python3Packages.mcp: 1.9.4 -> 1.12.2

I also had to disable some failing tests that I didn't mananage to catch in a
reproducible manner. They tend to happen when the system I'm running
nixpkgs-review on is under some load, but they don't happen all that often when
building the package in isolation.

Co-authored-by: Joshua Peek <josh@users.noreply.github.com>

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

@@ -11,6 +11,7 @@
   anyio,
   httpx,
   httpx-sse,
+  jsonschema,
   pydantic,
   pydantic-settings,
   python-multipart,
@@ -28,6 +29,7 @@
   websockets,
 
   # tests
+  dirty-equals,
   inline-snapshot,
   pytest-asyncio,
   pytest-examples,
@@ -38,20 +40,31 @@
 
 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 ];
@@ -64,6 +77,7 @@ buildPythonPackage rec {
     anyio
     httpx
     httpx-sse
+    jsonschema
     pydantic
     pydantic-settings
     python-multipart
@@ -88,6 +102,7 @@ buildPythonPackage rec {
   pythonImportsCheck = [ "mcp" ];
 
   nativeCheckInputs = [
+    dirty-equals
     inline-snapshot
     pytest-asyncio
     pytest-examples
@@ -97,29 +112,45 @@ buildPythonPackage rec {
   ]
   ++ 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
+    # ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+    "test_lifespan_cleanup_executed"
+
+    # AssertionError: Child process should be writing
+    "test_basic_child_process_cleanup"
+
+    # 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_client_session_version_negotiation_failure"
-
-    # AttributeError: 'coroutine' object has no attribute 'client_metadata'
-    "TestOAuthClientProvider"
-
-    # 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)
-    "test_notification_validation_error"
+    "test_tool_progress"
   ];
 
   __darwinAllowLocalNetworking = true;