New pkgdown theme

.github/workflows/pkgdown.yaml

@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  # build dev site on merged pushes
+  push:
+    branches: [main, master]
+  # build full site on releases
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::., any::withr, stan-dev/pkgdown-config
+
+      - name: Build site
+        run: |
+          withr::with_envvar(
+            c("NOT_CRAN" = "true"), # this should already be set by setup-r@v2? keeping because vignettes don't build otherwise
+            pkgdown::build_site_github_pages(
+              lazy = FALSE, # change to TRUE if runner times out.
+              run_dont_run = TRUE,
+              new_process = TRUE
+            )
+          )
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -52,7 +52,8 @@ Suggests:
     pkgload,
     roxygen2 (>= 6.0.1),
     rmarkdown,
-    rstudioapi
-RoxygenNote: 7.3.2
+    rstudioapi,
+    devtools
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

_pkgdown.yml

@@ -0,0 +1,80 @@
+url: https://mc-stan.org/rstantools
+
+destination: "."
+
+template:
+  package: pkgdownconfig
+
+navbar:
+  title: "rstantools"
+
+  structure:
+    left: [home, vignettes, functions, news, pkgs, stan]
+    right: [search, bluesky, forum, github, lightswitch]
+
+  components:
+    pkgs:
+      text: Other Packages
+      menu:
+        - text: bayesplot
+          href: https://mc-stan.org/bayesplot
+        - text: cmdstanr
+          href: https://mc-stan.org/cmdstanr
+        - text: loo
+          href: https://mc-stan.org/loo
+        - text: posterior
+          href: https://mc-stan.org/posterior
+        - text: projpred
+          href: https://mc-stan.org/projpred
+        - text: rstan
+          href: https://mc-stan.org/rstan
+        - text: rstanarm
+          href: https://mc-stan.org/rstanarm
+        - text: shinystan
+          href: https://mc-stan.org/shinystan
+
+articles:
+  - title: "Recommendations for R package development with Stan"
+    desc: >
+      This vignette provides many recommendations for developers interested in
+      creating an R package that interface with Stan. Topics include
+      development best practices, precompiling Stan programs, R code and
+      documentation, and more.
+    contents:
+      - developer-guidelines
+  - title: "Step-by-step guide"
+    desc: >
+      This vignette walks through the steps required to set up a package with
+      a precompiled Stan model, from creating the initial package structure to
+      adding the precompiled Stan program and writing the R function that users
+      will call to fit the model.
+    contents:
+      - minimal-rstan-package
+
+reference:
+  - title: "Package structure"
+    desc: >
+      Creating the basic structure of a Stan-based R package or add
+      Stan programs to an existing package.
+    contents:
+      - rstantools-package
+      - rstan_create_package
+      - use_rstan
+      - rstan_config
+      - rstantools_load_code
+  - title: "Generics"
+    desc: >
+      S3 generics (and some default methods) for adding functionality
+      to your package using the same naming conventions as **rstanarm**
+      and other Stan-based R packages.
+    contents:
+      - bayes_R2
+      - log_lik
+      - loo-prediction
+      - posterior_interval
+      - posterior_epred
+      - posterior_linpred
+      - posterior_predict
+      - predictive_error
+      - predictive_interval
+      - prior_summary

vignettes/minimal-rstan-package.Rmd

@@ -8,7 +8,7 @@ output:
 params:
   EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true")
 vignette: >
-  %\VignetteIndexEntry{Step by step guide}
+  %\VignetteIndexEntry{Step by step guide for creating a package that depends on RStan}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -235,16 +235,11 @@ information about the package.
 
 With __roxygen__ documentation enabled, we need to generate the documentation
 for `lm_stan` and update the `NAMESPACE` so the function is exported, i.e.,
-available to users when the package is installed.  This can be done with the
-function `roxygen2::roxygenize()`, which needs to be called twice initially.
+available to users when the package is installed. This can be done with the
+function `devtools::document()`.
 
-```{r, eval = FALSE}
-try(roxygen2::roxygenize(load_code = rstantools_load_code), silent = TRUE)
-roxygen2::roxygenize()
-```
-```{r, echo=FALSE, results="hide"}
-try(roxygen2::roxygenize(PATH, load_code = rstantools_load_code), silent = TRUE)
-roxygen2::roxygenize(PATH)
+```{r}
+devtools::document(PATH)
 ```
 
 ## Install and use