swcarpentry/shell-novice

tracking issue for https://github.com/swcarpentry/shell-novice

[x] add links to definition lists in glossary

[x] fix div/img workaround in episode 3 This is causing problems with the transition because the block is not being processed correctly. (to be fixed in https://github.com/swcarpentry/shell-novice/pull/1383)

 <div style="width:80%; margin: auto;"><img alt="screenshot of nano text editor in
 action with the text `It's not publish or perish any more, it's share and thrive`"
 src="../fig/nano-screenshot.png"></div>

[x] protect $ in episode 5 (note: this does not need protecting, but sandpaper should be updated to account for this: https://github.com/carpentries/sandpaper/issues/444)
[x] protect unescaped $ in episode 6 (to be fixed in https://github.com/swcarpentry/shell-novice/pull/1384)
[x] change HTML markup in setup.md to solution boxes. Because the HTML is immediately adjacent to the markdown, it is preventing the markdown from being processed and thus relative links are being turned into \[link text\], which mathjax sees as block math.

157:episodes/03-create.md:200 [missing file]: [](NA)

── Transforming Episodes ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
ℹ Converting 'swcarpentry/shell-novice/_episodes/01-intro.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/01-intro.md' to sandpaper ... done

ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'01-intro.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'01-intro.md'' ... done

ℹ Converting 'swcarpentry/shell-novice/_episodes/02-filedir.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/02-filedir.md' to sandpaper ... done

ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'02-filedir.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'02-filedir.md'' ... done

ℹ Converting 'swcarpentry/shell-novice/_episodes/03-create.md' to sandpaper
✖ Converting 'swcarpentry/shell-novice/_episodes/03-create.md' to sandpaper ... failed

Error in data.frame(node = rep(seq_along(divs), lengths(divs)), div = unlist(divs,  : 
  arguments imply differing number of rows: 57, 55
In addition: Warning message:
In lines[!fenced_divs] <- rep(get_linestart(nodes[!fenced_divs]),  :
  number of items to replace is not a multiple of replacement length
ℹ Converting 'swcarpentry/shell-novice/_episodes/04-pipefilter.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/04-pipefilter.md' to sandpaper ... done

ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'04-pipefilter.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'04-pipefilter.md'' ... done

ℹ Converting 'swcarpentry/shell-novice/_episodes/05-loop.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/05-loop.md' to sandpaper ... done

! Some math could not be parsed... likely because of shell variable examples
ℹ Below is the error
! Inline math delimiters are not balanced.

HINT: If you are writing BASIC code, make sure you wrap variable
      names and code in backtics like so: `INKEY$`.

Below are the pairs that were found:
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               start...end
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               -----...---
The for loop "for filename in .dat; do echo cp $filename original-$filename;done" will successively assign the names of all ".dat" files in your currentdirectory to the variable "$filename" and then execute the command. With thefiles "basilisk.dat", "minotaur.dat" and "unicorn.dat" in the current directorythe loop will successively call the echo command three times and print threelines: "cp basislisk.dat original-basilisk.dat", then "cp minotaur.datoriginal-minotaur.dat" and finally "cp unicorn.datoriginal-unicorn.dat"...
ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'05-loop.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'05-loop.md'' ... done

ℹ Converting 'swcarpentry/shell-novice/_episodes/06-script.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/06-script.md' to sandpaper ... done

! Some math could not be parsed... likely because of shell variable examples
ℹ Below is the error
! Inline math delimiters are not balanced.

HINT: If you are writing BASIC code, make sure you wrap variable
      names and code in backtics like so: `INKEY$`.

Below are the pairs that were found:
                                                                                start...end
                                                                                -----...---
The special variables $1, $2 and $3 represent the command line arguments given to the...
ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'06-script.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'06-script.md'' ... done

ℹ Converting 'swcarpentry/shell-novice/_episodes/07-find.md' to sandpaper
✔ Converting 'swcarpentry/shell-novice/_episodes/07-find.md' to sandpaper ... done

ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'07-find.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'07-find.md'' ... done

ℹ Committing...
ℹ Running '/home/zhian/Documents/Carpentries/Git/carpentries/lesson-transition/swcarpentry/shell-novice.R'
ℹ Converting 'sandpaper/swcarpentry/shell-novice/episodes/03-create.md' to sandpaper
✔ Converting 'sandpaper/swcarpentry/shell-novice/episodes/03-create.md' to sandpaper ... done

ℹ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'03-create.md''
✔ Writing ''sandpaper/swcarpentry/shell-novice/episodes'/'03-create.md'' ... done

carpentries / lesson-transition

swcarpentry/shell-novice #80