Develop Github Pull Request Template

- Added a PULL_REQUEST_TEMPLATE.md
- Minor adjustments to Makefile and README.md files

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,95 @@
+# Pull Request Submission - Clinical Assistant
+
+## Description
+
+
+**Related Issue(s):** 
+
+
+## Type of Change
+
+- [ ] Bug fix (non-breaking change that fixes an issue)
+- [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+- [ ] Documentation update
+- [ ] Refactoring (no functional changes)
+- [ ] CI/CD pipeline improvement
+
+## Technical Implementation Details
+
+
+**Modified Components:**
+
+- [ ] `app.py` (Gradio entry point)
+- [ ] `chat.py`
+- [ ] `main.py`
+- [ ] `chatlib/` (Core logic)
+  - [ ] `assistant_node.py`
+  - [ ] `guidlines_rag_agent_li.py`
+  - [ ] `idsr_check.py`
+  - [ ] `logger.py`
+  - [ ] `patient_all_data.py`
+  - [ ] `patient_sql_agent.py`
+  - [ ] `phi_filter.py`
+  - [ ] `state_types.py`
+- [ ] Requirements/dependencies
+- [ ] Makefile
+- [ ] Documentation
+
+## Testing Performed
+
+
+**Test Types Performed:**
+- [ ] Unit tests (pytest)
+- [ ] Integration tests
+- [ ] Manual testing (Gradio UI)
+- [ ] Security validation (PHI handling)
+- [ ] Performance testing
+
+**Test Results:**
+
+
+## Quality Assurance Checklist
+
+
+### Code Quality
+- [ ] Code follows PEP8 style guidelines
+- [ ] Docstrings added for new functions/classes
+- [ ] Type hints added for function signatures
+- [ ] No commented-out code
+- [ ] No debugging statements (print/logging.debug) committed
+
+### Validation
+- [ ] All existing tests pass
+- [ ] New tests added for changes
+- [ ] Ran `make lint` with no warnings
+- [ ] Ran `make format` before committing
+- [ ] Verified Gradio UI functionality
+- [ ] Confirmed SQL generation accuracy
+
+### Documentation
+- [ ] README.md updated if needed
+- [ ] Docstrings added/modified
+- [ ] Any new dependencies documented
+- [ ] Special instructions added if needed
+
+### Security
+- [ ] Verified PHI filtering remains effective
+- [ ] Confirmed no sensitive data exposure
+- [ ] Checked for potential SQL injection vulnerabilities
+
+## Deployment Notes
+- [ ] Requirements.txt updated (if dependency changes)
+- [ ] Migration steps required
+- [ ] Environment variables changes
+
+## Screenshots (if applicable)
+
+
+**Before:**
+
+
+**After:**
+
+
+## Additional Context

Makefile

@@ -12,7 +12,7 @@ else
 	RM := rm -rf
 endif
 
-.PHONY: venv install install-dev lint test format run clean
+.PHONY: venv install lint test format run clean
 
 venv:
 	uv venv $(VENV)

README.md

@@ -30,6 +30,8 @@ A conversational assistant designed to help clinicians in Kenya access patient d
 ```
 .
 ├── app.py                # Gradio web app entry point
+├── chat.py
+├── main.py
 ├── chatlib/              # Core logic, tools, and utilities
 │   ├── assistant_node.py
 │   ├── guidlines_rag_agent_li.py
@@ -39,9 +41,10 @@ A conversational assistant designed to help clinicians in Kenya access patient d
 │   ├── patient_sql_agent.py
 │   ├── phi_filter.py
 │   └── state_types.py
-├── requirements.txt      # Python dependencies
-├── Makefile              # Common dev commands (lint, test, format)
-└── README.md             # Project documentation
+├── Makefile              # Common dev commands (lint, test, format, install, run, clean)
+├── pyproject.toml      # Python dependencies
+├── README.md      # Project documentation
+└── uv.lock             
 ```
 
 ---
@@ -91,13 +94,18 @@ A conversational assistant designed to help clinicians in Kenya access patient d
 
 ## Requirements
 
-See `requirements.txt` for the full list. Key dependencies:
-- Python 3.10+
-- gradio
-- langchain_core, langchain_community, langchain_openai
-- langgraph
-- pandas
-- pydantic
+See `pyproject.toml` for the full list. Key dependencies:
+   - black>=25.1.0
+   - dateparser>=1.2.2
+   - faiss-cpu>=1.11.0
+   - gradio>=5.36.2
+   - langchain-community>=0.3.27
+   - langchain-openai>=0.3.27
+   - langgraph>=0.5.2
+   - llama-index>=0.12.48
+   - pandas>=2.3.1
+   - pylint>=3.3.7
+   - python-dotenv>=1.1.1
 
 ---