ci: add GitHub Actions workflow and .Rbuildignore

[lwaldron]

Adds .github/workflows/ci.yml using the reusable Bioconductor BiocCheck workflow (https://github.com/Bioconductor/workflows) and adds .github/ to .Rbuildignore. It's set to error only on error now, and is working. Open questions for core team:

1. OK to add .github/ directory and probably a README.md to display status badges, with these added to .Rbuildignore? Alternative is to make the default branch for active development main and leave these out of the devel branch. Seems unnecessarily complicated to me.
2. add codecov? Easy to do but needs a README.md and badge to be useful.

[Copilot]

Pull request overview

Adds CI automation for the package via a GitHub Actions workflow that reuses the waldronlab Bioconductor CMD check + pkgdown workflow, and ensures the .github/ directory is excluded from R package builds.

Changes:

• Add .github/workflows/ci.yml to run PR CMD check and (on selected pushes) build the pkgdown site via a reusable workflow.
• Add .github/ to .Rbuildignore so it is not included in the R build tarball.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
.Rbuildignore	Ignores the .github/ directory during R CMD build.
.github/workflows/ci.yml	Introduces a reusable-workflow-based CI job for PR checks and branch push events.

Comments suppressed due to low confidence (3)

.github/workflows/ci.yml:8

• The paths glob **.yml does not reliably match .yml files in subdirectories (e.g. .github/workflows/ci.yml), so pushes that change this workflow may not trigger CI. Use **/*.yml (and optionally **/*.yaml) to match nested workflow files.

    paths:
      - 'DESCRIPTION'
      - '**.yml'

.github/workflows/ci.yml:15

• The reusable workflow is referenced by a mutable branch (@devel). For supply-chain security and reproducibility, pin uses: to a tag or full commit SHA from waldronlab/.github instead of a branch name.

    uses: waldronlab/.github/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml@devel

.github/workflows/ci.yml:20

• This workflow requests write permissions (contents/pages/id-token) and inherits all secrets for the called workflow. Consider scoping permissions/secrets to the minimum required (especially for pull_request runs) to reduce blast radius if untrusted code executes.

    secrets: inherit
    permissions:
      contents: write
      pages: write
      id-token: write

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

.Rbuildignore:1

• .Rbuildignore entries are regular expressions. Using .github/ is unanchored and the leading . is a regex wildcard, which can unintentionally match other paths. Prefer an anchored, escaped pattern for the .github directory.

^\.github$

[vjcitn]

I am fine with these changes. Longer term we should arrange two signoffs from core.

[vjcitn]

Merging, hoping version was bumped.

[lwaldron]

No version bump because there was no change to the built .tar.gz package.