mandos.entries.common_args.CommonArgs.parse_taxon_id_or_name() - Code Metrics - Inspection of "refactor: simplify some code" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 7b3fbc...cf9f8c )

by Douglas

created 2021-06-30 21:05 UTC

CommonArgs.parse_taxon_id_or_name() A

↳ Parent: mandos.entries.common_args

Complexity

Conditions

Size

Total Lines	7
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	4
eloc	7
nop	1
dl	0
loc	7
rs	10
c	0
b	0
f	0

"""
Common argument processing and arguments for Typer.
"""

from inspect import cleandoc
from pathlib import Path
from typing import Optional, TypeVar, Sequence, Union

import typer

from mandos.model.settings import MANDOS_SETTINGS

T = TypeVar("T", covariant=True)



class _Args:
    @staticmethod
    def _arg(doc: str, *names, default: Optional[T] = None, req: bool = False, **kwargs):
        kwargs = dict(
            help=cleandoc(doc),
            **kwargs,
            allow_dash=True,
        )
        return typer.Argument(default, **kwargs) if req else typer.Option(default, *names, **kwargs)

    @staticmethod
    def _path(
        doc: str, *names, default: Optional[str], f: bool, d: bool, out: bool, req: bool, **kwargs

    ):
        # if it's None, we're going to have a special default set afterward, so we'll explain it in the doc

        if out and default is None:
            kwargs = dict(show_default=True, **kwargs)
        kwargs = {
            **dict(
                exists=not out,
                dir_okay=d,
                file_okay=f,
                readable=out,
                writable=not out,
            ),
            **kwargs,
        }
        return _Args._arg(doc, *names, default=default, req=req, **kwargs)


class Arg(_Args):

    @staticmethod
    def out_file(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=False, out=True, req=True, **kwargs
        )

    @staticmethod
    def out_dir(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=True, out=True, req=True, **kwargs
        )

    @staticmethod
    def out_path(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=True, out=False, req=True, **kwargs
        )

    @staticmethod
    def in_file(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=False, out=False, req=True, **kwargs
        )

    @staticmethod
    def in_dir(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=False, d=True, out=False, req=True, **kwargs
        )

    @staticmethod
    def in_path(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=True, out=False, req=True, **kwargs
        )

    @staticmethod
    def x(doc: str, *names, default: Optional[T] = None, **kwargs):

        return _Args._arg(doc, *names, default=default, req=True, **kwargs)


class Opt(_Args):

    @staticmethod
    def out_file(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=False, out=True, req=False, **kwargs
        )

    @staticmethod
    def out_dir(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=True, out=True, req=False, **kwargs
        )

    @staticmethod
    def out_path(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc,
            *names,
            default=default,
            f=True,
            d=True,
            out=False,
            req=False,
            exists=False,
            **kwargs,
        )

    @staticmethod
    def in_file(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=True, d=False, out=False, req=False, **kwargs
        )

    @staticmethod
    def in_dir(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc, *names, default=default, f=False, d=True, out=False, req=False, **kwargs
        )

    @staticmethod
    def in_path(doc: str, *names, default: Optional[str] = None, **kwargs):

        return _Args._path(
            doc,
            *names,
            default=default,
            f=True,
            d=True,
            out=False,
            req=False,
            exists=False,
            **kwargs,
        )

    @staticmethod
    def val(doc: str, *names, default: Optional[T] = None, **kwargs):

        return _Args._arg(doc, *names, default=default, req=False, **kwargs)

    @staticmethod
    def flag(doc: str, *names, **kwargs):

        return _Args._arg(doc, *names, default=False, req=False, **kwargs)


def _strip(s: str) -> str:

    return s.strip().strip("'").strip('"').strip()


class CommonArgs:

    @staticmethod
    def parse_taxon_id_or_name(taxon: Union[int, str]) -> Union[int, str]:

        if isinstance(taxon, str):

            return taxon
        elif isinstance(taxon, str) and taxon.isdigit():
            return int(taxon)
        raise ValueError(f"Taxon {taxon} must be an ID or name")

    @staticmethod
    def parse_taxon_id(taxon: Union[int, str]) -> int:

        try:
            return int(taxon)
        except ValueError:
            raise ValueError(f"Taxon {taxon} must be an exact ID") from None

    @staticmethod
    def parse_taxa(taxa: str) -> Sequence[Union[int, str]]:

        taxa = [_strip(t) for t in taxa.split(",")]
        return [CommonArgs.parse_taxon_id_or_name(t) for t in taxa]

    output_formats = r"""
        The filename extension must be one of: .feather; .snappy/.parquet;
        .csv, .tsv, .tab, .json (with optional .gz/.bz2/.zip/.xz);
        Feather (.feather) and Parquet (.snappy) are recommended.
        If only a filename suffix is provided, only sets the format and filename suffix.
        If no extension is provided, interprets that path as a directory and uses the default format (Feather).

        Will fail if the file exists, unless `--replace` is passed.
    """

    input_formats = r"""
        The filename extension must be one of: .feather; .snappy/.parquet;
        .csv, .tsv, .tab (with optional .gz/.bz2/.zip/.xz);
        Feather (.feather) and Parquet (.snappy) are recommended formats.
        (Some other formats, such as .json or .h5, may be permitted but are discouraged.)
    """

    file_input = Arg.in_file("The path to a file output by `:concat` or `:search`.", "input")

    compounds = Arg.in_file(
        """
        The path to the input file.
        One of:

          (A) *.txt, *.lines, or *.list (optionally with .gz/.zip/.xz/.bz2)), with one InChI Key per line;


          (B) A *.csv, *.tsv, *.tab file (or .gz/.zip/.xz/.bz2 variant) with a column called 'inchikey'; OR


          (C) An Arrow *.feather file or Parquet *.snappy file with a column called 'inchikey'
        """
    )

    dir_input = Arg.in_dir(
        rf"""
        The path to a directory containing files output from mandos search.

        {input_formats}
        Note that *all* matching files will be included.
        Provide ``--exclude`` if needed.
        """
    )

    to_single = Opt.out_file(
        rf"""
        The path to the output file.

        {output_formats}

        [default: <input-path>/{...}.{MANDOS_SETTINGS.default_table_suffix}.gz]
        """,
        "--to",
    )

    input_matrix: Path = Arg.in_file(
        rf"""
        The path to a similarity matrix file to write to.

        {input_formats}
        .txt/.txt.gz/etc. is assumed to be whitespace-delimited.
        TCompounds can be referenced by InChI Key or compound ID (matching what you provided for the search).

        The set of compounds here must exactly match the set of compounds in the input files.
        For Excel and text formats, the first row and the first column (header and index) indicate the compounds.


        Values must be floating-point.
        """
    )
    replace: bool = typer.Option(
        False, help="Replace output file(s) if they exist. See also: --skip"
    )

    taxa = Opt.val(
        r"""
        The IDs or names of UniProt taxa, comma-separated.
        Taxon names and common names can be used for vertebrate species (where available).

        This can have a significant effect on searches. See the docs for more info.

        [default: 7742] (Euteleostomi)
        """,
        "--taxa",
        "7742",
        show_default=False,
    )

    seed = Opt.val(r"A random seed (integer).", "--seed", default=0)

    n_samples = Opt.val(
        "Number of bootstrap samples (positive integer).",
        "--samples",
        min=1,
        default=2000,
    )

    exclude = Opt.val("A glob pattern matching input filenames to ignore.")

    verbose: bool = Opt.flag(
        r"Configure logger to output INFO (use ``--quiet`` for less info)",
        "-v",
        "--verbose",
    )

    quiet: bool = Opt.flag(
        r"Configure logger to output only ERROR (use ``--verbose`` for more info)",
        "-q",
        "--quiet",
    )

    in_cache: bool = Opt.flag(
        r"Do not download any data and fail if needed data is not cached.",
        hidden=True,
    )

    as_of: Optional[str] = Opt.val(
        f"""
        Restrict to data that was cached as of some date and time.
        This option can be useful for reproducibility.

        Note that this should imply that underlying data sources (such as of deposition or publication)

        are restricted by this datetime, but that is not checked.

        Examples:

            - --as-of 2021-10-11T14:12:13Z
            - --as-of 2021-10-11T14:12:13+14:00
            - --as-of 2021-10-11T14:12:13.496Z
            - --as-of "2021-10-11 14:12:13,496,915+14:00"
            - --as-of "2021-10-11 14:12:13-8:00 [America/Los_Angeles]"

        This is a subset of ISO 8601, represented as ``YYYY-mm-dd('T'|' '):hh:MM:ss(i)Z``.
        Precision must be nanosecond or less, and ``,`` and ``.`` are equivalent as a thousands separator.

        You can provide an IANA zone name in square brackets for context, but the offset is still required.

        """

    )

    log_path = Opt.out_path(
        r"""
        Also log to a file.
        The suffix can be .log, .log.gz, .log.zip, or .json, .json.gz, or .json.gz.
        You can prefix the path with :LEVEL: to control the level. For example, ``:INFO:out.log``
        """,
        "--log",
        show_default=True,
    )

    no_setup: bool = Opt.flag(
        r"Skip setup, such as configuring logging.",
        "--no-setup",
        hidden=True,
    )


cli = typer.Typer()


@cli.command()
def run(

    path: Path = CommonArgs.dir_input,

    x=CommonArgs.log_path,

):
    pass


if __name__ == "__main__":
    typer.run(run)


__all__ = ["CommonArgs", "Arg", "Opt"]


1			"""
2			Common argument processing and arguments for Typer.
3			"""
4
5			from inspect import cleandoc
6			from pathlib import Path
7			from typing import Optional, TypeVar, Sequence, Union
8
9			import typer
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Unable to import 'typer' Loading history...
10			from mandos.model.settings import MANDOS_SETTINGS
11
12			T = TypeVar("T", covariant=True)
			0 ignored issues – show Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Class name "T" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
13
14
15			class _Args:
16			@staticmethod
17			def _arg(doc: str, names, default: Optional[T] = None, req: bool = False, *kwargs):
18			kwargs = dict(
19			help=cleandoc(doc),
20			**kwargs,
21			allow_dash=True,
22			)
23			return typer.Argument(default, *kwargs) if req else typer.Option(default, names, **kwargs)
24
25			@staticmethod
26			def _path(
27			doc: str, names, default: Optional[str], f: bool, d: bool, out: bool, req: bool, *kwargs
			0 ignored issues – show Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Variable name "f" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history... Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Variable name "d" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
28			):
29			# if it's None, we're going to have a special default set afterward, so we'll explain it in the doc
			0 ignored issues – show Coding Style introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (107/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
30			if out and default is None:
31			kwargs = dict(show_default=True, **kwargs)
32			kwargs = {
33			**dict(
34			exists=not out,
35			dir_okay=d,
36			file_okay=f,
37			readable=out,
38			writable=not out,
39			),
40			**kwargs,
41			}
42			return _Args._arg(doc, names, default=default, req=req, *kwargs)
43
44
45			class Arg(_Args):
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46			@staticmethod
47			def out_file(doc: str, names, default: Optional[str] = None, *kwargs):
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48			return _Args._path(
49			doc, names, default=default, f=True, d=False, out=True, req=True, *kwargs
50			)
51
52			@staticmethod
53			def out_dir(doc: str, names, default: Optional[str] = None, *kwargs):
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54			return _Args._path(
55			doc, names, default=default, f=True, d=True, out=True, req=True, *kwargs
56			)
57
58			@staticmethod
59			def out_path(doc: str, names, default: Optional[str] = None, *kwargs):
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60			return _Args._path(
61			doc, names, default=default, f=True, d=True, out=False, req=True, *kwargs
62			)
63
64			@staticmethod
65			def in_file(doc: str, names, default: Optional[str] = None, *kwargs):
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66			return _Args._path(
67			doc, names, default=default, f=True, d=False, out=False, req=True, *kwargs
68			)
69
70			@staticmethod
71			def in_dir(doc: str, names, default: Optional[str] = None, *kwargs):
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72			return _Args._path(
73			doc, names, default=default, f=False, d=True, out=False, req=True, *kwargs
74			)
75
76			@staticmethod
77			def in_path(doc: str, names, default: Optional[str] = None, *kwargs):
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78			return _Args._path(
79			doc, names, default=default, f=True, d=True, out=False, req=True, *kwargs
80			)
81
82			@staticmethod
83			def x(doc: str, names, default: Optional[T] = None, *kwargs):
			0 ignored issues – show Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Method name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
84			return _Args._arg(doc, names, default=default, req=True, *kwargs)
85
86
87			class Opt(_Args):
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88			@staticmethod
89			def out_file(doc: str, names, default: Optional[str] = None, *kwargs):
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90			return _Args._path(
91			doc, names, default=default, f=True, d=False, out=True, req=False, *kwargs
92			)
93
94			@staticmethod
95			def out_dir(doc: str, names, default: Optional[str] = None, *kwargs):
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96			return _Args._path(
97			doc, names, default=default, f=True, d=True, out=True, req=False, *kwargs
98			)
99
100			@staticmethod
101			def out_path(doc: str, names, default: Optional[str] = None, *kwargs):
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102			return _Args._path(
103			doc,
104			*names,
105			default=default,
106			f=True,
107			d=True,
108			out=False,
109			req=False,
110			exists=False,
111			**kwargs,
112			)
113
114			@staticmethod
115			def in_file(doc: str, names, default: Optional[str] = None, *kwargs):
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116			return _Args._path(
117			doc, names, default=default, f=True, d=False, out=False, req=False, *kwargs
118			)
119
120			@staticmethod
121			def in_dir(doc: str, names, default: Optional[str] = None, *kwargs):
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122			return _Args._path(
123			doc, names, default=default, f=False, d=True, out=False, req=False, *kwargs
124			)
125
126			@staticmethod
127			def in_path(doc: str, names, default: Optional[str] = None, *kwargs):
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128			return _Args._path(
129			doc,
130			*names,
131			default=default,
132			f=True,
133			d=True,
134			out=False,
135			req=False,
136			exists=False,
137			**kwargs,
138			)
139
140			@staticmethod
141			def val(doc: str, names, default: Optional[T] = None, *kwargs):
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142			return _Args._arg(doc, names, default=default, req=False, *kwargs)
143
144			@staticmethod
145			def flag(doc: str, names, *kwargs):
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146			return _Args._arg(doc, names, default=False, req=False, *kwargs)
147
148
149			def _strip(s: str) -> str:
			0 ignored issues – show Coding Style Naming introduced 2021-06-30 21:07 UTC by Report Bug Copy Issue Report Argument name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
150			return s.strip().strip("'").strip('"').strip()
151
152
153			class CommonArgs:
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154			@staticmethod
155			def parse_taxon_id_or_name(taxon: Union[int, str]) -> Union[int, str]:
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156			if isinstance(taxon, str):
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157			return taxon
158			elif isinstance(taxon, str) and taxon.isdigit():
159			return int(taxon)
160			raise ValueError(f"Taxon {taxon} must be an ID or name")
161
162			@staticmethod
163			def parse_taxon_id(taxon: Union[int, str]) -> int:
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164			try:
165			return int(taxon)
166			except ValueError:
167			raise ValueError(f"Taxon {taxon} must be an exact ID") from None
168
169			@staticmethod
170			def parse_taxa(taxa: str) -> Sequence[Union[int, str]]:
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171			taxa = [_strip(t) for t in taxa.split(",")]
172			return [CommonArgs.parse_taxon_id_or_name(t) for t in taxa]
173
174			output_formats = r"""
175			The filename extension must be one of: .feather; .snappy/.parquet;
176			.csv, .tsv, .tab, .json (with optional .gz/.bz2/.zip/.xz);
177			Feather (.feather) and Parquet (.snappy) are recommended.
178			If only a filename suffix is provided, only sets the format and filename suffix.
179			If no extension is provided, interprets that path as a directory and uses the default format (Feather).
180
181			Will fail if the file exists, unless `--replace` is passed.
182			"""
183
184			input_formats = r"""
185			The filename extension must be one of: .feather; .snappy/.parquet;
186			.csv, .tsv, .tab (with optional .gz/.bz2/.zip/.xz);
187			Feather (.feather) and Parquet (.snappy) are recommended formats.
188			(Some other formats, such as .json or .h5, may be permitted but are discouraged.)
189			"""
190
191			file_input = Arg.in_file("The path to a file output by `:concat` or `:search`.", "input")
192
193			compounds = Arg.in_file(
194			"""
195			The path to the input file.
196			One of:
197
198			(A) .txt, .lines, or *.list (optionally with .gz/.zip/.xz/.bz2)), with one InChI Key per line;
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199
200			(B) A .csv, .tsv, *.tab file (or .gz/.zip/.xz/.bz2 variant) with a column called 'inchikey'; OR
			0 ignored issues – show Coding Style introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (107/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
201
202			(C) An Arrow .feather file or Parquet .snappy file with a column called 'inchikey'
203			"""
204			)
205
206			dir_input = Arg.in_dir(
207			rf"""
208			The path to a directory containing files output from mandos search.
209
210			{input_formats}
211			Note that all matching files will be included.
212			Provide ``--exclude`` if needed.
213			"""
214			)
215
216			to_single = Opt.out_file(
217			rf"""
218			The path to the output file.
219
220			{output_formats}
221
222			[default: <input-path>/{...}.{MANDOS_SETTINGS.default_table_suffix}.gz]
223			""",
224			"--to",
225			)
226
227			input_matrix: Path = Arg.in_file(
228			rf"""
229			The path to a similarity matrix file to write to.
230
231			{input_formats}
232			.txt/.txt.gz/etc. is assumed to be whitespace-delimited.
233			TCompounds can be referenced by InChI Key or compound ID (matching what you provided for the search).
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234			The set of compounds here must exactly match the set of compounds in the input files.
235			For Excel and text formats, the first row and the first column (header and index) indicate the compounds.
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236
237			Values must be floating-point.
238			"""
239			)
240			replace: bool = typer.Option(
241			False, help="Replace output file(s) if they exist. See also: --skip"
242			)
243
244			taxa = Opt.val(
245			r"""
246			The IDs or names of UniProt taxa, comma-separated.
247			Taxon names and common names can be used for vertebrate species (where available).
248
249			This can have a significant effect on searches. See the docs for more info.
250
251			[default: 7742] (Euteleostomi)
252			""",
253			"--taxa",
254			"7742",
255			show_default=False,
256			)
257
258			seed = Opt.val(r"A random seed (integer).", "--seed", default=0)
259
260			n_samples = Opt.val(
261			"Number of bootstrap samples (positive integer).",
262			"--samples",
263			min=1,
264			default=2000,
265			)
266
267			exclude = Opt.val("A glob pattern matching input filenames to ignore.")
268
269			verbose: bool = Opt.flag(
270			r"Configure logger to output INFO (use ``--quiet`` for less info)",
271			"-v",
272			"--verbose",
273			)
274
275			quiet: bool = Opt.flag(
276			r"Configure logger to output only ERROR (use ``--verbose`` for more info)",
277			"-q",
278			"--quiet",
279			)
280
281			in_cache: bool = Opt.flag(
282			r"Do not download any data and fail if needed data is not cached.",
283			hidden=True,
284			)
285
286			as_of: Optional[str] = Opt.val(
287			f"""
288			Restrict to data that was cached as of some date and time.
289			This option can be useful for reproducibility.
290
291			Note that this should imply that underlying data sources (such as of deposition or publication)
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292			are restricted by this datetime, but that is not checked.
293
294			Examples:
295
296			- --as-of 2021-10-11T14:12:13Z
297			- --as-of 2021-10-11T14:12:13+14:00
298			- --as-of 2021-10-11T14:12:13.496Z
299			- --as-of "2021-10-11 14:12:13,496,915+14:00"
300			- --as-of "2021-10-11 14:12:13-8:00 [America/Los_Angeles]"
301
302			This is a subset of ISO 8601, represented as ``YYYY-mm-dd('T'\|' '):hh:MM:ss(i)Z``.
303			Precision must be nanosecond or less, and ``,`` and ``.`` are equivalent as a thousands separator.
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304			You can provide an IANA zone name in square brackets for context, but the offset is still required.
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305			"""
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306			)
307
308			log_path = Opt.out_path(
309			r"""
310			Also log to a file.
311			The suffix can be .log, .log.gz, .log.zip, or .json, .json.gz, or .json.gz.
312			You can prefix the path with :LEVEL: to control the level. For example, ``:INFO:out.log``
313			""",
314			"--log",
315			show_default=True,
316			)
317
318			no_setup: bool = Opt.flag(
319			r"Skip setup, such as configuring logging.",
320			"--no-setup",
321			hidden=True,
322			)
323
324
325			cli = typer.Typer()
326
327
328			@cli.command()
329			def run(
			0 ignored issues – show Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Argument name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... introduced 2021-06-30 21:07 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
330			path: Path = CommonArgs.dir_input,
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331			x=CommonArgs.log_path,
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332			):
333			pass
334
335
336			if __name__ == "__main__":
337			typer.run(run)
338
339
340			__all__ = ["CommonArgs", "Arg", "Opt"]
341

dmyersturnbull / mandos

Push — main ( 7b3fbc...cf9f8c )

CommonArgs.parse_taxon_id_or_name() A

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