Allow for ids in figures

[muschellij2]

This PR allows for Ids for <div class="figure", which solves half of the problem in rstudio/bookdown#766, which will allow for id references in bookdown for figures in epub documents. An additional adaptation needs to be made in https://github.com/rstudio/bookdown/blob/master/R/html.R#L566, which I will make momentarily.

Otherwise, this reprex should show that adding the id causes fewer epub errors:

Clone the Repo

library(git2r)
library(bookdown)
library(knitr)
local_path = "bookdown-demo"
git2r::clone("https://github.com/rstudio/bookdown-demo.git",
             local_path = local_path)
#> cloning into 'bookdown-demo'...
#> Receiving objects:   1% (6/530),    8 kb
#> Receiving objects:  11% (59/530),   16 kb
#> Receiving objects:  21% (112/530),  120 kb
#> Receiving objects:  31% (165/530),  321 kb
#> Receiving objects:  41% (218/530),  409 kb
#> Receiving objects:  51% (271/530),  472 kb
#> Receiving objects:  61% (324/530),  544 kb
#> Receiving objects:  71% (377/530),  576 kb
#> Receiving objects:  81% (430/530),  584 kb
#> Receiving objects:  91% (483/530),  592 kb
#> Receiving objects: 100% (530/530),  723 kb, done.
#> Local:    master /private/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T/RtmpgLdL4z/reprexac002cc7d5c9/bookdown-demo
#> Remote:   master @ origin (https://github.com/rstudio/bookdown-demo.git)
#> Head:     [4e34630] 2018-10-22: Add now.json and Dockerfile for building HTML book and deploy to now.sh (#36)
setwd(local_path)


epub_file = bookdown::render_book(
  "index.Rmd",
  bookdown::epub_book(pandoc_args = "--reference-links"),
  clean = FALSE)
#> processing file: bookdown-demo.Rmd
#> output file: bookdown-demo.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS bookdown-demo.utf8.md --to epub3 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output bookdown-demo.epub --reference-links --number-sections --filter /usr/local/bin/pandoc-citeproc
#> 
#> Output created: _book/bookdown-demo.epub
epub_file = normalizePath(epub_file)

Test output

Simple epub checker function

The epubcheck R function will get the output from epubcheck.

epubcheck = function(epub_file) {
  res = system2("epubcheck", epub_file, stdout = TRUE, stderr = TRUE)
  res
}

Then num_errors will count the number of errors

num_errors = function(out) {
  out = grep("Messages", out, value = TRUE)
  out = sub(".* (.*) errors.*", "\\1", out)
  as.numeric(out)
}

Here we see we get 4 errors from the result (seemingly no problems were
fixed).
The issue is that one of the lines has both a table reference (not fixed)
and a figure reference (fixed by this PR).

result = epubcheck(epub_file)
#> Warning in system2("epubcheck", epub_file, stdout = TRUE, stderr
#> = TRUE): running command ''epubcheck' /private/var/folders/1s/
#> wrtqcpxn685_zk570bnx9_rr0000gr/T/RtmpgLdL4z/reprexac002cc7d5c9/bookdown-
#> demo/_book/bookdown-demo.epub 2>&1' had status 1
result
#>  [1] "Validating using EPUB version 3.2 rules."                                                                                                                                    
#>  [2] "ERROR(RSC-005): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/nav.xhtml(19,9): Error while parsing file: element \"ol\" incomplete; missing required element \"li\""         
#>  [3] "ERROR(RSC-005): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/text/ch002.xhtml(87,74): Error while parsing file: value of attribute \"width\" is invalid; must be an integer"
#>  [4] "ERROR(RSC-012): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/text/ch002.xhtml(82,247): Fragment identifier is not defined."                                                 
#>  [5] "ERROR(RSC-012): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/text/ch002.xhtml(92,252): Fragment identifier is not defined."                                                 
#>  [6] ""                                                                                                                                                                            
#>  [7] "Check finished with errors"                                                                                                                                                  
#>  [8] "Messages: 0 fatals / 4 errors / 0 warnings / 0 infos"                                                                                                                        
#>  [9] ""                                                                                                                                                                            
#> [10] "EPUBCheck completed"                                                                                                                                                         
#> attr(,"status")
#> [1] 1
num_errors(result)
#> [1] 4

^{Created on 2019-08-28 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       macOS Mojave 10.14.6        
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2019-08-28                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version     date       lib
#>  assertthat    0.2.1       2019-03-21 [1]
#>  backports     1.1.4       2019-04-10 [1]
#>  bookdown    * 0.13.2      2019-08-28 [1]
#>  callr         3.3.1       2019-07-18 [1]
#>  cli           1.1.0       2019-03-19 [1]
#>  crayon        1.3.4       2017-09-16 [1]
#>  curl          4.0         2019-07-22 [1]
#>  desc          1.2.0       2019-07-10 [1]
#>  devtools      2.1.0       2019-07-06 [1]
#>  digest        0.6.20      2019-07-04 [1]
#>  evaluate      0.14        2019-05-28 [1]
#>  fs            1.3.1       2019-05-06 [1]
#>  git2r       * 0.26.1      2019-06-29 [1]
#>  glue          1.3.1       2019-03-12 [1]
#>  highr         0.8         2019-03-20 [1]
#>  htmltools     0.3.6       2017-04-28 [1]
#>  httr          1.4.1       2019-08-05 [1]
#>  knitr       * 1.24.3      2019-08-28 [1]
#>  magrittr      1.5         2014-11-22 [1]
#>  memoise       1.1.0       2017-04-21 [1]
#>  mime          0.7         2019-06-11 [1]
#>  pkgbuild      1.0.3       2019-03-20 [1]
#>  pkgload       1.0.2       2018-10-29 [1]
#>  prettyunits   1.0.2       2015-07-13 [1]
#>  processx      3.4.1       2019-07-18 [1]
#>  ps            1.3.0       2018-12-21 [1]
#>  R6            2.4.0       2019-02-14 [1]
#>  Rcpp          1.0.2       2019-07-25 [1]
#>  remotes       2.1.0       2019-06-24 [1]
#>  rlang         0.4.0       2019-06-25 [1]
#>  rmarkdown     1.14        2019-07-12 [1]
#>  rprojroot     1.3-2       2018-01-03 [1]
#>  rstudioapi    0.10.0-9000 2019-07-30 [1]
#>  sessioninfo   1.1.1       2018-11-05 [1]
#>  stringi       1.4.3       2019-03-12 [1]
#>  stringr       1.4.0       2019-02-10 [1]
#>  testthat      2.1.1       2019-04-23 [1]
#>  usethis       1.5.1.9000  2019-08-15 [1]
#>  withr         2.1.2       2018-03-15 [1]
#>  xfun          0.8         2019-06-25 [1]
#>  xml2          1.2.1       2019-07-29 [1]
#>  yaml          2.2.0       2018-07-25 [1]
#>  source                             
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#>  local                              
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (muschellij2/desc@b0c374f)  
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (muschellij2/knitr@abcea3d) 
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (rstudio/rstudioapi@31d1afa)
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  local                              
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#> 
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Another Example, but a little editing

Clone the Repo

library(git2r)
library(bookdown)
library(knitr)

This is required because this line technically has a table reference and a
figure reference - if we edit this, we show that the figure reference
is indeed fixed. The warning from counting figures will be
addressed in a PR to bookdown.

local_path = "bookdown-demo"
git2r::clone("https://github.com/rstudio/bookdown-demo.git",
             local_path = local_path)
#> cloning into 'bookdown-demo'...
#> Receiving objects:   1% (6/530),    9 kb
#> Receiving objects:  11% (59/530),   17 kb
#> Receiving objects:  21% (112/530),  121 kb
#> Receiving objects:  31% (165/530),  321 kb
#> Receiving objects:  41% (218/530),  409 kb
#> Receiving objects:  51% (271/530),  472 kb
#> Receiving objects:  61% (324/530),  545 kb
#> Receiving objects:  71% (377/530),  576 kb
#> Receiving objects:  81% (430/530),  584 kb
#> Receiving objects:  91% (483/530),  592 kb
#> Receiving objects: 100% (530/530),  723 kb, done.
#> Local:    master /private/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T/RtmpgLdL4z/reprexac002d6b1666/bookdown-demo
#> Remote:   master @ origin (https://github.com/rstudio/bookdown-demo.git)
#> Head:     [4e34630] 2018-10-22: Add now.json and Dockerfile for building HTML book and deploy to now.sh (#36)
setwd(local_path)
x = readLines("01-intro.Rmd")
x = sub("\\@ref(tab:nice-tab)", "", x, fixed = TRUE)
writeLines(x, "01-intro.Rmd")
epub_file = bookdown::render_book(
  "index.Rmd",
  bookdown::epub_book(pandoc_args = "--reference-links"),
  clean = FALSE)
#> processing file: bookdown-demo.Rmd
#> output file: bookdown-demo.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS bookdown-demo.utf8.md --to epub3 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output bookdown-demo.epub --reference-links --number-sections --filter /usr/local/bin/pandoc-citeproc
#> 
#> Output created: _book/bookdown-demo.epub
epub_file = normalizePath(epub_file)

Test output

Simple epub checker function

The epubcheck R function will get the output from epubcheck.

epubcheck = function(epub_file) {
  res = system2("epubcheck", epub_file, stdout = TRUE, stderr = TRUE)
  res
}

Then num_errors will count the number of errors

num_errors = function(out) {
  out = grep("Messages", out, value = TRUE)
  out = sub(".* (.*) errors.*", "\\1", out)
  as.numeric(out)
}

Test output

Here we see we get fewer errors from the result

result = epubcheck(epub_file)
#> Warning in system2("epubcheck", epub_file, stdout = TRUE, stderr
#> = TRUE): running command ''epubcheck' /private/var/folders/1s/
#> wrtqcpxn685_zk570bnx9_rr0000gr/T/RtmpgLdL4z/reprexac002d6b1666/bookdown-
#> demo/_book/bookdown-demo.epub 2>&1' had status 1
result
#> [1] "Validating using EPUB version 3.2 rules."                                                                                                                                    
#> [2] "ERROR(RSC-005): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/nav.xhtml(19,9): Error while parsing file: element \"ol\" incomplete; missing required element \"li\""         
#> [3] "ERROR(RSC-005): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/text/ch002.xhtml(87,74): Error while parsing file: value of attribute \"width\" is invalid; must be an integer"
#> [4] "ERROR(RSC-012): ./bookdown-demo/_book/bookdown-demo.epub/EPUB/text/ch002.xhtml(82,247): Fragment identifier is not defined."                                                 
#> [5] ""                                                                                                                                                                            
#> [6] "Check finished with errors"                                                                                                                                                  
#> [7] "Messages: 0 fatals / 3 errors / 0 warnings / 0 infos"                                                                                                                        
#> [8] ""                                                                                                                                                                            
#> [9] "EPUBCheck completed"                                                                                                                                                         
#> attr(,"status")
#> [1] 1
num_errors(result)
#> [1] 3

^{Created on 2019-08-28 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       macOS Mojave 10.14.6        
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2019-08-28                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version     date       lib
#>  assertthat    0.2.1       2019-03-21 [1]
#>  backports     1.1.4       2019-04-10 [1]
#>  bookdown    * 0.13.2      2019-08-28 [1]
#>  callr         3.3.1       2019-07-18 [1]
#>  cli           1.1.0       2019-03-19 [1]
#>  crayon        1.3.4       2017-09-16 [1]
#>  curl          4.0         2019-07-22 [1]
#>  desc          1.2.0       2019-07-10 [1]
#>  devtools      2.1.0       2019-07-06 [1]
#>  digest        0.6.20      2019-07-04 [1]
#>  evaluate      0.14        2019-05-28 [1]
#>  fs            1.3.1       2019-05-06 [1]
#>  git2r       * 0.26.1      2019-06-29 [1]
#>  glue          1.3.1       2019-03-12 [1]
#>  highr         0.8         2019-03-20 [1]
#>  htmltools     0.3.6       2017-04-28 [1]
#>  httr          1.4.1       2019-08-05 [1]
#>  knitr       * 1.24.3      2019-08-28 [1]
#>  magrittr      1.5         2014-11-22 [1]
#>  memoise       1.1.0       2017-04-21 [1]
#>  mime          0.7         2019-06-11 [1]
#>  pkgbuild      1.0.3       2019-03-20 [1]
#>  pkgload       1.0.2       2018-10-29 [1]
#>  prettyunits   1.0.2       2015-07-13 [1]
#>  processx      3.4.1       2019-07-18 [1]
#>  ps            1.3.0       2018-12-21 [1]
#>  R6            2.4.0       2019-02-14 [1]
#>  Rcpp          1.0.2       2019-07-25 [1]
#>  remotes       2.1.0       2019-06-24 [1]
#>  rlang         0.4.0       2019-06-25 [1]
#>  rmarkdown     1.14        2019-07-12 [1]
#>  rprojroot     1.3-2       2018-01-03 [1]
#>  rstudioapi    0.10.0-9000 2019-07-30 [1]
#>  sessioninfo   1.1.1       2018-11-05 [1]
#>  stringi       1.4.3       2019-03-12 [1]
#>  stringr       1.4.0       2019-02-10 [1]
#>  testthat      2.1.1       2019-04-23 [1]
#>  usethis       1.5.1.9000  2019-08-15 [1]
#>  withr         2.1.2       2018-03-15 [1]
#>  xfun          0.8         2019-06-25 [1]
#>  xml2          1.2.1       2019-07-29 [1]
#>  yaml          2.2.0       2018-07-25 [1]
#>  source                             
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  local                              
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#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (muschellij2/desc@b0c374f)  
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
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#>  Github (muschellij2/knitr@abcea3d) 
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#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (rstudio/rstudioapi@31d1afa)
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
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#>  CRAN (R 3.6.0)                     
#>  local                              
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#> 
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

[cderv]

I think it has been wrongly closed as needed and referenced in rstudio/bookdown#767

[cderv]

@muschellij2 we can't really reopen this PR because you are working directly in master and not in branch. As you have another PR open (#1870) this one is no more possible.

Sorry we took some time to read all this.

If you still have the work you shared here, it would be useful.

When you do PR, please create a branch in your repo and PR from that branch. This way features won't impact each others.

Or Am I missing something and this is included somewhere else ? or not needed anymore ?

(I went there from bookdown)