seismicrna.core.arg package

CLI arguments/options: import directly from submodules (e.g. from ..arg.<submodule> import <name>).

Subpackages

Submodules

seismicrna.core.arg.cli.merge_params(*param_lists: list[Parameter], exclude: Iterable[Parameter] = ())

Merge lists of Click parameters, dropping duplicates.

seismicrna.core.arg.cli.optional_path(path_or_none: Path | str | None)
seismicrna.core.arg.docdef.auto(*, extra_defaults: dict[str, Any] | None = None, exclude_defaults: Iterable[str] = (), extra_docstrs: dict[str, str] | None = None, return_docstr: str = '')

Combine auto_defaults and auto_docstrs, in that order.

seismicrna.core.arg.docdef.auto_defaults(extra_defaults: dict[str, Any] | None = None, exclude_defaults: Iterable[str] = ())

Call paramdef and automatically infer default values from the CLI and API. Extra defaults (if needed) may be given as keyword arguments.

seismicrna.core.arg.docdef.auto_docstrs(extra_docstrs: dict[str, str] | None = None, return_docstr: str = '')

Call param_docstrs and automatically infer descriptions and type annotations about all parameters from the CLI and API. Documentation of any extra parameters may also be given.

seismicrna.core.arg.docdef.get_docstr_lines(func: Callable, param_lines: list[str], return_docstr: str)

Assemble docstring lines for a function.

Parameters:

  • func (Callable) – Function whose existing docstring and return annotation are used as the basis for the new docstring.

  • param_lines (list[str]) – Lines describing each parameter, as produced by get_param_lines.

  • return_docstr (str) – Description of the return value; included only when the function has a return annotation.

seismicrna.core.arg.docdef.get_param_default(param: Parameter, defaults: dict[str, Any], exclude_defaults: Iterable[str])

Return the parameter, possibly with a new default value.

seismicrna.core.arg.docdef.get_param_lines(func: Callable, docstrs: dict[str, str])
seismicrna.core.arg.docdef.param_defaults(defaults: dict[str, Any], exclude_defaults: Iterable[str] = ())

Give the keyword argments of a function default values.

seismicrna.core.arg.docdef.param_docstrs(docstrs: dict[str, str], return_docstr: str)

Give a function a new docstring where each parameter gets annotated with the text given in the keyword arguments (param_docs).

Parameters:

  • docstrs (dict[str, str]) – Description of each parameter, keyed by name

  • return_docstr (str) – Description of the return value; will occur at end of docstring

Returns:

Function with new docstring

Return type:

callable

class seismicrna.core.arg.glob.GlobPath(exists: bool = False, file_okay: bool = True, dir_okay: bool = True, writable: bool = False, readable: bool = True, resolve_path: bool = False, allow_dash: bool = False, path_type: type | None = None, executable: bool = False)

Bases: Path

A click.Path that expands glob patterns via Python’s glob module.

convert(value, param, ctx)

Convert the value to the correct type. This is not called if the value is None (the missing value).

This must accept string values from the command line, as well as values that are already the correct type. It may also convert other compatible types.

The param and ctx arguments may be None in certain situations, such as when converting prompt input.

If the value cannot be converted, call fail() with a descriptive message.

Parameters:

  • value – The value to convert.

  • param – The parameter that is using this type to convert its value. May be None.

  • ctx – The current context that arrived at this value. May be None.

name: str = 'glob_path'

the descriptive name of this type

seismicrna.core.arg.glob.expand_ct_pos_5(ctx, param, value)

Pair each glob-expanded path with its associated integer position.

seismicrna.core.arg.glob.flatten_glob_results(ctx, param, value)

Flatten a multiple=True value where entries may be tuples of paths.