aurelian 0.3.4__py3-none-any.whl → 0.4.2__py3-none-any.whl

aurelian/agents/biblio/biblio_agent.py

@@ -30,6 +30,7 @@ biblio_agent = Agent(
         " tables for this. Use your judgment in how to roll up tables, and whether values"
         " should be present/absent, increased/decreased, or more specific."
     ),
+    defer_model_check=True,
 )
 
 

aurelian/agents/checklist/checklist_agent.py

@@ -22,6 +22,7 @@ checklist_agent = Agent(
         "\nThe available checklists are:"
     ),
     deps_type=ChecklistDependencies,
+    defer_model_check=True,
 )
 
 

aurelian/agents/chemistry/chemistry_agent.py

@@ -39,7 +39,8 @@ chemistry_agent = Agent(
         Tool(retrieve_chemistry_web_page),
         Tool(inspect_file),
         Tool(list_files),
-    ]
+    ],
+    defer_model_check=True,
 )
 
 # Remove the chat import to avoid circular imports

aurelian/agents/d4d/__init__.py

@@ -3,7 +3,7 @@ D4D (Datasheets for Datasets) agent package for extracting dataset metadata.
 """
 
 # isort: skip_file
-from .d4d_agent import data_sheets_agent  # noqa: E402
+from .d4d_agent import d4d_agent  # noqa: E402
 from .d4d_config import D4DConfig, get_config  # noqa: E402
 from .d4d_gradio import chat  # noqa: E402
 from .d4d_tools import (  # noqa: E402
@@ -14,7 +14,7 @@ from .d4d_tools import (  # noqa: E402
 
 __all__ = [
     # Agent
-    "data_sheets_agent",
+    "d4d_agent",
     
     # Config
     "D4DConfig",

aurelian/agents/d4d/d4d_agent.py

@@ -8,7 +8,7 @@ from .d4d_tools import get_full_schema, process_website_or_pdf
 
 
 # Create the agent, the full schema will be loaded when needed
-data_sheets_agent = Agent(
+d4d_agent = Agent(
     model="openai:gpt-4o",
     deps_type=D4DConfig,
     system_prompt="""
@@ -21,10 +21,11 @@ content, extract all the relevant metadata, and output a YAML document that exac
 conforms to the above schema. The output must be valid YAML with all required fields 
 filled in, following the schema exactly.
 """,
+    defer_model_check=True,
 )
 
 
-@data_sheets_agent.system_prompt
+@d4d_agent.system_prompt
 async def add_schema(ctx: RunContext[D4DConfig]) -> str:
     """
     Add the full schema to the system prompt.
@@ -39,7 +40,7 @@ async def add_schema(ctx: RunContext[D4DConfig]) -> str:
     return schema
 
 
-@data_sheets_agent.tool
+@d4d_agent.tool
 async def extract_metadata(ctx: RunContext[D4DConfig], url: str) -> str:
     """
     Extract metadata from a dataset description document or webpage.

aurelian/agents/d4d/d4d_gradio.py

@@ -5,7 +5,7 @@ from typing import List, Optional
 
 import gradio as gr
 
-from .d4d_agent import data_sheets_agent
+from .d4d_agent import d4d_agent
 from .d4d_config import D4DConfig, get_config
 
 
@@ -22,7 +22,7 @@ async def process_url(url: str, history: List[str], config: D4DConfig) -> str:
         YAML formatted metadata
     """
     # Run the agent with the URL
-    result = await data_sheets_agent.run(url, deps=config)
+    result = await d4d_agent.run(url, deps=config)
     return result.data
 
 

aurelian/agents/diagnosis/diagnosis_agent.py

@@ -44,6 +44,7 @@ diagnosis_agent = Agent(
     deps_type=DiagnosisDependencies,
     result_type=str,
     system_prompt=DIAGNOSIS_SYSTEM_PROMPT,
+    defer_model_check=True,
 )
 
 # Register tools

aurelian/agents/gocam/__init__.py

@@ -3,11 +3,13 @@ GOCAM agent module for working with Gene Ontology Causal Activity Models.
 """
 from pathlib import Path
 
+from ...evaluators.substring_evaluator import SubstringEvaluator
+
 THIS_DIR = Path(__file__).parent
 DOCUMENTS_DIR = THIS_DIR / "documents"
 
 # isort: skip_file
-from .gocam_agent import gocam_agent  # noqa: E402
+from .gocam_agent import gocam_agent, gocam_reviewer_agent, gocam_review_summarizer_agent  # noqa: E402
 from .gocam_config import GOCAMDependencies, get_config  # noqa: E402
 from .gocam_gradio import chat  # noqa: E402
 from .gocam_tools import (  # noqa: E402
@@ -18,6 +20,7 @@ from .gocam_tools import (  # noqa: E402
     fetch_document,
     validate_gocam_model,
 )
+from .gocam_evals import create_eval_dataset  # noqa: E402
 
 __all__ = [
     # Constants
@@ -26,6 +29,8 @@ __all__ = [
     
     # Agent
     "gocam_agent",
+    "gocam_reviewer_agent",
+    "gocam_review_summarizer_agent",
     # Config
     "GOCAMDependencies",
     "get_config",
@@ -40,4 +45,8 @@ __all__ = [
     
     # Gradio
     "chat",
+    
+    # Evals
+    "create_eval_dataset",
+    "SubstringEvaluator",
 ]

aurelian/agents/gocam/gocam_agent.py

@@ -135,6 +135,7 @@ gocam_agent = Agent(
     deps_type=GOCAMDependencies,
     system_prompt=SYSTEM,
     tools=core_tools,
+    defer_model_check=True,
 )
 
 def get_documents_for_prompt() -> str:
@@ -208,6 +209,7 @@ gocam_reviewer_agent = Agent(
         Tool(lookup_gocam_local),
         #Tool(validate_gocam_model),
     ],
+    defer_model_check=True,
 )
 
 
@@ -237,4 +239,5 @@ gocam_review_summarizer_agent = Agent(
         #Tool(lookup_gocam_local),
     ],
     result_type=GOCamReviewSummary,
+    defer_model_check=True,
 )

aurelian/agents/gocam/gocam_evals.py

@@ -14,9 +14,6 @@ from pydantic_evals import Case, Dataset
 from aurelian.agents.gocam.gocam_agent import gocam_agent
 from aurelian.agents.gocam.gocam_config import GOCAMDependencies
 
-class GOCAMMetadata(Dict[str, Any]):
-    """Simple metadata dictionary for GO-CAM evaluations."""
-    pass
 
 # Define individual evaluation cases
 case1 = Case(

aurelian/agents/linkml/linkml_mcp.py

@@ -56,7 +56,6 @@ async def inspect_file(data_file: str) -> str:
     Inspect a file in the working directory.
 
     Args:
-        ctx:
         data_file: name of file
 
     Returns:
@@ -71,7 +70,6 @@ async def list_files() -> str:
     List files in the working directory.
 
     Args:
-        ctx:
 
     Returns:
 
@@ -84,7 +82,6 @@ async def write_to_file(data: str, file_name: str) -> str:
     Write data to a file in the working directory.
 
     Args:
-        ctx:
         data:
         file_name:
 
@@ -104,7 +101,6 @@ async def validate_data(schema: str, data_file: str) -> str:
     You can write data to the working directory using the `write_to_file` tool.
 
     Args:
-        ctx:
         schema: the schema (as a YAML string)
         data_file: the name of the data file in the working directory
 
@@ -167,7 +163,6 @@ async def download_web_page(url: str, local_file_name: str) -> str:
     Download contents of a web page.
 
     Args:
-        ctx:
         url: URL of the web page
         local_file_name: Name of the local file to save the
 
@@ -183,4 +178,4 @@ async def download_web_page(url: str, local_file_name: str) -> str:
 
 if __name__ == "__main__":
     # Initialize and run the server
-    mcp.run(transport='stdio')
+    mcp.run(transport='stdio')

aurelian/agents/literature/literature_agent.py

@@ -1,6 +1,7 @@
 """
 Agent for working with scientific literature and publications.
 """
+from aurelian.agents.web.web_tools import perplexity_query
 from aurelian.agents.literature.literature_config import LiteratureDependencies
 from aurelian.agents.literature.literature_tools import (
     lookup_pmid,
@@ -48,6 +49,25 @@ literature_agent = Agent(
         Tool(get_article_abstract),
         Tool(extract_text_from_pdf_url),
         Tool(search_literature_web),
+        #Tool(perplexity_query), 
+        Tool(retrieve_literature_page),
+        Tool(inspect_file),
+        Tool(list_files),
+    ]
+)
+
+advanced_literature_agent = Agent(
+    model="openai:gpt-4o",
+    deps_type=LiteratureDependencies,
+    system_prompt=SYSTEM,
+    tools=[
+        Tool(lookup_pmid),
+        Tool(lookup_doi),
+        Tool(convert_pmid_to_doi),
+        Tool(convert_doi_to_pmid),
+        Tool(get_article_abstract),
+        Tool(extract_text_from_pdf_url),
+        Tool(perplexity_query), 
         Tool(retrieve_literature_page),
         Tool(inspect_file),
         Tool(list_files),

aurelian/agents/monarch/__init__.py

@@ -1,25 +0,0 @@
-"""
-Monarch agent package for interacting with the Monarch Knowledge Base.
-"""
-
-from .monarch_agent import monarch_agent, MONARCH_SYSTEM_PROMPT
-from .monarch_config import MonarchDependencies, get_config
-from .monarch_gradio import chat
-from .monarch_tools import find_gene_associations, find_disease_associations
-
-__all__ = [
-    # Agent
-    "monarch_agent",
-    "MONARCH_SYSTEM_PROMPT",
-    
-    # Config
-    "MonarchDependencies",
-    "get_config",
-    
-    # Tools
-    "find_gene_associations",
-    "find_disease_associations",
-    
-    # Gradio
-    "chat",
-]

aurelian/agents/monarch/monarch_agent.py

@@ -37,6 +37,7 @@ monarch_agent = Agent(
     model="openai:gpt-4o",
     system_prompt=MONARCH_SYSTEM_PROMPT,
     deps_type=MonarchDependencies,
+    defer_model_check=True,
 )
 
 # Register the tools with the agent

aurelian/agents/monarch/monarch_tools.py

@@ -7,7 +7,6 @@ from typing import Dict, List, Optional
 from pydantic_ai import RunContext, ModelRetry
 
 from aurelian.utils.data_utils import obj_to_dict
-from aurelian.utils.async_utils import run_sync
 from .monarch_config import MonarchDependencies, get_config
 
 

aurelian/agents/ontology_mapper/ontology_mapper_agent.py

@@ -39,6 +39,7 @@ ontology_mapper_agent = Agent(
     deps_type=OntologyMapperDependencies,
     result_type=str,
     system_prompt=ONTOLOGY_MAPPER_SYSTEM_PROMPT,
+    defer_model_check=True,
 )
 
 # Register the tools with the agent

aurelian/agents/paperqa/paperqa_agent.py

@@ -55,6 +55,7 @@ paperqa_agent = Agent(
     deps_type=PaperQADependencies,
     result_type=str,
     system_prompt=PAPERQA_SYSTEM_PROMPT,
+    defer_model_check=True,
 )
 
 paperqa_agent.tool(search_papers)

aurelian/agents/rag/rag_agent.py

@@ -18,6 +18,7 @@ rag_agent = Agent(
         "  - `inspect_document` to retrieve a specific document (by title/name)"
         "You can also use `lookup_pmid` to retrieve the text of a PubMed ID, or `search_web` to search the web."
     ),
+    defer_model_check=True,
 )
 
 

aurelian/agents/talisman/talisman_mcp.py

@@ -1,168 +1,75 @@
 """
-MCP integration for the Talisman agent.
+MCP tools for retrieving gene information using the UniProt API and NCBI Entrez.
 """
-import json
 import os
-from typing import Dict, Any, List, Optional
 
-from anthropic import Anthropic
-from pydantic_ai import Agent
+from mcp.server.fastmcp import FastMCP
 
-# Import directly from the MCP module
-from .talisman_agent import talisman_agent, TALISMAN_SYSTEM_PROMPT
-from .talisman_config import TalismanConfig, get_config
+from aurelian.agents.talisman.talisman_agent import TALISMAN_SYSTEM_PROMPT
+from aurelian.agents.talisman.talisman_config import TalismanConfig, get_config
+from aurelian.agents.talisman.talisman_tools import (
+    get_gene_description,
+    get_gene_descriptions,
+    get_genes_from_list,
+    analyze_gene_set
+)
 
+from pydantic_ai import RunContext
 
-def tools_to_anthropic_tools(agent: Agent) -> List[Dict[str, Any]]:
-    """Convert pydantic-ai Agent tools to Anthropic tools format.
+# Initialize FastMCP server
+mcp = FastMCP("talisman", instructions=TALISMAN_SYSTEM_PROMPT)
+
+def deps() -> TalismanConfig:
+    """Get the Talisman dependencies."""
+    return get_config()
+
+def ctx() -> RunContext[TalismanConfig]:
+    """Get the run context with dependencies."""
+    rc: RunContext[TalismanConfig] = RunContext[TalismanConfig](
+        deps=deps(),
+        model=None, usage=None, prompt=None,
+    )
+    return rc
+
+@mcp.tool()
+async def get_gene_info(gene_id: str) -> str:
+    """
+    Get description for a single gene ID.
     
     Args:
-        agent: The pydantic-ai Agent with tools
+        gene_id: The gene identifier (UniProt ID, gene symbol, etc.)
         
     Returns:
-        A list of tools in the Anthropic format
+        The gene description in a structured format
     """
-    anthropic_tools = []
-    for tool in agent.tools:
-        anthropic_tool = {
-            "name": tool.name,
-            "description": tool.description,
-            "input_schema": {
-                "type": "object",
-                "properties": {},
-                "required": []
-            }
-        }
-        
-        for param_name, param in tool.params.items():
-            if param_name == "ctx":
-                continue
-                
-            param_schema = {"type": "string"}
-            if param.annotation.__origin__ == list:
-                param_schema = {
-                    "type": "array",
-                    "items": {"type": "string"}
-                }
-                
-            anthropic_tool["input_schema"]["properties"][param_name] = param_schema
-            if param.default == param.empty:
-                anthropic_tool["input_schema"]["required"].append(param_name)
-                
-        anthropic_tools.append(anthropic_tool)
-        
-    return anthropic_tools
-
+    return get_gene_description(ctx(), gene_id)
 
-def create_bedrock_compatible_resp(
-    response_id: str, 
-    model: str, 
-    role: str, 
-    content: List[Dict[str, Any]]
-) -> Dict[str, Any]:
-    """Create a response compatible with the Bedrock format.
+@mcp.tool()
+async def get_multiple_gene_info(gene_ids: str) -> str:
+    """
+    Get descriptions for multiple gene IDs provided as a string.
     
     Args:
-        response_id: The response ID
-        model: The model name
-        role: The role (usually 'assistant')
-        content: The content from the Anthropic response
+        gene_ids: String containing gene identifiers separated by commas, spaces, or newlines
         
     Returns:
-        A response in the Bedrock format
+        The gene descriptions in a structured format
     """
-    return {
-        "id": response_id,
-        "model": model,
-        "choices": [
-            {
-                "message": {
-                    "role": role,
-                    "content": content
-                }
-            }
-        ]
-    }
-
+    return get_genes_from_list(ctx(), gene_ids)
 
-def get_talisman_mcp_tools() -> List[Dict[str, Any]]:
-    """Get the MCP tools for the Talisman agent.
-
-    Returns:
-        A list of tools in the MCP format
+@mcp.tool()
+async def analyze_genes(gene_list: str) -> str:
     """
-    return tools_to_anthropic_tools(talisman_agent)
-
-
-def get_talisman_mcp_messages(
-    messages: Optional[List[Dict[str, Any]]] = None,
-    system: Optional[str] = None,
-) -> List[Dict[str, Any]]:
-    """Get MCP messages for the Talisman agent.
-
-    Args:
-        messages: Previous messages
-        system: System message override
-
-    Returns:
-        List of MCP messages
-    """
-    if messages is None:
-        messages = []
-    
-    if system is None:
-        system = TALISMAN_SYSTEM_PROMPT
+    Analyze a set of genes and generate a biological summary of their properties and relationships.
     
-    if not messages or messages[0].get("role") != "system":
-        messages = [{"role": "system", "content": system}] + messages
-    
-    return messages
-
-
-def handle_talisman_mcp_request(
-    messages: List[Dict[str, Any]],
-    config: Optional[TalismanConfig] = None,
-    model: str = "claude-3-5-sonnet-20240620",
-    max_tokens: int = 4096,
-    temperature: float = 0.0,
-) -> Dict[str, Any]:
-    """Handle an MCP request for the Talisman agent.
-
     Args:
-        messages: The messages from the client
-        config: The Talisman configuration (optional)
-        model: The model to use
-        max_tokens: The maximum number of tokens to generate
-        temperature: The temperature to use for generation
-
+        gene_list: String containing gene identifiers separated by commas, spaces, or newlines
+        
     Returns:
-        An MCP response
+        A structured biological summary of the gene set with Narrative, Functional Terms Table, and Gene Summary Table
     """
-    config = config or get_config()
-    
-    api_key = os.environ.get("ANTHROPIC_API_KEY")
-    if not api_key:
-        raise ValueError("ANTHROPIC_API_KEY environment variable is required for MCP")
-
-    client = Anthropic(api_key=api_key)
-    
-    # Prepare the messages and tools
-    mcp_messages = get_talisman_mcp_messages(messages)
-    mcp_tools = get_talisman_mcp_tools()
-    
-    # Send the request to Anthropic
-    response = client.messages.create(
-        model=model,
-        messages=mcp_messages,
-        tools=mcp_tools,
-        max_tokens=max_tokens,
-        temperature=temperature,
-    )
+    return analyze_gene_set(ctx(), gene_list)
 
-    # Return the response in a format compatible with the MCP protocol
-    return create_bedrock_compatible_resp(
-        response_id=response.id,
-        model=model,
-        role="assistant",
-        content=response.content,
-    )
+if __name__ == "__main__":
+    # Initialize and run the server
+    mcp.run(transport='stdio')

aurelian/agents/ubergraph/ubergraph_agent.py

@@ -50,6 +50,7 @@ ubergraph_agent = Agent(
     "openai:gpt-4o",
     deps_type=Dependencies,
     result_type=str,
+    defer_model_check=True,
 )
 
 # Register tools

aurelian/agents/ubergraph/ubergraph_tools.py

@@ -4,9 +4,9 @@ Tools for interacting with the UberGraph SPARQL endpoint.
 import asyncio
 from typing import Any, Dict, List, Optional
 
+import requests
 from pydantic import BaseModel
 from pydantic_ai import RunContext, ModelRetry
-from SPARQLWrapper import JSON, SPARQLWrapper
 
 from .ubergraph_config import Dependencies, get_config
 
@@ -88,13 +88,23 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
     print("##")
     
     try:
-        # Create SPARQL wrapper
-        sw = SPARQLWrapper(endpoint)
-        sw.setQuery(prefixed_query)
-        sw.setReturnFormat(JSON)
+        # Define a function to execute in a thread pool
+        def run_query():
+            response = requests.post(
+                endpoint,
+                data={
+                    'query': prefixed_query,
+                },
+                headers={
+                    'Accept': 'application/sparql-results+json',
+                    'Content-Type': 'application/x-www-form-urlencoded'
+                }
+            )
+            response.raise_for_status()  # Raise an exception for HTTP errors
+            return response.json()
         
         # Execute the query in a thread pool
-        ret = await asyncio.to_thread(sw.queryAndConvert)
+        ret = await asyncio.to_thread(run_query)
         
         # Process the results
         results = simplify_results(ret, prefixes, limit=config.max_results)
@@ -105,6 +115,8 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
             raise ModelRetry(f"No results found for SPARQL query. Try refining your query.")
             
         return QueryResults(results=results)
+    except requests.RequestException as e:
+        raise ModelRetry(f"Error connecting to SPARQL endpoint: {str(e)}")
     except Exception as e:
         if "ModelRetry" in str(type(e)):
             raise e

aurelian/agents/uniprot/__init__.py

@@ -1,37 +0,0 @@
-"""
-UniProt agent package for interacting with the UniProt database.
-"""
-
-from .uniprot_agent import uniprot_agent, UNIPROT_SYSTEM_PROMPT
-from .uniprot_config import UniprotConfig, get_config
-from .uniprot_gradio import chat
-from .uniprot_mcp import (
-    get_uniprot_mcp_tools,
-    get_uniprot_mcp_messages,
-    handle_uniprot_mcp_request,
-)
-from .uniprot_tools import lookup_uniprot_entry, search, uniprot_mapping, normalize_uniprot_id
-
-__all__ = [
-    # Agent
-    "uniprot_agent",
-    "UNIPROT_SYSTEM_PROMPT",
-    
-    # Config
-    "UniprotConfig",
-    "get_config",
-    
-    # Tools
-    "lookup_uniprot_entry",
-    "search",
-    "uniprot_mapping",
-    "normalize_uniprot_id",
-    
-    # Gradio
-    "chat",
-    
-    # MCP
-    "get_uniprot_mcp_tools",
-    "get_uniprot_mcp_messages",
-    "handle_uniprot_mcp_request",
-]

aurelian/agents/web/web_tools.py

@@ -43,9 +43,11 @@ async def search_web(query: str) -> str:
     return web_search(query)
 
 
-async def perplexity_query(query: str, model_name: str = "sonar") -> ResultWithCitations:
+async def perplexity_query(query: str, model_name: str = "sonar-pro") -> ResultWithCitations:
     """
     Query the Perplexity API and return structured results with citations.
+
+    The Perplexity API performs a web search and returns a structured response with citations.
     
     Args:
         query: The query to send to Perplexity
@@ -58,14 +60,25 @@ async def perplexity_query(query: str, model_name: str = "sonar") -> ResultWithC
         ValueError: If the Perplexity API key is not set
         RuntimeError: If the response parsing fails
     """
+    # TODO: consider using perplexity API directly, gives control over search domains, e.g. https://docs.perplexity.ai/guides/search-domain-filters
     perplexity_api_key = os.environ.get("PERPLEXITY_API_KEY")
     if not perplexity_api_key:
         raise ValueError("PERPLEXITY_API_KEY environment variable is not set")
         
+    # Use specific implementation instead of OpenAIModel directly
+    # since OpenAIModel doesn't accept base_url and api_key params directly
+    from pydantic_ai.models.openai import Provider
+    from pydantic_ai.providers.openai import OpenAIProvider
+
+    
+    provider = OpenAIProvider(
+        api_key=perplexity_api_key,
+        base_url='https://api.perplexity.ai'
+    )
+    
     sonar_model = OpenAIModel(
         model_name=model_name,
-        base_url='https://api.perplexity.ai',
-        api_key=perplexity_api_key,
+        provider=provider,
     )
     
     agent = Agent(sonar_model,

aurelian/cli.py

@@ -4,6 +4,7 @@ import logging
 import os
 from typing import Any, Awaitable, Callable, Optional, List
 
+from aurelian.utils.async_utils import run_sync
 import click
 from pydantic_ai.models.openai import OpenAIModel
 from pydantic_ai.providers.openai import OpenAIProvider
@@ -550,6 +551,14 @@ def websearch(term):
     txt = web_search(term)
     print(txt)
 
+@main.command()
+@click.argument("term")
+def perplexity(term):
+    """Search the web for a query term, with citations."""
+    from aurelian.agents.web.web_tools import perplexity_query
+    result = run_sync(perplexity_query(term))
+    import yaml
+    print(yaml.dump(result.model_dump(), indent=2))
 
 @main.command()
 @click.argument("url")

aurelian/evaluators/model.py

@@ -0,0 +1,9 @@
+# Use TypedDict for metadata
+from typing_extensions import TypedDict
+
+
+MetadataDict = TypedDict("Metadata", {"difficulty": str, "type": str})
+
+
+def metadata(difficulty: str, type: str) -> MetadataDict:
+    return {"difficulty": difficulty, "type": type}

aurelian/evaluators/substring_evaluator.py

@@ -0,0 +1,30 @@
+from pydantic_evals.evaluators import Evaluator, EvaluatorContext
+
+
+class SubstringEvaluator(Evaluator[str, str]):
+    """
+    Custom evaluator for GO-CAM agent responses.
+
+    This evaluator checks if the expected substring is present in the agent's response.
+    If no expected output is specified, it assumes the test passes (for cases where we
+    only want to verify the agent doesn't error out).
+    """
+
+    def evaluate(self, ctx: EvaluatorContext[str, str]) -> float:
+        """
+        Evaluate GO-CAM agent response by checking for expected substring.
+
+        Args:
+            ctx: The evaluator context containing input, output, and expected output
+
+        Returns:
+            Score between 0.0 and 1.0 (1.0 = pass, 0.0 = fail)
+        """
+        # If no expected output is specified, return 1.0 (success)
+        if ctx.expected_output is None:
+            return 1.0
+
+        # Check if expected string is in output
+        if ctx.expected_output.lower() in ctx.output.lower():
+            return 1.0
+        return 0.0

aurelian/utils/async_utils.py

@@ -1,11 +1,14 @@
 import asyncio
-from typing import Callable
+from typing import Callable, Coroutine
 
 
-def run_sync(f: Callable):
+def run_sync(f: Callable | Coroutine):
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
-    result = f()
+    if isinstance(f, Coroutine):
+        result = f
+    else:
+        result = f()
 
     # Ensure it's a coroutine before running it
     if asyncio.iscoroutine(result):

{aurelian-0.3.4.dist-info → aurelian-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aurelian
-Version: 0.3.4
+Version: 0.4.2
 Summary: aurelian
 License: MIT
 Author: Author 1
@@ -17,6 +17,7 @@ Provides-Extra: gocam
 Provides-Extra: gradio
 Provides-Extra: linkml
 Provides-Extra: pdfminer
+Provides-Extra: pypaperbot
 Provides-Extra: rdkit
 Requires-Dist: bioservices (>=1.12.0) ; extra == "bioservices"
 Requires-Dist: bs4 (>=0.0.2)
@@ -30,13 +31,14 @@ Requires-Dist: linkml ; extra == "linkml"
 Requires-Dist: linkml-store[llm,mongodb] (>=0.2.4)
 Requires-Dist: logfire (>=3.5.3)
 Requires-Dist: markdownify (>=0.14.1)
-Requires-Dist: markitdown (>=0.0.1a4)
+Requires-Dist: markitdown (>=0.1.1)
 Requires-Dist: mcp[cli] (>=1.3.0,<2.0.0)
 Requires-Dist: oaklib (>=0.6.19)
+Requires-Dist: onnxruntime (<=1.19.0)
 Requires-Dist: paper-qa (>=5.20.0,<6.0.0)
 Requires-Dist: pdfminer-six ; extra == "pdfminer"
-Requires-Dist: pydantic-ai (>=0.0.29)
-Requires-Dist: pypaperbot (>=1.4.1)
+Requires-Dist: pydantic-ai (>=0.2.0)
+Requires-Dist: pypaperbot (>=1.4.1) ; extra == "pypaperbot"
 Requires-Dist: pytest-asyncio (>=0.25.3,<0.26.0)
 Requires-Dist: rdkit ; extra == "rdkit" or extra == "chem"
 Requires-Dist: tabulate (>=0.9.0)

{aurelian-0.3.4.dist-info → aurelian-0.4.2.dist-info}/RECORD

@@ -8,14 +8,14 @@ aurelian/agents/amigo/amigo_gradio.py,sha256=UYJW2ZdDQJz77wZNetxejWEI5tz39lVRWXZ
 aurelian/agents/amigo/amigo_mcp.py,sha256=byLMDguj_osVV5Q4m1Fp_I1megZm28TzV3YVoi5qa1Q,3831
 aurelian/agents/amigo/amigo_tools.py,sha256=upTjjw4rKCFe3qX-633-9mlQZmXGcNsU8IV7Zd9XJvE,5561
 aurelian/agents/biblio/__init__.py,sha256=xBuwjRYjyWRbABMaa7NaMwJUmSDj0AATQ_55Oy_FitA,814
-aurelian/agents/biblio/biblio_agent.py,sha256=LmBFJhF_t10WYM7j0WrX-8eiKwR8YiBY-mgbm3_l4lw,3698
+aurelian/agents/biblio/biblio_agent.py,sha256=7icG6TzCr1vNgkMHju662IceRQOsEt5XLkipnybxHlw,3726
 aurelian/agents/biblio/biblio_config.py,sha256=K2crtuWIsvzLaoD0bINrx7_VPucp4Qwbfwj8DEn_09E,1254
 aurelian/agents/biblio/biblio_gradio.py,sha256=4YTqYn4Jw0MX29udZ4iCJP-YXKl9yQdPAwouPRr_B1I,1911
 aurelian/agents/biblio/biblio_mcp.py,sha256=zZpRHTc7tVAcBL190sDSPcmvous7vjYx0S0OD8-q4IE,3156
 aurelian/agents/biblio/biblio_tools.py,sha256=tTihpzOTjLBwvMm6QNAHsUb9yWdT4DziOt7t3XWe0_o,4936
 aurelian/agents/biblio_agent.py,sha256=0Uvh6N6AQdva-4NgjOlFHXQFPuEwLyAqUVGtRkokn-U,1241
 aurelian/agents/checklist/__init__.py,sha256=ZN70snI4C871K-76oRCMU3XZPYl_4lKH4VzPUx9tvCg,1034
-aurelian/agents/checklist/checklist_agent.py,sha256=J8IsDzYMc-Ejr3HSP6HCKTbmQYjdymCnUE6gOw3Sfe8,2760
+aurelian/agents/checklist/checklist_agent.py,sha256=G7NpLDSqKvqz3mti1t8SAceFnXHko0knjotqx1YpMQY,2788
 aurelian/agents/checklist/checklist_config.py,sha256=8V_fwWj3dPEyJmcle0nscfvcxdUFiAGsE1T17GnFNIk,828
 aurelian/agents/checklist/checklist_gradio.py,sha256=UOwL7BCjyRsnldP-3RVhzxQsRGLC5QztY8iuAxqjIsY,1981
 aurelian/agents/checklist/checklist_mcp.py,sha256=cQo_VmP_U-A0cQEHBMrgt5gYIr3nkVFTLv-8ucS0D20,2238
@@ -24,22 +24,22 @@ aurelian/agents/checklist/content/checklists.yaml,sha256=QVPp65lnPfRJvHxXgFEFu_W
 aurelian/agents/checklist/content/streams.csv,sha256=VjqssvA05-tdJC5Egr-ZR6RZVTSfHvucZRQFEOlqGm4,50132
 aurelian/agents/checklist_agent.py,sha256=2K1l2ctb8oIWGOqMuWBfuM0WEZ0pa2BiQUefXWAvnJI,1187
 aurelian/agents/chemistry/__init__.py,sha256=_a0iQB50o5cF-t-SI5EkaP8oCeDWc2QKvJ0m628Typ8,68
-aurelian/agents/chemistry/chemistry_agent.py,sha256=L_m-oLaAZsLh4rWS68Vp4HONLLFRsHwjEHBqK05dQfM,1565
+aurelian/agents/chemistry/chemistry_agent.py,sha256=ah8ba8-WLyi-5DIjmRfRURbmienbwyx_h1TXkR16o98,1594
 aurelian/agents/chemistry/chemistry_config.py,sha256=r348qJwBpvp6Q8MbnA3OOOSBjhFj-J_5J68OpKgTijE,1900
 aurelian/agents/chemistry/chemistry_evals.py,sha256=s_elRDsjle8fNrkL4c4Ud2NrFnoCM3goJkcwORhi-4Y,2611
 aurelian/agents/chemistry/chemistry_gradio.py,sha256=2tF6HhRhbJK_3zQfydBn0kwFAJiQQcHzeva8tax4DEM,1545
 aurelian/agents/chemistry/chemistry_mcp.py,sha256=ZS8lXMjCwj60RCv4t6BFxqU0uiiGxLFhWoG9vNb_Ld0,2892
 aurelian/agents/chemistry/chemistry_tools.py,sha256=sJ0FWMqwvf1cOd1XEmdOkViYY7FhWUZ_z0zMD8EyQ30,3387
 aurelian/agents/chemistry/image_agent.py,sha256=Taty5MYbhg7XPzpGgfMeu7Ll6D5f_grClGPF9M3boTE,562
-aurelian/agents/d4d/__init__.py,sha256=cWKTT72IZ1MDQbIjnJfIpufLGooPGfH3VdWmRABleJg,613
-aurelian/agents/d4d/d4d_agent.py,sha256=fMdNhOEdz5_cNAYRSvpVjOTMQMObBmLUO6HCtOav6MY,2115
+aurelian/agents/d4d/__init__.py,sha256=h7jmgzmu_zEU-5HpejrDs0Wsigq4kpvdNLC3s-MHXuI,597
+aurelian/agents/d4d/d4d_agent.py,sha256=tmWb3qnHQcS1o5GMyyePN-UaC7231KOGIPUDEK1-Tg0,2119
 aurelian/agents/d4d/d4d_config.py,sha256=vQz1ym2NDim2cQV4gFMXTDcAEeg5RAVBkWvVIdo7CNo,1471
-aurelian/agents/d4d/d4d_gradio.py,sha256=Xpq0ObbkYgmOa74iBJCDTM9QsdQtTZL4g3nwE-DjUAs,1860
+aurelian/agents/d4d/d4d_gradio.py,sha256=gJXImWqQv9PAPKVlexhdvXqTcDpQWbEi1xLWVGIly9Q,1844
 aurelian/agents/d4d/d4d_mcp.py,sha256=QjRqFd4miAbfFwzos5idHA-wfdN5-djpD2Ot0xogb58,1810
 aurelian/agents/d4d/d4d_tools.py,sha256=ymyWSOOYF6vgv06mpU_GQH7gecIUYluqvT3eXgEhfVA,4803
 aurelian/agents/d4d_agent.py,sha256=hDS5RVisPcKzDX202vYzz54kyGZ1_L8VfBCDfXPlpPk,1896
 aurelian/agents/diagnosis/__init__.py,sha256=HhW4NEjr8Zo6Lqxiq0AW3pzGZu1N8xEkdAd0EG_7fak,668
-aurelian/agents/diagnosis/diagnosis_agent.py,sha256=ID8EkZ8C-YMo3g5TY12ZZ_fBXWyRbp0_klBqd8HSous,2341
+aurelian/agents/diagnosis/diagnosis_agent.py,sha256=-nJ7gwZZ6N6I-A6y9SVxrqKV98b-DgrkAE82jpiZ20s,2369
 aurelian/agents/diagnosis/diagnosis_config.py,sha256=TCoJ9tPmXS0gvXgmziSqAMHKXdl48Mg5AFejS_0Wvxo,1565
 aurelian/agents/diagnosis/diagnosis_evals.py,sha256=FL42urNIAsWo9iMRmpynlrvMYLnazsC9tMPdPm86JG8,2582
 aurelian/agents/diagnosis/diagnosis_gradio.py,sha256=We_ZxhxmlvcxcvVmf2NuflmeHVIYmDJ_LvrO4hL1Y9U,1754
@@ -78,7 +78,7 @@ aurelian/agents/goann/goann_evals.py,sha256=foDikX0KBYcfBamf0G5UWcJstADbNrRB7q_T
 aurelian/agents/goann/goann_gradio.py,sha256=s_mx4Qh2_5SgXdR3NuY_Jr1h38vTjz__-Tv0yk8QLU0,2025
 aurelian/agents/goann/goann_mcp.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/agents/goann/goann_tools.py,sha256=m5nM41nbH45IZ8-BXCaWOX970j0spYwjQJhFs23EvAs,2059
-aurelian/agents/gocam/__init__.py,sha256=0jLnmPKRPv414TUmhOQyDU1WGopelFpIgvMslOM4fEA,883
+aurelian/agents/gocam/__init__.py,sha256=CuXryR9hlrCSdlDSctqKsorHO7jbrI2eGBwcoBDYEJY,1196
 aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.docx,sha256=aohQYDq-iI6dj4AWpWZO-6dG91i_UhJ9Cvre40hsO5I,946469
 aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.pdf,sha256=ffnp3EwWD-guJtv69IEo2y-Sw-mQn-ZiXPK-V2CvWC8,602114
 aurelian/agents/gocam/documents/DNA-binding_transcription_factor_activity_annotation_guidelines.md,sha256=m2C4wIk0snHbG5BEH2ys_u1bisdK6D-2l5rxbWYiDww,5604
@@ -136,10 +136,10 @@ aurelian/agents/gocam/documents/md/Transcription_coregulator_activity.md,sha256=
 aurelian/agents/gocam/documents/md/Transporter_activity_annotation_annotation_guidelines.md,sha256=7wrC8TryecwxXdXN6_XpUP7dHoUZ2-vzCHhLitCm42A,1688
 aurelian/agents/gocam/documents/md/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md,sha256=Ug84Aa640VBwpMom5blksjweKjCutHKUYqBBzwzgG-I,2653
 aurelian/agents/gocam/documents/pandoc_md/Signaling_receptor_activity_annotation_guidelines.md,sha256=TGw39vKs5XE0jF3s0A6XzP4_ovKS3nohqlrGlK7kVFo,11990
-aurelian/agents/gocam/gocam_agent.py,sha256=G5XGiNaVgJjDjv0VLn875Ts5cfNDDq7nLwSahJNtFgw,9413
+aurelian/agents/gocam/gocam_agent.py,sha256=5em_lS64D2eG_srlGU4B_76FTx3NABPAgmTrYcPr1a0,9497
 aurelian/agents/gocam/gocam_config.py,sha256=MU7jRhrkB05kRT-ruPDoPpHMPFCn2y2Od6B13XIj6R0,2492
 aurelian/agents/gocam/gocam_curator_agent.py,sha256=4OK3PoNCNA3pVLV6yq7Rm0ZN7YQ5todAvjJvYzAPPrY,1452
-aurelian/agents/gocam/gocam_evals.py,sha256=ZrzLQaLXkRaqZ3RJrkhYVxu8PWXWKAXzOCmnOp8u34M,2041
+aurelian/agents/gocam/gocam_evals.py,sha256=x9K04niguY2BVtPA99ifj3gb7dIlu5Xt_YEpqpPcky4,1934
 aurelian/agents/gocam/gocam_gradio.py,sha256=Ah1VnlGSYVzLPQel5SbZ-RNsI_QRg0PJBt6VGGIOOfo,3098
 aurelian/agents/gocam/gocam_mcp.py,sha256=S-KT5GuQKtzvq33Qemm1Wwg3jhl64GnGbic_tA4-XoQ,5915
 aurelian/agents/gocam/gocam_tools.py,sha256=tmhXLIYHDbXiteChzV6n-RzRhMiX2GSR9D2b47MmyxI,9671
@@ -148,32 +148,32 @@ aurelian/agents/linkml/linkml_agent.py,sha256=JhYfg-xMGhlj2VqaqeqTZEOhTcBkGzTj5a
 aurelian/agents/linkml/linkml_config.py,sha256=VIPPX7H5eGbw7Rx-YyDorOYVHZz1TQxqFtFKwFtmFwg,1450
 aurelian/agents/linkml/linkml_evals.py,sha256=odQ6unXhobBT6krqYVtdx1Jl91xh4m6avBk7-BlnHvc,2124
 aurelian/agents/linkml/linkml_gradio.py,sha256=XaaBQEZTJdW2HdENbs2LjlHjcfjAr2-setFePJKp6bg,1303
-aurelian/agents/linkml/linkml_mcp.py,sha256=rR31BiIId0rcq39Zpz4uuzyHzZhjHp1uslHezqw1CDw,4775
+aurelian/agents/linkml/linkml_mcp.py,sha256=8CttCtfiFrRU4FX4-JjXvDBnpMYnz3oOVvVuP2OlMjE,4711
 aurelian/agents/linkml/linkml_tools.py,sha256=-y53s1MIJdLsqJstZF-8t5ocigHOLtXTDxmRIhY7uyc,3684
 aurelian/agents/literature/__init__.py,sha256=8EY_j4JWf5Mbowv6mzUE6TLpkhwrbNZSKT-NEH65KpU,101
-aurelian/agents/literature/literature_agent.py,sha256=jmTNwBkEp-7mG53AvXNGIudigg0ys6iiPtTzMSS9l3U,1708
+aurelian/agents/literature/literature_agent.py,sha256=LB9RYOK4bzaQUfs8D6rmLQ-1NCwNAPSFsfu_hCY4f00,2275
 aurelian/agents/literature/literature_config.py,sha256=uDyhonTSdMP5L1dXgIGhgwlaHeyRPxjpVQkmt6kx7cE,947
 aurelian/agents/literature/literature_gradio.py,sha256=5GAef4fB8GgfOokwpL016MIpyIZ20gfb5snZJWGF-k8,1646
 aurelian/agents/literature/literature_mcp.py,sha256=fVBW7Vg8pW2vRq8RPio6Ltk_xe4KJCs_UCQzlsLDrJo,3925
 aurelian/agents/literature/literature_tools.py,sha256=vZMTV-V3xpo4SvkEPnuJAsbv6gGCwQGbcvLW6ec6jX8,5849
-aurelian/agents/monarch/__init__.py,sha256=8klP_zmBDbJoj7vUZTH_8WeGy-BC2fr1_SZ94AgfcVQ,563
-aurelian/agents/monarch/monarch_agent.py,sha256=7Oyo4HCSJu6p9-GVQUCOJKnSt-Qnb98F9x1bp42mRlI,1798
+aurelian/agents/monarch/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+aurelian/agents/monarch/monarch_agent.py,sha256=nve0m3BDj9_QwbUBy4Ht5ltVXElo1H_Hh3lPgc43rE4,1826
 aurelian/agents/monarch/monarch_config.py,sha256=3g5OXmMnuH0by1IZY9YLn4WPR6hr4XKCreq1SBGMzXo,1390
 aurelian/agents/monarch/monarch_gradio.py,sha256=GG5m4m8x4crFwP2a5z8s97nylG6gwuRXHa7RO82PPvY,1528
 aurelian/agents/monarch/monarch_mcp.py,sha256=U-K0XlpRIMPlAm5dKQkqemepz-DemCmFLMJWLASV0AI,1839
-aurelian/agents/monarch/monarch_tools.py,sha256=icghELlr5qvcjhpb5sK7iN6lWAIeH26Zyj2_jMLRSY8,3602
+aurelian/agents/monarch/monarch_tools.py,sha256=z6ohe4wzO8vBVSV_23FSPwLzFNhFrk6Hkdy7FCOmhos,3554
 aurelian/agents/oak/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/agents/oak/oak_config.py,sha256=Gc9_edlkZKF-8377xwx2QiIxVHGiHA2xWPgYVyG-tvE,675
 aurelian/agents/oak/oak_gradio.py,sha256=-y99MoEORea2sLIvcvEEbeKDojxm0I7bXzzZkoSHu_s,1669
 aurelian/agents/ontology_mapper/__init__.py,sha256=5SCUej1UyBJSuSwZrNHHO8rrTPElup_ufOClKom6_v8,646
-aurelian/agents/ontology_mapper/ontology_mapper_agent.py,sha256=fPIaEbLERvbO0Tj2Y8MhlFscSkI8IM_rXBWnWzw6ZaA,2768
+aurelian/agents/ontology_mapper/ontology_mapper_agent.py,sha256=sE22zXyAru9dc1nlZB-0uAWWmd2RsoUndqoiwvrL_yk,2796
 aurelian/agents/ontology_mapper/ontology_mapper_config.py,sha256=iqJzuZ6M7BSs0qGgeah5u7THOusZ3VjvH8lJ6IiYgSE,1639
 aurelian/agents/ontology_mapper/ontology_mapper_evals.py,sha256=6kympT8LV570rRozgeBIyEdZ3dDfRGH2o3x4x2F__9Q,3591
 aurelian/agents/ontology_mapper/ontology_mapper_gradio.py,sha256=nzkwPvK3k6Sze8oNS2R8z4k2XeXj4LU2wjV4G_Jn-Ec,1819
 aurelian/agents/ontology_mapper/ontology_mapper_mcp.py,sha256=YnXCKU2Yzy_RPqEba8hJPWwtb1H07Wo-zlZY-nnKurw,2208
 aurelian/agents/ontology_mapper/ontology_mapper_tools.py,sha256=S0azD3wR0pTh-9ipjVBUiNRkgsDEb30n1KMZD0qWvyw,4272
 aurelian/agents/paperqa/__init__.py,sha256=Dfff3fyx9PeoeqA4DcvyE_loW-UXegYM281alttwLvI,590
-aurelian/agents/paperqa/paperqa_agent.py,sha256=LimGkiN89gK-kD-AdrBXqIHw9FdC2JkBZTDZAuP1YX4,2615
+aurelian/agents/paperqa/paperqa_agent.py,sha256=FAPgHVeW63jT07trjV2HzNqq7OivRDlhp2Kn50Kb5Gs,2643
 aurelian/agents/paperqa/paperqa_cli.py,sha256=A0cwGUUTVcFVO1e_PsXusvBae9N5ElyeCtsZuQh-eGo,10357
 aurelian/agents/paperqa/paperqa_config.py,sha256=CUj3BARcII8AippAYJXAq9MsqrQlkRm36ucHyuCGnII,4554
 aurelian/agents/paperqa/paperqa_gradio.py,sha256=Thz82905TBeUQSiKcT40ZFs9MOqlN3YzYrJ5LNZPjHs,2844
@@ -187,7 +187,7 @@ aurelian/agents/phenopackets/phenopackets_gradio.py,sha256=KJdu5ZIgyYhAvpQLQ012J
 aurelian/agents/phenopackets/phenopackets_mcp.py,sha256=PzhqNW6RC9E5jRG9xBzMGVP3u-tQmTt6Idq_zDAeEsE,4677
 aurelian/agents/phenopackets/phenopackets_tools.py,sha256=3U8mjA_mi3K6Sb5VOSfT3Z-ytTx2cuz8zFLnFxxp-U8,4052
 aurelian/agents/rag/__init__.py,sha256=eqnU5tVCH52qW5KKSAgUzhh7WDYl-HZb84j-V5fs48g,749
-aurelian/agents/rag/rag_agent.py,sha256=xt1w1FYJdCceXXRHH16DEiuWXrV7v6mf6emyUjL0R4M,2526
+aurelian/agents/rag/rag_agent.py,sha256=vkOsAwDWyt-uexqdUuHQ1QehLiYjk8P8E83QK61f9-0,2554
 aurelian/agents/rag/rag_config.py,sha256=M5q56xOp7ZfK21mi0gOCJP8dXiWjPvbTHmv-36YyVq8,2692
 aurelian/agents/rag/rag_gradio.py,sha256=Vl9GicDP0xlL7126RUHx9f0loQGa_JnFwN0QtOT_58w,1844
 aurelian/agents/rag/rag_mcp.py,sha256=-o0c868DZdqfB38QOHFDqGHrwyWqI7vAK6aNAtDP3XA,2543
@@ -208,15 +208,15 @@ aurelian/agents/talisman/run_talisman.py,sha256=K_GX9eqA2wrhXIDjtTfpCh7UHRObniSY
 aurelian/agents/talisman/talisman_agent.py,sha256=KBvCCkzl-j_PObfMBrsyXg3kvCDmCpi2DAOnuaURdMI,6641
 aurelian/agents/talisman/talisman_config.py,sha256=bYjgMecVrKXwwZwv7n7Leseks6DFEfqVEZF9MqgoShQ,2301
 aurelian/agents/talisman/talisman_gradio.py,sha256=ogpFwnxVngvu5UmQ1GKz2JdbpCWlIK7duQDLJGisWs8,1617
-aurelian/agents/talisman/talisman_mcp.py,sha256=dOLpklOqDRmsvm4ZFGZwKrcrrsx_FcahxcIOUnvJYm8,4612
+aurelian/agents/talisman/talisman_mcp.py,sha256=yQbLR6ITvl3qsV-p4nnqEDYW_R5qRyQNl56CkEWiY8k,2189
 aurelian/agents/talisman/talisman_tools.py,sha256=ZzvpFxZBXpeZrIFV9aqtwVqa6O3z_5WvUReWOHh-aS4,42256
 aurelian/agents/ubergraph/__init__.py,sha256=Nl81e1H7XKBSQ2nIHoY0UCHgcOW5N-PJ1AugKh_YGOs,767
-aurelian/agents/ubergraph/ubergraph_agent.py,sha256=UUu-PQz9MPFZZIuRw0KPSokTaFh_cMVNjRVj3BsG1ek,3038
+aurelian/agents/ubergraph/ubergraph_agent.py,sha256=dW1IG35w7OgNgC5SDgNFB6K2RJCsRrfnTRd2nqrU9Tg,3066
 aurelian/agents/ubergraph/ubergraph_config.py,sha256=Fi2hFVu92v55IinNYFlLjdvt9THXtRFPkSEcXtTrC10,2774
 aurelian/agents/ubergraph/ubergraph_gradio.py,sha256=Gig_3AK0B4AkfvjlNklHkr87z2vcphll2I9DLgfdmdU,1372
 aurelian/agents/ubergraph/ubergraph_mcp.py,sha256=p_YbEkSF4yN0T5OJ8FKIkuOtutOYvFL3TJDtJydSnws,2475
-aurelian/agents/ubergraph/ubergraph_tools.py,sha256=9LLlOWXWu8crXCADpvzEJ0gQVNi9fuFYx8SkrDS175s,3428
-aurelian/agents/uniprot/__init__.py,sha256=Vj6vhxd8FtoLSKtT3u9yHiCrx__PA3iSDlZ3CoyJ6qE,821
+aurelian/agents/ubergraph/ubergraph_tools.py,sha256=OtyqOyRviuBInCuMwK5dn1jaFJRJIZq6QFImqK3uFWk,3909
+aurelian/agents/uniprot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/agents/uniprot/uniprot_agent.py,sha256=KMTRKGVpRpSchz7YEShh9ZSSGHzmeaGEUaNFKJPDWSI,1648
 aurelian/agents/uniprot/uniprot_config.py,sha256=YhL265Z0GnTeXINHawe5iMcpR2ETLmdY3XhNXcYIc8w,1404
 aurelian/agents/uniprot/uniprot_evals.py,sha256=aZAZAOYFfvywqWuWV1-6p3PpXCxEl_ZkHppl88z5GUw,3178
@@ -227,11 +227,13 @@ aurelian/agents/web/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSu
 aurelian/agents/web/web_config.py,sha256=uk-etu-DzYgeuS2zBs0SVfX_BvZ6QGs0X5PFsf1NR-Q,675
 aurelian/agents/web/web_gradio.py,sha256=T7qzuRuBaWCYckWjpLu3L0LzHPLEKkxUYp2rj-Og_ms,1334
 aurelian/agents/web/web_mcp.py,sha256=3mrUlxBqeMSOmtpnD2wWedsOiRJbtveEnbyJqQdfEXQ,1163
-aurelian/agents/web/web_tools.py,sha256=BfJJWlHz7tKh9VDjymIwzziahFKrqr2ZUO0QH3IcL6U,4070
+aurelian/agents/web/web_tools.py,sha256=oSS8MFxFqtcPfdEhmEuuiRKW8_NTg3ktLxahlF8h0Ec,4645
 aurelian/chat.py,sha256=hg9eGKiz_NAjwG5jNGwNqoFrhhx029XX3dWdMRrk-EU,563
-aurelian/cli.py,sha256=nRCLPZb__FpMsHqNnDeoYCc0KspESumIKQlrDe97594,34510
+aurelian/cli.py,sha256=-6r3w8H43fhoHrkzn3GQmpQ37McsFHjWP5wZIrnk0gQ,34856
 aurelian/dependencies/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/dependencies/workdir.py,sha256=G_eGlxKpHRjO3EL2hHN8lvtticgSZvJe300KkJP4vZQ,2228
+aurelian/evaluators/model.py,sha256=USfoHcYTMTlPJaM9-BPksb3asBoDd7amqSnHIbg9YYs,253
+aurelian/evaluators/substring_evaluator.py,sha256=cx1fF3f5FulEeD9iTkgtwo-zByt5qgdmk1XKWJ1_eqQ,1039
 aurelian/mcp/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/mcp/amigo_mcp_test.py,sha256=TtlYU-5AKcXf2XubFUNpZE2RxFHYi_cVbtte6KJQnzE,2902
 aurelian/mcp/config_generator.py,sha256=QIaLqURiuOPgGfOImItf89d4ZltYonpybzAcO2vjA2Y,4350
@@ -246,7 +248,7 @@ aurelian/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/tools/web/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/tools/web/url_download.py,sha256=Tpg41yx4Sd3dToV-kGBZggwYUq3hmeLwJttSQrnqz4M,1435
 aurelian/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-aurelian/utils/async_utils.py,sha256=nkuyNwGmykEfesZ0MUPRdnrSgxb66RD6-tEKVQPwzTo,328
+aurelian/utils/async_utils.py,sha256=mqjYPr8RlXlIXKYRgQ95ZcGTbdIeOw4PHvr37Clopd0,417
 aurelian/utils/data_utils.py,sha256=LFuSKWtApLJxFGuHLG4-Zhw42cbaQK0juCEXD44b3S4,1047
 aurelian/utils/documentation_manager.py,sha256=uvAnI_N1V1ITQX53ytOSgvDLbV0IIsSkxpKDg0y3E4g,1767
 aurelian/utils/doi_fetcher.py,sha256=BNIsYaS9cb2uOSY0jxdjnZAFI2VSk2odzP4ppz3ToHg,8553
@@ -257,8 +259,8 @@ aurelian/utils/pubmed_utils.py,sha256=Gk00lu1Lv0GRSNeF5M4zplp3UMSpe5byCaVKCJimUH
 aurelian/utils/pytest_report_to_markdown.py,sha256=WH1NlkVYj0UfUqpXjRD1KMpkMgEW3qev3fDdPvZG9Yw,1406
 aurelian/utils/robot_ontology_utils.py,sha256=aaRe9eyLgJCtj1EfV13v4Q7khFTWzUoFFEE_lizGuGg,3591
 aurelian/utils/search_utils.py,sha256=9MloT3SzOE4JsElsYlCznp9N6fv_OQK7YWOU8MIy1WU,2818
-aurelian-0.3.4.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
-aurelian-0.3.4.dist-info/METADATA,sha256=o6MapyVbBF6DMGrYZMYBNc-JKm2q-uv3qjSVCwuXR0E,3471
-aurelian-0.3.4.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-aurelian-0.3.4.dist-info/entry_points.txt,sha256=BInUyPfLrHdmH_Yvi71dx21MhkcNCEOPiqvpEIb2U5k,46
-aurelian-0.3.4.dist-info/RECORD,,
+aurelian-0.4.2.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
+aurelian-0.4.2.dist-info/METADATA,sha256=Wtded6_NxBHSXTCFxjUcXUrbLz00vOQgoy7xsHPM8YM,3557
+aurelian-0.4.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+aurelian-0.4.2.dist-info/entry_points.txt,sha256=EnGehbtRm0YmhdfwfcoGJjVG3Man-zgKvob20fTIBik,102
+aurelian-0.4.2.dist-info/RECORD,,

aurelian-0.4.2.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+aurelian=aurelian.cli:main
+aurelian-mcp-gocam=aurelian.agents.gocam.gocam_mcp:main
+

aurelian-0.3.4.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-aurelian=aurelian.cli:main
-