# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2016-2019
# (c) University of Strathclyde 2019-2022
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G4 0RE
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2016-2019 The James Hutton Institute
# Copyright (c) 2019-2022 University of Strathclyde
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
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# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# THE SOFTWARE.
"""Provides parser for plot subcommand."""
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, _SubParsersAction
from pathlib import Path
from typing import List, Optional
from pyani.scripts import subcommands
[docs]def build(
subps: _SubParsersAction, parents: Optional[List[ArgumentParser]] = None
) -> None:
"""Return a command-line parser for the plot subcommand.
:param subps: collection of subparsers in main parser
:param parents: parsers from which arguments are inherited
The plot subcommand takes specific arguments:
--method (graphics method to use)
"""
parser = subps.add_parser(
"plot", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
)
# Required arguments: output directory and run ID
parser.add_argument(
"-o",
"--outdir",
action="store",
dest="outdir",
default=None,
type=Path,
help="output directory",
required=True,
)
parser.add_argument(
"--run_ids",
action="store",
dest="run_ids",
default=None,
metavar="RUN_ID",
nargs="+",
help="run IDs to plot",
required=True,
)
# Other optional arguments
parser.add_argument(
"--dbpath",
action="store",
dest="dbpath",
default=Path(".pyani/pyanidb"),
type=Path,
help="path to pyani database",
)
# Graphics methods and formats
parser.add_argument(
"--formats",
dest="formats",
action="store",
default=["png"],
metavar="FORMAT",
nargs="+",
choices=["pdf", "png", "svg", "jpg"],
help="graphics output format; options: (pdf, png, svg, jpg)",
)
parser.add_argument(
"--method",
dest="method",
action="store",
default="seaborn",
metavar="METHOD",
nargs=1,
choices=["seaborn", "mpl", "plotly"],
help="graphics method to use for plotting; options (seaborn, mpl, plotly)",
)
parser.add_argument(
"--workers",
dest="workers",
action="store",
default=None,
type=int,
help="Number of worker processes for multiprocessing "
"(default zero, meaning use all available cores)",
)
parser.set_defaults(func=subcommands.subcmd_plot)