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GitHub Hosting Transition - Overview

For hands‑on instructions (remotes, redirects, authentication) see the Developer Implementation Guide.

Executive Summary

Bioconductor is migrating authoritative package repositories from a self‑hosted gitolite service (git.bioconductor.org) to GitHub under the bioconductor-source organization.

Implementation Overview

Current State

  • Packages live in a gitolite-managed server accessed via SSH (git@git.bioconductor.org:packages/<pkgname>.git).
  • Web access uses URLs like https://git.bioconductor.org/packages/<pkgname> (which historically exposed cgit or similar views).
  • Authentication / authorization is handled by gitolite keys maintained by the core team.
  • Package source code can be browsed at https://code.bioconductor.org separately.

Target State

  • Authoritative repositories: https://github.com/bioconductor-source/<pkgname>.
  • The existing Apache server (the same host that currently fronts gitolite) continues to answer for git.bioconductor.org, redirecting to the appropriate GitHub location
  • Apache issues permanent 301 redirects from legacy package paths to GitHub, preserving deep links, encouraging caches and clients to update remotes automatically over time.
  • The server for https://code.bioconductor.org is deprecated and rolled into the above Apache redirect, to also encourage browsing directly in GitHub.

Redirect Strategy

Permanent (301) redirects for git.bioconductor.org/packages/<pkg> paths to github.com/bioconductor-source/<pkg> so:

  • Search engines update indexing.
  • Tooling that follows redirects (most modern git clients for HTTPS) keeps functioning until remotes are updated.
  • A centralized switch reduces need for piecemeal communication of new URLs.

Impact on Package Maintainers

Pros:

  • Standard GitHub fork + Pull Request workflow increases visibility of external contributions.
  • Easier collaboration with broader open-source community (contributors already have GitHub accounts, no more auth registration process).
  • Optionally opens up space for public issues about packages,

Cons:

  • Need to update local origin remotes (SSH: git@github.com:bioconductor-source/<pkg>.git or HTTPS) and possibly adjust authentication (PAT vs legacy gitolite key).
  • Initial learning curve for those unfamiliar with PR review features / branch protection.

Mitigations:

  • Clear guide providing "cheat sheet" for common tasks and links to detailed documentation

Next: For technical implementation details proceed to the Developer Implementation Guide.