Fix BiocStyle & pkgdown interaction

R/pdf_document.R

@@ -80,12 +80,14 @@ pdf_document <- function(toc = TRUE,
 
   ## code chunks and code highlighting
   thm <- system.file("themes", "default.css", package = "BiocStyle")
-  opts_knit$set(out.format="latex");
+  out_fmt <- opts_knit$get("out.format")
+  opts_knit$set(out.format="latex")
   head = c(head,
            "% code highlighting",
            knit_theme$get(thm)$highlight,
            readLines(file.path(resources, "tex", "highlighting-macros.def")))
-
+  opts_knit$set(out.format=out_fmt)
+
   if (use_unsrturl)
     head = c(head, sprintf("\\AtBeginDocument{\\bibliographystyle{%s}}\n",  sub(".bst$", "", template_files[["bst"]])))
 

inst/unitTests/test_pdf_document.R

@@ -2,9 +2,27 @@ test_pdf_document <- function() {
   filename <- rmarkdown::draft(tempfile(fileext = ".Rmd"), edit = FALSE,
                                template="pdf_document", package = "BiocStyle")
   lines <- BiocStyle:::readUTF8(filename)
-  lines <- BiocStyle:::modifyLines(lines, from = "title:", replace = FALSE, 
+  lines <- BiocStyle:::modifyLines(lines, from = "title:", replace = FALSE,
                        insert='subtitle: "Vignette Subtitle"')
   BiocStyle:::writeUTF8(lines, filename)
   rmarkdown::render(filename)
   unlink(filename)
 }
+
+test_pdf_document_restores_out_format <- function() {
+  ## Regression test for https://github.com/Bioconductor/BiocStyle/pull/108
+  ##
+  ## BiocStyle::pdf_document() temporarily sets the global knitr option
+  ## 'out.format' to "latex" in order to look up the syntax highlighting
+  ## theme, but used to leave it set afterwards. This corrupted the knitr
+  ## state for anything rendered later in the same R session, e.g. pkgdown
+  ## building several articles (one of which uses BiocStyle::pdf_document)
+  ## within a single process, which itself relies on 'out.format' being
+  ## "html".
+  out_format_before <- knitr::opts_knit$get("out.format")
+  on.exit(knitr::opts_knit$set(out.format = out_format_before))
+
+  knitr::opts_knit$set(out.format = "html")
+  invisible(BiocStyle::pdf_document())
+  checkIdentical(knitr::opts_knit$get("out.format"), "html")
+}