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task: Changes required for FastMCP v3.x#425

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neelay-aign wants to merge 1 commit intomain from
task/changes-for-fastmcp-3
Open

task: Changes required for FastMCP v3.x #425
neelay-aign wants to merge 1 commit intomain from
task/changes-for-fastmcp-3

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@neelay-aign neelay-aign commented Feb 10, 2026

Merge when FastMCP releases a v3.x to PyPI and we switch to that in the pyproject.toml

Copilot AI review requested due to automatic review settings February 10, 2026 20:34 
Error: This repo is not allowlisted for Atlantis.

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Pull request overview

Prepare the MCP integration code for FastMCP v3.x API changes (mount namespacing and async tool listing) ahead of switching the dependency in pyproject.toml.

Changes:

  • Update mcp.mount(..., prefix=...) to mcp.mount(..., namespace=...).
  • Replace get_tools() (dict) with list_tools() (list) and adjust tool formatting output.
  • Update docstrings/comments to reflect the new FastMCP API terminology.

seen_names.add(server.name)
logger.info(f"Mounting MCP server: {server.name}")
mcp.mount(server, prefix=server.name)
mcp.mount(server, namespace=server.name)
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namespace on mount() and list_tools() are FastMCP v3.x API calls; if this PR lands before the dependency is bumped to v3.x, this will raise at runtime (unexpected keyword argument / missing attribute). To make this change safe (and keep CI green) until pyproject.toml is updated, consider supporting both APIs via capability detection (e.g., try namespace then fallback to prefix, and try list_tools() then fallback to get_tools()).

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# lazily initialize resources. We use asyncio.run() to bridge sync/async.
tools = asyncio.run(server.get_tools())
return [{"name": name, "description": tool.description or ""} for name, tool in tools.items()]
tools = asyncio.run(server.list_tools())
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namespace on mount() and list_tools() are FastMCP v3.x API calls; if this PR lands before the dependency is bumped to v3.x, this will raise at runtime (unexpected keyword argument / missing attribute). To make this change safe (and keep CI green) until pyproject.toml is updated, consider supporting both APIs via capability detection (e.g., try namespace then fallback to prefix, and try list_tools() then fallback to get_tools()).

Copilot uses AI. Check for mistakes.
tools = asyncio.run(server.get_tools())
return [{"name": name, "description": tool.description or ""} for name, tool in tools.items()]
tools = asyncio.run(server.list_tools())
return [{"name": tool.name, "description": tool.description or ""} for tool in tools]
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list_tools() returning a list can make output ordering depend on server/tool registration order, which may be non-deterministic across environments and can cause flaky CLI output/tests. Consider sorting the returned tools by tool.name before formatting the list so mcp_list_tools() has stable output.

Suggested change
return [{"name": tool.name, "description": tool.descriptionor""} fortoolintools]
# Sort tools by name to ensure deterministic output order across environments
sorted_tools = sorted(tools, key=lambda tool: tool.name)
return [{"name": tool.name, "description": tool.description or ""} for tool in sorted_tools]

Copilot uses AI. Check for mistakes.
Comment on lines +120 to +121
tools = asyncio.run(server.list_tools())
return [{"name": tool.name, "description": tool.description or ""} for tool in tools]
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Bug: Tests in mcp_test.py use the outdated FastMCP v2 API (get_tools()), while production code uses the new v3 API (list_tools()), guaranteeing future test failures.
Severity: CRITICAL

Suggested Fix

Update the test file tests/aignostics/utils/mcp_test.py to use the new FastMCP v3.x API. Replace calls to server.get_tools() with server.list_tools(). Update the test logic to handle a list of Tool objects instead of a dictionary, accessing tool names via the tool.name attribute.

Prompt for AI Agent 
Review the code at the location below. A potential bug has been identified by an AI
agent.
Verify if this is a real issue. If it is, propose a fix; if not, explain why it's not
valid.
Location: src/aignostics/utils/_mcp.py#L120-L121
Potential issue: The production code was updated to use the FastMCP v3.x API,
specifically changing from `server.get_tools()` to `server.list_tools()`. However, the
corresponding test file, `tests/aignostics/utils/mcp_test.py`, was not updated. It still
calls the old `get_tools()` method and expects a dictionary, while the new
`list_tools()` method returns a list of `Tool` objects. When the FastMCP dependency is
updated to v3.x as intended for this pull request, the tests will fail with an
`AttributeError`, blocking deployment.

Did we get this right? 👍 / 👎 to inform future reviews.

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codecov bot commented Feb 10, 2026

❌ 6 Tests Failed:

Tests completed Failed Passed Skipped
512 6 506 3
View the full list of 6 ❄️ flaky test(s) 
tests.aignostics.cli_test::test_cli_mcp_list_tools

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.036s run time 
runner = <typer.testing.CliRunner object at 0x7f89821ac710>
record_property = <function record_property.<locals>.append_property at 0x7f89821a3c10>
 @pytest.mark.unit
 def test_cli_mcp_list_tools(runner: CliRunner, record_property) -> None:
 """Test list-tools command displays discovered tools."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 test_server = FastMCP("test")
 
 @test_server.tool
 def test_tool() -> str:
 """A test tool."""
 return "test"
 
 with patch(PATCH_MCP_LOCATE_IMPLEMENTATIONS, return_value=[test_server]):
 result = runner.invoke(cli, ["mcp", "list-tools"])
> assert result.exit_code == 0
E assert 1 == 0
E + where 1 = <Result TypeError("FastMCP.mount() got an unexpected keyword argument 'namespace'")>.exit_code
tests/aignostics/cli_test.py:321: AssertionError
tests.aignostics.cli_test::test_cli_mcp_list_tools_empty

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.025s run time 
runner = <typer.testing.CliRunner object at 0x7f89820057b0>
record_property = <function record_property.<locals>.append_property at 0x7f8982059220>
 @pytest.mark.unit
 def test_cli_mcp_list_tools_empty(runner: CliRunner, record_property) -> None:
 """Test list-tools command with no tools."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 with patch(PATCH_MCP_LOCATE_IMPLEMENTATIONS, return_value=[]):
 result = runner.invoke(cli, ["mcp", "list-tools"])
> assert result.exit_code == 0
E assert 1 == 0
E + where 1 = <Result AttributeError("'FastMCP' object has no attribute 'list_tools'")>.exit_code
tests/aignostics/cli_test.py:332: AssertionError
tests.aignostics.utils.mcp_test::test_mcp_create_server_mounts_discovered

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.019s run time 
record_property = <function record_property.<locals>.append_property at 0x7f9763a15e80>
 @pytest.mark.unit
 def test_mcp_create_server_mounts_discovered(record_property) -> None:
 """Test that mcp_create_server mounts discovered servers with their tools."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 plugin1 = FastMCP("plugin1")
 plugin2 = FastMCP("plugin2")
 
 @plugin1.tool
 def plugin1_tool() -> str:
 """Plugin 1 tool."""
 return "p1"
 
 @plugin2.tool
 def plugin2_tool() -> str:
 """Plugin 2 tool."""
 return "p2"
 
 with patch(PATCH_LOCATE_IMPLEMENTATIONS, return_value=[plugin1, plugin2]):
> server = mcp_create_server()
 ^^^^^^^^^^^^^^^^^^^
.../aignostics/utils/mcp_test.py:91: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
server_name = 'Central Aignostics MCP Server'
 def mcp_create_server(server_name: str = MCP_SERVER_NAME) -> FastMCP:
 """Create and configure the MCP server with all discovered plugins mounted.
 
 Creates a new FastMCP server instance and mounts all discovered MCP servers
 from the SDK and plugins. Each mounted server's tools are namespaced
 automatically using FastMCP's built-in namespace feature.
 
 Args:
 server_name: Human-readable name for the MCP server.
 
 Returns:
 FastMCP: Configured MCP server ready to run.
 """
 mcp = FastMCP(name=server_name, version=__version__)
 
 # Mount discovered servers
 servers = mcp_discover_servers()
 seen_names: set[str] = set()
 count = 0
 
 for server in servers:
 if server is not mcp: # Don't mount self
 if server.name in seen_names:
 logger.warning(f"Duplicate MCP server name '{server.name}' - skipping to avoid tool collision")
 continue
 seen_names.add(server.name)
 logger.info(f"Mounting MCP server: {server.name}")
> mcp.mount(server, namespace=server.name)
E TypeError: FastMCP.mount() got an unexpected keyword argument 'namespace'
.../aignostics/utils/_mcp.py:79: TypeError
tests.aignostics.utils.mcp_test::test_mcp_create_server_skips_duplicate_names

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.023s run time 
caplog = <_pytest.logging.LogCaptureFixture object at 0x7f9763a87d20>
record_property = <function record_property.<locals>.append_property at 0x7f9763a7b110>
 @pytest.mark.unit
 def test_mcp_create_server_skips_duplicate_names(caplog: pytest.LogCaptureFixture, record_property) -> None:
 """Test that servers with duplicate names are skipped with warning."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 dup1 = FastMCP("duplicate_name")
 dup2 = FastMCP("duplicate_name")
 unique = FastMCP("unique_name")
 
 @dup1.tool
 def dup1_tool() -> str:
 """Dup1 tool."""
 return "dup1"
 
 @dup2.tool
 def dup2_tool() -> str:
 """Dup2 tool - should NOT be mounted."""
 return "dup2"
 
 @unique.tool
 def unique_tool() -> str:
 """Unique tool."""
 return "unique"
 
 with patch(PATCH_LOCATE_IMPLEMENTATIONS, return_value=[dup1, dup2, unique]):
> server = mcp_create_server()
 ^^^^^^^^^^^^^^^^^^^
.../aignostics/utils/mcp_test.py:131: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
server_name = 'Central Aignostics MCP Server'
 def mcp_create_server(server_name: str = MCP_SERVER_NAME) -> FastMCP:
 """Create and configure the MCP server with all discovered plugins mounted.
 
 Creates a new FastMCP server instance and mounts all discovered MCP servers
 from the SDK and plugins. Each mounted server's tools are namespaced
 automatically using FastMCP's built-in namespace feature.
 
 Args:
 server_name: Human-readable name for the MCP server.
 
 Returns:
 FastMCP: Configured MCP server ready to run.
 """
 mcp = FastMCP(name=server_name, version=__version__)
 
 # Mount discovered servers
 servers = mcp_discover_servers()
 seen_names: set[str] = set()
 count = 0
 
 for server in servers:
 if server is not mcp: # Don't mount self
 if server.name in seen_names:
 logger.warning(f"Duplicate MCP server name '{server.name}' - skipping to avoid tool collision")
 continue
 seen_names.add(server.name)
 logger.info(f"Mounting MCP server: {server.name}")
> mcp.mount(server, namespace=server.name)
E TypeError: FastMCP.mount() got an unexpected keyword argument 'namespace'
.../aignostics/utils/_mcp.py:79: TypeError
tests.aignostics.utils.mcp_test::test_mcp_list_tools_empty

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.009s run time 
record_property = <function record_property.<locals>.append_property at 0x7f9763ac5d20>
 @pytest.mark.unit
 def test_mcp_list_tools_empty(record_property) -> None:
 """Test mcp_list_tools with no discovered tools."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 with patch(PATCH_LOCATE_IMPLEMENTATIONS, return_value=[]):
> tools = mcp_list_tools()
 ^^^^^^^^^^^^^^^^
.../aignostics/utils/mcp_test.py:175: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
server_name = 'Central Aignostics MCP Server'
 def mcp_list_tools(server_name: str = MCP_SERVER_NAME) -> list[dict[str, Any]]:
 """List all available MCP tools.
 
 Creates the server and returns information about all registered tools
 including those from mounted servers.
 
 Note:
 This function must be called from a synchronous context. Calling it
 from within an async function will raise RuntimeError.
 
 Args:
 server_name: Human-readable name for the MCP server.
 
 Returns:
 list[dict[str, Any]]: List of tool information dictionaries with
 'name' and 'description' keys.
 """
 server = mcp_create_server(server_name)
 # FastMCP's list_tools() is async because mounted servers may need to
 # lazily initialize resources. We use asyncio.run() to bridge sync/async.
> tools = asyncio.run(server.list_tools())
 ^^^^^^^^^^^^^^^^^
E AttributeError: 'FastMCP' object has no attribute 'list_tools'. Did you mean: 'get_tools'?
.../aignostics/utils/_mcp.py:120: AttributeError
tests.aignostics.utils.mcp_test::test_mcp_list_tools_returns_tool_info

Flake rate in main: 100.00% (Passed 0 times, Failed 1 times)

Stack Traces | 0.014s run time 
record_property = <function record_property.<locals>.append_property at 0x7f9763aa64b0>
 @pytest.mark.unit
 def test_mcp_list_tools_returns_tool_info(record_property) -> None:
 """Test that mcp_list_tools returns correct tool information."""
 record_property("tested-item-id", "SPEC-UTILS-SERVICE")
 test_server = FastMCP("test")
 
 @test_server.tool
 def test_tool(param: str) -> str:
 """A test tool."""
 return param
 
 with patch(PATCH_LOCATE_IMPLEMENTATIONS, return_value=[test_server]):
> tools = mcp_list_tools()
 ^^^^^^^^^^^^^^^^
.../aignostics/utils/mcp_test.py:164: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../aignostics/utils/_mcp.py:117: in mcp_list_tools
 server = mcp_create_server(server_name)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
server_name = 'Central Aignostics MCP Server'
 def mcp_create_server(server_name: str = MCP_SERVER_NAME) -> FastMCP:
 """Create and configure the MCP server with all discovered plugins mounted.
 
 Creates a new FastMCP server instance and mounts all discovered MCP servers
 from the SDK and plugins. Each mounted server's tools are namespaced
 automatically using FastMCP's built-in namespace feature.
 
 Args:
 server_name: Human-readable name for the MCP server.
 
 Returns:
 FastMCP: Configured MCP server ready to run.
 """
 mcp = FastMCP(name=server_name, version=__version__)
 
 # Mount discovered servers
 servers = mcp_discover_servers()
 seen_names: set[str] = set()
 count = 0
 
 for server in servers:
 if server is not mcp: # Don't mount self
 if server.name in seen_names:
 logger.warning(f"Duplicate MCP server name '{server.name}' - skipping to avoid tool collision")
 continue
 seen_names.add(server.name)
 logger.info(f"Mounting MCP server: {server.name}")
> mcp.mount(server, namespace=server.name)
E TypeError: FastMCP.mount() got an unexpected keyword argument 'namespace'
.../aignostics/utils/_mcp.py:79: TypeError

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