aiagents4pharma 1.25.1__py3-none-any.whl → 1.26.1__py3-none-any.whl

aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py

@@ -22,10 +22,11 @@ def get_app(uniq_id, llm_model: BaseChatModel):
     '''
     This function returns the langraph app.
     '''
-    if llm_model.model_name == 'gpt-4o-mini':
-        llm_model = ChatOpenAI(model='gpt-4o-mini',
-                               temperature=0,
-                               model_kwargs={"parallel_tool_calls": False})
+    if hasattr(llm_model, 'model_name'):
+        if llm_model.model_name == 'gpt-4o-mini':
+            llm_model = ChatOpenAI(model='gpt-4o-mini',
+                                temperature=0,
+                                model_kwargs={"parallel_tool_calls": False})
     # Load hydra configuration
     logger.log(logging.INFO, "Launching AIAgents4Pharma_Agent with thread_id %s", uniq_id)
     with hydra.initialize(version_base=None, config_path="../configs"):
@@ -57,7 +58,7 @@ def get_app(uniq_id, llm_model: BaseChatModel):
         # Full history is needed to extract
         # the tool artifacts
         output_mode="full_history",
-        add_handoff_back_messages=False,
+        add_handoff_back_messages=True,
         prompt=system_prompt
     )
 

{aiagents4pharma-1.25.1.dist-info → aiagents4pharma-1.26.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.25.1
+Version: 1.26.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -67,6 +67,7 @@ Requires-Dist: scanpy==1.11.0
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
 ![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
 ![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 ![Docker Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?link=https%3A%2F%2Fhub.docker.com%2Frepository%2Fdocker%2Fvirtualpatientengine%2Ftalk2biomodels%2Fgeneral)
@@ -97,23 +98,77 @@ Our toolkit currently consists of the following agents:
 pip install aiagents4pharma
 ```
 
-Check out the tutorials on each agent for detailed instrcutions.
+Check out the tutorials on each agent for detailed instructions.
 
 #### Option 2: Docker Hub
 
-_Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
+_We now have `Talk2AIAgents4Pharma`, `Talk2Biomodels`, and `Talk2Scholars` available on Docker Hub._
 
-1. **Pull the Docker images**
+##### **Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs**
 
-   ```bash
-   docker pull virtualpatientengine/talk2biomodels
-   ```
+Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network.
 
-   ```bash
-   docker pull virtualpatientengine/talk2scholars
+###### **Setup Environment Variables**
+
+1. Choose the app you want to use:
+
+```sh
+# Navigate to the correct directory before setting up environment variables.
+# Use one of the following commands based on the agent you want to use:
+cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma
+cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs
+```
+
+2. Copy the `.env.example` file and rename it to `.env`:
+   ```sh
+   cp .env.example .env
    ```
+3. Open the `.env` file and add your API keys:
+
+   ```plaintext
+   OPENAI_API_KEY=your_openai_api_key
+   NVIDIA_API_KEY=your_nvidia_api_key
+   OLLAMA_HOST=http://ollama:11434
+   LANGCHAIN_TRACING_V2=true
+   LANGCHAIN_API_KEY=your_langchain_api_key_here
+   # Notes:
+   # - The API endpoint for Ollama is already set in env.example.
+   # - Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
+   # - If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
+   # - Langsmith API for tracing is optional for both, set it in env.example if required.
+   ```
+
+4. Save the file.
+
+To start the containers, run the following command:
+
+```sh
+docker compose --profile cpu up # for CPU mode
+docker compose --profile nvidia up # for GPU mode
+docker compose --profile amd up # for AMD mode
+```
+
+This will:
+
+- Pull the latest images if they are not already available.
+- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network.
+- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs.
 
-2. **Run the containers**
+To Access the web app, open your browser and go to:
+
+```
+http://localhost:8501
+```
+
+To stop the containers, run:
+
+```sh
+docker compose down
+```
+
+##### **Run Talk2Biomodels and Talk2Scholars**
+
+1. **Run the containers**
 
    ```bash
    docker run -d \
@@ -134,8 +189,8 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
      virtualpatientengine/talk2scholars
    ```
 
-3. **Access the Web App**
-    Open your browser and go to:
+2. **Access the Web App**
+   Open your browser and go to:
 
    ```
    http://localhost:8501
@@ -161,36 +216,43 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
    cd AIAgents4Pharma
    ```
 2. **Install dependencies:**
+
    ```bash
    pip install -r requirements.txt
    ```
-   The current version of T2KG requires additional Ollama library to be installed.
+
+   ⚠️ The current version of T2KG requires additional Ollama library to be installed.
 
    Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download)
 
    As an alternative, use the following commands to install the library using terminal and to pull necessary model:
 
    - Ubuntu:
-      ```
-      curl -fsSL https://ollama.com/install.sh | sh
-      ollama pull nomic-embed-text
-      ```
+     ```
+     curl -fsSL https://ollama.com/install.sh | sh
+     ollama pull nomic-embed-text
+     ```
    - Windows:
-      ```
-      curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
-      tar -xzf .\ollama-windows-amd64.zip
-      start ollama serve
-      ollama pull nomic-embed-text
-      ```
+     ```
+     curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
+     tar -xzf .\ollama-windows-amd64.zip
+     start ollama serve
+     ollama pull nomic-embed-text
+     ```
    - macOS:
-      ```
-      brew install ollama
-      ollama pull nomic-embed-text
-      ```
-   A list of pulled Ollama models can be checked using the following command:
+     ```
+     brew install ollama
+     ollama pull nomic-embed-text
+     ```
+     A list of pulled Ollama models can be checked using the following command:
+
    ```
    ollama list
    ```
+
+   ⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed.
+   You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
 
    ```bash
@@ -260,4 +322,4 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 
 ## Feedback
 
-Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀

{aiagents4pharma-1.25.1.dist-info → aiagents4pharma-1.26.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 aiagents4pharma/__init__.py,sha256=7xnvthMuxYurECWvyb0_yaPJ18SsqvmkKPTCxgbQlNQ,186
 aiagents4pharma/talk2aiagents4pharma/__init__.py,sha256=KOPe8cZ-ROQ6EGn8FeejRFUPokayKRMTgiXFyOpZGoA,122
 aiagents4pharma/talk2aiagents4pharma/agents/__init__.py,sha256=Cc1RitlLGzJ5d_dCSUdguZH417nlJux1qVCVS2M9t30,129
-aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py,sha256=s0mrOk4DuAg7IkzB1YGyl_8wjxF2T_ReZENZirvjr94,2810
+aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py,sha256=gnXBvvi3t8DjUtXImqgVJ9Rz7RqnDeHNTCMFiPo6bvc,2860
 aiagents4pharma/talk2aiagents4pharma/configs/__init__.py,sha256=5ah__-8XyRblwT0U1ByRigNjt_GyCheu7zce4aM-eZE,68
 aiagents4pharma/talk2aiagents4pharma/configs/config.yaml,sha256=VnbMbVSYfCh68cHZ0JLu00UjOUmapejN3EsN3lnBXtU,51
 aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py,sha256=zrJcq-4m0YUKfSlRGC8KzBmEooaASKuL_Y75yDp-ZoA,72
@@ -186,8 +186,8 @@ aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=i5KMFJWK31CjYtVT1McJpLzg
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=7PoZfcstxDThWX6NYOgxN_9M_nwgMPAALch8OmjraVY,5568
 aiagents4pharma/talk2scholars/tools/zotero/__init__.py,sha256=1UW4r5ECvAwYpo1Fjf7lQPO--M8I85baYCHocFOAq4M,53
 aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=NJ65fAJ4u2Zq15uvEajVOhI4QnNvyqA6FHPaEDqvMw0,4321
-aiagents4pharma-1.25.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.25.1.dist-info/METADATA,sha256=b6pqbn3KJ-oCdO-rupWLZegRk594gIE-tfA9BnFnBCg,10297
-aiagents4pharma-1.25.1.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-aiagents4pharma-1.25.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.25.1.dist-info/RECORD,,
+aiagents4pharma-1.26.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.26.1.dist-info/METADATA,sha256=q4jfiTPl4koFlScZw3k22S_iIIr9w7SV-tk0aEftH-Q,12585
+aiagents4pharma-1.26.1.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+aiagents4pharma-1.26.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.26.1.dist-info/RECORD,,