Dev

[Arvindiyer]

Summary

Prepares the package for CRAN submission and establishes automated CI/CD via GitHub Actions.

Changes

• CI: Add R-CMD-check workflow (ubuntu/macos/windows × release + R-devel)
• CI: Add pkgdown workflow — auto-builds and deploys site to gh-pages on every push to main
• Logo: Add man/figures/logo.svg (clean scalable version); update pkgdown navbar to use SVG
• pkgdown: Fix logo positioning and site styling via pkgdown/extra.css

Test plan

• devtools::document() run to regenerate NAMESPACE / man pages
• devtools::check(args = "--run-donttest") passes with 0 errors, 0 warnings, 0 notes
• All examples verified to run correctly (including estimate_p_val, r.effectSize, al.pairwise.alteration.stats)
• pkgdown site built and verified locally

Summary by CodeRabbit

• New Features

  • Added automated documentation build and deployment workflow that generates and publishes documentation to a dedicated hosting branch on each push and release.

• Documentation

  • Updated README with build status badge and website branding.
  • Enhanced documentation site configuration with logo and navigation improvements.

• Chores

  • Updated checkout action in build workflow to latest version.
  • Cleaned up static documentation files (will be auto-generated by new workflow).

[coderabbitai]

Wondering what really moved? Review this PR in Change Stack to inspect semantic changes, definitions, and references.

Caution

Review failed

Pull request was closed or merged during review

📝 Walkthrough

Walkthrough

This PR sets up automated documentation generation and deployment using GitHub Actions. It adds a new pkgdown workflow that builds and publishes documentation to gh-pages, updates repository branding with logos and CI status badges, and removes generated documentation files from version control since they will now be automatically produced.

Changes

Documentation automation and branding

Layer / File(s)	Summary
GitHub Actions CI/CD workflow for documentation .github/workflows/R-CMD-check.yaml, .github/workflows/pkgdown.yaml	Workflow checkout action updated from v4 to v5; new pkgdown workflow added to build and deploy documentation to gh-pages on push to main/master, release events, and manual dispatch. Includes R and Pandoc setup, pkgdown site building, and deployment via JamesIves/github-pages-deploy-action.
Repository branding and site configuration README.Rmd, README.md, _pkgdown.yml	README files updated with R-CMD-check GitHub Actions status badge and logo with alt text; pkgdown navbar configuration extended with logo asset path (logo.svg), alt text, width (30), and link target.
Generated documentation management .gitignore, docs/LICENSE-text.md, docs/articles/introduction.md	The docs/ directory is added to .gitignore to exclude generated content from version control. Generated documentation files removed as they will be automatically created by the new workflow.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Poem

🐰 A workflow springs to life with grace,
Docs build themselves in cyberspace!
With badges bright and logos fair,
Our README receives a care.
Old files fade—let automation reign,
No more to hand-update again! 🚀

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Dev' is vague and generic, providing no meaningful information about the changeset's primary objectives.	Use a more descriptive title that captures the main purpose, such as 'Prepare package for CRAN submission with CI/CD workflows' or 'Add GitHub Actions workflows and pkgdown documentation site'.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev

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