feat: deprecate roots sampling and logging

Warn when Roots, Sampling, or Logging APIs are used with MCP protocol version 2026-07-28, while leaving the latest stable default at 2025-11-25.

Add a shared protocol deprecation helper, YARD deprecation notes, and regression tests covering warnings for 2026-07-28 and no warnings for older protocol versions.

Closes #390

Author: atesgoral

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Warn when deprecated Roots, Sampling, or Logging APIs are used with protocol version `2026-07-28` (#390)
+
 ## [0.20.0] - 2026-06-14
 
 ### Added

lib/mcp.rb

@@ -2,6 +2,7 @@
 
 require_relative "json_rpc_handler"
 require_relative "mcp/configuration"
+require_relative "mcp/protocol_deprecations"
 require_relative "mcp/string_utils"
 require_relative "mcp/transport"
 require_relative "mcp/version"

lib/mcp/client/http.rb

@@ -4,6 +4,7 @@
 require_relative "../../json_rpc_handler"
 require_relative "../configuration"
 require_relative "../methods"
+require_relative "../protocol_deprecations"
 require_relative "../version"
 
 module MCP
@@ -155,6 +156,7 @@ def connect(client_info: nil, protocol_version: nil, capabilities: {})
             error_type: :internal_error,
           )
         end
+        MCP::ProtocolDeprecations.warn_for_client_capabilities(capabilities, protocol_version: negotiated_protocol_version, uplevel: 1)
 
         begin
           send_request(request: {

lib/mcp/client/stdio.rb

@@ -7,6 +7,7 @@
 require_relative "../../json_rpc_handler"
 require_relative "../configuration"
 require_relative "../methods"
+require_relative "../protocol_deprecations"
 require_relative "../version"
 
 module MCP
@@ -109,6 +110,7 @@ def connect(client_info: nil, protocol_version: nil, capabilities: {})
             error_type: :internal_error,
           )
         end
+        MCP::ProtocolDeprecations.warn_for_client_capabilities(capabilities, protocol_version: negotiated_protocol_version, uplevel: 1)
 
         begin
           notification = {

lib/mcp/configuration.rb

@@ -3,8 +3,9 @@
 module MCP
   class Configuration
     LATEST_STABLE_PROTOCOL_VERSION = "2025-11-25"
+    ROOTS_SAMPLING_LOGGING_DEPRECATED_PROTOCOL_VERSION = "2026-07-28"
     SUPPORTED_STABLE_PROTOCOL_VERSIONS = [
-      LATEST_STABLE_PROTOCOL_VERSION, "2025-06-18", "2025-03-26", "2024-11-05",
+      ROOTS_SAMPLING_LOGGING_DEPRECATED_PROTOCOL_VERSION, LATEST_STABLE_PROTOCOL_VERSION, "2025-06-18", "2025-03-26", "2024-11-05",
     ]
     DEFAULT_NEGOTIATED_PROTOCOL_VERSION = "2025-03-26"
 

lib/mcp/protocol_deprecations.rb

@@ -0,0 +1,49 @@
+# frozen_string_literal: true
+
+require_relative "configuration"
+
+module MCP
+  module ProtocolDeprecations
+    extend self
+
+    ROOTS_MESSAGE =
+      "MCP Roots (`roots/list` and `notifications/roots/list_changed`) is deprecated as of protocol version " \
+        "2026-07-28 (SEP-2577). Use tool parameters, resource URIs, server configuration, or environment " \
+        "variables instead."
+    SAMPLING_MESSAGE =
+      "MCP Sampling (`sampling/createMessage`) is deprecated as of protocol version 2026-07-28 (SEP-2577). " \
+        "Use direct LLM provider APIs instead."
+    LOGGING_MESSAGE =
+      "MCP Logging (`logging/setLevel` and `notifications/message`) is deprecated as of protocol version " \
+        "2026-07-28 (SEP-2577). Use stderr or OpenTelemetry instead."
+
+    MESSAGES = {
+      roots: ROOTS_MESSAGE,
+      sampling: SAMPLING_MESSAGE,
+      logging: LOGGING_MESSAGE,
+    }.freeze
+
+    def deprecated_roots_sampling_logging?(protocol_version)
+      protocol_version == Configuration::ROOTS_SAMPLING_LOGGING_DEPRECATED_PROTOCOL_VERSION
+    end
+
+    def warn_for(feature, protocol_version:, uplevel: 1)
+      return unless deprecated_roots_sampling_logging?(protocol_version)
+
+      Kernel.warn(MESSAGES.fetch(feature), uplevel: uplevel + 1)
+    end
+
+    def warn_for_client_capabilities(capabilities, protocol_version:, uplevel: 1)
+      return unless deprecated_roots_sampling_logging?(protocol_version)
+      return unless capabilities
+
+      warn_for(:roots, protocol_version: protocol_version, uplevel: uplevel + 1) if capability?(capabilities, :roots)
+      warn_for(:sampling, protocol_version: protocol_version, uplevel: uplevel + 1) if capability?(capabilities, :sampling)
+    end
+
+    def capability?(capabilities, key)
+      capabilities.key?(key) || capabilities.key?(key.to_s)
+    end
+    private :capability?
+  end
+end

lib/mcp/server.rb

@@ -7,6 +7,7 @@
 require_relative "methods"
 require_relative "logging_message_notification"
 require_relative "progress"
+require_relative "protocol_deprecations"
 require_relative "server_context"
 require_relative "server/pagination"
 require_relative "server/transports"
@@ -139,6 +140,7 @@ def initialize(
       self.page_size = page_size
       @configuration = MCP.configuration.merge(configuration)
       @client = nil
+      @client_protocol_version = nil
 
       validate!
 
@@ -250,10 +252,15 @@ def notify_resources_list_changed
       report_exception(e, { notification: "resources_list_changed" })
     end
 
+    # @deprecated MCP Logging (`logging/setLevel` and `notifications/message`)
+    #   is deprecated as of MCP protocol version 2026-07-28 (SEP-2577).
+    #   Use stderr or OpenTelemetry instead.
     def notify_log_message(data:, level:, logger: nil)
       return unless @transport
       return unless logging_message_notification&.should_notify?(level)
 
+      warn_if_deprecated_protocol_feature(:logging, uplevel: 1)
+
       params = { "data" => data, "level" => level }
       params["logger"] = logger if logger
 
@@ -266,7 +273,13 @@ def notify_log_message(data:, level:, logger: nil)
     # Called when a client notifies the server that its filesystem roots have changed.
     #
     # @yield [params] The notification params (typically `nil`).
+    # @deprecated MCP Roots (`roots/list` and
+    #   `notifications/roots/list_changed`) is deprecated as of MCP protocol
+    #   version 2026-07-28 (SEP-2577). Use tool parameters, resource URIs,
+    #   server configuration, or environment variables instead.
     def roots_list_changed_handler(&block)
+      warn_if_deprecated_protocol_feature(:roots, uplevel: 1)
+
       @handlers[Methods::NOTIFICATIONS_ROOTS_LIST_CHANGED] = block
     end
 
@@ -448,6 +461,8 @@ def handle_request(request, method, session: nil, related_request_id: nil)
           server_context: { request: request },
           exception_already_reported: ->(e) { reported_exception.equal?(e) },
         ) do
+          warn_if_deprecated_protocol_feature(:roots, session: session, uplevel: 0) if method == Methods::NOTIFICATIONS_ROOTS_LIST_CHANGED
+
           result = case method
           when Methods::INITIALIZE
             init(params, session: session)
@@ -562,7 +577,11 @@ def init(params, session: nil)
         response_instructions = nil
       end
 
-      session&.mark_initialized!
+      if session
+        session.mark_initialized!(protocol_version: negotiated_version)
+      else
+        @client_protocol_version = negotiated_version
+      end
 
       {
         protocolVersion: negotiated_version,
@@ -577,6 +596,8 @@ def configure_logging_level(request, session: nil)
         raise RequestHandlerError.new("Server does not support logging", request, error_type: :internal_error)
       end
 
+      warn_if_deprecated_protocol_feature(:logging, session: session, uplevel: 0)
+
       logging_message_notification = LoggingMessageNotification.new(level: request[:level])
       unless logging_message_notification.valid_level?
         raise RequestHandlerError.new("Invalid log level #{request[:level]}", request, error_type: :invalid_params)
@@ -588,6 +609,19 @@ def configure_logging_level(request, session: nil)
       {}
     end
 
+    def warn_if_deprecated_protocol_feature(feature, session: nil, uplevel: 1)
+      protocol_version = effective_deprecation_protocol_version(session)
+      MCP::ProtocolDeprecations.warn_for(feature, protocol_version: protocol_version, uplevel: uplevel + 1)
+    end
+
+    def effective_deprecation_protocol_version(session)
+      session&.protocol_version || @client_protocol_version || explicit_protocol_version
+    end
+
+    def explicit_protocol_version
+      configuration.protocol_version if configuration.protocol_version?
+    end
+
     def list_tools(request)
       page = paginate(@tools.values, cursor: cursor_from(request), page_size: @page_size, request: request, &:to_h)
 

lib/mcp/server_context.rb

@@ -35,10 +35,19 @@ def report_progress(progress, total: nil, message: nil)
     # @param data [Object] The log data to send.
     # @param level [String] Log level (e.g., `"debug"`, `"info"`, `"error"`).
     # @param logger [String, nil] Logger name.
+    # @deprecated MCP Logging (`logging/setLevel` and `notifications/message`)
+    #   is deprecated as of MCP protocol version 2026-07-28 (SEP-2577).
+    #   Use stderr or OpenTelemetry instead.
     def notify_log_message(data:, level:, logger: nil)
       return unless @notification_target
 
-      @notification_target.notify_log_message(data: data, level: level, logger: logger, related_request_id: @related_request_id)
+      @notification_target.notify_log_message(
+        data: data,
+        level: level,
+        logger: logger,
+        related_request_id: @related_request_id,
+        **server_session_deprecation_options,
+      )
     end
 
     # Sends a resource updated notification scoped to the originating session.
@@ -51,9 +60,13 @@ def notify_resources_updated(uri:)
     end
 
     # Delegates to the session so the request is scoped to the originating client.
+    # @deprecated MCP Roots (`roots/list` and
+    #   `notifications/roots/list_changed`) is deprecated as of MCP protocol
+    #   version 2026-07-28 (SEP-2577). Use tool parameters, resource URIs,
+    #   server configuration, or environment variables instead.
     def list_roots
       if @notification_target.respond_to?(:list_roots)
-        @notification_target.list_roots(related_request_id: @related_request_id)
+        @notification_target.list_roots(related_request_id: @related_request_id, **server_session_deprecation_options)
       else
         raise NoMethodError, "undefined method 'list_roots' for #{self}"
       end
@@ -84,9 +97,12 @@ def ping
     # Delegates to the session so the request is scoped to the originating client.
     # Falls back to `@context` (via `method_missing`) when `@notification_target`
     # does not support sampling.
+    # @deprecated MCP Sampling (`sampling/createMessage`) is deprecated as of
+    #   MCP protocol version 2026-07-28 (SEP-2577). Use direct LLM provider
+    #   APIs instead.
     def create_sampling_message(**kwargs)
       if @notification_target.respond_to?(:create_sampling_message)
-        @notification_target.create_sampling_message(**kwargs, related_request_id: @related_request_id)
+        @notification_target.create_sampling_message(**kwargs, related_request_id: @related_request_id, **server_session_deprecation_options)
       elsif @context.respond_to?(:create_sampling_message)
         @context.create_sampling_message(**kwargs, related_request_id: @related_request_id)
       else
@@ -141,5 +157,11 @@ def method_missing(name, ...)
     def respond_to_missing?(name, include_private = false)
       @context.respond_to?(name) || super
     end
+
+    private
+
+    def server_session_deprecation_options
+      @notification_target.is_a?(ServerSession) ? { deprecation_uplevel: 2 } : {}
+    end
   end
 end

lib/mcp/server_session.rb

@@ -7,7 +7,7 @@ module MCP
   # Holds per-connection state for a single client session.
   # Created by the transport layer; delegates request handling to the shared `Server`.
   class ServerSession
-    attr_reader :session_id, :client, :logging_message_notification
+    attr_reader :session_id, :client, :logging_message_notification, :protocol_version
 
     def initialize(server:, transport:, session_id: nil)
       @server = server
@@ -16,6 +16,7 @@ def initialize(server:, transport:, session_id: nil)
       @client = nil
       @client_capabilities = nil
       @logging_message_notification = nil
+      @protocol_version = nil
       @in_flight = {}
       @in_flight_mutex = Mutex.new
       @initialized = false
@@ -29,8 +30,9 @@ def initialized?
     # Called by `Server#init` after a successful `initialize` response, so subsequent
     # `initialize` requests on the same session can be rejected per MCP spec
     # (the initialization phase MUST be the first interaction).
-    def mark_initialized!
+    def mark_initialized!(protocol_version: nil)
       @initialized = true
+      @protocol_version = protocol_version
     end
 
     # Registers a `Cancellation` token for an in-flight request.
@@ -98,11 +100,17 @@ def client_capabilities
     end
 
     # Sends a `roots/list` request scoped to this session.
-    def list_roots(related_request_id: nil)
+    # @deprecated MCP Roots (`roots/list` and
+    #   `notifications/roots/list_changed`) is deprecated as of MCP protocol
+    #   version 2026-07-28 (SEP-2577). Use tool parameters, resource URIs,
+    #   server configuration, or environment variables instead.
+    def list_roots(related_request_id: nil, deprecation_uplevel: 1)
       unless client_capabilities&.dig(:roots)
         raise "Client does not support roots."
       end
 
+      @server.send(:warn_if_deprecated_protocol_feature, :roots, session: self, uplevel: deprecation_uplevel)
+
       send_to_transport_request(Methods::ROOTS_LIST, nil, related_request_id: related_request_id)
     end
 
@@ -115,8 +123,13 @@ def ping(related_request_id: nil)
     end
 
     # Sends a `sampling/createMessage` request scoped to this session.
-    def create_sampling_message(related_request_id: nil, **kwargs)
+    # @deprecated MCP Sampling (`sampling/createMessage`) is deprecated as of
+    #   MCP protocol version 2026-07-28 (SEP-2577). Use direct LLM provider
+    #   APIs instead.
+    def create_sampling_message(related_request_id: nil, deprecation_uplevel: 1, **kwargs)
       params = @server.build_sampling_params(client_capabilities, **kwargs)
+      @server.send(:warn_if_deprecated_protocol_feature, :sampling, session: self, uplevel: deprecation_uplevel)
+
       send_to_transport_request(Methods::SAMPLING_CREATE_MESSAGE, params, related_request_id: related_request_id)
     end
 
@@ -188,10 +201,15 @@ def notify_progress(progress_token:, progress:, total: nil, message: nil, relate
     end
 
     # Sends a log message notification to this session only.
-    def notify_log_message(data:, level:, logger: nil, related_request_id: nil)
+    # @deprecated MCP Logging (`logging/setLevel` and `notifications/message`)
+    #   is deprecated as of MCP protocol version 2026-07-28 (SEP-2577).
+    #   Use stderr or OpenTelemetry instead.
+    def notify_log_message(data:, level:, logger: nil, related_request_id: nil, deprecation_uplevel: 1)
       effective_logging = @logging_message_notification || @server.logging_message_notification
       return unless effective_logging&.should_notify?(level)
 
+      @server.send(:warn_if_deprecated_protocol_feature, :logging, session: self, uplevel: deprecation_uplevel)
+
       params = { "data" => data, "level" => level }
       params["logger"] = logger if logger