Documentation (#14)

---------

Co-authored-by: Adam Kells <[email protected]>

CONTRIBUTING.md

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+# Contributing 
+> If you're reading this, you're early! We're still finalising our guidelines as this is an early release so I asked ChatGPT to write some guidelines as a placeholder. [Drop us a message](https://discord.gg/jG4UWCUh) instead!
+>
+
+Thank you for considering contributing to this project! Here are some guidelines to help you get started.
+
+
+## How to Report a Bug
+
+If you find a bug, please create an issue on GitHub. Include as much detail as possible:
+- A clear and descriptive title
+- Steps to reproduce the issue
+- Expected and actual results
+- Any relevant screenshots or logs
+
+## How to Suggest a Feature
+
+If you have an idea for a new feature, please open an issue on GitHub with the following information:
+- A clear and descriptive title
+- A detailed description of the proposed feature
+- Any other information that might be useful
+
+## How to Contribute Code
+
+1. Fork the repository to your own GitHub account.
+2. Clone the forked repository to your local machine.
+3. Create a new branch for your feature or bugfix.
+   ```sh
+   git checkout -b my-feature-branch
+   ```
+4. Make your changes and commit them with descriptive commit messages.
+   ```sh
+   git commit -m "Add new feature to do X"
+   ```
+5. Push your changes to your forked repository.
+   ```sh
+   git push origin my-feature-branch
+   ```
+6. Open a pull request on the original repository.
+
+## Style Guide
+
+Please follow the project's coding style:
+- Use meaningful variable and function names.
+- Write comments to explain complex code.
+- Ensure your code is formatted consistently.
+
+## Testing
+
+Make sure to add tests for any new functionality you add. Run all tests to ensure that your changes do not break existing functionality.
+
+## Pull Request Process
+
+1. Ensure your changes comply with the style guide.
+2. Ensure all tests pass.
+3. Open a pull request with a clear title and description of your changes.
+4. A project maintainer will review your pull request and may request changes.
+5. Once approved, your pull request will be merged.
+
+Thank you for your contributions!

LICENSE

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README.md

@@ -1,9 +1,91 @@
-![GitHub License](https://img.shields.io/github/license/:user/:repo)
+![GitHub License](https://img.shields.io/github/license/dotimplement/healthchain)
 
 # HealthChain
 
-Simplify prototyping and testing LLM applications in healthcare context.
+Simplify prototyping and testing AI/NLP applications in a healthcare context 💫 🏥.
 
-## Quickstart
+Building applications that integrate in healthcare systems is complex, and so is designing reliable, reactive algorithms involving text and structured data. Let's try to change that.
 
-You can install this package by running:
+```bash
+pip install healthchain
+```
+> 🚧 This is a work in progress with a limited set of functionalities and resources implemented. Things might break. 💥 We are working towards a full release soon! 👀
+
+
+## Features
+- [x] 🍱 Create sandbox servers and clients that comply with real EHRs API and data standards.
+- [x] 🗃️ Generate synthetic FHIR resources or load your own data as free-text.
+- [x] 💾 Save generated request and response data for each sandbox run.
+- [x] 🎈 Streamlit dashboard to inspect generated data and responses.
+- [x] 🧪 Experiment with LLMs in a fully HL7 standard-compliant pipeline from day 1.
+
+## Clinical Decision Support (CDS)
+[CDS Hooks](https://cds-hooks.org/) is an [HL7](https://cds-hooks.hl7.org) published specification for clinical decision support.
+
+**When is this used?** CDS hooks are triggered at certain events during a clinician's workflow in an electronic health record (EHR), e.g. when a patient record is opened, when an order is elected.
+
+**What information is sent**: the context of the event and FHIR resources that are requested by your service, for example, the patient ID and information on the encounter and conditions they are being seen for.
+
+**What information is returned**: “cards” displaying text, actionable suggestions, or links to launch a [SMART](https://smarthealthit.org/) app from within the workflow.
+
+**What you need to decide**: What data do I want my EHR client to send, and how will my service process this data.
+
+
+```python
+import healthchain as hc
+
+from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.data_generator import DataGenerator
+
+# Decorate class with sandbox and pass in use case
+@hc.sandbox
+class myCDS(ClinicalDecisionSupport):
+    def __init__(self) -> None:
+        self.data_generator = DataGenerator()
+
+    # Sets up an instance of a mock EHR client of the specified workflow
+    @hc.ehr(workflow="patient-view")
+    def load_data(self):
+        self.data_generator.generate()
+        return self.data_generator.data
+
+    # Define your application logic here
+    @hc.api
+    def service(self, request: str):
+        result = "Hello " + request["patient_name"]
+        return result
+
+if __name__ == "__main__":
+    cds = myCDS()
+    cds.start_sandbox()
+```
+
+Then run:
+```bash
+healthchain mycds.py
+```
+This will populate your EHR client with the data generation method you have defined, send requests to your server for processing, and save the data in `./output' by default.
+
+### Streamlit dashboard
+Note this is currently not meant to be a frontend to the EHR client, so you will have to run it separately from the sandbox application.
+
+```bash
+streamlit streamlit-demo/app.py
+```
+
+## Road Map
+- [ ] 📝 Adding Clinical Documentation use case: CDA data generation, NoteReader API, and structured data extraction applications
+- [ ] 🎛️ Ability to test different EHR backend data configurations in client
+- [ ] 📦 Versioning of configurations and model artifacts
+- [ ] ✨ Improvements to synthetic data generator methods
+- [ ] 👾 Add proper frontend for EHR client which renders more complex cards
+- [ ] 🐳 Serve with Docker containers
+- [ ] 🚀 Use LLMs to parse configuration and modify integration code
+
+## Contribute
+We are always eager to hear feedback and suggestions, especially if you are a developer or researcher working with healthcare systems!
+- 💡 Let's chat! [Discord](https://discord.gg/jG4UWCUh)
+- 🛠️ [Contribution Guidelines](CONTRIBUTING.md)
+
+## Acknowledgement
+This repository makes use of CDS Hooks developed by Boston Children’s Hospital.

docs/api/index.md

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+# API Reference

docs/blog/index.md

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+# Blog

docs/community/index.md

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+# Community
+
+## Contribute
+
+[Contributing Guidelines](../../CONTRIBUTING.md)

docs/cookbook/index.md

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+# Cookbook