Utils

check_command_available(command)

Check if a command is available.

Parameters:

Name	Type	Description	Default
command	str	The command to check.	required

Returns:

Name	Type	Description
bool		True if the command is available, False otherwise.

Examples:

>>> check_command_available('ls')

Source code in src/snk_cli/utils.py

def check_command_available(command: str):
    """
    Check if a command is available.

    Args:
      command (str): The command to check.

    Returns:
      bool: True if the command is available, False otherwise.

    Examples:
      >>> check_command_available('ls')
    """
    from shutil import which

    return which(command) is not None

convert_key_to_snakemake_format(key, value, sep=':')

Convert key to a format that can be passed over the cli to snakemake.

Parameters:

Name	Type	Description	Default
key	str	The key to convert.	required
value	any	The value associated with the key.	required
sep	str	The separator to use between keys. Defaults to ':'.	':'

Returns:

Name	Type	Description
dict		The converted key-value pair in snakemake format.

Source code in src/snk_cli/utils.py

def convert_key_to_snakemake_format(key, value, sep=":"):
    """
    Convert key to a format that can be passed over the cli to snakemake.

    Args:
      key (str): The key to convert.
      value (any): The value associated with the key.
      sep (str, optional): The separator to use between keys. Defaults to ':'.

    Returns:
      dict: The converted key-value pair in snakemake format.
    """
    result_dict = {}
    parts = key.split(sep)
    current_dict = result_dict

    for part in parts[:-1]:
        current_dict = current_dict.setdefault(part, {})

    current_dict[parts[-1]] = value

    return result_dict

flatten(d, parent_key='', sep=':')

Flattens a nested dictionary.

Parameters:

Name	Type	Description	Default
d	dict	The dictionary to flatten.	required
parent_key	str	The parent key of the dictionary. Defaults to ''.	''
sep	str	The separator to use between keys. Defaults to ':'.	':'

Returns:

Name	Type	Description
dict		A flattened dictionary.

Examples:

>>> d = {'a': {'b': 1, 'c': 2}, 'd': 3}
>>> flatten(d)
{'a:b': 1, 'a:c': 2, 'd': 3}

Source code in src/snk_cli/utils.py

def flatten(d, parent_key="", sep=":"):
    """
    Flattens a nested dictionary.

    Args:
      d (dict): The dictionary to flatten.
      parent_key (str, optional): The parent key of the dictionary. Defaults to ''.
      sep (str, optional): The separator to use between keys. Defaults to ':'.

    Returns:
      dict: A flattened dictionary.

    Examples:
      >>> d = {'a': {'b': 1, 'c': 2}, 'd': 3}
      >>> flatten(d)
      {'a:b': 1, 'a:c': 2, 'd': 3}
    """
    items = []
    for k, v in d.items():
        new_key = parent_key + sep + k if parent_key else k
        if isinstance(v, MutableMapping):
            items.extend(flatten(v, new_key, sep=sep).items())
        else:
            items.append((new_key, v))
    return dict(items)

parse_config_args(args, options)

Parses a list of arguments and a list of options.

Parameters:

Name	Type	Description	Default
args	List[str]	A list of arguments.	required
options	List[Option]	A list of options.	required

Returns:

Type	Description
	Tuple[List[str], List[dict]]: A tuple of parsed arguments and config.

Examples:

>>> parse_config_args(['-name', 'John', '-age', '20'], [{'name': 'name', 'default': '', 'help': '', 'type': 'str', 'required': True}, {'name': 'age', 'default': '', 'help': '', 'type': 'int', 'required': True}])
(['John', '20'], [{'name': 'name', 'John'}, {'age': 20}])

Source code in src/snk_cli/utils.py

def parse_config_args(args: List[str], options: List[Option]):
    """
    Parses a list of arguments and a list of options.

    Args:
      args (List[str]): A list of arguments.
      options (List[Option]): A list of options.

    Returns:
      Tuple[List[str], List[dict]]: A tuple of parsed arguments and config.

    Examples:
      >>> parse_config_args(['-name', 'John', '-age', '20'], [{'name': 'name', 'default': '', 'help': '', 'type': 'str', 'required': True}, {'name': 'age', 'default': '', 'help': '', 'type': 'int', 'required': True}])
      (['John', '20'], [{'name': 'name', 'John'}, {'age': 20}])
    """
    names = [op.name for op in options]
    config = []
    parsed: List[str] = []
    flag = None
    for arg in args:
        if flag:
            name = flag.lstrip("-")
            op = next(op for op in options if op.name == name)
            if op.updated is False and op.default == serialise(arg):
                # skip args that don't change
                flag = None
                continue
            if ":" in op.original_key:
                samkemake_format_config = convert_key_to_snakemake_format(
                    op.original_key, arg
                )
                name = list(samkemake_format_config.keys())[0]
                arg = samkemake_format_config[name]
            config.append({name: serialise(arg)})
            flag = None
            continue
        if arg.startswith("-") and arg.lstrip("-") in names:
            flag = arg
            continue
        parsed.append(arg)
    parsed.sort()
    return parsed, config

serialise(d)

Serialises a data structure into a string.

Parameters:

Name	Type	Description	Default
d	any	The data structure to serialise.	required

Returns:

Name	Type	Description
any		The serialised data structure.

Examples:

>>> serialise({'a': 1, 'b': 2})
{'a': '1', 'b': '2'}

Source code in src/snk_cli/utils.py

def serialise(d):
    """
    Serialises a data structure into a string.

    Args:
      d (any): The data structure to serialise.

    Returns:
      any: The serialised data structure.

    Examples:
      >>> serialise({'a': 1, 'b': 2})
      {'a': '1', 'b': '2'}
    """
    if isinstance(d, Path) or isinstance(d, datetime):
        return str(d)

    if isinstance(d, list):
        return [serialise(x) for x in d]

    if isinstance(d, dict):
        for k, v in d.items():
            d.update({k: serialise(v)})

    # return anything else, like a string or number
    return d