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Technical Notes & Software Architecture

This document describes the software architecture and internal maintenance details of the bioconductor/workflows repository.

Architecture Decision Records (ADRs)

Any significant structural change or new design pattern in these reusable workflows is documented in the docs/adr/ directory using the Nygard format.

Please refer to the ADR Directory for the complete list of Architecture Decision Records that guide the architecture.

Copilot Instructions

When contributing to this repository using AI assistants, please review the rules and guidelines specified in .github/copilot-instructions.md.

Internal Workflows

actionlint.yml

This repository uses raven-actions/actionlint to validate the GitHub Actions workflow syntax. It runs automatically on push and pull requests for any changes within .github/workflows/.

canary.yml

The canary workflow runs on a weekly schedule (and on-demand) to verify that bioccheck.yml executes correctly end-to-end against the Bioconductor container tag derived from the main branch. It uses error_on: 'never' so that expected BiocCheck notes from the internal stub package do not cause a false failure.

This repo contains a DESCRIPTION file and basic vignette to make it a valid R package that can be checked without error (with enough disabling flags invoked).

Release & Version Tagging Checklist

When cutting a formal major release (e.g. v1, v2) or transitioning default references, maintainers must update the following four locations in lockstep:

  1. ci.yml: Update the template workflow call tag (bioconductor/workflows/.github/workflows/bioccheck.yml@v1).
  2. docs/index.html: Update the workflowObj.jobs.bioccheck.uses template string (uses: 'bioconductor/workflows/.github/workflows/bioccheck.yml@v1').
  3. README.md: Update the Overview table workflow reference.
  4. bioccheck_usage.md: Update the Versioning Strategy section notes and recommendations.

Git Tag Creation Commands

# Create or update the floating major version tag (e.g., v1)
git tag -fa v1 -m "Release v1"
git push origin v1 --force