docopt boolean arg python - python

I use following args for my script with doctopt
Usage:
GaussianMixture.py --snpList=File --callingRAC=File
Options:
-h --help Show help.
snpList list snp txt
callingRAC results snp
I would like to add an argument that have a conditional consequence on my script : correct my datas or don't correct my datas. Something like :
Usage:
GaussianMixture.py --snpList=File --callingRAC=File correction(--0 | --1)
Options:
-h --help Show help.
snpList list snp txt
callingRAC results snp
correction 0 : without correction | 1 : with correction
And I would like to add in my script an if in some functions
def func1():
if args[correction] == 0:
datas = non_corrected_datas
if args[correction] == 1:
datas = corrected_datas
But I don't know how to write it in the usage neither in my script.

EDIT:
My original answer didn't take into account OP's requirements for --correction to be mandatory. Syntax was incorrect in my original answer. Here's a tested working example:
#!/usr/bin/env python
"""Usage:
GaussianMixture.py --snpList=File --callingRAC=File --correction=<BOOL>
Options:
-h, --help Show this message and exit.
-V, --version Show the version and exit
--snpList list snp txt
--callingRAC results snp
--correction=BOOL Perform correction? True or False. [default: True]
"""
__version__ = '0.0.1'
from docopt import docopt
def main(args):
args = docopt(__doc__, version=__version__)
print(args)
if args['--correction'] == 'True':
print("True")
else:
print("False")
if __name__ == '__main__':
args = docopt(__doc__, version=__version__)
main(args)
Please let me know if this works for you.

Not all options have to have arguments in docopt. In other words, you can use flag arguments instead. This is the most straightforward way to get boolean values from a user. That being said, you can simply do the following.
"""
Usage:
GaussianMixture.py (--correction | --no-correction)
Options:
--correction With correction
--no-correction Without correction
-h --help Show help.
"""
import docopt
if __name__ == '__main__':
args = docopt.docopt(__doc__)
print(args)

Related

How to run a Python file with boolean arguments

I have a .py file with a single function that basically converts a .csv file to a .pkl file. This file, when invoked from the terminal, is supposed to convert the measurements between imperial and metrics depending on whether the input is true or not. For example
python3 file.py imperial_units=True or python3 file.py imperial_units=False and if there are no arguments provided like python3 file.py, imperial units should just default to True:
This is my attempt:
import json, sys
import pandas as pd
def log_to_pickle(units):
...
if units == True: # If units == True, convert all metric to imperial
print('Imperial True')
if imperial_unit == False:
...
elif units == False: # If units == False, convert all imperial to metric
print('Imperial False')
if imperial_unit == True:
...
...
if __name__ == "__main__":
if sys.argv == True or sys.argv == '':
log_to_pickle(True)
else:
log_to_pickle(False)
I've added the print statements inside the if/elif block to see whether my inputs work. I ran python3 file.py imperial_units=True and the output was 'Imperial False'
What am I doing wrong?
There are a few wrong things here but the root cause is that the code doesn't use sys.argv correctly. Try printing sys.argv:
if __name__ == "__main__":
import sys
print(sys.argv)
$ python3 argv.py imperial_units=True
['argv.py', 'imperial_units=True']
You need to parse the command line arguments.
if __name__ == "__main__":
if len(sys.argv) <= 1 or sys.argv[1] == "imperial_units=True":
log_to_pickle(True)
else:
log_to_pickle(False)
Take a look at the argparse package for more robust command line argument handling.
I would use argparse for this type of thing. Use a boolean flag argument. I also like to provide a positive and a negative version for ease of use.
import argparse
...
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='log-to-pickle')
parser.add_argument('--imperial-units', dest='imperial_units', action='store_true')
parser.add_argument('--no-imperial-units', dest='imperial_units', action='store_false')
parser.set_defaults(imperial_units=True)
args = parser.parse_args()
log_to_pickle(args.imperial_units)
Using argparse you'll get some nice help messages too:
$ python3 file.py -h
usage: log-to-pickle [-h] [--imperial-units] [--no-imperial-units]
optional arguments:
-h, --help show this help message and exit
--imperial-units
--no-imperial-units
Now you can call the application like this:
# These are the same given the default.
$ python3 file.py
$ python3 file.py --imperial-units
Or to do the negative version:
$ python3 file.py --no-imperial-units
If you really want to provide a string argument to the bool flag, then I would make a custom method to transform string to boolean:
import argparse
def bool_arg(val):
return val.lower() in ('y', 'yes', 't', 'true', 'on', '1')
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='log-to-pickle')
parser.add_argument('--imperial-units', type=bool_arg, default=True)
args = parser.parse_args()
print(args.imperial_units)
Examples:
$ python3 file.py --imperial-units y
True
$ python3 file.py --imperial-units True
True
$ python3 file.py --imperial-units 0
False
sys.argv provides a list of arguments. You can iterate through it to find an argument that contains "imperial_units". You can then process this to get the boolean.
if __name__ == "__main__":
#Find arguments which contain imperial_units
arg = [x.split("=")[1] for x in sys.argv if "imperial_units" in x]
#If the length is 0, no args were found, default to true
#Otherwise use value after = and convert it to bool
arg = True if len(arg) == 0 else bool(arg[0])
log_to_pickle(arg)
argparse results in a more user-friendly program with help text and uses an arguably more standard method of dash-delimited parameters. Since you only want one thing, the unit of measure, I think it is best implemented with a choice flag that includes a default, but you could make a single argument such as --use-metric that defaults to False.
#!/usr/bin/env python3
import argparse
parser = argparse.ArgumentParser(description='CSV to Pickle with unit conversion to metric')
parser.add_argument('-u', '--unit', default='imperial', choices=['imperial', 'metric'],
help='Source unit type (imperial or metric)')
parser.add_argument('from_file', help="CSV file to convert")
parser.add_argument('to_file', help="Converted Pickle file")
args = parser.parse_args()
print(args.unit)
Options for using the program are
$ ./test.py --help
usage: test.py [-h] [-u {imperial,metric}] from_file to_file
CSV to Pickle with unit conversion to metric
positional arguments:
from_file CSV file to convert
to_file Converted Pickle file
optional arguments:
-h, --help show this help message and exit
-u {imperial,metric}, --unit {imperial,metric}
Source unit type (imperial or metric)
$ ./test.py --unit metric aaa.csv aaa.pkl
metric
$ ./test.py -u imperial aaa.csv aaa.plk
imperial
$ ./test.py aaa.csv aaa.pkl
imperial
$ ./test.py --unit=other aaa.csv aaa.pkl
usage: test.py [-h] [-u {imperial,metric}] from_file to_file
test.py: error: argument -u/--unit: invalid choice: 'other' (choose from 'imperial', 'metric')

How to handle optional and mandatory positional arguments with argparse(python)

I have been trying to execute my python script with some arguments passed. The way I want it to be is something like this:
python script.py filepath
but also to support this
python script.py filepath1 filepath2
My implementation has been:
parser = argparse.ArgumentParser()
mand = parser.add_argument_group("Mandatory arguments")
mand.add_argument("path1", help = "path1")
opt = parser.add_argument_group("Optional arguments")
opt.add_argument("path2", help = "path2")
args = parser.parse_args()
It seems to ask for both arguments. Does anyone have any suggestion as to what is the proper way to do this? One of my thoughts was to do two argument groups; one with the path1 and the other with both paths, but it still requested both.
Thanks guys and gals!
P.S. Python 2.7
Use nargs="?" (with argparse)
import argparse
parser = argparse.ArgumentParser()
mand = parser.add_argument_group("Mandatory arguments")
mand.add_argument("path1", help = "path1")
opt = parser.add_argument_group("Optional arguments")
opt.add_argument("path2", help = "path2", nargs="?")
args = parser.parse_args()
print args
See usage string:
$ python argscript.py
usage: argscript.py [-h] path1 [path2]
argscript.py: error: too few arguments
Or with -h:
$ python argscript.py -h
usage: argscript.py [-h] path1 [path2]
optional arguments:
-h, --help show this help message and exit
Mandatory arguments:
path1 path1
Optional arguments:
path2 path2
and try it with one positional argument only:
$ python argscript.py alfa
Namespace(path1='alfa', path2=None)
And with two:
$ python argscript.py alfa beta
Namespace(path1='alfa', path2='beta')
Sorry for a bit off topic answer. I prefer using docopt so in case it would be of interest for you.
Using docopt
Install docopt first:
$ pip install docopt
and with the script:
"""script.py
Usage:
script.py <fname>...
"""
if __name__ == "__main__":
from docopt import docopt
args = docopt(__doc__)
print args
You can use it this way:
Asking for usage script:
$ python script.py
Usage:
script.py <fname>...
Calling with one file name:
$ python script.py alfa
{'<fname>': ['alfa']}
Using with two names:
$ python script.py alfa beta
{'<fname>': ['alfa', 'beta']}
Playing with alternative usage descriptions:
Following would allow one or two file names, but never three or more:
"""script.py
Usage:
script.py <input> [<output>]
"""
if __name__ == "__main__":
from docopt import docopt
args = docopt(__doc__)
print args

Parsing command line parameters

As an example of my problem consider the following situation:
A user launches a program from command line with a syntax similar to this
python prog.py "hi there" hi=Hello there=World!
The output of the program is "Hello World!".
My question refers to the part of parsing the arguments. How can I save the information contained in the "hi=Hello there=World!" part in order to use it? From there I should be able to do something with it.
I don't have the slightest idea of what the parameters are going to be so the solution needs to be as generic as possible.
you have to do something like this... save this as "argtest.py":
import sys
def main(x):
print(x)
if __name__ == "__main__":
print sys.argv #notice this is whatever you put in the arguments
print sys.argv[0] # this is the name of the file you used
main(sys.argv[1])
this will pass the first arg into main()
so if you are running from command line
python argtest.py hello
your output will be
hello
in your main() you would of course define whatever you want to do with the argument
personally i do my parsing in under the if __name__=="__main__": line usually something like arguments = [x.split('=') for x in sys.argv[1:]] #if you want to seperate arguments like "pie=apple fart=stinky"
sys.argv is a list of whatever you put after python argtest.py space seperated
for example if you do python argtest.py apple pie comma poop
sys.argv[1] == 'apple'
sys.argv[2] == 'pie'
sys.argv[3] == 'comma'
sys.argv[4] == 'poop'
Using docopt
install docopt:
$ pip install docopt
Write the code of prog.py:
"""
Usage:
prog.py <greeting> <name>
"""
if __name__ == "__main__":
from docopt import docopt
args = docopt(__doc__)
print args
print "------"
name = args["<name>"]
greeting = args["<greeting>"]
print "{greeting} {name}!".format(greeting=greeting, name=name)
Use it:
First see usage instructions:
$ python prog.py
Usage:
prog.py <greeting> <name>
Then use it:
$ python prog.py Ola Mundi
{'<greeting>': 'Ola',
'<name>': 'Mundi'}
------
Ola Mundi!
I ended up using simple string processing:
import sys
entry = {}
for i in sys.argv[1:]:
pos = i.find("=")
entry[i[:pos]] = i[pos+1:]

Simple argparse example wanted: 1 argument, 3 results

The documentation for the argparse python module, while excellent I'm sure, is too much for my tiny beginner brain to grasp right now. I don't need to do math on the command line or meddle with formatting lines on the screen or change option characters. All I want to do is "If arg is A, do this, if B do that, if none of the above show help and quit".
Here's the way I do it with argparse (with multiple args):
parser = argparse.ArgumentParser(description='Description of your program')
parser.add_argument('-f','--foo', help='Description for foo argument', required=True)
parser.add_argument('-b','--bar', help='Description for bar argument', required=True)
args = vars(parser.parse_args())
args will be a dictionary containing the arguments:
if args['foo'] == 'Hello':
# code here
if args['bar'] == 'World':
# code here
In your case simply add only one argument.
My understanding of the original question is two-fold. First, in terms of the simplest possible argparse example, I'm surprised that I haven't seen it here. Of course, to be dead-simple, it's also all overhead with little power, but it might get you started.
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("a")
args = parser.parse_args()
if args.a == 'magic.name':
print 'You nailed it!'
But this positional argument is now required. If you leave it out when invoking this program, you'll get an error about missing arguments. This leads me to the second part of the original question. Matt Wilkie seems to want a single optional argument without a named label (the --option labels). My suggestion would be to modify the code above as follows:
...
parser.add_argument("a", nargs='?', default="check_string_for_empty")
...
if args.a == 'check_string_for_empty':
print 'I can tell that no argument was given and I can deal with that here.'
elif args.a == 'magic.name':
print 'You nailed it!'
else:
print args.a
There may well be a more elegant solution, but this works and is minimalist.
The argparse documentation is reasonably good but leaves out a few useful details which might not be obvious. (#Diego Navarro already mentioned some of this but I'll try to expand on his answer slightly.) Basic usage is as follows:
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--my-foo', default='foobar')
parser.add_argument('-b', '--bar-value', default=3.14)
args = parser.parse_args()
The object you get back from parse_args() is a 'Namespace' object: An object whose member variables are named after your command-line arguments. The Namespace object is how you access your arguments and the values associated with them:
args = parser.parse_args()
print (args.my_foo)
print (args.bar_value)
(Note that argparse replaces '-' in your argument names with underscores when naming the variables.)
In many situations you may wish to use arguments simply as flags which take no value. You can add those in argparse like this:
parser.add_argument('--foo', action='store_true')
parser.add_argument('--no-foo', action='store_false')
The above will create variables named 'foo' with value True, and 'no_foo' with value False, respectively:
if (args.foo):
print ("foo is true")
if (args.no_foo is False):
print ("nofoo is false")
Note also that you can use the "required" option when adding an argument:
parser.add_argument('-o', '--output', required=True)
That way if you omit this argument at the command line argparse will tell you it's missing and stop execution of your script.
Finally, note that it's possible to create a dict structure of your arguments using the vars function, if that makes life easier for you.
args = parser.parse_args()
argsdict = vars(args)
print (argsdict['my_foo'])
print (argsdict['bar_value'])
As you can see, vars returns a dict with your argument names as keys and their values as, er, values.
There are lots of other options and things you can do, but this should cover the most essential, common usage scenarios.
Matt is asking about positional parameters in argparse, and I agree that the Python documentation is lacking on this aspect. There's not a single, complete example in the ~20 odd pages that shows both parsing and using positional parameters.
None of the other answers here show a complete example of positional parameters, either, so here's a complete example:
# tested with python 2.7.1
import argparse
parser = argparse.ArgumentParser(description="An argparse example")
parser.add_argument('action', help='The action to take (e.g. install, remove, etc.)')
parser.add_argument('foo-bar', help='Hyphens are cumbersome in positional arguments')
args = parser.parse_args()
if args.action == "install":
print("You asked for installation")
else:
print("You asked for something other than installation")
# The following do not work:
# print(args.foo-bar)
# print(args.foo_bar)
# But this works:
print(getattr(args, 'foo-bar'))
The thing that threw me off is that argparse will convert the named argument "--foo-bar" into "foo_bar", but a positional parameter named "foo-bar" stays as "foo-bar", making it less obvious how to use it in your program.
Notice the two lines near the end of my example -- neither of those will work to get the value of the foo-bar positional param. The first one is obviously wrong (it's an arithmetic expression args.foo minus bar), but the second one doesn't work either:
AttributeError: 'Namespace' object has no attribute 'foo_bar'
If you want to use the foo-bar attribute, you must use getattr, as seen in the last line of my example. What's crazy is that if you tried to use dest=foo_bar to change the property name to something that's easier to access, you'd get a really bizarre error message:
ValueError: dest supplied twice for positional argument
Here's how the example above runs:
$ python test.py
usage: test.py [-h] action foo-bar
test.py: error: too few arguments
$ python test.py -h
usage: test.py [-h] action foo-bar
An argparse example
positional arguments:
action The action to take (e.g. install, remove, etc.)
foo-bar Hyphens are cumbersome in positional arguments
optional arguments:
-h, --help show this help message and exit
$ python test.py install foo
You asked for installation
foo
Yet another summary introduction, inspired by this post.
import argparse
# define functions, classes, etc.
# executes when your script is called from the command-line
if __name__ == "__main__":
parser = argparse.ArgumentParser()
#
# define each option with: parser.add_argument
#
args = parser.parse_args() # automatically looks at sys.argv
#
# access results with: args.argumentName
#
Arguments are defined with combinations of the following:
parser.add_argument( 'name', options... ) # positional argument
parser.add_argument( '-x', options... ) # single-char flag
parser.add_argument( '-x', '--long-name', options... ) # flag with long name
Common options are:
help: description for this arg when --help is used.
default: default value if the arg is omitted.
type: if you expect a float or int (otherwise is str).
dest: give a different name to a flag (e.g. '-x', '--long-name', dest='longName'). Note: by default --long-name is accessed with args.long_name
action: for special handling of certain arguments
store_true, store_false: for boolean args '--foo', action='store_true' => args.foo == True
store_const: to be used with option const '--foo', action='store_const', const=42 => args.foo == 42
count: for repeated options, as in ./myscript.py -vv '-v', action='count' => args.v == 2
append: for repeated options, as in ./myscript.py --foo 1 --foo 2 '--foo', action='append' => args.foo == ['1', '2']
required: if a flag is required, or a positional argument is not.
nargs: for a flag to capture N args ./myscript.py --foo a b => args.foo = ['a', 'b']
choices: to restrict possible inputs (specify as list of strings, or ints if type=int).
Note the Argparse Tutorial in Python HOWTOs. It starts from most basic examples, like this one:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("square", type=int,
help="display a square of a given number")
args = parser.parse_args()
print(args.square**2)
and progresses to less basic ones.
There is an example with predefined choice for an option, like what is asked:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("square", type=int,
help="display a square of a given number")
parser.add_argument("-v", "--verbosity", type=int, choices=[0, 1, 2],
help="increase output verbosity")
args = parser.parse_args()
answer = args.square**2
if args.verbosity == 2:
print("the square of {} equals {}".format(args.square, answer))
elif args.verbosity == 1:
print("{}^2 == {}".format(args.square, answer))
else:
print(answer)
Here's what I came up with in my learning project thanks mainly to #DMH...
Demo code:
import argparse
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--flag', action='store_true', default=False) # can 'store_false' for no-xxx flags
parser.add_argument('-r', '--reqd', required=True)
parser.add_argument('-o', '--opt', default='fallback')
parser.add_argument('arg', nargs='*') # use '+' for 1 or more args (instead of 0 or more)
parsed = parser.parse_args()
# NOTE: args with '-' have it replaced with '_'
print('Result:', vars(parsed))
print('parsed.reqd:', parsed.reqd)
if __name__ == "__main__":
main()
This may have evolved and is available online: command-line.py
Script to give this code a workout: command-line-demo.sh
code file: argparseDemo.py
Simple: common case
name(abbr, full), with help
import argparse
argParser = argparse.ArgumentParser()
argParser.add_argument("-n", "--name", help="your name")
args = argParser.parse_args()
print("args=%s" % args)
print("args.name=%s" % args.name)
call
python argparseDemo.py -n Crifan
python argparseDemo.py --name Crifan
output: args=Namespace(name='Crifan') and args.name=Crifan
type
argParser.add_argument("-a", "--age", type=int, help="your current age")
print("type(args.age)=%s" % type(args.age))
call: python argparseDemo.py --age 30
output: type(args.age)=<class 'int'> and args.age=30
required
argParser.add_argument("-a", "--age", required=True, type=int, help="your current age")
call: python argparseDemo.py
output: error argparseDemo.py: error: the following arguments are required: -a/--age
default
argParser.add_argument("-a", "--age", type=int, default=20, help="your current age. Default is 20")
call: python argparseDemo.py
output: args.age=20
choices
argParser.add_argument("-f", "--love-fruit", choices=['apple', 'orange', 'banana'], help="your love fruits")
call: python argparseDemo.py -f apple
output: args=Namespace(love_fruit='apple') and args.love_fruit=apple
multi args
argParser.add_argument("-f", "--love-fruit", nargs=2, help="your love fruits")
call: python argparseDemo.py -f apple orange
output: args.love_fruit=['apple', 'orange']
Detail
most simple: -x
code:
import argparse
argParser = argparse.ArgumentParser()
argParser.add_argument("-a") # most simple -> got args.a, type is `str`
args = argParser.parse_args()
print("args.a=%s" % args.a)
usage = run in command line
python argparseDemo.py -a 30
or: ./argparseDemo.py -a 30
makesure argparseDemo.py is executable
if not, add it: chmod +x argparseDemo.py
output
args.a=30
Note
default type is str
argParser.add_argument("-a") == argParser.add_argument("-a", type=str)
print("type(args.a)=%s" % type(args.a)) -> type(args.a)=<class 'str'>
args type is Namespace
print("type(args)=%s" % type(args)) -> type(args)=<class 'argparse.Namespace'>
args value is Namespace(a='30')
print("args=%s" % args) -> args=Namespace(a='30')
so we can call/use args.a
parameter name
full parameter name: --xxx
code
argParser.add_argument("-a", "--age")
usage
python argparseDemo.py -a 30
or: python argparseDemo.py --age 30
get parsed value: args.age
Note: NOT args.a, and NOT exist args.a
full parameter name with multiple words: --xxx-yyy
code
argParser.add_argument("-a", "--current-age")
get parsed value: args.current_age
add help description: help
code
argParser.add_argument("-a", help="your age") # with help
output
use --help can see description
 python argparseDemo.py --help
usage: argparseDemo.py [-h] [-a A]
optional arguments:
-h, --help show this help message and exit
-a A your age
designate parameter type: type
code
argParser.add_argument("-a", type=int) # parsed arg is `int`, not default `str`
output
print("type(args.a)=%s" % type(args.a)) -> type(args.a)=<class 'int'>
print("args=%s" % args) -> args=Namespace(a=30)
add default value: default
code
argParser.add_argument("-a", type=int, default=20) # if not pass a, a use default value: 20
effect
usage: python argparseDemo.py
output: print("args.age=%s" % args.age) -> args=Namespace(a=20)
You could also use plac (a wrapper around argparse).
As a bonus it generates neat help instructions - see below.
Example script:
#!/usr/bin/env python3
def main(
arg: ('Argument with two possible values', 'positional', None, None, ['A', 'B'])
):
"""General help for application"""
if arg == 'A':
print("Argument has value A")
elif arg == 'B':
print("Argument has value B")
if __name__ == '__main__':
import plac
plac.call(main)
Example output:
No arguments supplied - example.py:
usage: example.py [-h] {A,B}
example.py: error: the following arguments are required: arg
Unexpected argument supplied - example.py C:
usage: example.py [-h] {A,B}
example.py: error: argument arg: invalid choice: 'C' (choose from 'A', 'B')
Correct argument supplied - example.py A :
Argument has value A
Full help menu (generated automatically) - example.py -h:
usage: example.py [-h] {A,B}
General help for application
positional arguments:
{A,B} Argument with two possible values
optional arguments:
-h, --help show this help message and exit
Short explanation:
The name of the argument usually equals the parameter name (arg).
The tuple annotation after arg parameter has the following meaning:
Description (Argument with two possible values)
Type of argument - one of 'flag', 'option' or 'positional' (positional)
Abbreviation (None)
Type of argument value - eg. float, string (None)
Restricted set of choices (['A', 'B'])
Documentation:
To learn more about using plac check out its great documentation:
Plac: Parsing the Command Line the Easy Way
To add to what others have stated:
I usually like to use the 'dest' parameter to specify a variable name and then use 'globals().update()' to put those variables in the global namespace.
Usage:
$ python script.py -i "Hello, World!"
Code:
...
parser.add_argument('-i', '--input', ..., dest='inputted_variable',...)
globals().update(vars(parser.parse_args()))
...
print(inputted_variable) # Prints "Hello, World!"
New to this, but combining Python with Powershell and using this template, being inspired by an in-depth and great Python Command Line Arguments – Real Python
There is a lot you can do within the init_argparse() and I am covering just the most simple scenario here.
import argparse
use if __name__ == "__main__": main() pattern to execute from terminal
parse arguments within the main() function that has no parameters as all
define a init_argparse() function
create a parser object by calling argparse.ArgumentParser()
declare one or more argumnent with parser.add_argument("--<long_param_name>")
return parser
parse args by creating an args object by calling parser.parse_args()
define a function proper with param1, param2, ...
call function_proper with params being assigned as attributes of an args object
e.g. function_proper(param1=args.param1, param2=args.param2)
within a shell call the module with named arguments:
e.g. python foobar.py --param1="foo" --param2=="bar"
#file: foobar.py
import argparse
def function_proper(param1, param2):
#CODE...
def init_argparse() -> argparse.ArgumentParser:
parser = argparse.ArgumentParser()
parser.add_argument("--param1")
parser.add_argument("--param2")
return parser
def main() -> None:
parser = init_argparse()
args = parser.parse_args()
function_proper(param1=args.param1, param2=args.param2)
if __name__ == "__main__":
main()
>>> python .\foobar.py --param1="foo" --param2=="bar"
I went through all the examples and answers and in a way or another they didn't address my need. So I will list her a scenario that I need more help and I hope this can explain the idea more.
Initial Problem
I need to develop a tool which is getting a file to process it and it needs some optional configuration file to be used to configure the tool.
so what I need is something like the following
mytool.py file.text -config config-file.json
The solution
Here is the solution code
import argparse
def main():
parser = argparse.ArgumentParser(description='This example for a tool to process a file and configure the tool using a config file.')
parser.add_argument('filename', help="Input file either text, image or video")
# parser.add_argument('config_file', help="a JSON file to load the initial configuration ")
# parser.add_argument('-c', '--config_file', help="a JSON file to load the initial configuration ", default='configFile.json', required=False)
parser.add_argument('-c', '--config', default='configFile.json', dest='config_file', help="a JSON file to load the initial configuration " )
parser.add_argument('-d', '--debug', action="store_true", help="Enable the debug mode for logging debug statements." )
args = parser.parse_args()
filename = args.filename
configfile = args.config_file
print("The file to be processed is", filename)
print("The config file is", configfile)
if args.debug:
print("Debug mode enabled")
else:
print("Debug mode disabled")
print("and all arguments are: ", args)
if __name__ == '__main__':
main()
I will show the solution in multiple enhancements to show the idea
First Round: List the arguments
List all input as mandatory inputs so second argument will be
parser.add_argument('config_file', help="a JSON file to load the initial configuration ")
When we get the help command for this tool we find the following outcome
(base) > python .\argparser_example.py -h
usage: argparser_example.py [-h] filename config_file
This example for a tool to process a file and configure the tool using a config file.
positional arguments:
filename Input file either text, image or video
config_file a JSON file to load the initial configuration
optional arguments:
-h, --help show this help message and exit
and when I execute it as the following
(base) > python .\argparser_example.py filename.txt configfile.json
the outcome will be
The file to be processed is filename.txt
The config file is configfile.json
and all arguments are: Namespace(config_file='configfile.json', filename='filename.txt')
But the config file should be optional, I removed it from the arguments
(base) > python .\argparser_example.py filename.txt
The outcome will be is:
usage: argparser_example.py [-h] filename config_file
argparser_example.py: error: the following arguments are required: c
Which means we have a problem in the tool
Second Round : Make it optimal
So to make it optional I modified the program as follows
parser.add_argument('-c', '--config', help="a JSON file to load the initial configuration ", default='configFile.json', required=False)
The help outcome should be
usage: argparser_example.py [-h] [-c CONFIG] filename
This example for a tool to process a file and configure the tool using a config file.
positional arguments:
filename Input file either text, image or video
optional arguments:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
a JSON file to load the initial configuration
so when I execute the program
(base) > python .\argparser_example.py filename.txt
the outcome will be
The file to be processed is filename.txt
The config file is configFile.json
and all arguments are: Namespace(config_file='configFile.json', filename='filename.txt')
with arguments like
(base) > python .\argparser_example.py filename.txt --config_file anotherConfig.json
The outcome will be
The file to be processed is filename.txt
The config file is anotherConfig.json
and all arguments are: Namespace(config_file='anotherConfig.json', filename='filename.txt')
Round 3: Enhancements
to change the flag name from --config_file to --config while we keep the variable name as is we modify the code to include dest='config_file' as the following:
parser.add_argument('-c', '--config', help="a JSON file to load the initial configuration ", default='configFile.json', dest='config_file')
and the command will be
(base) > python .\argparser_example.py filename.txt --config anotherConfig.json
To add the support for having a debug mode flag, we need to add a flag in the arguments to support a boolean debug flag. To implement it i added the following:
parser.add_argument('-d', '--debug', action="store_true", help="Enable the debug mode for logging debug statements." )
the tool command will be:
(carnd-term1-38) > python .\argparser_example.py image.jpg -c imageConfig,json --debug
the outcome will be
The file to be processed is image.jpg
The config file is imageConfig,json
Debug mode enabled
and all arguments are: Namespace(config_file='imageConfig,json', debug=True, filename='image.jpg')
A really simple way to use argparse and amend the '-h'/ '--help' switches to display your own personal code help instructions is to set the default help to False, you can also add as many additional .add_arguments as you like:
import argparse
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument('-h', '--help', action='help',
help='To run this script please provide two arguments')
parser.parse_args()
Run: python test.py -h
Output:
usage: test.py [-h]
optional arguments:
-h, --help To run this script please provide two arguments
As an addition to existing answers, if you are lazy enough, it is possible to use code generation tool called protoargs. It generates arguments parser from the configuration. For python it uses argparse.
Configuration with optional A and B:
syntax = "proto2";
message protoargs
{
optional string A = 1; // A param description
optional string B = 2; // B param description
}//protoargs
Configuration with required A and B:
syntax = "proto2";
message protoargs
{
required string A = 1; // A param description
required string B = 2; // B param description
}//protoargs
Configuration with positional A and B:
syntax = "proto2";
message protoargs
{
required string A = 1; // A param description
required string B = 2; // B param description
}//protoargs
message protoargs_links
{
}//protoargs_links
Now all you should run is:
python ./protoargs.py -i test.proto -o . --py
And use it (it is possible to take other examples here):
import sys
import test_pa
class ArgsParser:
program = "test"
description = "Simple A and B parser test."
def parse(self, argv):
self.config = test_pa.parse(self.program, self.description, argv)
def usage(self):
return test_pa.usage(self.program, self.description)
if __name__ == "__main__":
parser = ArgsParser()
if len(sys.argv) == 1:
print(parser.usage())
else:
parser.parse(sys.argv[1:])
if parser.config.A:
print(parser.config.A)
if parser.config.B:
print(parser.config.B)
If you want more - change configuration, regenerate parser, use an updated parser.config.
UPD: As mentioned in rules, I must specify that this is my own project
code:
import argparse
parser=argparse.ArgumentParser()
parser.add_argument('-A', default=False, action='store_true')
parser.add_argument('-B', default=False, action='store_true')
args=parser.parse_args()
if args.A:
print('do this')
elif args.B:
print('do that')
else:
print('help')
running result:
$ python3 test.py
help
$ python3 test.py -A
do this
$ python3 test.py -B
do that
$ python3 test.py -C
usage: test.py [-h] [-A] [-B]
test.py: error: unrecognized arguments: -C
As for the original request (if A ....), I would use argv to solve it, not using argparse at all:
import sys
if len(sys.argv)==2:
if sys.argv[1] == 'A':
print('do this')
elif sys.argv[1] == 'B':
print('do that')
else:
print('help')
else:
print('help')
Since you have not clarified wheather the arguments 'A' and 'B' are positional or optional, I'll make a mix of both.
Positional arguments are required by default. If not giving one will throw 'Few arguments given' which is not the case for the optional arguments going by their name. This program will take a number and return its square by default, if the cube option is used it shall return its cube.
import argparse
parser = argparse.ArgumentParser('number-game')
parser.add_argument(
"number",
type=int,
help="enter a number"
)
parser.add_argument(
"-c", "--choice",
choices=['square','cube'],
help="choose what you need to do with the number"
)
# all the results will be parsed by the parser and stored in args
args = parser.parse_args()
# if square is selected return the square, same for cube
if args.c == 'square':
print("{} is the result".format(args.number**2))
elif args.c == 'cube':
print("{} is the result".format(args.number**3))
else:
print("{} is not changed".format(args.number))
usage
$python3 script.py 4 -c square
16
Here the optional arguments are taking value, if you just wanted to use it like a flag you can too. So by using -s for square and -c for cube we change the behaviour, by adding action = "store_true". It is changed to true only when used.
parser.add_argument(
"-s", "--square",
help="returns the square of number",
action="store_true"
)
parser.add_argument(
"-c", "--cube",
help="returns the cube of number",
action="store_true"
)
so the conditional block can be changed to,
if args.s:
print("{} is the result".format(args.number**2))
elif args.c:
print("{} is the result".format(args.number**3))
else:
print("{} is not changed".format(args.number))
usage
$python3 script.py 4 -c
64
The simplest answer!
P.S. the one who wrote the document of argparse is foolish
python code:
import argparse
parser = argparse.ArgumentParser(description='')
parser.add_argument('--o_dct_fname',type=str)
parser.add_argument('--tp',type=str)
parser.add_argument('--new_res_set',type=int)
args = parser.parse_args()
o_dct_fname = args.o_dct_fname
tp = args.tp
new_res_set = args.new_res_set
running code
python produce_result.py --o_dct_fname o_dct --tp father_child --new_res_set 1

What's the best way to parse command line arguments? [duplicate]

This question already has answers here:
How to read/process command line arguments?
(22 answers)
Closed 8 months ago.
What's the easiest, tersest, and most flexible method or library for parsing Python command line arguments?
argparse is the way to go. Here is a short summary of how to use it:
1) Initialize
import argparse
# Instantiate the parser
parser = argparse.ArgumentParser(description='Optional app description')
2) Add Arguments
# Required positional argument
parser.add_argument('pos_arg', type=int,
help='A required integer positional argument')
# Optional positional argument
parser.add_argument('opt_pos_arg', type=int, nargs='?',
help='An optional integer positional argument')
# Optional argument
parser.add_argument('--opt_arg', type=int,
help='An optional integer argument')
# Switch
parser.add_argument('--switch', action='store_true',
help='A boolean switch')
3) Parse
args = parser.parse_args()
4) Access
print("Argument values:")
print(args.pos_arg)
print(args.opt_pos_arg)
print(args.opt_arg)
print(args.switch)
5) Check Values
if args.pos_arg > 10:
parser.error("pos_arg cannot be larger than 10")
Usage
Correct use:
$ ./app 1 2 --opt_arg 3 --switch
Argument values:
1
2
3
True
Incorrect arguments:
$ ./app foo 2 --opt_arg 3 --switch
usage: convert [-h] [--opt_arg OPT_ARG] [--switch] pos_arg [opt_pos_arg]
app: error: argument pos_arg: invalid int value: 'foo'
$ ./app 11 2 --opt_arg 3
Argument values:
11
2
3
False
usage: app [-h] [--opt_arg OPT_ARG] [--switch] pos_arg [opt_pos_arg]
convert: error: pos_arg cannot be larger than 10
Full help:
$ ./app -h
usage: app [-h] [--opt_arg OPT_ARG] [--switch] pos_arg [opt_pos_arg]
Optional app description
positional arguments:
pos_arg A required integer positional argument
opt_pos_arg An optional integer positional argument
optional arguments:
-h, --help show this help message and exit
--opt_arg OPT_ARG An optional integer argument
--switch A boolean switch
This answer suggests optparse which is appropriate for older Python versions. For Python 2.7 and above, argparse replaces optparse. See this answer for more information.
As other people pointed out, you are better off going with optparse over getopt. getopt is pretty much a one-to-one mapping of the standard getopt(3) C library functions, and not very easy to use.
optparse, while being a bit more verbose, is much better structured and simpler to extend later on.
Here's a typical line to add an option to your parser:
parser.add_option('-q', '--query',
action="store", dest="query",
help="query string", default="spam")
It pretty much speaks for itself; at processing time, it will accept -q or --query as options, store the argument in an attribute called query and has a default value if you don't specify it. It is also self-documenting in that you declare the help argument (which will be used when run with -h/--help) right there with the option.
Usually you parse your arguments with:
options, args = parser.parse_args()
This will, by default, parse the standard arguments passed to the script (sys.argv[1:])
options.query will then be set to the value you passed to the script.
You create a parser simply by doing
parser = optparse.OptionParser()
These are all the basics you need. Here's a complete Python script that shows this:
import optparse
parser = optparse.OptionParser()
parser.add_option('-q', '--query',
action="store", dest="query",
help="query string", default="spam")
options, args = parser.parse_args()
print 'Query string:', options.query
5 lines of python that show you the basics.
Save it in sample.py, and run it once with
python sample.py
and once with
python sample.py --query myquery
Beyond that, you will find that optparse is very easy to extend.
In one of my projects, I created a Command class which allows you to nest subcommands in a command tree easily. It uses optparse heavily to chain commands together. It's not something I can easily explain in a few lines, but feel free to browse around in my repository for the main class, as well as a class that uses it and the option parser
Using docopt
Since 2012 there is a very easy, powerful and really cool module for argument parsing called docopt. Here is an example taken from its documentation:
"""Naval Fate.
Usage:
naval_fate.py ship new <name>...
naval_fate.py ship <name> move <x> <y> [--speed=<kn>]
naval_fate.py ship shoot <x> <y>
naval_fate.py mine (set|remove) <x> <y> [--moored | --drifting]
naval_fate.py (-h | --help)
naval_fate.py --version
Options:
-h --help Show this screen.
--version Show version.
--speed=<kn> Speed in knots [default: 10].
--moored Moored (anchored) mine.
--drifting Drifting mine.
"""
from docopt import docopt
if __name__ == '__main__':
arguments = docopt(__doc__, version='Naval Fate 2.0')
print(arguments)
So this is it: 2 lines of code plus your doc string which is essential and you get your arguments parsed and available in your arguments object.
Using python-fire
Since 2017 there's another cool module called python-fire. It can generate a CLI interface for your code with you doing zero argument parsing. Here's a simple example from the documentation (this small program exposes the function double to the command line):
import fire
class Calculator(object):
def double(self, number):
return 2 * number
if __name__ == '__main__':
fire.Fire(Calculator)
From the command line, you can run:
> calculator.py double 10
20
> calculator.py double --number=15
30
The new hip way is argparse for these reasons. argparse > optparse > getopt
update: As of py2.7 argparse is part of the standard library and optparse is deprecated.
I prefer Click. It abstracts managing options and allows "(...) creating beautiful command line interfaces in a composable way with as little code as necessary".
Here's example usage:
import click
#click.command()
#click.option('--count', default=1, help='Number of greetings.')
#click.option('--name', prompt='Your name',
help='The person to greet.')
def hello(count, name):
"""Simple program that greets NAME for a total of COUNT times."""
for x in range(count):
click.echo('Hello %s!' % name)
if __name__ == '__main__':
hello()
It also automatically generates nicely formatted help pages:
$ python hello.py --help
Usage: hello.py [OPTIONS]
Simple program that greets NAME for a total of COUNT times.
Options:
--count INTEGER Number of greetings.
--name TEXT The person to greet.
--help Show this message and exit.
Pretty much everybody is using getopt
Here is the example code for the doc :
import getopt, sys
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "ho:v", ["help", "output="])
except getopt.GetoptError:
# print help information and exit:
usage()
sys.exit(2)
output = None
verbose = False
for o, a in opts:
if o == "-v":
verbose = True
if o in ("-h", "--help"):
usage()
sys.exit()
if o in ("-o", "--output"):
output = a
So in a word, here is how it works.
You've got two types of options. Those who are receiving arguments, and those who are
just like switches.
sys.argv is pretty much your char** argv in C. Like in C you skip the first element which is the name of your program and parse only the arguments : sys.argv[1:]
Getopt.getopt will parse it according to the rule you give in argument.
"ho:v" here describes the short arguments : -ONELETTER. The : means that -o accepts one argument.
Finally ["help", "output="] describes long arguments ( --MORETHANONELETTER ).
The = after output once again means that output accepts one arguments.
The result is a list of couple (option,argument)
If an option doesn't accept any argument (like --help here) the arg part is an empty string.
You then usually want to loop on this list and test the option name as in the example.
I hope this helped you.
Use optparse which comes with the standard library. For example:
#!/usr/bin/env python
import optparse
def main():
p = optparse.OptionParser()
p.add_option('--person', '-p', default="world")
options, arguments = p.parse_args()
print 'Hello %s' % options.person
if __name__ == '__main__':
main()
Source: Using Python to create UNIX command line tools
However as of Python 2.7 optparse is deprecated, see: Why use argparse rather than optparse?
Lightweight command line argument defaults
Although argparse is great and is the right answer for fully documented command line switches and advanced features, you can use function argument defaults to handles straightforward positional arguments very simply.
import sys
def get_args(name='default', first='a', second=2):
return first, int(second)
first, second = get_args(*sys.argv)
print first, second
The 'name' argument captures the script name and is not used. Test output looks like this:
> ./test.py
a 2
> ./test.py A
A 2
> ./test.py A 20
A 20
For simple scripts where I just want some default values, I find this quite sufficient. You might also want to include some type coercion in the return values or command line values will all be strings.
Just in case you might need to, this may help if you need to grab unicode arguments on Win32 (2K, XP etc):
from ctypes import *
def wmain(argc, argv):
print argc
for i in argv:
print i
return 0
def startup():
size = c_int()
ptr = windll.shell32.CommandLineToArgvW(windll.kernel32.GetCommandLineW(), byref(size))
ref = c_wchar_p * size.value
raw = ref.from_address(ptr)
args = [arg for arg in raw]
windll.kernel32.LocalFree(ptr)
exit(wmain(len(args), args))
startup()
Argparse code can be longer than actual implementation code!
That's a problem I find with most popular argument parsing options is that if your parameters are only modest, the code to document them becomes disproportionately large to the benefit they provide.
A relative new-comer to the argument parsing scene (I think) is plac.
It makes some acknowledged trade-offs with argparse, but uses inline documentation and wraps simply around main() type function function:
def main(excel_file_path: "Path to input training file.",
excel_sheet_name:"Name of the excel sheet containing training data including columns 'Label' and 'Description'.",
existing_model_path: "Path to an existing model to refine."=None,
batch_size_start: "The smallest size of any minibatch."=10.,
batch_size_stop: "The largest size of any minibatch."=250.,
batch_size_step: "The step for increase in minibatch size."=1.002,
batch_test_steps: "Flag. If True, show minibatch steps."=False):
"Train a Spacy (http://spacy.io/) text classification model with gold document and label data until the model nears convergence (LOSS < 0.5)."
pass # Implementation code goes here!
if __name__ == '__main__':
import plac; plac.call(main)
I prefer optparse to getopt. It's very declarative: you tell it the names of the options and the effects they should have (e.g., setting a boolean field), and it hands you back a dictionary populated according to your specifications.
http://docs.python.org/lib/module-optparse.html
I think the best way for larger projects is optparse, but if you are looking for an easy way, maybe http://werkzeug.pocoo.org/documentation/script is something for you.
from werkzeug import script
# actions go here
def action_foo(name=""):
"""action foo does foo"""
pass
def action_bar(id=0, title="default title"):
"""action bar does bar"""
pass
if __name__ == '__main__':
script.run()
So basically every function action_* is exposed to the command line and a nice
help message is generated for free.
python foo.py
usage: foo.py <action> [<options>]
foo.py --help
actions:
bar:
action bar does bar
--id integer 0
--title string default title
foo:
action foo does foo
--name string
consoleargs deserves to be mentioned here. It is very easy to use. Check it out:
from consoleargs import command
#command
def main(url, name=None):
"""
:param url: Remote URL
:param name: File name
"""
print """Downloading url '%r' into file '%r'""" % (url, name)
if __name__ == '__main__':
main()
Now in console:
% python demo.py --help
Usage: demo.py URL [OPTIONS]
URL: Remote URL
Options:
--name -n File name
% python demo.py http://www.google.com/
Downloading url ''http://www.google.com/'' into file 'None'
% python demo.py http://www.google.com/ --name=index.html
Downloading url ''http://www.google.com/'' into file ''index.html''
Here's a method, not a library, which seems to work for me.
The goals here are to be terse, each argument parsed by a single line, the args line up for readability, the code is simple and doesn't depend on any special modules (only os + sys), warns about missing or unknown arguments gracefully, use a simple for/range() loop, and works across python 2.x and 3.x
Shown are two toggle flags (-d, -v), and two values controlled by arguments (-i xxx and -o xxx).
import os,sys
def HelpAndExit():
print("<<your help output goes here>>")
sys.exit(1)
def Fatal(msg):
sys.stderr.write("%s: %s\n" % (os.path.basename(sys.argv[0]), msg))
sys.exit(1)
def NextArg(i):
'''Return the next command line argument (if there is one)'''
if ((i+1) >= len(sys.argv)):
Fatal("'%s' expected an argument" % sys.argv[i])
return(1, sys.argv[i+1])
### MAIN
if __name__=='__main__':
verbose = 0
debug = 0
infile = "infile"
outfile = "outfile"
# Parse command line
skip = 0
for i in range(1, len(sys.argv)):
if not skip:
if sys.argv[i][:2] == "-d": debug ^= 1
elif sys.argv[i][:2] == "-v": verbose ^= 1
elif sys.argv[i][:2] == "-i": (skip,infile) = NextArg(i)
elif sys.argv[i][:2] == "-o": (skip,outfile) = NextArg(i)
elif sys.argv[i][:2] == "-h": HelpAndExit()
elif sys.argv[i][:1] == "-": Fatal("'%s' unknown argument" % sys.argv[i])
else: Fatal("'%s' unexpected" % sys.argv[i])
else: skip = 0
print("%d,%d,%s,%s" % (debug,verbose,infile,outfile))
The goal of NextArg() is to return the next argument while checking for missing data, and 'skip' skips the loop when NextArg() is used, keeping the flag parsing down to one liners.
I extended Erco's approach to allow for required positional arguments and for optional arguments. These should precede the -d, -v etc. arguments.
Positional and optional arguments can be retrieved with PosArg(i) and OptArg(i, default) respectively.
When an optional argument is found the start position of searching for options (e.g. -i) is moved 1 ahead to avoid causing an 'unexpected' fatal.
import os,sys
def HelpAndExit():
print("<<your help output goes here>>")
sys.exit(1)
def Fatal(msg):
sys.stderr.write("%s: %s\n" % (os.path.basename(sys.argv[0]), msg))
sys.exit(1)
def NextArg(i):
'''Return the next command line argument (if there is one)'''
if ((i+1) >= len(sys.argv)):
Fatal("'%s' expected an argument" % sys.argv[i])
return(1, sys.argv[i+1])
def PosArg(i):
'''Return positional argument'''
if i >= len(sys.argv):
Fatal("'%s' expected an argument" % sys.argv[i])
return sys.argv[i]
def OptArg(i, default):
'''Return optional argument (if there is one)'''
if i >= len(sys.argv):
Fatal("'%s' expected an argument" % sys.argv[i])
if sys.argv[i][:1] != '-':
return True, sys.argv[i]
else:
return False, default
### MAIN
if __name__=='__main__':
verbose = 0
debug = 0
infile = "infile"
outfile = "outfile"
options_start = 3
# --- Parse two positional parameters ---
n1 = int(PosArg(1))
n2 = int(PosArg(2))
# --- Parse an optional parameters ---
present, a3 = OptArg(3,50)
n3 = int(a3)
options_start += int(present)
# --- Parse rest of command line ---
skip = 0
for i in range(options_start, len(sys.argv)):
if not skip:
if sys.argv[i][:2] == "-d": debug ^= 1
elif sys.argv[i][:2] == "-v": verbose ^= 1
elif sys.argv[i][:2] == "-i": (skip,infile) = NextArg(i)
elif sys.argv[i][:2] == "-o": (skip,outfile) = NextArg(i)
elif sys.argv[i][:2] == "-h": HelpAndExit()
elif sys.argv[i][:1] == "-": Fatal("'%s' unknown argument" % sys.argv[i])
else: Fatal("'%s' unexpected" % sys.argv[i])
else: skip = 0
print("Number 1 = %d" % n1)
print("Number 2 = %d" % n2)
print("Number 3 = %d" % n3)
print("Debug = %d" % debug)
print("verbose = %d" % verbose)
print("infile = %s" % infile)
print("outfile = %s" % outfile)

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