EvoScientist 0.0.1.dev3__py3-none-any.whl → 0.1.0rc1__py3-none-any.whl

EvoScientist/EvoScientist.py

@@ -21,17 +21,11 @@ from deepagents import create_deep_agent
 from deepagents.backends import FilesystemBackend, CompositeBackend
 from langchain.chat_models import init_chat_model
 
-from .backends import CustomSandboxBackend, MergedReadOnlyBackend
-from .middleware import create_skills_middleware, create_memory_middleware
+from .backends import CustomSandboxBackend, ReadOnlyFilesystemBackend
+from .middleware import create_skills_middleware
 from .prompts import RESEARCHER_INSTRUCTIONS, get_system_prompt
 from .utils import load_subagents
-from .tools import tavily_search, think_tool, skill_manager
-from .paths import (
-    ensure_dirs,
-    default_workspace_dir,
-    MEMORY_DIR as _MEMORY_DIR_PATH,
-    USER_SKILLS_DIR as _USER_SKILLS_DIR_PATH,
-)
+from .tools import tavily_search, think_tool
 
 # =============================================================================
 # Configuration
@@ -45,11 +39,8 @@ MAX_CONCURRENT = 3  # Max parallel sub-agents
 MAX_ITERATIONS = 3  # Max delegation rounds
 
 # Workspace settings
-ensure_dirs()
-WORKSPACE_DIR = str(default_workspace_dir())
-MEMORY_DIR = str(_MEMORY_DIR_PATH)  # Shared across sessions (not per-session)
-SKILLS_DIR = str(Path(__file__).parent / "skills")
-USER_SKILLS_DIR = str(_USER_SKILLS_DIR_PATH)
+WORKSPACE_DIR = "./workspace/"
+SKILLS_DIR = "./skills/"
 SUBAGENTS_CONFIG = Path(__file__).parent / "subagent.yaml"
 
 # =============================================================================
@@ -85,25 +76,16 @@ else:
         virtual_mode=True,
     )
 
-# Skills backend: merge user-installed (./skills/) and system (package) skills
-_skills_backend = MergedReadOnlyBackend(
-    primary_dir=USER_SKILLS_DIR,                        # user-installed, takes priority
-    secondary_dir=SKILLS_DIR,                           # package built-in, fallback
-)
-
-# Memory backend: persistent filesystem for long-term memory (shared across sessions)
-_memory_backend = FilesystemBackend(
-    root_dir=MEMORY_DIR,
+# Skills backend: read-only access to ./skills/
+_skills_backend = ReadOnlyFilesystemBackend(
+    root_dir=SKILLS_DIR,
     virtual_mode=True,
 )
 
-# Composite backend: workspace as default, skills and memory mounted
+# Composite backend: workspace as default, skills mounted at /skills/
 backend = CompositeBackend(
     default=_workspace_backend,
-    routes={
-        "/skills/": _skills_backend,
-        "/memory/": _memory_backend,
-    },
+    routes={"/skills/": _skills_backend},
 )
 
 tool_registry = {
@@ -125,13 +107,10 @@ subagents = load_subagents(
 _AGENT_KWARGS = dict(
     name="EvoScientist",
     model=chat_model,
-    tools=[think_tool, skill_manager],
+    tools=[think_tool],
     backend=backend,
     subagents=subagents,
-    middleware=[
-        create_memory_middleware(MEMORY_DIR, extraction_model=chat_model),
-        create_skills_middleware(SKILLS_DIR, user_skills_dir=USER_SKILLS_DIR),
-    ],
+    middleware=[create_skills_middleware(SKILLS_DIR, WORKSPACE_DIR)],
     system_prompt=SYSTEM_PROMPT,
 )
 
@@ -145,7 +124,7 @@ def create_cli_agent(workspace_dir: str | None = None):
     Args:
         workspace_dir: Optional per-session workspace directory. If provided,
             creates a fresh backend rooted at this path. If None, uses the
-            module-level default backend (./workspace).
+            module-level default backend (./workspace/).
     """
     from langgraph.checkpoint.memory import InMemorySaver  # type: ignore[import-untyped]
 
@@ -155,26 +134,15 @@ def create_cli_agent(workspace_dir: str | None = None):
             virtual_mode=True,
             timeout=300,
         )
-        sk_backend = MergedReadOnlyBackend(
-            primary_dir=USER_SKILLS_DIR,
-            secondary_dir=SKILLS_DIR,
-        )
-        # Memory always uses SHARED directory (not per-session) for cross-session persistence
-        mem_backend = FilesystemBackend(
-            root_dir=MEMORY_DIR,
+        sk_backend = ReadOnlyFilesystemBackend(
+            root_dir=SKILLS_DIR,
             virtual_mode=True,
         )
         be = CompositeBackend(
             default=ws_backend,
-            routes={
-                "/skills/": sk_backend,
-                "/memory/": mem_backend,
-            },
+            routes={"/skills/": sk_backend},
         )
-        mw = [
-            create_memory_middleware(MEMORY_DIR, extraction_model=chat_model),
-            create_skills_middleware(SKILLS_DIR, user_skills_dir=USER_SKILLS_DIR),
-        ]
+        mw = [create_skills_middleware(SKILLS_DIR, workspace_dir)]
         kwargs = dict(
             _AGENT_KWARGS,
             backend=be,

EvoScientist/backends.py

@@ -9,8 +9,6 @@ from deepagents.backends import FilesystemBackend
 from deepagents.backends.filesystem import WriteResult, EditResult
 from deepagents.backends.protocol import (
     ExecuteResponse,
-    FileDownloadResponse,
-    FileUploadResponse,
     SandboxBackendProtocol,
 )
 
@@ -225,30 +223,6 @@ class MergedReadOnlyBackend:
     async def aedit(self, file_path: str, old_string: str, new_string: str, replace_all: bool = False) -> EditResult:
         return self.edit(file_path, old_string, new_string, replace_all)
 
-    # -- download / upload (required by BackendProtocol) --
-
-    def download_files(self, paths: list[str]) -> list[FileDownloadResponse]:
-        """Download files, trying primary then secondary."""
-        responses: list[FileDownloadResponse] = []
-        for path in paths:
-            resp = self._primary.download_files([path])[0]
-            if resp.error is not None:
-                resp = self._secondary.download_files([path])[0]
-            responses.append(resp)
-        return responses
-
-    async def adownload_files(self, paths: list[str]) -> list[FileDownloadResponse]:
-        return self.download_files(paths)
-
-    def upload_files(self, files: list[tuple[str, bytes]]) -> list[FileUploadResponse]:
-        return [
-            FileUploadResponse(path=path, error="permission_denied")
-            for path, _ in files
-        ]
-
-    async def aupload_files(self, files: list[tuple[str, bytes]]) -> list[FileUploadResponse]:
-        return self.upload_files(files)
-
 
 class CustomSandboxBackend(FilesystemBackend, SandboxBackendProtocol):
     """