misc/build.R

In sahilseth/flowr: Streamlining Design and Deployment of Complex Workflows

#' ---
#' output: html_document
#' ---
#' 
#' Description:
#' This script is used by packagedocs.
#' After making a change to the vignettes in flowr, 
#' run this script to update the docs.
#' The last step is to commit the change to gh-pages branch.

#rmarkdown::render("~/Dropbox/public/github_flow/misc/build.R")

message("installing required packages....", getwd())
options(repos = c(CRAN = "http://cran.rstudio.com"))
if(!require(drat))
  install.packages("drat")

library(drat)
repo = addRepo("sahilseth")

#devtools::install_github("sahilseth/ngsflows")
if(!require(ultraseq))
  install.packages("ultraseq")
library(ultraseq)

library(staticdocs)
library(packagedocs)
require(flowr)
require(knitr)


if(Sys.info()['sysname'] == "Darwin"){
  outwd = "~/Dropbox/public/flow-r/flowrpages"
  code_path <- "~/Dropbox/public/github_flow"
}else{
  outwd = "gh-pages"
  code_path <- "../"
}

if(!file.exists(outwd))
  dir.create(outwd, recursive = TRUE)

## ---------------------------

## load packages (and install if not on system)
# if(!require("staticdocs"))
#   devtools::install_github("hadley/staticdocs")
# if(!require("packagedocs"))
#   devtools::install_github("hafen/packagedocs")
# if(!require("rmarkdown"))
#   install.packages("rmarkdown")
# if(!require("flowr"))
#   devtools::install_github("sahilseth/flowr")

library(staticdocs)
library(packagedocs)
library(flowr)
library(rmarkdown)

# make sure your working directory is set to repo base directory
setwd(outwd)
#setwd("~/Dropbox/public/github_flowrdocs2/flowr")

## this make file uses several files, from flowr folder
# ├── README.Rmd
# ├── NEWS.md
# ├── man/*Rd
# └── vignettes/build-pipes.Rmd

theme="flatly"
theme = list(htmltools::htmlDependency(name = "bootswatch",
                                       version = "3.3.5",
                                       src = "assets/bootswatch-3.3.5",
                                       #system.file("html_assets/bootswatch", theme, package = "packagedocs"),
                                       stylesheet = "bootstrap.css"))

# set some options
pd <- package_docs(lib_dir = "assets", toc = FALSE, template = "template.html", extra_dependencies = theme)
pd_collapsed <- package_docs(lib_dir = "assets", toc_collapse = TRUE, template = "template.html", extra_dependencies = theme)
pd_expand <- package_docs(lib_dir = "assets", toc_collapse = FALSE, toc_depth = 2, template = "template.html", extra_dependencies = theme)
knitr::opts_knit$set(root.dir = normalizePath("."))

# generate index.html, get new from template.
#unlink("assets", recursive = TRUE)

message("Copying RMD files ....", getwd())
fls = c(
  #  "README.Rmd" = "index.Rmd",
  "NEWS.md" = "news.Rmd",
  "vignettes/flowr_overview.Rmd" = "overview.Rmd",
  "vignettes/flowr_install.Rmd" = "install.Rmd",
  "vignettes/flowr_tutorial.Rmd" = "tutorial.Rmd"
)

unlink(fls)
file.copy(from = file.path(code_path, names(fls)), to = fls)
dir.create("files", showWarnings = FALSE)
file.copy(file.path(code_path, "vignettes/files"), to = ".", recursive = TRUE)

message("rendering RMD files ....", getwd())

#undebug(rmarkdown:::html_extras_for_document)
render("index.Rmd", output_format = pd)
check_output("index.html"); #system("open index.html")
render("overview.Rmd", output_format = pd_expand)
check_output("overview.html")
render("tutorial.Rmd", output_format = pd_expand)
check_output("tutorial.html")
render("news.Rmd", output_format = pd_expand)
check_output("news.html")
render("install.Rmd", output_format = pd_expand)
check_output("install.html")

message("rendering RD files ....", getwd())
if(!file.exists(file.path(code_path, "inst/staticdocs")))
  dir.create(file.path(code_path, "inst/staticdocs"))
#devtools::load_all("~/Dropbox/public/github_packagedocs/")
#debug(packagedocs:::get_rd_data)
#debug(rd_template)
#undebug(staticdocs:::to_html.Rd_content)
#debug(staticdocs:::to_html.Rd_doc)
render_rd("rd_skeleton.Rmd", "flowr", code_path,
          rd_index = "rd_index.yaml", output_format = pd_expand)
check_output("rd.html")

# create pdf manual
#render("flowr_manual.Rmd")



## stuff for MAC ONLY
if(Sys.info()['sysname'] == "Darwin"){
  system("open index.html")
  setwd("~/Dropbox/public/flow-r/flowrpages")
  system("rm flowr_pkg_ref.pdf;R CMD Rd2pdf --no-preview -o flowr_pkg_ref.pdf ~/Dropbox/public/github_flow")
  system("git commit -a -m 'update website'")
  system("git push")
}

## ---- create a PDF manual as well
if(FALSE){
  #setwd("~/Dropbox/public/github_flowrpages/flowr")
  rd = "../../github_flow/man/to_flow.Rd"
  require(tools)
  Rd2latex(rd, out = "rd/to_flow.tex")
  library(pander)
  system("pandoc -f html -t markdown rd.html > rd2.md")
  render("pdf.Rmd", pdf_document())
}


# copy the PDFs to github, to make them easier to see:
file.copy(c("flowr_manual.pdf", "flowr_pkg_ref.pdf"), code_path, overwrite = TRUE)
setwd(code_path)