Added a function to get binary paths from a yaml file.

    process_item,

    reorder_items_list,

)

from ivas_processing_scripts.utils import DirManager, apply_func_parallel

from ivas_processing_scripts.utils import (

    DirManager,

    apply_func_parallel,

    get_binary_paths,

)

def logging_init(args, cfg):

        # set up logging

        logger = logging_init(args, cfg)

        # updating binary paths

        if cfg.binary_paths is not None:

            get_binary_paths(cfg, cfg.binary_paths)

        # Re-ordering items based on concatenation order

        if cfg.concatenate_input and cfg.concatenation_order is not None:

            cfg.items_list = reorder_items_list(cfg.items_list, cfg.concatenation_order)

    "preamble": None,

    "pad_noise_preamble": False,

    "metadata_path": None,

    "binary_paths": None,

    # postprocessing

    "postprocessing": {

        "hp50": False,

import shutil

import subprocess as sp

import sys

import yaml

from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor

from itertools import repeat, tee

from os import devnull

    binary: str,

    raise_error: Optional[bool] = True,

    logger: Optional[logging.Logger] = None,

    binary_path: Optional[str] = None,

) -> Union[Path, None]:

    """Attempt to find and return the path to the given binary"""

    # prioritise binaries placed in the directory over $PATH

    if binary_path is not None:

        bin = which(binary, path=binary_path)

    else:

        bin = which(binary, path=BIN_DIR)

    if not bin:

        bin = which(binary)

    if not bin and raise_error:

        raise FileNotFoundError(

            f"Binary {binary} was not found in $PATH or in {BIN_DIR.absolute()}!"

            f"Binary {binary} was neither found in {binary_path.absolute()} nor in {BIN_DIR.absolute()} or in $PATH!"

        )

    elif not bin:

        if logger:

        yield item

        update(i + 1)

    print("\n", flush=True, file=sys.stdout)

def get_binary_paths(obj, binary_path):

    with open(binary_path, "r") as f:

        data = yaml.safe_load(f)

    for key, value in data.items():

        p = Path(value)

        setattr(obj, key + "_binary_path", p)