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import csv def read_csv_file(filename): """ Read the CSV file with the image and mask filenames """ imgFiles = [] mskFiles = [] with open(filename, "rt") as f: data = csv.reader(f) for row in data: if len(row) > 0: imgFiles.append(row[0]) ...
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def check_numeric(value_string): """ This function tries to determine if a string would be better represented with a numeric type, either int or float. If neither works, for example ``10 Mb``, it will simply return the same string provided :param value_string: input string to be parsed. :retu...
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import torch import math def shifted_softplus(x: torch.Tensor) -> torch.Tensor: """ Shifted softplus activation function. """ return torch.nn.functional.softplus(x) - math.log(2)
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from typing import Any from typing import Optional from typing import Tuple from typing import Type from typing import Union def _union_args(cls: Any) -> Optional[Tuple[Type]]: """Convert ``Union[T1, T2]`` to (T1, T2). Returns ``None`` if `cls` is not a specific :class:`typing.Union` type. """ if not...
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def get_all(client, query_params): """Requests the list of roles.""" return client.get_roles(**query_params)
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def calculate_midpoint(l, r): """ @param l left index, included in the range of elements to consider @param r right index, included in range of elements to consider @return None if there's no elements to range over. Returns the midpoint from the "left side" or "left half" if there's an even num...
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import math def yrlygrowth(total_growth, years): """ Determine the annual growth from the growth over an arbitrary time span. """ return math.exp(math.log(total_growth) / years)
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def bpm2msec(bpm): """ Obtains the rr duration in msec corresponding to a specific frequency in beats per minute. """ return 60000 / bpm
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def palindrome(value:str) -> bool: """ Returns true if value/string is a palindrome.""" return str(value) == str(value)[::-1]
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def wpa_validation_check(words=[]): """ Function to optimise wordlist for wpa cracking > Removes Duplicates. > Removes passwords < 8 or > 63 characters in length. """ custom_list = list(set(words)) custom_list = [x for x in custom_list if not (len(x) < 8 or len(x) > 63)] return custom...
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def _count_occurences(needle, haystack): """ Count occurences of the string needle in haystack """ return len(haystack.split(needle)) - 1
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import re def to_snake_case(input): """Convert a string into its snake case representation.""" str1 = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", input).replace("-", "_") return re.sub("([a-z0-9])([A-Z])", r"\1_\2", str1).lower()
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def is_truncate(q): """ True if `q` is a TRUNCATE table statement :param q: :return: """ return 'truncate' in q.lower()
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def common_substr_2( seq1, seq2, sorting=None): """ Find the longest common consecutive subsequence(s). This version works for two iterables. This is known as the `longest common substring` problem, or LCS for short. Args: seq1 (iterable): The first input sequence. ...
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import random import math def calculate_pi(attempts): """ This function calculates an approximation of Pi using a raw MonteCarlo integration technique :param: attempts: the number of iterations for the MonteCarlo method :type: attemts: int :return: the approximated value of Pi """ ass...
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def strftime_with_precision(tick, format, sub_secs_precision=2): """ Returns a formatted string for a datetime (tick). :param tick: The datetime for this tick :param format: The formatting string :param sub_secs_precision: Number of digits to used for sub-seconds. If None, will choose it "sm...
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def read_file(dbx, from_file): """Read file from Dropbox Args: dbx (Dropbox object): Dropbox object generated from API token from_file (string): File location in Dropbox accounts Returns: int32: Percentage value """ _, f = dbx.files_download(from_file) percentage = f.con...
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def zip_lsts(lsts): """ zip a list of lists """ lengths = [len(lst) for lst in lsts] assert len(list(set(lengths))) == 1 # assert that the lsts have the same lengths zipped_lst = [list(tp) for tp in list(zip(*lsts))] return zipped_lst
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from typing import Iterable def flatten(iter, unlist=False): """ Flatten an arbitrarily nested iterable whose innermost items are strings into a flat list of strings. Parameters ---------- iter : iterable unlist : bool If True, convert single-item lists into a bare string """...
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def without(dict_in: dict, keys: list): """ Utility that copies a dictionary excluding a specific list of keys. """ if not isinstance(keys, list): keys = [keys] new_d = dict_in.copy() for key in keys: new_d.pop(key) return new_d
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def _MakeDispatchListIntoYaml(application, dispatch_list): """Converts list of DispatchEntry objects into a YAML string.""" statements = [] if application: statements.append('application: %s' % application) statements.append('dispatch:') for entry in dispatch_list: statements += entry.ToYaml() retur...
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def purity(rho): """ Calculate the purity of a quantum state. Parameters ---------- rho : :class:`qutip.Qobj` Density matrix of a quantum system. Returns ---------- purity_rho : float Purity of the quantum system, p (p=1 if pure, 1/N<=p<1 if mixed). """ if rho.type=="ket": rho=rho*rho.dag() purity_...
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import pathlib def to_path(*p, as_string=True): """Convert string to pathlib path. INFO: Path resolving removes stuff like ".." with 'strict=False' the path is resolved as far as possible -- any remainder is appended without checking whether it really exists. """ pl_path = pathlib.Path(*p) ...
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def predicatize(term): """Formats a term (string) to look like a Predicate.""" # Replace spaces by underscores and lowercase first letter of a Predicate term term = term.replace(" ", "_") return term[0].lower() + term[1:]
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def get_match_filter(barcode): """Return a function for filtering a pair of (seq, bc) namedtuple pairs; the function returns True if bc.seq == barcode """ def filterfun(pair): seq, bc = pair return str(bc.seq) == barcode return filterfun
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def _IsSpecified(args, name): """Returns true if an arg is defined and specified, false otherwise.""" return hasattr(args, name) and args.IsSpecified(name)
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def _is_symmetric_padding(padding, data_dim): """ Check whether padding is symmetrical. """ assert len(padding) == data_dim * 2 or len(padding) == data_dim is_sys = True if len(padding) == data_dim * 2: for i in range(data_dim): if padding[i * 2] != padding[i * 2 + 1]: ...
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def min_power_rule(mod, g, tmp): """ **Constraint Name**: GenCommitCap_Min_Power_Constraint **Enforced Over**: GEN_COMMIT_CAP_OPR_TMPS Power minus downward services cannot be below a minimum stable level. """ return mod.GenCommitCap_Provide_Power_MW[g, tmp] \ - mod.GenCommitCap_Downward...
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import re def swap_twitter_subject(subject, body): """If subject starts from 'Tweet from...' then we need to get first meaning line from the body.""" if subject.startswith('Tweet from'): lines = body.split('\n') for idx, line in enumerate(lines): if re.match(r'.*, ?\d{2}:\d{2}...
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import csv def parse_csv(filename): """ Convert CSV file to list of dictionaries. Source: https://stackoverflow.com/a/21572244/4562156 :param filename: filename containing CSV data (relative to project root) :return: list of dictionaries representing each row with CSV schema as keys """ with...
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import re def _valid_date(date): """ Whether the date requested matches the desired format (starts between 1 and 8 digits) :param date: The date to check :return: True if valid, false otherwise """ return re.compile('^\d{1,8}').search(date)
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def pairwise_analogy_func(wrap, a1, b1, a2, b2, weight_direct, weight_transpose): """ Rate the quality of the analogy a1 : b1 :: a2 : b2. """ va1 = wrap.get_vector(a1) vb1 = wrap.get_vector(b1) va2 = wrap.get_vector(a2) vb2 = wrap.get_vector(b2) value = ( weight_direct * (vb2 - ...
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def discrete_colorscale(bvals, colors): """ bvals - list of values bounding intervals/ranges of interest colors - list of rgb or hex colorcodes for values in [bvals[k], bvals[k+1]],0<=k < len(bvals)-1 returns the plotly discrete colorscale """ if len(bvals) != len(colors)+1: raise Value...
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def convertListDomainToDict(list_domains:list): """ convert a list of domains objects to a dictionary with the designation in the key and the id in value :param list_domains: list of domains json objects :type list_domains: list[DomainJ] :return: dictionary :rtype: dict[designation] = id ...
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import requests import json def get(url, params=None): """ Performs a GET request to the given url with supplied params. If an error happens that will be printed to the console and None is returned """ response = requests.get(url, params) if response.status_code == 200: return json.loads(respo...
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def target_subnet(model, subnet_idx): """ model = Keras model subnet_idx = indexes of the subnet you want to target. ex: subnet_idx = [1,0] -> targets model.layers[1].layers[0] """ subnet = model for idx in subnet_idx: subnet = subnet.layers[idx] return subnet
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def annual_metrics( globvars, mass, prodloss, wetdep, drydep ): """ Computes the following terms: 1. "dyn": Ox subsiding from the stratosphere 2 "net": Net Ox = (POx-LOx) + Dyn - Drydep - Wetdep 3. "life": Ox lifetime (d) = Ox burden / (LOx + Drydep + Wetd...
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def find_distance(df): """ Finds the number of words between the gender pronoun word, and the entity word. """ df = df.values g_idx = df[0] p_idx = df[1] return abs(g_idx - p_idx)
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import string def pre_process_sentence(sentence: str) -> str: """ Given a sentence, return a new one all lower-cased and without punctuation. """ # lower case lower_sentence = sentence.lower() # remove punctuation exclude = set(string.punctuation) return ''.join(ch for ch in lower_...
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import math def heuristic(p1, p2): """ Heuristic for a* algorithm. :param p1: tuple :param p2: tuple :return: int """ x1, y1 = p1 x2, y2 = p2 return math.fabs(x1 - x2) + math.fabs(y1 - y2)
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def _add_coordinates(domcfg): """ If existing in the domcfg dataset, adds the lat/lon/depth variables as coordinates """ coordinates = [ "glamt", "glamu", "glamv", "glamf", "gphit", "gphiu", "gphiv", "gphif", "gdept_0", "gde...
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def list_journals(config): """List the journals specified in the configuration file""" sep = "\n" journal_list = sep.join(config['journals']) return journal_list
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def get_labels(cs): """Return list of every label.""" records = [] for c in cs: records.extend(c.get('labels', [])) return records
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def le(x, y): """Implement `le`.""" return x <= y
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def are_close(a, b, epsilon): """Check if a and b are relative (to epsilon) close.""" return (a - epsilon) <= b and (a + epsilon) >= b
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import tempfile import pickle def _dump(partition): """ Dump the given partition to an external source. The default implementation is to pickle the list of objects to a temporary file. :param partition: The partition of objects to dump. :return: Unique id which can be used to reload the seriali...
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def keep_last_labtest_instance(df): """ select last instance of every type of test for a patient """ df = df.sort_values('charttime', axis=0) df = df.drop_duplicates(subset=['hadm_id', 'itemid'], keep='last', ignore_index=True) return df
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def expand_boxes(boxes, scale): """Expand an array of boxes by a given scale.""" w_half = (boxes[:, 2] - boxes[:, 0]) * .5 h_half = (boxes[:, 3] - boxes[:, 1]) * .5 x_c = (boxes[:, 2] + boxes[:, 0]) * .5 y_c = (boxes[:, 3] + boxes[:, 1]) * .5 w_half *= scale h_half *= scale boxes_exp =...
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from typing import Dict import requests from typing import cast def default_headers() -> Dict: """ Return default headers with a custom user agent """ headers = requests.utils.default_headers() # type: ignore headers.update({'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) ' ...
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def fitness_func_oob(vector): """ out of bounds fitness func, returns a negative fitness""" return -1
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import operator def get_field_set(items, getter=operator.attrgetter('id'), cast=int): """ Get ids via getter and collect them in a set """ return {cast(getter(item)) for item in items}
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def commands_not_installed(commands, completer_content): """ Checking for installed commands in exists completer file :param commands: List of commands found in completions directory :param completer_content: Content of current installed complete file :return: List of not installed commands """ ...
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def get_model_cache_key(model): """ Returns a part of cache key used to identify mode. :param model: model, on which cache depends :return: Part of cache key used to identify model """ return f'{model._meta.app_label}.{model.__name__}'
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def get_inputs( filename ): """ The input file has intructions in each line with a command and a value. This function returns the instructions as a list of lists. """ with open( filename, 'r') as input_file: inputs = [ [ item[:1], int(item[1:]) ] for item in input_file...
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def fetch_courses(job_config, data_bucket, data_dir ="morf-data/"): """ Fetch list of course names in data_bucket/data_dir. :param job_config: MorfJobConfig object. :param data_bucket: name of bucket containing data; s3 should have read/copy access to this bucket. :param data_dir: path to directory ...
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def read_keywords(args): """This function reads the keywords from the input file and creates: - a dictionary where the key is the old name and the value is the new name, these keywords will be further processed. - a list of keywords which will not be processed, typically keywords with argument(s)...
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import importlib def get_suite_amount_of_workers(workspace, project, suite): """Get the amount of workers defined in a suite. Default is 1 if suite does not have workers defined""" amount = 1 suite_module = importlib.import_module('projects.{0}.suites.{1}'.format(project, suite), ...
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def mk_find_in_field_logical_query(field, query): """ Allows one to create "find in field" query of any logical complexity (since AND, OR, and NOT are supported). field is the field to consider query can be a string, a tuple, or a list, and can be nested: if query is a string, it is is conside...
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def get_decimal(f, aprox=2): """Gets the decimal part of a float Args: f (float): Real number to get the decimal part from aprox (int)(optional): Number of decimal digits, default is 2. Returns: float: Decimal part of f """ f = round((f - int(f)), aprox) ret...
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def fitness_fn(turns, energy, isDead): """Fitness function that scores based on turns and energy. Provides a score to a creature, with 3 times the amount of turns plus the energy, with a bonus for surviving. Args: turns: number of turns a creature survived. energy: amount of energy lef...
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def create_epoch(f, name, start_time, stop_time): """ add an <epoch_X>. f is the h5gate file object. name is name of epoch start_time and stop_time should both be float64 Returns the group for the created epoch. """ epoch = f.make_group("<epoch_X>", name) epoch.set_dataset("start_time", sta...
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def CheckChangeHasNoTabs(input_api, output_api, source_file_filter=None): """Checks that there are no tab characters in any of the text files to be submitted. """ # In addition to the filter, make sure that makefiles are blacklisted. if not source_file_filter: # It's the default filter. source_file_fi...
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def parse_filename(filename, full_output=False): """ Return the basic stellar parameters from the filename. """ basename = filename.split("/")[-1] teff = basename[1:5] logg = basename.split("_")[1][1:] feh = basename.split("_")[5][1:] parameters = map(float, [teff, logg, feh, int(basena...
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def retrieve_termination_obj(nb,termination_type,dev_name,termination_name): """Searches for a NetBox termination object of a given name from a given device Args: nb: PyNetbox connection to a Netbox instance termination_type: NetBox termination object type (ie. dcim.interface) dev_nam...
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def setup_method_arguments(method, bounds): """ prepare method specific arguments """ kwargs = {} # pass bounds to methods that support it if method in ["L-BFGS-B", "TNC", "SLSQP"]: kwargs['bounds'] = bounds return kwargs
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import re def _valid_name(tensor_name): """Return a valid tensor name (strips '/', ':', etc).""" return re.sub('[^a-zA-Z0-9_-]+', '', tensor_name)
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def parse_name(text): """Split an arbitrary (maybe empty) word from the beginning of a string.""" lth = 0 while text[lth] not in ' ,*%();': lth += 1 return text[:lth], text[lth:]
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import time def wait_for_computation(predicate, timeout, retry_after): """Return wrapped function retrying computation until result satisfies given predicate or timeout is reached.""" def wrapper(func): def compute(*args, time_left=timeout, **kwargs): if time_left <= 0: rai...
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def trim_text(text, nbytes): # type: (str, int) -> str """Trim text such that its utf-8 encoded size does not exceed `nbytes`.""" return text.encode("utf-8")[:nbytes].decode("utf-8", "ignore").strip()
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import torch def get_test_tensor(max_value=10, float=False): """Create simple test tensor.""" tensor = torch.LongTensor(list(range(max_value))) if float: tensor = tensor.float() return tensor
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def task_eta(eta): """Converts a datetime.datetime into a taskqueue ETA. Args: eta: Naive datetime.datetime of the task's ETA. Returns: The ETA formatted as a string. """ return eta.strftime('%Y/%m/%d %H:%M:%S')
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def bad_request(message: str, code: int = 400): """Format bad request response from a message.""" return { 'result': 'error', 'message': message }, code
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def _arg(bytes, signed, dvi, _): """Read *bytes* bytes, returning the bytes interpreted as a signed integer if *signed* is true, unsigned otherwise.""" return dvi._arg(bytes, signed)
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def solar_geometric_mean_anomaly(julian_century): """Returns the Anomaly of Solar Geometric Mean with Julian Century, julian_century.""" solar_geometric_mean_anomaly = 357.52911 + julian_century * ( 35999.05029 - 0.0001537 * julian_century ) return solar_geometric_mean_anomaly
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def splitPackageName(packageName): """e.g. given com.example.appname.library.widgetname returns com com.example com.example.appname etc. """ result = [] end = packageName.find('.') while end > 0: result.append(packageName[0:end]) end = packageNa...
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def valid_csv_header(headers, expected_headers): """return True if all of expected headers are present in headers""" return all(h in headers for h in expected_headers)
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def calc_set(pos, n): """ Computes the subset of {1, 2, ..., `n`} with given rank `pos` in the ordering induces by gray ordering of indicator vectors. """ binary = [1 & (pos >> (n - k - 1)) for k in range(n)] assoc_seq = list(map(lambda x: x[0] ^ x[1], zip([0] + binary[:-1], binary))) return [x + 1 for x...
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def instr_to_intcode(instructions): """ Takes a string of instructions written in ASCII and converts them to integers for using as input for the intcode program. """ output = [] for char in instructions: output.append(ord(char)) output.append(ord('\n')) re...
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def names_in_graph(list_of_names, graph): """ Return true if all names are in the graph """ return all([name in graph.keys() for name in list_of_names])
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import re def prettify_keys(string): """Utility function used to clean keys with numerical values, so that they can be ordered alphabetically the way they should be.""" r = re.compile("bandwidth_([0-9]{1,3})") def replacer(match): m = match.groups()[0] return "bandwidth " + m re...
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import inspect def hasarg(func, arg): """ simple check whether a function takes a parameter as input Parameters ---------- func: function the function to be ckecked arg: str the argument name to be found Returns ------- bool does the function take this...
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def _extract_first_from_str(content: str) -> str: """Extract first line from str without splitting by line.""" if not content: return content newline_pos = content.find("\n") if newline_pos == -1: return content return content[:newline_pos]
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import inspect def get_init_params(cls): """Return the parameters expected when calling the class.""" initializer = cls.__init__ if initializer is object.__init__ and cls.__new__ is not object.__new__: initializer = cls.__new__ try: return list(inspect.signature(initializer).parameters...
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def _match_linear_pattern(root, pattern): """ Use Depth First Search to match the pattern :param root: operation :param pattern: List[Node] :return: Return List[operation] if pattern matches entirely else [] """ op = root if not pattern or len(op.outputs) != 1: return [] no...
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def to_iterable(var): """ convert things to list treat string as not iterable! """ try: if type(var) is str: raise Exception iter(var) except Exception: return [var] else: return var
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def generate_tld_cols(hostname_split_df, hostnames, col_len): """ This function generates tld columns. :param hostname_split_df: Hostname splits. :type hostname_split_df: cudf.DataFrame :param hostnames: Hostnames. :type hostnames: cudf.DataFrame :param col_len: Hostname splits dataframe co...
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from typing import Dict from typing import List def counts_to_list(counts: Dict[str, int]) -> List[int]: """Converts counts to a list representation :param counts: a Qiskit-style counts dictionary :return: a list of integers """ num_bits = len(list(counts.keys())[0].replace(' ', '')) counts_l...
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def get_shape_from_label(label): """ Extract the output shape of a flattened pyNN layer from the layer name generated during parsing. Parameters ---------- label: str Layer name containing shape information after a '_' separator. Returns ------- : list The layer s...
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import re def _ClientIDFromSessionID(session_id): """Extracts the client id from a session id.""" parts = session_id.Split(4) client_id = parts[0] if re.match(r"C\.[0-9a-f]{16}", client_id): return client_id raise ValueError("Unable to parse client id from session_id: %s" % session_id)
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def generate_ena_api_endpoint(result: str, data_portal: str, fields: str, optional: str = ''): """ Generate the url for ENA API endpoint :param result: either be read_run (for experiment, file, dataset import) or analysis (for analysis import) :param data_portal: either ena (legacy data) or faang (faang...
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def gf_int(a, p): """Coerce `a mod p` to an integer in `[-p/2, p/2]` range. """ if a <= p // 2: return a else: return a - p
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import re def is_abspath(pathname): """ Return True if pathname is an absolute pathname, else False. """ return bool(re.match(r"^([/\\])|([a-zA-Z]:)", pathname))
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def format_to_string(obj): """ Formatter to print strings and bytes without leading/trailing quotes """ if isinstance(obj, bytes): return repr(obj.decode()).strip('"\'') if isinstance(obj, str): return repr(obj).strip('"\'') return obj
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def calculate_prediction_coverage(y_actual, y_predicted): """ Calculates the percentage of known user-item pairs which were predicted by the algorithm. It is different from the item_coverage in that only the user's actual ratings are analyzed vs all potential ratings In this manner it is likely that ver...
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import re def find_at(text): """ @ - Used to mention someone in tweets Parameters ---------- text: str Text selected to apply transformation Examples: --------- ```python sentence="@David,can you help me out" find_at(sentence) >>> 'David' ``` "...
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def parse_float(str_value): """ This fuction converts a string to float just like the built-in float() function. In addition to "normal" numbers it also handles numbers such as 1.2D3 (equivalent to 1.2E3) """ try: return float(str_value) except ValueError: return float(str_va...
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def fetch_page(base_url, page, session): """ Fetch a particular page number for a GitHub API resource. :param unicode base_url: the URL of the GitHub API resource. :param int page: the page number to request (0 indexed). :param requests.Session session: the requests Session to use for the r...
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import collections import csv def read_value_file(filename, delim): """Read value file. The value file is a simple csv structure with a key and value. Arguments: filename (str): file to read delim (str): csv delimiter Returns: OrderedDict with results. """ result = c...
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def clean_ns(tag): """Return a tag and its namespace separately.""" if '}' in tag: split = tag.split('}') return split[0].strip('{'), split[-1] return '', tag
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def get_e_continued_fraction(n): """ Return the first n digits of the continued fraction of e.""" if not n: return [] result = [2] # First digit n -= 1 k = 1 # Pattern is 1,2k,1... for i in range(n): if i % 3 == 1: result.append(k * 2) k += 1 else: result.append(1) return r...
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