7117316673

Committed 06 Dec 2023 04:24PM UTC coverage: 75.413% (-0.07%) from 75.482%

Build # 7117316673

Build Type

push

github

Committed by

cokelaer

Commit Message

Update all codes to fulfill pre-commit hooks

Run Details

392 of 456 new or added lines in 116 files covered. (85.96%)

1819 existing lines in 87 files now uncovered.

13680 of 18140 relevant lines covered (75.41%)

1.51 hits per line

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95.65

/sequana/scripts/utils.py

#  This file is part of Sequana software
#
#  Copyright (c) 2016-2020 - Sequana Development Team
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
import functools

import rich_click as click

CONTEXT_SETTINGS = {"help_option_names": ["-h", "--help"]}

click.rich_click.USE_MARKDOWN = True
click.rich_click.SHOW_METAVARS_COLUMN = False
click.rich_click.APPEND_METAVARS_HELP = True
click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
click.rich_click.SHOW_ARGUMENTS = True


# This is a recipe from https://stackoverflow.com/questions/48391777/nargs-equivalent-for-options-in-click
# to allow command line such as
# sequana enrichment-panther --ontologies MF BP CC
class OptionEatAll(click.Option):
    def __init__(self, *args, **kwargs):
        self.save_other_options = kwargs.pop("save_other_options", True)
        nargs = kwargs.pop("nargs", -1)
        assert nargs == -1, "nargs, if set, must be -1 not {}".format(nargs)
        super(OptionEatAll, self).__init__(*args, **kwargs)
        self._previous_parser_process = None
        self._eat_all_parser = None

    def add_to_parser(self, parser, ctx):
        def parser_process(value, state):
            # method to hook to the parser.process
            done = False
            value = [value]
            if self.save_other_options:
                # grab everything up to the next option
                while state.rargs and not done:
                    for prefix in self._eat_all_parser.prefixes:
                        if state.rargs[0].startswith(prefix):
                            done = True
                    if not done:
                        value.append(state.rargs.pop(0))
            else:
                # grab everything remaining
                value += state.rargs
                state.rargs[:] = []
            value = tuple(value)

            # call the actual process
            self._previous_parser_process(value, state)

        retval = super(OptionEatAll, self).add_to_parser(parser, ctx)
        for name in self.opts:
            our_parser = parser._long_opt.get(name) or parser._short_opt.get(name)
            if our_parser:
                self._eat_all_parser = our_parser
                self._previous_parser_process = our_parser.process
                our_parser.process = parser_process
                break
        return retval


# This can be used by all commands as a simple decorator
def common_logger(func):
    @click.option(
        "--logger",
        default="INFO",
        type=click.Choice(["INFO", "DEBUG", "WARNING", "CRITICAL", "ERROR"]),
    )
    @functools.wraps(func)
    def wrapper(*args, **kwargs):
        return func(*args, **kwargs)

    return wrapper

1	# This file is part of Sequana software
2	#
3	# Copyright (c) 2016-2020 - Sequana Development Team
4	#
5	# Distributed under the terms of the 3-clause BSD license.
6	# The full license is in the LICENSE file, distributed with this software.
7	#
8	# website: https://github.com/sequana/sequana
9	# documentation: http://sequana.readthedocs.io
10	#
11	##############################################################################
12	import functools	3✔
13
14	import rich_click as click	3✔
15
16	CONTEXT_SETTINGS = {"help_option_names": ["-h", "--help"]}	3✔
17
18	click.rich_click.USE_MARKDOWN = True	3✔
19	click.rich_click.SHOW_METAVARS_COLUMN = False	3✔
20	click.rich_click.APPEND_METAVARS_HELP = True	3✔
21	click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"	3✔
22	click.rich_click.SHOW_ARGUMENTS = True	3✔
23
24
25	# This is a recipe from https://stackoverflow.com/questions/48391777/nargs-equivalent-for-options-in-click
26	# to allow command line such as
27	# sequana enrichment-panther --ontologies MF BP CC
28	class OptionEatAll(click.Option):	3✔
29	def __init__(self, args, *kwargs):	3✔
30	self.save_other_options = kwargs.pop("save_other_options", True)	3✔
31	nargs = kwargs.pop("nargs", -1)	3✔
32	assert nargs == -1, "nargs, if set, must be -1 not {}".format(nargs)	3✔
33	super(OptionEatAll, self).__init__(args, *kwargs)	3✔
34	self._previous_parser_process = None	3✔
35	self._eat_all_parser = None	3✔
36
37	def add_to_parser(self, parser, ctx):	3✔
38	def parser_process(value, state):	3✔
39	# method to hook to the parser.process
40	done = False	3✔
41	value = [value]	3✔
42	if self.save_other_options:	3✔
43	# grab everything up to the next option
44	while state.rargs and not done:	3✔
45	for prefix in self._eat_all_parser.prefixes:	3✔
46	if state.rargs[0].startswith(prefix):	3✔
47	done = True	3✔
48	if not done:	3✔
49	value.append(state.rargs.pop(0))	3✔
50	else:
51	# grab everything remaining
52	value += state.rargs	×
UNCOV 53	state.rargs[:] = []	×
54	value = tuple(value)	3✔
55
56	# call the actual process
57	self._previous_parser_process(value, state)	3✔
58
59	retval = super(OptionEatAll, self).add_to_parser(parser, ctx)	3✔
60	for name in self.opts:	3✔
61	our_parser = parser._long_opt.get(name) or parser._short_opt.get(name)	3✔
62	if our_parser:	3✔
63	self._eat_all_parser = our_parser	3✔
64	self._previous_parser_process = our_parser.process	3✔
65	our_parser.process = parser_process	3✔
66	break	3✔
67	return retval	3✔
68
69
70	# This can be used by all commands as a simple decorator
71	def common_logger(func):	3✔
72	@click.option(	3✔
73	"--logger",
74	default="INFO",
75	type=click.Choice(["INFO", "DEBUG", "WARNING", "CRITICAL", "ERROR"]),
76	)
77	@functools.wraps(func)	3✔
78	def wrapper(args, *kwargs):	3✔
79	return func(args, *kwargs)	3✔
80
81	return wrapper	3✔

cokelaer / sequana / 7117316673

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