Skip to content

Navigation Menu

Appearance settings

GitHub Copilot
Write better code with AI

GitHub Spark New
Build and deploy intelligent apps

GitHub Models New
Manage and compare prompts

GitHub Advanced Security
Find and fix vulnerabilities

Actions
Automate any workflow
Codespaces
Instant dev environments

Issues
Plan and track work

Code Review
Manage code changes

Discussions
Collaborate outside of code

Code Search
Find more, search less
Explore

Why GitHub

Documentation

GitHub Skills

Blog
Integrations

GitHub Marketplace

MCP Registry
View all features
By company size

Enterprises

Small and medium teams

Startups

Nonprofits
By use case

App Modernization

DevSecOps

DevOps

CI/CD

View all use cases
By industry

Healthcare

Financial services

Manufacturing

Government

View all industries
View all solutions
Topics

AI

DevOps

Security

Software Development

View all
Explore

Learning Pathways

Events & Webinars

Ebooks & Whitepapers

Customer Stories

Partners

Executive Insights
GitHub Sponsors
Fund open source developers
The ReadME Project
GitHub community articles
Repositories

Topics

Trending

Collections
Enterprise platform
AI-powered developer platform
Available add-ons

GitHub Advanced Security
Enterprise-grade security features

Copilot for business
Enterprise-grade AI features

Premium Support
Enterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

nextstrain / augur Public

Notifications You must be signed in to change notification settings
Fork 136
Star 275

Code
Issues 235
Pull requests 41
Actions
Security
Insights

Additional navigation options

Code
Issues
Pull requests
Actions
Security
Insights

subsample: Improve default search paths, allow customization#1918

Open

victorlin wants to merge 8 commits intomasternextstrain/augur:masterfrom

victorlin/subsample-filepath-configsnextstrain/augur:victorlin/subsample-filepath-configsCopy head branch name to clipboard

Conversation Commits8 (8)Checks Files changed

Open

subsample: Improve default search paths, allow customization#1918
victorlin wants to merge 8 commits intomasterfrom
victorlin/subsample-filepath-configs

Commits

Commits on Oct 31, 2025

Remove numbering from comments
victorlin
committed
Mark filepath values in schema
victorlin
committed
Load schema outside of config parsing
victorlin
committed
Add CLI option for custom search paths
victorlin
committed
Add config's parent directory as first default search path
victorlin
committed
Add env var for custom search paths
victorlin
committed
Add helper function to get resolved filepaths
victorlin
committed
Update changelog
victorlin
committed

Footer

© 2025 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.