cytosnake.guards package#

Submodules#

module: ext_guards.py

Checks if the correct extensions are provided

cytosnake.guards.ext_guards.has_parquet_ext(file_name: str | Path) → TypeGuard[str]#

Checks if the provided file path contains parquet file extension . :param file_name: path to file :type file_name: str | pathlib.Path

cytosnake.guards.ext_guards.has_sqlite_ext(file_name: str | Path) → TypeGuard[str]#

Checks if the provided file path contains parquet file extension .

module: input_guards.py

This module will handle the CytoSnake’s CLI logic mostly interacting with user defined parameters from CytoSnake’s CLI.

There the logic establishes some rules of what inputs are required or what functionality is or not allowed.

cytosnake.guards.input_guards.check_init_parameter_inputs(user_params: NameSpace) → bool#

Main wrapper to check init mode parameter logic.

Parameters:: user_params (NameSpace) – Argparse.NameSpace object that contains all user provided parameters.
Returns:: True if all logic checks passed
Return type:: bool
Raises:: BarcodeMissingError – Raised if a multiple platemaps are found but no barcode file was provided

cytosnake.guards.input_guards.is_barcode_required(user_params: NameSpace) → bool#

user_params: NameSpace: Argparse.NameSpace object that contains all user provided parameters

Returns:: With the given parameter inputs, True if barcodes are required else False
Return type:: bool

Module: path_guards.py

Functions for checking paths.

This includes:

cytosnake.guards.path_guards.is_valid_path(val: object) → TypeGuard[Path]#

checks if provided value is a valid path