knit

#!/usr/bin/Rscript

## ./knit [epub|github|html|pdf] to generate different types of output

library(knitr)

## global chunk options: use high quality Cairo PNG device
pdf.options(pointsize = 10)  # smaller pointsize for recording plots
opts_chunk$set(cache=TRUE, cache.path = 'cache-local/',
               fig.width=5, fig.height=5, par=TRUE)
## xtable options (generate HTML by default)
options(xtable.type = 'html', xtable.html.table.attributes = '',
        table.placement = '', xtable.comment = FALSE)

## chunk hooks
knit_hooks$set(par=function(before, options, envir){
  if (before && options$fig.show!='none') 
    par(mar=c(4,4,.1,.1), cex.lab=.95, cex.axis=.9, mgp=c(2,.7,0), tcl=-.3)
})

local({
  fmt = commandArgs(TRUE)
  if (length(fmt) == 0L) fmt = 'epub'
  if (fmt %in% c('github', 'html')) {
    # upload to Imgur when output is for github or html
    opts_knit$set(upload.fun = imgur_upload)
    opts_chunk$set(cache.path = 'cache-upload/')
  } else if (fmt == 'pdf') {
    options(xtable.type = 'latex')
    opts_chunk$set(cache.path = 'cache-pdf/')
    # use high quality tikz graphics for PDF output
    opts_chunk$set(dev = 'tikz', fig.width=4, fig.height=4)
    x = readLines('template.tex')
    options(tikzDocumentDeclaration = x[1], tikzDefaultEngine = 'xetex')
    assign('tikzPackages', c(x[2:13], '\n'), envir = knitr:::.knitEnv)
  }
  
  # knit all md files under ./source
  for (f in list.files('./source/', '\\.md$', full.names = TRUE)) {
    unlink(basename(f))
    knit(f, output = basename(f))
    # make sure you do not do stupid things (edit output instead of source)
    Sys.chmod(basename(f), mode = '0444')
  }
})

## convert to an ebook (EPUB) or other formats
source('mdconvert.sh')