getopt/0000755000176200001440000000000014506210752011556 5ustar liggesusersgetopt/NAMESPACE0000644000176200001440000000017214130057213012767 0ustar liggesusers# Generated by roxygen2: do not edit by hand export(get_Rscript_filename) export(getopt) export(sort_list) import(stats) getopt/exec/0000755000176200001440000000000013400340627012477 5ustar liggesusersgetopt/exec/example.R0000644000176200001440000000214113400340622014246 0ustar liggesusers#!/path/to/Rscript library('getopt') library('stats') #get options, using the spec as defined by the enclosed list. #we read the options from the default: commandArgs(TRUE). spec = matrix(c( 'verbose', 'v', 2, "integer", 'help' , 'h', 0, "logical", 'count' , 'c', 1, "integer", 'mean' , 'm', 1, "double", 'sd' , 's', 1, "double" ), byrow=TRUE, ncol=4) opt = getopt(spec) # if help was asked for print a friendly message # and exit with a non-zero error code if ( !is.null(opt$help) ) { cat(getopt(spec, usage=TRUE)) q(status=1) } #set some reasonable defaults for the options that are needed, #but were not specified. if ( is.null(opt$mean ) ) { opt$mean = 0 } if ( is.null(opt$sd ) ) { opt$sd = 1 } if ( is.null(opt$count ) ) { opt$count = 10 } if ( is.null(opt$verbose ) ) { opt$verbose = FALSE } #print some progress messages to stderr, if requested. if ( opt$verbose ) { write("writing...",stderr()) } #do some operation based on user input. cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n")) cat("\n") #signal success and exit. q(status=0) getopt/README.md0000644000176200001440000000507514505725505013052 0ustar liggesusers# getopt [![CRAN Status Badge](https://www.r-pkg.org/badges/version/getopt)](https://cran.r-project.org/package=getopt) [![R-CMD-check](https://github.com/trevorld/r-getopt/workflows/R-CMD-check/badge.svg)](https://github.com/trevorld/r-getopt/actions) [![Coverage Status](https://codecov.io/github/trevorld/r-getopt/branch/master/graph/badge.svg)](https://app.codecov.io/github/trevorld/r-getopt?branch=master) [![RStudio CRAN mirror downloads](https://cranlogs.r-pkg.org/badges/getopt)](https://cran.r-project.org/package=getopt) [![Number of dependencies](https://tinyverse.netlify.com/badge/getopt)](https://cran.r-project.org/package=getopt) optparse hex sticker `getopt` is an R package designed to be used with `Rscript` to write "#!"-shebang scripts that accept short and long flags/options. Many users will prefer using instead the package [optparse](https://github.com/trevorld/r-optparse) which adds extra features (automatically generated help option and usage, support for default values, basic positional argument support). To install the last version released on CRAN use the following command: install.packages("getopt") To install the development version use the following command: install.packages("remotes") remotes:install_github("trevorld/r-getopt") ## example An example Rscript using `getopt`: #!/path/to/Rscript library('getopt') # get options, using the spec as defined by the enclosed list. # we read the options from the default: commandArgs(TRUE). spec = matrix(c( 'verbose', 'v', 2, "integer", 'help' , 'h', 0, "logical", 'count' , 'c', 1, "integer", 'mean' , 'm', 1, "double", 'sd' , 's', 1, "double" ), byrow=TRUE, ncol=4) opt = getopt(spec) # if help was asked for print a friendly message # and exit with a non-zero error code if ( !is.null(opt$help) ) { cat(getopt(spec, usage=TRUE)) q(status=1) } # set some reasonable defaults for the options that are needed, # but were not specified. if ( is.null(opt$mean ) ) { opt$mean = 0 } if ( is.null(opt$sd ) ) { opt$sd = 1 } if ( is.null(opt$count ) ) { opt$count = 10 } if ( is.null(opt$verbose ) ) { opt$verbose = FALSE } # print some progress messages to stderr, if requested. if ( opt$verbose ) { write("writing...",stderr()) } # do some operation based on user input. cat(rnorm(opt$count,mean=opt$mean,sd=opt$sd),sep="\n") # signal success and exit. # q(status=0) getopt/man/0000755000176200001440000000000014505724727012344 5ustar liggesusersgetopt/man/sort_list.Rd0000644000176200001440000000057114505721643014652 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/utils.R \name{sort_list} \alias{sort_list} \title{Recursively sorts a list} \usage{ sort_list(unsorted_list) } \arguments{ \item{unsorted_list}{A list.} } \value{ A sorted list. } \description{ \code{sort_list()} returns a recursively sorted list } \examples{ l <- list(b = 2, a = 1) sort_list(l) } getopt/man/getopt.Rd0000644000176200001440000001576114506176406014143 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/getopt.R \name{getopt} \alias{getopt} \alias{getopt-package} \title{C-like getopt behavior} \usage{ getopt( spec = NULL, opt = NULL, command = get_Rscript_filename(), usage = FALSE, debug = FALSE ) } \arguments{ \item{spec}{The getopt specification, or spec of what options are considered valid. The specification must be either a 4-5 column matrix, or a character vector coercible into a 4 column matrix using \code{matrix(x,ncol=4,byrow=TRUE)} command. The matrix/vector contains: Column 1: the \emph{long flag} name. A multi-character string. Column 2: \emph{short flag} alias of Column 1. A single-character string. Column 3: \emph{Argument} mask of the \emph{flag}. An integer. Possible values: 0=no argument, 1=required argument, 2=optional argument. Column 4: Data type to which the \emph{flag}'s argument shall be cast using \code{\link[=storage.mode]{storage.mode()}}. A multi-character string. This only considered for same-row Column 3 values of 1,2. Possible values: logical, integer, double, complex, character. If numeric is encountered then it will be converted to double. Column 5 (optional): A brief description of the purpose of the option. The terms \emph{option}, \emph{flag}, \emph{long flag}, \emph{short flag}, and \emph{argument} have very specific meanings in the context of this document. Read the \dQuote{Description} section for definitions.} \item{opt}{This defaults to the return value of \code{commandArgs(TRUE)} unless \code{argv} is in the global environment in which case it uses that instead (this is for compatibility with \code{littler}). If R was invoked directly via the \code{R} command, this corresponds to all arguments passed to R after the \code{--args} flag. If R was invoked via the \code{Rscript} command, this corresponds to all arguments after the name of the R script file. Read about \code{\link[=commandArgs]{commandArgs()}} and \link{Rscript} to learn more.} \item{command}{The string to use in the usage message as the name of the script. See argument \emph{usage}.} \item{usage}{If \code{TRUE}, argument \code{opt} will be ignored and a usage statement (character string) will be generated and returned from \code{spec}.} \item{debug}{This is used internally to debug the \code{getopt()} function itself.} } \description{ \code{getopt} is primarily intended to be used with \code{Rscript}. It facilitates writing \verb{#!} shebang scripts that accept short and long flags/options. It can also be used from \code{R} directly, but is probably less useful in this context. } \details{ \code{\link[=getopt]{getopt()}} returns a list data structure containing names of the flags that were present in the character vector passed in under the \code{opt} argument. Each value of the list is coerced to the data type specified according to the value of the \code{spec} argument. See below for details. Notes on naming convention: \enumerate{ \item An \emph{option} is one of the shell-split input strings. \item A \emph{flag} is a type of \emph{option}. a \emph{flag} can be defined as having no \emph{argument} (defined below), a required \emph{argument}, or an optional \emph{argument}. \item An \emph{argument} is a type of \emph{option}, and is the value associated with a flag. \item A \emph{long flag} is a type of \emph{flag}, and begins with the string \verb{--}. If the \emph{long flag} has an associated \emph{argument}, it may be delimited from the \emph{long flag} by either a trailing \code{=}, or may be the subsequent \emph{option}. \item A \emph{short flag} is a type of \emph{flag}, and begins with the string \code{-}. If a \emph{short flag} has an associated \emph{argument}, it is the subsequent \emph{option}. \emph{short flags} may be bundled together, sharing a single leading \code{-}, but only the final \emph{short flag} is able to have a corresponding \emph{argument}. } Many users wonder whether they should use the \code{getopt} package, \code{optparse} package, or \code{argparse} package. Here is some of the major differences: Features available in \code{getopt} unavailable in \code{optparse} \enumerate{ \item As well as allowing one to specify options that take either no argument or a required argument like \code{optparse}, \code{getopt} also allows one to specify option with an optional argument. } Some features implemented in \code{optparse} package unavailable in \code{getopt} \enumerate{ \item Limited support for capturing positional arguments after the optional arguments when \code{positional_arguments} set to \code{TRUE} in \code{optparse::parse_args()} \item Automatic generation of an help option and printing of help text when encounters an \code{-h} \item Option to specify default arguments for options as well the variable name to store option values } There is also new package \code{argparse} introduced in 2012 which contains all the features of both getopt and optparse but which has a dependency on Python 2.7 or 3.2+. Some Features unlikely to be implemented in \code{getopt}: \enumerate{ \item Support for multiple, identical flags, e.g. for \verb{-m 3 -v 5 -v}, the trailing \code{-v} overrides the preceding \verb{-v 5}, result is \code{v=TRUE} (or equivalent typecast). \item Support for multi-valued flags, e.g. \verb{--libpath=/usr/local/lib --libpath=/tmp/foo}. \item Support for lists, e.g. \verb{--define os=linux --define os=redhat} would set \code{result$os$linux=TRUE} and \code{result$os$redhat=TRUE}. \item Support for incremental, argument-less flags, e.g. \verb{/path/to/script -vvv} should set \code{v=3}. \item Support partial-but-unique string match on options, e.g. \code{--verb} and \code{--verbose} both match long flag \code{--verbose}. \item No support for mixing in positional arguments or extra arguments that don't match any options. For example, you can't do \verb{my.R --arg1 1 foo bar baz} and recover \code{foo}, \code{bar}, \code{baz} as a list. Likewise for \verb{my.R foo --arg1 1 bar baz}. } } \examples{ #!/path/to/Rscript library('getopt') # get options, using the spec as defined by the enclosed list. # we read the options from the default: commandArgs(TRUE). spec = matrix(c( 'verbose', 'v', 2, "integer", 'help' , 'h', 0, "logical", 'count' , 'c', 1, "integer", 'mean' , 'm', 1, "double", 'sd' , 's', 1, "double" ), byrow=TRUE, ncol=4) opt = getopt(spec) # if help was asked for print a friendly message # and exit with a non-zero error code if (!is.null(opt$help)) { cat(getopt(spec, usage = TRUE)) q(status = 1) } # set some reasonable defaults for the options that are needed, # but were not specified. if (is.null(opt$mean)) opt$mean <- 0 if (is.null(opt$sd)) opt$sd <- 1 if (is.null(opt$count)) opt$count <- 10 if (is.null(opt$verbose)) opt$verbose <- FALSE # print some progress messages to stderr, if requested. if (opt$verbose) write("writing...", stderr()) # do some operation based on user input. cat(rnorm(opt$count, mean = opt$mean, sd = opt$sd), sep = "\n") # signal success and exit. # q(status=0) } \author{ Allen Day } \keyword{data} getopt/man/get_Rscript_filename.Rd0000644000176200001440000000073714505722072016756 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/utils.R \name{get_Rscript_filename} \alias{get_Rscript_filename} \title{Returns file name being interpreted by Rscript} \usage{ get_Rscript_filename() } \value{ A string with the filename of the calling script. If not found (i.e. you are in a interactive session) returns \code{NA_character_}. } \description{ \code{get_Rscript_filename()} returns the file name that \code{Rscript} is interpreting. } getopt/man/figures/0000755000176200001440000000000014127752175014006 5ustar liggesusersgetopt/man/figures/logo.png0000644000176200001440000000177414127752175015465 0ustar liggesusersPNG  IHDR PLTE2zdjtRNSDP! pHYs  ~IDATxے0 P{gUe]Y 7:EbZ f?S-e#޳(=Rά]h=ϿB'AvaҺ4v].RXilʺj,Vf堉Xi#`EMf~]Y +KScŢtNX޴,Oڊ"em'=͌eL3uɌYV4m'~@:vbЂNX-Z` Z:f~BZdaY-rZhV%%`piIX-ZOwI_<`\fG]irVh?S]1_+ M*qVMeHZ+m ˝U?.Sb'k!͛U֬r4u#KբF*ZdQEdLҢ1,6EDjar wՂ/1 Y&V -eUW-rs+j!iY-]Z~Vʶp mVK{**W<ٔղ)dS,) YIENDB`getopt/man/figures/logo.svg0000644000176200001440000000317714127752175015477 0ustar liggesusers getopt/DESCRIPTION0000644000176200001440000000234114506210752013264 0ustar liggesusersEncoding: UTF-8 Package: getopt Type: Package Title: C-Like 'getopt' Behavior Version: 1.20.4 Authors@R: c(person("Trevor L", "Davis", role=c("aut", "cre"), email="trevor.l.davis@gmail.com", comment = c(ORCID = "0000-0001-6341-4639")), person("Allen", "Day", role="aut", comment="Original package author"), person("Roman", "Zenka", role="ctb")) URL: https://github.com/trevorld/r-getopt Imports: stats BugReports: https://github.com/trevorld/r-getopt/issues Description: Package designed to be used with Rscript to write '#!' shebang scripts that accept short and long flags/options. Many users will prefer using instead the packages optparse or argparse which add extra features like automatically generated help option and usage, support for default values, positional argument support, etc. License: GPL (>= 2) Suggests: testthat RoxygenNote: 7.2.3 Config/testthat/edition: 3 NeedsCompilation: no Packaged: 2023-10-01 05:01:35 UTC; trevorld Author: Trevor L Davis [aut, cre] (), Allen Day [aut] (Original package author), Roman Zenka [ctb] Maintainer: Trevor L Davis Repository: CRAN Date/Publication: 2023-10-01 06:30:01 UTC getopt/tests/0000755000176200001440000000000012660247705012727 5ustar liggesusersgetopt/tests/testthat/0000755000176200001440000000000014506176407014570 5ustar liggesusersgetopt/tests/testthat/test-getopt.R0000644000176200001440000002320614505713020017160 0ustar liggesuserstest_that("getopt works as expected", { spec <- matrix(c( "verbose", "v", 2, "integer", "help", "h", 0, "logical", "dummy1", "d", 0, "logical", "dummy2", "e", 2, "logical", "count", "c", 1, "integer", "mean", "m", 1, "double", "sd", "s", 1, "double", "output", "O", 1, "character" ), ncol = 4, byrow = TRUE) expect_equal(sort_list(getopt(spec, c("-c", "-1", "-m", "-1.2"))), sort_list(list(ARGS = character(0), count = -1, mean = -1.2))) expect_equal(sort_list(getopt(spec, c("-v", "-m", "3"))), sort_list(list(ARGS = character(0), verbose = 1, mean = 3))) expect_equal(sort_list(getopt(spec, c("-m", "3", "-v"))), sort_list(list(ARGS = character(0), mean = 3, verbose = 1))) expect_equal(sort_list(getopt(spec, c("-m", "3", "-v", "2", "-v"))), sort_list(list(ARGS = character(0), mean = 3, verbose = 1))) expect_equal(sort_list(getopt(spec, c("-O", "-", "-m", "3"))), sort_list(list(ARGS = character(0), output = "-", mean = 3))) expect_equal(sort_list(getopt(spec, c("-O", "-", "-m", "3"))), sort_list(getopt(spec, c("-m", "3", "-O", "-")))) expect_equal(sort_list(getopt(spec, c("-de"))), sort_list(getopt(spec, c("-ed")))) expect_equal(sort_list(getopt(spec, c("-de"))), sort_list(list(ARGS = character(0), dummy1 = TRUE, dummy2 = TRUE))) expect_equal(sort_list(getopt(spec, c("-de", "1"))), sort_list(list(ARGS = character(0), dummy1 = TRUE, dummy2 = NA))) expect_equal(sort_list(getopt(spec, c("--verbose"))), sort_list(list(ARGS = character(0), verbose = 1))) expect_equal(sort_list(getopt(spec, c("--verbose", "--help"))), sort_list(list(ARGS = character(0), verbose = 1, help = TRUE))) expect_equal(sort_list(getopt(spec, c("--verbose", "--mean", "5"))), sort_list(list(ARGS = character(0), verbose = 1, mean = 5))) expect_equal(sort_list(getopt(spec, c("--mean=5"))), sort_list(list(ARGS = character(0), mean = 5))) expect_equal(sort_list(getopt(spec, c("--verbose", "--mean=5", "--sd", "5"))), sort_list(list(ARGS = character(0), verbose = 1, mean = 5, sd = 5))) expect_equal(sort_list(getopt(spec, c("--verbose", "--mean=5", "--sd", "5"))), sort_list(getopt(spec, c("--mean=5", "--sd", "5", "--verbose")))) spec <- c( "date", "d", 1, "character", "help", "h", 0, "logical", "getdata", "g", 0, "logical", "market", "m", 1, "character", "threshold", "t", 1, "double" ) spec2 <- matrix(spec, ncol = 4, byrow = TRUE) # should give warning is spec is not matrix expect_warning(getopt(spec, c("--date", "20080421", "--market", "YM", "--getdata"))) expect_equal(sort_list(getopt(spec2, c("--date", "20080421", "--market", "YM", "--getdata"))), sort_list(list(ARGS = character(0), date = "20080421", market = "YM", getdata = TRUE))) expect_equal(sort_list(getopt(spec2, c("--date", "20080421", "--market", "YM", "--getdata"))), sort_list(getopt(spec2, c("--date", "20080421", "--getdata", "--market", "YM")))) expect_output(getopt(spec2, c("--date", "20080421", "--getdata", "--market", "YM"), debug = TRUE), "processing ") expect_output(print(getopt(spec2, c("--date", "20080421", "--getdata", "--market", "YM"), usage = TRUE)), "Usage: ") }) test_that("numeric is cast to double", { # Feature reported upstream (optparse) by Miroslav Posta spec <- matrix(c("count", "c", 1, "integer"), ncol = 4, byrow = TRUE) opt <- getopt(spec, c("-c", "-55")) expect_equal(typeof(opt$count), "integer") spec <- matrix(c("count", "c", 1, "numeric"), ncol = 4, byrow = TRUE) opt <- getopt(spec, c("-c", "-55.0")) expect_equal(typeof(opt$count), "double") }) test_that("empty strings are handled correctly for mandatory character arguments", { spec <- matrix(c("string", "s", 1, "character", "number", "n", 1, "numeric"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("--string=foo"))$string, "foo") expect_equal(getopt(spec, c("--string="))$string, "") expect_warning(getopt(spec, c("--number="))) }) test_that("negative numbers are handled correctly", { # Issue if negative number preceded by space instead of '=' reported by Roman Zenka spec <- matrix(c("count", "c", 1, "integer"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("-c", "5"))$count, 5) spec <- matrix(c("count", "c", 1, "integer"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("-c", "-5"))$count, -5) spec <- matrix(c("count", "c", 1, "integer"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("--count=-1E5"))$count, -1E5) spec <- matrix(c("count", "c", 1, "double"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("-c", "-5"))$count, -5) spec <- matrix(c("count", "c", 1, "double"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("-c", "-1e5"))$count, -1e5) spec <- matrix(c("count", "c", 1, "double"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("--count=-1.2e5"))$count, -1.2e5) spec <- matrix(c("count", "c", 1, "double"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("--count", "-1e5"))$count, -1e5) }) test_that("more helpful warnings upon incorrect input", { # Give more pointed warning upon wildly incorrect input spec <- matrix(c("count", "c", 1, "integer"), ncol = 4, byrow = TRUE) expect_warning(getopt(spec, c("-c", "hello"))$count, paste("integer expected, got", dQuote("hello"))) spec <- NULL expect_error(getopt(spec, ""), 'argument "spec" must be non-null.') spec <- c("foo", "f", 0) expect_error(getopt(spec, ""), "or a character vector with length divisible by 4, rtfm") spec <- matrix(c("foo", "f", 0, "integer"), ncol = 2) expect_error(getopt(spec, ""), '"spec" should have at least 4 columns.') spec <- matrix(c("foo", "f", 0, "integer", "bar", "b", 0, "integer"), ncol = 8) expect_error(getopt(spec, ""), '"spec" should have no more than 6 columns.') }) test_that("don't throw error if multiple matches match one argument fully", { # test if partial name matches fully, # still throw error if multiple matches and doesn't match both fully # feature request from Jonas Zimmermann spec <- matrix(c( "foo", "f", 0, "logical", "foobar", "b", 0, "logical", "biz", "z", 0, "logical" ), ncol = 4, byrow = TRUE) expect_error(getopt(spec, c("--fo"))) expect_equal(getopt(spec, c("--foo")), sort_list(list(ARGS = character(0), foo = TRUE))) }) test_that("sort_list works as expected", { expect_equal(sort_list(list(a = 3, b = 2)), sort_list(list(b = 2, a = 3))) expect_false(identical(sort_list(list(b = 3, a = 2)), list(b = 3, a = 2))) expect_false(identical(sort_list(list(b = list(b = 3, c = 2), a = 2)), list(b = list(c = 2, b = 3), a = 2))) }) test_that("Use h flag for non help", { spec <- matrix(c("foo", "h", 0, "logical"), ncol = 4, byrow = TRUE) expect_equal(getopt(spec, c("-h")), sort_list(list(ARGS = character(0), foo = TRUE))) spec <- matrix(c("foo", "h", 0, "logical", "help", "h", 0, "logical"), ncol = 4, byrow = TRUE) expect_error(getopt(spec, c("-h")), "redundant short names for flags") spec <- matrix(c("foo", "f", 0, "logical", "foo", "h", 0, "logical"), ncol = 4, byrow = TRUE) expect_error(getopt(spec, c("-h")), "redundant long names for flags") }) test_that("Optional usage strings work as expected", { spec <- matrix(c( "foo", "f", 0, "logical", "foo usage", "foobar", "b", 1, "character", "foobar usage", "biz", "z", 2, "logical", "biz usage", "number", "n", 1, "numeric", "number usage", "help", "h", 0, "logical", "help" ), ncol = 5, byrow = TRUE) expect_output(cat(getopt(spec, usage = TRUE)), "foobar usage") }) test_that("tests to get coverage up", { spec <- matrix(c( "foo", "f", 0, "logical", "foo usage", "foobar", "b", 1, "character", "foobar usage", "biz", "z", 2, "logical", "biz usage", "number", "n", 1, "numeric", "number usage", "help", "h", 0, "logical", "help" ), ncol = 5, byrow = TRUE) expect_error(getopt(spec, "--whodunit"), 'long flag "whodunit" is invalid') expect_error(getopt(spec, "--foo=4"), 'long flag "foo" accepts no arguments') # expect_error(getopt(spec, c("--foo", "4")), 'long flag "foo" accepts no arguments') # nolint expect_equal(getopt(spec, "--biz", "4"), sort_list(list(ARGS = character(0), biz = TRUE))) expect_warning(getopt(spec, c("-n", "bar")), paste("double expected, got", dQuote("bar"))) expect_warning(getopt(spec, c("--number=bar")), paste("double expected, got", dQuote("bar"))) expect_error(getopt(spec, "-n"), 'flag "n" requires an argument') expect_error(getopt(spec, "-p"), 'short flag "p" is invalid') expect_error(getopt(spec, "-nh"), 'short flag "n" requires an argument, but has none') expect_error(getopt(spec, "-fn"), 'flag "n" requires an argument') expect_error(getopt(spec, c("--number", 3, 4)), '"4" is not a valid option, or does not support an argument') expect_error(getopt(spec, c("-b")), '"b" requires an argument') expect_error(getopt(spec, c("--foobar")), 'flag "foobar" requires an argument') expect_error(getopt(spec, c("--foobar", "--help")), 'flag "foobar" requires an argument') expect_output(getopt(spec, c("-n", "2"), debug = TRUE), "short option: -n") expect_output(getopt(spec, c("-b", "-"), debug = TRUE), "lone dash") expect_warning(getopt(spec, c("-n", "-")), paste("double expected, got", dQuote("-"))) }) getopt/tests/run-all.R0000644000176200001440000000005212255510214014405 0ustar liggesuserslibrary("testthat") test_check("getopt") getopt/COPYING0000644000176200001440000004325412206012161012606 0ustar liggesusers GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. getopt/R/0000755000176200001440000000000014506176457011774 5ustar liggesusersgetopt/R/getopt.R0000644000176200001440000004575614506176353013435 0ustar liggesusers# Copyright (c) 2008-2010 Allen Day # Copyright (c) 2011-2018 Trevor L. Davis # # This file is free software: you may copy, redistribute and/or modify it # under the terms of the GNU General Public License as published by the # Free Software Foundation, either version 2 of the License, or (at your # option) any later version. # # This file is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . #' C-like getopt behavior #' #' `getopt` is primarily intended to be used with `Rscript`. It #' facilitates writing `#!` shebang scripts that accept short and long #' flags/options. It can also be used from `R` directly, but is probably less #' useful in this context. #' #' [getopt()] returns a list data structure containing names of the #' flags that were present in the character vector passed in under #' the `opt` argument. Each value of the list is coerced to the #' data type specified according to the value of the `spec` argument. See #' below for details. #' #' Notes on naming convention: #' #' 1. An \emph{option} is one of the shell-split input strings. #' #' 2. A \emph{flag} is a type of \emph{option}. a \emph{flag} can be defined as #' having no \emph{argument} (defined below), a required \emph{argument}, or an #' optional \emph{argument}. #' #' 3. An \emph{argument} is a type of \emph{option}, and is the value associated #' with a flag. #' #' 4. A \emph{long flag} is a type of \emph{flag}, and begins with the string #' `--`. If the \emph{long flag} has an associated \emph{argument}, it may be #' delimited from the \emph{long flag} by either a trailing `=`, or may be #' the subsequent \emph{option}. #' #' 5. A \emph{short flag} is a type of \emph{flag}, and begins with the string #' `-`. If a \emph{short flag} has an associated \emph{argument}, it is the #' subsequent \emph{option}. \emph{short flags} may be bundled together, #' sharing a single leading `-`, but only the final \emph{short flag} is able #' to have a corresponding \emph{argument}. #' #' Many users wonder whether they should use the `getopt` package, `optparse` package, #' or `argparse` package. #' Here is some of the major differences: #' #' Features available in `getopt` unavailable in `optparse` #' #' 1. As well as allowing one to specify options that take either #' no argument or a required argument like `optparse`, #' `getopt` also allows one to specify option with an optional argument. #' #' Some features implemented in `optparse` package unavailable in `getopt` #' #' 1. Limited support for capturing positional arguments after the optional arguments #' when `positional_arguments` set to `TRUE` in `optparse::parse_args()` #' #' 2. Automatic generation of an help option and printing of help text when encounters an `-h` #' #' 3. Option to specify default arguments for options as well the #' variable name to store option values #' #' There is also new package `argparse` introduced in 2012 which contains #' all the features of both getopt and optparse but which has a dependency on #' Python 2.7 or 3.2+. #' #' Some Features unlikely to be implemented in `getopt`: #' #' 1. Support for multiple, identical flags, e.g. for `-m 3 -v 5 -v`, the #' trailing `-v` overrides the preceding `-v 5`, result is `v=TRUE` (or equivalent #' typecast). #' #' 2. Support for multi-valued flags, e.g. `--libpath=/usr/local/lib #' --libpath=/tmp/foo`. #' #' 3. Support for lists, e.g. `--define os=linux --define os=redhat` would #' set `result$os$linux=TRUE` and `result$os$redhat=TRUE`. #' #' 4. Support for incremental, argument-less flags, e.g. `/path/to/script #' -vvv` should set `v=3`. #' #' 5. Support partial-but-unique string match on options, e.g. `--verb` and #' `--verbose` both match long flag `--verbose`. #' #' 6. No support for mixing in positional arguments or extra arguments that #' don't match any options. For example, you can't do `my.R --arg1 1 foo bar #' baz` and recover `foo`, `bar`, `baz` as a list. Likewise for `my.R foo #' --arg1 1 bar baz`. #' #' @aliases getopt getopt-package #' @param spec The getopt specification, or spec of what options are considered #' valid. The specification must be either a 4-5 column matrix, or a #' character vector coercible into a 4 column matrix using #' `matrix(x,ncol=4,byrow=TRUE)` command. The matrix/vector #' contains: #' #' Column 1: the \emph{long flag} name. A multi-character string. #' #' Column 2: \emph{short flag} alias of Column 1. A single-character #' string. #' #' Column 3: \emph{Argument} mask of the \emph{flag}. An integer. #' Possible values: 0=no argument, 1=required argument, 2=optional argument. #' #' Column 4: Data type to which the \emph{flag}'s argument shall be cast using #' [storage.mode()]. A multi-character string. This only considered #' for same-row Column 3 values of 1,2. Possible values: logical, #' integer, double, complex, character. #' If numeric is encountered then it will be converted to double. #' #' Column 5 (optional): A brief description of the purpose of the option. #' #' The terms \emph{option}, \emph{flag}, \emph{long flag}, \emph{short flag}, #' and \emph{argument} have very specific meanings in the context of this #' document. Read the \dQuote{Description} section for definitions. #' @param opt This defaults to the return value of `commandArgs(TRUE)` unless #' `argv` is in the global environment in which case it uses that instead #' (this is for compatibility with `littler`). #' #' If R was invoked directly via the `R` command, this corresponds to all #' arguments passed to R after the `--args` flag. #' #' If R was invoked via the `Rscript` command, this corresponds to all #' arguments after the name of the R script file. #' #' Read about [commandArgs()] and \link{Rscript} to learn more. #' @param command The string to use in the usage message as the name of the #' script. See argument \emph{usage}. #' @param usage If `TRUE`, argument `opt` will be ignored and a usage #' statement (character string) will be generated and returned from `spec`. #' @param debug This is used internally to debug the `getopt()` function itself. #' @author Allen Day #' @keywords data #' @export #' @examples #' #!/path/to/Rscript #' library('getopt') #' # get options, using the spec as defined by the enclosed list. #' # we read the options from the default: commandArgs(TRUE). #' spec = matrix(c( #' 'verbose', 'v', 2, "integer", #' 'help' , 'h', 0, "logical", #' 'count' , 'c', 1, "integer", #' 'mean' , 'm', 1, "double", #' 'sd' , 's', 1, "double" #' ), byrow=TRUE, ncol=4) #' opt = getopt(spec) #' #' # if help was asked for print a friendly message #' # and exit with a non-zero error code #' if (!is.null(opt$help)) { #' cat(getopt(spec, usage = TRUE)) #' q(status = 1) #' } #' #' # set some reasonable defaults for the options that are needed, #' # but were not specified. #' if (is.null(opt$mean)) opt$mean <- 0 #' if (is.null(opt$sd)) opt$sd <- 1 #' if (is.null(opt$count)) opt$count <- 10 #' if (is.null(opt$verbose)) opt$verbose <- FALSE #' #' # print some progress messages to stderr, if requested. #' if (opt$verbose) write("writing...", stderr()) #' #' # do some operation based on user input. #' cat(rnorm(opt$count, mean = opt$mean, sd = opt$sd), sep = "\n") #' #' # signal success and exit. #' # q(status=0) #' @import stats getopt <- function(spec = NULL, opt = NULL, command = get_Rscript_filename(), usage = FALSE, debug = FALSE) { # nolint # littler compatibility - map argv vector to opt if (is.null(opt)) { if (exists("argv", where = .GlobalEnv, inherits = FALSE)) { opt <- get("argv", envir = .GlobalEnv) # nocov } else { opt <- commandArgs(TRUE) } } ncol <- 4 maxcol <- 6 col_long_name <- 1 col_short_name <- 2 col_has_argument <- 3 col_mode <- 4 col_description <- 5 flag_no_argument <- 0 flag_required_argument <- 1 flag_optional_argument <- 2 result <- list() result$ARGS <- vector(mode = "character") # nolint # no spec. fail. if (is.null(spec)) { stop('argument "spec" must be non-null.') # spec is not a matrix. attempt to coerce, if possible. issue a warning. } else if (!is.matrix(spec)) { if (length(spec) / 4 == as.integer(length(spec) / 4)) { warning('argument "spec" was coerced to a 4-column (row-major) matrix. use a matrix to prevent the coercion') spec <- matrix(spec, ncol = ncol, byrow = TRUE) } else { stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.') } # spec is a matrix, but it has too few columns. } else if (dim(spec)[2] < ncol) { stop(paste('"spec" should have at least ', ncol, " columns.", sep = "")) # spec is a matrix, but it has too many columns. } else if (dim(spec)[2] > maxcol) { stop(paste('"spec" should have no more than ', maxcol, " columns.", sep = "")) # spec is a matrix, and it has some optional columns. } else if (dim(spec)[2] != ncol) { ncol <- dim(spec)[2] } # sanity check. make sure long names are unique, and short names are unique. if (length(unique(spec[, col_long_name])) != length(spec[, col_long_name])) { stop(paste("redundant long names for flags (column ", col_long_name, " of spec matrix).", sep = "")) } if (length(stats::na.omit(unique(spec[, col_short_name]))) != length(stats::na.omit(spec[, col_short_name]))) { stop(paste("redundant short names for flags (column ", col_short_name, " of spec matrix).", sep = "")) } # convert numeric type to double type spec[, 4] <- gsub("numeric", "double", spec[, 4]) # if usage=TRUE, don't process opt, but generate a usage string from the data in spec if (usage) { ret <- "" ret <- paste(ret, "Usage: ", command, sep = "") for (j in 1:(dim(spec))[1]) { ret <- paste(ret, " [-[-", spec[j, col_long_name], "|", spec[j, col_short_name], "]", sep = "") if (spec[j, col_has_argument] == flag_no_argument) { ret <- paste(ret, "]", sep = "") } else if (spec[j, col_has_argument] == flag_required_argument) { ret <- paste(ret, " <", spec[j, col_mode], ">]", sep = "") } else if (spec[j, col_has_argument] == flag_optional_argument) { ret <- paste(ret, " [<", spec[j, col_mode], ">]]", sep = "") } } # include usage strings if (ncol >= 5) { max.long <- max(apply(cbind(spec[, col_long_name]), 1, function(x)length(strsplit(x, "")[[1]]))) ret <- paste(ret, "\n", sep = "") for (j in 1:(dim(spec))[1]) { ret <- paste(ret, sprintf(paste(" -%s|--%-", max.long, "s %s\n", sep = ""), spec[j, col_short_name], spec[j, col_long_name], spec[j, col_description] ), sep = "") } } else { ret <- paste(ret, "\n", sep = "") } return(ret) } # XXX check spec validity here. e.g. column three should be convertible to integer i <- 1 while (i <= length(opt)) { if (debug) print(paste("processing", opt[i])) current_flag <- 0 # XXX use NA optstring <- opt[i] # long flag if (substr(optstring, 1, 2) == "--") { if (debug) print(paste(" long option:", opt[i])) optstring <- substring(optstring, 3) this_flag <- NA this_argument <- NA kv <- strsplit(optstring, "=")[[1]] # if (!is.na(kv[2])) { if (grepl("=", optstring)) { this_flag <- kv[1] this_argument <- paste(kv[-1], collapse = "=") } else { this_flag <- optstring } rowmatch <- grep(this_flag, spec[, col_long_name], fixed = TRUE) # long flag is invalid, matches no options if (length(rowmatch) == 0) { stop(paste('long flag "', this_flag, '" is invalid', sep = "")) # long flag is ambiguous, matches too many options } else if (length(rowmatch) > 1) { # check if there is an exact match and use that rowmatch <- which(this_flag == spec[, col_long_name]) if (length(rowmatch) == 0) { stop(paste('long flag "', this_flag, '" is ambiguous', sep = "")) } } # if we have an argument if (!is.na(this_argument)) { # if we can't accept the argument, bail out if (spec[rowmatch, col_has_argument] == flag_no_argument) { stop(paste('long flag "', this_flag, '" accepts no arguments', sep = "")) # otherwise assign the argument to the flag } else { mode <- spec[rowmatch, col_mode] warning_msg <- tryCatch(storage.mode(this_argument) <- mode, warning = function(w) warning(paste(mode, "expected, got", dQuote(this_argument)))) if (is.na(this_argument) && !grepl("expected, got", warning_msg)) { warning(paste("long flag", this_flag, "given a bad argument")) } result[spec[rowmatch, col_long_name]] <- this_argument i <- i + 1 next } # otherwise, we don't have an argument } else { # nolint start # if we require an argument, bail out ### if (spec[rowmatch, col_has_argument] == flag_required_argument) { ### stop(paste('long flag "', this_flag, '" requires an argument', sep = "")) # long flag has no attached argument. set flag as present. # set current_flag so we can peek ahead later and consume the argument if it's there # nolint end ###} else { result[spec[rowmatch, col_long_name]] <- TRUE current_flag <- rowmatch ###} } # short flag(s) } else if (substr(optstring, 1, 1) == "-") { if (debug) print(paste(" short option:", opt[i])) these_flags <- strsplit(optstring, "")[[1]] done <- FALSE for (j in 2:length(these_flags)) { this_flag <- these_flags[j] rowmatch <- grep(this_flag, spec[, col_short_name], fixed = TRUE) # short flag is invalid, matches no options if (length(rowmatch) == 0) { stop(paste('short flag "', this_flag, '" is invalid', sep = "")) # short flag has an argument, but is not the last in a compound flag string } else if (j < length(these_flags) & spec[rowmatch, col_has_argument] == flag_required_argument) { stop(paste('short flag "', this_flag, '" requires an argument, but has none', sep = "")) # short flag has no argument, flag it as present } else if (spec[rowmatch, col_has_argument] == flag_no_argument) { result[spec[rowmatch, col_long_name]] <- TRUE done <- TRUE # can't definitively process this_flag flag yet, need to see if next option is an argument or not } else { result[spec[rowmatch, col_long_name]] <- TRUE current_flag <- rowmatch done <- FALSE } } if (done) { i <- i + 1 next } } # invalid opt if (current_flag == 0) { stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep = "")) # nolint start # TBD support for positional args # if (debug) print(paste('"', optstring, '" not a valid option. It is appended to getopt(...)$ARGS', sep = "")) # result$ARGS = append(result$ARGS, optstring) # nolint end # some dangling flag, handle it } else if (current_flag > 0) { if (debug) print(" dangling flag") if (length(opt) > i) { peek_optstring <- opt[i + 1] if (debug) print(paste(' peeking ahead at: "', peek_optstring, '"', sep = "")) # got an argument. attach it, increment the index, and move on to the next option. # we don't allow arguments beginning with "-" UNLESS specfile indicates the value is an "integer" or "double", # in which case we allow a leading dash (and verify trailing digits/decimals). if (substr(peek_optstring, 1, 1) != "-" | # match negative double (substr(peek_optstring, 1, 1) == "-" & regexpr("^-[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", peek_optstring) > 0 & spec[current_flag, col_mode] == "double" ) | # match negative integer (substr(peek_optstring, 1, 1) == "-" & regexpr("^-[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", peek_optstring) > 0 & spec[current_flag, col_mode] == "integer" ) ) { if (debug) print(paste(" consuming argument *", peek_optstring, "*", sep = "")) mode <- spec[current_flag, col_mode] tryCatch(storage.mode(peek_optstring) <- mode, warning = function(w) warning(paste(mode, "expected, got", dQuote(peek_optstring)))) result[spec[current_flag, col_long_name]] <- peek_optstring i <- i + 1 # a lone dash } else if (substr(peek_optstring, 1, 1) == "-" & length(strsplit(peek_optstring, "")[[1]]) == 1) { if (debug) print(' consuming "lone dash" argument') mode <- spec[current_flag, col_mode] tryCatch(storage.mode(peek_optstring) <- mode, warning = function(w) warning(paste(mode, "expected, got", dQuote(peek_optstring)))) # nocov result[spec[current_flag, col_long_name]] <- peek_optstring i <- i + 1 # no argument } else { if (debug) print(" no argument!") # if we require an argument, bail out if (spec[current_flag, col_has_argument] == flag_required_argument) { stop(paste('flag "', this_flag, '" requires an argument', sep = "")) # otherwise set flag as present. } else if ( spec[current_flag, col_has_argument] == flag_optional_argument | spec[current_flag, col_has_argument] == flag_no_argument ) { x <- TRUE storage.mode(x) <- spec[current_flag, col_mode] result[spec[current_flag, col_long_name]] <- x } else { stop(paste("This should never happen.", # nocov "Is your spec argument correct? Maybe you forgot to set", # nocov "ncol=4, byrow=TRUE in your matrix call?")) # nocov } } # trailing flag without required argument } else if (spec[current_flag, col_has_argument] == flag_required_argument) { stop(paste('flag "', this_flag, '" requires an argument', sep = "")) # trailing flag without optional argument } else if (spec[current_flag, col_has_argument] == flag_optional_argument) { x <- TRUE storage.mode(x) <- spec[current_flag, col_mode] result[spec[current_flag, col_long_name]] <- x # trailing flag without argument } else if (spec[current_flag, col_has_argument] == flag_no_argument) { x <- TRUE storage.mode(x) <- spec[current_flag, col_mode] result[spec[current_flag, col_long_name]] <- x } else { stop("this should never happen (2). please inform the author.") # nocov } } # no dangling flag, nothing to do. i <- i + 1 } return(result) } getopt/R/utils.R0000644000176200001440000000325014505722057013247 0ustar liggesusers# Copyright (c) 2011-2013 Trevor L. Davis # # This file is free software: you may copy, redistribute and/or modify it # under the terms of the GNU General Public License as published by the # Free Software Foundation, either version 2 of the License, or (at your # option) any later version. # # This file is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . #' Returns file name being interpreted by Rscript #' #' `get_Rscript_filename()` returns the file name that `Rscript` is interpreting. #' @return A string with the filename of the calling script. #' If not found (i.e. you are in a interactive session) returns `NA_character_`. #' @export get_Rscript_filename <- function() { # nolint prog <- sub("--file=", "", grep("--file=", commandArgs(), value = TRUE)[1]) if (.Platform$OS.type == "windows") { prog <- gsub("\\\\", "\\\\\\\\", prog) } prog } #' Recursively sorts a list #' #' `sort_list()` returns a recursively sorted list #' @param unsorted_list A list. #' @return A sorted list. #' @examples #' l <- list(b = 2, a = 1) #' sort_list(l) #' @export sort_list <- function(unsorted_list) { for (ii in seq(along = unsorted_list)) { if (is.list(unsorted_list[[ii]])) { unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]]) } } unsorted_list[sort(names(unsorted_list))] } getopt/NEWS.md0000644000176200001440000000355414505725736012677 0ustar liggesusersgetopt 1.20.4 ============= * Documentation tweaks eliminating a CRAN check NOTE. * `{covr}` is no longer a "suggested" package in the `DESCRIPTION` file. getopt 1.20.3 ============= * Now by default ``getopt()`` won't override a user specified ``opt`` argument if ``argv`` is in the global environment. Will continue to use ``argv`` as a default for ``opt`` if it is in the global environment and the user does not specify an ``opt`` argument (for ``littler`` compatibility). getopt 1.20.2 ============= * Now allows one to pass an empty string to a character option. Thanks Matthew Flickinger for bug report. getopt 1.20.1 ============= * Now explicitly imports the ``na.omit()`` method from the ``stats`` package. Thanks Derrick Oswald for bug report. * Improved parsing for negative numbers preceded by a space instead of a '=' sign. Thanks Roman Zenka for improved regular expression. * Slightly more informative error message if `storage.mode()` coercion results in an `NA`. Thanks Roman Zenka for suggestion. getopt 1.20.0 ============= * Type of "numeric" in spec automatically cast to "double". Previously users might have had an error passing negative numbers if they accidentally specified "numeric" instead of "double". * Project website moved to https://github.com/trevorld/getopt * Exports new function ``sort_list()``. getopt 1.19.1 ============= * If a passed in option matches multiple options in the getopt specification but matches one exactly then `getopt` now uses that value instead of throwing a "long flag is ambiguous" error. getopt 1.19.0 ============= * Exports new function ``get_Rscript_filename()`` that returns name of calling script, `{getopt}` now uses this function value as default for ``command`` argument. * Documentation improved and now highlights differences between `{getopt}` and `{optparse}` packages for new undecided users. getopt/MD50000644000176200001440000000134414506210752012070 0ustar liggesusersb234ee4d69f5fce4486a80fdaf4a4263 *COPYING bebd5c240f8d6e3420f13362cd57ba08 *DESCRIPTION d400adb3d8a7edbac587ac399fdeb451 *NAMESPACE a88b14eddc259381cb4310885a38ca4c *NEWS.md 9ae1ed63c65ad65e31b0d999b23f7899 *R/getopt.R eb7f853b737aa33b19f3004b22c6924a *R/utils.R bf7de6cec8f715eabbf4b28fc4fe9c91 *README.md 74d919a70588c23dcd41197ec49cd73f *exec/example.R c490bcc00c95ea60beabd5fa4d2966ae *man/figures/logo.png 6ad4ceffc3fc4ca978c3c52aabdaf818 *man/figures/logo.svg 01a6dd5b80177220ce6fc05c8bbacd13 *man/get_Rscript_filename.Rd 1da9c4924243fb316c1041e81f4eedcb *man/getopt.Rd b465f884c7143520847d5735d1f10481 *man/sort_list.Rd 35fe6c4707e36c320771156c47cc943f *tests/run-all.R 9dd4b87cb0144d77630395e07047c246 *tests/testthat/test-getopt.R