mandos.entry._arg_utils

Complexity

Total Complexity

36

Size/Duplication

Total Lines	210
Duplicated Lines	0 %

Importance

Changes

0

24 Methods

Rating	Name	Duplication	Size	Complexity
A	Opt.out_file()	0	4	1
A	Opt.out_path()	0	12	1
A	_Args._arg()	0	11	2
A	Arg.val()	0	3	1
A	Opt.in_path()	0	12	1
A	Arg.out_path()	0	4	1
A	Arg.in_path()	0	4	1
A	ArgUtils.parse_taxon_id_or_name()	0	7	4
B	ArgUtils.list()	0	18	6
A	Opt.in_file()	0	4	1
A	_Args._path()	0	18	3
A	Opt.out_dir()	0	4	1
A	Arg.out_dir()	0	4	1
A	Opt.in_dir()	0	4	1
A	Opt.val()	0	3	1
A	ArgUtils.parse_taxon_id()	0	6	2
A	Opt.flag()	0	3	1
A	ArgUtils.definition_bullets()	0	5	1
A	Arg.out_file()	0	4	1
A	ArgUtils.parse_taxa()	0	4	1
A	ArgUtils.definition_list()	0	4	1
A	Arg.in_dir()	0	4	1
A	ArgUtils.df_description()	0	7	1
A	Arg.in_file()	0	4	1

import enum

Missing module docstring

import os
from inspect import cleandoc
from typing import Optional, Iterable, Any, Mapping, Union, Callable, Sequence, Type

import typer

Unable to import 'typer'

from typeddfs import TypedDf

Unable to import 'typeddfs'

from mandos.entry._common_args import T


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,
        )
        if req:

Unnecessary "else" after "return"

            return typer.Argument(default, **kwargs)
        else:
            return typer.Option(default, *names, **kwargs)

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

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)

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)

Wrong hanging indentation before block (add 4 spaces).

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

This line is too long as per the coding-style (107/100).

        if out and default is None:
            kwargs = dict(show_default=False, **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):

Missing class docstring

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

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

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

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

Missing function or method docstring

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


class Opt(_Args):

Missing class docstring

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

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

        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):

Missing function or method docstring

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

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

Missing function or method docstring

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


class ArgUtils:

Missing class docstring

    @classmethod
    def definition_bullets(cls, dct: Mapping[Any, Any], colon: str = ": ", indent: int = 12) -> str:

Missing function or method docstring

        joiner = os.linesep * 2 + " " * indent
        jesus = [f" - {k}{colon}{v}" for k, v in dct.items()]
        return joiner.join(jesus)

    @classmethod
    def definition_list(cls, dct: Mapping[Any, Any], colon: str = ": ", sep: str = "; ") -> str:

Missing function or method docstring

        jesus = [f"{k}{colon}{v}" for k, v in dct.items()]
        return sep.join(jesus)

    @classmethod
    def df_description(cls, tdf: Type[TypedDf]) -> str:

Missing function or method docstring

        req = tdf.get_typing().required_columns
        res = [*tdf.get_typing().reserved_index_names, *tdf.get_typing().reserved_columns]
        line1 = "Required columns: " + ", ".join(req)
        line2 = "Optional columns: " + ", ".join(res)
        return line1 + "\n\n" + line2

    @classmethod
    def list(

Missing function or method docstring

        cls,

Wrong hanging indentation before block (add 4 spaces).

        lst: Iterable[Any],

Wrong hanging indentation before block (add 4 spaces).

        attr: Union[None, str, Callable[[Any], Any]] = None,

Wrong hanging indentation before block (add 4 spaces).

        sep: str = "; ",

Wrong hanging indentation before block (add 4 spaces).

    ) -> str:
        x = []

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        for v in lst:

Variable name "v" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            if attr is None and isinstance(v, enum.Enum):
                x += [v.name]

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            elif attr is None:
                x += [str(v)]

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            elif isinstance(attr, str):
                x += [str(getattr(v, attr))]

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            else:
                x += [str(attr(v))]

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        return sep.join(x)

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

Missing function or method docstring

        if isinstance(taxon, str):

Unnecessary "elif" after "return"

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

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

Missing function or method docstring

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

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

Missing function or method docstring

        taxa = [t.strip() for t in taxa.split(",")]
        return [ArgUtils.parse_taxon_id_or_name(t) for t in taxa]


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