Revamp README with detailed usage and features

README.md

@@ -1,14 +1,140 @@
-# ChatAnalysis
-Chat with your CSV/TSV data using OpenAI models (more models will be supported soon)
+# ChatAnalysis: Galaxy Data Analysis Agent
 
-# Run the app locally
-Created a virtual env:
-```
-python -m venv .env
+## Introduction
+
+**ChatAnalysis** is an interactive Galaxy tool that lets you perform data analysis via **natural language**. Built on Large Language Models (LLMs) and the **DSPy** prompt framework, ChatAnalysis interprets plain-English requests (e.g. “Generate a heatmap of columns A vs B”) and returns:
+
+- **Data processing** (filtering, aggregations, summary statistics)
+- **Visualizations** (plots, charts)
+- **Code snippets** (Python / Pandas / AutoGluon)
+- **Explanations** (how the analysis was done)
+
+All results appear in a split-pane chat interface **inside Galaxy**—no coding required!
+
+---
+
+## v0.3 Highlights (DSPy Agent)
+
+- **DSPy + Few-Shot Learning**  
+  Uses curated Q&A examples to improve prompt accuracy.
+
+- **Split-Pane UI**  
+  - **Left:** Conversation  
+  - **Right:** Details & Preview (code, tables, plots)  
+  Click past queries to revisit full outputs.
+
+- **Faster, Multi-Step Analyses**  
+  Optimized logic for chaining data cleaning, visualization, modeling in one session.
+
+- **Advanced ML Support**  
+  Integrates AutoGluon, scikit-learn, and more for model training, evaluation, and explanation.
+
+- **Bookmarking & History**  
+  Easily revisit previous queries without rerunning; suggested follow-up shortcuts.
+
+---
+
+## Use on Galaxy Main (usegalaxy.org)
+
+1. **Upload Data**  
+   Log in to [usegalaxy.org](https://usegalaxy.org), upload your CSV/TSV/Excel file into your history.
+
+2. **Set Your LLM API Key**  
+   - Obtain an OpenAI API key (or other supported backend).  
+   - In Galaxy: **User → Preferences → OpenAI API Key** → paste your key.
+
+3. **Launch ChatAnalysis**  
+   - Find **ChatAnalysis** under **Interactive Tools**.  
+   - Select your dataset (and model if prompted) → **Launch**.
+
+4. **Chat & Analyze**  
+   - Type queries like “Summarize this dataset.”  
+   - View text, code, tables, and plots in the split-pane UI.
+
+5. **Follow-Ups & Refinement**  
+   - Context is retained: ask “Filter to 2022 and rerun.”  
+   - Click suggested follow-up buttons for one-click analyses.
+
+6. **Stop & Save**  
+   - Click **Stop** to end the session.  
+   - Outputs are saved back to your Galaxy history.
+
+---
+
+## Install on Your Own Galaxy
+
+### 1. ToolShed Installation (Admin)
+
+- **Repo:** `goeckslab/chatanalysis`  
+- Install via ToolShed; enable Interactive Tool support and Docker.
+
+### 2. Local Development
+
+```bash
+git clone https://github.com/goeckslab/ChatAnalysis.git
+cd ChatAnalysis
+
+# 1. Create & activate a virtual environment
+python3.11 -m venv .env
 source .env/bin/activate
+
+# 2. Install dependencies
+pip install --upgrade pip
+pip install -r dspy_agent/requirements_nicegui_dspy.txt
+
+# 3. Provide your OpenAI API key
+# Option A: Key file (default)
+echo YOUR_OPENAI_KEY > dspy_agent/user_config_openai.key
+
+# Option B: CLI argument
+# python dspy_agent/chat_dspy.py --openai_key_file /full/path/to/user_config_openai.key
+
+# Option C: provide on the app UI.
+
+# 4. Run the DSPy agent
+python dspy_agent/chat_dspy.py
+
+# 5. Open in browser:
+# http://localhost:9090
 ```
-Run the app 
+
+_or_
+
+```bash
+docker build -t chatanalysis:dspy -f dspy_agent/Dockerfile .
+docker run -p 9090:9090 chatanalysis:dspy
+# then visit http://localhost:9090
 ```
-pip install -r requirements.txt
-streamlit run chat_analysis.py
+
+> **Note:** Internet access is required for the LLM API.
+
+---
+
+## Legacy Agents (Reference Only)
+
+These prior versions are now **deprecated**—moved to `legacy_agents/`:
+
+- **v0.1** – `pandasai_agent/`  
+- **v0.2** – `smolagents_agent/`  
+
+---
+
+## Repository Structure
+
+```
+/
+├── .github/workflows/        # CI/CD pipelines
+├── dspy_agent/               # **v0.3 DSPy agent** (primary code)
+├── legacy_agents/            # pandasai_agent/ & smolagents_agent/
+├── tools/                    # Galaxy tool XML & support files
+├── seq_diagram.md            # Sequence diagram
+├── LICENSE
+├── README.md
+├── .gitignore
+└── .dockerignore
 ```
+
+
+---
+
+*Feel free to open issues or pull requests for questions or improvements!*