feat: Improve testing framework

.coveragerc

@@ -0,0 +1,26 @@
+[run]
+source = chatbot_api/src, chatbot_frontend/src, hospital_neo4j_etl/src
+omit =
+    */tests/*
+    */test_*
+    */__init__.py
+    */conftest.py
+    */migrations/*
+    */venv/*
+    */.venv/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+    class .*\bProtocol\):
+    @(abc\.)?abstractmethod
+
+[html]
+directory = htmlcov

.github/workflows/ci.yml

@@ -0,0 +1,142 @@
+name: CI
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
+
+jobs:
+  code-quality:
+    name: Code Quality
+    runs-on: ubuntu-latest
+    if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: "**/pyproject.toml"
+
+    - name: Set up Python 3.11
+      run: uv python install 3.11
+
+    - name: Create virtual environment and install dependencies
+      run: |
+        uv venv --python 3.11
+        uv pip install -e "chatbot_api[dev]" -e "chatbot_frontend[dev]" -e "hospital_neo4j_etl[dev]"
+
+    - name: Run linting and formatting checks
+      run: |
+        uv run ruff check chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
+        uv run ruff format --check chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
+
+    - name: Run type checking
+      run: uv run mypy chatbot_api/src/
+
+  unit-tests:
+    name: Unit Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: "**/pyproject.toml"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Create virtual environment and install dependencies
+      run: |
+        uv venv --python ${{ matrix.python-version }}
+        uv pip install -e "chatbot_api[dev]" -e "chatbot_frontend[dev]" -e "hospital_neo4j_etl[dev]"
+
+    - name: Run unit tests with coverage
+      run: make test-unit
+
+  integration-tests:
+    name: Integration Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: "**/pyproject.toml"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Create virtual environment and install dependencies
+      run: |
+        uv venv --python ${{ matrix.python-version }}
+        uv pip install -e "chatbot_api[dev]" -e "chatbot_frontend[dev]" -e "hospital_neo4j_etl[dev]"
+
+    - name: Run integration tests with coverage
+      run: |
+        uv run pytest tests/integration/ -v --cov=chatbot_api/src --cov=chatbot_frontend/src --cov=hospital_neo4j_etl/src
+
+    - name: Upload coverage to Codecov
+      if: matrix.python-version == '3.11'  # Only upload once
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false
+
+  build-validation:
+    name: Docker Build Validation
+    runs-on: ubuntu-latest
+    if: ${{ contains(github.event.head_commit.message, 'docker') || contains(github.event.head_commit.message, 'Docker') || github.event_name == 'pull_request' }}
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Check for Docker-related changes
+      uses: dorny/paths-filter@v2
+      id: docker-changes
+      with:
+        filters: |
+          docker:
+            - 'docker-compose.yml'
+            - '**/Dockerfile'
+            - '.dockerignore'
+
+    - name: Create dummy .env file for Docker build
+      if: steps.docker-changes.outputs.docker == 'true' || github.event_name == 'pull_request'
+      run: |
+        cat > .env << 'EOF'
+        # Dummy environment variables for CI build validation
+        OPENAI_API_KEY=sk-dummy-key-for-ci-build-only
+        NEO4J_URI=neo4j://localhost:7687
+        NEO4J_USERNAME=neo4j
+        NEO4J_PASSWORD=password
+        HOSPITAL_AGENT_MODEL=gpt-3.5-turbo
+        HOSPITAL_CYPHER_MODEL=gpt-3.5-turbo
+        HOSPITAL_QA_MODEL=gpt-3.5-turbo
+        CHATBOT_URL=http://localhost:8000/hospital-rag-agent
+        EOF
+
+    - name: Validate Docker Compose build
+      if: steps.docker-changes.outputs.docker == 'true' || github.event_name == 'pull_request'
+      run: |
+        docker compose build --no-cache
+        docker compose config --quiet

.gitignore

@@ -8,3 +8,6 @@ __pycache__
 *.pyc
 .DS_Store
 
+*.egg-info
+*.coverage
+htmlcov/

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.8
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-requests]
+        args: [--ignore-missing-imports, --explicit-package-bases]
+        files: ^chatbot_api/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files

Makefile

@@ -8,8 +8,29 @@ start:
 stop:
 	docker compose down chatbot_api chatbot_frontend
 
-format:
+test:
+	uv run pytest tests/ -v --cov=chatbot_api/src --cov=chatbot_frontend/src --cov=hospital_neo4j_etl/src --ignore=tests/performance
+
+test-unit:
+	uv run pytest tests/unit/ -v
 
+test-integration:
+	uv run pytest tests/integration/ -v
+
+format:
+	uv run ruff format chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
 
 lint:
+	uv run ruff check chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
+
+format-check:
+	uv run ruff format --check chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
+
+lint-fix:
+	uv run ruff check --fix chatbot_api/src/ chatbot_frontend/src/ hospital_neo4j_etl/src/ tests/
+
+pre-commit:
+	uv run pre-commit run --all-files
 
+install-dev:
+	uv pip install -e "chatbot_api[dev]" -e "chatbot_frontend[dev]" -e "hospital_neo4j_etl[dev]"

README.md

@@ -1,6 +1,8 @@
-# Healthcare RAG Agent 
+# Healthcare RAG Agent
 
-[![Python](https://img.shields.io/badge/Python-3.8+-blue.svg)](https://www.python.org/)
+[![CI](https://github.com/asanmateu/medgraph-ai/workflows/CI/badge.svg)](https://github.com/asanmateu/medgraph-ai/actions)
+[![codecov](https://codecov.io/gh/asanmateu/medgraph-ai/branch/master/graph/badge.svg)](https://codecov.io/gh/asanmateu/medgraph-ai)
+[![Python](https://img.shields.io/badge/Python-3.9%20|%203.11-blue.svg)](https://www.python.org/)
 [![LangChain](https://img.shields.io/badge/LangChain-Latest-green.svg)](https://langchain.com/)
 [![Neo4j](https://img.shields.io/badge/Neo4j-5.0+-blue.svg)](https://neo4j.com/)
 [![Docker](https://img.shields.io/badge/Docker-Required-blue.svg)](https://www.docker.com/)
@@ -16,6 +18,7 @@ A Retrieval-Augmented Generation (RAG) agent designed for healthcare information
 - [Example Queries](#-example-queries)
 - [Database Design](#database-design)
 - [Technical Stack](#technical-stack)
+- [Contributing](#-contributing)
 - [Acknowledgments](#acknowledgments)
 
 ## 🎯 Overview
@@ -24,10 +27,10 @@ This project implements a healthcare-focused RAG chatbot that leverages LangChai
 
 ## ✨ Key Features
 
-✅ **Knowledge Graph Integration** - Neo4j for healthcare data relationships  
-✅ **RESTful API** - FastAPI-powered scalable backend  
-✅ **Interactive UI** - Intuitive Streamlit interface  
-✅ **Containerized** - Docker-based deployment  
+✅ **Knowledge Graph Integration** - Neo4j for healthcare data relationships
+✅ **RESTful API** - FastAPI-powered scalable backend
+✅ **Interactive UI** - Intuitive Streamlit interface
+✅ **Containerized** - Docker-based deployment
 ✅ **Multi-Model Support** - Configurable OpenAI models
 
 <a name="architecture"></a>
@@ -147,7 +150,10 @@ Relationships between nodes contain additional contextual information:
 - **Docker**: Containerization platform
 - **OpenAI GPT-3.5**: Language model for natural language understanding
 
-## Acknowledgments
+## 🤝 Contributing
 
-This project builds upon the excellent foundation provided by Real Python's LLM RAG Chatbot [tutorial](https://realpython.com/build-llm-rag-chatbot-with-langchain).
+Contributions are welcome. Please ensure that any pull requests maintain the existing code style and include appropriate tests and documentation updates.
+
+## 🙏 Acknowledgments
 
+This project builds upon the excellent foundation provided by Real Python's LLM RAG Chatbot [tutorial](https://realpython.com/build-llm-rag-chatbot-with-langchain).

chatbot_api/mypy.ini

@@ -0,0 +1,41 @@
+[mypy]
+python_version = 3.9
+warn_return_any = True
+warn_unused_configs = True
+disallow_untyped_defs = False
+disallow_incomplete_defs = False
+check_untyped_defs = True
+disallow_untyped_decorators = False
+no_implicit_optional = True
+warn_redundant_casts = True
+warn_unused_ignores = True
+warn_no_return = True
+warn_unreachable = True
+strict_equality = True
+namespace_packages = True
+explicit_package_bases = True
+
+# Ignore missing imports for third-party libraries
+[mypy-langchain.*]
+ignore_missing_imports = True
+
+[mypy-langchain_openai.*]
+ignore_missing_imports = True
+
+[mypy-langchain_community.*]
+ignore_missing_imports = True
+
+[mypy-neo4j.*]
+ignore_missing_imports = True
+
+[mypy-openai.*]
+ignore_missing_imports = True
+
+[mypy-pydantic.*]
+ignore_missing_imports = True
+
+[mypy-fastapi.*]
+ignore_missing_imports = True
+
+[mypy-uvicorn.*]
+ignore_missing_imports = True

chatbot_api/pyproject.toml

@@ -16,4 +16,13 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["black", "flake8"]
+dev = [
+    "ruff",
+    "mypy",
+    "pre-commit",
+    "pytest>=7.0.0",
+    "pytest-asyncio>=0.21.0",
+    "pytest-mock>=3.10.0",
+    "httpx>=0.24.0",
+    "pytest-cov>=4.0.0"
+]

chatbot_api/src/agents/hospital_rag_agent.py

@@ -1,24 +1,26 @@
 import os
+from typing import List, Optional
 from langchain_openai import ChatOpenAI
 from langchain.agents import (
     create_openai_functions_agent,
     Tool,
     AgentExecutor,
 )
 from langchain import hub
+from langchain.schema import BasePromptTemplate
 from chains.hospital_review_chain import reviews_vector_chain
 from chains.hospital_cypher_chain import hospital_cypher_chain
 from tools.wait_times import (
     get_current_wait_times,
     get_most_available_hospital,
 )
 
-HOSPITAL_AGENT_MODEL = os.getenv("HOSPITAL_AGENT_MODEL")
+HOSPITAL_AGENT_MODEL: Optional[str] = os.getenv("HOSPITAL_AGENT_MODEL")
 
-hospital_agent_prompt = hub.pull("hwchase17/openai-functions-agent")
+hospital_agent_prompt: BasePromptTemplate = hub.pull("hwchase17/openai-functions-agent")
 
 
-tools = [
+tools: List[Tool] = [
     Tool(
         name="Experiences",
         func=reviews_vector_chain.invoke,
@@ -68,7 +70,7 @@
 ]
 
 
-chat_model = ChatOpenAI(
+chat_model: ChatOpenAI = ChatOpenAI(
     model=HOSPITAL_AGENT_MODEL,
     temperature=0,
 )
@@ -79,7 +81,7 @@
     tools=tools,
 )
 
-hospital_rag_agent_executor = AgentExecutor(
+hospital_rag_agent_executor: AgentExecutor = AgentExecutor(
     agent=hospital_rag_agent,
     tools=tools,
     return_intermediate_steps=True,