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def strip_string_to_integer(string): """ :param string: :return: """ return int("".join(filter(lambda x: x.isdigit(), string)))
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def totalMemory(): """The total amount of memory installed in this computer, in bytes.""" return int
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import math def _linspace_args(start, stop, step_size=None, length=None): """ Parameters ---------- start : stop : step_size : (Default value = None) length : (Default value = None) Returns ------- type where step_size OR length is ...
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def config_handler(cfg): """ Separates the explainability values from the models. :param cfg: Loaded config file. """ explainability_measures = [] models_to_use = [] for model in cfg["models to use"]: models_to_use.append(list(model.keys())[0]) values = list(mod...
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def unique_proportion(_metrics): """Computes the proportion of unique non-null values out of all non-null values""" total_values = _metrics.get("table.row_count") unique_values = _metrics.get("column.distinct_values.count") null_count = _metrics.get("column_values.nonnull.unexpected_count") # Ensur...
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def parsed_variant(): """Return variant information for a parsed variant with minimal information""" variant = {'alternative': 'C', 'callers': { 'freebayes': None, 'gatk': None, 'samtools': None }, 'case_id': '...
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def binval(b): """ Renvoie la valeur du nombre binaire b (big endian). Seulement dans [0,15]. """ s = 0 for i in b: s = 2*s + i return s
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import argparse def get_config_from_args(): """ Reads the arguments and returns a config used by the rest of the script """ parser = argparse.ArgumentParser(description='Parse converter cli args') parser.add_argument('infile', help='The file containing the input json') parser.add_argument('-o'...
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import math def signed_distance_point_to_line(a, b, c, p): """ Distance between a point p and a line defined by a, b and c. a, b, c: the line $x + by + c = 0$ p: the point """ d1 = (a*p[0] + b*p[1] + c) d2 = math.sqrt(math.pow(a, 2.) + math.pow(b, 2.)) #d = abs(d1)/d2 d = d1/d2 ...
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import yaml def validate_spackyaml(filename): """ Ensure that a spack.yaml file has a spack or env directive """ try: with open(filename, "r") as fd: data = yaml.load(fd, Loader=yaml.FullLoader) if "env" not in data and "spack" not in data: return False ...
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def ResetStNum(N=0): """Reset the state numbering counter. """ global NXTSTATENUM NXTSTATENUM = N return NXTSTATENUM
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import binascii def bytes_str(val): """ Converts bytes into hex string. Returns: hex string """ assert isinstance(val, (bytes, bytearray)) return binascii.hexlify(val).decode('ascii')
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def distinct(l): """Builds a new list with all duplicates removed.""" s = [] for i in l: if i not in s: s.append(i) return s
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import os import subprocess import re def run_camb(params_fname, camb_exec_dir): """ Run CAMB, using a given (pre-written) params file (see camb_params). Waits for CAMB to finish before returning. Returns a dictionary of derived values output by CAMB to stdout. """ # Change directory and cal...
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import argparse def parseArgs(): """ Parse arguments from the command line. Uses the `argparse` package to establish all positional and optional arguments. """ parser = argparse.ArgumentParser(description='Find coincidence lattices within combinations of 2D crystals.', epilog= "If you find this script u...
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def get_gap_segments(segments): """ Get the gap segments. {(start1, end1), (start2, end2), (start3, end3)} -> {(end1, start2), (end2, start3)} """ segments = [list(i) for i in segments] segments.sort(key=lambda x: x[0]) gap_segments = set() for i in range(len(segments) - 1): gap_segm...
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def pull_key(key_fun): """Return a new dict with members of objs as values and values generated by key_fun as keys. pull_key(key_fun)(objs) :: Hashable K => (X -> K) -> Seq[X] -> {K : X} Equivalent to the following in Python 3: {key_fun(v):v for v in objs} >>> from operator import itemgett...
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import re def word_tokenizer(sentence): """ 将一句话分成单词的列表, 会顺便承担清除标点符号的工作 Parameters ---------- sentence : string Returns -------- words : the list of word """ solve_sentence = re.sub(r'\W+|\s+', ' ', sentence) words = solve_sentence.lower().strip(' ').split(' ') return...
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def _hexify(num): """ Converts and formats to hexadecimal """ num = "%x" % num if len(num) % 2: num = '0'+num return num.decode('hex')
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def flatten(list_of_lists: list) -> list: """Given a list of lists, flatten all the items into one list. >>> flatten([ [1, 2, 3], [4, 5, 6]]) [1, 2, 3, 4, 5, 6] """ return [val for sublist in list_of_lists for val in sublist]
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def timeseries_train_test_split(df, test_size=0.2, gap=0, ascending=True): """Split DataFrame or matrices into random train and test subsets for timeseries Parameters ---------- df : pd.DataFrame, shape (n_samples, n_features) Training data, where n_samples is the number of samples an...
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import random def pad_password(password: str): """ Passwords are 6 characters long. But are sent as 10 characters where the last 4 characters are insignificant. """ possible_chars = "abcdefghijklmnopqrstuvxyzABCDEFGHIJKLMNOPQRSTUVXYZ0123456789" two_random = random.choices(possible_chars, k=2) ...
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import yaml def _get_definitions(definition_file): """Parses "algos.yaml".""" with open(definition_file, "r") as f: return yaml.load(f, yaml.SafeLoader)
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def list_to_string(l): """ Converts a string list in to a string @param l is the string list @returns a concatentation of each element in the list """ res = "" for elem in l: res += elem return res
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def is_aware( time_point): """ Return whether ``time_point`` is aware of the timezone """ return time_point.tzinfo is not None and \ time_point.utcoffset() is not None
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def string(params): """Define a string parameter to be used within this YAML file""" return {params.name: params.value}
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def mrr_roundtrip_phase_to_tr_fused(rt_phi, a: float = 0.8, r: float = 0.9, intensity: bool = False): """ description: round trip phase shift to field transmission rt_phi {torch.Tensor or np.ndarray} abs of roundtrip phase shift (abs(phase lag)). range from abs([-pi, 0])=[0, pi]\\ a {scalar} attenuatio...
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def interpolate2d(x,y,X,Y,Z): """ Used to need it but no longer necessary Here is just a placeholder for future implementation if needed again """ return ""
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import logging from pathlib import Path def get_filelist(paths: list[str], recursive: bool = False) -> list[str]: """Get a list of files (but not directories) from a path. Args: paths (list[str]): The path(s) to search for files. recursive (bool, optional): Whether to recursively search the p...
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import re def size2integer(value): """Try to convert a string representing a size to an integer value in bytes. Supported formats: * K|k for KB * M|m for MB * G|g for GB :param value: the string to convert :return: the corresponding integer value """ m = re.match("(\d+)\s*(\w...
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def find_domain_zone_matches(domains, zones): """ Finds matches between Amazon SES verified domains and Route 53 hosted zones. Subdomain matches are taken when found, otherwise root domain matches are taken. :param domains: The list of domains to match. :param zones: The list of hosted zones to mat...
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def format_seconds(s): """ Format a seconds value into a human-readable form """ years, s = divmod(s, 31556952) min, s = divmod(s, 60) h, min = divmod(min, 60) d, h = divmod(h, 24) return '%sy, %sd, %sh, %sm, %ss' % (years, d, h, min, s)
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import os def get_filename(file_dir): """ :param file_dir: """ file_name = os.listdir(file_dir) if len(file_name) is not 1: print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!') print('There are {} files in [{}]'.format(len(file_name), file_dir)) print(file_name) new_fil...
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def question1(records): """quantité d'ammoniac (en t/an) a été émise en Alsace en 2004""" # On code en dur l'indice de colonne de 2004 col_2004 = 4 for r in records: if ( r.region == "ALSACE" and r.substance == "Ammoniac" and r.metric == "Quantités annuelles é...
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def sanitize_string(input_string): """Removes unwanted characters from a string and returns the result """ return input_string.replace('"', '')
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def z_vprod(a, b): """ Computes the z component of the vector product of the input vector fields """ return a[:,:,0]*b[:,:,1] - a[:,:,1]*b[:,:,0]
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import glob import os def glob_directory(base): """Return a list of files matching base Parameters ---------- base: str string you wish to match e.g. "./", "./*.py" """ if "*" not in base: base = os.path.join(base, "*") return glob.glob(base)
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def checkDict(d): """Check a dict recursively for non serializable types""" allowed = [str,int,float,list,tuple,bool] for k, v in d.items(): if isinstance(v, dict): checkDict(v) else: if type(v) not in allowed: return 0 return 1
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def parse_distro_info_path(path): """Break distro_info path into repo + file""" path = path.strip().rsplit("/", 1) info_repo = path[0] info_file = path[1] remote = False if info_repo.startswith("http"): remote = True return info_file, info_repo, remote
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import math def volatilization_rate(k, mass, dz, dt): """ Compute the transfer of the volatilization (kg/s) source : (“CHEMMAP technical User’s manual 6.10,” 2014) params ------ k : volatilization coefficient [m/s] dz : vertical diffusivity [m²/s] dt : length of a timestep [s] mas...
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def extractFeatures(featureExtractors, pacmanData): """ Run all of the feature extractors on the game state training data """ features = {} # pacmanData is a list of GameState instances with the snapshots of the pacman game for gameState in pacmanData: # for each game state, apply all feature extractors and co...
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def on_demand_resource_renderer(request, registry, settings): """Active instance of :py:class:`websauna.system.core.render.OnDemandResourceRenderer` managing dynamic CSS and JS. May be None.""" on_demand_resource_renderer = getattr(request, "on_demand_resource_renderer", None) return on_demand_resource_rend...
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def _FlattenToScoresList(config_param_score_dict): """Extracts a list of scores from input data structure. Args: config_param_score_dict: of the form {'capture_name': {'param_name' : score_value,.. } ..} Returns: Plain list of all score value present in input data structure """ result = [] ...
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def absoluteDeg(deg: float = 0): """ absoluteDeg(float degrees) Returns: float degrees """ return deg % 360
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def filter_dataset(dataset, filter_indices): """ Filter a dataset consisting of a dictionary for the different variables by a vector of True/False indicating if the data point (a row index) should be kept or not. Returning a copy to leave the original dataset untouched. """ dataset_copy = datase...
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from typing import Mapping def check_dict_nested_attrs(item: Mapping, dict_data: Mapping) -> bool: """ Checks the values from `dict_data` are contained in `item` >>> d = {'a': 1, 'b': {'c': 2}} >>> check_dict_nested_attrs(d, {'a': 1}) True >>> check_dict_nested_attrs(d, {'b': {'c': 2}}) True ...
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def calculateEncryptionKey(subjectNumber: int, numLoops: int) -> int: """ Calculates encryption key """ val: int = 1 for _ in range(numLoops): val *= subjectNumber val %= 20201227 return val
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import itertools def is_almost_simplicial(G, n): """Determines whether a node n in G is almost simplicial. Parameters ---------- G : NetworkX graph The graph on which to check whether node n is almost simplicial. n : node A node in graph G. Returns ------- is_almost_s...
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def correct_name(row): """Correct known misspelled names from the data.""" if row["last_name"] == "Digiorgio" and row["first_name"] == "Kevin": row["last_name"] = "DiGiorgio" elif row["last_name"] == "Huynk" and row["first_name"] == "Nho": row["last_name"] = "Huynh" elif row["last_name"]...
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def wang_ind(x, a, b): """Wang method: indicator fucntion of interval.""" return (x >= a) * (x <= b)
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def showBoard(players): """Returns a string representing the current game""" return (player.name for player in players)
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def compute_abundances(sam_transcripts, dataset): """ Iterates over sam transcripts and records the transcript assignment of each in a dictionary. This dictionary is then converted to a list of tuples that can later be added to the TALON database""" abundance_dict = {} for sam_tran...
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import csv def create_csv_table(table_path, rows_list): """Create csv file from list of lists. Args: table_path (str): file path to table. rows_list (list): nested list of elements to write to table. Returns: table_path (str): filepath to table. """ with open(table_path, ...
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def processReducedResult(key_value_tuple): """ input: (TW-100917-125717-1537514430, 4.03) output: [TW, 100917, 125717, 1537514430, 4.03] """ values = key_value_tuple[0].split("-") values.append(str(key_value_tuple[1])) return values
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def projective(nodes): """Identifies if a tree is non-projective or not.""" for leaf1 in nodes: v1,v2 = sorted([int(leaf1.id), int(leaf1.parent)]) for leaf2 in nodes: v3, v4 = sorted([int(leaf2.id), int(leaf2.parent)]) if leaf1.id == leaf2.id:continue if (v1 <...
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import json def load_srl(input_file): """Loads cached SRL predictions for an input file.""" verb_srl_dict, nom_srl_dict = {}, {} if "ACE" in input_file: dataset = "ACE" elif "ERE" in input_file: dataset = "ERE" else: raise ValueError("Unknown dataset") split = input_file.split('/')[-1].split('.')[0] ...
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def DBC_to_SBC(text): """ 转义 半角竖线/半角空格 -> 全角竖线/全角空格 """ rules = ( (" ", "\u3000"), #全角空格 ("|", "\uFF5C"), #全角竖线 ) for DBC, SBC in rules: text = SBC.join(w for w in text.split(DBC) if w != '') # 合并连续空格 return text
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def respond_alert(**kwargs): """Returns a response to `alert`.""" arguments = kwargs['arguments'] bot = kwargs['bot'] message = kwargs['message'] if arguments[0] == 'list': alarms = [f'T-{h}h' for h, c in bot.alarms if c == message.channel.id] msg = "I'm alerting at: " + ', '.join(a...
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import os def reader(path, encoding="utf-8"): """ read txt file from given path """ if os.path.exists(path): with open(path, "r", encoding=encoding) as f: # return list of without line breaks return [line.strip() for line in f] else: print("path does not exi...
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def _split_csv(string): """Split string into a list, excluding empty strings""" if string is None: return [] return [n.strip() for n in string.split(',') if n]
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import random def selectNRandom(nodes, N): """ Selects n random nodes from a list of nodes and returns the list """ random.shuffle(nodes) return nodes[:N]
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def socketio_handler(event, namespace=None): """Register a socketio handler via decorator.""" def wrapper(func): """Decorate a ws event handler.""" # pylint: disable=protected-access func._ws_event = event func._ws_namespace = namespace return func return wrapper
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import sys def is_macos(): """ Returns True if the environment is Microsoft Windows. """ return sys.platform == "darwin"
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def padding(msg: str, num_bytes: int) -> bytes: """ 문자열 메시지를 UTF-8 인코딩 후 `num_bytes`에 맞게 조정합니다, :param msg: 인코딩할 메시지 :param num_bytes: 바이트 수 :return: 인코딩 된 bytes 객체 """ data = msg.encode('utf-8')[:num_bytes] if len(data) < num_bytes: data += b'\x00' * (num_bytes-len(data)) r...
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def globify_time_descriptors(path): """Convert strftime time descriptors to a glob-compatible expression. For example, convert,'%Y' to '[12][0-9][0-9][0-9]'. Then the glob expression can be used to match path names containing a four digit year. """ path = path.replace('%Y', '[12][0-9][0-9][0-9...
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def MakeTuple(object_): """ Returns the given object as a tuple, if it is not, creates one with it inside. @param: Any object or tuple The object to tupleIZE """ if isinstance(object_, tuple): return object_ else: return (object_,)
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def reorder_exons(exon_ids): """ Reorder exons if they were out of order. Parameters: exon_ids (list of str): List of exons 'chrom_coord1_coord2_strand_exon' Returns: exons (list of str): List of same exon IDs ordered based on strand and genomic location """ strand = exon_ids[0].split('_')[-2] coords = ...
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def parseAddress(address): """ Resolve the IP address of the device :param address: :return: add_str """ add_list = [] for i in range(4): add_list.append(int(address.hex()[(i * 2): (i + 1) * 2], 16)) add_str = ( str(add_list[0]) + "." + str(add_list[1]) ...
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import re def clean_stmt(stmt): """ Apache Superset tests a specified schema, table & field definition with SQL database query. The built SQL, however, cannot be interpreted by Apache Ignite, as it contains the table name extended by the schema: "<schema>"."<table>" We expect that a user defi...
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def get_reaction_from_name(reactions, name): """Return reaction with name. Args: reactions (list(reactions)): the reactions. name (str): name of the desired reaction. Returns: reaction: the corresponding reaction. """ matches = [r for r in reactions if r.name == name] ...
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import os def get_latest_trained_model_path(): """ Used to find the latest saved model's path. :return: path of the latest model's Tensorboard, Generated_Images and Saved_Models. """ latest_run_dir = os.listdir("./Results/roses") latest_run_dir.sort() latest_run_dir = latest_run_dir[-1] ...
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def extract_sub_ids(file, naive=False, label_of_interest=0): """ Extracts sub_ids from dataset_x.txt files of the following format: SubjectID,Network,Station,Latitude,Longitude,PercentageEarthquakes,PercentageTremor, PercentageNoise,PercentageUnclearEvent Args: file (path): Path to file con...
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def format_api_output(response): """Format retrieved json from API call""" data = response["items"][0] return { "rep": data["reputation"], "gold": data["badge_counts"]["gold"], "silver": data["badge_counts"]["silver"], "bronze": data["badge_counts"]["bronze"], }
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def _call_string(*args, **kwargs): """Return format of args and kwargs as viewed when typed out""" arg_strings = [] for arg in args: arg_strings.append(repr(arg)) for key, arg in kwargs.items(): arg_strings.append(key+'='+repr(arg)) return "(%s)" % ', '.join(arg_strings)
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def get_partial_link_text_from_selector(selector): """ A basic method to get the partial link text from a partial link selector. """ if selector.startswith("partial_link="): return selector[len("partial_link="):] elif selector.startswith("partial_link_text="): return selector[len("pa...
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def longest_positive_sequence(the_list): """ Function that given a list, it returns the longest number of positive numbers. If it returns 3, then there exists 3 consecutive positive numbers. @param the_list: an array of integers @complexity: best-case and worst-case is O(N) where N is the length of the list ...
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def add_flist( flist, progress_json, scenario, stage='train', file_type='wav', channel_type='observed', channel='CH1' ): """ Adds a file list to the current progress_json object Example:: ....<flists> ......<file_type> (z.B. wav) ........<scenario> (z.B. tr05_simu, tr05_real...) ...
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from sys import _getframe from pathlib import Path def relpath(file): """ Always locate to the correct relative path. :param file: The wanted-to-get file location :return: An absolute path to the file requested """ frame = _getframe(1) curr_file = Path(frame.f_code.co_filename) return...
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def ticket_bucketizer(row): """.""" try: bucket = int(row[0][0]) if bucket == 1 or bucket == 2: return [bucket, row[1]] else: return [3, row[1]] except ValueError: bucket = ord(row[0][0]) if bucket == 80: return [bucket, row[1]] ...
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import os def get_subid_sesid(in_file, caps_directory): """ This is to extract the base_directory for the DataSink including participant_id and sesion_id in CAPS directory, also the tuple_list for substitution :param subject_id: :return: base_directory for DataSink """ identifier = (in_file.s...
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def compute_mass(struct_mass, n_golf_balls=13, n_ping_pong_balls=13): """ Used to estimate the empty mass of the plane. Should scale up with surface area of body and wings in some principled manner. """ non_structural_mass = 0.326 #kg ball_mass = n_golf_balls*0.04593 + n_ping_pong_balls*0.0027 ...
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def relativize_paths(root, paths): """ Take a list of fully-qualified paths and remove the root, thus making them relative to something. """ clean_paths = [] for path in paths: clean_paths.append(path.replace("%s/" % root, '')) return clean_paths
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def runner(app): """Using test app, create and return a CLI runner object.""" return app.test_cli_runner()
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def set_force_update_on_page_load(forceUpdateOnPageLoad: bool) -> dict: """ Parameters ---------- forceUpdateOnPageLoad: bool """ return { "method": "ServiceWorker.setForceUpdateOnPageLoad", "params": {"forceUpdateOnPageLoad": forceUpdateOnPageLoad}, }
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def _is_descendant(index, target): """ Return true if index is a parent of target. """ while target.isValid(): if target == index: return True target = target.parent() return False
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import time def benchmark(f): """A simple decorator for timing output for publish_body.""" def inner(*args, **kwargs): before = time.time() ret = f(*args, **kwargs) print('Took %f secs for sending %d messages.' % (time.time() - before, len(args[1]['messages']))) r...
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def cost_deriv(y, t): """ gradient. dcost / dy """ return 2 * (y - t)
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def pybtex_unescape(string: str) -> str: """ Reverts the escaping applied by Pybtex. :param str: Input string with pybtex-escape characters. :return: Output string where this has been reverted. """ return string.replace('\\_', '_').replace('\\textasciitilde ', '~')
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def isPointInsideRect(x, y, rect): """ This function determines if the point x, y is within the rectangle rect. Returns TRUE if it is and FALSE if it is not. """ if ((x > rect.left) and (x < rect.right) and (y > rect.top) and (y < rect.bottom)): return True else: ...
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import inspect import sys def get_model_cls(model): """Return the corresponding class to the model specified in params""" classes = [obj for name, obj in inspect.getmembers(sys.modules[__name__]) if inspect.isclass(obj)] for cls in classes: if cls.__name__.lower() == model: return cls ...
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import torch def zero_loss(*args, **kwargs): """Dummy loss that always returns zero. Parameters ---------- args : list Can take any number of positional arguments (without using them). kwargs : dict Can take any number of keyword arguments (without using th...
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import os def get_timeout(servername, default=None): """Get timeout for server communication from environment variables. Args: servername (str): The name of application (e.g. plantuml) default (int): The result when timeout does not exist in environment variables. Returns: ...
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def subcmd(f): """subcmd Decorator - used in combination with a subclassed Command class to enable its methods that act as sub-commands. These subcommand methods get auto-registered with an Application when the main command is registered. When a command is executed, the default execute method will aut...
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def get_attribute_from_tag(tag, attribute): """Returns a xml attribute from a given tag""" element = None try: element = tag.attrib[attribute] except KeyError: pass # print("Error: attribute {} was not defined in this tag.".format(e)) return element
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def showPage(request): """Show the page when the URL is called. """ if 'geneset' in request.session: # restore previous list of genes gs = request.session['geneset'] genes = [] for item in gs.dataframe().reset_index().to_dict(orient="records"): # won't return TranscriptLengths genes.append(dict([(key,val) ...
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def _to_blob(b): """Convert a bytestring into a type SQLite will accept for a blob.""" return b
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def calc_frag_lengths(x, y, orientation, merged_frags): """ given a merged fragments table, calculate the fragment lengths assuming the fragments span the provided x and y breakpoints; adds frag lengths inplace """ if orientation[0] == "+": partlen_x = x - merged_frags["start_pos_x"] el...
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def _func_any(_current, _checks): """Implementation of Any.""" return True
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import argparse import sys def add_arguments_get_values(): """ Add arguments to the command line and get the values passed. Returns: argparse.Namespace: Argument values passed. """ # instanciate command line argument parser parser = argparse.ArgumentParser(prog=f"python {sys.argv[0]}"...
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def fib (n: int) -> int: """ Returns the n'th Fibonacci number. Note that this function uses zero style indexing, meaning that the first Fibonacci number has an index of zero (n=0).""" f_p, f_c= 0, 1 for i in range(n): f_n = f_c + f_p f_p = f_c f_c = f_n return f_c
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