## ----echo = FALSE, message = FALSE--------------------------------------------
library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    comment = NA,
    fig.align = "center")
library(GetoptLong)

## ----echo = FALSE, out.width = "600px"----------------------------------------
include_graphics("workflow.png")

## ----simple, eval = FALSE-----------------------------------------------------
# library(GetoptLong)
# 
# cutoff = 0.05
# GetoptLong(
#     "number=i", "Number of items.",
#     "cutoff=f", "Cutoff for filtering results.",
#     "verbose",  "Print message."
# )

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["simple"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
GetoptLong.options("help_style" = "two-column")
local({ eval(parse(text = chunks[["simple"]])) })
GetoptLong.options("__argv_str__" = NULL)
GetoptLong.options("help_style" = "one-column")

## ----template, eval = FALSE---------------------------------------------------
# spec = "
# This is an example of using template to specify options.
# 
# Usage: Rscript foo.R [options]
# 
# Options:
#   <number=i> Number of items.
#   <cutoff=f> Cutoff for filtering results.
#   <verbose> Print messages.
# 
# Contact: name@address
# "
# 
# GetoptLong(spec, template_control = list(opt_width = 21))

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["template"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----print_var, eval = FALSE--------------------------------------------------
# library(GetoptLong)
# 
# cutoff = 0.05
# GetoptLong(
#     "number=i{1,}", "Number of items.",
#     "cutoff=f", "Cutoff for filtering results.",
#     "param=s%", "Parameters specified by name=value pairs.",
#     "verbose",  "Print message."
# )
# 
# print(number)
# print(cutoff)
# print(param)
# print(verbose)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--number 1 2 --param var1=a var2=b --verbose")
local({ eval(parse(text = chunks[["print_var"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----eval = FALSE-------------------------------------------------------------
# verbose = TRUE
# GetoptLong(
#     "verbose!",  "Print message."
# )

## ----with_env, eval = FALSE---------------------------------------------------
# opt = new.env()
# 
# opt$cutoff = 0.05
# GetoptLong(
#     "number=i@", "Number of items.",
#     "cutoff=f", "Cutoff for filtering results.",
#     "param=s%", "Parameters specified by name=value pairs.",
#     "verbose",  "Print message.",
# 
#     envir = opt
# )
# print(as.list(opt))

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--number 1 2 --param var1=a var2=b --verbose")
local({ eval(parse(text = chunks[["with_env"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----multi_word, eval = FALSE-------------------------------------------------
# # or a default can be set for `bar_value`
# # bar_value = 2
# GetoptLong(
#     "bar_value=i", "Some value."
# )
# print(bar_value)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--bar-value 1")
local({ eval(parse(text = chunks[["multi_word"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----multi_word_logical, eval = FALSE-----------------------------------------
# GetoptLong(
#     "show_messages!", "Whether to show messages?"
# )
# print(show_messages)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--show-messages")
local({ eval(parse(text = chunks[["multi_word_logical"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--no-show-messages")
local({ eval(parse(text = chunks[["multi_word_logical"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----complex_example, eval = FALSE--------------------------------------------
# GetoptLong(
#     "count=i",  paste("This is a count. This is a count. This is a count.",
#                       "This is a count.  This is a count. This is a count."),
#     "number=f", paste("This is a number. This is a number. This is a number.",
#                       "This is a number. This is a number. This is a number."),
#     "array=f@", paste("This is an array. This is an array. This is an array.",
#                       "This is an array. This is an array. This is an array."),
#     "hash=s%",  paste("This is a hash. This is a hash. This is a hash.",
#                       "This is a hash. This is a hash. This is a hash."),
#     "verbose!", "Whether show messages",
#     "flag",     "a non-sense option"
# )

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["complex_example"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ count = 1
    number = 0.1
    array = c(1, 2)
    hash = list("foo" = "a", "bar" = "b")
    verbose = TRUE
    eval(parse(text = chunks[["complex_example"]])) 
})
GetoptLong.options("__argv_str__" = NULL)

## ----eval = FALSE-------------------------------------------------------------
# GetoptLong.options(help_style = "two-column")
# # specifying the defaults
# GetoptLong{
#     ...
# }

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
GetoptLong.options("help_style" = "two-column")
local({ count = 1
    number = 0.1
    array = c(1, 2)
    hash = list("foo" = "a", "bar" = "b")
    verbose = TRUE
    eval(parse(text = chunks[["complex_example"]])) 
})
GetoptLong.options("__argv_str__" = NULL)
GetoptLong.options("help_style" = "one-column")

## ----sub_opt, eval = FALSE----------------------------------------------------
# foo = list(a = 1, b = 2)
# GetoptLong(
#     "foo=i%", paste("This is foo. This is foo. This is foo. This is foo.",
#                     "This is foo. This is foo. This is foo. This is foo."),
#     "foo$name1", paste("name1 in foo. name1 in foo. name1 in foo. name1 in foo.",
#                        "name1 in foo. name1 in foo. name1 in foo. name1 in foo."),
#     "foo$name2", paste("name2 in foo. name2 in foo. name2 in foo. name2 in foo.",
#                        "name2 in foo. name2 in foo. name2 in foo. name2 in foo."),
#     "bar=s%", paste("This is bar. This is bar. This is bar. This is bar.",
#                     "This is bar. This is bar. This is bar. This is bar."),
#     "bar$name3", paste("name3 in bar. name3 in bar. name3 in bar. name3 in bar.",
#                        "name3 in bar. name3 in bar. name3 in bar. name3 in bar."),
#     "bar$name4", paste("name4 in bar. name4 in bar. name4 in bar. name4 in bar.",
#                        "name4 in bar. name4 in bar. name4 in bar. name4 in bar.")
# )

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["sub_opt"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----eval = FALSE-------------------------------------------------------------
# GetoptLong.options(help_style = "two-column")
# GetoptLong{
#     ...
# }

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
GetoptLong.options(help_style = "two-column")
local({ eval(parse(text = chunks[["sub_opt"]])) })
GetoptLong.options("__argv_str__" = NULL)
GetoptLong.options(help_style = "one-column")

## ----head_and_foot, eval = FALSE----------------------------------------------
# GetoptLong(
#     help_head = "This is a demonstration of adding usage head and foot.",
# 
#     "number=i", "Number of items.",
#     "cutoff=f", "Cutoff for filtering results.",
#     "verbose",  "Print message.",
# 
#     help_foot = "Please contact name@address."
# )

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["head_and_foot"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----grouped_options, eval = FALSE--------------------------------------------
# count = 1
# array = c(0.1, 0.2)
# GetoptLong(
#     "--------", "Binary options:",
#     "verbose!", "Whether show messages",
#     "flag",     "a non-sense option",
# 
#     "-------", "Single-value options:",
#     "count=i",  paste("This is a count. This is a count. This is a count.",
#                       "This is a count.  This is a count. This is a count."),
#     "number=f", paste("This is a number. This is a number. This is a number.",
#                       "This is a number. This is a number. This is a number."),
# 
#     "--------", paste("Multiple-vlaue options: long text long text long text",
#                       " long text long text long text long text long text"),
#     "array=f@", paste("This is an array. This is an array. This is an array.",
#                       "This is an array. This is an array. This is an array."),
#     "hash=s%",  paste("This is a hash. This is a hash. This is a hash.",
#                       "This is a hash. This is a hash. This is a hash."),
# 
#     "-------", "Other options:"
# )

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["grouped_options"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----eval = FALSE-------------------------------------------------------------
# GetoptLong.options(help_style = "two-column")
# GetoptLong{
#     ...
# }

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
GetoptLong.options(help_style = "two-column")
local({ eval(parse(text = chunks[["grouped_options"]])) })
GetoptLong.options("__argv_str__" = NULL)
GetoptLong.options(help_style = "one-column")

## ----complex_template, eval = FALSE-------------------------------------------
# GetoptLong("
# This is a demonstration of using template as the option specification.
# 
# Usage: Rscript foo.R [options]
# 
# Binary options:
#   <verbose!> Whether show messages
#   <flag> A non-sense option
# 
# Single-value options:
#   <count=i> This is a count. This is a count.
#   <number=f> This is a number. This is a number.
# 
# Multiple-vlaue options:
#   <array=f@> This is an array. This is an array.
#   <hash=s%> This is a hash. This is a hash.
# 
# Questions, please contact your.name@email
# ", template_control = list(opt_width = c(verbose = 23, flag = 23,
#                                          count = 22, number = 22,
#                                          array = 30, hash = 30)
# ))

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["complex_template"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----template_multi_line, eval = FALSE----------------------------------------
# GetoptLong("
# Usage: Rscript foo.R [options]
# 
#   <count=i{2,}> This is a count. This is a count. This is a count.
#                 This is a count. This is a count.
#   <number=f> This is a number. This is a number. This is a number.
#              This is a number. This is a number.
# ")

## ----echo = FALSE-------------------------------------------------------------
chunks <- knitr:::knit_code$get()
GetoptLong.options("__argv_str__" = "--help")
local({ eval(parse(text = chunks[["template_multi_line"]])) })
GetoptLong.options("__argv_str__" = NULL)

## ----version, eval = FALSE----------------------------------------------------
# VERSION = "0.0.1"
# GetoptLong(
#     "tag=i", "...",
# )

## ----version2, eval = FALSE---------------------------------------------------
# VERSION = numeric_version("1.1-1")
# GetoptLong(
#     "tag=i", "...",
# )

## ----eval = FALSE-------------------------------------------------------------
# GetoptLong.options("config" = "bundling")
# GetoptLong.options("config" = c("no_ignore_case", "bundling"))

## ----eval = FALSE-------------------------------------------------------------
# source_script("foo.R", argv_str = "--cutoff 0.01 --input file=foo.txt --verbose")

## ----eval = TRUE--------------------------------------------------------------
sessionInfo()

## ----echo = FALSE, results = "asis"-------------------------------------------
get_os <- function(){
  sysinf <- Sys.info()
  if (!is.null(sysinf)){
  os <- sysinf['sysname']
  if (os == 'Darwin')
    os <- "osx"
  } else { ## mystery machine
    os <- .Platform$OS.type
    if (grepl("^darwin", R.version$os))
      os <- "osx"
    if (grepl("linux-gnu", R.version$os))
      os <- "linux"
  }
  tolower(os)
}

is.solaris = function() {
  os = get_os()
  !(os %in% c("windows", "unix", "linux", "osx"))
}

if(is.solaris()) {
  cat("**GetoptLong** is not supported on Solaris platform.\n")
} else {
  if(!is.solaris()) {
      invisible(knit("GetoptLong.Rmd2", "GetoptLong.md2"))
  }

  if(Sys.info()["user"] == "jokergoo") {
      invisible(file.copy("GetoptLong.md2", "/Users/jokergoo/project/GetoptLong/vignettes/GetoptLong.md2", overwrite = TRUE))
  }

  ln = readLines("GetoptLong.md2")
  cat(paste(ln, collapse = "\n"))
}