Python default parameter if no command line arguments are passed - python

I'l like to build a program with this behaviour:
usage: sage 4ct.py [-h] (-r R | -i I | -p P) [-o O]
But if you don't give any parameter, I'd like to have "-r 100" as the default.
Is it possible?
parser = argparse.ArgumentParser(description = '4ct args')
group_input = parser.add_mutually_exclusive_group(required = True)
group_input.add_argument("-r", "-random", help = "Random graph: dual of a triangulation of N vertices", nargs = 1, type = int, default = 100)
group_input.add_argument("-i", "-input", help = "Input edgelist filename (networkx)", nargs = 1)
group_input.add_argument("-p", "-planar", help = "Load a planar embedding of the graph G.faces() - Automatically saved at each run: input_planar_file.serialized", nargs = 1)
parser.add_argument("-o", "-output", help="Output edgelist filename (networkx)", nargs = 1, required = False)
args = parser.parse_args()

Just remove the requiredargument of the add_mutually_exclusive_group function call (or set it to False) and you're done:
import argparse
parser = argparse.ArgumentParser(description = '4ct args')
group_input = parser.add_mutually_exclusive_group(required = False)
group_input.add_argument("-r", "--random", help = "Random graph: dual of a triangulation of N vertices", type = int, default = 100)
group_input.add_argument("-i", "--input", help = "Input edgelist filename (networkx)")
group_input.add_argument("-p", "--planar", help = "Load a planar embedding of the graph G.faces() - Automatically saved at each run: input_planar_file.serialized")
parser.add_argument("-o", "--output", help="Output edgelist filename (networkx)", required = False)
print(parser.parse_args())
# Namespace(input=None, output=None, planar=None, random=100)
print(parser.parse_args("-r 77".split()))
# Namespace(input=None, output=None, planar=None, random=77)
print(parser.parse_args("-o some/path".split()))
# Namespace(input=None, output='some/path', planar=None, random=100)
print(parser.parse_args("-i some/path".split()))
# Namespace(input='some/path', output=None, planar=None, random=100)
print(parser.parse_args("-i some/path -o some/other/path".split()))
# Namespace(input='some/path', output='some/other/path', planar=None, random=100)
print(parser.parse_args("-r 42 -o some/other/path".split()))
# Namespace(input=None, output='some/other/path', planar=None, random=42)
As you can see, the random option is defaulted to 100 even if:
the output option is provided, which seems normal
an option from the mutual exclusive group other than random is provided, which can be problematic. you will have to check in your code if random is the only exclusive option which has a value before taking it in account.
This example also includes some tiny improvement to your option parser:
use long option names with two dashes (it is a convention but it also allows argparse to correctly recognise option name).
remove the nargs=1 in your options definitions which makes you retrieve a list of one value. By removing it, you could retrieve directly the value.

Give the following a try:
import argparse
import sys
parser = argparse.ArgumentParser(description='4ct args')
group_input = parser.add_mutually_exclusive_group(required=True)
group_input.add_argument("-r", "-random", help="Random graph: dual of a triangulation of N vertices", nargs=1, type=int, default=100)
group_input.add_argument("-i", "-input", help="Input edgelist filename (networkx)", nargs=1)
group_input.add_argument("-p", "-planar", help="Load a planar embedding of the graph G.faces() - Automatically saved at each run: input_planar_file.serialized",nargs=1)
parser.add_argument("-o", "-output", help="Output edgelist filename (networkx)", nargs=1, required=False)
if not sys.argv[1:]:
sys.argv.extend(['-r', '100'])
args = parser.parse_args(sys.argv[1:])
Essentially you are checking if any commandline parameters are given at all, and if not, you append the desired -r 100

Related

How to take bulk inputs in python using input function

Code as following:
#enter code here
source_input = input("enter source url: ")
destination_input = input("enter the destination url: ")
new_source = source_input.replace("https://www.domain.com.au","")
new_destination = destination_input.replace("https://www.domain.com.au","")
symbol = "=>"
symbol_space = len(symbol)
center = symbol.center(symbol_space)
source_final = f" '{new_source}' "
destination_final = f" '{new_destination}' "
print(source_final+center+destination_final)
but this code is not taking multiline inputs. I want to provide multiple source and destination inputs like:
Actual source input
https://www.domain.com.au/shop
Actual destination input
https://www.domain.com.au/shopwithus
Actual output
'/shop' => '/shopwithus'
desired source inputs to be taken
https://www.domain.com.au/shop
https://www.domain.com.au/main
https://www.domain.com.au/home
https://www.domain.com.au/contactus
desired destiantion inputs to be taken
https://www.domain.com.au/shopwithus
https://www.domain.com.au/gomain
https://www.domain.com.au/homemain
https://www.domain.com.au/contactus
Desired outputs
'/shop' => '/shopwithus'
'/main' => '/gomain'
'/home' => 'homemain'
'/contactus' => '/contactus'
is there any way to achieve this kind of inputs and outputs?
This may be a lateral move but you could use command line arguments with argparse:
#!/usr/bin/env python3
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-s', '--source', help='The source.', required=True, type=str)
parser.add_argument('-d', '--destination', help='The desitnation.', required=True, type=str)
cmd_args = parser.parse_args()
def main() -> None:
print("source :", cmd_args.source)
print("destination:", cmd_args.destination)
if __name__ == "__main__":
main()
Then when executing just specify the arguments like follows (to script is called tmp.py)
python3 tmp.py -s "www.source.com" -d "www.destination.com"
# source : www.source.com
# destination: www.destination.com

Resolve argparse alias back to the original command

I'm using a subparser/subcommand that has an alias.
I'm using the dest option for the subparser to store the name of the subcommand so I can get it later.
Currently if the subcommand's name is reallyLongName and the alias is r (say) then the dest option stores either reallyLongName or r exactly - whatever I typed in gets stored. This is annoying because I now have to check for the name of the command or any of its aliases in order to identify the command.
Is there a way to get argparse to store the subcommand's name in the dest field in some sort of single, canonical text string?
For example, given the following code:
import argparse
parser = argparse.ArgumentParser()
subparsers = parser.add_subparsers(dest='command', help='sub-command help')
parser_ag = subparsers.add_parser( 'mySubcommand',
aliases=['m'],
help='Subcommand help')
print(parser.parse_args('mySubcommand'.split()))
print(parser.parse_args('m'.split()))
the following output is produced:
Namespace(command='mySubcommand')
Namespace(command='m')
Desired result: command has a single, canonical value for both, for example:
Namespace(command='mySubcommand')
Namespace(command='mySubcommand')
There was a Python bug/issue requesting this - saving the 'base' name, rather than the alias. You can't change that without changing argparse.py code. I think the change would limited to the Action subclass that handles subparsers. https://bugs.python.org/issue36664
But I point out that there's simpler way of handling this. Just use set_defaults as documented near the end of the https://docs.python.org/3/library/argparse.html#sub-commands section. There
parser_foo.set_defaults(func=foo)
is used to set a subparser specific function, but it could just as well be used to set the 'base' name.
parser_foo.set_defaults(name='theIncrediblyLongAlias')
This was surprisingly difficult to dig out. When you add a subparser, it gets stored in the parents ._actions attribute. From there it is just digging through attributes to get what you need. Below I create dictionaries to reference the subparser arguments by the dest name, and then added a function that lets us remap the inputted arguments to the primary argument name.
from collections import defaultdict
def get_subparser_aliases(parser, dest):
out = defaultdict(list)
prog_str = parser.prog
dest_dict = {a.dest: a for a in parser._actions}
try:
choices = dest_dict.get(dest).choices
except AttributeError:
raise AttributeError(f'The parser "{parser}" has no subparser with a `dest` of "{dest}"')
for k, v in choices.items():
clean_v = v.prog.replace(prog_str, '', 1).strip()
out[clean_v].append(k)
return dict(out)
def remap_args(args, mapping, dest):
setattr(args, dest, mapping.get(getattr(args, dest)))
return args
Using your example, we can remap the parse args using:
import argparse
parser = argparse.ArgumentParser()
subparsers = parser.add_subparsers(dest='command', help='sub-command help')
parser_ag = subparsers.add_parser('mySubcommand',
aliases=['m'],
help='Subcommand help')
args = parser.parse_args('m'.split())
mapping = get_subparser_aliases(parser, 'command')
remap_args(args, mapping, 'command')
print(args)
# prints:
Namespace(command='mySubcommand')
Here is an example of it at work with multiple subparser levels.. We have a parser with an optional argument and a subparser. The subparser has 3 possible arguments, the last of which invoke another subparser (a sub-subparser), with 2 possible arguments.
You can examine either the top level parser or the first level subparser to see alias mappings.
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--someoption', '-s', action='store_true')
subparser1 = parser.add_subparsers(help='sub-command help', dest='sub1')
parser_r = subparser1.add_parser('reallyLongName', aliases=['r'])
parser_r.add_argument('foo', type=int, help='foo help')
parser_s = subparser1.add_parser('otherReallyLong', aliases=['L'])
parser_s.add_argument('bar', choices='abc', help='bar help')
parser_z = subparser1.add_parser('otherOptions', aliases=['oo'])
subparser2 = parser_z.add_subparsers(help='sub-sub-command help', dest='sub2')
parser_x = subparser2.add_parser('xxx', aliases=['x'])
parser_x.add_argument('fizz', type=float, help='fizz help')
parser_y = subparser2.add_parser('yyy', aliases=['y'])
parser_y.add_argument('blip', help='blip help')
get_subparser_aliases(parser, 'sub1')
# returns:
{'reallyLongName': ['reallyLongName', 'r'],
'otherReallyLong': ['otherReallyLong', 'L'],
'otherOptions': ['otherOptions', 'oo']}
get_subparser_aliases(parser_z, 'sub2')
# returns:
{'xxx': ['xxx', 'x'], 'yyy': ['yyy', 'y']}
Using this with the function above, we can remap the collected args to their longer names.
args = parser.parse_args('-s oo x 1.23'.split())
print(args)
# prints:
Namespace(fizz=1.23, someoption=True, sub1='oo', sub2='x')
for p, dest in zip((parser, parser_z), ('sub1', 'sub2')):
mapping = get_subparser_aliases(p, dest)
remap_args(args, mapping, dest)
print(args)
# prints:
Namespace(fizz=1.23, someoption=True, sub1='otherOptions', sub2='xxx')

Command-line argument overwritten by default value when using subparser

I have a program with sub commands, but they all have common arguments (e.g. they all require input and output directories) which I included in the parent parser to avoid redundancies. However, I want each subcommand to have a different default value, but this causes the value provided in the command-line to be ignored.
MWE:
import argparse
top_parser = argparse.ArgumentParser()
top_parser.add_argument("--input-dir", type=str)
subparsers = top_parser.add_subparsers()
generate_parser = subparsers.add_parser("generate")
generate_parser.set_defaults(input_dir=".")
process_parser = subparsers.add_parser("process")
process_parser.set_defaults(input_dir="SOME_OTHER_DIR")
generate_args = top_parser.parse_args("--input-dir USE_THIS_DIR generate".split())
print("generate_args = ", generate_args)
process_args = top_parser.parse_args("--input-dir USE_THIS_DIR process".split())
print("process_args = ", process_args)
This gives:
generate_args = Namespace(input_dir='.')
process_args = Namespace(input_dir='SOME_OTHER_DIR')
but I want:
generate_args = Namespace(input_dir='USE_THIS_DIR')
process_args = Namespace(input_dir='USE_THIS_DIR')
I can circumvent this by separately adding the argument to each subparser, but I would like to avoid this redundancy if possible.
One workaround would be to check the value of input_dir after parsing, and substitute a subparser-specific default at that time.
import argparse
top_parser = argparse.ArgumentParser()
top_parser.add_argument("--input-dir", type=str)
subparsers = top_parser.add_subparsers()
generate_parser = subparsers.add_parser("generate")
generate_parser.set_defaults(alt_input_dir=".")
process_parser = subparsers.add_parser("process")
process_parser.set_defaults(alt_input_dir="SOME_OTHER_DIR")
args = top_parser.parse_args()
if args.input_dir is None:
args.input_dir = args.alt_input_dir
del args.alt_input_dir

Cannot output file: no file created

I'm brand new to python, and am struggling to understand why my program will not print despite my best efforts to understand I/O and file handling.
The below code should take in a fastQ or fasta file (for DNA or protein sequences) and prune the sequences according to user-specified quality, then create a new file with the pruned sequences.
The trouble comes when I attempt to run the program from the command line:
python endtrim --min_q 35 --in_33 fQ.txt --out_33 fQ_out.txt
The program runs without incident (no errors or trace issues), but I don't see the file fQ_out.txt being created. Methinks the problem lies somewhere with argparse, since I don't get a help message when running:
python endtrim --help
Can someone please point me in the right direction?
from __future__ import division, print_function
import argparse
import collections
import sys
import re
from string import punctuation
from fastRead import *
ready2trim = ()
def parse_arguments():
"""Creates a bevvy of possible sort arguments from command line and
binds them to their respective names"""
parser = argparse.ArgumentParser("--h", "--help", description=__doc__, \
formatter_class=argparse.\
RawDescriptionHelpFormatter)
options = parse_arguments()
#quality argument
parser.add_argument("--min_qual", action='store', default=30, \
dest='min_qual', help="""Lowest quality value
that can appear in the output""")
#input arguments
parser.add_argument("--in_33", action='store', default=sys.stdin, \
dest='in_33', nargs='?', help="""Input file in fastq format, using Phred+33 coding""")
parser.add_argument("--in_64", action='store', default=sys.stdin, \
dest='in_64', nargs='?', help="""Input file in fastq format, using Phred+64 coding""")
parser.add_argument("--in_fasta", action='store', default=sys.stdin, \
dest='in_fasta', nargs='?', help="""Input fasta format, requires concurrent --in_qual argument""")
parser.add_argument("--in_qual", action='store', default=sys.stdin, \
dest='in_qual', nargs='?', help="""Input quality format, requires concurrent --in_fasta argument""")
#output arguments
parser.add_argument("--out_33", action='store', default=sys.stdout, \
dest='out_33', nargs='?', help="""Output file in fastq format,
using Phred+33 coding""")
parser.add_argument("--out_64", action='store', default=sys.stdout, \
dest='out_64', nargs='?', help="""Output file in fastq format,
using Phred+33 coding""")
parser.add_argument("--out_fasta", action='store', default=sys.stdout, \
dest='out_fasta', nargs='?', help="""Output fasta format,
""")
parser.add_argument("--out_qual", action='store', default=False, \
dest='out_qual', nargs='?', help="""Output quality format,
""")
args = parser.parse_args()
return args
def incoming(args):
"""interprets argparse command and assigns appropriate format for
incoming file"""
if options.in_fasta and options.in_qual:
#ready2trim is the input after being read by fastRead.py
ready2trim = read_fasta_with_quality(open(options.in_fasta), \
open(options.in_qual))
return ready2trim
elif options.in_33:
ready2trim = read_fastq(open(options.in_33))
#phredCode_in specifies the Phred coding of the input fastQ
phredCode_in = 33
return ready2trim
elif options.in_64:
ready2trim = read_fastq(open(options.in_64))
phredCode_in = 64
return ready2trim
else: sys.stderr.write("ERR: insufficient input arguments")
def print_output(seqID, seq, comm, qual):
"""interprets argparse command and creates appropriate format for
outgoing file"""
#Printing a fastQ
if options.out_33 or options.out_64:
if options.out_33:
#phredCode_out specifies the Phred coding of the output fastQ
phredCode_out = 33
if comm:
#outputfh is the file handle of new output file
with open(options.out_33,'a') as outputfh:
outputfh.write("#{}\n{}\n{}\n+".format(seqID, seq, comm))
else:
with open(options.out_33,'a') as outputfh:
outputfh.write("#{}\n{}\n+".format(seqID, seq))
else:
phredCode_out = 64
if comm:
#outputfh is the file handle of new output file
with open(options.out_33,'a') as outputfh:
outputfh.write("#{}\n{}\n{}\n+".format(seqID, seq, comm))
else:
with open(options.out_33,'a') as outputfh:
outputfh.write("#{}\n{}\n+".format(seqID, seq))
print(''.join(str(chr(q+phredCode_out)) for q in qual))
#Print a fasta
if options.out_fasta:
outputfh = open(options.out_fasta, "a")
if(comment == ''):
output.write('>{}\n{}\n'.format(seqID, seq))
else: output.write('>{} {}\n{}\n'.format(seqID, comm, seq))
#Print a qual
if options.out_qual:
outputfh = open(options.out_qual, "a")
if(comment == ''):
output.write('>{}\n{}\n'.format(seqID, seq))
else: output.write('>{} {}\n{}\n'.format(seqID, comm, seq))
def main(args):
"""Prints combined fastq sequence from separate fasta and quality
files according to user-generated arguments """
for (seqID, seq, comm, qual) in ready2trim:
for q in qual:
#i counts satisfactory bases to later print that number of
i = 0
if ord(q) - phredCode_in >= min_qual:
i += 1
print_output(seqID, seq[0:i], comm, qual[0:i])
sys.stderr.write("ERR: sys.stdin is without sequence data")
if __name__ == "__main__" :
sys.exit(main(sys.argv))
parse_arguments seems to be calling itself recursively, while it is not called at all from anywhere else in the program
def parse_arguments():
"""Creates a bevvy of possible sort arguments from command line and
binds them to their respective names"""
parser = argparse.ArgumentParser("--h", "--help", description=__doc__, \
formatter_class=argparse.\
RawDescriptionHelpFormatter)
options = parse_arguments()
Perhaps this options line should be in the main function, or global?

How to parse multiple nested sub-commands using python argparse?

I am implementing a command line program which has interface like this:
cmd [GLOBAL_OPTIONS] {command [COMMAND_OPTS]} [{command [COMMAND_OPTS]} ...]
I have gone through the argparse documentation. I can implement GLOBAL_OPTIONS as optional argument using add_argument in argparse. And the {command [COMMAND_OPTS]} using Sub-commands.
From the documentation it seems I can have only one sub-command. But as you can see I have to implement one or more sub-commands. What is the best way to parse such command line arguments useing argparse?
I came up with the same qustion, and it seems i have got a better answer.
The solution is we shall not simply nest subparser with another subparser, but we can add subparser following with a parser following another subparser.
Code tell you how:
parent_parser = argparse.ArgumentParser(add_help=False)
parent_parser.add_argument('--user', '-u',
default=getpass.getuser(),
help='username')
parent_parser.add_argument('--debug', default=False, required=False,
action='store_true', dest="debug", help='debug flag')
main_parser = argparse.ArgumentParser()
service_subparsers = main_parser.add_subparsers(title="service",
dest="service_command")
service_parser = service_subparsers.add_parser("first", help="first",
parents=[parent_parser])
action_subparser = service_parser.add_subparsers(title="action",
dest="action_command")
action_parser = action_subparser.add_parser("second", help="second",
parents=[parent_parser])
args = main_parser.parse_args()
#mgilson has a nice answer to this question. But problem with splitting sys.argv myself is that i lose all the nice help message Argparse generates for the user. So i ended up doing this:
import argparse
## This function takes the 'extra' attribute from global namespace and re-parses it to create separate namespaces for all other chained commands.
def parse_extra (parser, namespace):
namespaces = []
extra = namespace.extra
while extra:
n = parser.parse_args(extra)
extra = n.extra
namespaces.append(n)
return namespaces
argparser=argparse.ArgumentParser()
subparsers = argparser.add_subparsers(help='sub-command help', dest='subparser_name')
parser_a = subparsers.add_parser('command_a', help = "command_a help")
## Setup options for parser_a
## Add nargs="*" for zero or more other commands
argparser.add_argument('extra', nargs = "*", help = 'Other commands')
## Do similar stuff for other sub-parsers
Now after first parse all chained commands are stored in extra. I reparse it while it is not empty to get all the chained commands and create separate namespaces for them. And i get nicer usage string that argparse generates.
parse_known_args returns a Namespace and a list of unknown strings. This is similar to the extra in the checked answer.
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--foo')
sub = parser.add_subparsers()
for i in range(1,4):
sp = sub.add_parser('cmd%i'%i)
sp.add_argument('--foo%i'%i) # optionals have to be distinct
rest = '--foo 0 cmd2 --foo2 2 cmd3 --foo3 3 cmd1 --foo1 1'.split() # or sys.argv
args = argparse.Namespace()
while rest:
args,rest = parser.parse_known_args(rest,namespace=args)
print args, rest
produces:
Namespace(foo='0', foo2='2') ['cmd3', '--foo3', '3', 'cmd1', '--foo1', '1']
Namespace(foo='0', foo2='2', foo3='3') ['cmd1', '--foo1', '1']
Namespace(foo='0', foo1='1', foo2='2', foo3='3') []
An alternative loop would give each subparser its own namespace. This allows overlap in positionals names.
argslist = []
while rest:
args,rest = parser.parse_known_args(rest)
argslist.append(args)
The solution provide by #Vikas fails for subcommand-specific optional arguments, but the approach is valid. Here is an improved version:
import argparse
# create the top-level parser
parser = argparse.ArgumentParser(prog='PROG')
parser.add_argument('--foo', action='store_true', help='foo help')
subparsers = parser.add_subparsers(help='sub-command help', dest='subparser_name')
# create the parser for the "command_a" command
parser_a = subparsers.add_parser('command_a', help='command_a help')
parser_a.add_argument('bar', type=int, help='bar help')
# create the parser for the "command_b" command
parser_b = subparsers.add_parser('command_b', help='command_b help')
parser_b.add_argument('--baz', choices='XYZ', help='baz help')
# parse some argument lists
argv = ['--foo', 'command_a', '12', 'command_b', '--baz', 'Z']
while argv:
print(argv)
options, argv = parser.parse_known_args(argv)
print(options)
if not options.subparser_name:
break
This uses parse_known_args instead of parse_args. parse_args aborts as soon as a argument unknown to the current subparser is encountered, parse_known_args returns them as a second value in the returned tuple. In this approach, the remaining arguments are fed again to the parser. So for each command, a new Namespace is created.
Note that in this basic example, all global options are added to the first options Namespace only, not to the subsequent Namespaces.
This approach works fine for most situations, but has three important limitations:
It is not possible to use the same optional argument for different subcommands, like myprog.py command_a --foo=bar command_b --foo=bar.
It is not possible to use any variable length positional arguments with subcommands (nargs='?' or nargs='+' or nargs='*').
Any known argument is parsed, without 'breaking' at the new command. E.g. in PROG --foo command_b command_a --baz Z 12 with the above code, --baz Z will be consumed by command_b, not by command_a.
These limitations are a direct limitation of argparse. Here is a simple example that shows the limitations of argparse -even when using a single subcommand-:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('spam', nargs='?')
subparsers = parser.add_subparsers(help='sub-command help', dest='subparser_name')
# create the parser for the "command_a" command
parser_a = subparsers.add_parser('command_a', help='command_a help')
parser_a.add_argument('bar', type=int, help='bar help')
# create the parser for the "command_b" command
parser_b = subparsers.add_parser('command_b', help='command_b help')
options = parser.parse_args('command_a 42'.split())
print(options)
This will raise the error: argument subparser_name: invalid choice: '42' (choose from 'command_a', 'command_b').
The cause is that the internal method argparse.ArgParser._parse_known_args() it is too greedy and assumes that command_a is the value of the optional spam argument. In particular, when 'splitting' up optional and positional arguments, _parse_known_args() does not look at the names of the arugments (like command_a or command_b), but merely where they occur in the argument list. It also assumes that any subcommand will consume all remaining arguments.
This limitation of argparse also prevents a proper implementation of multi-command subparsers. This unfortunately means that a proper implementation requires a full rewrite of the argparse.ArgParser._parse_known_args() method, which is 200+ lines of code.
Given these limitation, it may be an options to simply revert to a single multiple-choice argument instead of subcommands:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--bar', type=int, help='bar help')
parser.add_argument('commands', nargs='*', metavar='COMMAND',
choices=['command_a', 'command_b'])
options = parser.parse_args('--bar 2 command_a command_b'.split())
print(options)
#options = parser.parse_args(['--help'])
It is even possible to list the different commands in the usage information, see my answer https://stackoverflow.com/a/49999185/428542
You can always split up the command-line yourself (split sys.argv on your command names), and then only pass the portion corresponding to the particular command to parse_args -- You can even use the same Namespace using the namespace keyword if you want.
Grouping the commandline is easy with itertools.groupby:
import sys
import itertools
import argparse
mycommands=['cmd1','cmd2','cmd3']
def groupargs(arg,currentarg=[None]):
if(arg in mycommands):currentarg[0]=arg
return currentarg[0]
commandlines=[list(args) for cmd,args in intertools.groupby(sys.argv,groupargs)]
#setup parser here...
parser=argparse.ArgumentParser()
#...
namespace=argparse.Namespace()
for cmdline in commandlines:
parser.parse_args(cmdline,namespace=namespace)
#Now do something with namespace...
untested
Improving on the answer by #mgilson, I wrote a small parsing method which splits argv into parts and puts values of arguments of commands into hierarchy of namespaces:
import sys
import argparse
def parse_args(parser, commands):
# Divide argv by commands
split_argv = [[]]
for c in sys.argv[1:]:
if c in commands.choices:
split_argv.append([c])
else:
split_argv[-1].append(c)
# Initialize namespace
args = argparse.Namespace()
for c in commands.choices:
setattr(args, c, None)
# Parse each command
parser.parse_args(split_argv[0], namespace=args) # Without command
for argv in split_argv[1:]: # Commands
n = argparse.Namespace()
setattr(args, argv[0], n)
parser.parse_args(argv, namespace=n)
return args
parser = argparse.ArgumentParser()
commands = parser.add_subparsers(title='sub-commands')
cmd1_parser = commands.add_parser('cmd1')
cmd1_parser.add_argument('--foo')
cmd2_parser = commands.add_parser('cmd2')
cmd2_parser.add_argument('--foo')
cmd2_parser = commands.add_parser('cmd3')
cmd2_parser.add_argument('--foo')
args = parse_args(parser, commands)
print(args)
It behaves properly, providing nice argparse help:
For ./test.py --help:
usage: test.py [-h] {cmd1,cmd2,cmd3} ...
optional arguments:
-h, --help show this help message and exit
sub-commands:
{cmd1,cmd2,cmd3}
For ./test.py cmd1 --help:
usage: test.py cmd1 [-h] [--foo FOO]
optional arguments:
-h, --help show this help message and exit
--foo FOO
And creates a hierarchy of namespaces containing the argument values:
./test.py cmd1 --foo 3 cmd3 --foo 4
Namespace(cmd1=Namespace(foo='3'), cmd2=None, cmd3=Namespace(foo='4'))
You could try arghandler. This is an extension to argparse with explicit support for subcommands.
Built a full Python 2/3 example with subparsers, parse_known_args and parse_args (running on IDEone):
from __future__ import print_function
from argparse import ArgumentParser
from random import randint
def main():
parser = get_parser()
input_sum_cmd = ['sum_cmd', '--sum']
input_min_cmd = ['min_cmd', '--min']
args, rest = parser.parse_known_args(
# `sum`
input_sum_cmd +
['-a', str(randint(21, 30)),
'-b', str(randint(51, 80))] +
# `min`
input_min_cmd +
['-y', str(float(randint(64, 79))),
'-z', str(float(randint(91, 120)) + .5)]
)
print('args:\t ', args,
'\nrest:\t ', rest, '\n', sep='')
sum_cmd_result = args.sm((args.a, args.b))
print(
'a:\t\t {:02d}\n'.format(args.a),
'b:\t\t {:02d}\n'.format(args.b),
'sum_cmd: {:02d}\n'.format(sum_cmd_result), sep='')
assert rest[0] == 'min_cmd'
args = parser.parse_args(rest)
min_cmd_result = args.mn((args.y, args.z))
print(
'y:\t\t {:05.2f}\n'.format(args.y),
'z:\t\t {:05.2f}\n'.format(args.z),
'min_cmd: {:05.2f}'.format(min_cmd_result), sep='')
def get_parser():
# create the top-level parser
parser = ArgumentParser(prog='PROG')
subparsers = parser.add_subparsers(help='sub-command help')
# create the parser for the "sum" command
parser_a = subparsers.add_parser('sum_cmd', help='sum some integers')
parser_a.add_argument('-a', type=int,
help='an integer for the accumulator')
parser_a.add_argument('-b', type=int,
help='an integer for the accumulator')
parser_a.add_argument('--sum', dest='sm', action='store_const',
const=sum, default=max,
help='sum the integers (default: find the max)')
# create the parser for the "min" command
parser_b = subparsers.add_parser('min_cmd', help='min some integers')
parser_b.add_argument('-y', type=float,
help='an float for the accumulator')
parser_b.add_argument('-z', type=float,
help='an float for the accumulator')
parser_b.add_argument('--min', dest='mn', action='store_const',
const=min, default=0,
help='smallest integer (default: 0)')
return parser
if __name__ == '__main__':
main()
I had more or less the same requirements: Being able to set global arguments and being able to chain commands and execute them in order of command line.
I ended up with the following code. I did use some parts of the code from this and other threads.
# argtest.py
import sys
import argparse
def init_args():
def parse_args_into_namespaces(parser, commands):
'''
Split all command arguments (without prefix, like --) in
own namespaces. Each command accepts extra options for
configuration.
Example: `add 2 mul 5 --repeat 3` could be used to a sequencial
addition of 2, then multiply with 5 repeated 3 times.
'''
class OrderNamespace(argparse.Namespace):
'''
Add `command_order` attribute - a list of command
in order on the command line. This allows sequencial
processing of arguments.
'''
globals = None
def __init__(self, **kwargs):
self.command_order = []
super(OrderNamespace, self).__init__(**kwargs)
def __setattr__(self, attr, value):
attr = attr.replace('-', '_')
if value and attr not in self.command_order:
self.command_order.append(attr)
super(OrderNamespace, self).__setattr__(attr, value)
# Divide argv by commands
split_argv = [[]]
for c in sys.argv[1:]:
if c in commands.choices:
split_argv.append([c])
else:
split_argv[-1].append(c)
# Globals arguments without commands
args = OrderNamespace()
cmd, args_raw = 'globals', split_argv.pop(0)
args_parsed = parser.parse_args(args_raw, namespace=OrderNamespace())
setattr(args, cmd, args_parsed)
# Split all commands to separate namespace
pos = 0
while len(split_argv):
pos += 1
cmd, *args_raw = split_argv.pop(0)
assert cmd[0].isalpha(), 'Command must start with a letter.'
args_parsed = commands.choices[cmd].parse_args(args_raw, namespace=OrderNamespace())
setattr(args, f'{cmd}~{pos}', args_parsed)
return args
#
# Supported commands and options
#
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--print', action='store_true')
commands = parser.add_subparsers(title='Operation chain')
cmd1_parser = commands.add_parser('add', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
cmd1_parser.add_argument('add', help='Add this number.', type=float)
cmd1_parser.add_argument('-r', '--repeat', help='Repeat this operation N times.',
default=1, type=int)
cmd2_parser = commands.add_parser('mult', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
cmd2_parser.add_argument('mult', help='Multiply with this number.', type=float)
cmd2_parser.add_argument('-r', '--repeat', help='Repeat this operation N times.',
default=1, type=int)
args = parse_args_into_namespaces(parser, commands)
return args
#
# DEMO
#
args = init_args()
# print('Parsed arguments:')
# for cmd in args.command_order:
# namespace = getattr(args, cmd)
# for option_name in namespace.command_order:
# option_value = getattr(namespace, option_name)
# print((cmd, option_name, option_value))
print('Execution:')
result = 0
for cmd in args.command_order:
namespace = getattr(args, cmd)
cmd_name, cmd_position = cmd.split('~') if cmd.find('~') > -1 else (cmd, 0)
if cmd_name == 'globals':
pass
elif cmd_name == 'add':
for r in range(namespace.repeat):
if args.globals.print:
print(f'+ {namespace.add}')
result = result + namespace.add
elif cmd_name == 'mult':
for r in range(namespace.repeat):
if args.globals.print:
print(f'* {namespace.mult}')
result = result * namespace.mult
else:
raise NotImplementedError(f'Namespace `{cmd}` is not implemented.')
print(10*'-')
print(result)
Below an example:
$ python argstest.py --print add 1 -r 2 mult 5 add 3 mult -r 5 5
Execution:
+ 1.0
+ 1.0
* 5.0
+ 3.0
* 5.0
* 5.0
* 5.0
* 5.0
* 5.0
----------
40625.0
Another package which supports parallel parsers is "declarative_parser".
import argparse
from declarative_parser import Parser, Argument
supported_formats = ['png', 'jpeg', 'gif']
class InputParser(Parser):
path = Argument(type=argparse.FileType('rb'), optional=False)
format = Argument(default='png', choices=supported_formats)
class OutputParser(Parser):
format = Argument(default='jpeg', choices=supported_formats)
class ImageConverter(Parser):
description = 'This app converts images'
verbose = Argument(action='store_true')
input = InputParser()
output = OutputParser()
parser = ImageConverter()
commands = '--verbose input image.jpeg --format jpeg output --format gif'.split()
namespace = parser.parse_args(commands)
and namespace becomes:
Namespace(
input=Namespace(format='jpeg', path=<_io.BufferedReader name='image.jpeg'>),
output=Namespace(format='gif'),
verbose=True
)
Disclaimer: I am the author. Requires Python 3.6. To install use:
pip3 install declarative_parser
Here is the documentation and here is the repo on GitHub.
In order to parse the sub commands, I used the following (referred from argparse.py code). It parses the sub parser arguments and retains the help for both. Nothing additional passed there.
args, _ = parser.parse_known_args()
you can use the package optparse
import optparse
parser = optparse.OptionParser()
parser.add_option("-f", dest="filename", help="corpus filename")
parser.add_option("--alpha", dest="alpha", type="float", help="parameter alpha", default=0.5)
(options, args) = parser.parse_args()
fname = options.filename
alpha = options.alpha

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