Feat agent toml

aiagents4pharma/talk2biomodels/README.md

@@ -0,0 +1,33 @@
+**Talk2BioModels** is an AI agent designed to facilitate interaction with mathematical models in systems biology. Systems biology models are critical in understanding complex biological mechanisms, but they’re often inaccessible to those without coding or mathematical expertise. Talk2BioModels simplifies this, enabling researchers to focus on analysis and interpretation rather than on programming. With Talk2BioModels, users can interact directly with these models through natural language. By simply asking questions or making requests, users can:
+
+- Forward simulation of both internal and open-source models (BioModels).
+- Adjust parameters within the model to simulate different conditions.
+- Query simulation results.
+
+## Installation
+
+### Prerequisites
+- Python 3.10 or higher
+
+### Installing Talk2BioModels in two ways
+
+#### Option 1: Git
+
+1. Clone the repository:
+
+    git clone https://github.com/<your-repo>/ aiagents4pharma.git
+    cd aiagents4pharma/talk2biomodels
+
+2. Install the package and its dependencies:
+
+    pip install .
+
+3. Alternatively, install from source:
+
+    pip install -e .
+
+
+#### Option 2: PyPI *(coming soon)*
+   ```bash
+   pip install aiagents4pharma 
+   ```

aiagents4pharma/talk2biomodels/pyproject.toml

@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "talk2biomodels"
+
+description = "A submodule of AIAgents4Pharma for interacting with systems biology models "
+
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "copasi_basico==0.78",
+    "openai==1.59.4",
+    "pandas==2.2.3",
+    "langchain==0.3.7",
+    "langchain-community==0.3.5",
+    "langchain-core==0.3.15",
+    "langchain-experimental==0.3.3",
+    "langchain-openai==0.2.5",
+    "matplotlib==3.9.2",
+    "plotly==5.24.1",
+    "pydantic==2.9.2",
+    "pytest==8.3.3",
+    "streamlit==1.39.0"
+]
+dynamic = ["version"]
+
+# Package discovery for the submodule
+[tool.setuptools]
+packages = [
+    "talk2biomodels",
+    "talk2biomodels.models",
+    "talk2biomodels.tools"
+]

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "langchain-experimental==0.3.3",
     "langchain-openai==0.2.5",
     "matplotlib==3.9.2",
-    "openai==1.55.3",
+    "openai==1.59.4",
     "pandas==2.2.3",
     "plotly==5.24.1",
     "pydantic==2.9.2",

requirements.txt

@@ -6,7 +6,7 @@ langchain-core==0.3.15
 langchain-experimental==0.3.3
 langchain-openai==0.2.5
 matplotlib==3.9.2
-openai==1.55.3
+openai==1.59.4
 pandas==2.2.3
 plotly==5.24.1
 pydantic==2.9.2