fix: apply code formatting fixes for linting compliance

- Fix trailing whitespace in core source files
- Apply ruff formatting to search.py, epics.py, and models
- Address code style violations for PR compliance

Author: Jose Luis Moreno

src/mcp_atlassian/jira/epics.py

@@ -780,10 +780,9 @@ def _find_sample_epic(self) -> list[dict]:
         try:
             # Search for issues with type=Epic
             jql = "issuetype = Epic ORDER BY updated DESC"
-            response = self.jira.post("rest/api/3/search/jql", json={
-                "jql": jql,
-                "maxResults": 1
-            })
+            response = self.jira.post(
+                "rest/api/3/search/jql", json={"jql": jql, "maxResults": 1}
+            )
             if not isinstance(response, dict):
                 msg = f"Unexpected return value type from `jira.jql`: {type(response)}"
                 logger.error(msg)
@@ -814,10 +813,9 @@ def _find_issues_linked_to_epic(self, epic_key: str) -> list[dict]:
                 f"issueFunction in issuesScopedToEpic('{epic_key}')",
             ]:
                 try:
-                    response = self.jira.post("rest/api/3/search/jql", json={
-                        "jql": query,
-                        "maxResults": 5
-                    })
+                    response = self.jira.post(
+                        "rest/api/3/search/jql", json={"jql": query, "maxResults": 5}
+                    )
                     if not isinstance(response, dict):
                         msg = f"Unexpected return value type from `jira.jql`: {type(response)}"
                         logger.error(msg)

src/mcp_atlassian/jira/search.py

@@ -96,7 +96,7 @@ def search_issues(
                     payload = {
                         "jql": jql,
                         "fields": fields_param.split(",") if fields_param else [],
-                        "maxResults": min(limit, 100)
+                        "maxResults": min(limit, 100),
                     }
                     if expand:
                         payload["expand"] = expand.split(",")
@@ -120,12 +120,14 @@ def search_issues(
 
                     # Check for more pages - new API uses isLast instead of nextPageToken
                     is_last = response.get("isLast", True)
-                    next_page_token = response.get("nextPageToken")  # May not be present
-                    
+                    next_page_token = response.get(
+                        "nextPageToken"
+                    )  # May not be present
+
                     # Break if this is the last page or we've reached the limit
                     if is_last or len(all_issues) >= limit:
                         break
-                    
+
                     # For pagination, we may need to use different approach
                     # If nextPageToken is not available, we might need to use startAt
                     if not next_page_token:
@@ -142,7 +144,7 @@ def search_issues(
                     "issues": all_issues,
                     "total": actual_total,
                     "maxResults": limit,
-                    "startAt": 0
+                    "startAt": 0,
                 }
 
                 search_result = JiraSearchResult.from_api_response(
@@ -159,9 +161,9 @@ def search_issues(
                     fields=fields_param,
                     start=start,
                     limit=min(limit, 50),
-                    expand=expand
+                    expand=expand,
                 )
-                
+
                 if not isinstance(response, dict):
                     msg = f"Unexpected return value type from jql: {type(response)}"
                     logger.error(msg)

src/mcp_atlassian/models/jira/issue.py

@@ -268,7 +268,7 @@ def from_api_response(cls, data: dict[str, Any], **kwargs: Any) -> "JiraIssue":
         key = str(data.get("key", JIRA_DEFAULT_KEY))
         summary = str(fields.get("summary", EMPTY_STRING))
         description = fields.get("description")
-        
+
         # Handle ADF (Atlassian Document Format) description
         if isinstance(description, dict):
             # Extract plain text from ADF format if possible

src/mcp_atlassian/models/jira/search.py

@@ -69,7 +69,7 @@ def from_api_response(
         raw_total = data.get("total")
         raw_start_at = data.get("startAt")
         raw_max_results = data.get("maxResults")
-        
+
         # New API may not include these fields, especially when empty
         # For new API, we need to infer values from available data
         if raw_total is None and "isLast" in data:

tests/unit/jira/test_epics.py

@@ -6,7 +6,7 @@
 
 from mcp_atlassian.jira import JiraFetcher
 from mcp_atlassian.jira.epics import EpicsMixin
-from mcp_atlassian.models.jira import JiraIssue, JiraSearchResult
+from mcp_atlassian.models.jira import JiraIssue
 
 
 class TestEpicsMixin: