Add project setup scaffolding and Dockerfile

.dockerignore

@@ -0,0 +1,16 @@
+.git
+.idea
+.pytest_cache
+.ruff_cache
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.env
+.env.*
+tests/
+docs/
+notebooks/
+output/
+*.md
+!README.md

Dockerfile

@@ -0,0 +1,48 @@
+# HealthChain application Dockerfile
+#
+# Usage:
+#   Build:  docker build -t my-healthcare-app .
+#   Run:    docker run -p 8000:8000 --env-file .env my-healthcare-app
+#
+# Required environment variables (set in .env or pass via -e):
+#   APP_MODULE   Python module path to your app, e.g. "myapp:app" (default: "app:app")
+#
+# FHIR source credentials (if connecting to Epic/Cerner):
+#   FHIR_BASE_URL, CLIENT_ID, CLIENT_SECRET or CLIENT_SECRET_PATH
+#
+# See docs: https://dotimplement.github.io/HealthChain/reference/gateway/gateway/
+
+FROM python:3.11-slim
+
+# Keeps Python from buffering stdout/stderr
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    APP_MODULE=app:app \
+    PORT=8000
+
+WORKDIR /app
+
+# Install system dependencies needed by lxml and spaCy
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    gcc \
+    g++ \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install healthchain from PyPI
+RUN pip install --no-cache-dir healthchain
+
+# Install any additional dependencies your application needs
+# (copy requirements first to leverage Docker layer caching)
+COPY requirements.txt* ./
+RUN if [ -f requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi
+
+# Copy application code
+COPY . .
+
+# Run as non-root user
+RUN useradd -m appuser && chown -R appuser /app
+USER appuser
+
+EXPOSE $PORT
+
+CMD uvicorn $APP_MODULE --host 0.0.0.0 --port $PORT

README.md

@@ -26,16 +26,25 @@
 
 <div align="center">
 
-HealthChain is an open-source developer framework to build healthcare AI applications with native protocol understanding. Skip months of custom integration with **built-in FHIR support**, **real-time EHR connectivity**, and **production-ready deployment** - all in Python.
+HealthChain is an open-source SDK for production-ready healthcare AI. Skip months of custom integration work with **built-in FHIR support**, **real-time EHR connectivity**, and **deployment tooling for healthcare AI/ML systems** — all in Python.
 
 </div>
 
 ## Installation
 
 ```bash
 pip install healthchain
+
+# Scaffold a new project
+healthchain new my-app
+cd my-app
+
+# Run locally
+healthchain serve
 ```
 
+See the [CLI reference](https://dotimplement.github.io/HealthChain/cli/) for all commands.
+
 ## Core Features
 
 HealthChain is the **quickest way for AI/ML engineers to integrate their models with real healthcare systems**.
@@ -232,7 +241,7 @@ client.save_results("./output/")
 - [ ] 🔍 Data provenance and observability
 - [ ] 🔒 Production security and compliance (Authentication, audit logging, HIPAA)
 - [ ] 🔄 HL7v2 parsing, FHIR profile conversion and OMOP mapping support
-- [ ] 🚀 Enhanced deployment support (Docker, Kubernetes, telemetry)
+- [ ] 🚀 Kubernetes and telemetry support
 - [ ] 📊 Model performance monitoring with MLFlow integration
 - [ ] 🤖 MCP server integration
 

docs/cli.md

@@ -0,0 +1,94 @@
+# CLI Reference
+
+HealthChain ships with a CLI to help you scaffold, run, and customize projects.
+
+```bash
+healthchain --help
+```
+
+---
+
+## `healthchain new`
+
+Scaffold a new project directory with everything you need to get started.
+
+```bash
+healthchain new my-app
+```
+
+Creates:
+
+```
+my-app/
+├── app.py            # your application entry point
+├── .env.example      # FHIR credential template — copy to .env and fill in
+├── requirements.txt  # add extra dependencies here
+├── Dockerfile
+└── .dockerignore
+```
+
+---
+
+## `healthchain serve`
+
+Start your app locally with uvicorn.
+
+```bash
+healthchain serve              # defaults to app:app on port 8000
+healthchain serve app:app
+healthchain serve app:app --port 8080
+healthchain serve app:app --host 127.0.0.1 --port 8080
+```
+
+The `app_module` argument is the Python import path to your FastAPI app instance — `<module>:<variable>`. If your app is defined as `app = HealthChainAPI()` in `app.py`, the default `app:app` works as-is.
+
+To run in Docker instead:
+
+```bash
+docker build -t my-app .
+docker run -p 8000:8000 --env-file .env my-app
+```
+
+---
+
+## `healthchain eject-templates`
+
+Copy the built-in interop templates into your project so you can customize them.
+
+```bash
+healthchain eject-templates ./my_configs
+```
+
+Only needed if you're using the [InteropEngine](reference/interop/interop.md) and want to customize FHIR↔CDA conversion beyond the defaults. After ejecting:
+
+```python
+from healthchain.interop import create_interop
+
+engine = create_interop(config_dir="./my_configs")
+```
+
+See [Interoperability](reference/interop/interop.md) for details.
+
+---
+
+## Typical workflow
+
+```bash
+# 1. Scaffold a new project
+healthchain new my-cds-service
+cd my-cds-service
+
+# 2. Build your app in app.py
+#    See https://dotimplement.github.io/HealthChain/cookbook/ for examples
+
+# 3. Set credentials
+cp .env.example .env
+# edit .env with your FHIR_BASE_URL, CLIENT_ID, CLIENT_SECRET
+
+# 4. Run locally
+healthchain serve
+
+# 5. Ship it
+docker build -t my-cds-service .
+docker run -p 8000:8000 --env-file .env my-cds-service
+```

docs/index.md

@@ -53,7 +53,7 @@ HealthChain is an open-source Python toolkit that streamlines productionizing he
 
 ## Getting Started with Healthcare AI
 
-HealthChain provides the missing middleware layer between healthcare systems and modern AI/ML development. Whether you're building clinical decision support tools, processing medical documents, or creating multi-system integrations, these docs will guide you through:
+HealthChain is production-ready healthcare AI infrastructure: built-in FHIR support, real-time EHR connectivity, and deployment tooling for healthcare AI/ML systems. Skip months of custom integration work. Whether you're building clinical decision support tools, processing medical documents, or creating multi-system integrations, these docs will guide you through:
 
 - **🔧 Core concepts** - Understand FHIR resources, pipelines, and gateway patterns
 - **📚 Real examples** - Step-by-step tutorials for common healthcare AI use cases

docs/reference/interop/configuration.md

@@ -27,8 +27,8 @@ engine = create_interop(config_dir="/path/to/custom/configs")
 To create editable configuration templates:
 
 ```bash
-# Create customizable config templates
-healthchain init-configs ./my_configs
+# Eject built-in templates for customization
+healthchain eject-templates ./my_configs
 
 # Then use them in your code
 engine = create_interop(config_dir="./my_configs")

docs/reference/interop/engine.md

@@ -43,10 +43,10 @@ engine = create_interop(validation_level="warn", environment="production")
 
 
 > **💡 Tip:**
-> To create editable configuration templates, run:
+> To eject the built-in templates for customization, run:
 >
 > ```bash
-> healthchain init-configs ./my_configs
+> healthchain eject-templates ./my_configs
 > ```
 > This will create a `my_configs` directory with editable default configuration templates.
 

docs/reference/interop/experimental.md

@@ -28,7 +28,7 @@ This page tracks templates that are under development or have known issues. Use
 
 1. Copy experimental files to your custom config:
    ```bash
-   # After running: healthchain init-configs my_configs
+   # After running: healthchain eject-templates my_configs
    cp dev-templates/allergies/allergies.yaml my_configs/interop/cda/sections/
    cp dev-templates/allergies/allergy_*.liquid my_configs/templates/cda_fhir/
    cp dev-templates/allergies/allergy_*.liquid my_configs/templates/fhir_cda/

docs/reference/interop/interop.md

@@ -65,11 +65,11 @@ cda_document = engine.from_fhir(fhir_resources, dest_format="cda")
 ```
 ### Custom Configs
 
-The default templates that come with the package are limited to problems, medications, and notes and are meant for basic testing and prototyping. Use the `healthchain init-configs` command to create editable configuration templates:
+The default templates that come with the package are limited to problems, medications, and notes and are meant for basic testing and prototyping. Use the `healthchain eject-templates` command to create editable configuration templates:
 
 ```bash
-# Create editable configuration templates
-healthchain init-configs ./my_configs
+# Eject built-in templates for customization
+healthchain eject-templates ./my_configs
 ```
 
 Then use the `config_dir` parameter to specify the path to your custom configs: