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import importlib def dynamic_import(import_path, alias=dict()): """dynamic import module and class :param str import_path: syntax 'module_name:class_name' e.g., 'deepspeech.models.u2:U2Model' :param dict alias: shortcut for registered class :return: imported class """ if import_path n...
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from typing import Optional def create_next_start_key(last_evaluated_key: Optional[dict]) -> Optional[dict]: """ Create the 'next_start_key' that will be returned in the response body of this Lambda function. Is identical to the 'LastEvaluatedKey' returned from DynamoDB, except the 'player_id' is removed...
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def elgamal_keygen(params): """ generate an El Gamal key pair """ (G, o, g1, hs, g2, e) = params d = o.random() gamma = d * g1 return (d, gamma)
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def align_decision_ref(id_human, title): """ In German, decisions are either referred to as 'Beschluss' or 'Entscheidung'. This function shall align the term used in the title with the term used in id_human. """ if 'Beschluss' in title: return id_human return id_human.replace('Be...
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from typing import Dict def get_fields(index_dict: Dict) -> Dict: """ :param index_dict: Elasticsearch index mapping :return: simplified dictionary of structure with keys are field names and values as types """ ret_dict = {} for key, value in index_dict.items(): if "properties" in valu...
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def restrict_common_genes(X1, X2, genes1, genes2): """ Given two expression matrices and two lists of gene identifiers corresponding to the two columns of the matrices, re-configure the matrices to keep only columns for genes that are common between the two datasets. """ gene_to_index1 =...
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def _get_host_string(config): """ Take appropriate elements from a config dictionary and convert them into a string of format 'host:port'. :param dict config: Application configuration dictionary, including ES config. """ host = config["es-configuration"]["es-host"] port = config["es-configu...
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def str_to_bool(user_input): """ Convert string to Boolean value """ if isinstance(user_input, bool): return user_input else: if user_input.lower() in ['1', 'true']: return True else: return False
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import json def read_json(fname): """ Read data from a JSON file. Parameters ---------- fname : str Full path to the data-containing file Returns ------- dict """ with open(fname, 'w') as ff: out = json.load(ff) return out
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def clamp(val, at_least, at_most): """ Clamps a value so it doesn't exceed specified limits. If one of the edges is not needed, it should be passed as None (consider using at_most / at_least functions). :param at_least: Minimum possible value. :param at_most: Maxium possible value. :return: The ...
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def get_cells(worksheet, get_range: str): """ Get cells from sheet params ------ workbook: openpyxl.WorkSheet loaded worksheet. get_range: str Get cells range. Ex: "A1:B3" return ------ cells: Tuple[Cell] Got cells tuple """ cells = worksheet[...
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import shlex def parse_line(line_or_args): """Parse line or list of text into (cmd, rest of args).""" if isinstance(line_or_args, list): return (line_or_args[0], line_or_args[1:]) try: if " " in line_or_args: (cmd, args) = line_or_args.split(maxsplit=1) return (cmd, shlex.split(args)) exce...
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def _GetSSHKeyListFromMetadataEntry(metadata_entry): """Returns a list of SSH keys (without whitespace) from a metadata entry.""" keys = [] for line in metadata_entry.split('\n'): line_strip = line.strip() if line_strip: keys.append(line_strip) return keys
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def rank_genes_or_pathways(col_to_rank, DE_summary_stats, is_template): """ Returns the input dataframe (`DE_summary_stats`) that has been modified such that genes are ranked by the selected statistic, `col_to_rank` (if the input is the template experiment) or the median of the selected statistic (i...
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def mean(num_list): """ Computes the mean of a list Parameters ------------- num_lists: list list to calculate mean of Returns ------------- mean: float Mean of list of numbers """ list_mean=sum(num_list)/len(num_list) return list_mean
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def format_str(val, counter, values): """ Format the given value (with method ``format``) when it is a string. """ if isinstance(val, str): return val.format(counter=counter, values=values) return val
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def authenticated_user(client, account): """Create an authenticated user for a test""" # user = G(User, email='test@gmail.com') account.email = 'test@gmail.com' account.set_password('my_password123') account.save() client.login(email='test@gmail.com', password='my_password123') return accoun...
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def drude(x, x0=4.59, gamma=0.90, **extras): """Drude profile for the 2175AA bump. :param x: Inverse wavelength (inverse microns) at which values for the drude profile are requested. :param gamma: Width of the Drude profile (inverse microns). :param x0: Center of the Dr...
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def get_class(kls): """Returns a class given a fully qualified class name""" parts = kls.split('.') module = ".".join(parts[:-1]) mod = __import__(module) for comp in parts[1:]: mod = getattr(mod, comp) return mod
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def calculate_ttc( state, risk_args, verbose=True): """ This first method to calculate ttc (time-to-collision) is just brute force. Propagate the scene forward by tenths of a second until a collision is detected, or the maximum horizon is reached. Assume horizon...
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def quantile(x, q): """Generate the q'th quantile of x Arguments: x: a numpy array q: the quantile of interest (a float) Returns: the element of x closest to the qth quantile. """ if len(x.shape) != 1: return None x = x.tolist() x.sort() return x[int((len(...
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def get_doi_from_request(request, method): """ Extract the doi from the request. Args: request (HTTPRequest): The HTTP request Return: a str, the DOI """ full_path = request.get_full_path() bits = full_path.split(method + '/') try: return bits[1] except Ind...
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def remove_special_chars(text: str, char_set=0) -> str: """Removes special characters from a text. :param text: String to be cleaned. :param char_set: 0 -> remove all ASCII special chars except for '_' & 'space'; 1 -> remove invalid chars from file names :return: Clean text. ""...
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def setTeamQorStateUsage(err=''): """ Prints the Usage() statement for this method """ m = '%s\n\n' %err m += ' This script set the status of a Team Branch QOR bin in Salesforce.\n' m += ' Use one of the forms below to meet your needs.\n' m += ' \n' m += ' Set the sf team\'s blast5_sf1 Q...
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def irc_prefix(var): """ Prefix a string with the irc_ :param var: Variable to prefix :return: Prefixed variable """ if isinstance(var, str): return 'irc_%s' % var.lower()
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def string_to_list(string) -> list: """Convert comma separated text to list.""" if string is None or string == "": return [] return list(map(lambda x: x.strip("'\" "), string.split(",")))
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def colorbrewer(values, alpha=255): """ Return a dict of colors for the unique values. Colors are adapted from Harrower, Mark, and Cynthia A. Brewer. "ColorBrewer. org: an online tool for selecting colour schemes for maps." The Cartographic Journal 40.1 (2003): 27-37. :param values: values ...
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def load_e3d_par(fp: str, comment_chars=("#",)): """ Loads an emod3d parameter file as a dictionary As the original file does not have type data all values will be strings. Typing must be done manually. Crashes if duplicate keys are found :param fp: The path to the parameter file :param comment_...
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def listfmt(lst: list) -> str: """ Format a list as a str with 4 decimal places of accuracy. """ return "(" + ", ".join([f"{x:.4f}" for x in lst]) + ")"
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def generate_id(name, data_id: int) -> str: """ Overview: Use ``self.name`` and input ``id`` to generate a unique id for next data to be inserted. Arguments: - data_id (:obj:`int`): Current unique id. Returns: - id (:obj:`str`): Id in format "BufferName_DataId". """ retur...
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def get_cc_feature_configuration(feature_configuration): """Returns the C++ feature configuration in a Swift feature configuration. Args: feature_configuration: The Swift feature configuration, as returned from `swift_common.configure_features`. Returns: A C++ `FeatureConfigura...
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def kth_largest_element(nums, left, right, k): """ Find kth largest element in given array (like quick sort) :param nums: given array :type nums: list[int] :param left: left position to begin :type left: int :param right: right position to end :type right: int :param k: kth :typ...
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def linear_search(sequence, target): """Pure implementation of linear search algorithm in Python :param sequence: some sorted collection with comparable items :param target: item value to search :return: index of found item or None if item is not found Examples: >>> linear_search([0, 5, 7, 10,...
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def dependence_label(dep): """Return a string representing dep.""" reason, kind = dep if kind == u'trg': label = "%s" % (kind, ) elif kind != u'unknown': label = "%s_%s" % (reason, kind) else: label = "%s" % reason return label
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from bs4 import BeautifulSoup def get_links(file): """Get links from a webpage snapshot.""" with open(file, 'r', encoding='utf-8') as f: soup = BeautifulSoup(f, 'html5lib') links = soup.find_all("a", {"class": "proditem__link"}) return [link['href'] for link in links]
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def _pprint_strs(strs, max_chars=80, delimiter=', ', suffix='...',): """Pretty-print an iterable of strings, truncating if necessary.""" # Adapted from http://stackoverflow.com/a/250373 joined_str = delimiter.join(repr(s) for s in strs) if len(joined_str) > max_chars: truncated = joined_str[:ma...
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import json def get(last_state_file_location): """ Get the last_state.json file and return a dict """ last_state_json = None last_state_dict = {} with open(last_state_file_location, 'r') as a_file: last_state_json=a_file.read() last_state_dict = json.loads(last_state_json) ...
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def _convert_params(sql, params): """convert sql and params args to DBAPI2.0 compliant format""" args = [sql] if params is not None: args += list(params) return args
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def cleanup_ocr_text(txt): """Do some basic cleanup to make OCR text better. Err on the side of safety. Don't make fixes that could cause other issues. :param txt: The txt output from the OCR engine. :return: Txt output, cleaned up. """ simple_replacements = ( (u"Fi|ed", u"Filed"), ...
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def get_item(where, key, defaultvalue=None): """ Finds the key in the dict. The key can be made up of multiple pieces seperated with a period. :param where: dict to search :param key: multiple keywords combined with a period :param defaultvalue: if the key is not found return this value :return...
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def sgn(x): """Return the sign of x.""" return -1 if x < 0 else 1
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from datetime import datetime def datetime_string_to_datetime(string: str): """ Convert datetime formatted string to datetime :param string: str "%Y-%m-%d %H:%M:%S" :return: datetime """ return datetime.strptime(string, "%Y-%m-%d %H:%M:%S")
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def get_form_model(form): """Returns the model of a modelform.""" return form._meta.model
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import inspect def get_caller_frame(i=1): """Get the caller's frame (utilizing the inspect module). You can adjust `i` to find the i-th caller, default is 1. """ # We can't use inspect.stack()[1 + i][1] for the file name because ST sets # that to a different value when inside a zip archive. r...
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import math def absolute_error(y, yhat): """Returns the maximal absolute error between y and yhat. :param y: true function values :param yhat: predicted function values Lower is better. >>> absolute_error([0,1,2,3], [0,0,1,1]) 2.0 """ return float(max(map(lambda x, y: math.fabs(x-y...
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import csv def create_dictionary(filename): """ Creates a dict that contains, patientid as key and diagnosis + month as value Parameters ---------- filename: str, path to csv file Returns ------- dictionary with all patient data """ dictionary =...
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import random import string def random_string(length): """ This function generates a crytographically secure random string of alphanumeric characters of the appropriate length using the system random libraries. """ return ''.join(random.SystemRandom().choice(string.ascii_uppercase + string...
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import math def distance(x1: float, y1: float, x2: float, y2: float): """ Return distance between two 2D points. """ dx = x2 - x1 dy = y2 - y1 return math.sqrt(dx * dx + dy * dy)
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import re def is_fraction(s): """ Determine if the input string appears to represent a fraction. This does not include mixed numbers such as 1 1/3 :param s: A string value to check if it is formatted as a fraction. """ return bool(re.match(r'^-?\d+/\d+$', s))
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def fitting_function(x, a, b): """ My fitting function to be fit to the v_out to sfr surface density data Parameters ---------- x : (vector) the SFR surface density a, b : (int) constants to be fit Returns ------- y : (vector) the outflow velocity """ ...
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def merge_dicts(source, destination): """ Deeply merges two dictionaries, included nested keys, merging lists, and updating values. NOTE: source has precendence over duplicated keys """ for key, value in source.items(): if isinstance(value, dict): # get node or create one ...
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def replace_value(value, arguments, parameters): """Test whether the string is a reference to a template parameter and (if True) replace the value with the given argument or default value. In the current implementation template parameters are referenced using $[[..]] syntax. Parameters -------...
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def arnonA_mono_to_string(mono, latex=False, p=2): """ String representation of element of Arnon's A basis. This is used by the _repr_ and _latex_ methods. INPUT: - ``mono`` - tuple of pairs of non-negative integers (m,k) with `m >= k` - ``latex`` - boolean (optional, default False),...
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import ast def _convert_str_to_tuple(string): """Function to convert a Python `str` object to a `tuple`. Args: string: The `str` to be converted. Returns: A `tuple` version of the string. Raises: ValueError: If the string is not a well formed `tuple`. """ # literal_eval converts strings to ...
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def get_limited_to(headers): """Return the user and project the request should be limited to. :param headers: HTTP headers dictionary :return: A tuple of (user, project), set to None if there's no limit on one of these. """ return headers.get('X-User-Id'), headers.get('X-Project-Id')
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def alphabets_input(min_length=None, max_length=None, description="", filter_null=True): """ Read a string from standard. And filter input by length. If length of input is out of defined length, read a string again. Parameters ---------- min_length : int Minimum len...
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def trim_float(value: float, places: int = 2) -> float: """Trim a float to N places. Args: value: float to trim places: decimal places to trim value to """ if isinstance(places, int): value = float(f"{value:.{places}f}") return value
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def get_bag_of_communities(network, partition): """ :param network: dictionary containing for each key (each node/page) a dictionary containing the page categories. :param partition: list of the community assignment :return: list of dictionaries, one dictionary per community. Each dictionary contains th...
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def message_history(request): """ Returns message edit history for a message. """ return request.param
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import math def max_uv_distance(max_fact, radius_deg, freq_hz): """Function to evaluate maximum uv distance for given amplitude drop. Follows equation 1 from: ftp://ftp.cv.nrao.edu/NRAO-staff/bcotton/Obit/BLAverage.pdf Args: max_fact (float) : amplitude reduction factor radius_deg (f...
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import yaml def _load_yaml(path: str): """ Load yaml file from path. """ with open(path) as file: return yaml.load(file, Loader=yaml.SafeLoader)
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def is_sorted(lst): """Checks whether the input list is sorted.""" for i in range(len(lst) - 1): if lst[i] > lst[i + 1]: print(lst) return False return True
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def ImportStoryIDs(path_to_file): """ .. versionadded:: 0.1.0 Reads FanFiction.Net story-ids from a file, where each story-id is on a separate line. Returns a list of strings representing story-ids. :param path_to_file: path to a file containing story-ids from FanFiction.N...
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def split_element(s, elements): """Split a string using a list of starting elements""" candidates = [] for element in elements: if not s.startswith(element): continue candidates.append(element) if len(candidates) == 0: return if len(candidates) > 2: rais...
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import torch def thwc_to_cthw(data: torch.Tensor) -> torch.Tensor: """ Permute tensor from (time, height, weight, channel) to (channel, height, width, time). """ return data.permute(3, 0, 1, 2)
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def apply_bitshift_scale(x, bitshift, do_round=True): """ applies bitshift scale to the vector x Parameters: - x: np.array(dtype=int), input array - bitshift: int: bitshift to the right - do_round: add the rounding factor if this is enabled Returns: np.array(dtype=int), scaled vector """ ...
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def _columnExists(cursor, name, colname): """Tests whether a column exists in a table.""" schemaname, tablename = name.split(".") sql = "select column_name from information_schema.columns where table_schema='{0}' and table_name='{1}' and column_name='{2}'".format( schemaname, tablename, colname) ...
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def validate(result, selectors): """Check whether a result does satisfy the selectors Parameters ---------- result : (string, dictionary) A tuple describing a file with a valid header. The parsed header data is saved in the dictionary. selectors : array-like, shape (n,) The...
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import errno def _convert_errno_parm(code_should_be): """ Convert the code_should_be value to an integer If code_should_be isn't an integer, then try to use the code_should_be value as a errno "name" and extract the errno value from the errno module. """ try: code = int(code_should_be)...
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def remove_nodes_from_graph_and_dict(nodes_to_remove, gsc_SC_KM, nodes_statuses_pre_treatment): """Remove nodes from graph and nodes_statuses dict.""" treated_graph = gsc_SC_KM.copy() nodes_statuses_post_treatment = nodes_statuses_pre_treatment.copy() for node_id in nodes_to_remove: treated_grap...
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def pylong_join(count, digits_ptr='digits', join_type='unsigned long'): """ Generate an unrolled shift-then-or loop over the first 'count' digits. Assumes that they fit into 'join_type'. (((d[2] << n) | d[1]) << n) | d[0] """ return ('(' * (count * 2) + "(%s)" % join_type + ' | '.join( ...
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import struct def int_to_bytes(int_data): """ For a 32 bit signed int in little endian :param int_data: :return: bytes(); len == 4 """ result = struct.pack('<i', int_data) return result
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import itertools def sparse_dict_from_array(array, magnitude_threshold=0): """Converts a array to a dict of nonzero-entries keyed by index-tuple.""" ret = {} for index_tuple in itertools.product(*(map(range, array.shape))): v = array[index_tuple] if abs(v) > magnitude_threshold: ret[index_tuple] =...
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def GetChrom(chrom): """ Extract a numerical chromosome Parameters ---------- chrom : str Chromosome string Returns ------- chrom : int Integer-value for the chromosome X gets set to 23 """ if "X" in chrom: return 23 if "Y" in chrom: return 24 if ch...
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def camel_to_snake(name): """ Converts camelCase to snake_case variable names Used in the Fleur parser to convert attribute names from the xml files """ name = name.replace('-', '') return ''.join(['_' + c.lower() if c.isupper() else c for c in name]).lstrip('_')
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def first_signal(stock_data, base_price, gain_loss_threshold): """ This function detects the first market signal after certain days. If the price went above the threshold we set return 1. If the price went below we return -1. If the price did not go either way we return 0 :param stock_data: a list of di...
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def validate_ip(ip): """ Validate if a string have an correct IP format. Args: ip (str): The string to be verified. Returns: ip (str): The string with a valid IP format. Raises: ValueError: In case the string hasn't a valid IP format. """ split...
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import time def get_s3_bucket_and_dir(bucket_arg): """Return the name of the S3 bucket and path to upload Lambda artifacts to. If no additional path is provided a default value will be used. Bucket Only: ``my-bucket`` Bucket with Path: ``my-bucket/my-path`` :param str bucket_arg: The string pass...
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def get_cloudgov_service_creds_by_instance_name(services, instance_name): """Retrieve credentials for a bound Cloud.gov service by instance name.""" return next( (service.get('credentials', {}) for service in services if service.get('instance_name') == instance_name), {} )
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def compare_partial_dicts(result, expected): """ Make sure all the keys in expected are matched by keys in result, and that the values stored in those keys match. Result can contain more items than expected - those are ignored. Used in the test_lvs, test_pvs and test_vgs tests. """ # retur...
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def with_graph(f): """Call a function with self.graph.as_default() context.""" def wrapper(*args, **kwargs): # the first argument is always the model instance model = args[0] with model.graph.as_default(): return f(*args, **kwargs) return wrapper
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import re def get_relvaldata_id(file): """Returns unique relvaldata ID for a given file.""" run_id = re.search('R\d{9}', file) run = re.search('_RelVal_([\w\d]*)-v\d__', file) if not run: run = re.search('GR_R_\d*_V\d*C?_([\w\d]*)-v\d__', file) if run_id and run: return (run_id.gro...
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def evaluate(node, case): """ Evaluate a node recursively. The node's symbol string is evaluated. :param node: Evaluated node :type node: list :param case: Current fitness case :type case: list :returns: Value of the evaluation :rtype: float """ symbol = node[0] # Identify ...
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def range_check(low, high): """\ Verifies that that given range has a low lower than the high. If the condition is not met, a ValueError is raised. Otherwise, the values are returned, but as floats. """ low, high = float(low), float(high) if low >= high: raise ValueError('low >= high...
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def apply_mask(image, mask): """ Applies a mask to an image. The size of the image should be N x M x 3. The mask should be a N x M array with 0.0 or 1.0 values. """ image[:,:,0] = image[:,:,0]*mask image[:,:,1] = image[:,:,1]*mask image[:,:,2] = image[:,:,2]*mask return image
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def build_raw_view(lines_layout, stats_human, no_stat_human='-'): """Convert the lines_layout to human reading stats list""" raw = [] for v in lines_layout: try: raw.append(v.format(**stats_human)) except KeyError: raw.append(no_stat_human) return raw
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def _countries_to_dict(ls: list) -> dict: """ convert countries db in the form of a list to a dict :param ls: list :return: dict """ res = dict() for i in ls: res[i[0]] = i[1] return res
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def GetXMLTag(node): """ Get XML tag of current node.""" return node.tag
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import collections def array_to_points(points): """Transform an array of floats into a list of 2 tuples.""" point_list = [] array = collections.deque(points) while array: lat = array.popleft() long = array.popleft() point = (lat, long) point_list.append(point) ret...
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def pretty_str(element, encoding="us-ascii", xml_declaration=True, indent=4): """ Gets a string of the provided XML element. Args: element (xml.etree.ElementTree.Element): The element to get as a string. encoding (str): The encoding of the XML string. xml_declaration (bool): If the ...
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def update_docstring_references(obj, ref="ref"): """ Updates docstring reference names to strings including the function name. Decorator will return the same function with a modified docstring. Sphinx likes unique names - specifically for citations, not so much for footnotes. Parameters -------...
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def blockshaped(arr, nrows, ncols): """ Return an array of shape (n, nrows, ncols) where n * nrows * ncols = arr.size If arr is a 2D array, the returned array should look like n subblocks with each subblock preserving the "physical" layout of arr. """ h, w = arr.shape return (arr.resha...
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import requests def request_ct(url): """Performs a get request that provides a (somewhat) useful error message.""" try: response = requests.get(url) except: raise IOError( "Couldn't retrieve the data, check your search expression or try again later." ) else: ...
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def _signature_map(map_dict, parsed_sig): """Map values found in parsed gufunc signature. Parameters ---------- map_dict : dict of str to int Mapping from `str` dimension names to `int`. All strings in `parsed_sig` must have entries in `map_dict`. parsed_sig : list-like of tuples of...
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def get_referer(self, request): """ Retrieves the referer value for the current request being used for the handling. The referer value shall not be trusted as it may not be defined in the request. :type request: Request :param request: The request to be used. :rtype: String :return:...
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def _build_params(dt): """Takes a date and builds the parameters needed to scrape the dgm website. :param dt: the `datetime` object :returns: the `params` that contain the needed api information """ params = (('yr', dt.year), ('month', dt.month), ('dy', dt.day), ...
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def length(iterator): """A length function for iterators Returns the number of items in the specified iterator. Note that this function consumes the iterator in the process. """ return sum(1 for _item in iterator)
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def unique_edge_sizes(H): """A function that returns the unique edge sizes. Parameters ---------- H : Hypergraph object The hypergraph of interest Returns ------- list() The unique edge sizes """ return list({len(H.edges.members(edge)) for edge in H.edges})
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from pathlib import Path from typing import Tuple def _get_cache_info(path: Path) -> Tuple[float, int]: """ Returns a tuple of (modified_time, file_size) for the path; this tuple is persisted to the cache, and we check the files on disk against this cached value to determine if we need to format the f...
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def get_number_of_outputs(output_data): """Get the number of output variables for a given output array.""" if not hasattr(output_data, 'shape'): raise AttributeError( 'Output data types must have attribute "shape".' ) if len(output_data.shape) == 1: return 1 return ...
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