python3Packages.mcp: 1.9.4 -> 1.12.2, and fix dependent packages build failures (#428733)

pkgs/by-name/mc/mcp-proxy/package.nix

···
     pytest-asyncio
   ];
 
+  disabledTests = [
+    # AssertionError: expected call not found.
+    # Expected: mock(PromptReference(type='ref/prompt', name='name'), CompletionArgument(name='name', value='value'))
+    #   Actual: mock(PromptReference(type='ref/prompt', name='name'), CompletionArgument(name='name', value='value'), None)
+    "test_call_tool[server-AsyncMock]"
+    "test_call_tool[proxy-AsyncMock]"
+    "test_complete[server-AsyncMock]"
+    "test_complete[proxy-AsyncMock]"
+  ];
+
+  __darwinAllowLocalNetworking = true;
+
   meta = {
     description = "MCP server which proxies other MCP servers from stdio to SSE or from SSE to stdio";
     homepage = "https://github.com/sparfenyuk/mcp-proxy";

pkgs/by-name/ot/oterm/package.nix

···
     "pydantic"
     "textual"
     "typer"
+    "fastmcp"
   ];
 
   build-system = with python3Packages; [ hatchling ];

pkgs/development/python-modules/fastapi-mcp/default.nix

···
 
 buildPythonPackage rec {
   pname = "fastapi-mcp";
-  version = "0.3.4";
+  version = "0.3.7";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "tadata-org";
     repo = "fastapi_mcp";
     tag = "v${version}";
-    hash = "sha256-t6p/jXQjbhUmIlwoqszRj3GGSrLS0Gcoh1BtizNaw8o=";
+    hash = "sha256-WQ+Y/TM5fz0lHjCKvEuYGY6hzxo2ePcgRnq7piNC+KQ=";
   };
 
   build-system = [
···
     pytest-asyncio
     pytest-cov-stub
     pytestCheckHook
+  ];
+
+  disabledTestPaths = [
+    # Flaky, would try to allocate a port on Darwin
+    "tests/test_sse_real_transport.py"
   ];
 
   __darwinAllowLocalNetworking = true;

pkgs/development/python-modules/fastmcp/default.nix

···
 
   # dependencies
   authlib,
+  cyclopts,
   exceptiongroup,
   httpx,
   mcp,
   openapi-pydantic,
+  pydantic,
+  pyperclip,
   python-dotenv,
   rich,
-  typer,
 
   # tests
   dirty-equals,
+  email-validator,
   fastapi,
+  pytest-asyncio,
   pytest-httpx,
   pytestCheckHook,
 }:
 
 buildPythonPackage rec {
   pname = "fastmcp";
-  version = "2.8.0";
+  version = "2.10.6";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "jlowin";
     repo = "fastmcp";
     tag = "v${version}";
-    hash = "sha256-FleJkqdUIhGsV+DVYv/Nf5IORntH/aFq9abKn2r/6Is=";
+    hash = "sha256-Wxugk2ocuur710WZLG7xph2R/n02Y9BvH7Lf4BuEMYs=";
   };
 
   postPatch = ''
···
 
   dependencies = [
     authlib
+    cyclopts
     exceptiongroup
     httpx
     mcp
     openapi-pydantic
+    pyperclip
     python-dotenv
     rich
-    typer
   ];
 
   pythonImportsCheck = [ "fastmcp" ];
 
   nativeCheckInputs = [
     dirty-equals
+    email-validator
     fastapi
+    pydantic
+    pytest-asyncio
     pytest-httpx
     pytestCheckHook
     writableTmpDirAsHomeHook
-  ];
+  ]
+  ++ pydantic.optional-dependencies.email;
 
   disabledTests = [
     # AssertionError: assert 'INFO' == 'DEBUG'
     "test_temporary_settings"
+
+    # RuntimeError: Client failed to connect: Connection close
+    "test_keep_alive_maintains_session_across_multiple_calls"
+    "test_keep_alive_false_starts_new_session_across_multiple_calls"
+    "test_keep_alive_starts_new_session_if_manually_closed"
+    "test_keep_alive_maintains_session_if_reentered"
+    "test_close_session_and_try_to_use_client_raises_error"
+
+    # RuntimeError: Client failed to connect: Timed out while waiting for response
+    "test_timeout"
+    "test_timeout_tool_call_overrides_client_timeout_even_if_lower"
+
+    # assert 0 == 2
+    "test_multi_client"
+
+    # fastmcp.exceptions.ToolError: Unknown tool
+    "test_multi_client_with_logging"
+    "test_multi_client_with_elicitation"
   ];
 
   disabledTestPaths = lib.optionals stdenv.hostPlatform.isDarwin [

pkgs/development/python-modules/gradio/default.nix

···
 
 buildPythonPackage rec {
   pname = "gradio";
-  version = "5.38.0";
+  version = "5.38.2";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "gradio-app";
     repo = "gradio";
     tag = "gradio@${version}";
-    hash = "sha256-NbVRbwqHUSwyG+v+cDKCrVtzjj6ThxGRfO+xjqXOy5I=";
+    hash = "sha256-zKAH/tbF1S+LIi1i+BuKBUWDSI0+Ii5FhsZ3sQaFtto=";
   };
 
   pnpmDeps = pnpm_9.fetchDeps {
     inherit pname version src;
     fetcherVersion = 1;
-    hash = "sha256-E6dBajJoKzaJF67KRrSB/LNAyLDmT78mCmTar5G6P6g=";
+    hash = "sha256-sIEsolHffX3cpAJU79w+ndRY4vvmWLxp2efTryv+j38=";
   };
 
   pythonRelaxDeps = [

pkgs/development/python-modules/mcp/default.nix

···
   anyio,
   httpx,
   httpx-sse,
+  jsonschema,
   pydantic,
   pydantic-settings,
   python-multipart,
···
   websockets,
 
   # tests
+  dirty-equals,
   inline-snapshot,
   pytest-asyncio,
   pytest-examples,
···
 
 buildPythonPackage rec {
   pname = "mcp";
-  version = "1.9.4";
+  version = "1.12.2";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "modelcontextprotocol";
     repo = "python-sdk";
     tag = "v${version}";
-    hash = "sha256-VXbu/wHbXGS+cISJVUgCVEpTmZc0VfckNRoMj3GDi/A=";
+    hash = "sha256-K3S+2Z4yuo8eAOo8gDhrI8OOfV6ADH4dAb1h8PqYntc=";
   };
 
   postPatch = ''
     substituteInPlace pyproject.toml \
       --replace-fail ', "uv-dynamic-versioning"' "" \
       --replace-fail 'dynamic = ["version"]' 'version = "${version}"'
+  ''
+  + lib.optionalString stdenv.buildPlatform.isDarwin ''
+    # time.sleep(0.1) feels a bit optimistic and it has been flaky whilst
+    # testing this on macOS under load.
+    substituteInPlace \
+      "tests/client/test_stdio.py" \
+      "tests/server/fastmcp/test_integration.py" \
+      "tests/shared/test_ws.py" \
+      "tests/shared/test_sse.py" \
+      "tests/shared/test_streamable_http.py" \
+      --replace-fail "time.sleep(0.1)" "time.sleep(1)"
   '';
 
   build-system = [ hatchling ];
···
     anyio
     httpx
     httpx-sse
+    jsonschema
     pydantic
     pydantic-settings
     python-multipart
···
   pythonImportsCheck = [ "mcp" ];
 
   nativeCheckInputs = [
+    dirty-equals
     inline-snapshot
     pytest-asyncio
     pytest-examples
···
     requests
   ]
   ++ lib.flatten (lib.attrValues optional-dependencies);
-
-  pytestFlags = [
-    "-Wignore::pydantic.warnings.PydanticDeprecatedSince211"
-  ];
 
   disabledTests = [
     # attempts to run the package manager uv
     "test_command_execution"
 
-    # performance-dependent test
-    "test_messages_are_executed_concurrently"
-
     # ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
-    "test_client_session_version_negotiation_failure"
+    "test_lifespan_cleanup_executed"
 
-    # AttributeError: 'coroutine' object has no attribute 'client_metadata'
-    "TestOAuthClientProvider"
+    # AssertionError: Child process should be writing
+    "test_basic_child_process_cleanup"
 
-    # inline_snapshot._exceptions.UsageError: snapshot value should not change. Use Is(...) for dynamic snapshot parts
-    "test_build_metadata"
-  ]
-  ++ lib.optionals stdenv.hostPlatform.isDarwin [
-    # Flaky: ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+    # AssertionError: parent process should be writing
+    "test_nested_process_tree"
+
+    # AssertionError: Child should be writing
+    "test_early_parent_exit"
+
+    # pytest.PytestUnraisableExceptionWarning: Exception ignored in: <_io.FileIO ...
+    "test_list_tools_returns_all_tools"
+
+    # AssertionError: Server startup marker not created
+    "test_stdin_close_triggers_cleanup"
+
+    # pytest.PytestUnraisableExceptionWarning: Exception ignored in: <function St..
+    "test_resource_template_client_interaction"
+
+    # Flaky: https://github.com/modelcontextprotocol/python-sdk/pull/1171
     "test_notification_validation_error"
+
+    # Flaky: httpx.ConnectError: All connection attempts failed
+    "test_sse_security_"
+    "test_streamable_http_"
+
+    # This just feels a bit optimistic...
+    #     	assert duration < 3 * _sleep_time_seconds
+    # AssertionError: assert 0.0733884589999434 < (3 * 0.01)
+    "test_messages_are_executed_concurrently"
+
+    # ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+    "test_tool_progress"
   ];
 
   __darwinAllowLocalNetworking = true;
···
     description = "Official Python SDK for Model Context Protocol servers and clients";
     homepage = "https://github.com/modelcontextprotocol/python-sdk";
     license = lib.licenses.mit;
-    maintainers = with lib.maintainers; [ josh ];
+    maintainers = with lib.maintainers; [
+      bryanhonof
+      josh
+    ];
   };
 }

pkgs/development/python-modules/openai-agents/default.nix

···
 {
   lib,
-  nix-update-script,
   buildPythonPackage,
   fetchPypi,
   hatchling,
···
 
 buildPythonPackage rec {
   pname = "openai-agents";
-  version = "0.0.13";
+  version = "0.2.3";
   pyproject = true;
 
   src = fetchPypi {
     inherit version;
     pname = "openai_agents";
-    hash = "sha256-a4AxXnXAa1MCxfKtui+eo4RflGFdrtRwa/uHF0D1YaU=";
+    hash = "sha256-ldStGUxcDPGkADjLcB7ujs2q92mNh7sT48LFz/gMS00=";
   };
 
-  # OpenAI 1.76.0 seems to not build currently
-  postPatch = ''
-    substituteInPlace pyproject.toml --replace-fail "openai>=1.76.0" "openai"
-  '';
-
   build-system = [
     hatchling
   ];
···
   pythonImportsCheck = [
     "agents"
   ];
-
-  passthru.updateScript = nix-update-script { };
 
   meta = {
     changelog = "https://github.com/openai/openai-agents-python/releases/tag/${version}";

pkgs/development/python-modules/smolagents/default.nix

···
 
   pythonImportsCheck = [ "smolagents" ];
 
+  disabledTestPaths = [
+    # ImportError: cannot import name 'require_soundfile' from 'transformers.testing_utils'
+    "tests/test_types.py"
+  ];
+
   disabledTests = [
     # Missing dependencies
     "test_cleanup"

pkgs/servers/home-assistant/default.nix

···
           tag = "v${version}";
           hash = "sha256-Z2NN6k4mD6NixDON1MUOELpBZW9JvMvFErcCbFPdg2o=";
         };
+        pytestFlagsArray = [
+          "-W"
+          "ignore::pydantic.warnings.PydanticDeprecatedSince211"
+        ];
       });
 
       notifications-android-tv = super.notifications-android-tv.overridePythonAttrs (oldAttrs: rec {