make .qmd files autobehave the same as standard knitr files

R/Eqn.R

@@ -5,7 +5,8 @@
 #' The \code{Eqn} function is designed to produce LaTeX expressions of mathematical
 #' equations for writing.
 #' The output can be copied/pasted into documents or
-#' used directly in chunks in \code{.Rmd} or \code{.qmd} documents to compile to equations.
+#' used directly in chunks in \code{.Rmd}, \code{.Rnw}, or \code{.qmd}
+#' documents to compile to equations.
 #' It wraps the equations generated by its arguments
 #' in either a \code{\\begin{equation} ...\\end{equation}} or
 #' \code{\\begin{align} ...\\end{align}} LaTeX environment. \code{ref()} provides for
@@ -32,10 +33,11 @@
 #'   then the equations will be labelled  via \code{(\#eq:myeqn)} and references via \code{\@ref(eq:myeqn)},
 #'   or again via \code{\link{ref}} for convenience
 #' @param html_output logical; use labels for HTML outputs instead of the LaTeX? Automatically
-#'   changed for compiled documents that support \code{knitr}
+#'   changed for compiled documents that support \code{knitr}. Generally not
+#'   required or recommended for the user to modify, except to view the generated syntax
 #' @param quarto logical; use Quarto referencing syntax? When \code{TRUE}
-#'   the \code{html_output} will be irrelevant. Can be set globally via
-#'   \code{\link{options}} with \code{options(quartoEqn=TRUE)}
+#'   the \code{html_output} will be irrelevant. Generally not recommended for the
+#'   user to modify, except to view the generated syntax
 #' @param align logical; use the \code{align} environment with explicit \code{&} representing alignment
 #'   points. Default: \code{FALSE}
 #' @param mat_args list of arguments to be passed to \code{\link{latexMatrix}} to change the
@@ -64,18 +66,13 @@
 #' Eqn('e=mc^2', label = 'eq:einstein')
 #' Eqn("X=U \\lambda V", label='eq:svd')
 #'
-#' # html_output and quarto outputs only show code:
-#' #   (auto detected in compiled documents)
+#' # html_output and quarto outputs only show code
+#' #   (both auto detected in compiled documents)
 #' Eqn('e=mc^2', label = 'eq:einstein', html_output = TRUE)
 #'
 #' # Quarto output
 #' Eqn('e=mc^2', label = 'eq-einstein', quarto = TRUE)
 #'
-#' # Set Quarto option globally for all calls to Eqn()
-#' options(quartoEqn=TRUE)
-#' Eqn('e=mc^2', label = 'eq-einstein')
-#' options(quartoEqn=FALSE) ## reset
-#'
 #' # Multiple expressions
 #' Eqn("e=mc^2",
 #'     Eqn_newline(),
@@ -127,11 +124,10 @@ Eqn <- function(...,
     }
   }
   on.exit(sink.reset())
-  if(is.null(quarto)) quarto <- FALSE
+  quarto <- setQuartoEqn(quarto)
   preview <- preview && interactive()
   if(html_output || quarto) preview <- FALSE
   if(preview){
-      quarto <- FALSE
       tmpfile <- tempfile()
       # everything except the kitchen ...
       sink(tmpfile)
@@ -189,6 +185,30 @@ title: '&nbsp;'
   invisible(NULL)
 }
 
+setQuartoEqn <- function(quarto){
+    if(interactive()){
+        if(is.null(quarto)) quarto <- FALSE
+        return(quarto)
+    }
+    if(isTRUE(getOption('knitr.in.progress')) && is.null(getOption('quartoEqn'))){
+        finp <- knitr::current_input()
+        stripped <- gsub('.rmarkdown', '', finp)
+        files <- dir()
+        if(sum(grepl(paste0(stripped, '.qmd'), files)) == 1)
+            options('quartoEqn' = TRUE)
+        else options('quartoEqn' = FALSE)
+        if(getOption('quartoEqn')){
+            matched_files <- files[grepl(paste0(stripped, '.'), files, fixed=TRUE)]
+            exts <- gsub(paste0(stripped, '.'), "", matched_files, fixed=TRUE)
+            if(any(tolower(exts) %in% c('rmd', 'rnw')))
+                stop(c('Detected files with identical names but different extensions. ',
+                       '\n\n  Please use unique file names when a mix of .qmd and R markdown files',
+                       ' (e.g., .Rmd, .Rnw) are in the same directory.'))
+        }
+    }
+    invisible(getOption('quartoEqn'))
+}
+
 #' Emit a newline in an equation
 #'
 #' \code{Eqn_newline()} emits a newline (\code{\\}) in an equation
@@ -396,7 +416,7 @@ ref <- function(label,
                 parentheses = TRUE,
                 html_output = knitr::is_html_output(),
                 quarto = getOption('quartoEqn')) {
-    if(is.null(quarto)) quarto <- FALSE
+    quarto <- setQuartoEqn(quarto)
     ret <- if(quarto){
         if(parentheses)
             sprintf('([-@%s])', label)

dev/Eqn_test_quarto.qmd

@@ -51,35 +51,9 @@ Will also work within an equation, not that this is particularly useful.
 "@eq-binom"
 ```
 
-# Test if .qmd file used
-
-Set global to TRUE if .qmd file detected from input. Warning raised if files have the same name but different extension (`Eqn.qmd` and `Eqn.Rmd` will raise error if in same dir).
-
-```{r echo=FALSE}
-setQuartoEqn <- function(){
-    if(isTRUE(getOption('knitr.in.progress')) && is.null(getOption('quartoEqn'))){
-        finp <- knitr::current_input()
-        stripped <- gsub('.rmarkdown', '', finp)
-        files <- dir()
-        if(sum(grepl(paste0(stripped, '.qmd'), files)) == 1)
-            options('quartoEqn' = TRUE)
-        else options('quartoEqn' = FALSE)
-        if(getOption('quartoEqn')){
-            matched_files <- files[grepl(paste0(stripped, '.'), files, fixed=TRUE)]
-        exts <- gsub(paste0(stripped, '.'), "", matched_files, fixed=TRUE)
-        if(any(tolower(exts) %in% c('rmd', 'rnw')))
-           stop(c('Detected files with identical names but different extensions. ',
-                '\n\n  Please use unique file names when a mix of .qmd and R markdown files',
-                ' (e.g., .Rmd, .Rnw) are in the same directory.'))
-        }
-    }
-    invisible(NULL)
-}
-```
+# Auto use `quarto=TRUE` if .qmd file used
 
-```{r echo=FALSE}
-setQuartoEqn()
-```
+Internally, set global to TRUE if .qmd file detected. Error raised if files have the same name but different extension (`Eqn.qmd` and `Eqn.Rmd` will raise error if in same dir).
 
 
 ```{r}
@@ -88,4 +62,4 @@ Eqn("f\\left(k\\right) = \\binom{n}{k} p^k\\left(1-p\\right)^{n-k}", label = 'eq
 ```
 
 
-See `{r} ref("eq-auto", quarto=TRUE)` for auto-detected quarto label.
+See `{r} ref("eq-auto", quarto=TRUE)` for auto-detected quarto label. Of course, the @ notation still works too; e.g., see @eq-auto for details