aurelian 0.3.3__tar.gz → 0.4.1__tar.gz

{aurelian-0.3.3 → aurelian-0.4.1}/PKG-INFO

@@ -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 → aurelian-0.4.1}/README.md

@@ -1,3 +1,4 @@
+[![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 → aurelian-0.4.1}/pyproject.toml

@@ -1,6 +1,9 @@
+[project]
+name = "aurelian"
+
 [tool.poetry]
 name = "aurelian"
-version = "0.3.3"
+version = "0.4.1"
 description = "aurelian"
 authors = ["Author 1 <author@org.org>"]
 license = "MIT"
@@ -17,20 +20,22 @@ rdkit = {optional=true, version="*"}
 gocam = {optional=true, version="*"}
 linkml = {optional=true, version="*"}
 gradio = "^5.23.3"
-pydantic-ai = ">=0.0.29"
+pydantic-ai = ">=0.2.0"
 logfire = ">=3.5.3"
 bs4 = ">=0.0.2"
 duckduckgo-search = ">=7.3.2"
 markdownify = ">=0.14.1"
 wikipedia = ">=1.4.0"
-markitdown = ">=0.0.1a4"
-pypaperbot = ">=1.4.1"
+onnxruntime = "<=1.19.0"
+markitdown = ">=0.1.1"
+pypaperbot = {optional=true, version=">=1.4.1"}
 undetected-chromedriver = ">=3.5.5"
 bioservices = ">=1.12.0"
 pdfminer-six = {optional=true, version="*"}
 mcp = {extras = ["cli"], version = "^1.3.0"}
 pytest-asyncio = "^0.25.3"
 cairosvg = "^2.7.1"
+paper-qa = "^5.20.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = {version = ">=8.3.2"}
@@ -53,6 +58,7 @@ bioservices = ["bioservices"]
 linkml = ["linkml"]
 chem = ["rdkit"]
 pdfminer = ["pdfminer-six"]
+pypaperbot = ["pypaperbot"]
 
 [tool.pytest.ini_options]
 markers = [
@@ -77,6 +83,7 @@ typer = ">=0.9.0"  # Required for mkdocs-click
 
 [tool.poetry.scripts]
 aurelian = "aurelian.cli:main"
+aurelian-mcp-gocam = "aurelian.agents.gocam.gocam_mcp:main"
 
 [tool.poetry-dynamic-versioning]
 enable = false

{aurelian-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.3.3 → aurelian-0.4.1}/src/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-0.4.1/src/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-0.4.1/src/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)