aiagents4pharma 1.39.1__py3-none-any.whl → 1.39.3__py3-none-any.whl

aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml

@@ -0,0 +1,5 @@
+_target_: agents.paper_download_agent.get_app
+paper_download_agent: |
+  You are the Paper Download Agent.
+
+  You are responsible for downloading PDFs of papers using their IDs. Use all the provied Ids to download the papers. Only when the user asks a question related to PDFs, please forward the query to the `question_and_answer` tool from the `pdf_agent`

aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml

@@ -0,0 +1,5 @@
+_target_: agents.pdf_agent.get_app
+pdf_agent: |
+  You are the PDF Agent.
+
+  You are responsible for performing question-and-answer tasks on papers, articles, or PDFs

aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml

@@ -0,0 +1,4 @@
+api_url: "http://export.arxiv.org/api/query"
+request_timeout: 10
+chunk_size: 1024
+pdf_base_url: "https://arxiv.org/pdf"

aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml

@@ -0,0 +1,2 @@
+api_url: "https://api.biorxiv.org/details/biorxiv/"
+request_timeout: 20

aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml

@@ -0,0 +1,2 @@
+api_url: "https://api.biorxiv.org/details/medrxiv"
+request_timeout: 20

aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml

@@ -0,0 +1,22 @@
+# Default configuration for the PDF question_and_answer Tool
+chunk_size: 1200 # Number of characters per text chunk
+chunk_overlap: 200 # Overlap between adjacent chunks
+top_k_papers: 5 # Number of papers to rank and retrieve
+top_k_chunks: 25 # Number of chunks to retrieve
+reranker:
+  model: "nvidia/nv-rerankqa-mistral-4b-v3"
+  api_key: ${oc.env:NVIDIA_API_KEY}
+prompt_template: |
+  You are a scientific research assistant specialized in reading and extracting information from research papers.
+  Your role is to answer questions by retrieving relevant information from the provided context.
+
+  - Provide detailed, structured, and well-argued explanations—not just brief summaries.
+  - Cite specific sources using onky the title of the paper.
+  - If the context is insufficient, clearly state that more information is needed.
+
+  Context:
+  {context}
+
+  Question: {question}
+
+  Your answer should be comprehensive, accurate, and clearly structured for a scientific audience.

{aiagents4pharma-1.39.1.dist-info → aiagents4pharma-1.39.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.39.1
+Version: 1.39.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -114,18 +114,19 @@ _We now have all the agents available on Docker Hub._
 
 Both agents require [Ollama](https://ollama.com/) to run embedding models like `nomic-embed-text`. We use a **single startup script** that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.
 
-##### **1. Clone the repository and navigate to the agent directory**
+##### **1. Download docker-compose.yml, .env.example and startup.sh from GitHub**
 
-```sh
-git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+###### Talk2Agents4Pharma
 
-cd AIAgents4Pharma/aiagents4pharma/<agent>
+```sh
+mkdir talk2aiagents4pharma && cd talk2aiagents4pharma && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/startup.sh
 ```
 
-Replace `<agent>` with either:
+###### Talk2KnowledgeGraphs
 
-- `talk2aiagents4pharma`
-- `talk2knowledgegraphs`
+```sh
+mkdir talk2knowledgegraphs && cd talk2knowledgegraphs && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/startup.sh
+```
 
 ##### **2. Setup environment variables**
 
@@ -145,7 +146,7 @@ LANGCHAIN_TRACING_V2=true           # Optional for both agents
 LANGCHAIN_API_KEY=...               # Optional for both agents
 ```
 
-[Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
+[Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users)
 
 ##### **3. Start the application**
 
@@ -154,7 +155,7 @@ chmod +x startup.sh
 ./startup.sh        # Add --cpu flag to force CPU mode if needed
 ```
 
-[More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
+[More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#about-startupsh)
 
 ##### **To Run Talk2Biomodels / Talk2Scholars**
 
@@ -196,11 +197,11 @@ To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key
 
 Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
 
-If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma).
+If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users).
 
 **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
 
-[More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
+[More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#to-run-multiple-agents-simultaneously)
 
 #### Option 2: git (for developers and contributors)
 
@@ -209,8 +210,7 @@ If you are using docker on Windows, please follow these [Windows Setup Notes](ht
 1. **Clone the repository:**
 
 ```sh
-git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-cd AIAgents4Pharma
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma && cd AIAgents4Pharma
 ```
 
 2. **Install dependencies:**
@@ -321,9 +321,10 @@ git push origin feat/your-feature-name
 
 #### Contacts for contributions
 
-- **Talk2Biomodels / Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330), [@lilijap](https://github.com/lilijap), [@dmccloskey](https://github.com/dmccloskey)
-- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi), [@dmccloskey](https://github.com/dmccloskey)
-- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info), [@gurdeep330](https://github.com/gurdeep330), [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Biomodels**: [@lilijap](https://github.com/lilijap), [@gurdeep330](https://github.com/gurdeep330)
+- **Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330)
+- **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.
 

{aiagents4pharma-1.39.1.dist-info → aiagents4pharma-1.39.3.dist-info}/RECORD

@@ -158,7 +158,9 @@ aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=D9
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=hew5vyrhLeJktoN6DTPRRpnINrXqKZ4trLJQDOuDGOA,4712
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml,sha256=D-IanUKvd2yhrFJjQCMnIG8UNQ3fbkW_bOdhHWRKmq8,357
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml,sha256=p3hFJi-1xbHCNagTG13WHvsrPt11XQg1nHS7VJx2XOY,166
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=N3a_brrB1ilUCeqHQrqu97Olz2snko3tTNPMNR8yTHI,208
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
@@ -168,11 +170,15 @@ aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcb
 aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
 aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=6pHPF0ZGY78SD6KPMukd_xrfO1ocVXcyrsrB-kz-OnI,402
 aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml,sha256=VT3f-E6QGtqUjLEX0eaw9b_7f1Fp83cnnMOpqOufK4I,120
 aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml,sha256=d5_dl1_FYWseBGTVGkvC41jfJMsMUaDMOmC_av3aL4Q,72
 aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml,sha256=NaWmyVZ71rIF3ZRUm912wQgRL0cgDTWA-hVKeu60rtg,70
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=comNgL9hRpH--IWuEsrN6hV5WdrJmh-ZsRh7hbryVhg,631
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml,sha256=lZ_DM0UIj8j2Xryt90YOEj4Bl9_FZ-Z4dhLxaAbgNFY,977
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml,sha256=HG-N8yRjlX9zFwbIBvaDI9ndKjfL-gqPTCCPMLgdUpw,271
 aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
@@ -245,8 +251,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9y
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
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