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buildRef.R
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## install packages required to build the docs
#install.packages("devtools")
#library(devtools)
#install_github("staticdocs", "hadley")
#install_github("buildDocs", "hafen")
## load the pacakge
library(buildDocs)
my.buildref <- function (docsLoc, outLoc = NULL, pageList = NULL, navPill = "",
editHref = "", copyrightText, windowTitle = NULL, root.dir = NULL,
knit = TRUE, purl = TRUE)
{
if (is.null(outLoc))
outLoc <- docsLoc
outFigLoc <- file.path(outLoc, "figures", "knitr/")
if (!file.exists(outFigLoc))
dir.create(outFigLoc, recursive = TRUE)
outCacheLoc <- file.path(outLoc, "cache/")
if (!file.exists(outCacheLoc))
dir.create(outCacheLoc, recursive = TRUE)
opts_knit$set(base.dir = outLoc)
opts_chunk$set(comment = NA, tidy = FALSE, dpi = 150, base.dir = outLoc,
fig.path = "figures/knitr/", cache.path = outCacheLoc)
if (!is.null(root.dir))
opts_knit$set(root.dir = normalizePath(root.dir))
if (!file.exists(file.path(outLoc, "markdown")))
dir.create(file.path(outLoc, "markdown"))
if (!file.exists(file.path(outLoc, "code")))
dir.create(file.path(outLoc, "code"))
ff <- list.files(docsLoc, full.names = TRUE, pattern = "\\.Rmd$",
recursive = TRUE)
ff2 <- list.files(docsLoc, pattern = "\\.Rmd$", recursive = TRUE)
if (!is.null(pageList)) {
ff <- ff[ff2 %in% pageList]
}
else {
pageList <- ff2
}
for (.file in ff) {
ll <- readLines(.file)
if (grepl("^\\`\\`\\`$", ll[1]))
ll <- ll[-1]
f2 <- textConnection(paste(ll, collapse = "\n"))
if (purl)
purl(f2, output = file.path(outLoc, "code", gsub("\\.Rmd",
".R", basename(.file))), documentation = 0)
f2 <- textConnection(paste(ll, collapse = "\n"))
if (knit)
knit(f2, output = file.path(outLoc, "markdown", gsub("\\.Rmd",
".md", basename(.file))))
}
ff <- list.files(file.path(outLoc, "markdown"))
if (length(ff) == 0)
stop("There were no markdown files")
ff <- ff[gsub("md$", "Rmd", basename(ff)) %in% basename(pageList)]
aList <- suppressWarnings(lapply(file.path(outLoc, "markdown",
ff), readLines))
a <- do.call(c, aList)
aFileIdx <- do.call(c, lapply(seq_along(aList), function(x) rep(x,
length(aList[[x]]))))
if (grepl("^\\`\\`\\`$", a[1]))
a <- a[-1]
knitrProblemInd <- which(grepl("\\\\```", a))
if (length(knitrProblemInd) > 0) {
a[knitrProblemInd] <- gsub("(.*)\\\\(```.*)", "\\1\\2",
a[knitrProblemInd])
}
titleInd <- which(grepl("^# (.*) #$", a))
if (length(titleInd) == 0) {
pageTitle <- "No Title"
}
else {
pageTitle <- gsub("^# (.*) #$", "\\1", a[titleInd])
}
if (is.null(windowTitle))
windowTitle <- pageTitle
a <- a[-titleInd]
aFileIdx <- aFileIdx[-titleInd]
chInd <- which(grepl("^## (.*) ##$", a))
chNames <- gsub("^## (.*) ##$", "\\1", a[chInd])
chFiles <- ff[aFileIdx[chInd]]
chFiles <- gsub("\\.md$", ".Rmd", chFiles)
if (is.null(editHref)) {
chFileEditLink <- "#"
}
else {
chFileEditLink <- paste(editHref, chFiles, sep = "")
}
a[chInd] <- ""
chStart <- chInd
chEnd <- c(chStart[-1] - 1, length(a))
toc <- list()
contents <- list()
c_ind <- 1
firstSection <- ""
for (i in seq_along(chStart)) {
b <- a[chStart[i]:chEnd[i]]
secInd <- which(grepl("^### (.*) ###$", b))
secNames <- gsub("^### (.*) ###$", "\\1", b[secInd])
secID <- buildDocs:::validID(secNames)
tmp <- paste(sprintf("\n <li class='active'>\n <a target='_self' class='nav-not-header' href='#%s'>%s</a>\n </li>\n",
secID, secNames), collapse = "\n")
toc[[i]] <- sprintf("<li class='nav-header unselectable' data-edit-href='%s'>%s</li>\n %s",
chFileEditLink[i], chNames[i], tmp)
secStart <- secInd
secEnd <- c(secInd[-1] - 1, length(b))
for (j in seq_along(secInd)) {
if (c_ind == 1)
firstSection <- secID[j]
contents[[c_ind]] <- paste("<div class='tab-pane",
ifelse(c_ind == 1, " active", ""), "' id='",
secID[j], "'>\n", markdownToHTML(text = paste(b[secStart[j]:secEnd[j]],
collapse = "\n"), options = "fragment_only"),
"\n</div>\n", sep = "")
c_ind <- c_ind + 1
}
}
toc <- paste(toc, collapse = "\n\n")
contents <- paste(contents, collapse = "\n\n")
if (!"package:buildDocs" %in% search()) {
message("* ---- running dev version - getting templates from source")
templatePath <- "~/Documents/Code/buildDocs/inst/templates"
assetsLoc <- "~/Documents/Code/buildDocs/inst/assets"
}
else {
templatePath <- file.path(system.file(package = "buildDocs"),
"templates")
assetsLoc <- file.path(system.file(package = "buildDocs"),
"assets")
}
extraHeader <- "<script type=\"text/javascript\" src=\"assets/MathJax/MathJax.js?config=TeX-AMS-MML_HTMLorMML\">\n MathJax.Hub.Config({ \n extensions: [\"tex2jax.js\"], \n \"HTML-CSS\": { scale: 100} \n });\n </script>"
ll <- list(title = windowTitle, extra_css = "", navpills = navPill,
header = pageTitle, side_span = "3", main_span = "9",
toc = toc, content = contents, copyright = paste(copyrightText,
", ", format(Sys.time(), "%Y"), sep = ""), first_section = firstSection,
extra_header = extraHeader)
pageTemplate <- readLines(file.path(templatePath, "page_template.html"))
b <- whisker.render(pageTemplate, ll)
if (!file.exists(outLoc))
dir.create(outLoc, recursive = TRUE)
cat(b, file = file.path(outLoc, "functionref.html")) ##original is index.html
digestMatch <- function(dirName, outLoc, assetsLoc) {
d1 <- digest(as.character(md5sum(list.files(file.path(assetsLoc,
dirName), recursive = TRUE, full.names = TRUE))))
d2 <- digest(as.character(md5sum(list.files(file.path(outAssetsLoc,
dirName), recursive = TRUE, full.names = TRUE))))
d1 == d2
}
outAssetsLoc <- file.path(outLoc, "assets")
if (!file.exists(outAssetsLoc))
dir.create(outAssetsLoc)
for (dirName in c("bootstrap", "custom", "font-awesome",
"jquery", "MathJax", "prism", "svgeezy")) {
if (!digestMatch(dirName, outAssetsLoc, assetsLoc)) {
message("copying ", dirName)
file.copy(file.path(assetsLoc, dirName), normalizePath(outAssetsLoc),
overwrite = TRUE, recursive = TRUE)
}
}
}
my.buildref(
docsLoc = "./ref",
outLoc = ".",
copyrightText = NULL,
# pageList = c("01.intro.Rmd", "02.wordcount.Rmd"),
navPill = packageNavPill("https://github.com/delta-rho/RHIPE", docsActive = FALSE),
# editHref = "https://github.com/user/project/edit/gh-pages/docs/",
knit = TRUE,
purl = FALSE
)