Merge branch 'main' into verbose_quiet

etiennebacher · Jul 4, 2024 · d1548e8 · d1548e8
2 parents 7e46e82 + 0dcc577
commit d1548e8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: altdoc
 Title: Package Documentation Websites with 'Quarto', 'Docsify', 'Docute', or 'MkDocs'
-Version: 0.3.0.9003
+Version: 0.3.0.9004
 Authors@R: 
     c(person(given = "Etienne",
              family = "Bacher",
@@ -24,14 +24,14 @@ Imports:
     cli,
     desc,
     evaluate,
-    downlit,
     fs,
     quarto,
     tools,
     utils
 Suggests: 
     covr,
     digest,
+    downlit,
     future,
     future.apply,
     knitr,

diff --git a/NEWS.md b/NEWS.md
@@ -17,7 +17,7 @@
   execute:
     freeze: auto
   ```
-* `render_docs(autolink = TRUE)` uses the `downlit` package to automatically link function calls to their documentation on the web.
+* For Quarto websites, `render_docs()` can use the `downlit` package to automatically link function calls to their documentation on the web. Turn off by modifying the `code-link` line in `altdoc/quarto_website.yml`
 
 ### Other changes
 

diff --git a/R/autolink.R b/R/autolink.R
diff --git a/R/render_docs.R b/R/render_docs.R
@@ -7,7 +7,6 @@
 #' @param verbose Logical. Print Rmarkdown or Quarto rendering output.
 #' @param parallel Logical. Render man pages and vignettes in parallel using the `future` framework. In addition to setting this argument to TRUE, users must define the parallelism plan in `future`. See the examples section below.
 #' @param freeze Logical. If TRUE and a man page or vignette has not changed since the last call to `render_docs()`, that file is skipped. File hashes are stored in `altdoc/freeze.rds`. If that file is deleted, all man pages and vignettes will be rendered anew.
-#' @param autolink Logical. TRUE to link function names and calls to web-based documentation. See the Autolink section below for details.
 #' @param ... Additional arguments are ignored.
 #' @inheritParams setup_docs
 #' @export
@@ -47,6 +46,7 @@
 #'   render_docs(parallel = TRUE)
 #'
 #' }
+<<<<<<< HEAD
 render_docs <- function(path = ".", verbose = FALSE, parallel = FALSE, freeze = FALSE, autolink = FALSE, ...) {
 
   # Quarto sometimes raises errors encouraging users to set `quiet=FALSE` to get more information. 
@@ -55,6 +55,9 @@ render_docs <- function(path = ".", verbose = FALSE, parallel = FALSE, freeze =
   if ("quiet" %in% names(dots) && is.logical(dots[["quiet"]]) && isTRUE(length(dots[["quiet"]]) == 1)) {
     verbose <- !dots[["quiet"]]
   }
+=======
+render_docs <- function(path = ".", verbose = FALSE, parallel = FALSE, freeze = FALSE) {
+>>>>>>> main
 
   path <- .convert_path(path)
   tool <- .doc_type(path)
@@ -115,11 +118,6 @@ render_docs <- function(path = ".", verbose = FALSE, parallel = FALSE, freeze =
   cli::cli_h1("Update HTML")
   .import_settings(path = path, tool = tool, verbose = verbose, freeze = freeze)
 
-  if (isTRUE(autolink)) {
-    cli::cli_h1("Auto-Link")
-    .autolink(path)
-  }
-
   cli::cli_h1("Complete")
   cli::cli_alert_success("Documentation updated.")
 }

diff --git a/inst/quarto_website/quarto_website.yml b/inst/quarto_website/quarto_website.yml
@@ -8,6 +8,7 @@ project:
 
 website:
   title: "$ALTDOC_PACKAGE_NAME"
+  code-links: true
   navbar:
     search: true
     right:
@@ -34,7 +35,8 @@ website:
       - text: Citation
         file: $ALTDOC_CITATION
 
-# format:
-#   html:
+format:
+  html:
+    code-link: true
 #     theme: cosmo
 #     number-sections: false
diff --git a/man-roxygen/altdoc_autolink.R b/man-roxygen/altdoc_autolink.R
@@ -1,9 +1,8 @@
-#' @section Auto-link:
-#' 
-#' When the `autolink` argument is `TRUE`, `altdoc` will use the `downlit` package to replace the function names on the package website by links to web-based package documentation. This works for base R libraries and any package published on CRAN.
+#' @section Auto-link for Quarto websites:
 #'
-#' To allow internal links to functions documented by `altdoc`, we need to include links to correct URLs in the `altdoc/pkgdown.yml` file. By default, this file is populated with links to the first URL in the `DESCRIPTION`. When calling `render_docs(autolink=TRUE)`, the `pkgdown.yml` file is moved to the root of the website.
+#' When the `code-link` format setting is `true` in `altdoc/quarto_website.yml` and the `downlit` package is installed, `altdoc` will use the `downlit` package to replace the function names on the package website by links to web-based package documentation. This works for base R libraries and any package published on CRAN.
 #'
-#' Importantly, `downlit` requires the `pkgdown.yml` to be live on the website to create links. This means that links will generally not be updated when making purely local changes. Also, links may not be updated the first time an `altdoc` website is published to the web.
+#' To allow internal links to functions documented by `altdoc`, we need to include links to correct URLs in the `altdoc/pkgdown.yml` file. By default, this file is populated with links to the first URL in the `DESCRIPTION`.
+#'
+#' Importantly, `downlit` requires the `pkgdown.yml` file to be live on the website to create links. This means that links will generally not be updated when making purely local changes. Also, links may not be updated the first time an `altdoc` website is published to the web.
 #'
-#' Note that the `autolink` argument works best for Quarto-based websites. `mkdocs` appears to ignore `downlit` annotations altogether. `docute` and `docsify` display `downlit` annotations, but CSS styling and code highlighting sometimes suffer.
diff --git a/man/render_docs.Rd b/man/render_docs.Rd
diff --git a/tests/testthat/_snaps/docsify/render_docs.md b/tests/testthat/_snaps/docsify/render_docs.md
@@ -146,7 +146,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"hello_base_:_x\">x</code>"                                           
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    
@@ -359,7 +359,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"examplesIf_true_:_x\">x</code>"                                      
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    
@@ -405,7 +405,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"examplesIf_false_:_x\">x</code>"                                     
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    

diff --git a/tests/testthat/_snaps/docute/render_docs.md b/tests/testthat/_snaps/docute/render_docs.md
@@ -137,7 +137,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"hello_base_:_x\">x</code>"                                           
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    
@@ -350,7 +350,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"examplesIf_true_:_x\">x</code>"                                      
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    
@@ -396,7 +396,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"examplesIf_false_:_x\">x</code>"                                     
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    

diff --git a/tests/testthat/_snaps/mkdocs/render_docs.md b/tests/testthat/_snaps/mkdocs/render_docs.md
@@ -36,7 +36,7 @@
       [16] "<table>"                                                                        
       [17] "<tr>"                                                                           
       [18] "<td style=\"white-space: nowrap; font-family: monospace; vertical-align: top\">"
-      [19] "<code id=\"hello_base_:_x\">x</code>"                                           
+      [19] "<code id=\"x\">x</code>"                                                        
       [20] "</td>"                                                                          
       [21] "<td>"                                                                           
       [22] "A parameter"                                                                    

diff --git a/tests/testthat/test-render_docs.R b/tests/testthat/test-render_docs.R
@@ -158,7 +158,7 @@ test_that("quarto: autolink", {
   install.packages(".", repos = NULL, type = "source")
   fs::file_move("README.Rmd", "README.qmd") # special thing quarto
   setup_docs("quarto_website")
-  expect_no_error(render_docs(verbose = .on_ci(), autolink = TRUE))
+  expect_no_error(render_docs(verbose = .on_ci()))
 
   tmp <- .readlines("docs/vignettes/test.html")
   expect_true(any(grepl("https://rdrr.io/r/base/library.html", tmp, fixed = TRUE)))