aurelian 0.3.3__py3-none-any.whl → 0.4.1__py3-none-any.whl

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/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")
@@ -958,6 +967,33 @@ def reaction(ui, query, **kwargs):
 
 
 
+@main.command()
+@model_option
+@workdir_option
+@share_option
+@server_port_option
+@ui_option
+@click.argument("query", nargs=-1, required=False)
+def paperqa(ui, query, **kwargs):
+    """Start the PaperQA Agent for scientific literature search and analysis.
+    
+    The PaperQA Agent helps search, organize, and analyze scientific papers. It can
+    find papers on specific topics, add papers to your collection, and answer questions
+    based on the papers in your collection.
+    
+    Run with a query for direct mode or with --ui for interactive chat mode.
+    
+    Use `aurelian paperqa` subcommands for paper management:
+      - `aurelian paperqa index` to index papers for searching
+      - `aurelian paperqa list` to list papers in your collection
+    """
+    run_agent("paperqa", "aurelian.agents.paperqa", query=query, ui=ui, **kwargs)
+
+
+# Import and register PaperQA CLI commands
+from aurelian.agents.paperqa.paperqa_cli import paperqa_cli
+main.add_command(paperqa_cli)
+
 # DO NOT REMOVE THIS LINE
 # added this for mkdocstrings to work
 # see https://github.com/bruce-szalwinski/mkdocs-typer/issues/18

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-0.3.3.dist-info → aurelian-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aurelian
-Version: 0.3.3
+Version: 0.4.1
 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)
@@ -30,12 +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)
@@ -43,6 +46,7 @@ Requires-Dist: undetected-chromedriver (>=3.5.5)
 Requires-Dist: wikipedia (>=1.4.0)
 Description-Content-Type: text/markdown
 
+[![DOI](https://zenodo.org/badge/932483388.svg)](https://doi.org/10.5281/zenodo.15299996)
 
 # Aurelian: Agentic Universal Research Engine for Literature, Integration, Annotation, and Navigation
 

{aurelian-0.3.3.dist-info → aurelian-0.4.1.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
@@ -148,30 +148,37 @@ 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
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 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
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 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
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 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=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
+aurelian/agents/paperqa/paperqa_mcp.py,sha256=ApnH43iZpM4ToPpSpE1KQf2mF4o7HCTXPb_X6tjX0ic,4665
+aurelian/agents/paperqa/paperqa_tools.py,sha256=k0WtWPhkyAndnpPjP7XRF5llkW-Ktkxx2JhChO-SKU4,20238
 aurelian/agents/phenopackets/__init__.py,sha256=TrXNpK2KDUjxok4nCuhepVPGH4RvALOZJoXjD4S-i1g,73
 aurelian/agents/phenopackets/phenopackets_agent.py,sha256=R--xoY558TaVcAG2HoQvj7lWwCr_PrpfG7xl33rCIpk,2229
 aurelian/agents/phenopackets/phenopackets_config.py,sha256=hpc3m2IboYlQoJselVMPf_EK0Z1YJBNp7qbj3TLk7PM,2304
@@ -180,7 +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
@@ -201,15 +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/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
@@ -220,11 +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=RvIl2Y4DtyEqXNTsY71n-0t_ZXCK3nTmzWAcnFmMvrE,33532
+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
@@ -239,7 +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
@@ -250,8 +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-0.3.3.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
-aurelian-0.3.3.dist-info/METADATA,sha256=zuOveEkQXBoEtZe5gOlQeTby9eIGowh4Pzp8QOwbVuc,3339
-aurelian-0.3.3.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-aurelian-0.3.3.dist-info/entry_points.txt,sha256=BInUyPfLrHdmH_Yvi71dx21MhkcNCEOPiqvpEIb2U5k,46
-aurelian-0.3.3.dist-info/RECORD,,
+aurelian-0.4.1.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
+aurelian-0.4.1.dist-info/METADATA,sha256=jQhaYsfYEvlpDSotKJrxSYgXLxprb_Ictzd33LVqbco,3557
+aurelian-0.4.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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+aurelian-0.4.1.dist-info/RECORD,,

{aurelian-0.3.3.dist-info → aurelian-0.4.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.2
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any