Source code for shennong.utils

"""Provides some utilities functions used by the *shennong* library

Those fonctions are not designed to be used by the end-user.


import multiprocessing
import os
import re
import sys

import numpy as np
import pkg_resources

from shennong.logger import null_logger

[docs]def get_njobs(njobs=None, log=null_logger()): """Returns the number of parallel jobs to run The returned number of jobs is adapted from the input `njobs` value, considering the number of CPU cores available on the machine. Parameters ---------- njobs : int, optional The desired number of jobs to use, default to the number of cores available on the machine. log : logging.Logger, optional A logger where to send messages, no logging by default. Returns ------- njobs : int The returned value is min(njobs, ncpus). Raises ------ ValueError If `njobs` is not a strictly positive integer. """ max_njobs = multiprocessing.cpu_count() if njobs is None: return max_njobs if njobs <= 0: raise ValueError( 'njobs must be strictly positive, it is {}'.format(njobs)) if njobs > max_njobs: log.warning( 'asking %d CPU cores but reducing to %d (max available)', njobs, max_njobs) return max_njobs return njobs
[docs]def list2array(seq): """Converts lists in `seq` into numpy arrays""" if isinstance(seq, list): return np.asarray(seq) if isinstance(seq, dict): return {k: list2array(v) for k, v in seq.items()} return seq
[docs]def array2list(seq): """Converts numpy arrays in `seq` into lists""" if isinstance(seq, dict): return { k: array2list(v) for k, v in seq.items()} if isinstance(seq, np.ndarray): return seq.tolist() return seq
[docs]def dict_equal(dict1, dict2): """Returns True if `dict1` and `dict2` are equals The dictionnaries `dict1` and `dict2` can contain numpy arrays. Parameters ---------- dict1 : dict The first dictionnary to compare dict2 : dict The second dictionnary to compare Returns ------- equal : bool True if `dict1` == `dict2`, False otherwise """ return array2list(dict1) == array2list(dict2)
[docs]def list_files_with_extension( directory, extension, abspath=False, realpath=True, recursive=True): """Return all files of given extension in directory hierarchy Parameters ---------- directory : str The directory where to search for files extension : str The extension of the targeted files (e.g. '.wav') abspath : bool, optional If True, return the absolute path to the file/link, default to False. realpath : bool, optional If True, return resolved links, default to True. recursive : bool, optional If True, list files in the whole subdirectories tree, if False just list the top-level directory, default to True. Returns ------- files : list The files are returned in a sorted list with a path relative to 'directory', except if `abspath` or `realpath` is True """ # the regular expression to match in filenames expr = r'(.*)' + extension + '$' # build the list of matching files if recursive: matched = [] for path, _, files in os.walk(directory): matched += [ os.path.join(path, f) for f in files if re.match(expr, f)] else: matched = ( os.path.join(directory, f) for f in os.listdir(directory) if re.match(expr, f)) if abspath: matched = (os.path.abspath(m) for m in matched) if realpath: matched = (os.path.realpath(m) for m in matched) return sorted(matched)
[docs]class CatchExceptions: """Decorator wrapping a function in a try/except block When an exception occurs, display a user friendly message on standard output before exiting with error code 1. The detected exceptions are ValueError, OSError, RuntimeError, AssertionError, KeyboardInterrupt and pkg_resources.DistributionNotFound. Parameters ---------- function : The function to wrap in a try/except block """ def __init__(self, function): self.function = function def __call__(self): """Executes the wrapped function and catch common exceptions""" try: self.function() except (IOError, ValueError, OSError, RuntimeError, AssertionError) as err: self.exit('fatal error: {}'.format(err)) except pkg_resources.DistributionNotFound: # pragma: nocover self.exit( 'fatal error: shennong package not found\n' 'please install shennong on your system') except KeyboardInterrupt: self.exit('keyboard interruption, exiting')
[docs] @staticmethod def exit(msg): """Write `msg` on stderr and exit with error code 1""" sys.stderr.write(msg.strip() + '\n') sys.exit(1)