R/argparse.R

Defines functions .print_message_and_exit .stop find_python_cmd detects_python assert_python_cmd get_Rscript_filename needs_prog convert_..._to_arguments `%||%` should_as_list get_python_type convert_argument parse_args_output ArgumentParser

Documented in ArgumentParser

# Copyright (c) 2012-2021 Trevor L. Davis <trevor.l.davis@gmail.com>
#
#  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 <http://www.gnu.org/licenses/>.
#
# This file incorporates work from the argparse module in Python 2.7.3.
#
#     Copyright (c) 2001-2012 Python Software Foundation; All Rights Reserved
#
# See (inst/)COPYRIGHTS or http://docs.python.org/2/license.html for the full
# Python (GPL-compatible) license stack.

#' Create a command line parser
#'
#' \code{ArgumentParser} creates a parser object that acts as
#' a wrapper to Python's argparse module
#'
#' @param ... Arguments cleaned and passed to Pythons argparse.ArgumentParser()
#' @param python_cmd Python executable for \code{argparse} to use.
#'      Must have argparse and json modules (automatically included Python 2.7 and 3.2+).
#'      If you need Unicode argument support then you must use Python 3.0+.
#'      Default will be to use \code{findpython} package to find suitable Python binary.
#' @return  \code{ArgumentParser} returns a parser object which contains
#'    an \code{add_argument} function to add arguments to the parser,
#'    a \code{parse_args} function to parse command line arguments into
#'    a list, a \code{print_help} and \code{print_usage} function to print
#'    usage information.  See code examples, package vignette,
#'    and corresponding python module for more information on how to use it.
#'
#' @references Python's \code{argparse} library, which this package is based on,
#'  is described here: \url{https://docs.python.org/3/library/argparse.html}
#'
#' @import jsonlite
#' @import R6
#' @export
#' @examples
#'
#' if (argparse:::detects_python()) {
#'   parser <- ArgumentParser(description='Process some integers')
#'   parser$add_argument('integers', metavar='N', type = "integer", nargs='+',
#'                      help='an integer for the accumulator')
#'   parser$add_argument('--sum', dest='accumulate', action='store_const',
#'                      const='sum', default='max',
#'                      help='sum the integers (default: find the max)')
#'   parser$print_help()
#'   # default args for ArgumentParser()$parse_args are commandArgs(TRUE)
#'   # which is what you'd want for an Rscript but not for interactive use
#'   args <- parser$parse_args(c("--sum", "1", "2", "3"))
#'   accumulate_fn <- get(args$accumulate)
#'   print(accumulate_fn(args$integers))
#' }
ArgumentParser <- function(..., python_cmd = NULL) { # nolint
    python_cmd <- find_python_cmd(python_cmd)
    assert_python_cmd(python_cmd)
    initial_python_code <- c("import argparse",
        "try:",
        "    import json",
        "except ImportError:",
        "    import simplejson as json",
        "",
        sprintf("parser = argparse.ArgumentParser(%s)",
                convert_..._to_arguments("ArgumentParser", ...)),
        "")
    Parser$new(Code$new(python_cmd, initial_python_code), "parser")
}

Code <- R6Class("Code", # nolint
    public = list(
        append = function(new_code) {
            private$code <- c(private$code, new_code)
        },
        run = function(new_code) {
            code <- c(private$code, new_code)
            suppressWarnings(system2(private$cmd, input = code,
                                    stdout = TRUE, stderr = TRUE))
        },
        initialize = function(cmd, code = character(0)) {
            private$cmd <- cmd
            private$code <- code
        }
    ),
    private = list(code = NULL, cmd = NULL)
)

Group <- R6Class("Group", # nolint
    public = list(
        initialize = function(python_code, name) {
            private$python_code <- python_code
            private$name <- name
        },
        add_argument = function(...) {
            private$python_code$append(sprintf("%s.add_argument(%s)",
                private$name, convert_..._to_arguments("add_argument", ...)))
            return(invisible(NULL))
        }
    ),
    private = list(python_code = NULL, name = NULL)
)

Subparsers <- R6Class("Subparsers", # nolint
    public = list(
        initialize = function(python_code, name) {
            private$python_code <- python_code
            private$name <- name
        },
        add_parser = function(...) {
            parser_name <- paste0(private$name, "_subparser", private$n_subparsers)
            private$n_subparsers <- private$n_subparsers + 1
            private$python_code$append(sprintf("%s = %s.add_parser(%s)",
                            parser_name, private$name,
                            convert_..._to_arguments("ArgumentParser", ...)))
            Parser$new(private$python_code, parser_name)
        }
    ),
    private = list(python_code = NULL, name = NULL, n_subparsers = 0)
)

Parser <- R6Class("Parser", # nolint
    public = list(
        parse_args = function(args = commandArgs(TRUE)) {
            new_code <- c(sprintf("args = %s.parse_args([%s])", private$name,
                            paste(sprintf("'%s'", args), collapse = ", ")),
                    "print(json.dumps(args.__dict__, sort_keys=True))")
            output <- private$python_code$run(new_code)
            parse_args_output(output)
        },
        parse_known_args = function(args = commandArgs(TRUE)) {
            new_code <- c(sprintf("args_remainder = %s.parse_known_args([%s])", private$name,
                            paste(sprintf("'%s'", args), collapse = ", ")),
                    "print(json.dumps((args_remainder[0].__dict__, args_remainder[1])))")
            output <- private$python_code$run(new_code)
            parse_args_output(output)
        },
        print_help = function() {
            cat(private$python_code$run(sprintf("%s.print_help()", private$name)), sep = "\n")
            invisible(NULL)
        },
        print_usage = function() {
            cat(private$python_code$run(sprintf("%s.print_usage()", private$name)), sep = "\n")
            invisible(NULL)
        },
        add_argument = function(...) {
            private$python_code$append(sprintf("%s.add_argument(%s)", private$name,
                            convert_..._to_arguments("add_argument", ...)))
            invisible(NULL)
        },
        add_argument_group = function(...) {
            group_name <- paste0(private$name, "_group", private$n_groups)
            private$n_groups <- private$n_groups + 1
            private$python_code$append(sprintf("%s = %s.add_argument_group(%s)",
                           group_name, private$name,
                            convert_..._to_arguments("add_argument", ...)))
            Group$new(private$python_code, group_name)
        },
        add_mutually_exclusive_group = function(required = FALSE) {
            group_name <- paste0(private$name, "_mutually_exclusive_group",
                                 private$n_mutually_exclusive_groups)
            private$n_mutually_exclusive_groups <- private$n_mutually_exclusive_groups + 1
            private$python_code$append(sprintf("%s = %s.add_mutually_exclusive_group(%s)",
                           group_name, private$name,
                           ifelse(required, "required=True", "")))
            Group$new(private$python_code, group_name)
        },
        add_subparsers = function(...) {
            subparsers_name <- paste0(private$name, "_subparsers")
            private$python_code$append(sprintf("%s = %s.add_subparsers(%s)",
                            subparsers_name, private$name,
                            convert_..._to_arguments("add_argument", ...)))
            Subparsers$new(private$python_code, subparsers_name)
        },
        initialize = function(python_code, name) {
            private$python_code <- python_code
            private$name <- name
        }
    ),
    private = list(python_code = NULL, name = NULL,
                   n_mutually_exclusive_groups = 0, n_groups = 0)
)

parse_args_output <- function(output) {
    if (grepl("^usage:", output[1])) {
        has_positional_arguments <- any(grepl("^positional arguments:", output))
        has_optional_arguments <- any(grepl("^optional arguments:|^options:", output))
        if (has_positional_arguments || has_optional_arguments) {
            .print_message_and_exit(output, "help requested:")
        } else {
            .stop(output, "parse error:")
        }
    } else if (grepl("^Traceback", output[1])) {
        .stop(output, "Error: python error")
    } else if (any(grepl("^SyntaxError: Non-ASCII character", output))) {
        message <- paste("Non-ASCII character detected.",
                       "If you wish to use Unicode arguments/options",
                       "please upgrade to Python 3.2+",
                       "Please see file INSTALL for more details.")
        .stop(message, "non-ascii character error:")
    } else if (any(grepl("^SyntaxError: positional argument follows keyword argument", output)) ||
               grepl("^SyntaxError: non-keyword arg after keyword arg", output[2])) {
        message <- "Positional argument following keyword argument."
        .stop(message, "syntax error:")
    } else if (grepl("^\\{|^\\[", output)) {
        args <- jsonlite::fromJSON(paste(output, collapse = ""))
        return(args)
    } else { # presumably version number request
        .print_message_and_exit(output, "version requested:")
    }
}

# @param argument argument to be converted from R to Python
convert_argument <- function(argument, as_list = FALSE) {
    if (is.character(argument)) argument <- shQuote(argument, type = "sh")
    if (is.numeric(argument)) argument <- as.character(argument)
    if (is.logical(argument)) argument <- ifelse(argument, "True", "False")
    if (is.null(argument)) argument <- "None"
    if (as_list) {
        argument <- sprintf("[%s]", paste(argument, collapse = ", "))
    } else if (length(argument) > 1) {
        argument <- sprintf("(%s)", paste(argument, collapse = ", "))
    }
    argument
}

get_python_type <- function(type, proposed_arguments) {
    python_type <- switch(type,
            character = "str",
            double = "float",
            integer = "int",
            logical = "bool",
            stop(paste(sprintf("type %s not supported,", type),
                    "supported types:",
                    "'logical', 'integer', 'double' or 'character'")))
    # warn if type set to "logical" and action set to "store"
    if (python_type == "bool" && any(grepl("action='store'", proposed_arguments)))
        warning("You almost certainly want to use action='store_true' or action='store_false' instead")
    sprintf("type=%s", python_type)
}

should_as_list <- function(name, argument_list) {
    if (name == "default" &&
        (argument_list[["action"]] %||% "store") == "append") {
        TRUE
    } else {
        FALSE
    }
}

`%||%` <- function(x, y) if (is.null(x)) y else x # nolint

# @param mode Either "add_argument" or "ArgumentParser"
convert_..._to_arguments <- function(mode, ...) { # nolint

    argument_list <- list(...)
    argument_names <- names(argument_list)
    if (is.null(argument_names))
        argument_names <- rep_len("", length(argument_list))
    equals <- ifelse(argument_names == "", "", "=")
    proposed_arguments <- c()
    for (ii in seq_along(argument_list)) {
        name <- argument_names[ii]
        equal <- equals[ii]
        as_list <- should_as_list(name, argument_list)
        argument <- convert_argument(argument_list[[ii]], as_list)
        proposed_arguments <- append(proposed_arguments,
                                     paste0(name, equal, argument))
    }
    # Make sure types are what Python wants
    if (mode == "add_argument" && any(grepl("type=", proposed_arguments))) {
        ii <- grep("type=", proposed_arguments)
        type <- argument_list[[ii]]
        proposed_arguments[ii] <- get_python_type(type, proposed_arguments)
    }
    # Don't put quotes around formatter_class argument
    if (mode == "ArgumentParser" && any(grepl("formatter_class=", proposed_arguments))) {
        ii <- grep("formatter_class=", proposed_arguments)
        formatter_class <- argument_list[[ii]]
        proposed_arguments[ii] <- sprintf("formatter_class=%s", formatter_class)
    }
    # Set right default prog name if not specified, if possible
    # Do last to not screw up other fixes with prog insertion
    if (mode == "ArgumentParser" && needs_prog(argument_names)) {
        prog <- get_Rscript_filename()
        if (is.na(prog)) prog <- "PROGRAM"
        proposed_arguments <- c(sprintf("prog='%s'", prog), proposed_arguments)
    }
    return(paste(proposed_arguments, collapse = ", "))
}

needs_prog <- function(argument_names) {
    if (length(argument_names) == 0L) {
        TRUE
    } else if (argument_names[1L] == "") {
        FALSE
    } else if (any(argument_names == "prog")) {
        FALSE
    } else {
        TRUE
    }
}

# Manually copied over from getopt to eliminate it as a dependency
get_Rscript_filename <- function() { # nolint
    prog <- sub("--file=", "", grep("--file=", commandArgs(), value = TRUE)[1])
    if (.Platform$OS.type == "windows") {
        prog <- gsub("\\\\", "\\\\\\\\", prog)
    }
    prog
}

# Internal function to check python cmd is okay
# @param python_cmd Python cmd to use
assert_python_cmd <- function(python_cmd) {
    if (!findpython::is_python_sufficient(python_cmd, required_modules = c("argparse", "json | simplejson"))) {
        stop(paste(sprintf("python executable %s either is not installed,", python_cmd),
                "is not on the path, or does not have argparse, json modules",
                "please see INSTALL file"))
    }
}

detects_python <- function() {
    python_cmd <- try(find_python_cmd())
    !inherits(python_cmd, "try-error")
}

# Internal function to find python cmd
# @param python_cmd  Python cmd to use
find_python_cmd <- function(python_cmd = NULL) {
    if (is.null(python_cmd)) {
        python_cmd <- getOption("python_cmd")
    }
    if (is.null(python_cmd)) {
        required_modules <- c("argparse", "json | simplejson")
        did_find_python3 <- findpython::can_find_python_cmd(minimum_version = "3.0",
                                                required_modules = required_modules,
                                                silent = TRUE)
        if (did_find_python3) {
            python_cmd <- attr(did_find_python3, "python_cmd")
        } else {
            python_cmd <- findpython::find_python_cmd(required_modules = required_modules)
        }
    }
    python_cmd
}

.stop <- function(message, r_note) {
        stop(paste(r_note, paste(message, collapse = "\n"), sep = "\n"))
}

# Internal function to print message
.print_message_and_exit <- function(message, r_note) {
    if (interactive()) {
        .stop(message, r_note)
    } else {
        cat(message, sep = "\n")
        quit(status = 0)
    }
}

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argparse documentation built on Nov. 26, 2021, 5:16 p.m.