[docs] Add development setup guide and contribution guidelines#18
[docs] Add development setup guide and contribution guidelines#18NobleCoder69 wants to merge 1 commit intoga4gh:mainfrom
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- Created SETUP.md with Python environment and installation instructions - Created CONTRIBUTING.md with development workflow and code style guidelines - Added .env.example template for environment configuration - Updated requirements.txt with version pins and package descriptions - Enhanced README.md with quick start guide and project structure Fixes ga4gh#17
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Pull request overview
Adds onboarding documentation and templates to make local development setup and contributions clearer for new contributors to GA4GH-RegBot (per issue #17).
Changes:
- Added new documentation files:
SETUP.md(dev setup) andCONTRIBUTING.md(contribution guide). - Added
.env.examplefor environment variable configuration. - Updated
requirements.txtwith pinned dependencies and inline descriptions; updatedREADME.mdwith a quick start.
Reviewed changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
requirements.txt |
Adds dependency comments and adjusts pinned packages (notably PDF dependency). |
SETUP.md |
Introduces development setup instructions and a quick-start flow. |
README.md |
Replaces the minimal overview with a formatted README + quick start steps. |
CONTRIBUTING.md |
Adds initial contribution guidance (fork/clone/upstream remote). |
.env.example |
Provides a template for required/optional environment variables. |
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| \## Getting Started | ||
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| 1\. \*\*Fork the repository\*\* on GitHub | ||
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| 2\. \*\*Clone your fork\*\* locally | ||
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| 3\. \*\*Create a feature branch\*\* for your changes | ||
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| 4\. \*\*Follow the development workflow\*\* below | ||
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| 5\. \*\*Submit a pull request\*\* with a clear description | ||
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| \## Development Workflow | ||
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CONTRIBUTING.md currently covers forking/cloning but doesn’t yet include the development workflow details mentioned in the PR description/issue (#17) (branch naming, commit conventions, lint/format tools, code style expectations, PR process, etc.). Either expand this document accordingly or adjust the PR description/scope so expectations match what’s delivered.
| \# GA4GH-RegBot: Development Setup Guide | ||
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| Welcome! This guide will help you set up GA4GH-RegBot for local development and testing. | ||
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| \## Prerequisites | ||
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| \- \*\*Python 3.8+\*\* |
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The markdown headings/lists are escaped (e.g., \#, \##, \-) so they will render as literal backslashes instead of proper Markdown formatting. Please remove the backslashes so headings and bullets render correctly.
| \# 2. Create a virtual environment | ||
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| python -m venv venv | ||
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| venv\\Scripts\\activate # Windows | ||
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| \# 3. Install dependencies | ||
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| pip install -r requirements.txt | ||
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| \# 4. Set up environment | ||
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| copy .env.example .env | ||
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The Quick Start only includes Windows-specific environment activation (venv\\Scripts\\activate) and .env creation (copy ...). Since this guide is meant for general onboarding, add the Mac/Linux equivalents (source venv/bin/activate and cp .env.example .env) or clearly label the section as Windows-only.
| \# GA4GH-RegBot: Compliance Assistant | ||
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| Overview | ||
| RegBot is an LLM-powered tool designed to help researchers map their consent forms against GA4GH regulatory frameworks. It uses RAG (Retrieval-Augmented Generation) to flag compliance gaps automatically. | ||
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| Architecture (Planned) | ||
| Core: Python | ||
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| LLM Framework: LangChain / LlamaIndex | ||
| \*\*Status:\*\* Proposal Stage for GSoC 2026 | ||
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| Vector Store: ChromaDB / FAISS | ||
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| UI: Streamlit | ||
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| Roadmap | ||
| Phase 1: Ingest GA4GH "Framework for Responsible Sharing" policy documents. | ||
| GA4GH-RegBot is an LLM-powered tool designed to help researchers map their consent forms against GA4GH regulatory frameworks. It uses RAG (Retrieval-Augmented Generation) to flag compliance gaps automatically. | ||
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| \## Quick Start (5 minutes) | ||
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There was a problem hiding this comment.
The README markdown is also escaped (e.g., \#, \*\*Status\*\*, \##), which will prevent proper rendering on GitHub. Remove the backslashes so the README displays correctly.
| GA4GH-RegBot is an LLM-powered tool designed to help researchers map their consent forms against GA4GH regulatory frameworks. It uses RAG (Retrieval-Augmented Generation) to flag compliance gaps automatically. | ||
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| \## Quick Start (5 minutes) |
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This README update adds a Quick Start but does not include the “project structure”/architecture overview referenced in the PR description and issue #17 acceptance criteria, nor a link to the full setup guide. Consider adding a short “Project Structure” section (even a brief tree) and a link to SETUP.md near the Quick Start so the README matches the stated goals.
| \# Contributing to GA4GH-RegBot | ||
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| Thank you for your interest in contributing to GA4GH-RegBot! | ||
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| \## Getting Started | ||
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| 1\. \*\*Fork the repository\*\* on GitHub | ||
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| 2\. \*\*Clone your fork\*\* locally | ||
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| 3\. \*\*Create a feature branch\*\* for your changes | ||
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| 4\. \*\*Follow the development workflow\*\* below | ||
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| 5\. \*\*Submit a pull request\*\* with a clear description | ||
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| \## Development Workflow | ||
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| \### 1. Fork and Clone | ||
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| ```bash | ||
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| \# Fork on GitHub, then clone your fork | ||
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There was a problem hiding this comment.
Like the other docs, headings and comments are escaped (e.g., \#, \##, \###, and \# Fork on GitHub...) which will render incorrectly in Markdown and in the fenced code block. Remove the leading backslashes so both the Markdown and shell comments display as intended.
Fixes #17