Repository Organization

Naming conventions and structure for lab repositories

Overview

All Rashid Lab repositories live in the rashidlab GitHub organization. We use a flat structure with consistent naming conventions and GitHub Topics to keep repositories organized and discoverable.

Repository Types

Prefix	Purpose	Example
lab-*	Lab infrastructure	lab-handbook, lab-meetings, lab-computing
template-*	Project templates	template-research-project, template-r-package
pkg-*	R packages	pkg-baton, pkg-adapthr
paper-*	Publication repositories	paper-adaptive-basket-design
{username}-*	Student projects	tylerbhumpherys-pancreatic-rl

Naming Conventions

Student Project Repositories

When creating a new repository for your research, use this format:

{github-username}-{short-project-name}

Guidelines:

• Use your GitHub username (not your name) as the prefix
• Keep the project name short but descriptive (2-4 words)
• Use hyphens to separate words
• Use lowercase only
• Avoid dates in the name (use Topics instead)

Good examples:

• tylerbhumpherys-pancreatic-rl
• andrew-walther-spatial-spillover
• dinelka97-biomarker-validation
• ayoung31-survival-methods
• jialiux22-adaptive-enrichment

Avoid:

• tyler-project-1 (not descriptive)
• 2026-02-pancreatic-analysis (dates don’t help)
• PancreaticCancerRLAnalysis (not lowercase, no hyphens)
• my-awesome-project (not prefixed with username)

Publication Repositories

When a project is ready for publication, you may optionally rename or create a clean repository:

paper-{short-title}

Examples:

• paper-adaptive-basket-design
• paper-spatial-spillover-trials
• paper-biomarker-surrogacy

R Package Repositories

For reusable R packages:

pkg-{package-name}

Or simply use the package name if it’s distinctive:

• pkg-baton or just BATON
• pkg-adapthr or just adapthr

GitHub Topics

Every repository should have relevant topics to enable filtering and discovery. Add topics via Settings → Topics or the “About” gear icon on the repo page.

Required Topics

Topic	When to Use
student-project	All student research repos
Your GitHub username	All your repos (e.g., tylerbhumpherys)

Recommended Topics

Topic	Description
methods-paper	Methodology development
applied-paper	Applied data analysis
clinical-trials	Trial design projects
spatial-statistics	Spatial methods
machine-learning	ML/AI projects
survival-analysis	Time-to-event methods
bayesian	Bayesian methods
simulation-study	Contains simulation studies
r-package	R package development

Filtering by Topic

To find all repositories with a specific topic:

https://github.com/rashidlab?q=topic:tylerbhumpherys
https://github.com/rashidlab?q=topic:clinical-trials

Or use the GitHub search bar with topic:NAME.

Creating a New Repository

From a Template

1. Go to the appropriate template repository:

   • template-research-project — General research
   • template-methods-paper — Methods papers
   • template-clinical-trial — Trial designs
   • template-r-package — R packages

2. Click “Use this template” → “Create a new repository”

3. Configure:

   • Owner: rashidlab (not your personal account)
   • Repository name: Follow naming convention above
   • Visibility: Private (can make public later)

4. After creation:

   • Add relevant Topics
   • Update README with project description
   • Update CLAUDE.md with project-specific guidance

From Scratch

If no template fits:

1. Go to github.com/organizations/rashidlab/repositories/new
2. Follow the naming convention
3. Initialize with README
4. Add .gitignore for R or Python
5. Add MIT license
6. Add Topics after creation

Repository Visibility

Stage	Visibility	Notes
Active development	Private	Default for new repos
Submitted for publication	Private	Until acceptance
Published/Preprint	Public	Make public when paper is available
Lab infrastructure	Public	lab-handbook, templates, etc.

To change visibility: Settings → Danger Zone → Change visibility

GitHub Teams

The lab uses GitHub Teams for access control:

Team	Access	Members
lab-admin	Admin on all repos	Dr. Rashid
students	Read on lab-* repos	All students
{username}	Write on their repos	Individual student

When you create a new repository, your team will automatically have access. For collaboration, add other student teams with appropriate permissions.

Directory Structure on Longleaf

Repositories are cloned to your Longleaf workspace. Recommended structure:

/proj/rashidlab/users/{onyen}/
├── projects/
│   ├── tylerbhumpherys-pancreatic-rl/    # Git repo
│   ├── tylerbhumpherys-biomarker-study/  # Git repo
│   └── ...
└── data/
    ├── pancreatic-rl/                     # Symlinked from repos
    └── biomarker-study/

See Lab Computing for more details on Longleaf setup.

Archiving and Cleanup

When a project is complete:

1. Ensure reproducibility — README has full reproduction instructions
2. Tag a release — git tag -a v1.0 -m "Publication version"
3. Update status — Add archived topic if no longer active
4. Consider archiving — Settings → Archive repository (makes read-only)

TipDon’t Delete

Avoid deleting repositories. Archive them instead to preserve history and links.

Quick Reference

# Clone your project
git clone git@github.com:rashidlab/tylerbhumpherys-pancreatic-rl.git

# Check all your repos
gh repo list rashidlab --topic tylerbhumpherys

# Check all clinical trial repos
gh repo list rashidlab --topic clinical-trials

# Create new repo from template
gh repo create rashidlab/tylerbhumpherys-new-project \
  --template rashidlab/template-research-project \
  --private