aurelian 0.3.3__py3-none-any.whl → 0.4.1__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/__init__.py

@@ -0,0 +1,27 @@
+"""
+PaperQA agent package for scientific literature search and analysis.
+"""
+
+# isort: skip_file
+from .paperqa_agent import paperqa_agent  # noqa: E402
+from .paperqa_config import PaperQADependencies, get_config  # noqa: E402
+from .paperqa_gradio import chat  # noqa: E402
+from .paperqa_tools import (  # noqa: E402
+    search_papers,
+    query_papers,
+    add_paper,
+    add_papers,
+    list_papers,
+)
+
+__all__ = [
+    "paperqa_agent",
+    "PaperQADependencies",
+    "get_config",
+    "search_papers",
+    "query_papers",
+    "add_paper",
+    "add_papers",
+    "list_papers",
+    "chat",
+]

aurelian/agents/paperqa/paperqa_agent.py

@@ -0,0 +1,66 @@
+"""
+Agent for PaperQA integration with Aurelian.
+"""
+import logging
+from pydantic_ai import Agent
+
+paperqa_logger = logging.getLogger("aurelian.agents.paperqa")
+paperqa_logger.setLevel(logging.INFO)
+
+for handler in list(paperqa_logger.handlers):
+    paperqa_logger.removeHandler(handler)
+
+console = logging.StreamHandler()
+console.setLevel(logging.INFO)
+formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+console.setFormatter(formatter)
+paperqa_logger.addHandler(console)
+
+paperqa_logger.propagate = False
+
+from .paperqa_config import PaperQADependencies
+from .paperqa_tools import (
+    search_papers,
+    query_papers,
+    add_paper,
+    add_papers,
+    list_papers,
+    build_index
+)
+
+PAPERQA_SYSTEM_PROMPT = """
+        You are an AI assistant that helps explore scientific literature using PaperQA.
+        You can use different functions to search for papers and analyze them:
+          - `search_papers` to find papers by topic or keyword from outside this repository.
+          - `query_papers` to ask questions about the papers in the repository
+          - `add_paper` to add a specific paper by file path or URL (with auto_index=True by default)
+          - `add_papers` to add multiple papers from a directory (with auto_index=True by default)
+          - `list_papers` to see all papers in the collection
+          - `build_index` to manually rebuild the search index
+        
+        When adding papers with `add_paper` or `add_papers`:
+        - For `add_paper`, the URL must be a direct link to a PDF (e.g., "https://example.com/paper.pdf")
+        - For `add_paper`, you can provide a citation string to attribute the source
+        - For `add_papers`, you provide a directory containing papers and an optional citation format
+        - By default, auto_index=True, which automatically rebuilds the index after adding papers
+        - You can set auto_index=False if you want to add multiple papers before indexing
+        - After adding papers with auto_index=False, use `build_index()` to make them searchable
+        
+        When showing paper information, format using Markdown for readability.
+        When papers have been successfully retrieved, proceed to analyzing them.
+                        """
+
+paperqa_agent = Agent(
+    model="openai:gpt-4o-2024-11-20",
+    deps_type=PaperQADependencies,
+    result_type=str,
+    system_prompt=PAPERQA_SYSTEM_PROMPT,
+    defer_model_check=True,
+)
+
+paperqa_agent.tool(search_papers)
+paperqa_agent.tool(query_papers)
+paperqa_agent.tool(add_paper)
+paperqa_agent.tool(add_papers)
+paperqa_agent.tool(list_papers)
+paperqa_agent.tool(build_index)