mandos.entries.common_args.Arg.out_path() - Code Metrics - Inspection of "feat: massive changes" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( ddff4b...7b3fbc )

by Douglas

created 2021-06-30 04:47 UTC

mandos.entries.common_args.Arg.out_path() A

↳ Parent: mandos.entries.common_args

Complexity

Conditions

Size

Total Lines	4
Code Lines	4

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	4
nop	4
dl	0
loc	4
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 Mapping, Optional, TypeVar, Sequence


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)


class CommonArgs:


    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 Mapping, Optional, TypeVar, Sequence
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8
9			import typer
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10			from mandos.model.settings import MANDOS_SETTINGS
11
12			T = TypeVar("T", covariant=True)
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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
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28			):
29			# if it's None, we're going to have a special default set afterward, so we'll explain it in the doc
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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			class CommonArgs:
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150
151			output_formats = r"""
152			The filename extension must be one of: .feather; .snappy/.parquet;
153			.csv, .tsv, .tab, .json (with optional .gz/.bz2/.zip/.xz);
154			Feather (.feather) and Parquet (.snappy) are recommended.
155			If only a filename suffix is provided, only sets the format and filename suffix.
156			If no extension is provided, interprets that path as a directory and uses the default format (Feather).
157
158			Will fail if the file exists, unless `--replace` is passed.
159			"""
160
161			input_formats = r"""
162			The filename extension must be one of: .feather; .snappy/.parquet;
163			.csv, .tsv, .tab (with optional .gz/.bz2/.zip/.xz);
164			Feather (.feather) and Parquet (.snappy) are recommended formats.
165			(Some other formats, such as .json or .h5, may be permitted but are discouraged.)
166			"""
167
168			file_input = Arg.in_file("The path to a file output by `:concat` or `:search`.", "input")
169
170			compounds = Arg.in_file(
171			"""
172			The path to the input file.
173			One of:
174
175			(A) .txt, .lines, or *.list (optionally with .gz/.zip/.xz/.bz2)), with one InChI Key per line;
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176
177			(B) A .csv, .tsv, *.tab file (or .gz/.zip/.xz/.bz2 variant) with a column called 'inchikey'; OR
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178
179			(C) An Arrow .feather file or Parquet .snappy file with a column called 'inchikey'
180			"""
181			)
182
183			dir_input = Arg.in_dir(
184			rf"""
185			The path to a directory containing files output from mandos search.
186
187			{input_formats}
188			Note that all matching files will be included.
189			Provide ``--exclude`` if needed.
190			"""
191			)
192
193			to_single = Opt.out_file(
194			rf"""
195			The path to the output file.
196
197			{output_formats}
198
199			[default: <input-path>/{...}.{MANDOS_SETTINGS.default_table_suffix}.gz]
200			""",
201			"--to",
202			)
203
204			input_matrix: Path = Arg.in_file(
205			rf"""
206			The path to a similarity matrix file to write to.
207
208			{input_formats}
209			.txt/.txt.gz/etc. is assumed to be whitespace-delimited.
210			TCompounds can be referenced by InChI Key or compound ID (matching what you provided for the search).
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211			The set of compounds here must exactly match the set of compounds in the input files.
212			For Excel and text formats, the first row and the first column (header and index) indicate the compounds.
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213
214			Values must be floating-point.
215			"""
216			)
217			replace: bool = typer.Option(
218			False, help="Replace output file(s) if they exist. See also: --skip"
219			)
220
221			taxa = Opt.val(
222			r"""
223			The IDs or names of UniProt taxa, comma-separated.
224			Taxon names and common names can be used for vertebrate species (where available).
225
226			This can have a significant effect on searches. See the docs for more info.
227
228			[default: 7742] (Euteleostomi)
229			""",
230			"--taxa",
231			"7742",
232			show_default=False,
233			)
234
235			seed = Opt.val(r"A random seed (integer).", "--seed", default=0)
236
237			n_samples = Opt.val(
238			"Number of bootstrap samples (positive integer).",
239			"--samples",
240			min=1,
241			default=2000,
242			)
243
244			exclude = Opt.val("A glob pattern matching input filenames to ignore.")
245
246			verbose: bool = Opt.flag(
247			r"Configure logger to output INFO (use ``--quiet`` for less info)",
248			"-v",
249			"--verbose",
250			)
251
252			quiet: bool = Opt.flag(
253			r"Configure logger to output only ERROR (use ``--verbose`` for more info)",
254			"-q",
255			"--quiet",
256			)
257
258			in_cache: bool = Opt.flag(
259			r"Do not download any data and fail if needed data is not cached.",
260			hidden=True,
261			)
262
263			as_of: Optional[str] = Opt.val(
264			f"""
265			Restrict to data that was cached as of some date and time.
266			This option can be useful for reproducibility.
267
268			Note that this should imply that underlying data sources (such as of deposition or publication)
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269			are restricted by this datetime, but that is not checked.
270
271			Examples:
272
273			- --as-of 2021-10-11T14:12:13Z
274			- --as-of 2021-10-11T14:12:13+14:00
275			- --as-of 2021-10-11T14:12:13.496Z
276			- --as-of "2021-10-11 14:12:13,496,915+14:00"
277			- --as-of "2021-10-11 14:12:13-8:00 [America/Los_Angeles]"
278
279			This is a subset of ISO 8601, represented as ``YYYY-mm-dd('T'\|' '):hh:MM:ss(i)Z``.
280			Precision must be nanosecond or less, and ``,`` and ``.`` are equivalent as a thousands separator.
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281			You can provide an IANA zone name in square brackets for context, but the offset is still required.
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282			"""
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283			)
284
285			log_path = Opt.out_path(
286			r"""
287			Also log to a file.
288			The suffix can be .log, .log.gz, .log.zip, or .json, .json.gz, or .json.gz.
289			You can prefix the path with :LEVEL: to control the level. For example, ``:INFO:out.log``
290			""",
291			"--log",
292			show_default=True,
293			)
294
295			no_setup: bool = Opt.flag(
296			r"Skip setup, such as configuring logging.",
297			"--no-setup",
298			hidden=True,
299			)
300
301
302			cli = typer.Typer()
303
304
305			@cli.command()
306			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 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
307			path: Path = CommonArgs.dir_input,
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308			x=CommonArgs.log_path,
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309			):
310			pass
311
312
313			if __name__ == "__main__":
314			typer.run(run)
315
316
317			__all__ = ["CommonArgs", "Arg", "Opt"]
318

dmyersturnbull / mandos

Push — main ( ddff4b...7b3fbc )

mandos.entries.common_args.Arg.out_path() A

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