CI & Scheduled Jobs

Every GitHub Actions workflow in the public bioc repos, what it tests, how they relate, and whether it is green right now

One page for the question “what is red, and does it matter?” Status badges are live. The table under Workflows is generated at site build by ci-inventory.py from the GitHub API, so it matches the workflows in each repo; the description column is each workflow’s leading comment block, so a workflow with no header comment shows only its name. Everything else on this page is hand-written.

How the new-system workflows relate

flowchart LR
  subgraph RU[r-universe, upstream, no badges here]
    G[git.bioconductor.org<br/>maintainer push] --> CR[control-room<br/>hourly cron 25 * * * *]
    CR --> SY[sync<br/>bioc · bioc-release monorepos]
    SY --> BU[workflows/build.yml<br/>build + check]
    BU --> API[r-universe API<br/>bioc · bioc-release]
  end
  API -- poll every 15 min --> OB[(observations<br/>R2 obs/…)]
  OB --> GT{evaluate<br/>the gate}
  GT --> R[(propagated index<br/>/repo)]
  R --> F[freshness<br/>serves?]
  R --> I[install<br/>installs?]
  subgraph X[Experimental: standalone build path]
    M[bioc-manifest<br/>validate]
    D[bioc-build<br/>dispatch, manual → build-package → build.yml]
  end
  M -. read by .-> D
  D -. attested tarballs .-> P[publish] -.-> GT
  W[bioc-website<br/>site] -- static site --> R2[(R2)]
  S[systemd bioc-sync<br/>master.bioconductor.org → R2<br/>+ purge, manifest] --> R2
  R2 --> E[bioc-edge worker]
  E --> H[health] & PA[parity<br/>vs master] & L[bioc-website<br/>links]

The r-universe components are not ours and have no badge on this page. A stalled r-universe shows up here as freshness red on “latest observation under 36 hours”, since the registry polls its API and nothing else changes when r-universe stops. bioc-build’s build.yml is a pinned verbatim copy of r-universe’s, so the two build boxes run the same engine. bioc-manifest does not trigger bioc-build: bioc-build’s dispatch.yml is workflow_dispatch only, and its schedule is deferred until the registry publisher is proven.

This diagram shows the new-system checks, not the production publishing path. bioconductor.org’s packages are still built by BBS (source tarballs) and mostly r-universe (binaries), and reach R2 through the hourly bioc-sync from master.bioconductor.org. The registry path above publishes only at the registry’s own host; switching to it is the registry switch plan. The production path is on how bioconductor.org works.

Reading a red badge:

• publish red: the bioc-build → registry ingest broke. Experimental path; software packages from r-universe are unaffected.
• freshness red, publish green: the Worker is down, the observer stalled, or the served index is inconsistent (the #34 invariant).
• install red, freshness green: what the registry serves does not install. Since #47 the canary runs in the r-universe build image, so this is no longer “the runner lacks a system library”.
• health or parity red: the served site, not the data plane. Health probes bioconductor.org (since 2026-09-29). Parity compares bioconductor.org with master.bioconductor.org path by path; the known differences are tracked in bioc-edge #43 to #46.
• links red: link rot on the served site, a content problem.

Scheduled jobs outside GitHub Actions

The systemd --user timers on onclappc02, following the platform scheduling convention. All of them run on that one host, mostly from development checkouts of their repos (bioc-site-refresh uses its own clone of main) (for example ~/Documents/git/bioc-edge); moving them to separate operations checkouts is planned in bioc-infrastructure#43. There is no live status column: these alert on failure only (a GitHub issue or an ntfy push), and the heartbeat that would prove “ran OK today” is not set up yet.

Unit	Repo	Cadence	What it does	On failure
bioc-sync	bioc-edge	hourly	rsync from master.bioconductor.org to the local mirror, upload changes to R2, purge them from the edge cache, regenerate the mirror manifest	GitHub issue
bioc-site-refresh	bioc-website	every 20 min	When Bioconductor/bioconductor.org devel moves: regenerate prose and assets into the site data snapshot, upload it, dispatch the site build. Keeps replaced snapshots in /data/davsean/bioc-site-refresh/snapshots	GitHub issue
bioc-reconcile	bioc-edge	weekly, Sun 04:00	Checksum drift check: does R2 match the local mirror	GitHub issue
bioc-logpush-check	bioc-edge	daily 07:15	Alert if yesterday’s Logpush access-log delivery to GCS is missing	GitHub issue
biocintel-refresh	bioc-intelligence	monthly, 1st 06:00 UTC	Enrichment pipeline: extract → link → enrich → marts → publish	ntfy

Private repos with timers are not listed.

Workflows

The repos that make up the new system and its platform services, active workflows only. Dynamic workflows GitHub injects (Pages deploy, Copilot) are excluded; which repos appear is the GROUPS map in the script.

New system pipeline

bioc-edge

Serving side of bioconductor.org: Cloudflare Worker + R2 mirror

Workflow	Status	Triggers	What it does
health.yml		schedule, workflow_dispatch (17 6 * * *)	Daily black-box probe of the serving stack at bioconductor.org. The badge on this workflow is the status light: red means a probe failed.
parity.yml		schedule, workflow_dispatch (52 6 * * *)	Daily parity probe: does bioconductor.org (the new stack) answer like master.bioconductor.org (the legacy origin)? master stays up until parity is reached; this is the gate for turning it off. The logic is in parity.sh (unit-tested by…
test.yml		push, pull_request	test

bioc-infrastructure

How bioconductor.org is built, served, and being replaced — and the decisions behind it

Workflow	Status	Triggers	What it does
docs-check.yml		schedule, workflow_dispatch (37 7 * * 1)	Weekly stale-content check (docs-check.sh): phrases that only made sense before the 2026-09-28 cutover, retired repo names, and dead external links. Findings go to one open issue labelled docs-review (opened, or commented on if already…
docs.yml		push, workflow_dispatch	docs
test.yml		push, pull_request	test

bioc-registry

The Bioconductor package registry: metadata, propagated versions, installable artifacts, provenance, and build/check state behind one HTTP API

Workflow	Status	Triggers	What it does
freshness.yml		schedule, workflow_dispatch (43 6 * * *)	Daily probe of the live registry: is the worker up, and has the observer actually observed something recently? The 15-minute poll previously had no alerting at all — a silent stop was detected by someone remembering to look. The badge…
install.yml		schedule, workflow_dispatch (27 8 * * *)	Daily installation canary: freshness.yml proves the registry serves; this proves what it serves actually installs into a real R session. The badge is the status light: red means the repo surface is broken for the pinned canaries. (#27)
publish.yml		schedule, workflow_dispatch (7,37 * * * *)	The bioc-build publisher (issue #13, SPEC-014). Sweeps completed build.yml runs on seandavi/bioc-build, verifies each staged package, and publishes it through the guarded POST /publish route — see scripts/publish.sh for the algorithm….
test.yml		push, pull_request	test

bioc-website

Next-generation bioconductor.org: static Astro build fed by a data pipeline over primary sources (r-universe, the site git repo, the bioc-prop data plane)

Workflow	Status	Triggers	What it does
links.yml		schedule, workflow_dispatch (31 7 * * *)	Daily link-rot check over the maintained pages of the served site. (#18) A fresh build enumerates the pages; the checks then run against the served dev host, where mirror-backed internal links resolve for real and external links are…
preview-cleanup.yml		pull_request	Delete a PR’s preview build from R2 when the PR closes.
site.yml		push, pull_request, workflow_dispatch	Build the site and publish it to R2. push to main -> s3://bioc-site/site/-/ (immutable, pointer in site/latest) dispatch -> same, after ops/refresh-content.sh refreshes the snapshot pull request ->…

Platform services

bioc-intelligence

Research-intelligence & impact analytics for the Bioconductor ecosystem (DuckDB + Parquet, lake-sourced enrichment)

Workflow	Status	Triggers	What it does
ci.yml		push, pull_request	CI
deploy-pages.yml		push, workflow_dispatch	Deploy Pages
frontend-ci.yml		push, pull_request	Frontend CI

Experimental

Prototypes of a standalone build path for the packages r-universe does not build (data-experiment, annotation, workflows; ADR 0010). Not the production route: software packages reach the registry from r-universe. A red badge here is not a production incident.

bioc-build

Bioconductor’s standalone package build system on GitHub Actions: configuration-driven build and check workflows for every package type, feeding the bioc-registry data plane

Workflow	Status	Triggers	What it does
build-package.yml		workflow_dispatch, workflow_call	Our entry point: resolves package+stream against seandavi/bioc-manifest into r-universe’s input shape (universe/repository/ref/…), then calls the mostly-verbatim build.yml engine with our_output set. See README.md “Relationship to…
build.yml		workflow_call	Verbatim copy of r-universe-org/workflows/.github/workflows/build.yml Upstream: https://github.com/r-universe-org/workflows Pinned at commit 2025515d8de93f38f70bb8ff6384e06821a3b5bd (2026-09-03). Every uses: below is pinned to the…
dispatch.yml		schedule, workflow_dispatch (17 */6 * * *)	Manual-trigger-only for now: decides which (package, stream) pairs need a build and fans them out as a matrix of build.yml calls (issue #16, SPEC-014 §dispatch.yml). Never touches secrets; job 1 only reads public data (bioc-manifest,…

bioc-manifest

Bioconductor build manifest: one YAML per package the build system is authorized to build, plus the policy file. The trust root; changes by human PR.

Workflow	Status	Triggers	What it does
validate.yml		push, pull_request	validate