EvoScientist_agent = None
+
+
+# =============================================================================
+# Lazy initialization helpers
+# =============================================================================
+
+
+def _ensure_config(config=None):
+    """Return cached config.  If *config* is passed, cache and use it."""
+    global _config
+    if config is not None:
+        _config = config
+        apply_config_to_env(_config)
+    if _config is None:
+        _config = get_effective_config()
+        apply_config_to_env(_config)
+    return _config
+
+
+def _ensure_chat_model():
+    """Return cached chat model, creating it on first call."""
+    global _chat_model
+    if _chat_model is None:
+        from .llm import get_chat_model
+
+        cfg = _ensure_config()
+        _chat_model = get_chat_model(model=cfg.model, provider=cfg.provider)
+    return _chat_model
+
+
+def _ensure_system_prompt():
+    """Return cached system prompt, creating it on first call."""
+    global _system_prompt
+    if _system_prompt is None:
+        _system_prompt = get_system_prompt()
+    return _system_prompt
+
+
+# =============================================================================
+# MCP caching
+# =============================================================================
+
+
+def _mcp_config_signature() -> str:
+    """Return a stable signature for the effective MCP config."""
+    from .mcp.client import load_mcp_config
+
+    cfg = load_mcp_config()
+    if not cfg:
+        return ""
+    try:
+        return json.dumps(cfg, sort_keys=True, ensure_ascii=True)
+    except TypeError:
+        # Fallback for non-JSON-serializable values (should be rare)
+        return repr(cfg)
+
+
+def _load_mcp_tools_cached() -> dict[str, list]:
+    """Load MCP tools with config-aware caching."""
+    global _MCP_TOOLS_CACHE_KEY, _MCP_TOOLS_CACHE_VALUE
+
+    from .mcp import load_mcp_tools
+
+    cfg_key = _mcp_config_signature()
+    if not cfg_key:
+        _MCP_TOOLS_CACHE_KEY = ""
+        _MCP_TOOLS_CACHE_VALUE = {}
+        return {}
+
+    if _MCP_TOOLS_CACHE_KEY == cfg_key and _MCP_TOOLS_CACHE_VALUE is not None:
+        return {k: list(v) for k, v in _MCP_TOOLS_CACHE_VALUE.items()}
+
+    loaded = load_mcp_tools()
+    _MCP_TOOLS_CACHE_KEY = cfg_key
+    _MCP_TOOLS_CACHE_VALUE = {k: list(v) for k, v in loaded.items()}
+    return {k: list(v) for k, v in loaded.items()}
+
+
+# =============================================================================
+# Agent construction helpers
+# =============================================================================
+
+
+def _inject_subagent_middleware(subs: list[dict]) -> None:
+    """Ensure every subagent gets ToolErrorHandlerMiddleware.
+
+    Without this, subagent tool errors are caught by LangGraph's default
+    ToolNode handler which produces terse messages without tracebacks or
+    retry guidance — reducing the subagent's ability to self-recover.
+    """
+    from .middleware import ToolErrorHandlerMiddleware
+
+    for sa in subs:
+        sa.setdefault("middleware", []).append(ToolErrorHandlerMiddleware())
+
+
+def _build_prompt_refs() -> dict:
+    """Build prompt references with the current date (not frozen at import)."""
+    return {
+        "RESEARCHER_INSTRUCTIONS": RESEARCHER_INSTRUCTIONS.format(
+            date=datetime.now().strftime("%Y-%m-%d"),
+        ),
+    }
+
+
+def _build_base_kwargs(base_backend, base_middleware):
+    """Build agent kwargs *without* MCP (fast, no subprocess spawning)."""
+    from .utils import load_subagents
+    from .tools import tavily_search, think_tool, skill_manager
+
+    tool_registry = {"think_tool": think_tool, "tavily_search": tavily_search}
+    base_tools = [think_tool, skill_manager]
+
+    subs = load_subagents(
+        SUBAGENTS_CONFIG,
+        tool_registry=tool_registry,
+        prompt_refs=_build_prompt_refs(),
+    )
+    _inject_subagent_middleware(subs)
+    return dict(
+        name="EvoScientist",
+        model=_ensure_chat_model(),
+        tools=list(base_tools),
+        backend=base_backend,
+        subagents=subs,
+        middleware=base_middleware,
+        system_prompt=_ensure_system_prompt(),
+        skills=["/skills/"],
+    )
+
+
+def load_mcp_and_build_kwargs(base_backend, base_middleware):
+    """Load MCP tools (cached by config) and build agent kwargs.
+
+    Re-connects to MCP servers only when the effective MCP config changes.
+    Falls back to base kwargs if no MCP configured.
+    """
+    from .utils import load_subagents
+    from .tools import tavily_search, think_tool, skill_manager
+
+    mcp_by_agent = _load_mcp_tools_cached()
+    if not mcp_by_agent:
+        return _build_base_kwargs(base_backend, base_middleware)
+
+    tool_registry = {"think_tool": think_tool, "tavily_search": tavily_search}
+    base_tools = [think_tool, skill_manager]
+
+    # Fresh tool registry — start from base tools + MCP tools
+    registry = dict(tool_registry)
+    for tools in mcp_by_agent.values():
+        for t in tools:
+            registry[t.name] = t
+
+    mcp_main = mcp_by_agent.pop("main", [])
+
+    subs = load_subagents(
+        SUBAGENTS_CONFIG,
+        tool_registry=registry,
+        prompt_refs=_build_prompt_refs(),
+    )
+
+    _inject_subagent_middleware(subs)
+
+    # Inject MCP tools into subagents by name
+    for sa in subs:
+        if sa_tools := mcp_by_agent.get(sa["name"], []):
+            sa.setdefault("tools", []).extend(sa_tools)
+
+    return dict(
+        name="EvoScientist",
+        model=_ensure_chat_model(),
+        tools=base_tools + mcp_main,
+        backend=base_backend,
+        subagents=subs,
+        middleware=base_middleware,
+        system_prompt=_ensure_system_prompt(),
+        skills=["/skills/"],
+    )
+
+
+# =============================================================================
+# Default agent (langgraph dev / notebooks)
+# =============================================================================
+
+
+def _get_default_backend():
+    """Build the default composite backend from current paths."""
+    from deepagents.backends import FilesystemBackend, CompositeBackend
+    from .backends import CustomSandboxBackend, MergedReadOnlyBackend
+
+    workspace_dir = str(_paths_mod.WORKSPACE_ROOT)
+    set_active_workspace(workspace_dir)
+    memory_dir = str(_paths_mod.MEMORY_DIR)
+    user_skills_dir = str(_paths_mod.USER_SKILLS_DIR)
+
+    ws_backend = CustomSandboxBackend(
+        root_dir=workspace_dir,
+        virtual_mode=True,
+        timeout=300,
+    )
+    sk_backend = MergedReadOnlyBackend(
+        primary_dir=user_skills_dir,
+        secondary_dir=SKILLS_DIR,
+    )
+    mem_backend = FilesystemBackend(
+        root_dir=memory_dir,
+        virtual_mode=True,
+    )
+    return CompositeBackend(
+        default=ws_backend,
+        routes={
+            "/skills/": sk_backend,
+            "/memory/": mem_backend,
+        },
+    )
+
+
+def _get_default_middleware():
+    """Build the default middleware list."""
+    from .middleware import create_memory_middleware, ToolErrorHandlerMiddleware
+
+    cfg = _ensure_config()
+    memory_dir = str(_paths_mod.MEMORY_DIR)
+    mw = [
+        ToolErrorHandlerMiddleware(),
+        create_memory_middleware(memory_dir, extraction_model=_ensure_chat_model()),
+    ]
+    if cfg.enable_ask_user and not cfg.auto_approve:
+        from .middleware.ask_user import AskUserMiddleware
+        mw.insert(0, AskUserMiddleware())
+    return mw
+
+
+def _get_default_agent():
+    """Build the default agent (with MCP, no checkpointer) on first access."""
+    global _EvoScientist_agent
+    if _EvoScientist_agent is None:
+        from deepagents import create_deep_agent
+
+        be = _get_default_backend()
+        mw = _get_default_middleware()
+        kwargs = load_mcp_and_build_kwargs(be, mw)
+        _EvoScientist_agent = create_deep_agent(**kwargs).with_config(
+            {"recursion_limit": 1000}
+        )
+    return _EvoScientist_agent
+
+
+def __getattr__(name: str):
+    if name == "EvoScientist_agent":
+        return _get_default_agent()
+    # Backward compat for module-level names
+    if name == "chat_model":
+        return _ensure_chat_model()
+    if name == "SYSTEM_PROMPT":
+        return _ensure_system_prompt()
+    if name == "backend":
+        return _get_default_backend()
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+# =============================================================================
+# CLI agent factory
+# =============================================================================
+
+
+def create_cli_agent(workspace_dir: str | None = None, checkpointer=None, config=None):
+    """Create agent with checkpointer for CLI multi-turn support.
+
+    A fresh backend is constructed on every call using the current
+    ``paths.WORKSPACE_ROOT`` (or the explicit *workspace_dir*), so
+    runtime ``set_workspace_root()`` changes are always respected.
+
+    Args:
+        workspace_dir: Per-session workspace directory. If ``None``,
+            defaults to the current ``paths.WORKSPACE_ROOT``.
+        checkpointer: Optional LangGraph checkpointer. If ``None``,
+            falls back to ``InMemorySaver`` (non-persistent).
+        config: Optional pre-loaded ``EvoScientistConfig``.  If ``None``,
+            loads from file/env/defaults.  Passing this avoids double
+            loading when the CLI has already loaded config.
+    """
+    import os as _os
+
+    from deepagents import create_deep_agent
+    from deepagents.backends import FilesystemBackend, CompositeBackend
+    from .backends import CustomSandboxBackend, MergedReadOnlyBackend
+    from .middleware import create_memory_middleware, ToolErrorHandlerMiddleware
+    from . import paths as _paths
+
+    cfg = _ensure_config(config)
+
+    if checkpointer is None:
+        from langgraph.checkpoint.memory import InMemorySaver  # type: ignore[import-untyped]
+        checkpointer = InMemorySaver()
+
+    # When no explicit workspace_dir is provided, apply config.default_workdir
+    # as a fallback.  This covers direct callers (notebooks, iMessage server)
+    # that never call set_workspace_root() themselves.  CLI callers always
+    # pass workspace_dir explicitly, so their --workdir is never overwritten.
+    if workspace_dir is None:
+        if cfg.default_workdir:
+            set_workspace_root(
+                _os.path.abspath(_os.path.expanduser(cfg.default_workdir))
+            )
+        workspace_dir = str(_paths.WORKSPACE_ROOT)
+
+    # Read paths dynamically so runtime set_workspace_root() changes are picked up
+    _mem_dir = str(_paths.MEMORY_DIR)
+    _usr_skills_dir = str(_paths.USER_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(
+        root_dir=workspace_dir,
+        virtual_mode=True,
+        timeout=300,
+    )
+    sk_backend = MergedReadOnlyBackend(
+        primary_dir=_usr_skills_dir,
+        secondary_dir=SKILLS_DIR,
+    )
+    # Memory always uses SHARED directory (not per-session) for cross-session persistence
+    mem_backend = FilesystemBackend(
+        root_dir=_mem_dir,
+        virtual_mode=True,
+    )
+    be = CompositeBackend(
+        default=ws_backend,
+        routes={
+            "/skills/": sk_backend,
+            "/memory/": mem_backend,
+        },
+    )
+
+    mw = [
+        ToolErrorHandlerMiddleware(),
+        create_memory_middleware(_mem_dir, extraction_model=_ensure_chat_model()),
+    ]
+    if cfg.enable_ask_user and not cfg.auto_approve:
+        from .middleware.ask_user import AskUserMiddleware
+        mw.insert(0, AskUserMiddleware())
+
+    # Re-load MCP tools from current config (picks up /mcp add changes)
+    kwargs = load_mcp_and_build_kwargs(be, mw)
+
+    # HITL: gate shell execution for user approval
+    _interrupt_on: dict[str, bool] | None = None
+    if not cfg.auto_approve:
+        _interrupt_on = {"execute": True}
+
+    return create_deep_agent(
+        **kwargs,
+        checkpointer=checkpointer,
+        interrupt_on=_interrupt_on,
+    ).with_config({"recursion_limit": 1000})

evoscientist-0.0.1/EvoScientist/__init__.py

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+"""EvoScientist Agent - AI-powered research and code execution.
+
+This package exposes a convenience API at the package root while keeping
+imports lazy, so lightweight modules (for example config helpers) can be used
+without importing heavy runtime dependencies.
+"""
+
+from __future__ import annotations
+
+from importlib import import_module
+
+
+_EXPORTS: dict[str, tuple[str, str]] = {
+    # Agent graph (lazy to avoid expensive initialization at import time)
+    "EvoScientist_agent": (".EvoScientist", "EvoScientist_agent"),
+    "create_cli_agent": (".EvoScientist", "create_cli_agent"),
+    # Backends
+    "CustomSandboxBackend": (".backends", "CustomSandboxBackend"),
+    "ReadOnlyFilesystemBackend": (".backends", "ReadOnlyFilesystemBackend"),
+    # Configuration
+    "EvoScientistConfig": (".config", "EvoScientistConfig"),
+    "load_config": (".config", "load_config"),
+    "save_config": (".config", "save_config"),
+    "get_effective_config": (".config", "get_effective_config"),
+    "get_config_path": (".config", "get_config_path"),
+    # LLM
+    "get_chat_model": (".llm", "get_chat_model"),
+    "MODELS": (".llm", "MODELS"),
+    "list_models": (".llm", "list_models"),
+    "DEFAULT_MODEL": (".llm", "DEFAULT_MODEL"),
+    # Prompts
+    "get_system_prompt": (".prompts", "get_system_prompt"),
+    "RESEARCHER_INSTRUCTIONS": (".prompts", "RESEARCHER_INSTRUCTIONS"),
+    # Tools
+    "tavily_search": (".tools", "tavily_search"),
+    "think_tool": (".tools", "think_tool"),
+    # Sessions
+    "get_checkpointer": (".sessions", "get_checkpointer"),
+    "generate_thread_id": (".sessions", "generate_thread_id"),
+    "list_threads": (".sessions", "list_threads"),
+    "delete_thread": (".sessions", "delete_thread"),
+}
+
+
+def __getattr__(name: str):
+    """Lazily import and cache package-level attributes.
+
+    Args:
+        name: The attribute name to look up.
+
+    Returns:
+        The resolved attribute value.
+
+    Raises:
+        AttributeError: If the name is not in _EXPORTS.
+    """
+    target = _EXPORTS.get(name)
+    if target is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+    module_name, attr_name = target
+    module = import_module(module_name, package=__name__)
+    value = getattr(module, attr_name)
+    # Cache after first load to avoid repeated import lookups.
+    globals()[name] = value
+    return value
+
+
+def __dir__() -> list[str]:
+    """List available public attributes including lazy exports."""
+    return sorted(set(globals()) | set(_EXPORTS))
+
+
+__all__ = list(_EXPORTS)

evoscientist-0.0.1/EvoScientist/__main__.py

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+"""Enable `python -m EvoScientist` execution."""
+from EvoScientist.cli import main
+
+main()