Flags do not work in v 0.3

[Former user]

after updating to 0.3 (and changing nothing else), for my flag arguments, I get the error

Insufficient number of arguments supplied for --offline

which worked in previous versions with identical call.

[David Shih]

Hello,

Thanks for your bug report. In order for me to diagnose this, can you provide some code to demonstrate the bug?

Thanks, David

[David Shih]

I just tested flags using the example given in add_argument(). Flags seem to be working as expected.

library(argparser)

p <- arg_parser("A text file modifying program")

p <- add_argument(p, "input", help="input file")
p <- add_argument(p, "--output", help="output file", default="output.txt")
p <- add_argument(p, "--append", help="append to file", flag=TRUE)

argv <- parse_args(p, "input.txt");
stopifnot(argv$append == FALSE);
stopifnot(argv$input == "input.txt");

argv <- parse_args(p, c("--append", "input.txt"));
stopifnot(argv$append == TRUE);

argv <- parse_args(p, c("-a", "input.txt"));
stopifnot(argv$append == TRUE);

# this should throw an error as expected, because <input> is not specified
argv <- parse_args(p, c("--append"));

You might be using a special combination of flags, positional arguments, and optional arguments, and I cannot diagnose your problem without some example code. Alternatively, the error checking is more stringent in v0.3. If you can provide some minimal code, I could help.

[Dmytro Lituiev]

Maybe it is not the behaviour you imply, but by analogy with the pythonic argparse flags and bash optarg, I expected that one can use flags to switch between TRUE/FALSE:

###############################################################################################
library(argparser)
# Create a parser
p <- arg_parser("plot p-value QQ-plot")

# Add command line arguments
p <- add_argument(p,'--permute', flag = FALSE,
                   help='')

# Parse the command line arguments
argv <- parse_args(p)

################################################################################################

library(methods)

if (argv$permute){
    write("permuting", file=stderr() )
} else {
    write(" - ", file=stderr() )
}

calling: Rscript argtest.R -p

results in:

Error in preprocess_argv(argv, parser) :
  Insufficient number of arguments supplied for --permute
Calls: parse_args -> preprocess_argv
Execution halted

[David Shih]

The flag parameter to add_argument simply indicates whether an argument is a flag or not.

In your code,

# Add command line arguments
p <- add_argument(p,'--permute', flag = FALSE, help='')

--permute is treated as an optional argument, because you set flag = FALSE Therefore, it would expect an argument.

If you want to set a default value for --permute, then you would do

# Add command line arguments
p <- add_argument(p,'--permute', default = FALSE, help='')

You have to call Rscript argtest.R -p TRUE. If you call Rscript argtest.R, then argv$permute will be FALSE, due to the default value.

[David Shih]

If you want to use a flag, so that

• Rscript argtest.R runs with argv$permute as FALSE, and
• Rscript argtest.R -p runs with argv$permute as TRUE.

Then you would do:

###############################################################################################
library(argparser)
# Create a parser
p <- arg_parser("plot p-value QQ-plot")

# Add command line arguments
p <- add_argument(p, '--permute', flag = TRUE, help='')

# Parse the command line arguments
argv <- parse_args(p)

################################################################################################

library(methods)

if (argv$permute){
    write("permuting", file=stderr() )
} else {
    write(" - ", file=stderr() )
}

By default, all flag arguments take on a value of FALSE, unless the flag parameter is passed in the command line.

So if you want the program to permute by default,

• Rscript argtest.R runs with permute as TRUE, and
• Rscript argtest.R --nopermute runs with permute as FALSE.

Then you would write:

###############################################################################################
library(argparser)
# Create a parser
p <- arg_parser("plot p-value QQ-plot")

# Add command line arguments
p <- add_argument(p, '--nopermute', flag = TRUE, help='')

# Parse the command line arguments
argv <- parse_args(p)

################################################################################################

library(methods)
permute <- ! argv$nopermute

if (permute){
    write("permuting", file=stderr() )
} else {
    write(" - ", file=stderr() )
}

Notice that you set permute manually. You could also work with argv$nopermute directly if you want.

I implemented flags the way they behave in most programs I know. Suppose --flag is a flag, then

• program --flag causes program to run with flag as TRUE
• program (without --flag) causes program to run with flag as FALSE

Flags in Python's argparse are more flexible, but I didn't see the need for more complexity.

[Dmytro Lituiev]

yes, i meant pythonic behaviour of argparse, where True and False are whether default or action values:

parser.add_argument('--foo', action='store_true')
parser.add_argument('--bar', action='store_false')

which is a nice-to-have feature seemingly important for mutually exclusive flags. It was just confusing after the Python.