tooluniverse 1.0.9__py3-none-any.whl → 1.0.10__py3-none-any.whl

tooluniverse/core_tool.py

@@ -43,7 +43,7 @@ class CoreTool(BaseTool):
             year_to: End year filter
             language: Language filter (e.g., 'en', 'es', 'fr')
 
-        Returns:
+        Returns
             List of paper dictionaries
         """
         try:
@@ -134,7 +134,7 @@ class CoreTool(BaseTool):
         Args:
             tool_arguments: Dictionary containing search parameters
 
-        Returns:
+        Returns
             List of paper dictionaries
         """
         query = tool_arguments.get("query", "")

tooluniverse/ctg_tool.py

@@ -34,7 +34,7 @@ class ClinicalTrialsTool(RESTfulTool):
         Args:
             arguments (dict): Runtime arguments provided to the tool's run method.
 
-        Returns:
+        Returns
             dict: A new dictionary with mapped parameter names.
         """
 
@@ -54,7 +54,7 @@ class ClinicalTrialsTool(RESTfulTool):
         Args:
             arguments (dict): Runtime arguments provided to the tool's run method.
 
-        Returns:
+        Returns
             dict: A dictionary of parameters ready for the API requests.
         """
         api_params = {}
@@ -77,7 +77,7 @@ class ClinicalTrialsTool(RESTfulTool):
         Args:
             arguments (dict): Runtime arguments provided to the tool's run method.
 
-        Returns:
+        Returns
             str: The formatted endpoint URL.
         """
         url_to_format = self.endpoint_url
@@ -185,7 +185,7 @@ class ClinicalTrialsSearchTool(ClinicalTrialsTool):
         Args:
             arguments (dict): A dictionary containing parameters provided by the user/LLM
 
-        Returns:
+        Returns
             dict or str: The JSON response from the API as a dictionary,
                          or raw text for non-JSON responses, or an error dictionary.
         """

tooluniverse/custom_tool.py

@@ -81,7 +81,7 @@ class CustomTool(BaseTool):
         Args:
             arguments: Input arguments for the tool
 
-        Returns:
+        Returns
             Dict containing the result of tool execution
         """
         try:

tooluniverse/dataset_tool.py

@@ -123,7 +123,7 @@ class DatasetTool(BaseTool):
                 - exact_match (bool): Whether to perform exact matching
                 - limit (int): Maximum number of results
 
-        Returns:
+        Returns
             dict: Search results with matched records and metadata
         """
         query = arguments.get("query", "")
@@ -206,7 +206,7 @@ class DatasetTool(BaseTool):
                 - value (str): Value to filter by (optional for not_empty condition)
                 - limit (int): Maximum number of results
 
-        Returns:
+        Returns
             dict: Filtered results with matched records and applied filters
         """
         field = arguments.get("field")

tooluniverse/default_config.py

@@ -157,7 +157,7 @@ def get_default_hook_config():
     """
     Get default hook configuration.
 
-    Returns:
+    Returns
         dict: Default hook configuration with basic settings
     """
     return {

tooluniverse/enrichr_tool.py

@@ -37,10 +37,10 @@ class EnrichrTool(BaseTool):
         """
         Retrieve the official gene symbol for a given gene name or synonym using the MyGene.info API.
 
-        Parameters:
+        Parameters
             gene_name (str): The gene name or synonym to query.
 
-        Returns:
+        Returns
             str: The official gene symbol if found; otherwise, raises an Exception.
         """
         # URL-encode the gene_name to handle special characters
@@ -89,10 +89,10 @@ class EnrichrTool(BaseTool):
         """
         Submit the gene list to Enrichr and return the user list ID.
 
-        Parameters:
+        Parameters
             gene_list (str): Newline-separated string of gene names.
 
-        Returns:
+        Returns
             str: The user list ID from Enrichr.
         """
         payload = {
@@ -110,11 +110,11 @@ class EnrichrTool(BaseTool):
         """
         Fetch enrichment results for a specific library.
 
-        Parameters:
+        Parameters
             user_list_id (str): The user list ID from Enrichr.
             library (str): The name of the enrichment library.
 
-        Returns:
+        Returns
             dict: The enrichment results.
         """
         query_string = f"?userListId={user_list_id}&backgroundType={library}"
@@ -129,11 +129,11 @@ class EnrichrTool(BaseTool):
         """
         Initialize and build the graph with gene nodes and enriched terms.
 
-        Parameters:
+        Parameters
             genes (list): List of gene names.
             enrichment_results (dict): Dictionary of enrichment results by library.
 
-        Returns:
+        Returns
             networkx.Graph: The constructed graph.
         """
         G = nx.Graph()
@@ -159,12 +159,12 @@ class EnrichrTool(BaseTool):
         """
         Find and rank paths between source and target based on total edge weight.
 
-        Parameters:
+        Parameters
             G (networkx.Graph): The graph to search.
             source (str): The source node.
             target (str): The target node.
 
-        Returns:
+        Returns
             list: List of tuples (path, weight) sorted by weight descending.
         """
         all_paths = list(nx.all_simple_paths(G, source=source, target=target))
@@ -182,12 +182,12 @@ class EnrichrTool(BaseTool):
         """
         Find and rank paths from each gene to a specified term based on total edge weight.
 
-        Parameters:
+        Parameters
             G (networkx.Graph): The graph to search.
             gene (str): The source gene.
             term (str): The target term.
 
-        Returns:
+        Returns
             list or None: List of tuples (path, weight) sorted by weight descending, or None if no paths.
         """
         all_paths = list(nx.all_simple_paths(G, source=gene, target=term))
@@ -207,11 +207,11 @@ class EnrichrTool(BaseTool):
         """
         Main API function to perform gene enrichment analysis.
 
-        Parameters:
+        Parameters
             genes (list): List of gene names.
             libs (list): List of enrichment libraries to use.
 
-        Returns:
+        Returns
             tuple: (connected_path, connections) dictionaries.
         """
         # Convert each gene to its official name and log the result