Adding parameters modifies logical values

[dchiu911]

I'm trying to create a template _output.yml and then allow the user to add certain parameters. However, this modifies the logical values (e.g. true -> yes) because the initial yaml was created with ymlthis::use_output_yml() and subsequent modification uses yaml::write_yaml(). My modified output_yml object no longer nests the entire yaml under output: so I cannot use ymlthis::use_output_yml(). Is there a more robust way to handle this workflow without calling ymlthis::yml_output() again with all the original parameters?

output_yml <- ymlthis::yml_output(
  .yml = ymlthis::yml_empty(),
  bookdown::gitbook(
    lib_dir = "assets",
    split_by = "chapter",
    config = list(download = "pdf")
  ),
  bookdown::pdf_book(
    keep_tex = TRUE,
    includes = ymlthis::includes2(in_header = "preamble.tex")
  )
)
print(output_yml)
#> ---
#> output:
#>   bookdown::gitbook:
#>     lib_dir: assets
#>     split_by: chapter
#>     config:
#>       download: pdf
#>   bookdown::pdf_book:
#>     keep_tex: true
#>     includes:
#>       in_header: preamble.tex
#> ---
options(ymlthis.remove_blank_line = TRUE)
ymlthis::use_output_yml(.yml = output_yml, path = tempdir(), quiet = TRUE)
options(ymlthis.remove_blank_line = FALSE)
tmpyml <- file.path(tempdir(), "_output.yml")
# The TRUE values are "true"
readLines(tmpyml)
#> [1] "bookdown::gitbook:"          "  lib_dir: assets"          
#> [3] "  split_by: chapter"         "  config:"                  
#> [5] "    download: pdf"           "bookdown::pdf_book:"        
#> [7] "  keep_tex: true"            "  includes:"                
#> [9] "    in_header: preamble.tex"

output_yml <- yaml::read_yaml(tmpyml)
bib_opts <- list(citation_package = "natbib", toc_bib = TRUE)
output_yml[["bookdown::pdf_book"]] <-
  c(output_yml[["bookdown::pdf_book"]], bib_opts)
ymlthis::as_yml(output_yml)
#> ---
#> bookdown::gitbook:
#>   lib_dir: assets
#>   split_by: chapter
#>   config:
#>     download: pdf
#> bookdown::pdf_book:
#>   keep_tex: true
#>   includes:
#>     in_header: preamble.tex
#>   citation_package: natbib
#>   toc_bib: true
#> ---
yaml::write_yaml(x = output_yml, file = tmpyml)
# The TRUE values are "yes"
readLines(tmpyml)
#>  [1] "bookdown::gitbook:"          "  lib_dir: assets"          
#>  [3] "  split_by: chapter"         "  config:"                  
#>  [5] "    download: pdf"           "bookdown::pdf_book:"        
#>  [7] "  keep_tex: yes"             "  includes:"                
#>  [9] "    in_header: preamble.tex" "  citation_package: natbib" 
#> [11] "  toc_bib: yes"

^{Created on 2022-09-14 with reprex v2.0.2}