Python: Updated instructions/system_message logic in GitHub Copilot agent (#3625)

* Updated instructions handling

* Small improvement

* Included runtime options in session creation logic

python/packages/github_copilot/tests/test_github_copilot_agent.py

@@ -135,12 +135,52 @@ class TestGitHubCopilotAgentInit:
         agent = GitHubCopilotAgent(tools=[my_tool])
         assert len(agent._tools) == 1  # type: ignore
 
-    def test_init_with_instructions(self) -> None:
-        """Test initialization with custom instructions."""
+    def test_init_with_instructions_parameter(self) -> None:
+        """Test initialization with instructions parameter."""
+        agent = GitHubCopilotAgent(instructions="You are a helpful assistant.")
+        assert agent._default_options.get("system_message") == {  # type: ignore
+            "mode": "append",
+            "content": "You are a helpful assistant.",
+        }
+
+    def test_init_with_system_message_in_default_options(self) -> None:
+        """Test initialization with system_message object in default_options."""
         agent: GitHubCopilotAgent[GitHubCopilotOptions] = GitHubCopilotAgent(
-            default_options={"instructions": "You are a helpful assistant."}
+            default_options={"system_message": {"mode": "append", "content": "You are a helpful assistant."}}
         )
-        assert agent._instructions == "You are a helpful assistant."  # type: ignore
+        assert agent._default_options.get("system_message") == {  # type: ignore
+            "mode": "append",
+            "content": "You are a helpful assistant.",
+        }
+
+    def test_init_with_system_message_replace_mode(self) -> None:
+        """Test initialization with system_message in replace mode."""
+        agent: GitHubCopilotAgent[GitHubCopilotOptions] = GitHubCopilotAgent(
+            default_options={"system_message": {"mode": "replace", "content": "Custom system prompt."}}
+        )
+        assert agent._default_options.get("system_message") == {  # type: ignore
+            "mode": "replace",
+            "content": "Custom system prompt.",
+        }
+
+    def test_instructions_parameter_takes_precedence_for_content(self) -> None:
+        """Test that direct instructions parameter takes precedence for content but preserves mode."""
+        agent: GitHubCopilotAgent[GitHubCopilotOptions] = GitHubCopilotAgent(
+            instructions="Direct instructions",
+            default_options={"system_message": {"mode": "replace", "content": "Options system_message"}},
+        )
+        assert agent._default_options.get("system_message") == {  # type: ignore
+            "mode": "replace",
+            "content": "Direct instructions",
+        }
+
+    def test_instructions_parameter_defaults_to_append_mode(self) -> None:
+        """Test that instructions parameter defaults to append mode when no system_message provided."""
+        agent = GitHubCopilotAgent(instructions="Direct instructions")
+        assert agent._default_options.get("system_message") == {  # type: ignore
+            "mode": "append",
+            "content": "Direct instructions",
+        }
 
 
 class TestGitHubCopilotAgentLifecycle:
@@ -462,10 +502,10 @@ class TestGitHubCopilotAgentSessionManagement:
         mock_client: MagicMock,
         mock_session: MagicMock,
     ) -> None:
-        """Test that session config includes instructions."""
-        agent: GitHubCopilotAgent[GitHubCopilotOptions] = GitHubCopilotAgent(
+        """Test that session config includes instructions from direct parameter."""
+        agent = GitHubCopilotAgent(
+            instructions="You are a helpful assistant.",
             client=mock_client,
-            default_options={"instructions": "You are a helpful assistant."},
         )
         await agent.start()
 
@@ -476,6 +516,31 @@ class TestGitHubCopilotAgentSessionManagement:
         assert config["system_message"]["mode"] == "append"
         assert config["system_message"]["content"] == "You are a helpful assistant."
 
+    async def test_runtime_options_take_precedence_over_default(
+        self,
+        mock_client: MagicMock,
+        mock_session: MagicMock,
+    ) -> None:
+        """Test that runtime options from run() take precedence over default_options."""
+        agent = GitHubCopilotAgent(
+            instructions="Default instructions",
+            client=mock_client,
+        )
+        await agent.start()
+
+        runtime_options: GitHubCopilotOptions = {
+            "system_message": {"mode": "replace", "content": "Runtime instructions"}
+        }
+        await agent._get_or_create_session(  # type: ignore
+            AgentThread(),
+            runtime_options=runtime_options,
+        )
+
+        call_args = mock_client.create_session.call_args
+        config = call_args[0][0]
+        assert config["system_message"]["mode"] == "replace"
+        assert config["system_message"]["content"] == "Runtime instructions"
+
     async def test_session_config_includes_streaming_flag(
         self,
         mock_client: MagicMock,