prevent to_md() from clobbering document (and friends!)

[zkamvar]

Description

I've done a couple of things here (I apologize for shoving too many things in a single PR, but I figured they were all roughly related):

1. Fixed a bug I introduced in add sourcepos argument #13/ensure Rmd chunks retain sourcepos attribute #14 where code chunks would have an extra sourcepos option added if read in with sourcepos = TRUE (whoops 😳)
2. Updated to_xml() to only post-process code blocks that have a language attribute to allow bare or unevaluated code fences.
3. I noticed that the original xml document was being affected by the round trip (because xml2 objects operate on pass-by-reference, which is summarized SO WELL in this coffee cup gif), so I have updated the processing to copy the document before processing and it no longer goes through a disk write (there was a weird namespace issue with this process that was affecting the block processing, so I use the technique I found in my own package)

Example

library(tinkr)
library(magrittr)
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
rmd <- tinkr::to_xml(path, sourcepos = TRUE)
rmd$body %>%
  xml2::xml_find_first(".//d1:code_block") %>%
  xml2::xml_attrs()
#>  sourcepos      space   language       name    include       eval 
#>  "2:1-4:3" "preserve"        "r"    "setup"    "FALSE"     "TRUE"
tmp <- tempfile()
to_md(rmd, tmp)
# blocks are processed correctly
readLines(tmp) %>%
  head(10) %>%
  cat(sep = "\n")
#> ---
#> title: "Untitled"
#> author: "M. Salmon"
#> date: "September 6, 2018"
#> output: html_document
#> ---
#> 
#> ```{r setup, include=FALSE, eval=TRUE}
#> knitr::opts_chunk$set(echo = TRUE)
#> ```
# unevaluated blocks are processed correctly
readLines(tmp) %>%
  tail(29) %>%
  head(10) %>%
  cat(sep = "\n")
#> 
#> Non-RMarkdown blocks are also considered
#> 
#> ```bash
#> echo "this is an unevaluted bash block"
#> ```
#> 
#> ```
#> This is an ambiguous code block
#> ```
# The attributes have not changed
rmd$body %>%
  xml2::xml_find_first(".//d1:code_block") %>%
  xml2::xml_attrs()
#>  sourcepos      space   language       name    include       eval 
#>  "2:1-4:3" "preserve"        "r"    "setup"    "FALSE"     "TRUE"

^{Created on 2020-05-28 by the reprex package (v0.3.0)}

[maelle]

Thanks a ton!!

[maelle]

much better! should I submit this to CRAN one day? If I do you'll have to become an author.

[zkamvar]

It would be nice to have on CRAN at some point, but I might like to give #9 a shot first 😉

[maelle]

so much more elegant! ✨

[maelle]

Would it be fine to add you as an author before merging? If so, please go ahead and add your metadata.