refactor: adopt toolregistry-server 0.4.0 App/ServerIdentity pattern

AGENTS.md

@@ -16,7 +16,7 @@ which provide:
   Code, and any MCP-compatible client.
 - **OpenAPI / REST** (optional extra) for curl, OpenAI Assistants,
   Anthropic Messages API, Gemini, LangChain, plain scripts.
-- **Python API** — `from uxarray_mcp.server import make_registry`.
+- **Python API** — `from uxarray_mcp.app import make_registry`.
 
 It supports local execution and optional remote execution on HPC clusters via
 [Globus Compute](https://globus-compute.readthedocs.io/).

docs/api.rst

@@ -86,6 +86,6 @@ State
 Server
 ------
 
-.. automodule:: uxarray_mcp.server
+.. automodule:: uxarray_mcp.app
    :members:
    :undoc-members:

docs/getting-started.md

@@ -161,7 +161,7 @@ Edit the config:
         "run",
         "python",
         "-m",
-        "uxarray_mcp.server"
+        "uxarray_mcp"
       ]
     }
   }

pyproject.toml

@@ -25,7 +25,7 @@ license = { file = "LICENSE" }
 # support and broaden requires-python back to >=3.11.
 requires-python = ">=3.12,<3.13"
 dependencies = [
-    "toolregistry-server[mcp]>=0.3.3",
+    "toolregistry-server[mcp]>=0.4.0",
     "holoviews>=1.19.0",
     "matplotlib>=3.9.0",
     "pyyaml>=6.0",
@@ -34,7 +34,7 @@ dependencies = [
 
 [project.optional-dependencies]
 openapi = [
-    "toolregistry-server[openapi]>=0.3.3",
+    "toolregistry-server[openapi]>=0.4.0",
 ]
 hpc = [
     "academy-py>=0.3.1",

src/uxarray_mcp/__init__.py

@@ -1,7 +1,6 @@
 """UXarray MCP Server - AI tools for unstructured mesh analysis."""
 
-from uxarray_mcp.server import make_mcp_server, make_registry
 from uxarray_mcp.tools import inspect_mesh
 
-__all__ = ["make_mcp_server", "make_registry", "inspect_mesh"]
+__all__ = ["inspect_mesh"]
 __version__ = "0.2.0"

src/uxarray_mcp/app.py

@@ -0,0 +1,77 @@
+"""UXarray application — subclass of toolregistry_server.App.
+
+Provides :class:`UXarrayApp`, the central server application that builds
+the UXarray tool registry and dispatches to protocol adapters (MCP, OpenAPI).
+
+Identity (product name, version, description) flows automatically to
+MCP server name, OpenAPI title, and CLI banner.
+
+Example::
+
+    from uxarray_mcp.app import UXarrayApp
+
+    app = UXarrayApp()
+    app.serve_mcp(transport="stdio", profile="core")
+"""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from toolregistry_server import ServerIdentity
+from toolregistry_server.app import App
+
+from . import __version__
+from .registry import Profile
+
+if TYPE_CHECKING:
+    from toolregistry import ToolRegistry
+
+UXARRAY_IDENTITY = ServerIdentity(
+    name="UXarray MCP",
+    version=__version__,
+    description="Mesh analysis tools for AI agents",
+)
+
+
+class UXarrayApp(App):
+    """UXarray-specific server application.
+
+    Overrides :meth:`prepare_registry` to build the UXarray tool
+    registry with profile-based tool surface selection.
+    """
+
+    def __init__(self, identity: ServerIdentity | None = None) -> None:
+        super().__init__(identity=identity or UXARRAY_IDENTITY)
+
+    def prepare_registry(self, **kwargs) -> ToolRegistry:
+        """Build the UXarray tool registry.
+
+        Keyword Args:
+            profile: Tool surface profile (``"core"`` or
+                ``"deferred-full"``). Defaults to ``"core"``.
+        """
+        from .registry import build_registry
+
+        profile = kwargs.get("profile", "core")
+        return build_registry(profile=profile)
+
+
+# ---------------------------------------------------------------------------
+# Convenience helpers for tests and scripts
+# ---------------------------------------------------------------------------
+
+
+def make_registry(*, profile: Profile = "core") -> ToolRegistry:
+    """Build the tool registry for the requested profile."""
+    return UXarrayApp().prepare_registry(profile=profile)
+
+
+def make_mcp_server(*, profile: Profile = "core"):
+    """Build a configured MCP server ready for any transport."""
+    from toolregistry_server.adapters.mcp import route_table_to_mcp_server
+    from toolregistry_server.route_table import RouteTable
+
+    registry = make_registry(profile=profile)
+    route_table = RouteTable(registry)
+    return route_table_to_mcp_server(route_table, name="UXarray MCP")

src/uxarray_mcp/cli.py

@@ -65,13 +65,29 @@ def _ensure_hpc_block(data: dict[str, Any]) -> dict[str, Any]:
 
 def cmd_serve(args: argparse.Namespace) -> int:
     """Run the MCP server."""
-    from uxarray_mcp.server import run
+    from uxarray_mcp.app import UXarrayApp
 
-    run(
-        profile=getattr(args, "profile", "core"),
-        transport=getattr(args, "transport", "stdio"),
+    app = UXarrayApp()
+    transport = getattr(args, "transport", "stdio")
+    mcp_transport = "streamable-http" if transport == "http" else transport
+    app.serve_mcp(
+        transport=mcp_transport,
         host=getattr(args, "host", "127.0.0.1"),
         port=getattr(args, "port", 8001),
+        profile=getattr(args, "profile", "core"),
+    )
+    return 0
+
+
+def cmd_openapi(args: argparse.Namespace) -> int:
+    """Run the OpenAPI/REST server."""
+    from uxarray_mcp.app import UXarrayApp
+
+    app = UXarrayApp()
+    app.serve_openapi(
+        host=getattr(args, "host", "0.0.0.0"),
+        port=getattr(args, "port", 8000),
+        profile=getattr(args, "profile", "core"),
     )
     return 0
 
@@ -285,6 +301,7 @@ def build_parser() -> argparse.ArgumentParser:
     )
     sub = p.add_subparsers(dest="command", required=True)
 
+    # --- serve (MCP) ---
     serve = sub.add_parser("serve", help="Run the MCP server.")
     serve.add_argument(
         "--profile",
@@ -306,6 +323,24 @@ def build_parser() -> argparse.ArgumentParser:
     serve.add_argument("--port", type=int, default=8001, help="Port for SSE/HTTP.")
     serve.set_defaults(func=cmd_serve)
 
+    # --- openapi ---
+    openapi = sub.add_parser("openapi", help="Run the OpenAPI/REST server.")
+    openapi.add_argument(
+        "--profile",
+        choices=("core", "deferred-full"),
+        default="core",
+        help=(
+            "core: gateway + control + list_datasets + prompts (~27 tools). "
+            "deferred-full: also load 30 raw tools as deferred, gated "
+            "behind discover_tools / admin promotion."
+        ),
+    )
+    openapi.add_argument(
+        "--host", default="0.0.0.0", help="Bind host (default: 0.0.0.0)."
+    )
+    openapi.add_argument("--port", type=int, default=8000, help="Port (default: 8000).")
+    openapi.set_defaults(func=cmd_openapi)
+
     setup = sub.add_parser("setup", help="Write a starter user config.")
     setup.add_argument("--path", default=None, help="Override target path.")
     setup.add_argument(

tests/test_server.py

@@ -2,7 +2,7 @@
 
 These tests replace the previous FastMCP-based assertions. They
 exercise ``uxarray_mcp.registry.build_registry`` and
-``uxarray_mcp.server.make_registry`` to confirm the tool surface
+``uxarray_mcp.app.make_registry`` to confirm the tool surface
 matches the agreed design spec.
 """
 
@@ -13,6 +13,7 @@
 
 import pytest
 
+from uxarray_mcp.app import make_mcp_server, make_registry
 from uxarray_mcp.registry import (
     _CONTROL_TOOLS,
     _CORE_EXTRA_TOOLS,
@@ -21,7 +22,6 @@
     FRONTDOOR_NAMES,
     build_registry,
 )
-from uxarray_mcp.server import make_mcp_server, make_registry
 
 EXPECTED_FRONTDOOR = 11
 EXPECTED_CONTROL = 12  # 8 session + 4 hpc
@@ -298,4 +298,4 @@ def test_live_call_through_registry():
 async def test_mcp_server_constructs():
     """make_mcp_server() returns a working MCP Server object."""
     server = make_mcp_server(profile="core")
-    assert server.name == "uxarray-mcp-server"
+    assert server.name == "UXarray MCP"

tests/test_vector_calc.py

@@ -330,7 +330,7 @@ def test_accepts_use_remote_endpoint_session_params(self):
 
 def test_vector_calc_operations_available_through_run_analysis():
     """run_analysis must advertise vector calc operations in its description."""
-    from uxarray_mcp.server import make_registry
+    from uxarray_mcp.app import make_registry
 
     registry = make_registry(profile="core")
     tool = registry.get_tool("run_analysis")
@@ -343,7 +343,7 @@ def test_vector_calc_operations_available_through_run_analysis():
 
 def test_prompts_registered_as_tools():
     """Former @mcp.prompt() decorators are now prompt/ namespace tools."""
-    from uxarray_mcp.server import make_registry
+    from uxarray_mcp.app import make_registry
 
     registry = make_registry(profile="core")
     tools = registry.list_tools()