# This code was provided by Michael Stewart, Feb. 2020.
#
# Knitr is a successor to Sweave (see sweave_latexmkrc) which allows the embedding
# of R code (and its output) into LaTeX files. A .Rnw file (including LaTeX code
# and R code) is "knitted" to produce a LaTeX file, which also includes the output
# obtained from running the R code. Knitr also works with other plain-text markup 
# languages (e.g. Rmarkdown and brew) but they are not supported here. 
# See https://yihui.org/knitr for more information.
#
# This latexmkrc file permits using knitr, allowing SyncTeX to work properly. 
# It also works for a multiple-file project under one caveat: the "native"
# knitr child document inclusion method which uses chunks like
#
# <<child='child.Rnw'>>=     
# @
#
# is *not* used. Rather, each .Rnw file is "knitted" in a standalone fashion 
# and the "inputting" is done purely at the LaTeX phase. 
#
# Thus if we have a main document "main.Rnw" and a child document "child.Rnw"
# the successful workflow is:
# 0. put a line 
#      
#    \input child.tex
# 
#    at the deisred location in main.Rnw;
# 1. knit('main.Rnw')  # to produce main.tex (which inherits the \input line above);
# 2. knit('child.Rnw') # to produce child.tex;
# 3. pdflatex -synctex=1 main.tex;
# 4. patchSynctex('main.Rnw');
# 5. patchSynctex('child.Rnw',syncfile='main');  
# All steps except 3. are R commands (note that the add-on R package "patchSynctex" 
# needs to be installed); 3. is an ordinary shell command.
#
# The configuration below handles both single-file and multiple-file projects (using
# the workflow described above).

# In the line below replace 'main.tex' with the name of the main *LaTeX* file. 
# This line is optional for single-file projects; using it means that latexmk 
# may be invoked without a filename, even if the file main.tex doesn't yet exist:
#
# $ latexmk
#
# If the line is not used, and the target LaTeX file does not yet exist, 
# its name must be supplied, e.g.:
#
# $ latexmk main
#
# It is compulsory for multiple file projects, so we avoid running pdflatex 
# on child documents.
@default_files=('main.tex');  

$pdf_mode=1;

# The definition of $pdflatex below runs pdflatex on the main LaTeX file
# and runs patchSynctex(...,syncfile='main') once for each .Rnw file appearing
# in the working directory:
$pdflatex = "pdflatex -interaction=nonstopmode -synctex=1 %O %B ;"
          . "Rscript -e \"library(patchSynctex); "
          . "Rnw.files=system(\\\"ls *.Rnw\\\",intern=T); "
          . "Rnw.stems=unlist(strsplit(Rnw.files,split=\\\".Rnw\\\")); "
          . "for (i in 1:length(Rnw.stems)) "
          . "patchSynctex(Rnw.stems[i],syncfile=\\\"%B\\\",verbose=T)\" " ;


# The remaining code defines a custom dependency to ensure that each LaTeX file
# is updated whenever the corresponding .Rnw file is updated. See below for how
# to adapt this for use with Sweave instead of knitr.
add_cus_dep( 'Rnw', 'tex', 0 , 'knit' ); 
sub knit {
	system( "Rscript -e \"library(knitr); "
              . "opts_knit\\\$set(concordance=T); "
              . "knitr::knit(\\\"$_[0].Rnw\\\",output=\\\"$_[0].tex\\\")\" " ); 
}

# For use with Sweave (rather than knitr) make the following adjustments:
#
# 1. Ensure that 
#
# \SweaveOpts{concordance=T}
#
# (possibly with other global options e.g. stylepath=T) appears near the top of each 
# .Rnw file *after* \begin{document} (at the time of writing there seems to be a bug 
# in Sweave() so that this is the only reliable way to pass the global 
# concordance=T option; neither Sweave(...,concordance=T) nor # the setting of the 
# SWEAVE_OPTIONS environment variable seems to work).
#
# 2. Replace the last 6 lines of code above this comment block with the commented-out 
# code below:
#
#add_cus_dep( 'Rnw', 'tex', 0, 'Sweave');
#sub Sweave {
#	system("Rscript -e \"Sweave(\\\"$_[0].Rnw\\\")\" ");
#}

# You will need to uncomment the two lines below if you are using this with a version
# of latexmk older than version 4.68:
#$force_mode=1;
#push @file_not_found, '^\\! I can\\\'t find file `([^\\\']*)\\\'\\.';