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shigella (development version)

  • Initial CRAN submission.

New API features

Bug fixes

Internal changes

  • added .lintr configuration file

  • Moved helper functions into R/ subdirectory (#1)

  • simplified spell-check GitHub Action (#3)

  • Migrated the Claude Code and NEWS-changelog workflows to d-morrison/gha reusable workflows, and removed the obsolete upstream-fix watcher (#29)

  • Finished the Morrison-Lab/gha migration: replaced the hand-maintained spellcheck, changed-file lint, and version-check workflows with their gha counterparts, added the bump-dev-version companion, and added checks for workflow, YAML, and Markdown lint, junk files, typos, committed secrets, PHI, broken links, and semantic line breaks (#32)

  • Moved the Claude, Claude-review, and NEWS callers from @v1 to @v2, fixing the startup failure every Claude Code run hit because @v1 does not declare the ANTHROPIC_API_KEY secret the callers pass (#32)

  • Recorded the roxygen2 version in Config/roxygen2/version, which roxygen2 8.1.0 uses in place of RoxygenNote (#32)

  • Added dissertation and standalone chapter manuscript source files with automated DOCX rendering (#31)

  • Pinned use-ai-config: true explicitly on the Claude and Claude-review Morrison-Lab/gha@v2 callers (#36). The reusable workflows already default that input to true, so the bot and the reviewer were already installing the shared ai-config plugin on every run. Setting it in the caller records that intent and keeps it from changing if the @v2 default ever moves.

  • Added AGENTS.md and CLAUDE.md, short orientation files for AI coding agents that defer to .github/copilot-instructions.md as the source of truth, plus a .claude/settings.json permissions allowlist (#35)

  • Corrected .github/copilot-instructions.md, whose CI section was stale, and recorded the inverted version convention and the two separate spelling accept-lists there (#35)

  • Made the Claude reviewer on-request only: dropped the pull_request trigger from .github/workflows/claude-code-review.yml, so a push to a pull request no longer starts a review by itself (#44). A review is now requested with an @claude review comment or a manual dispatch. Two automatic paths survive upstream, in gha's claude.yml, neither with a caller-side opt-out: an @claude run that pushes commits to a pull request dispatches a review of them, and an @claude run on an issue that pushes a branch opens a draft pull request and dispatches a review of that. Both are tracked as Morrison-Lab/gha#778. Because the check no longer appears on every pull request, review / require-review must not be listed as a required status check.

shigella 0.0.0

Started development.