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

tooluniverse/openalex_tool.py

@@ -37,14 +37,14 @@ class OpenAlexTool(BaseTool):
         """
         Search for literature using OpenAlex API.
 
-        Parameters:
+        Parameters
             search_keywords (str): Keywords to search for in title, abstract, and content.
             max_results (int): Maximum number of results to return (default: 10).
             year_from (int): Start year for publication date filter (optional).
             year_to (int): End year for publication date filter (optional).
             open_access (bool): Filter for open access papers only (optional).
 
-        Returns:
+        Returns
             list: List of dictionaries containing paper information.
         """
         # Encode search keywords for URL
@@ -98,10 +98,10 @@ class OpenAlexTool(BaseTool):
         """
         Extract relevant information from a work object returned by OpenAlex API.
 
-        Parameters:
+        Parameters
             work (dict): Work object from OpenAlex API response.
 
-        Returns:
+        Returns
             dict: Formatted paper information.
         """
         # Extract title
@@ -204,10 +204,10 @@ class OpenAlexTool(BaseTool):
         """
         Retrieve a specific paper by its DOI.
 
-        Parameters:
+        Parameters
             doi (str): DOI of the paper to retrieve.
 
-        Returns:
+        Returns
             dict: Paper information or None if not found.
         """
         try:
@@ -229,11 +229,11 @@ class OpenAlexTool(BaseTool):
         """
         Retrieve papers by a specific author.
 
-        Parameters:
+        Parameters
             author_name (str): Name of the author to search for.
             max_results (int): Maximum number of results to return.
 
-        Returns:
+        Returns
             list: List of papers by the author.
         """
         try:

tooluniverse/openfda_tool.py

@@ -85,11 +85,11 @@ def extract_sentences_with_keywords(text_list, keywords):
     """
     Extracts sentences containing any of the specified keywords from the text.
 
-    Parameters:
+    Parameters
     - text (str): The input text from which to extract sentences.
     - keywords (list): A list of keywords to search for in the text.
 
-    Returns:
+    Returns
     - list: A list of sentences containing any of the keywords.
     """
     sentences_with_keywords = []

tooluniverse/output_hook.py

@@ -65,7 +65,7 @@ class HookRule:
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Additional context information
 
-        Returns:
+        Returns
             bool: True if conditions are met, False otherwise
         """
         # Evaluate output length conditions
@@ -158,7 +158,7 @@ class OutputHook:
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Additional context information
 
-        Returns:
+        Returns
             bool: True if hook should trigger, False otherwise
         """
         if not self.enabled:
@@ -184,7 +184,7 @@ class OutputHook:
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Additional context information
 
-        Returns:
+        Returns
             Any: The processed output
 
         Raises:
@@ -290,7 +290,7 @@ class SummarizationHook(OutputHook):
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Additional context information
 
-        Returns:
+        Returns
             Any: The summarized output, or original output if summarization fails
         """
         try:
@@ -408,7 +408,7 @@ class SummarizationHook(OutputHook):
         Args:
             context (Dict[str, Any]): Execution context containing arguments and metadata
 
-        Returns:
+        Returns
             str: Extracted query context or fallback description
         """
         arguments = context.get("arguments", {})
@@ -519,7 +519,7 @@ class HookManager:
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Additional context information
 
-        Returns:
+        Returns
             Any: The processed output after applying all applicable hooks
         """
         if not self.enabled:
@@ -553,7 +553,7 @@ class HookManager:
         """
         Validate that LLM API keys are available for hook tools.
 
-        Returns:
+        Returns
             bool: True if API keys are available, False otherwise
         """
         from .agentic_tool import AgenticTool
@@ -641,7 +641,7 @@ class HookManager:
         Args:
             hook_name (str): Name of the hook to retrieve
 
-        Returns:
+        Returns
             Optional[OutputHook]: Hook instance if found, None otherwise
         """
         for hook in self.hooks:
@@ -684,7 +684,7 @@ class HookManager:
         """
         Get the path to the hook configuration file.
 
-        Returns:
+        Returns
             Path: Path to the configuration file
         """
         try:
@@ -934,7 +934,7 @@ class HookManager:
         Args:
             tool_name (str): Name of the tool to check
 
-        Returns:
+        Returns
             bool: True if the tool is a hook tool and should be excluded from hook processing
         """
         hook_tool_names = [
@@ -956,7 +956,7 @@ class HookManager:
         Args:
             hook_config (Dict[str, Any]): Hook configuration
 
-        Returns:
+        Returns
             Optional[OutputHook]: Created hook instance or None if type not supported
         """
         hook_type = hook_config.get("type", "SummarizationHook")
@@ -985,7 +985,7 @@ class HookManager:
         Args:
             hook_config (Dict[str, Any]): Original hook configuration
 
-        Returns:
+        Returns
             Dict[str, Any]: Enhanced configuration with defaults applied
         """
         hook_type = hook_config.get("type", "SummarizationHook")
@@ -1052,7 +1052,7 @@ class HookManager:
             tool_name (str): Name of the current tool
             context (Dict[str, Any]): Execution context
 
-        Returns:
+        Returns
             bool: True if hook is applicable, False otherwise
         """
         # Check tool-specific hooks
@@ -1138,7 +1138,7 @@ class FileSaveHook(OutputHook):
             arguments (Dict[str, Any]): Arguments passed to the tool
             context (Dict[str, Any]): Execution context
 
-        Returns:
+        Returns
             Dict[str, Any]: Dictionary containing file information:
                 - file_path: Path to the saved file
                 - data_format: Format of the data (json, text, binary, etc.)
@@ -1213,7 +1213,7 @@ class FileSaveHook(OutputHook):
         Args:
             data (Any): The data to analyze
 
-        Returns:
+        Returns
             tuple[str, str]: (data_format, data_structure)
         """
         if isinstance(data, dict):

tooluniverse/package_tool.py

@@ -27,7 +27,7 @@ class PackageTool(BaseTool):
         Args:
             arguments (dict): Optional parameters for customization
 
-        Returns:
+        Returns
             dict: Package information including name, description, installation, docs, usage
         """
         include_examples = arguments.get("include_examples", True)

tooluniverse/pmc_tool.py

@@ -43,7 +43,7 @@ class PMCTool(BaseTool):
             date_to: End date filter (YYYY/MM/DD)
             article_type: Article type filter (e.g., 'research-article', 'review')
 
-        Returns:
+        Returns
             List of paper dictionaries
         """
         try:
@@ -158,7 +158,7 @@ class PMCTool(BaseTool):
         Args:
             tool_arguments: Dictionary containing search parameters
 
-        Returns:
+        Returns
             List of paper dictionaries
         """
         query = tool_arguments.get("query", "")

tooluniverse/remote/boltz/boltz_mcp_server.py

@@ -35,7 +35,7 @@ def run_boltz2(query: dict):
             - without_potentials (bool): Whether to run without potentials (default: False)
             - diffusion_samples (int): Number of diffusion samples to generate (default: 1)
             - Additional constraint keys may be included as needed
-    Returns:
+    Returns
         dict: A dictionary containing the docking results with the following structure:
             - predicted_structure (str): The predicted protein-ligand complex structure in CIF format
             - structure_format (str): Format of the structure file (typically 'cif')

tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py

@@ -163,7 +163,7 @@ class DepmapCorrelationTool:
             gene_a (str): First gene symbol (e.g., 'BRAF', 'TP53'). Must be present in dataset.
             gene_b (str): Second gene symbol (e.g., 'MAPK1', 'MDM2'). Must be present in dataset.
 
-        Returns:
+        Returns
             Dict[str, float]: Dictionary containing correlation analysis results:
                 - 'correlation': Pearson correlation coefficient (-1.0 to 1.0)
                 - 'p_value': Statistical significance of correlation
@@ -272,7 +272,7 @@ async def compute_depmap24q2_gene_correlations(
         gene_b (str): Second gene symbol for correlation analysis (e.g., 'MAPK1', 'MDM2').
                      Must use standard HUGO gene nomenclature.
 
-    Returns:
+    Returns
         dict: Comprehensive correlation analysis results containing:
             - 'correlation_data' (dict): Statistical measures including:
                 * 'correlation': Pearson correlation coefficient (-1.0 to 1.0)

tooluniverse/remote/immune_compass/compass_tool.py

@@ -118,7 +118,7 @@ class CompassTool:
             exclude (List[str]): List of column names to exclude from results.
                                Defaults to ['CANCER', 'Reference'].
 
-        Returns:
+        Returns
             List[List[Tuple[str, float]]]: For each sample, a list of tuples containing
                                          (concept_name, concept_score) sorted by score descending.
         """
@@ -161,7 +161,7 @@ class CompassTool:
             batch_size (int): Batch size for model inference. Larger values may improve speed
                             but require more memory. Defaults to 128.
 
-        Returns:
+        Returns
             Tuple[bool, List[Tuple[str, float]]]: A tuple containing:
                 - bool: True if predicted as responder (probability ≥ threshold), False otherwise
                 - List[Tuple[str, float]]: Top immune cell concepts ranked by importance,
@@ -222,7 +222,7 @@ async def run_compass_prediction(
                          Default 0.5 provides balanced sensitivity/specificity.
                          Consider lower thresholds (~0.3) for higher sensitivity.
 
-    Returns:
+    Returns
         dict: Structured prediction results containing:
             - 'prediction' (dict): Core prediction results with:
                 * 'is_responder' (bool): True if predicted responder (probability ≥ threshold)

tooluniverse/remote/pinnacle/pinnacle_tool.py

@@ -101,7 +101,7 @@ class PinnaclePPITool:
                            The method handles various naming conventions including spaces,
                            hyphens, underscores, and capitalization differences.
 
-        Returns:
+        Returns
             Tuple[Dict[str, torch.Tensor], str]: A tuple containing:
                 - Dict mapping protein/gene names to their embedding tensors (empty if no match)
                 - Status message indicating match quality and selected cell type
@@ -198,7 +198,7 @@ async def run_pinnacle_ppi_retrieval(cell_type: str, embed_path: Optional[str] =
                         - Tissue types: 'liver', 'heart', 'brain', 'immune'
                         The tool performs intelligent matching to find the best available match.
 
-    Returns:
+    Returns
         dict: Comprehensive embedding retrieval results containing:
             - 'embeddings' (dict, optional): Protein-to-embedding mapping where:
                 * Keys: Gene/protein symbols (e.g., 'TP53', 'EGFR', 'BRCA1')

tooluniverse/remote/transcriptformer/transcriptformer_tool.py

@@ -105,7 +105,7 @@ class TranscriptformerEmbeddingTool:
         Args:
             disease (str): Disease identifier (normalized to lowercase with underscores).
 
-        Returns:
+        Returns
             Dict: Cached metadata dictionary containing:
                 - store_path: Path to disease-specific embedding store
                 - ensembl_ids_ordered: Ordered list of Ensembl gene IDs
@@ -213,7 +213,7 @@ class TranscriptformerEmbeddingTool:
             disease (str): Disease context identifier (e.g., 'breast_cancer', 'diabetes').
                          Must match available disease stores.
 
-        Returns:
+        Returns
             Tuple[Optional[Dict[str, np.ndarray]], List[str]]: A tuple containing:
                 - Dictionary mapping gene names to embedding vectors (None if failed)
                 - List of context information and error messages
@@ -416,7 +416,7 @@ async def run_transcriptformer_embedding_retrieval(
                     - 'alzheimer': Alzheimer's disease contexts
                     Must match available disease stores.
 
-    Returns:
+    Returns
         dict: Comprehensive embedding retrieval results containing:
             - 'embeddings' (dict, optional): Gene-to-embedding mapping where:
                 * Keys: Gene identifiers (symbols or Ensembl IDs as provided)

tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py

@@ -29,7 +29,7 @@ def download_abst(query: dict):
     """Retrieve the abstract of a patent application by its application number.
     Args:
         "query" dict: A dictionary containing the application number under the key "applicationNumberText".
-    Returns:
+    Returns
         dict: A dictionary containing the abstract text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.
     """
     return agents["get_abstract_from_patent_app_number"].run(query)
@@ -40,7 +40,7 @@ def download_claims(query: dict):
     """Retrieve the claims of a patent application by its application number.
     Args:
         "query" dict: A dictionary containing the application number under the key "applicationNumberText".
-    Returns:
+    Returns
         dict: A dictionary containing the claims text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.
     """
     return agents["get_claims_from_patent_app_number"].run(query)
@@ -51,7 +51,7 @@ def download_full_text(query: dict):
     """Retrieve the full text of a patent application by its application number.
     Args:
         "query" dict: A dictionary containing the application number under the key "applicationNumberText".
-    Returns:
+    Returns
         dict: A dictionary containing the full text under the 'result' key or an error message under the 'error' key if the document could not be retrieved.
     """
     return agents["get_full_text_from_patent_app_number"].run(query)

tooluniverse/remote_tool.py

@@ -45,7 +45,7 @@ class RemoteTool(BaseTool):
         Args:
             arguments (dict, optional): Tool arguments (ignored)
 
-        Returns:
+        Returns
             dict: Error message indicating the tool is not available locally
         """
         server_type = self.remote_info.get("server_type", "Unknown")
@@ -69,7 +69,7 @@ class RemoteTool(BaseTool):
         """
         Get information about the remote server hosting this tool.
 
-        Returns:
+        Returns
             dict: Remote server information including server type, URL, and original tool type
         """
         return self.remote_info.copy()
@@ -78,7 +78,7 @@ class RemoteTool(BaseTool):
         """
         Check if this tool is available for local execution.
 
-        Returns:
+        Returns
             bool: Always False for RemoteTool instances
         """
         return False
@@ -87,7 +87,7 @@ class RemoteTool(BaseTool):
         """
         Get server connection information for this remote tool.
 
-        Returns:
+        Returns
             dict: Server connection details
         """
         return {

tooluniverse/scripts/filter_tool_files.py

@@ -46,7 +46,7 @@ def filter_tool_relationship_graph(data, valid_tool_names):
         data: The loaded JSON data
         valid_tool_names: Set of valid tool names
 
-    Returns:
+    Returns
         Filtered data
     """
     if not isinstance(data, dict):
@@ -111,7 +111,7 @@ def filter_v4_all_tools(data, valid_tool_names):
         data: The loaded JSON data
         valid_tool_names: Set of valid tool names
 
-    Returns:
+    Returns
         Filtered data
     """
     if not isinstance(data, list):

tooluniverse/smcp.py

@@ -10,8 +10,8 @@ The SMCP module provides a complete solution for exposing scientific computation
 resources through the standardized MCP protocol, making it easy for AI agents to
 discover, understand, and execute scientific tools in a unified manner.
 
-Usage Patterns:
-===============
+Usage Patterns
+--------------
 
 Quick Start:
 
@@ -47,8 +47,8 @@ result = await client.call_tool("UniProt_get_entry_by_accession", {
 })
 ```
 
-Architecture:
-=============
+Architecture
+------------
 
 ┌─────────────────┐    ┌──────────────────┐    ┌─────────────────┐
 │   MCP Client    │◄──►│      SMCP        │◄──►│  ToolUniverse   │
@@ -69,8 +69,8 @@ The SMCP server acts as an intelligent middleware layer that:
 4. Returns formatted results via MCP protocol
 5. Provides intelligent tool discovery and recommendation
 
-Integration Points:
-==================
+Integration Points
+------------------
 
 MCP Protocol Layer:
     - Standard MCP methods (tools/list, tools/call, etc.)
@@ -219,6 +219,21 @@ class SMCP(FastMCP):
         during tool loading. Useful for excluding entire categories of tools
         (e.g., all ToolFinder types or all OpenTarget tools).
 
+    space : str or list of str, optional
+        Space configuration URI(s) to load. Can be a single URI string or a list
+        of URIs for loading multiple Space configurations. Supported formats:
+        - Local file: "./config.yaml" or "/path/to/config.yaml"
+        - HuggingFace: "hf:username/repo" or "hf:username/repo/file.yaml"
+        - HTTP URL: "https://example.com/config.yaml"
+
+        When provided, Space configurations are loaded after tool initialization,
+        applying LLM settings, hooks, and tool selections from the configuration files.
+        Multiple spaces can be loaded sequentially, with later configurations
+        potentially overriding earlier ones.
+
+        Example: space="./my-workspace.yaml"
+        Example: space=["hf:community/bio-tools", "./custom-tools.yaml"]
+
     auto_expose_tools : bool, default True
         Whether to automatically expose ToolUniverse tools as MCP tools.
         When True, all loaded tools become available via the MCP interface
@@ -281,6 +296,7 @@ class SMCP(FastMCP):
         tool_config_files: Optional[Dict[str, str]] = None,
         include_tool_types: Optional[List[str]] = None,
         exclude_tool_types: Optional[List[str]] = None,
+        space: Optional[Union[str, List[str]]] = None,
         auto_expose_tools: bool = True,
         search_enabled: bool = True,
         max_workers: int = 5,
@@ -325,6 +341,7 @@ class SMCP(FastMCP):
         self.tool_config_files = tool_config_files or {}
         self.include_tool_types = include_tool_types or []
         self.exclude_tool_types = exclude_tool_types or []
+        self.space = space
         self.auto_expose_tools = auto_expose_tools
         self.search_enabled = search_enabled
         self.max_workers = max_workers
@@ -332,18 +349,61 @@ class SMCP(FastMCP):
         self.hook_config = hook_config
         self.hook_type = hook_type
 
+        # Space configuration storage
+        self.space_llm_config = None
+        self.space_metadata = None
+
         # Thread pool for concurrent tool execution
         self.executor = ThreadPoolExecutor(max_workers=max_workers)
 
         # Track exposed tools to avoid duplicates
         self._exposed_tools = set()
 
-        # Initialize SMCP-specific features
+        # Load Space configurations first if provided
+        if space:
+            self._load_space_configs(space)
+
+        # Initialize SMCP-specific features (after Space is loaded)
         self._setup_smcp_tools()
 
         # Register custom MCP methods
         self._register_custom_mcp_methods()
 
+    def _load_space_configs(self, space: Union[str, List[str]]):
+        """
+        Load Space configurations.
+
+        This method loads Space configuration(s) and retrieves the LLM config
+        and metadata from ToolUniverse. It completely reuses ToolUniverse's
+        load_space functionality without reimplementing any logic.
+
+        Args:
+            space: Space URI or list of URIs (e.g., "./config.yaml",
+                      "hf:user/repo", or ["config1.yaml", "config2.yaml"])
+        """
+        space_list = [space] if isinstance(space, str) else space
+
+        for uri in space_list:
+            print(f"📦 Loading Space: {uri}")
+
+            # Directly call ToolUniverse's method (complete reuse)
+            config = self.tooluniverse.load_space(uri)
+
+            # Get configurations from ToolUniverse (complete reuse)
+            self.space_metadata = self.tooluniverse.get_space_metadata()
+            self.space_llm_config = self.tooluniverse.get_space_llm_config()
+
+            print(f"✅ Space loaded: {config.get('name', 'Unknown')}")
+
+    def get_llm_config(self) -> Optional[Dict[str, Any]]:
+        """
+        Get the current Space LLM configuration.
+
+        Returns:
+            LLM configuration dictionary or None if not set
+        """
+        return self.space_llm_config
+
     def _register_custom_mcp_methods(self):
         """
         Register custom MCP protocol methods for enhanced functionality.
@@ -857,9 +917,28 @@ class SMCP(FastMCP):
         - All setup phases include comprehensive error handling
         - Performance scales with the number of tools being loaded and exposed
         """
-        # Always ensure full tool set is loaded (hooks may have preloaded a minimal set)
-        # Deduplication in ToolUniverse.load_tools prevents duplicates, so reloading is safe
-        if self.tool_categories:
+        # Determine if ToolUniverse already has tools loaded (e.g., provided pre-configured instance)
+        preloaded_tools = getattr(self.tooluniverse, "all_tools", [])
+        preloaded_count = (
+            len(preloaded_tools) if isinstance(preloaded_tools, list) else 0
+        )
+
+        if preloaded_count > 0:
+            self.logger.info(
+                f"ToolUniverse already pre-configured with {preloaded_count} tool(s); skipping automatic loading."
+            )
+
+        # Check if Space has already loaded specific tools
+        if (
+            self.space
+            and hasattr(self.tooluniverse, "_current_space_config")
+            and preloaded_count > 0
+        ):
+            # Space has already loaded specific tools, don't reload all tools
+            self.logger.info(
+                f"Space configuration loaded {preloaded_count} tool(s), skipping additional loading"
+            )
+        elif preloaded_count == 0 and self.tool_categories:
             try:
                 # Validate categories first
                 valid_categories = self._get_valid_categories()
@@ -924,8 +1003,10 @@ class SMCP(FastMCP):
                     include_tool_types=self.include_tool_types,
                     exclude_tool_types=self.exclude_tool_types,
                 )
-        elif self.auto_expose_tools:
-            # Load all tools by default
+        elif self.auto_expose_tools and not (
+            self.space and hasattr(self.tooluniverse, "_current_space_config")
+        ):
+            # Load all tools by default (unless Space already handled tool loading)
             self.tooluniverse.load_tools(
                 exclude_tools=self.exclude_tools,
                 exclude_categories=self.exclude_categories,