Upgrade Fast MCP dependency

.env.example

@@ -142,3 +142,36 @@ CONFLUENCE_URL=https://your-company.atlassian.net/wiki
 
 # Confluence-specific custom headers.
 #CONFLUENCE_CUSTOM_HEADERS=X-Confluence-Service=mcp-integration,X-Custom-Auth=confluence-token,X-ALB-Token=secret-token
+
+# =============================================
+# INTEGRATION TESTING CONFIGURATION
+# =============================================
+# These variables are used for integration testing with real Atlassian instances.
+# They are optional and only needed when running tests with --use-real-data flag.
+
+# --- Test Data Configuration ---
+# Specific test issue key for integration tests
+#JIRA_TEST_ISSUE_KEY=PROJ-123
+
+# Specific test epic key for epic-related integration tests
+#JIRA_TEST_EPIC_KEY=PROJ-456
+
+# Specific test project key for project-specific integration tests
+#JIRA_TEST_PROJECT_KEY=PROJ
+
+# Specific test board ID for agile/sprint integration tests
+#JIRA_TEST_BOARD_ID=1000
+
+# Specific test sprint ID for sprint-related integration tests
+#JIRA_TEST_SPRINT_ID=10001
+
+# --- Confluence Test Configuration ---
+# Specific test page ID for Confluence integration tests
+#CONFLUENCE_TEST_PAGE_ID=123456789
+
+# Specific test space key for Confluence integration tests
+#CONFLUENCE_TEST_SPACE_KEY=DEV
+
+# --- Proxy Testing Configuration ---
+# Test proxy URL for proxy-related integration tests
+#TEST_PROXY_URL=http://test-proxy.example.com:8080

.gitignore

@@ -75,3 +75,7 @@ playground/
 
 # Claude
 .claude/
+
+# Amazon Q
+.amazonq/
+AmazonQ.md

pyproject.toml

@@ -10,13 +10,12 @@ dependencies = [
     "beautifulsoup4>=4.12.3",
     "httpx>=0.28.0",
     "mcp>=1.8.0,<2.0.0",
-    "fastmcp>=2.3.4,<2.4.0",
+    "fastmcp>=2.9.0,<3.0.0",
     "python-dotenv>=1.0.1",
     "markdownify>=0.11.6",
     "markdown>=3.7.0",
     "markdown-to-confluence>=0.3.0,<0.4.0",
     "pydantic>=2.10.6",
-    "trio>=0.29.0",
     "click>=8.1.7",
     "uvicorn>=0.27.1",
     "starlette>=0.37.1",
@@ -99,40 +98,29 @@ line-ending = "auto"
 
 [tool.mypy]
 python_version = "3.10"
-warn_return_any = true
-warn_unused_configs = true
-disallow_untyped_defs = true
-disallow_incomplete_defs = true
-check_untyped_defs = true
-disallow_untyped_decorators = false
-no_implicit_optional = true
-warn_redundant_casts = true
+ignore_missing_imports = true
+follow_imports = "silent"
+allow_untyped_defs = true
+allow_incomplete_defs = true
+allow_untyped_calls = true
+allow_untyped_decorators = true
+no_implicit_optional = false
+strict_optional = false
+warn_return_any = false
 warn_unused_ignores = false
-warn_no_return = true
-warn_unreachable = true
-strict_equality = true
-strict_optional = true
-disallow_subclassing_any = true
-warn_incomplete_stub = true
-exclude = "^src/"
-explicit_package_bases = true
-
-[[tool.mypy.overrides]]
-module = "tests.*"
-disallow_untyped_defs = false
+warn_redundant_casts = false
+warn_no_return = false
+warn_unreachable = false
 check_untyped_defs = false
+disallow_any_generics = false
+disallow_subclassing_any = false
+explicit_package_bases = true
 
-[[tool.mypy.overrides]]
-module = "atlassian.*"
-ignore_missing_imports = true
 
-[[tool.mypy.overrides]]
-module = "markdownify.*"
-ignore_missing_imports = true
 
-[[tool.mypy.overrides]]
-module = "src.mcp_atlassian.*"
-disallow_untyped_defs = false
+[tool.pytest.ini_options]
+asyncio_mode = "auto"
+asyncio_default_fixture_loop_scope = "function"
 
 [tool.hatch.version]
 source = "uv-dynamic-versioning"

src/mcp_atlassian/__init__.py

@@ -306,6 +306,8 @@ def was_option_provided(ctx: click.Context, param_name: str) -> bool:
     if click_ctx and was_option_provided(click_ctx, "jira_projects_filter"):
         os.environ["JIRA_PROJECTS_FILTER"] = jira_projects_filter
 
+    from fastmcp import settings as fastmcp_settings
+
     from mcp_atlassian.servers import main_mcp
 
     run_kwargs = {
@@ -325,9 +327,9 @@ def was_option_provided(ctx: click.Context, param_name: str) -> bool:
         log_display_path = final_path
         if log_display_path is None:
             if final_transport == "sse":
-                log_display_path = main_mcp.settings.sse_path or "/sse"
+                log_display_path = fastmcp_settings.sse_path or "/sse"
             else:
-                log_display_path = main_mcp.settings.streamable_http_path or "/mcp"
+                log_display_path = fastmcp_settings.streamable_http_path or "/mcp"
 
         logger.info(
             f"Starting server with {final_transport.upper()} transport on http://{final_host}:{final_port}{log_display_path}"

src/mcp_atlassian/jira/epics.py

@@ -44,21 +44,17 @@ def _try_discover_fields_from_existing_epic(
 
             # Find an Epic in the system
             epics_jql = "issuetype = Epic ORDER BY created DESC"
-            results = self.jira.jql(epics_jql, fields="*all", limit=1)
-            if not isinstance(results, dict):
-                msg = f"Unexpected return value type from `jira.jql`: {type(results)}"
-                logger.error(msg)
-                raise TypeError(msg)
+            results = self.search_issues(epics_jql, fields="*all", limit=1)
 
             # If no epics found, we can't use this method
-            if not results or not results.get("issues"):
+            if not results or not results.issues:
                 logger.warning("No existing Epics found to analyze field structure")
                 return
 
             # Get the most recent Epic
-            epic = results["issues"][0]
-            fields = epic.get("fields", {})
-            logger.debug(f"Found existing Epic {epic.get('key')} to analyze")
+            epic = results.issues[0]
+            fields = epic.custom_fields
+            logger.debug(f"Found existing Epic {epic.key} to analyze")
 
             # Look for Epic Name and other Epic fields
             for field_id, value in fields.items():
@@ -780,14 +776,14 @@ def _find_sample_epic(self) -> list[dict]:
         try:
             # Search for issues with type=Epic
             jql = "issuetype = Epic ORDER BY updated DESC"
-            response = self.jira.jql(jql, limit=1)
-            if not isinstance(response, dict):
-                msg = f"Unexpected return value type from `jira.jql`: {type(response)}"
-                logger.error(msg)
-                raise TypeError(msg)
+            result = self.search_issues(jql, limit=1)
 
-            if response and "issues" in response and response["issues"]:
-                return response["issues"]
+            if result and result.issues:
+                # Convert JiraIssue model back to dict format for compatibility
+                issue = result.issues[0]
+                return [
+                    {"key": issue.key, "id": issue.id, "fields": issue.custom_fields}
+                ]
         except Exception as e:
             logger.warning(f"Error finding sample epic: {str(e)}")
         return []
@@ -811,13 +807,17 @@ def _find_issues_linked_to_epic(self, epic_key: str) -> list[dict]:
                 f"issueFunction in issuesScopedToEpic('{epic_key}')",
             ]:
                 try:
-                    response = self.jira.jql(query, limit=5)
-                    if not isinstance(response, dict):
-                        msg = f"Unexpected return value type from `jira.jql`: {type(response)}"
-                        logger.error(msg)
-                        raise TypeError(msg)
-                    if response.get("issues"):
-                        return response["issues"]
+                    result = self.search_issues(query, limit=5)
+                    if result and result.issues:
+                        # Convert JiraIssue models back to dict format for compatibility
+                        return [
+                            {
+                                "key": issue.key,
+                                "id": issue.id,
+                                "fields": issue.custom_fields,
+                            }
+                            for issue in result.issues
+                        ]
                 except Exception:
                     # Try next query format
                     continue

src/mcp_atlassian/jira/issues.py

@@ -208,6 +208,7 @@ def get_issue(
                 issue,
                 base_url=self.config.url if hasattr(self, "config") else None,
                 requested_fields=fields,
+                is_cloud=self.config.is_cloud,
             )
         except HTTPError as http_err:
             if http_err.response is not None and http_err.response.status_code in [
@@ -645,7 +646,9 @@ def create_issue(
                 msg = f"Unexpected return value type from `jira.get_issue`: {type(issue_data)}"
                 logger.error(msg)
                 raise TypeError(msg)
-            return JiraIssue.from_api_response(issue_data)
+            return JiraIssue.from_api_response(
+                issue_data, is_cloud=self.config.is_cloud
+            )
 
         except Exception as e:
             self._handle_create_issue_error(e, issue_type)
@@ -1080,7 +1083,9 @@ def update_issue(
                 msg = f"Unexpected return value type from `jira.get_issue`: {type(issue_data)}"
                 logger.error(msg)
                 raise TypeError(msg)
-            issue = JiraIssue.from_api_response(issue_data)
+            issue = JiraIssue.from_api_response(
+                issue_data, is_cloud=self.config.is_cloud
+            )
 
             # Add attachment results to the response if available
             if attachments_result:
@@ -1123,7 +1128,9 @@ def _update_issue_with_status(
                 msg = f"Unexpected return value type from `jira.get_issue`: {type(issue_data)}"
                 logger.error(msg)
                 raise TypeError(msg)
-            return JiraIssue.from_api_response(issue_data)
+            return JiraIssue.from_api_response(
+                issue_data, is_cloud=self.config.is_cloud
+            )
 
         # Get available transitions (uses TransitionsMixin's normalized implementation)
         transitions = self.get_available_transitions(issue_key)  # type: ignore[attr-defined]
@@ -1222,7 +1229,7 @@ def _update_issue_with_status(
             msg = f"Unexpected return value type from `jira.get_issue`: {type(issue_data)}"
             logger.error(msg)
             raise TypeError(msg)
-        return JiraIssue.from_api_response(issue_data)
+        return JiraIssue.from_api_response(issue_data, is_cloud=self.config.is_cloud)
 
     def delete_issue(self, issue_key: str) -> bool:
         """
@@ -1466,6 +1473,7 @@ def batch_create_issues(
                                 base_url=self.config.url
                                 if hasattr(self, "config")
                                 else None,
+                                is_cloud=self.config.is_cloud,
                             )
                         )
                     except Exception as e: