Add support for .yml and .yaml files (#83)

NEWS.md

@@ -1,5 +1,7 @@
 # plume (development version)
 
+* `PlumeQuarto` now supports `.yml` and `.yaml` files (#82).
+
 # plume 0.2.4
 
 * Tweak some examples in the vignettes and expand the `Contributions` section in `vignette("plume")`.

R/checkers.R

@@ -293,15 +293,15 @@ file_ext <- function(x) {
   str_extract(x, "(?<=\\.)[^.]+$")
 }
 
-check_file <- function(x, extension, ..., param = caller_arg(x)) {
+check_file <- function(x, extensions, ..., param = caller_arg(x)) {
   check_string(x, allow_empty = FALSE, param = param)
   ext <- file_ext(x)
-  if (is_not_na(ext) && vec_in(ext, extension)) {
+  if (is_not_na(ext) && vec_in(ext, extensions)) {
     check_path(x, param = param)
     return(invisible())
   }
-  extension <- wrap(predot(extension), "`")
-  abort_check(paste("a", extension, "file"), ..., param = param)
+  extensions <- enumerate(wrap(predot(extensions), "`"), last = " or ")
+  abort_check(paste("a", extensions, "file"), ..., param = param)
 }
 
 is_glueish <- function(x) {

R/plume-quarto.R

@@ -11,8 +11,8 @@
 ))
 
 #' @title PlumeQuarto class
-#' @description Class that pushes author metadata in the YAML header
-#'   of Quarto files.
+#' @description Class that pushes author metadata in YAML files or the YAML
+#'   header of Quarto files.
 #' @examples
 #' # Create a simple temporary file with a YAML header
 #' # containing a title
@@ -53,7 +53,7 @@ PlumeQuarto <- R6Class(
   public = list(
     #' @description Create a `PlumeQuarto` object.
     #' @param data A data frame containing author-related data.
-    #' @param file A `.qmd` file to insert author data into.
+    #' @param file A `.qmd`, `.yml` or `.yaml` file to insert author data into.
     #' @param names A vector of key-value pairs specifying custom names to use,
     #'   where keys are default names and values their respective replacements.
     #' @param roles A vector of key-value pairs defining roles where keys
@@ -76,18 +76,19 @@ PlumeQuarto <- R6Class(
       initials_given_name = FALSE,
       by = NULL
     ) {
-      check_file(file, extension = "qmd")
+      check_file(file, extensions = c("qmd", "yml", "yaml"))
       super$initialize(data, names, roles, credit_roles, initials_given_name, by = by)
       private$file <- file
       private$id <- private$pick("id")
     },
 
-    #' @description Push or update author information in a YAML header. The
-    #'   generated YAML complies with Quarto's `r link("quarto_schemas")`.
+    #' @description Push or update author information in a YAML file or YAML
+    #'   header. The generated YAML complies with Quarto's
+    #'   `r link("quarto_schemas")`.
     #' @details
-    #' If missing, `to_yaml()` pushes author information into a YAML header. If
-    #' already existing, the function replaces old `author` and `affiliations`
-    #' values with the ones provided in the input data.
+    #' If missing, `to_yaml()` inserts author information into the desired file.
+    #' Otherwise, the function replaces old `author` and `affiliations` values
+    #' with the ones provided in the input data.
     #' @return The input `file` invisibly.
     to_yaml = function() {
       yaml_push(private$get_template(), file = private$file)
@@ -105,10 +106,11 @@ PlumeQuarto <- R6Class(
     },
 
     get_template = function() {
-      list(
+      out <- list(
         author = private$author_tbl(),
         affiliations = private$affiliation_tbl()
       )
+      add_class(out, cls = file_ext(private$file))
     },
 
     author_tbl = function() {

R/utils-list.R

@@ -47,3 +47,9 @@ list_replace <- function(x, y) {
   }
   x
 }
+
+list_drop_empty <- function(x) {
+  are_empty <- map_vec(x, \(.x) is_empty(.x))
+  x[are_empty] <- NULL
+  x
+}

R/utils.R

@@ -192,3 +192,8 @@ unstructure <- function(x) {
   attributes(x) <- NULL
   x
 }
+
+add_class <- function(x, cls) {
+  class(x) <- c(cls, class(x))
+  x
+}

R/yaml.R

@@ -1,17 +1,30 @@
-schemas_are_up_to_date <- function(current, new) {
-  current <- current[c("author", "affiliations")]
-  identical(current, new)
+eol <- function() {
+  if (.Platform$OS.type == "unix") "\n" else "\r\n" # nocov
 }
 
-json_update <- function(x, json) {
-  x <- yaml.load(x)
-  if (is.null(x)) {
-    return(json)
-  }
-  if (schemas_are_up_to_date(x, json)) {
+as_verbatim_lgl <- function(x) {
+  x <- if_else(x, "true", "false")
+  structure(x, class = "verbatim")
+}
+
+.yaml_args <- list(
+  line.sep = eol(),
+  indent.mapping.sequence = TRUE,
+  handlers = list(logical = as_verbatim_lgl)
+)
+
+schemas_are_up_to_date <- function(old, new) {
+  old <- old[c("author", "affiliations")]
+  identical(old, new)
+}
+
+json_update <- function(old, new) {
+  new <- as_json(new)
+  if (schemas_are_up_to_date(old, new)) {
     return()
   }
-  list_assign(x, !!!json)
+  out <- if (is.null(old)) new else list_assign(old, !!!new)
+  list_drop_empty(out)
 }
 
 as_json <- function(x) {
@@ -23,28 +36,10 @@ separate_yaml_header <- function(x) {
   str_split_1(x, "(?m:^|\\R\\K)-{3}(?:\\R|$)")
 }
 
-as_verbatim_lgl <- function(x) {
-  x <- if_else(x, "true", "false")
-  structure(x, class = "verbatim")
-}
-
-get_eol <- function() {
-  if (.Platform$OS.type == "unix") "\n" else "\r\n" # nocov
-}
-
 yaml_inject <- function(x, lines) {
-  eol <- get_eol()
-  if (is_empty(x$affiliations)) {
-    x$affiliations <- NULL
-  }
-  yaml <- as.yaml(
-    x,
-    line.sep = eol,
-    indent.mapping.sequence = TRUE,
-    handlers = list(logical = as_verbatim_lgl)
-  )
+  yaml <- do.call(as.yaml, c(list(x), .yaml_args))
   out <- replace(lines, 2, yaml)
-  collapse(out, paste0("---", eol))
+  collapse(out, paste0("---", eol()))
 }
 
 has_yaml <- function(x) {
@@ -80,15 +75,28 @@ add_yaml_header <- function(x) {
   c("", "", x)
 }
 
-yaml_push <- function(what, file) {
+yaml_push <- function(x, file) {
+  UseMethod("yaml_push")
+}
+
+yaml_push.default <- function(x, file) {
+  old <- yaml::read_yaml(file)
+  json <- json_update(old, x)
+  if (is.null(json)) {
+    return(invisible())
+  }
+  do.call(yaml::write_yaml, c(list(json), file, .yaml_args))
+}
+
+yaml_push.qmd <- function(x, file) {
   text <- read_file(file)
   check_has_yaml(text)
   items <- separate_yaml_header(text)
   if (yaml_has_strippable(items[[2]])) {
     items <- add_yaml_header(items)
   }
-  json <- as_json(what)
-  json <- json_update(items[[2]], json)
+  old <- yaml.load(items[[2]])
+  json <- json_update(old, x)
   if (is.null(json)) {
     return(invisible())
   }

README.Rmd

@@ -26,7 +26,7 @@ knitr::opts_chunk$set(
 
 plume provides tools for handling and generating author-related information for scientific writing in R Markdown and Quarto. The package implements two R6 classes:
 
-- `PlumeQuarto`: class that allows you to push author metadata in the YAML header of Quarto files. The generated YAML complies with Quarto's [author and affiliations schemas](https://quarto.org/docs/journals/authors.html). This is the class to use if you work with journal templates.
+- `PlumeQuarto`: class that allows you to push author metadata in YAML files or the YAML header of Quarto files. The generated YAML complies with Quarto's [author and affiliations schemas](https://quarto.org/docs/journals/authors.html). This is the class to use if you work with journal templates.
 
 - `Plume`: class that generates author lists and other author-related information as character strings. This is an easy and convenient solution when you don't need preformatted documents.
 
@@ -64,7 +64,7 @@ tmp_file <- withr::local_tempfile(
 )
 ```
 
-`PlumeQuarto` lets you push author metadata in the YAML header of any `.qmd` file using the `to_yaml()` method.
+`PlumeQuarto` lets you push author metadata in YAML files or the YAML header of any `.qmd` file using the `to_yaml()` method.
 
 Consider the following example:
 

README.md

@@ -18,9 +18,9 @@ plume provides tools for handling and generating author-related
 information for scientific writing in R Markdown and Quarto. The package
 implements two R6 classes:
 
-- `PlumeQuarto`: class that allows you to push author metadata in the
-  YAML header of Quarto files. The generated YAML complies with Quarto’s
-  [author and affiliations
+- `PlumeQuarto`: class that allows you to push author metadata in YAML
+  files or the YAML header of Quarto files. The generated YAML complies
+  with Quarto’s [author and affiliations
   schemas](https://quarto.org/docs/journals/authors.html). This is the
   class to use if you work with journal templates.
 
@@ -74,8 +74,8 @@ Plume$new(encyclopedists)
 #> # ℹ 2 more variables: affiliation <list>, role <list>
 ```
 
-`PlumeQuarto` lets you push author metadata in the YAML header of any
-`.qmd` file using the `to_yaml()` method.
+`PlumeQuarto` lets you push author metadata in YAML files or the YAML
+header of any `.qmd` file using the `to_yaml()` method.
 
 Consider the following example:
 

tests/testthat/_snaps/initialize.md

@@ -146,7 +146,7 @@
     Output
       <error/rlang_error>
       Error:
-      ! `file` must be a `.qmd` file.
+      ! `file` must be a `.qmd`, `.yml` or `.yaml` file.
     Code
       (expect_error(PlumeQuarto$new(basic_df, file = "~/test.qmd")))
     Output

tests/testthat/_snaps/to-yaml.md

@@ -220,6 +220,17 @@
         Vivamus quis
       ---
 
+# to_yaml() can push data into YAML files
+
+    Code
+      read_test_file(tmp_file)
+    Output
+      title: foo
+      author:
+        - name:
+            given: Zip
+            family: Zap
+
 # to_yaml() errors if no YAML headers is found
 
     Code

tests/testthat/test-to-yaml.R

@@ -113,6 +113,21 @@ test_that("to_yaml() writes in a separate header to preserve strippable data (#5
   expect_snapshot(read_test_file(tmp_file))
 })
 
+test_that("to_yaml() can push data into YAML files", {
+  tmp_file <- withr::local_tempfile(
+    lines = "title: foo",
+    fileext = ".yaml"
+  )
+
+  aut <- PlumeQuarto$new(
+    data.frame(given_name = "Zip", family_name = "Zap"),
+    tmp_file
+  )
+  aut$to_yaml()
+
+  expect_snapshot(read_test_file(tmp_file))
+})
+
 # Errors ----
 
 test_that("to_yaml() errors if no YAML headers is found", {

vignettes/plume.Rmd

@@ -202,9 +202,9 @@ aut$set_corresponding_authors(everyone())
 aut
 ```
 
-## Pushing data into YAML headers
+## Pushing data into a YAML or Quarto file
 
-`PlumeQuarto` allows you to inject author metadata directly into the YAML header of `.qmd` files.
+`PlumeQuarto` allows you to inject author metadata directly into YAML files or the YAML header of `.qmd` files.
 
 Consider the following Quarto document:
 
@@ -219,7 +219,7 @@ tmp_file <- withr::local_tempfile(
 cat(read_file(tmp_file))
 ```
 
-You can push information from the input data into the YAML header using the `to_yaml()` method:
+You can push information from the input data into the YAML or Quarto file using the `to_yaml()` method:
 
 ```{r, eval = FALSE}
 aut <- PlumeQuarto$new(
@@ -237,7 +237,7 @@ cat(read_file(tmp_file))
 
 Authors are listed in the order they're defined in the input data.
 
-If the YAML header already has an `author` and `affiliations` keys, `to_yaml()` replaces old values with new ones.
+If the YAML or Quarto file already has an `author` and `affiliations` keys, `to_yaml()` replaces old values with new ones.
 
 ```{r, eval = FALSE}
 aut <- PlumeQuarto$new(