aiagents4pharma 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py

@@ -5,15 +5,16 @@ Utility for zotero write tool.
 """
 
 import logging
-from typing import Any, Dict
+from typing import Any
+
 import hydra
 from pyzotero import zotero
+
 from .zotero_path import (
-    find_or_create_collection,
     fetch_papers_for_save,
+    find_or_create_collection,
 )
 
-
 # Configure logging
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -41,9 +42,7 @@ class ZoteroWriteData:
     def _load_config(self) -> Any:
         """Load hydra configuration."""
         with hydra.initialize(version_base=None, config_path="../../../configs"):
-            cfg = hydra.compose(
-                config_name="config", overrides=["tools/zotero_write=default"]
-            )
+            cfg = hydra.compose(config_name="config", overrides=["tools/zotero_write=default"])
             logger.info("Loaded configuration for Zotero write tool")
             return cfg.tools.zotero_write
 
@@ -107,9 +106,7 @@ class ZoteroWriteData:
                     if " " in name
                     else {"creatorType": "author", "lastName": name}
                 )
-                for name in [
-                    author.split(" (ID: ")[0] for author in paper.get("Authors", [])
-                ]
+                for name in [author.split(" (ID: ")[0] for author in paper.get("Authors", [])]
             ]
 
             self.zotero_items.append(
@@ -152,13 +149,13 @@ class ZoteroWriteData:
         top_papers = list(self.fetched_papers.values())[:2]
         top_papers_info = "\n".join(
             [
-                f"{i+1}. {paper.get('Title', 'N/A')} ({paper.get('URL', 'N/A')})"
+                f"{i + 1}. {paper.get('Title', 'N/A')} ({paper.get('URL', 'N/A')})"
                 for i, paper in enumerate(top_papers)
             ]
         )
         self.content += "Here are a few of these articles:\n" + top_papers_info
 
-    def process_write(self) -> Dict[str, Any]:
+    def process_write(self) -> dict[str, Any]:
         """Process the write operation and return results."""
         self._validate_papers()
         matched_collection_key = self._find_collection()

aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py

@@ -29,9 +29,7 @@ def get_item_collections(zot):
 
     # Create mappings: collection key → name and collection key → parent key
     collection_map = {col["key"]: col["data"]["name"] for col in collections}
-    parent_map = {
-        col["key"]: col["data"].get("parentCollection") for col in collections
-    }
+    parent_map = {col["key"]: col["data"].get("parentCollection") for col in collections}
 
     # Build full paths for collections
     def build_collection_path(col_key):
@@ -49,9 +47,7 @@ def get_item_collections(zot):
 
     for collection in collections:
         collection_key = collection["key"]
-        collection_items = zot.collection_items(
-            collection_key
-        )  # Fetch items in the collection
+        collection_items = zot.collection_items(collection_key)  # Fetch items in the collection
 
         for item in collection_items:
             item_key = item["data"]["key"]
@@ -67,9 +63,7 @@ def get_item_collections(zot):
 
 def find_or_create_collection(zot, path, create_missing=False):
     """find collection or create if missing"""
-    logger.info(
-        "Finding collection for path: %s (create_missing=%s)", path, create_missing
-    )
+    logger.info("Finding collection for path: %s (create_missing=%s)", path, create_missing)
     # Normalize path: remove leading/trailing slashes and convert to lowercase
     normalized = path.strip("/").lower()
     path_parts = normalized.split("/") if normalized else []
@@ -136,9 +130,7 @@ def get_all_collection_paths(zot):
 
     # Create mappings: collection key → name and collection key → parent key
     collection_map = {col["key"]: col["data"]["name"] for col in collections}
-    parent_map = {
-        col["key"]: col["data"].get("parentCollection") for col in collections
-    }
+    parent_map = {col["key"]: col["data"].get("parentCollection") for col in collections}
 
     # Build full paths for collections
     def build_collection_path(col_key):

aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py

@@ -3,10 +3,10 @@
 Utility functions for downloading PDFs from Zotero.
 """
 
+import concurrent.futures
 import logging
 import tempfile
-from typing import Optional, Tuple, Dict
-import concurrent.futures
+
 import requests
 
 logger = logging.getLogger(__name__)
@@ -18,7 +18,7 @@ def download_zotero_pdf(
     api_key: str,
     attachment_key: str,
     **kwargs,
-) -> Optional[Tuple[str, str]]:
+) -> tuple[str, str] | None:
     """
     Download a PDF from Zotero by attachment key.
 
@@ -40,18 +40,12 @@ def download_zotero_pdf(
     # Log configured parameters for verification
     logger.info("download_zotero_pdf params -> timeout=%s, chunk_size=%s", timeout, chunk_size)
     # Log download start
-    logger.info(
-        "Downloading Zotero PDF for attachment %s from Zotero API", attachment_key
-    )
-    zotero_pdf_url = (
-        f"https://api.zotero.org/users/{user_id}/items/" f"{attachment_key}/file"
-    )
+    logger.info("Downloading Zotero PDF for attachment %s from Zotero API", attachment_key)
+    zotero_pdf_url = f"https://api.zotero.org/users/{user_id}/items/{attachment_key}/file"
     headers = {"Zotero-API-Key": api_key}
 
     try:
-        response = session.get(
-            zotero_pdf_url, headers=headers, stream=True, timeout=timeout
-        )
+        response = session.get(zotero_pdf_url, headers=headers, stream=True, timeout=timeout)
         response.raise_for_status()
 
         # Download to a temporary file first
@@ -65,9 +59,7 @@ def download_zotero_pdf(
         # Determine filename from Content-Disposition header or default
         if "filename=" in response.headers.get("Content-Disposition", ""):
             filename = (
-                response.headers.get("Content-Disposition", "")
-                .split("filename=")[-1]
-                .strip('"')
+                response.headers.get("Content-Disposition", "").split("filename=")[-1].strip('"')
             )
         else:
             filename = "downloaded.pdf"
@@ -75,9 +67,7 @@ def download_zotero_pdf(
         return temp_file_path, filename
 
     except (requests.exceptions.RequestException, OSError) as e:
-        logger.error(
-            "Failed to download Zotero PDF for attachment %s: %s", attachment_key, e
-        )
+        logger.error("Failed to download Zotero PDF for attachment %s: %s", attachment_key, e)
         return None
 
 
@@ -85,9 +75,9 @@ def download_pdfs_in_parallel(
     session: requests.Session,
     user_id: str,
     api_key: str,
-    attachment_item_map: Dict[str, str],
+    attachment_item_map: dict[str, str],
     **kwargs,
-) -> Dict[str, Tuple[str, str, str]]:
+) -> dict[str, tuple[str, str, str]]:
     """
     Download multiple PDFs in parallel using ThreadPoolExecutor.
 
@@ -108,20 +98,16 @@ def download_pdfs_in_parallel(
     chunk_size = kwargs.get("chunk_size")
     # Log configured parameters for verification
     logger.info(
-        "download_pdfs_in_parallel params -> max_workers=%s, chunk_size=%s", 
+        "download_pdfs_in_parallel params -> max_workers=%s, chunk_size=%s",
         max_workers,
         chunk_size,
     )
-    results: Dict[str, Tuple[str, str, str]] = {}
+    results: dict[str, tuple[str, str, str]] = {}
     if not attachment_item_map:
         return results
 
     with concurrent.futures.ThreadPoolExecutor(
-        max_workers=(
-            max_workers
-            if max_workers is not None
-            else min(10, len(attachment_item_map))
-        )
+        max_workers=(max_workers if max_workers is not None else min(10, len(attachment_item_map)))
     ) as executor:
         future_to_keys = {
             executor.submit(

aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py

@@ -10,13 +10,14 @@ for each found item and makes the results available as an artifact.
 
 import logging
 from typing import Annotated, Any
+
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import tool
 from langchain_core.tools.base import InjectedToolCallId
 from langgraph.types import Command
 from pydantic import BaseModel, Field
-from .utils.read_helper import ZoteroSearchData
 
+from .utils.read_helper import ZoteroSearchData
 
 # Configure logging
 logging.basicConfig(level=logging.INFO)
@@ -34,16 +35,12 @@ class ZoteroSearchInput(BaseModel):
         tool_call_id (str): Internal identifier for this tool invocation.
     """
 
-    query: str = Field(
-        description="Search query string to find papers in Zotero library."
-    )
+    query: str = Field(description="Search query string to find papers in Zotero library.")
     only_articles: bool = Field(
         default=True,
         description="Whether to only search for journal articles/conference papers.",
     )
-    limit: int = Field(
-        default=2, description="Maximum number of results to return", ge=1, le=100
-    )
+    limit: int = Field(default=2, description="Maximum number of results to return", ge=1, le=100)
     download_pdfs: bool = Field(
         default=False,
         description="Whether to download PDF attachments immediately (default True).",

aiagents4pharma/talk2scholars/tools/zotero/zotero_review.py

@@ -5,15 +5,17 @@ This tool implements human-in-the-loop review for Zotero write operations.
 """
 
 import logging
-from typing import Annotated, Any, Optional, Literal
+from typing import Annotated, Any, Literal
+
+from langchain_core.messages import HumanMessage, ToolMessage
 from langchain_core.tools import tool
-from langchain_core.messages import ToolMessage, HumanMessage
 from langchain_core.tools.base import InjectedToolCallId
 from langgraph.prebuilt import InjectedState
 from langgraph.types import Command, interrupt
 from pydantic import BaseModel, Field
-from .utils.zotero_path import fetch_papers_for_save
+
 from .utils.review_helper import ReviewData
+from .utils.zotero_path import fetch_papers_for_save
 
 # Configure logging
 logging.basicConfig(level=logging.INFO)
@@ -28,7 +30,7 @@ class ZoteroReviewDecision(BaseModel):
     """
 
     decision: Literal["approve", "reject", "custom"]
-    custom_path: Optional[str] = None
+    custom_path: str | None = None
 
 
 class ZoteroReviewInput(BaseModel):
@@ -83,9 +85,7 @@ def zotero_review(
             raise ValueError("LLM model is not available in the state.")
         structured_llm = llm_model.with_structured_output(ZoteroReviewDecision)
         # Convert the raw human response to a message for structured parsing
-        decision_response = structured_llm.invoke(
-            [HumanMessage(content=str(human_review))]
-        )
+        decision_response = structured_llm.invoke([HumanMessage(content=str(human_review))])
 
         # Process the structured response
         if decision_response.decision == "approve":
@@ -105,9 +105,7 @@ def zotero_review(
                 }
             )
         if decision_response.decision == "custom" and decision_response.custom_path:
-            logger.info(
-                "User approved with custom path: %s", decision_response.custom_path
-            )
+            logger.info("User approved with custom path: %s", decision_response.custom_path)
             return Command(
                 update={
                     "messages": [

aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py

@@ -6,14 +6,15 @@ This tool is used to save fetched papers to Zotero library after human approval.
 
 import logging
 from typing import Annotated, Any
+
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import tool
 from langchain_core.tools.base import InjectedToolCallId
-from langgraph.types import Command
 from langgraph.prebuilt import InjectedState
+from langgraph.types import Command
 from pydantic import BaseModel, Field
-from .utils.write_helper import ZoteroWriteData
 
+from .utils.write_helper import ZoteroWriteData
 
 # Configure logging
 logging.basicConfig(level=logging.INFO)

{aiagents4pharma-1.43.0.dist-info → aiagents4pharma-1.45.0.dist-info}/METADATA

@@ -1,71 +1,92 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.43.0
+Version: 1.45.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
-Classifier: Programming Language :: Python :: 3
+License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: copasi_basico==0.84
+Requires-Dist: anndata==0.11.3
+Requires-Dist: beautifulsoup4==4.13.4
+Requires-Dist: cell2sentence==1.1.0
+Requires-Dist: cloudscraper==1.2.71
+Requires-Dist: copasi-basico==0.84
 Requires-Dist: coverage==7.6.4
+Requires-Dist: datasets==4.0.0
 Requires-Dist: einops==0.8.0
 Requires-Dist: gdown==5.2.0
 Requires-Dist: gravis==0.1.0
-Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: gseapy==1.1.8
+Requires-Dist: h5py==3.13.0
+Requires-Dist: huggingface-hub==0.34.4
 Requires-Dist: hydra-core==1.3.2
+Requires-Dist: igraph==0.11.8
+Requires-Dist: ipykernel==6.29.5
+Requires-Dist: ipython==8.32.0
 Requires-Dist: joblib==1.4.2
-Requires-Dist: langchain==0.3.7
 Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.40
 Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-milvus==0.2.0
 Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
-Requires-Dist: langchain-openai==0.2.5
-Requires-Dist: langchain_ollama==0.2.3
-Requires-Dist: langgraph_supervisor==0.0.9
+Requires-Dist: langchain-ollama==0.2.3
+Requires-Dist: langchain-openai==0.3.0
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langgraph-supervisor==0.0.9
+Requires-Dist: langgraph==0.3.34
 Requires-Dist: matplotlib==3.9.2
-Requires-Dist: openai==1.59.4
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocs-jupyter==0.25.1
+Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocstrings-python==1.12.2
+Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: nbformat==5.10.4
+Requires-Dist: numpy==1.26.4
 Requires-Dist: ollama==0.4.7
+Requires-Dist: openai==1.59.6
+Requires-Dist: openpyxl==3.1.5
 Requires-Dist: pandas==2.2.3
-Requires-Dist: pcst_fast==1.0.10
+Requires-Dist: pcst-fast==1.0.10
+Requires-Dist: plotly-express==0.4.1
 Requires-Dist: plotly==5.24.1
 Requires-Dist: pubchempy==1.0.4
-Requires-Dist: pydantic==2.9.2
+Requires-Dist: pyarrow==21.0.0
+Requires-Dist: pydantic==2.10.5
+Requires-Dist: pygeneconverter==0.3
 Requires-Dist: pylint==3.3.1
-Requires-Dist: pypdf==5.2.0
-Requires-Dist: pytest==8.3.3
+Requires-Dist: pymilvus==2.5.11
+Requires-Dist: pypdf2==3.0.1
+Requires-Dist: pypdf==6.0.0
 Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: pytest==8.3.3
+Requires-Dist: python-magic==0.4.27
 Requires-Dist: pyzotero==1.6.9
-Requires-Dist: pymilvus==2.5.11
-Requires-Dist: streamlit==1.39.0
-Requires-Dist: sentence_transformers==3.3.1
-Requires-Dist: tabulate==0.9.0
-Requires-Dist: torch==2.2.2
-Requires-Dist: torch_geometric==2.6.1
-Requires-Dist: transformers==4.48.0
-Requires-Dist: mkdocs==1.6.1
-Requires-Dist: mkdocs-jupyter==0.25.1
-Requires-Dist: mkdocs-material==9.5.47
-Requires-Dist: mkdocstrings-python==1.12.2
-Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
-Requires-Dist: mkdocstrings==0.27.0
-Requires-Dist: streamlit-feedback
-Requires-Dist: anndata==0.11.3
-Requires-Dist: h5py==3.13.0
-Requires-Dist: igraph==0.11.8
-Requires-Dist: ipykernel==6.29.5
-Requires-Dist: ipython==8.32.0
-Requires-Dist: nbformat==5.10.4
+Requires-Dist: requests==2.32.4
+Requires-Dist: scanpy==1.11.0
 Requires-Dist: scipy==1.15.2
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: sentence-transformers==3.3.1
+Requires-Dist: setuptools==80.9.0
+Requires-Dist: streamlit-feedback==0.1.4
+Requires-Dist: streamlit==1.41.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch-geometric==2.6.1
+Requires-Dist: torch==2.8.0
 Requires-Dist: tqdm==4.67.1
+Requires-Dist: transformers==4.55.2
 Requires-Dist: umap-learn==0.5.7
-Requires-Dist: plotly-express==0.4.1
-Requires-Dist: seaborn==0.13.2
-Requires-Dist: scanpy==1.11.0
-Requires-Dist: openpyxl==3.1.5
-Dynamic: license-file
+Requires-Dist: xlsxwriter==3.2.5
+Provides-Extra: dev
+Requires-Dist: bandit==1.8.6; extra == 'dev'
+Requires-Dist: mypy==1.17.1; extra == 'dev'
+Requires-Dist: pip-audit==2.9.0; extra == 'dev'
+Requires-Dist: pre-commit==4.3.0; extra == 'dev'
+Requires-Dist: ruff==0.12.8; extra == 'dev'
+Requires-Dist: safety==3.2.9; extra == 'dev'
+Requires-Dist: twine==6.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
 
 <img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
 
@@ -149,12 +170,16 @@ git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma && cd AIAgents
 
 2. **Install dependencies:**
 
-We use Conda as our environment manager, Follow the official [Quickstart](https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions) install instructions provided by anaconda/miniconda.
+We use `uv` for fast and reliable dependency management. Install uv first following the [official installation guide](https://docs.astral.sh/uv/getting-started/installation/).
 
-```python
-conda create --name AIAgents4Pharma python=3.12 -y && conda activate AIAgents4Pharma && pip install --upgrade pip && pip install -r requirements.txt
+> **For developers**: See [docs/developer/README.md](docs/developer/README.md) for detailed setup instructions including system prerequisites.
+
+```sh
+uv sync --extra dev --frozen
 ```
 
+> 💡 **Recommended**: Use `--frozen` flag to ensure exact reproducible builds using the pinned versions from `uv.lock`.
+
 3. **Initialize API Keys**
 
 ```env
@@ -168,7 +193,21 @@ export LANGCHAIN_API_KEY=...        # Optional for all agents
 
 4. **Launch the app:**
 
+**Option A: Using UV (recommended)**
+
 ```sh
+uv run streamlit run app/frontend/streamlit_app_<agent>.py
+```
+
+**Option B: Traditional approach**
+
+```sh
+# Activate virtual environment
+source .venv/bin/activate  # Linux/macOS
+# or
+.venv\Scripts\activate     # Windows
+
+# Then run the app
 streamlit run app/frontend/streamlit_app_<agent>.py
 ```
 
@@ -187,6 +226,8 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 To use the **Agents**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
 
+**Talk2Biomodels** supports integration with multiple LLMs: gpt-4o-mini (via OpenAI API) and open-source llama (3.1 and 3.3) models (via NVIDIA API). An **OpenAI API** key may be generated [here](https://platform.openai.com/settings/organization/api-keys). OpenAI may provide initial free credits for API calls with the API key, after which additional credits may be purchased [here](https://platform.openai.com/settings/organization/billing). More information on pricing is available [here](https://openai.com/api/pricing/).
+
 **Talk2Scholars** and **Talk2KnowledgeGraphs** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
 
 > By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
@@ -214,9 +255,19 @@ Check out the tutorials on each agent for detailed instructions.
 
 ## Contributing
 
-We welcome your support to make **AIAgents4Pharma** even better.  
+We welcome your support to make **AIAgents4Pharma** even better.
 All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.
 
+#### Development Setup
+
+For contributors and developers, we have comprehensive documentation:
+
+- **[Developer Setup Guide](docs/developer/README.md)** - Complete setup instructions with UV, security implementation, and tooling
+- **[Testing & Linting Guide](docs/developer/TESTING_LINTING.md)** - How to run tests, coverage, and code quality checks
+- **[SonarCloud Integration](docs/developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
+- **[GitHub Workflows](docs/developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
+- **[Streamlit Security](docs/developer/STREAMLIT_SECURITY.md)** - File upload security implementation
+
 #### How to contribute
 
 1. Star this repository to show your support.
@@ -227,19 +278,33 @@ All types of contributions are appreciated — whether you're fixing bugs, addin
 git checkout -b feat/your-feature-name
 ```
 
-4. Make your changes and commit them:
+4. Set up your development environment:
 
 ```sh
-git commit -m "feat: add a brief description of your change"
+uv sync --extra dev --frozen  # Install development dependencies
+uv run pre-commit install    # Set up code quality hooks
+```
+
+5. Make your changes and run quality checks:
+
+```sh
+uv run ruff check --fix .  # Lint and fix code
+uv run ruff format .  # Format code
+uv run pre-commit run --all-files  # Run all checks (linting, formatting, security)
+
+# Run submodule-specific checks (pylint configuration in pyproject.toml)
+uv run pylint aiagents4pharma/talk2scholars/
+uv run coverage run --include="aiagents4pharma/talk2scholars/*" -m pytest --cache-clear aiagents4pharma/talk2scholars/tests/ && uv run coverage report
 ```
 
-5. Push your branch:
+6. Commit and push your changes:
 
 ```sh
+git commit -m "feat: add a brief description of your change"
 git push origin feat/your-feature-name
 ```
 
-6. Open a Pull Request.
+7. Open a Pull Request.
 
 #### Areas where you can help
 
@@ -253,9 +318,9 @@ git push origin feat/your-feature-name
 - **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi)
 - **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info), [@gurdeep330](https://github.com/gurdeep330)
 
-Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
+Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) and [developer documentation](docs/developer/) for detailed contribution guidelines and setup instructions.
 
 ## Feedback
 
-If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.  
+If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.
 Please open an `issue` or start a `discussion`