[WIP] Fix pkgdown website rendering issues

[Copilot]

• Remove unnecessary Windows and macOS JAGS installation steps from test-coverage workflow (only runs on Ubuntu)
• Add JAGS installation to pkgdown workflow (required for building vignettes that use JAGS)
• Test pkgdown build locally to verify it renders properly
• Perform final code review

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

[d-morrison]

@copilot can we skip any of the jags system dependencies?

[Copilot]

@copilot can we skip any of the jags system dependencies?

Yes, we can skip JAGS dependencies in some workflows:

1. test-coverage.yaml: This workflow only runs on ubuntu-latest but includes install steps for Windows and macOS. We can remove those unused steps.

2. pkgdown.yaml: Currently has NO JAGS installation, which is likely why the site isn't rendering properly. The vignettes (dobson.Rmd and getting-started.qmd) both use JAGS/runjags, so we need to ADD JAGS here, not skip it.

3. R-CMD-check.yaml: Should keep all JAGS installations since it runs on multiple platforms (Windows, macOS, Ubuntu with different R versions).

I'll clean up the test-coverage workflow and add JAGS to pkgdown.

[d-morrison]

are these changes still helpful?

[Copilot]

are these changes still helpful?

Yes, these changes are still helpful:

1. Adding JAGS to pkgdown.yaml (commit 6ff113f):

• Main branch currently has NO JAGS installation in pkgdown workflow
• Both vignettes/dobson.Rmd and vignettes/articles/getting-started.qmd use JAGS/runjags
• Without JAGS, pkgdown cannot properly render these vignettes with executable code
• This likely explains why there are debugging instructions for "Quarto errors in pkgdown builds" (commit 6e41ef0 on main)

2. Removing unused platform steps from test-coverage.yaml (commit 6ff113f):

• Main branch has Windows and macOS JAGS install steps even though the workflow only runs on ubuntu-latest (line 14)
• The if: runner.os == 'Windows' and if: runner.os == 'macOS' conditions will never be true
• Removing these steps makes the workflow cleaner and faster

Both changes are valid optimizations that should be kept.

[d-morrison]

why didn't the pkgdown workflow run on the last commit?

[Copilot]

The pkgdown workflow didn't run because of the branch targeting:

The workflow is configured to only run on pull requests targeting the main branch (line 10 of pkgdown.yaml: branches: - main).

Based on the PR description ("this PR merges into #163") and the commit history (grafted from test-mcp branch), this PR is targeting another branch (likely test-mcp or a branch related to PR #163), not main.

The workflow WOULD have triggered since .github/workflows/pkgdown.yaml was modified (which matches the paths filter on lines 16-23), but the branch target condition prevents it from running.

[d-morrison]

is rjags not already installed by the setup-r-dependencies step?

[Copilot]

No, rjags is not automatically installed by setup-r-dependencies for several reasons:

1. rjags is in Suggests, not Imports (line 49 of DESCRIPTION), so it's not a hard dependency
2. needs: connect, website doesn't include all Suggests packages - it installs Imports and VignetteBuilder dependencies
3. rjags requires special installation from source (type = "source") to properly link against the JAGS system library

This is why all other workflows (R-CMD-check.yaml line 69-80, test-coverage.yaml line 35-46) also have an explicit "install rjags" step after setup-r-dependencies.

The explicit installation is necessary because:

• vignettes/dobson.Rmd uses library(rjags)
• rjags must be compiled against the JAGS system library installed in the previous step
• setup-r-dependencies would skip it or install a pre-built binary that won't work without JAGS

[github-actions]

📕 Preview documentation for this PR has been cleaned up.