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def build_tile_url( image_path: str, rgb: bool = False, url_root: str = "/", is_product: bool = False ) -> str: """Build a Tile URL for the given image path. Args: image_path: the path to the image to be processed rgb (optional): if the path should be to the DEM RGB version of tiles Re...
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def summarize_packet(pkt): """ Summarizes a packet into a human-legible string. Five key fields are represented in the summary - source/destination IP, source/destination MAC address, source/ destination TCP/UDP port, and the transport protocol in use (such as TCP/UDP). If any of the five key fields...
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import json def platform2gates(platform_fname, gates_fname): """Tries to convert an OpenQL platform JSON file to a gatemap JSON file for use with the DQCsim operator wrapper for OpenQL. Heuristics are applied to convert common gate names to DQCsim equivalents, but you may need to do some manual adjust...
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def parse_control(c): """ Parse a carla.VehicleControl to a json object. """ return { "brake": c.brake, "gear": c.gear, "hand_brake": c.hand_brake, "manual_gear_shift": c.manual_gear_shift, "reverse": c.reverse, "steer": c.steer, "throttle": c.thro...
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def eval_f(f, xs): """Takes a function f = f(x) and a list xs of values that should be used as arguments for f. The function eval_f should apply the function f subsequently to every value x in xs, and return a list fs of function values. I.e. for an input argument xs=[x0, x1, x2,..., xn] the function e...
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import requests def get_download_id(pql_query: str, datatype: str = "ssm", output_format: str = "TSV") -> str: """ Calls an ICGC Data Portal API to retrieve a download ID for the dataset specified by a PQL query, a data type, and an output format. :param pql_qu...
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import torch def exponential_transition(perturbations, norm, epsilon=0.3, gamma=1): """ Exponential transition rule. :param perturbations: perturbations :type perturbations: torch.autograd.Variable :param norm: norm :type norm: attacks.norms.Norm :param epsilon: epsilon :type epsilon:...
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def _create_vn_str(novice_status): """Creates varsity-novice status string from the integer pseudo-enum used by the model""" if novice_status is 0: return "varsity" if novice_status is 1: return "novice" return novice_status
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from typing import Optional from typing import BinaryIO import io import tarfile def merge_tar_gz(a: Optional[BinaryIO], b: Optional[BinaryIO]) -> Optional[BinaryIO]: """Merge <a> and <b>, returning a new tarfile.TarFile object. If two files in <a> and <b> have the same name, the one in <a> prevails. ...
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def make_zero_based_midi(defs): """ The official MIDI spec is 1 based (why???), but clearly most things are 0 based. So this function shifts all of the program numbers down by one and keeps 0 as piano. :param defs: :return: """ for k, v in defs.items(): pgms = [max(i - 1, 0) for ...
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def intdivceil(x, y): """ Returns the exact value of ceil(x // y). No floating point calculations are used. Requires positive integer types. The result is undefined if at least one of the inputs is floating point. """ result = x // y if (x % y): result += 1 return result
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import six from typing import OrderedDict def ordered_recurse(value): """Recursively order nested dicts and lists at all levels.""" if isinstance(value, list): return [ordered_recurse(v) for v in value] if isinstance(value, dict): items = sorted( ((key, ordered_recurse(value)) ...
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def _get_queue_arguments(conf): """Construct the arguments for declaring a queue. If the rabbit_ha_queues option is set, we declare a mirrored queue as described here: http://www.rabbitmq.com/ha.html Setting x-ha-policy to all means that the queue will be mirrored to all nodes in the cluste...
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from typing import Union from pathlib import Path from typing import Dict import yaml def read_config(path: Union[str, Path]) -> Dict: """ Reading configuration file based on the given path :param path: str or Path, path to the config file :return: Dict, dictionary generated by the config file which h...
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def clean_text(identifica, ementa, fulltext): """ Given a DOU article titles `identifica` and an abstract `ementa`, remove the first title in `identifica`, `ementa` and the hard-coded footnote from the full text of the DOU article `fulltext`. """ # ATTENTION: this code should reproduce the clea...
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import functools import aiohttp def http_session_method(f): """Decorator for a method that uses an async http session""" @functools.wraps(f) async def wrapper(self, *args, **kwargs): async with aiohttp.ClientSession() as session: return await f(self, session, *args, **kwargs) ...
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def mc_to_float(value): """ Convert from millicents to float Args: value: millicent number Returns: value in float """ return float(value) / (100 * 1000)
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def indices_to_sentence(indices, vocabulary): """ Turn a list of indices of a vocabulary into a sentence. """ y = indices words = [vocabulary[idx] for idx in y] return " ".join(words)
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import csv def _get_dsv_reader(dsv_file): """ Detect the delimiter used in opened dsv (delimiter-separated values) file and return csv.DictReader object initialized to iterate over file contents Args: dsv_file(file object): opened dsv file object Returns: csv.DictReader: reader o...
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def task_builder(generator, n_train=1000, n_test=250): """ creates the task generator :generator: generator for the wanted task :n_train: number of samples to generate for training :n_test: number of samples to generate for testing :returns: dictionary of the task of generated samples ...
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from typing import Tuple def parse_project_name(name: str, ssh: bool = True) -> Tuple[str, str, str, bool]: """Parse the name argument for get_project Returns (name, url, branch, is_url). If name is not a full url, the returned url will be a https or ssh url depending on the boolean argument ssh. ...
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def createZeroMat(m,n): """Return a matrix (m x n) filled with zeros.""" ret = [0] * m for i in range(m): ret[i] = [0] * n return ret
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def clamp(num, min_val, max_val): """Clamps `min` within the range [`min_val`..`max_val`].""" return max(min_val, min(num, max_val))
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def split_semicolon_filter(s): """ Filter to take semicolon-delimited text and convert it to a list """ if s is not None: return s.strip().split(';') return None
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import torch def effective_sample_size(log_weights): """Kish effective sample size; log weights don't have to be normalized""" return torch.exp(2*torch.logsumexp(log_weights, dim=0) - torch.logsumexp(2*log_weights, dim=0))
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def enable_squash(input): """ Convert long specific enable strings to 'enabled' Takes in a dictionary of parsed output, iterates over the keys and looks for key names containing the string "enabled" at the end of the key name. Specifically the end of the key name is matched for safety. Replaces th...
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import torch def get_ans_idx(p_s, p_e, max_len=15, no_answer=False): """ Discretize soft predictions (probs) to get start and end indices Choose (i, j) which maximizes p1[i]*p2[j], s.t. (i <= j) & (j-i+1 <= max_len) Args: p_s: [batch_size, c_len], probs for start index p_e: [batch_size...
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def dump_dataclass_object(packet_obj: object) -> bytes: """Given a dataclass object, will return it as bytes Args: packet_obj: A dataclass object Returns: bytes representing given dataclass object """ raw_packet = bytearray() for _, value in packet_obj.__dict__.items(): raw_pac...
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def _validate_timezone(hours_offset: int): """Creates an int from -48 to 36 that represents the timezone offset in 15-minute increments as per the FlashAir docs""" param_value = int(hours_offset * 4) assert -48 <= param_value <= 36 return param_value
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def dataToString(var, data): """Given a tuple of data, and a name to save it as returns var <- c(data) """ #convert data to strings d = [str(d) for d in data] return "%s <- c(%s)" % (var, ",".join(d))
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def _is_private_port_speed_item(item): """Determine if the port speed item is private network only.""" for attribute in item['attributes']: if attribute['attributeTypeKeyName'] == 'IS_PRIVATE_NETWORK_ONLY': return True return False
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def GetStateMessagesStrings(state_messages): """Returns the list of string representations of the state messages.""" return map(lambda st: '[{}] {}'.format(str(st.severity), st.message), state_messages)
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def get_uncrop(img,size,h_cent): """ Returns a method to convert cropped coordinate to full frame coordinate. Parameters ---------- img : numpy.ndarray The full framed image. size : int The size of the cropped images. h_cent : int The horizontal centre used for cropp...
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def check_assignments(csp, var1, var2) : """Check if all constraints between var1 and var2 are satisfied for the given assignment values""" return all(constraint.check(var1[1], var2[1]) for constraint in csp.constraints_between(var1[0], var2[0]))
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def _class_get_plugin(cls): """ Class method that retrieves the plugin instance associated with the current model class. This method should not overlap the get plugin method on the instance, and you should used this one to retrieve the absolute related system instance, avoiding problems with inh...
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from typing import Union from typing import Iterable import re def clean_uids(uid_set: Union[str, Iterable[str]]) -> str: """ Prepare set of uid for use in IMAP commands uid RE patterns are not strict and allow invalid combinations, but simple. Example: 2,4:7,9,12:* :param uid_set: str, that i...
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import time def retry(times, exceptions, scaling_duration=1): """ Retry Decorator Retries the wrapped function/method `times` times if the exceptions listed in ``exceptions`` are thrown :param times: The number of times to repeat the wrapped function/method :type times: Int :param Exceptio...
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import binascii def stringio_to_base64(stringio_obj): """Get base64 encoded version of a BytesIO object.""" return binascii.b2a_base64(stringio_obj.getvalue())
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def filter_frontier(frontier, pred_fns, cfg_pred_fns=None): """Filter out points from the frontier that don't pass all the pred_fns. If a pred_fn is None, ignore that metric. """ new_frontier = [] for result in frontier: cfg, qos = result keep = True if not all(f(x) for x, f ...
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def get_value_safe(d=None, key=None): """ Return value of a given dictionary for a key. @return: value for a key, None otherwise """ if d is None or key is None: return None if key not in d: return None return d[key]
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def Ndavies(r,g,eta,drho,rho): """Davies (Best) number Args: r: particle size (cm) g: gravity (cm/s2) eta: dynamic viscosity (g/s/cm) drho: density difference between condensates and atmosphere (g/cm3) rho: atmosphere density (g/cm3) Returns: Davies number (B...
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import random def random_matrix (nrow, colmean, colsd): """Generate a random matrix of independent Gaussians, with nrow being the number of rows, and with colmean and colsd being vectors of column means and SDs, respectively.""" assert(len(colmean) == len(colsd)) assert(nrow > 0) ncol = len(colmean) # ge...
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def derivative_colors(colors): """Return the names of valid color variants, given the base colors.""" return set([('on_' + c) for c in colors] + [('bright_' + c) for c in colors] + [('on_bright_' + c) for c in colors])
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def moving_avg(xyw, avg_len): """ Calculate a moving average for a given averaging length :param xyw: output from collapse_into_single_dates :type xyw: dict :param avg_len: average of these number of points, i.e., look-back window :type avg_len: int :return: list of x values, list of y value...
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def perspective_request(perspective, comment): """ Generates a request to run the toxicity report""" analyze_request = { 'comment':{'text': comment}, 'requestedAttributes': {'TOXICITY': {}, 'THREAT': {}, 'INSULT': {}} } response = perspective.comments().analyze(body=analyze_request).execute() retu...
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def remove_quotes(string): """ remove all (double) quotes""" return string.replace("'", "").replace('"', '')
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import struct def pack_word(word, big_endian=False): """ Packs a 32-bit word into a binary data string. """ endian = ">" if big_endian else "<" return struct.pack("%sL" % endian, word)
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def _no_convert(_, start, end=None): """Dummy function for when no conversion is needed.""" if end: return start, end else: return start, start
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from functools import reduce def _bit_list_to_bytes(bits): """Convert a sequence of truthy values into a byte string, MSB first.""" return bytes( reduce(lambda a, b: (a << 1) | b, (int(bool(x)) for x in byte_bits)) for byte_bits in zip(*[iter(bits)]*8) )
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def load_config_auth(config_parser): """Convert an auth cfparser config into a dictionary :param config_parser: configparser configuration :type paths: class:`configparser.ConfigParser` :return: configuration as a dictionary :rtype: dict """ config = {'github': {'token': config_parser['gi...
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def sort_2metals(metals): """ Handles iterable or string of 2 metals and returns them in alphabetical order Args: metals (str || iterable): two metal element names Returns: (tuple): element names in alphabetical order """ # return None's if metals is None if metals is None:...
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def pretty_bytes(byte_value, base_shift=0): """Pretty-print the given bytes value. Args: byte_value (float): Value base_shift (int): Base value of byte_value (0 = bytes, 1 = KiB, 2 = MiB, etc.) Returns: str: Pretty-printed byte string such as "1.00 GiB" Examples: :...
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import calendar import time def build_filename(option, quarter): """ Function to build filename based on current day and month :return: Name of the file. Example: 'teacher_q1_timestamp' """ timestamp = calendar.timegm(time.gmtime()) underscore = "_" name = [option, underscore, "q" + str(qu...
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from re import compile, findall def filterSpilloverFilename(filename): """ Remove any unwanted spill-over filename endings (i.e. _NNN or ._NNN) """ # Create the search pattern pattern = compile(r'(\.?\_\d+)') found = findall(pattern, filename) if found: # Make sure that the _NNN substring...
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def remove_comma(in_str): """ Remove comma from given string """ return str(in_str).replace(",", " ").replace(" ", " ")
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def is_ascii(str_data: str) -> bool: """Checks if string contains only ascii chars. Necessary because python 3.6 does not have a str.isascii() method. Parameters ---------- str_data : str string to check if it contains only ascii characters Returns ------- bool True if...
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def _wfdb_fmt(bit_res, single_fmt=True): """ Return the most suitable WFDB format(s) to use given signal resolutions. Parameters ---------- bit_res : int, list The resolution of the signal, or a list of resolutions, in bits. single_fmt : bool, optional Whether to return the ...
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def construct_res_tuple(res): """ Build the BigDFT fragment tuple given the residue of the structure Args: res(Residue): A residue Class on the Biopython package Returns: tuple: the (chain,fragname,fragno) tuple """ chain = res.full_id[2] if len(chain.lstrip(' ')) == 0: ...
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def id(args, premise): """Return ID.""" return args[0].id
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def bin2x2(arr): """Bin 2-d ``arr`` in 2x2 blocks. Requires that ``arr`` has even shape sizes""" shape = (arr.shape[0] // 2, 2, arr.shape[1] // 2, 2) return arr.reshape(shape).sum(-1).sum(1)
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def decode_bytes(s, encoding='utf-8', errors='replace'): """Decodes bytes to str, str to unicode.""" return s.decode(encoding, errors=errors) if isinstance(s, bytes) else s
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def dead_state(height, width): """ Construct a dead state with all cells set to DEAD. :arg height: The height of the state, in cells. :arg width: The width of the state, in cells. :returns: A state of dimensions height x width, with all cells set to DEAD. """ return [[0 for _ in r...
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def str_time(t): """ Return the time such as %H:%M:%S. Parameters ---------- t : int Time in seconds. Returns ------- str Time in hours, minutes and seconds. """ txt = '' s, t = t % 60, t // 60 if s < 10: s = '0' + str(s) m, h = t % 60, t // 60...
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def get_lower_case_dict(value_list): """ Create a dictionary whose key is the provided key value in lower case and whose value is the original key value. :param value_list: List of key strings. :return: Dictionary with lower case key and original value """ lower_case_map = dict() for value i...
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def spridning(data): """Returns the size of the range of values in the data.""" return max(data) - min(data)
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def split_vectors(vectors): """Splits vectors into their x, y and z components.""" return vectors[..., 0], vectors[..., 1], vectors[..., 2]
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import csv def real_edges_from_csv_file(real_edges_file: str) -> dict: """ Reads the csv file and returns a dict of edges with the real distance between the nodes. real_edges_file: str = csv path Returns: real_edges: dict = { from_station: [ (to_station, distance), ....
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from typing import List def primes(n_max: int = 100) -> List[int]: """Implements the Eratosthene's sieve """ if n_max < 2: raise ValueError t = list(range(2, n_max + 1)) for i in t: for j in (k for k in t if k > i): if j % i == 0: t.remove(j) retur...
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def module_name(instance): """Return the instance module name.""" return instance.__class__.__module__.split('.')[0]
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def soma_volume(morph): """Get the volume of a morphology's soma.""" return morph.soma.volume
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def _make_times(delta_hours): """ Creates the list of times that a map will be downloaded for each day starting a '00' UTC. :param delta_hours: The change in hours between subsequent maps :return: The list of times represented as list of strings >>> _make_times(6) ['00', '06', '12', '18'] ...
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def items(json_struct): """ Gets all items of the json_struct """ return json_struct._data.items()
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def sales_growth_rate(sales_period_1, sales_period_2): """Return the sales growth rate for the current period versus the previous period. Args: sales_period_1 (float): Total company sales for previous the period. sales_period_2 (float): Total company sales for the current period. Returns: ...
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def iqr(x): """Return the interquartile range of the input numpy array arguments: x: numpy array of numeric type returns: the interquartile range of x""" return x.quantile(0.75) - x.quantile(0.25)
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def check_ext(file_name, ext): """Check the extension for a file name, and add if missing. Parameters ---------- file_name : str The name of the file. ext : str The extension to check and add. Returns ------- str File name with the extension added. """ ...
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def prepare_querystring(*query_arguments, **kw_query_arguments): """Prepare a querystring dict containing all query_arguments and kw_query_arguments passed. :return: Querystring dict. :rtype: dict """ querystring = dict() for argument_dict in query_arguments: if isinstance(argument_...
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def contour_enclosed_area_py(verts): """ Compute the area enclosed by a contour. Copied from https://arachnoid.com/area_irregular_polygon/ Parameters ---------- verts : array_like 2D shape (N,2) array of vertices. Uses scikit image convetions (j,i indexing) Ret...
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def prefer_safest(graph, next_sys): """Return a weight for prefering the safest route.""" if graph.security(next_sys) < 0.45: # low/null return 50000.0 return 1.0
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def get_iftable(snmp_data): """ Gets the interface table (if_index and interface) for a given device for further snmp lookups Args: snmp_data - snmp data returned by cmdgen.nextCmd() for mib = .1.3.6.1.2.1.2.2.1.2 Returns: if_table - dict formatted as if:if_index ...
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def calculate_time_match_fifo(ai, aj, times0=None): """ Associate the times between two lists of timestamps using FIFO Parameters -------------- ai First list of timestamps aj Second list of timestamps times0 Correspondence between execution times Returns ...
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def _get_port_to_string(iface): """Simple helper which allows to get string representation for interface. Args: iface(list): Which IXIA interface to use for packet sending (list in format [chassis_id, card_id, port_id]) Returns: str: string in format "chassis_id/card_id/port_id" """ ...
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def str_day(day): """Transforms datetime day object into a "%d/%m/%y" string. Args: day (datetime/datetime.date): Day. Returns: A "%d/%m/%y" string representation. """ return day.strftime("%d/%m/%y")
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def get_chunk_region(chunkX, chunkZ): """ Returns the name of the region file given global chunk coords """ regionX = chunkX / 32 regionZ = chunkZ / 32 region_name = 'r.' + str(regionX) + '.' + str(regionZ) + '.mcr' return region_name
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def make_feature(wordlist, toplist): """Return a feature vector corresponding to a wordlist. The wordlist represents an article. We count the incidences in wordlist of each word in toplist. """ # This could be optimized if necessary. feature = [wordlist.count(word) for word in toplist] ...
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def xmlbool(bool): """Convert a boolean into the string expected by the elfweaver XML.""" # Is there a smarter way of doing this? if bool: return "true" else: return "false"
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import math def binom(n, r): """ return binomial coefficient: n choose k""" return math.factorial(n) // math.factorial(n - r) // math.factorial(r)
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import click def selection_prompt(prompt: str, choices: list) -> str: """ Prompts the user to select an option from an list of choices. :param prompt: The text of the prompt. :param choices: A list of choices. :return: The user's selection. """ joiner = "\n* " selection = click.prompt...
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def list_generator(start: int, step: int, number: int) -> list: """ Generates a list with 'number' of integers. The first one equals to 'start' and every consequtive is increased by 'step'. """ i = start retval = [i] for n in range(number): i += step retval.append(i) retu...
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from typing import List def _format_predicted_class_strings(class_names: List[str]) -> List[str]: """Format the class names by replacing underscores with spaces and capitilize every word's first letter. Args: class_names (List[str]): A List of class names. Returns: List[str]: A List of f...
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import re def squish(text): """Turn any run of whitespace into one space.""" return re.sub(r"\s+", " ", text)
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import torch def prepare_batch(batch, device, non_blocking, new_shape=None): """Prepare the batch data for training/inference, move data to GPU, reshape the target if necessary. Args: batch (torch.Tensor): A batch of data. device (torch.device or str): Device to load the backbone and data...
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def get_local_file_content(file_path): """Gets the contents of a local file. Args: file_path: The path of the file. Returns: The content fetched from the local file. """ with open(file_path, "r") as opened_file: return opened_file.read()
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def rec_cmp_releases(one, two): """Recursive function that compares two version strings represented as lists to determine which one comes "after" / takes precedence, or if they are equivalent. List items must be integers (will throw TypeError otherwise). If the left argument ("one") is a later version...
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def tokenize_mutation_seq(seq, placeholder_token='_'): """Converts a variable-length mutation sequence to a fixed-length sequence. For an N-residue reference sequence, the encoding is shape (N+1, M, A), where A is the alphabet size (e.g., A=20 for the canonical peptide alphabet) and M is the number of distinct...
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def prod(l): """ l: iterable of numbers. returns: product of all numbers in l """ p = 1 for i in l: p *= i return p
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def lv1_consts(key=None): """ defines consts used while reading Sciamachy level 0 data """ consts = {} consts['mds_size'] = 1247 consts['max_clusters'] = 64 consts['uvn_channels'] = 5 consts['swir_channels'] = 3 consts['all_channels'] = consts['uvn_channels'] + consts['swir_channels...
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def getDistance(interval_a, interval_b): """Returns the distance between two intervals""" return max(interval_a[0] - interval_b[1], interval_b[0] - interval_a[1])
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def align(offset): """Align an offset to a multiple of 4 Args: offset (int): Offset to align Returns: int: Resulting aligned offset (rounds up to nearest multiple) """ return (offset + 3) & ~3
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def date_formatter(date_val): """ Auto formats date values (month, day, hour, minute) to two digits. This is needed for proper date formatting by Plotly. i.e. the month of March is represented in the database as and integer of 3. This needs to be changed to a string of '03' to be plotted properly....
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def get_param_groups(net, weight_decay, norm_suffix='weight_g', verbose=False): """Get two parameter groups from `net`: One named "normalized" which will override the optimizer with `weight_decay`, and one named "unnormalized" which will inherit all hyperparameters from the optimizer. Args: net ...
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