Made tool selection configurable

More things:
- list tools using .subclasses instead of inspect
- entrypoint for listing tools
- util for listing selected tools
- documentation

README.md

@@ -74,7 +74,7 @@ We thus built Serena with the prospect of being able to cancel most other subscr
     "mcpServers": {
         "serena": {
             "command": "/abs/path/to/uv",
-            "args": ["run", "--directory", "/abs/path/to/serena", "serena", "/abs/path/to/myproject.yml"]
+            "args": ["run", "--directory", "/abs/path/to/serena", "serena-mcp-server", "/abs/path/to/myproject.yml"]
         }
     }
 }

myproject.demo.yml

@@ -4,7 +4,50 @@ project_root: /path/to/project
 language: python
 # list of directories to ignore: either names (e.g. "temp") or relative paths (e.g. "build/foo")
 ignored_dirs: [".git", "temp"]
-# whether to open a graphical window with Serena's logs (not supported on MacOS)
+
+# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions, 
+# execute `uv run serena-list-tools`.
+#
+# check_onboarding_performed
+# create_text_file
+# delete_lines
+# delete_memory
+# execute_shell_command
+# find_referencing_symbols
+# find_symbol
+# get_dir_overview
+# get_document_overview
+# insert_after_symbol
+# insert_at_line
+# insert_before_symbol
+# list_dir
+# list_memories
+# onboarding
+# prepare_for_new_conversation
+# read_file
+# read_memory
+# replace_symbol_body
+# search_in_all_code
+# summarize_changes
+# think_about_collected_information
+# think_about_task_adherence
+# think_about_whether_you_are_done
+# write_memory
+excluded_tools: []
+
+
+
+# Whether to open a graphical window with Serena's logs (not supported on MacOS).
+# This is useful both for troubleshooting and for monitoring the tool calls,
+# especially when using the agno playground, since the tool calls are not always shown,
+# and the input params are never shown in the agno UI.
+# When used as MCP server for Claude Desktop, the logs are primarily for troubleshooting.
+# Note: unfortunately, the various entities starting the Serena server or agent do so in
+# mysterious ways, often starting multiple instances of the process without shutting down
+# previous instances. This leads to multiple log windows being opened, and only the last
+# window being updated. Since we can't control how agno or Claude Desktop starts Serena, we have to live with this limitation for now.
 gui_log_window: True
 # minimum log level for the GUI log window (10 = debug, 20 = info, 30 = warning, 40 = error)
 gui_log_level: 20

pyproject.toml

@@ -33,7 +33,8 @@ dependencies = [
 ]
 
 [project.scripts]
-serena = "serena.mcp:start_mcp_server"
+serena-mcp-server = "serena.mcp:start_mcp_server"
+serena-list-tools = "serena.agent:print_tool_overview"
 
 [project.license]
 text = "MIT"

scripts/agno_agent.py

@@ -1,19 +1,13 @@
 import os
 from logging import Logger
 
-from agno.agent.agent import Agent
-from agno.memory.agent import AgentMemory
 from agno.models.anthropic.claude import Claude
 from agno.models.google.gemini import Gemini
-from agno.playground.playground import Playground
-from agno.playground.serve import serve_playground_app
-from agno.storage.agent.sqlite import SqliteAgentStorage
 from dotenv import load_dotenv
 from sensai.util import logging
 from sensai.util.helper import mark_used
 
 from serena.agent import SerenaAgent
-from serena.agno import SerenaAgnoToolkit
 
 mark_used(Gemini, Claude)
 
@@ -36,27 +30,30 @@ os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
 if os.path.exists(sql_db_path):
     os.remove(sql_db_path)
 
-model = Claude(id="claude-3-7-sonnet-20250219")
-# model = Gemini(id="gemini-2.5-pro-exp-03-25")
+for tool_name in serena_agent.list_tool_names():
+    print(tool_name)
 
-agno_agent = Agent(
-    name="Serena",
-    model=model,
-    storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
-    description="A fully-featured coding assistant",
-    tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
-    show_tool_calls=False,
-    markdown=True,
-    system_message=serena_agent.prompt_factory.create_system_prompt(),
-    read_tool_call_history=False,
-    telemetry=False,
-    memory=AgentMemory(),
-    add_history_to_messages=True,
-    num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
-)
+# model = Claude(id="claude-3-7-sonnet-20250219")
+# # model = Gemini(id="gemini-2.5-pro-exp-03-25")
 
-# The app object must be in the module scope so that the server can access it for hot reloading
-app = Playground(agents=[agno_agent]).get_app()
+# agno_agent = Agent(
+#     name="Serena",
+#     model=model,
+#     storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
+#     description="A fully-featured coding assistant",
+#     tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
+#     show_tool_calls=False,
+#     markdown=True,
+#     system_message=serena_agent.prompt_factory.create_system_prompt(),
+#     read_tool_call_history=False,
+#     telemetry=False,
+#     memory=AgentMemory(),
+#     add_history_to_messages=True,
+#     num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
+# )
 
-if __name__ == "__main__":
-    serve_playground_app("agno_agent:app", reload=False)
+# # The app object must be in the module scope so that the server can access it for hot reloading
+# app = Playground(agents=[agno_agent]).get_app()
+
+# if __name__ == "__main__":
+#     serve_playground_app("agno_agent:app", reload=False)

scripts/list_tools.py

@@ -1,10 +0,0 @@
-from serena.agent import SerenaAgent
-
-if __name__ == "__main__":
-    agent = SerenaAgent("myproject.yml")
-    tools = {}
-    for tool in agent.tools.values():
-        tools[tool.get_name()] = tool
-    for tool_name in sorted(tools.keys()):
-        tool = tools[tool_name]
-        print(f" * `{tool_name}`: {tool.get_tool_description().strip()}")

src/serena/agent.py

@@ -11,7 +11,7 @@ import traceback
 import warnings
 from abc import ABC
 from collections import defaultdict
-from collections.abc import Callable, Iterator
+from collections.abc import Callable, Generator, Iterable, Iterator
 from contextlib import contextmanager
 from logging import Logger
 from pathlib import Path
@@ -29,6 +29,7 @@ from serena.gui_log_viewer import GuiLogViewer, GuiLogViewerHandler
 from serena.llm.prompt_factory import PromptFactory
 from serena.symbol import SymbolLocation, SymbolManager
 from serena.util.file_system import scan_directory
+from serena.util.inspection import iter_subclasses
 from serena.util.shell import execute_shell_command
 
 log = logging.getLogger(__name__)
@@ -87,11 +88,12 @@ class SerenaAgent:
         self.memories_manager = MemoriesManager(memories_dir)
 
         # find all tool classes and instantiate them
+        excluded_tools = project_config.get("excluded_tools", [])
         self.tools: dict[type[Tool], Tool] = {}
-        tool_classes = [
-            cls for name, cls in inspect.getmembers(sys.modules[__name__], inspect.isclass) if issubclass(cls, Tool) and cls is not Tool
-        ]
-        for tool_class in tool_classes:
+        for tool_class in iter_tool_classes():
+            if (tool_name := tool_class.get_name()) in excluded_tools:
+                log.info(f"Skipping tool {tool_name} because it is in the exclude list")
+                continue
             tool_instance = tool_class(self)
             self.tools[tool_class] = tool_instance
         log.info(f"Loaded tools: {', '.join([tool.get_name() for tool in self.tools.values()])}")
@@ -101,11 +103,12 @@ class SerenaAgent:
             log.info("Starting the language server ...")
             self.language_server.start()
 
-        self._is_initialized = True
-
     def get_tool(self, tool_class: type[TTool]) -> TTool:
         return self.tools[tool_class]  # type: ignore
 
+    def print_tool_overview(self) -> None:
+        _print_tool_overview(self.tools.values())
+
     def get_serena_managed_dir(self) -> str:
         return os.path.join(self.project_root, ".serena")
 
@@ -195,8 +198,9 @@ class Tool(Component):
             raise Exception(f"{self} does not define method apply")
         return apply_fn
 
-    def get_tool_description(self) -> str:
-        docstring = self.__class__.__doc__
+    @classmethod
+    def get_tool_description(cls) -> str:
+        docstring = cls.__doc__
         if docstring is None:
             return ""
         return docstring.strip()
@@ -878,3 +882,20 @@ class ExecuteShellCommandTool(Tool):
         result = execute_shell_command(command, cwd=_cwd, capture_stderr=capture_stderr)
         result = result.json()
         return self._limit_length(result, max_answer_chars)
+
+
+def iter_tool_classes() -> Generator[type[Tool], None, None]:
+    return iter_subclasses(Tool)
+
+
+def print_tool_overview() -> None:
+    _print_tool_overview(iter_tool_classes())
+
+
+def _print_tool_overview(tools: Iterable[type[Tool] | Tool]) -> None:
+    tool_dict: dict[str, type[Tool] | Tool] = {}
+    for tool in tools:
+        tool_dict[tool.get_name()] = tool
+    for tool_name in sorted(tool_dict.keys()):
+        tool = tool_dict[tool_name]
+        print(f" * `{tool_name}`: {tool.get_tool_description().strip()}")

src/serena/util/inspection.py

@@ -0,0 +1,12 @@
+from collections.abc import Generator
+from typing import TypeVar
+
+T = TypeVar("T")
+
+
+def iter_subclasses(cls: type[T], recursive: bool = True) -> Generator[type[T], None, None]:
+    """Iterate over all subclasses of a class. If recursive is True, also iterate over all subclasses of all subclasses."""
+    for subclass in cls.__subclasses__():
+        yield subclass
+        if recursive:
+            yield from iter_subclasses(subclass, recursive)