Merge pull request #3512 from infotroph/pkgdown-tweaks

mdietze · web-flow · commit 8f39a30d3a03 · 2025-04-30T16:46:09.000Z
Pkgdown tweaks
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -63,7 +63,7 @@ jobs:
         fi
         cd package-documentation
         mkdir -p $VERSION
-        rsync -a --delete pkgdocs/ ${VERSION}/
+        rsync -a --delete ../_pkgdown_docs/ ${VERSION}/
         git add --all *
         git commit -m "Build pkgdown docs from pecan revision ${GITHUB_SHA}" || true
         git push -q origin main
diff --git a/.gitignore b/.gitignore
@@ -26,6 +26,7 @@ cache
 *.so
 *.Rproj*
 book_source/**/*.html
+_pkgdown_docs/
 # files generated by fia2ed script
 modules/data.land/contrib/FIA/data/*.log
 modules/data.land/contrib/FIA/data/*.ZIP
diff --git a/base/all/.Rbuildignore b/base/all/.Rbuildignore
@@ -1 +1,2 @@
-^data-raw$
+^data-raw$
+^docs$
diff --git a/base/all/.gitignore b/base/all/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/db/.Rbuildignore b/base/db/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 try\.sqlite
+^docs$
diff --git a/base/db/.gitignore b/base/db/.gitignore
@@ -1,2 +1,3 @@
 try.sqlite
 inst/import-try/data-proc
+docs/
diff --git a/base/logger/.Rbuildignore b/base/logger/.Rbuildignore
@@ -1 +1,2 @@
 cran-comments.md
+^docs$
diff --git a/base/logger/.gitignore b/base/logger/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/qaqc/.Rbuildignore b/base/qaqc/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/base/qaqc/.gitignore b/base/qaqc/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/remote/.Rbuildignore b/base/remote/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/base/remote/.gitignore b/base/remote/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/settings/.Rbuildignore b/base/settings/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/base/settings/.gitignore b/base/settings/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/utils/.Rbuildignore b/base/utils/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^scripts
+^docs$
diff --git a/base/utils/.gitignore b/base/utils/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/visualization/.Rbuildignore b/base/visualization/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/base/visualization/.gitignore b/base/visualization/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/base/workflow/.Rbuildignore b/base/workflow/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/base/workflow/.gitignore b/base/workflow/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/docker/docs/Dockerfile b/docker/docs/Dockerfile
@@ -51,7 +51,7 @@ RUN apt-get update \
 
 COPY docker/docs/index.html /usr/local/apache2/htdocs/
 COPY --from=pecandocs /src/book_source/_book/ /usr/local/apache2/htdocs/docs/pecan/
-COPY --from=pecandocs /pkgdoc/package_documentation/pkgdocs/ /usr/local/apache2/htdocs/pkgdocs/
+COPY --from=pecandocs /pkgdoc/_pkgdown_docs/ /usr/local/apache2/htdocs/pkgdocs/
 
 # ----------------------------------------------------------------------
 # PEcAn version information
diff --git a/models/basgra/.Rbuildignore b/models/basgra/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
 model_info.json
+^docs$
diff --git a/models/basgra/.gitignore b/models/basgra/.gitignore
@@ -1,4 +1,4 @@
 *.so
 *.o
 *.mod
-
+docs/
diff --git a/models/biocro/.Rbuildignore b/models/biocro/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
 model_info.json
+^docs$
diff --git a/models/biocro/.gitignore b/models/biocro/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/cable/.Rbuildignore b/models/cable/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/cable/.gitignore b/models/cable/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/clm45/.Rbuildignore b/models/clm45/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/clm45/.gitignore b/models/clm45/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/dalec/.Rbuildignore b/models/dalec/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/dalec/.gitignore b/models/dalec/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/dvmdostem/.Rbuildignore b/models/dvmdostem/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/dvmdostem/.gitignore b/models/dvmdostem/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/ed/.Rbuildignore b/models/ed/.Rbuildignore
@@ -5,3 +5,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 vignettes/ed_run_data/
+^docs$
diff --git a/models/ed/.gitignore b/models/ed/.gitignore
@@ -1 +1,2 @@
 vignettes/ed_run_data
+docs/
diff --git a/models/fates/.Rbuildignore b/models/fates/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/fates/.gitignore b/models/fates/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/gday/.Rbuildignore b/models/gday/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/gday/.gitignore b/models/gday/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/jules/.Rbuildignore b/models/jules/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/jules/.gitignore b/models/jules/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/ldndc/.Rbuildignore b/models/ldndc/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
 model_info.json
+^docs$
diff --git a/models/ldndc/.gitignore b/models/ldndc/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/linkages/.Rbuildignore b/models/linkages/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/linkages/.gitignore b/models/linkages/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/lpjguess/.Rbuildignore b/models/lpjguess/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/lpjguess/.gitignore b/models/lpjguess/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/maat/.Rbuildignore b/models/maat/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/maat/.gitignore b/models/maat/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/maespa/.Rbuildignore b/models/maespa/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
-model_info.json
+model_info.json
+^docs$
diff --git a/models/maespa/.gitignore b/models/maespa/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/preles/.Rbuildignore b/models/preles/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/preles/.gitignore b/models/preles/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/sibcasa/.Rbuildignore b/models/sibcasa/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/sibcasa/.gitignore b/models/sibcasa/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/sipnet/.Rbuildignore b/models/sipnet/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
 model_info.json
+^docs$
diff --git a/models/sipnet/.gitignore b/models/sipnet/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/stics/.Rbuildignore b/models/stics/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/models/stics/.gitignore b/models/stics/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/models/template/.Rbuildignore b/models/template/.Rbuildignore
@@ -1,2 +1,3 @@
 Dockerfile
 model_info.json
+^docs$
diff --git a/models/template/.gitignore b/models/template/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/allometry/.Rbuildignore b/modules/allometry/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/modules/allometry/.gitignore b/modules/allometry/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/assim.batch/.Rbuildignore b/modules/assim.batch/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/assim.batch/.gitignore b/modules/assim.batch/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/assim.sequential/.Rbuildignore b/modules/assim.sequential/.Rbuildignore
@@ -1,2 +1,3 @@
 inst/sda_backup
-inst/fluxnet_sandbox
+inst/fluxnet_sandbox
+^docs$
diff --git a/modules/assim.sequential/.gitignore b/modules/assim.sequential/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/benchmark/.Rbuildignore b/modules/benchmark/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/benchmark/.gitignore b/modules/benchmark/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/data.atmosphere/.Rbuildignore b/modules/data.atmosphere/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/modules/data.atmosphere/.gitignore b/modules/data.atmosphere/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/data.land/.Rbuildignore b/modules/data.land/.Rbuildignore
@@ -1,2 +1,3 @@
 contrib
 data-raw
+^docs$
diff --git a/modules/data.land/.gitignore b/modules/data.land/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/data.mining/.Rbuildignore b/modules/data.mining/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/data.mining/.gitignore b/modules/data.mining/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/data.remote/.Rbuildignore b/modules/data.remote/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
diff --git a/modules/data.remote/.gitignore b/modules/data.remote/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/emulator/.Rbuildignore b/modules/emulator/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/emulator/.gitignore b/modules/emulator/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/meta.analysis/.Rbuildignore b/modules/meta.analysis/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/meta.analysis/.gitignore b/modules/meta.analysis/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/photosynthesis/.Rbuildignore b/modules/photosynthesis/.Rbuildignore
@@ -1 +1,2 @@
 code/
+^docs$
diff --git a/modules/photosynthesis/.gitignore b/modules/photosynthesis/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/priors/.Rbuildignore b/modules/priors/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/priors/.gitignore b/modules/priors/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/modules/rtm/.Rbuildignore b/modules/rtm/.Rbuildignore
@@ -2,4 +2,7 @@
 ^\.Rproj\.user$
 ^dev
 ^tests
+^doc$
+^Meta$
+^docs$
 vignettes/.*.rds
diff --git a/modules/rtm/.gitignore b/modules/rtm/.gitignore
@@ -19,3 +19,6 @@ check
 **/Rprof.out
 
 **/.scratch.R
+/doc/
+/Meta/
+docs/
diff --git a/modules/uncertainty/.Rbuildignore b/modules/uncertainty/.Rbuildignore
@@ -0,0 +1 @@
+^docs$
diff --git a/modules/uncertainty/.gitignore b/modules/uncertainty/.gitignore
@@ -0,0 +1 @@
+docs/
diff --git a/scripts/build_pkgdown.R b/scripts/build_pkgdown.R
@@ -9,6 +9,7 @@ if (length(args) == 0) {
 }
 
 packages <- args
+output_dir <- "_pkgdown_docs"
 
 if (requireNamespace("PEcAn.logger", quietly = TRUE)) {
   logger <- PEcAn.logger::logger.info
@@ -35,11 +36,17 @@ for (pkg in packages) {
       warning(paste("No docs folder created for:", pkg))
       next 
     }
-    dest <- file.path("package_documentation/pkgdocs", pkg)
-    if (!dir.exists(dest)) {  
+    pkgname <- desc::desc_get("Package", pkg)
+    dest <- file.path(output_dir, pkgname)
+    if (!dir.exists(dest)) {
       dir.create(dest, recursive = TRUE, showWarnings = FALSE)
     }
-    file.copy(from = source_docs, to = dest, recursive = TRUE, overwrite = TRUE)
+    file.copy(
+      from = list.files(source_docs, full.names = TRUE),
+      to = dest,
+      recursive = TRUE,
+      overwrite = TRUE
+    )
     logger("✅ Successfully copied docs from", pkg, "to", dest)
   }, error = function(e) {
     warning(paste("❌ Error building pkgdown site for", pkg, ":", e$message))
@@ -50,4 +57,35 @@ for (pkg in packages) {
   })
 }
 
+logger("Creating index page")
+built_pkg_dirs <- list.dirs(output_dir, recursive=FALSE, full.names = FALSE)
+before_text <- c(
+  '<!DOCTYPE html>',
+  '<html lang="en">',
+  '<head>',
+  '  <title>Package-specific documentation for the PEcAn R packages</title>',
+  '</head>',
+  '<body>',
+  '<h1>PEcAn package documentation</h1>',
+  '<p>Function documentation and articles for each PEcAn package,',
+  '   generated from the package source using <code>{pkgdown}</code>.</p>',
+  '',
+  '<ul>'
+)
+listing_text <- paste0(
+  '  <li><a href="', built_pkg_dirs, '/index.html">',
+  built_pkg_dirs,
+  '</a></li>'
+)
+after_text <- c(
+  '  </ul>',
+  '',
+  '</body>',
+  '</html>'
+)
+writeLines(
+  text = c(before_text, listing_text, after_text),
+  con = file.path(output_dir, "index.html")
+)
+
 logger("✅ All packages processed.")
diff --git a/shiny/workflowPlot/.gitignore b/shiny/workflowPlot/.gitignore
@@ -1 +1,2 @@
 test.bm.R
+docs/

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
`1`	`1`	`try.sqlite`
`2`	`2`	`inst/import-try/data-proc`
	`3`	`+docs/`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
`1`	`1`	`^.*\.Rproj$`
`2`	`2`	`^\.Rproj\.user$`
	`3`	`+^docs$`