R/processTex.R
In vladchimescu/RdocsJupyter: Conversion of Rmd, knitr and Sweave docs into Jupyter notebook format
process.tex <- function(filename) {
replace.environment(filename)
replace.macros(filename)
remove.figures(filename)
} ## end process.tex()
knit.vignette <- function(filename) {
## works for now but this is dangerous...
opts_chunk$set(eval = TRUE)
## Also need to catch that warning from knitr (twice)
suppressWarnings(knit(filename))
opts_chunk$set(results = "hide", highlight = FALSE, eval = FALSE)
suppressWarnings(knit(filename))
if(dirname(filename) != ".") {
system2('mv', paste(getwd(), '/',
sub("^([^.]*).*", "\\1", basename(filename)),
".tex ", dirname(filename), "/", sep = ""))
} ## end if(dirname(filename != "."))
} ## end knit.vignette()
sweave.vignette <- function(filename) {
## not sure if it's such a good idea to use try on Sweave...
options(prompt=" ", continue=" ")
try(Sweave(filename, eval = TRUE))
try(Sweave(filename, eval = FALSE))
if(dirname(filename) != ".") {
system2('mv', paste(getwd(), '/',
sub("^([^.]*).*", "\\1", basename(filename)),
".tex ", dirname(filename), "/", sep = ""))
} ## end if(dirname(filename) != ".")
## this is dangerous...
options(prompt = "> ", continue = "+ ")
} ## end sweave.vignette
render.markdown <- function(filename) {
opts_chunk$set(results = "hide", fig.show = "hide")
render(filename, md_document(variant = "markdown_github+tex_math_dollars"))
} ## end render.markdown
#' @title Extract figure parameters from code chunks.
#' @description \code{extract.fig.params} extracts figure width and height from
#' code chunks
#' @param filename File name of the vignette. Absolute path has to be prepended
#' if the document is not in R working directory
#' @param type Vignette type. Valid values are "Rmd" for R markdown and "Rnw"
#' for Sweave and knitr vignette
#' @details The function extracts figure parameters from code chunks and
#' places these figure options right before the code chunk, from which the
#' figure dimensions were read out.
#' \cr\cr Suppose, there is a code chunk
#' in which a figure is plotted and the figure's width and height are set as follows:
#' \cr\cr\code{<<someplot, fig.width=6, fig.height=4.5>>=\cr
#' plot(x, f(x))\cr
#' @@ }
#' \cr\cr The function \code{extract.fig.params} would extract width and height
#' and pass them to \code{set_plot_options} function from package \pkg{IRkernel}.
#' Thus the former code chunk will be preceded by the following : \cr\cr
#' \code{<<>>=\cr
#' IRkernel::set_plot_options(width = 6, height = 4.5)\cr
#' @@}
#' \cr\cr The purpose of this code chunk is to make sure the aspect ratio of the
#' figure is communicated to Jupyter Notebook via R kernel (\pkg{IRkernel})
extract.fig.params <- function(filename, type) {
if(type == "Rmd") {
if (length(grep("IRkernel", readLines(filename), fixed = TRUE)) == 0) {
text <- gsub("(^[\t >]*```+\\s*\\{[.]?)([a-zA-Z]+.*)(fig+.*)\\}\\s*$",
"IRkernel::set_plot_options\\(\\2\\3\\)\n\\1\\2\\3\\}",
readLines(filename))
text <- gsub("(IRkernel::set_plot_options\\()([a-zA-Z]+.*)(width+.*|height+.*)fig.(height+.*|width+.*)\\)",
"```{r, eval=FALSE}\n\\1\\3\\4\\)\n```", text)
writeLines(text, con = filename, sep = "\n")
} ## end if (length(...))
} ## end if (type == "Rmd")
else {
if (length(grep("IRkernel", readLines(filename), fixed = TRUE)) == 0) {
text <- gsub("(^\\s*<<)(.*)(fig+.*)>>=.*$",
"IRkernel::set_plot_options\\(\\2\\3\\)\n\\1\\2\\3>>=",
readLines(filename))
text <- gsub("(IRkernel::set_plot_options\\()([a-zA-Z]+.*)(width+.*|height+.*)fig.(height+.*|width+.*)\\)",
"<<\\3\\4>>=\n\\1\\3\\4\\)\n@", text)
writeLines(text, con = filename, sep = "\n")
} ## end if(length...)
} ## end else
} ## end extract.fig.params() function
run.notedown <- function(filename) {
## check if notedown is installed
notedown.installed <- system2('notedown', '--version', stdout = FALSE)==0
if(notedown.installed) {
if (dirname(filename) == ".") {
out_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1",
basename(filename)), ".md", sep = "")
}
else {
out_name <- paste(dirname(filename), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)),
".md", sep = "")
}
## also test if system(...) command was successful and if yes
## print a message(): created a file dirname/file.ipynb
if(system2('notedown', paste('-o ', out_name, '.ipynb --nomagic ',
in_name, sep = "")) == 0)
if(dirname(filename) == ".") {
message(paste("Wrote ", basename(out_name), ".ipynb in ", getwd(), sep = ""))
}
else {
message(paste("Wrote ", basename(out_name), ".ipynb in ", dirname(filename), sep = ""))
} ## end else (dirname != ".")
else {
message("Error: notedown exited with non-zero status")
} ## end else (notedown not successful)
vignette <- paste(out_name, ".ipynb", sep = "")
# produce Dockerfile and packages.R script
produce.dockerfile(vignette)
if(dirname(filename) == ".") {
message(paste("Produced Dockerfile and packages.R in", getwd()))
}
else {
message(paste("Produced Dockerfile and packages.R in", dirname(filename)))
}
} ## end if(notedown.status)
else {
message("notedown executable not found.\n You need notedown utility for md -> ipynb conversion")
} ## end else ...
} ## end run.notedown() function
run.pandoc <- function(filename) {
pandoc.installed <- system2('pandoc', '--version', stdout = FALSE) == 0
if(pandoc.installed) {
if (dirname(filename) == ".") {
in_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1",
basename(filename)), ".tex", sep = "")
out_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
}
else {
out_name <- paste(dirname(filename), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)),
".tex", sep = "")
}
if(system2('pandoc', paste(' -s --toc --to=markdown_github+tex_math_dollars ',
in_name, ' -o ',
out_name, '.md', sep = "")) == 0)
if(dirname(filename) == ".") {
message(paste("Wrote ", basename(out_name), ".md in ", getwd(), sep = ""))
}
else {
message(paste("Wrote ", basename(out_name), ".md in ", dirname(filename), sep = ""))
}
else {
message("Error: pandoc exited with non-zero status")
}
} ## end if (pandoc.installed)
else {
message("pandoc executable not found. For TeX -> Md conversion pandoc has to be installed!")
} ## end else (!pandoc.installed)
} ## end run.pandoc() function
#' @title Convert vignettes into Jupyter notebooks.
#' @description \code{process.vignette} converts R markdown, Sweave and knitr vignettes
#' into Jupyter notebook format and automatically produces a Dockerfile for running
#' the notebook in Docker virtual environment.
#' @param filename File name of the R documentation (.Rmd or .Rnw) to be converted.
#' Absolute path has to be prepended if the file is not in the working directory.
#' The file extension must be included in the file name.
#' @details The function expects as input the file name of the .Rmd or .Rnw documentation
#' that needs to be converted to Jupyter notebook format. Absolute path has to be prepended
#' if the file is not in the working directory.
#' The file extension must be included in the file name.
#' \cr\cr R markdown (.Rmd) vignettes are first rendered to Markdown Github and
#' subsequently converted with the \strong{notedown}
#' command line utility to .ipynb format.
#' The produced Jupyter notebook is scanned for dependencies using \code{get.dependencies}
#' function and an R script \emph{packages.R} is produced. \emph{packages.R} and the
#' Jupyter notebook are used to make a Docker image for the vignette.
#' \cr\cr Note, however, that the Docker image has to be built first from the produced
#' Dockerfile. All generated files, i.e. Jupyter notebook, packages.R and Dockerfile
#' are written in the \strong{same} directory where the input file is located.
#' In order to build a Docker image for running the vignette you don't need
#' IPython Notebook installed on your machine. If you installed Docker,
#' simply run in command line \cr\cr
#' \code{$ docker build -t imagename .}
#' \cr\cr in the same directory as the Dockerfile. After building the Docker image for
#' your Jupyter notebook, check the operating system-specific commands for running
#' Jupyter notebooks in Docker containers on the following
#' web page \url{https://hub.docker.com/r/vladkim/rnaseq/}
#' \cr\cr Similarly, Sweave and knitr vignettes are compiled to a TeX file, which
#' is in turn converted to Markdown with \strong{pandoc}. The remaining processing
#' steps are identical to those for R markdown vignettes.
process.vignette <- function(filename) {
if(file_ext(filename) == "Rmd") {
## extract figure parameters from code chunks
extract.fig.params(filename, "Rmd")
## render Markdown file
render.markdown(filename)
## use notedown utility to convert the md file to ipynb
run.notedown(filename)
} ## end if (Rmd)
else if(file_ext(filename) == "Rnw") {
extract.fig.params(filename, "Rnw")
## here process Sweave and knitr vignettes separately
repeat {
vignette_type <- readline("Is this a knitr or Sweave vignette? \nknitr --- enter 1\nSweave --- enter 2\n ")
if(vignette_type == 1 || vignette_type == 2) {
break
}
message("Please enter 1 or 2 to choose knitr or Sweave!")
} ## end repeat
if(as.character(vignette_type) == 1) {
knit.vignette(filename)
} ## end if (knitr)
else if(as.character(vignette_type) == 2) {
## Sweave the vignette
sweave.vignette(filename)
} ## end else if (Sweave)
## after generating a TeX file, process it
process.tex(paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)), ".tex", sep = ""))
run.pandoc(filename)
## right now this is not strictly speaking right
run.notedown(filename)
} ## end else if (Rnw)
else {
message("Only Rmd and Rnw formats are supported!")
} ## end else (if !"Rmd" && !"Rnw")
} ## end process.vignette()
vladchimescu/RdocsJupyter documentation built on May 3, 2019, 6:15 p.m.
R Package Documentation
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process.tex <- function(filename) {
replace.environment(filename)
replace.macros(filename)
remove.figures(filename)
} ## end process.tex()
knit.vignette <- function(filename) {
## works for now but this is dangerous...
opts_chunk$set(eval = TRUE)
## Also need to catch that warning from knitr (twice)
suppressWarnings(knit(filename))
opts_chunk$set(results = "hide", highlight = FALSE, eval = FALSE)
suppressWarnings(knit(filename))
if(dirname(filename) != ".") {
system2('mv', paste(getwd(), '/',
sub("^([^.]*).*", "\\1", basename(filename)),
".tex ", dirname(filename), "/", sep = ""))
} ## end if(dirname(filename != "."))
} ## end knit.vignette()
sweave.vignette <- function(filename) {
## not sure if it's such a good idea to use try on Sweave...
options(prompt=" ", continue=" ")
try(Sweave(filename, eval = TRUE))
try(Sweave(filename, eval = FALSE))
if(dirname(filename) != ".") {
system2('mv', paste(getwd(), '/',
sub("^([^.]*).*", "\\1", basename(filename)),
".tex ", dirname(filename), "/", sep = ""))
} ## end if(dirname(filename) != ".")
## this is dangerous...
options(prompt = "> ", continue = "+ ")
} ## end sweave.vignette
render.markdown <- function(filename) {
opts_chunk$set(results = "hide", fig.show = "hide")
render(filename, md_document(variant = "markdown_github+tex_math_dollars"))
} ## end render.markdown
#' @title Extract figure parameters from code chunks.
#' @description \code{extract.fig.params} extracts figure width and height from
#' code chunks
#' @param filename File name of the vignette. Absolute path has to be prepended
#' if the document is not in R working directory
#' @param type Vignette type. Valid values are "Rmd" for R markdown and "Rnw"
#' for Sweave and knitr vignette
#' @details The function extracts figure parameters from code chunks and
#' places these figure options right before the code chunk, from which the
#' figure dimensions were read out.
#' \cr\cr Suppose, there is a code chunk
#' in which a figure is plotted and the figure's width and height are set as follows:
#' \cr\cr\code{<<someplot, fig.width=6, fig.height=4.5>>=\cr
#' plot(x, f(x))\cr
#' @@ }
#' \cr\cr The function \code{extract.fig.params} would extract width and height
#' and pass them to \code{set_plot_options} function from package \pkg{IRkernel}.
#' Thus the former code chunk will be preceded by the following : \cr\cr
#' \code{<<>>=\cr
#' IRkernel::set_plot_options(width = 6, height = 4.5)\cr
#' @@}
#' \cr\cr The purpose of this code chunk is to make sure the aspect ratio of the
#' figure is communicated to Jupyter Notebook via R kernel (\pkg{IRkernel})
extract.fig.params <- function(filename, type) {
if(type == "Rmd") {
if (length(grep("IRkernel", readLines(filename), fixed = TRUE)) == 0) {
text <- gsub("(^[\t >]*```+\\s*\\{[.]?)([a-zA-Z]+.*)(fig+.*)\\}\\s*$",
"IRkernel::set_plot_options\\(\\2\\3\\)\n\\1\\2\\3\\}",
readLines(filename))
text <- gsub("(IRkernel::set_plot_options\\()([a-zA-Z]+.*)(width+.*|height+.*)fig.(height+.*|width+.*)\\)",
"```{r, eval=FALSE}\n\\1\\3\\4\\)\n```", text)
writeLines(text, con = filename, sep = "\n")
} ## end if (length(...))
} ## end if (type == "Rmd")
else {
if (length(grep("IRkernel", readLines(filename), fixed = TRUE)) == 0) {
text <- gsub("(^\\s*<<)(.*)(fig+.*)>>=.*$",
"IRkernel::set_plot_options\\(\\2\\3\\)\n\\1\\2\\3>>=",
readLines(filename))
text <- gsub("(IRkernel::set_plot_options\\()([a-zA-Z]+.*)(width+.*|height+.*)fig.(height+.*|width+.*)\\)",
"<<\\3\\4>>=\n\\1\\3\\4\\)\n@", text)
writeLines(text, con = filename, sep = "\n")
} ## end if(length...)
} ## end else
} ## end extract.fig.params() function
run.notedown <- function(filename) {
## check if notedown is installed
notedown.installed <- system2('notedown', '--version', stdout = FALSE)==0
if(notedown.installed) {
if (dirname(filename) == ".") {
out_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1",
basename(filename)), ".md", sep = "")
}
else {
out_name <- paste(dirname(filename), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)),
".md", sep = "")
}
## also test if system(...) command was successful and if yes
## print a message(): created a file dirname/file.ipynb
if(system2('notedown', paste('-o ', out_name, '.ipynb --nomagic ',
in_name, sep = "")) == 0)
if(dirname(filename) == ".") {
message(paste("Wrote ", basename(out_name), ".ipynb in ", getwd(), sep = ""))
}
else {
message(paste("Wrote ", basename(out_name), ".ipynb in ", dirname(filename), sep = ""))
} ## end else (dirname != ".")
else {
message("Error: notedown exited with non-zero status")
} ## end else (notedown not successful)
vignette <- paste(out_name, ".ipynb", sep = "")
# produce Dockerfile and packages.R script
produce.dockerfile(vignette)
if(dirname(filename) == ".") {
message(paste("Produced Dockerfile and packages.R in", getwd()))
}
else {
message(paste("Produced Dockerfile and packages.R in", dirname(filename)))
}
} ## end if(notedown.status)
else {
message("notedown executable not found.\n You need notedown utility for md -> ipynb conversion")
} ## end else ...
} ## end run.notedown() function
run.pandoc <- function(filename) {
pandoc.installed <- system2('pandoc', '--version', stdout = FALSE) == 0
if(pandoc.installed) {
if (dirname(filename) == ".") {
in_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1",
basename(filename)), ".tex", sep = "")
out_name <- paste(getwd(), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
}
else {
out_name <- paste(dirname(filename), "/", sub("^([^.]*).*", "\\1", basename(filename)),
sep = "")
in_name <- paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)),
".tex", sep = "")
}
if(system2('pandoc', paste(' -s --toc --to=markdown_github+tex_math_dollars ',
in_name, ' -o ',
out_name, '.md', sep = "")) == 0)
if(dirname(filename) == ".") {
message(paste("Wrote ", basename(out_name), ".md in ", getwd(), sep = ""))
}
else {
message(paste("Wrote ", basename(out_name), ".md in ", dirname(filename), sep = ""))
}
else {
message("Error: pandoc exited with non-zero status")
}
} ## end if (pandoc.installed)
else {
message("pandoc executable not found. For TeX -> Md conversion pandoc has to be installed!")
} ## end else (!pandoc.installed)
} ## end run.pandoc() function
#' @title Convert vignettes into Jupyter notebooks.
#' @description \code{process.vignette} converts R markdown, Sweave and knitr vignettes
#' into Jupyter notebook format and automatically produces a Dockerfile for running
#' the notebook in Docker virtual environment.
#' @param filename File name of the R documentation (.Rmd or .Rnw) to be converted.
#' Absolute path has to be prepended if the file is not in the working directory.
#' The file extension must be included in the file name.
#' @details The function expects as input the file name of the .Rmd or .Rnw documentation
#' that needs to be converted to Jupyter notebook format. Absolute path has to be prepended
#' if the file is not in the working directory.
#' The file extension must be included in the file name.
#' \cr\cr R markdown (.Rmd) vignettes are first rendered to Markdown Github and
#' subsequently converted with the \strong{notedown}
#' command line utility to .ipynb format.
#' The produced Jupyter notebook is scanned for dependencies using \code{get.dependencies}
#' function and an R script \emph{packages.R} is produced. \emph{packages.R} and the
#' Jupyter notebook are used to make a Docker image for the vignette.
#' \cr\cr Note, however, that the Docker image has to be built first from the produced
#' Dockerfile. All generated files, i.e. Jupyter notebook, packages.R and Dockerfile
#' are written in the \strong{same} directory where the input file is located.
#' In order to build a Docker image for running the vignette you don't need
#' IPython Notebook installed on your machine. If you installed Docker,
#' simply run in command line \cr\cr
#' \code{$ docker build -t imagename .}
#' \cr\cr in the same directory as the Dockerfile. After building the Docker image for
#' your Jupyter notebook, check the operating system-specific commands for running
#' Jupyter notebooks in Docker containers on the following
#' web page \url{https://hub.docker.com/r/vladkim/rnaseq/}
#' \cr\cr Similarly, Sweave and knitr vignettes are compiled to a TeX file, which
#' is in turn converted to Markdown with \strong{pandoc}. The remaining processing
#' steps are identical to those for R markdown vignettes.
process.vignette <- function(filename) {
if(file_ext(filename) == "Rmd") {
## extract figure parameters from code chunks
extract.fig.params(filename, "Rmd")
## render Markdown file
render.markdown(filename)
## use notedown utility to convert the md file to ipynb
run.notedown(filename)
} ## end if (Rmd)
else if(file_ext(filename) == "Rnw") {
extract.fig.params(filename, "Rnw")
## here process Sweave and knitr vignettes separately
repeat {
vignette_type <- readline("Is this a knitr or Sweave vignette? \nknitr --- enter 1\nSweave --- enter 2\n ")
if(vignette_type == 1 || vignette_type == 2) {
break
}
message("Please enter 1 or 2 to choose knitr or Sweave!")
} ## end repeat
if(as.character(vignette_type) == 1) {
knit.vignette(filename)
} ## end if (knitr)
else if(as.character(vignette_type) == 2) {
## Sweave the vignette
sweave.vignette(filename)
} ## end else if (Sweave)
## after generating a TeX file, process it
process.tex(paste(dirname(filename), "/",
sub("^([^.]*).*", "\\1", basename(filename)), ".tex", sep = ""))
run.pandoc(filename)
## right now this is not strictly speaking right
run.notedown(filename)
} ## end else if (Rnw)
else {
message("Only Rmd and Rnw formats are supported!")
} ## end else (if !"Rmd" && !"Rnw")
} ## end process.vignette()
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