.github

We help organizations understand biological systems through data and decision analysis, database design, and software development.

Continuous integration

This repo centrally manages GitHub Actions for the org's R packages. CI logic lives in reusable workflows here; each package carries thin caller workflows that pass its classification (tier, plus auto-detected private/jags/cmdstan/tex/CRAN), so updating a reusable workflow propagates to every package on its next run.

Day-to-day use:

• tools/sync-ci.sh (dry run) classifies every package and shows the planned action.
• tools/sync-ci.sh --apply [pkg ...] renders the callers and opens routed PRs.
• tools/package-tiers.tsv is the tier registry; list a package there only to promote it to important or force a tier.

To promote a package to important, or to keep a manually promoted one important, run --apply from a real terminal: a pre-flight prompts before it would otherwise downgrade such a package.

See CI-SYSTEM.md for the full reference (components, classification, tier matrices, the candidate gate, and common tasks). Related: fledge-automation.md, GO-LIVE.md, CI-ROLLOUT-STATUS.md.