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from typing import Any import pickle def read_pickled(filepath: str, encoding: str = "latin1") -> Any: """Read the pickled data in the file Args: filepath (str): The file path encoding (str): File encoding. Defaults to :data:`"latin1"` Returns: The unpickled data""" with open(filepath,...
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def norm_array(Array, Minval=0.001): """Normalise array by largest abs value if >Minval (avoids trying to renormalise zero array)""" greatest = 0.0 flatarray = Array.flat for i in range(len(flatarray)): if abs(flatarray[i]) > abs(greatest): greatest = flatarray[i] if abs(greatest...
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import hashlib def compute_file_hashsum(filename): """ Compute SHA256 file hashsum for {filename}. """ algo=hashlib.sha256() maximum_block_size_in_bytes = 65536 with open(filename, 'rb') as file: while True: block = file.read(maximum_block_size_in_bytes) if ...
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def stringify_cookies(cookies: list[dict]) -> str: """ Creates a cookie string from a list of cookie dicts. """ return ";".join([f"{c['name']}={c['value']}" for c in cookies])
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import pickle def load_pk_file(file_name): """ Load data from a file using Pickle path: the path to the required file Return: the data in the form before saved """ with open(file_name,'rb') as f: data = pickle.load(f) return data
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import torch def atanh(x: torch.Tensor) -> torch.Tensor: """ Return atanh of the input. Modified torch.atanh in case the output is nan. Parameters ---------- x: torch.Tensor input Returns ------- y: torch.Tensor atanh(x) """ return 0.5 * (torch.log(1 + x + 1e-...
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def getNbins(h): """ To be used in loops on bin number with range() For each dimension there are GetNbinsX()+2 bins including underflow and overflow, and range() loops starts from 0. So the total number of bins as upper limit of a range() loop already includes the next to last value needed. """ biny=h...
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def format_key(tag, key): """ Format a key for insertion into the Redis cache. :param tag: Tag associated with this key. :param key: The actual key. :return: A formatted key for insertion into the cache. """ return '{tag}:{key}'.format(tag=tag, key=key)
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def _computeforwardmissing(a, b, match=None): """Computes which files are in b but not a. This is its own function so extensions can easily wrap this call to see what files _forwardcopies is about to process. """ ma = a.manifest() mb = b.manifest() return mb.filesnotin(ma, match=match)
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import glob def _get_post_file(stub): """Locate a post's markdown file from its stub""" files = glob.glob(f"../_posts/*{stub}.md") if not files: raise FileNotFoundError(f"Could not locate file with stub {stub}") elif len(files) > 1: raise ValueError(f"Multiple files located with stub {...
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import random def weighted_random_selection(obj1, obj2): """Randomly return one of the following, obj1 or obj2 :arg obj1: An instance of class AbstractGameUnit. It can be any object. The calling code should ensure the correct object is passed to this function. :arg obj2: Ano...
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def matches(open_symbol: str, close_symbol: str) -> bool: """Checks if the opening and closing sybols match""" symbol_close_map = {"(": ")", "[": "]", "{": "}"} return close_symbol == symbol_close_map.get(open_symbol)
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def construct_hex(hex1, hex2, _bytes=2): """ Helper method to construct hex from two decomposed hex values """ bin1 = format(int(str(hex1), 16), f"0{_bytes * 4}b") bin2 = format(int(str(hex2), 16), f"0{_bytes * 4}b") bin_total = "".join(["0b", bin1, bin2]) return f'0x{format(int(bin_total, 2...
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def apiname(field): """The full (qualified) programmatic name of a field""" if field["prefix"]: fieldname = u"{}.{}".format(field["prefix"], field["name"]) else: fieldname = field["name"] return fieldname
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def symbol_template(address, function_name): """Return an entry in the symbol array: {0xdeadbeef, "function"},""" return "\t{0x" + address + ", " + "\"" + function_name + "\"" + "},\n"
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def remove_empty_leading_trailing(lines): """ Removes leading and trailing empty lines. A list of strings is passed as argument, some of which may be empty. This function removes from the start and end of the list a contiguous sequence of empty lines and returns the result. Embedded sequences of ...
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def _data_header(cols, parent_dict): """Constructs a header row for the worksheet based on the columns in the table and contents of the parent row""" out = [] for col in cols: if col == 'gau_id': out.append(parent_dict['geography_id']) elif col == 'oth_1_id': out.appe...
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import json def read_json(json_file: str): """ Read a json file. Args: json_file (str): name of the json file. Must be 'name.json'. Returns: dict: returns a dict of the json file. """ with open(json_file, 'r', encoding='utf8') as file: return json.load(file)
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import random def rand_hex_str(str_len:int = 2) -> str: """ Random hex string of specified length Parameters ---------- str_len : int Length of random hex string, default 2 (characters) Returns ------- rand_str : str String with random hexadecimal characters "...
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def length_of_elements(elementList, index=0, lengths=None): """ Returns the length of each row (sub-array) in a single array """ if lengths is None: lengths = [] # Will only calculate len if index is lower than the len of the array. # If it isn't less, will return the final array of leng...
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def orth(string): """Returns a feature label as a string based on the capitalization and other orthographic characteristics of the string.""" if string.isdigit(): return 'DIGIT' elif string.isalnum(): if string.islower(): return 'LOWER' elif string.istitle(): ...
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from typing import Tuple def parse(line: str) -> Tuple[str, str]: """Parses import lines for comments and returns back the import statement and the associated comment. """ comment_start = line.find("#") if comment_start != -1: return (line[:comment_start], line[comment_start + 1 :].strip()...
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def rsync(s, d, test=False, config='dts', reverse=False): """Set up rsync command. Parameters ---------- s : :class:`str` Source directory. d : :class:`str` Destination directory. test : :class:`bool`, optional If ``True``, add ``--dry-run`` to the command. config : ...
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def validate_uniform_range(range): """ Validate a uniform range Args: range (:obj:`data_model.UniformRange`): range Returns: nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique) """ errors = [] if range.number_of_steps < 1: ...
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def notifier_title_cleaner(otitle): """ Simple function to replace problematic Markdown characters like `[` or `]` that can mess up links. These characters can interfere with the display of Markdown links in notifications. :param otitle: The title of a Reddit post. :return otitle: The cleaned-up ve...
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def delete_comments(line): """Deletes comments in parentheses from a line.""" fields = line.split(')') result = [] for f in fields: if '(' in f: result.append(f.split('(',1)[0]) else: result.append(f) return ''.join(result)
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import sqlite3 def connect_to_db(db_name = "rpg_db.sqlite3"): """ Function to connect to a SQL database """ return sqlite3.connect(db_name)
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def flip_cold(ds): """Flip mhw intensities if cold spell. Parameters ---------- ds: xarray Dataset Includes MHW properties Returns ------- ds: xarray Dataset Includes MHW properties with flipped values for intensities """ for varname in ds.keys(): if 'inten...
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import requests def pulsar_create(addr, auth, **kwargs): """ Create a new pulsar. Args: addr: hostname or ip address of database server. auth: tuple of username and password. name: name of pulsar. ra: right ascension of pulsar. dec: declination of pulsar. ...
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def convert_camel_case(s: str) -> str: """convert to camel case Args: s (str): str Returns: str: camel case str """ return s.title().replace("_", "").replace("-", "")
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def DecodeFATTime(FATdate, FATtime): """Convert the 2x16 bits of time in the FAT system to a tuple""" day = FATdate & 0x1f month = (FATdate >> 5) & 0xf year = 1980 + (FATdate >> 9) sec = 2 * (FATtime & 0x1f) min = (FATtime >> 5) & 0x3f hour = FATtime >> 11 return (year, day, month, hour,...
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def dB_function(dB): """ Convert dB into linear units """ linear = 10**(dB/10.) return linear
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def fast_replace(t, sep, sub=None): """ Replace separators (sep) with substitute char, sub. Many-to-one substitute. "a.b, c" SEP='.,' :param t: input text :param sep: string of chars to replace :param sub: replacement char :return: text with separators replaced """ result = [] ...
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import json def read_dataformat(file): """ Reads a dataformat .json file and returns it as a dict. Parameters ---------- file : str Path to dataformat.json file. """ return json.load(open(file))
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from typing import List def compute_columns_width(data: List[List[str]], padding: int = 2) -> List[int]: """Compute columns width for display purposes: Find size for each columns in the data and add padding. Args: data (List[List[str]]): Tabular data containing rows and columns. padding (i...
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def replace_none(idx, dim): """ Normalize slices to canonical form, i.e. replace ``None`` with the appropriate integers. Parameters ---------- idx: slice or other index dim: dimension length Examples -------- >>> replace_none(slice(None, None, None), 10) slice(0, 10, 1) ...
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from typing import List from typing import Any def list_copy(lst: List[Any]) -> List[Any]: """Copy the given list and returns new copied list""" new_list = [each_element for each_element in lst] return new_list
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def _ExtractObsoleteNode(node, recursive=True): """Extracts obsolete child from |node|. Returns None if not exists.""" if not recursive: obsolete = [ element for element in node.getElementsByTagName('obsolete') if element.parentNode == node ] else: obsolete = node.getElementsByTagName(...
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from typing import Sequence from typing import Callable from typing import Any def remove_if_possible(options: Sequence[str], predicate: Callable[[Any], bool]): """ Removes all entries in options where the predicate is true, unless that would leave an empty list of options. """ pred_vec = [predica...
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def ltc_public_byte_prefix(is_test): """LITECOIN Address prefix. Returns b'\30' for main network and b'\x6f' for testnet""" # XXX guessing at LTC-testnet value, can't find a reference. return b'\x6f' if is_test else b'\x30'
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def subpartition(quadtree, nmin, nmax): """ Recursive core of the ``QuadTree.partition`` method. Just five lines of code, amazingly. Parameters ---------- quadtree : QuadTree object instance The QuadTree object instance being partitioned. nmin : int The splitting threshold. If t...
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import requests def check_asa_network_object(name, asa): """ This function searches for an existing network object :param name: Name of the network object. :param asa: The ASA which is searched. :return: Returns True if the object exsists, else False """ url = asa.url() + "/api/objects/net...
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def fqdn_split(fqdn): """split a fully qualified domain and return the host name and dns domain, when no domain has been specified an empty string will be returned as dns domain""" split_host = fqdn.split('.') if len(split_host) == 1: host_name = split_host[0] dns_domain = '' el...
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def footer_length(header): """Calculates the ciphertext message footer length, given a complete header. :param header: Complete message header object :type header: aws_encryption_sdk.structures.MessageHeader :rtype: int """ footer_length = 0 if header.algorithm.signing_algorithm_info is not...
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def intToBinary(number, size): """ Converts a decimal number to binary form Parameters: ========== number: Integer The Number to be converted into binary form size: Integer The maximum length of the returning binary list Returns: ======= list: Returns a lis...
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def pyqtSlot(*args, **kwargs): """Declare dummy function for environments without pyqt5.""" return lambda *x: None
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import json def parse_json(json_file): """ Parse a JSON configuration file Parameters ---------- json_file : obj File handle to the file to be parsed Returns ------- config : dict Parsed configuration file """ config = json.load(json_file) re...
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def _rear_left_tire_pressure_supported(data): """Determine if rear left tire pressure is supported.""" return data["status"]["tirePressure"]["rearLeftTirePressurePsi"] is not None
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def series_cdf(series): """Calculate cdf of series preserving the index Parameters ---------- series : series like Returns ------- cdf : series """ index = series.index.tolist() total = series.sum(skipna=True) cdf = series.cumsum(skipna=True) / total return cdf
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import math def get_distance(atom1, atom2): """ Returns distance between atom1 and atom2. """ return math.sqrt(sum((atom1[i]-atom2[i])**2 for i in 'xyz'))
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import yaml import logging def get_config_by_path(config_filepath, parse_yaml=True): """Read in the file given at specified config path Args: config_filepath (str): File path to klio config file parse_yaml (bool): Whether to parse the given file path as yaml Returns: p...
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def _extractFeatureClasses(lookupIndex, subtableIndex, classDefs, coverage=None): """ Extract classes for a specific lookup in a specific subtable. This is relatively straightforward, except for class 0 interpretation. Some fonts don't have class 0. Some fonts have a list of class members that are c...
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import re def get_indentation(line): """ Take a line, and return its indentation as string """ pattern = re.compile(r"(.*?)(\w|\})") match = pattern.search(line) if not match: return indentation = match.group(1) add_extra_indent = ('public', '}') if any(s in line for s in a...
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def get_version(user_id, version, client): """Requests a certain version of certain user.""" return client.get_user_version(str(user_id), version)
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def _CalcEta(time_taken, written, total_size): """Calculates the ETA based on size written and total size. @param time_taken: The time taken so far @param written: amount written so far @param total_size: The total size of data to be written @return: The remaining time in seconds """ avg_time = time_tak...
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def all_subclasses(cls): """Recursively retrieve all subclasses of the specified class""" return cls.__subclasses__() + [ g for s in cls.__subclasses__() for g in all_subclasses(s) ]
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def to_string(lista_ref): """ Constrói uma string a partir dos elementos de uma lista Args: lista_ref (list): lista de referência para construção da string Returns: [str]: string formada pelos elementos da lista_ref """ return ''.join(lista_ref)
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def get_gap(numberlist: list): """Get gap Can take an integer list returned by :meth:`get_numbers` and determine the missing sequence number. Args: numberlist: List of numbers to find a gap in. Returns: Missing number in the sequence or None if there is no gap. """ seqlist...
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def exact_dp4(a_v, b_v): """ Exact version (formal) of 4D dot-product :param a_v: left-hand-side vector :type a_v: list(SollyaObject) :param b_v: right-hand-side vector :type b_v: list(SollyaObject) :return: exact 4D dot-product :rtype: SollyaObject (value or express...
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import difflib def create_patch(filename: str, modified: str): """Create a unified diff between original and modified""" with open(filename, "r") as f: original = f.read() patch = "\n".join( difflib.unified_diff( original.splitlines(), modified.splitlines(), ...
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import hashlib import math def deterministic_random(input_string): """ Returns a deterministically random number between 0 and 1 based on the value of the string. The same input should always produce the same output. """ if isinstance(input_string, str): input_string = input_string.encode(...
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from typing import Iterable def scheduler_story(keys: set, transition_log: Iterable) -> list: """Creates a story from the scheduler transition log given a set of keys describing tasks or stimuli. Parameters ---------- keys : set A set of task `keys` or `stimulus_id`'s log : iterable ...
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import functools def collect_keys(table): """ Collects all names of keys (columns) used throughout the data """ just_keys = map(lambda entry: set(entry.keys()), table) return sorted(list(functools.reduce(set.union, just_keys)))
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def get_simult_lines(tests, results, test_line_num=0): """Returns a line from the input/output, ensuring that we are sync'd up between the two.""" test = tests.pop(0) result = results.pop(0) test_line_num += 1 if test != result: raise Exception("Lost sync between files at input...
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def _to_pandas_from_pandas(obj): """ Convert Pandas DataFrame etc. to a Pandas DataFrame. A no-op, in short. """ return obj
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def get_closer(a, b, test_val): """Returns which ever of a or b is closer to test_val""" diff_a = abs(a - test_val) diff_b = abs(b - test_val) if diff_a < diff_b: return a else: return b
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def bias(obs, mod): """ Bias = mean(obs) - mean(mod) """ return obs.mean(axis=0) - mod.mean(axis=0)
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def _get_start_end(location): """ Get the start and the end of a location object. For point locations both start and end equal the position value. """ if location["type"] == "range": return location["start"]["position"], location["end"]["position"] elif location["type"] == "point": ...
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def response(code, description): """ Decorates a function with a set of possible HTTP response codes that it can return. Args: code: The HTTP code (i.e 404) description: A human readable description """ def response_inner(function): if not hasattr(function, 'doc_response...
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def uniq(ls): """ uniqify a list """ return list(set(ls))
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import io def bfh(s): """utility function to convert string of hex into a BytesIO stream""" return io.BytesIO(bytes.fromhex(s))
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def sort_batch_of_lists(uids, batch_of_lists, lens): """Sort batch of lists according to len(list). Descending""" sorted_idx = [i[0] for i in sorted(enumerate(lens), key=lambda x: x[1], reverse=True)] uids = [uids[i] for i in sorted_idx] lens = [lens[i] for i in sorted_idx] batch_of_lists = [batch_o...
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from math import ceil def round_up(x,step): """Rounds x up to the next multiple of step.""" if step == 0: return x return ceil(float(x)/float(step))*step
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def list_records(full_record): """Fixture list of records.""" list_records = { "hits": {"hits": [full_record, full_record]}, } return list_records
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def define_outfile_cols_expand(samp_grps, ontology, mode): """ define columns for writing the expand output file :param samp_grps: SampleGroups object :param ontology: functional ontology. only required for 'f' or 'ft' modes :param mode: f, t, or ft :return: a list of relevant columns in the co...
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def is_return_value(parameter: dict) -> bool: """Whether the parameter is marked as a return_value.""" return parameter.get("return_value", False)
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import math def cos(degrees) -> float: """Calculate the cosine of the given degrees.""" return math.cos(math.radians(degrees))
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def return_list_smart(lst): """ If the list has length > returns the list if it has length == 1 it returns the element if it has length == 0 it returns None """ if len(lst) > 1: return lst elif len(lst) == 1: return lst[0] else: return None
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def grid_maker(width, height): """Accepts width, height (ints). Returns widthxheight grid with '.' as values.""" grid = [['.' for i in range(width)] for j in range(height)] return grid
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def adjust_indel_rates(expected): """ adapt indel rates for lower rate estimate from validated de novos The indel mutation rates from Samocha et al., Nature Genetics 46:944-950 assume that the overall indel mutation rate is 1.25-fold greater than the overall nonsense mutation rate, ie there are 1.2...
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import zipfile def create_archive(archive_path, file_path, file_name=None, if_exists='replace'): """ Create and fill an archive. `Args:` archive_path: str The file name of zip archive file_path: str The path of the file file_name: str The name o...
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def rotToQuat(obj): """ return the rotation of the object as quaternion""" if obj.rotation_mode == 'QUATERNION' or obj.rotation_mode == 'AXIS_ANGLE': return obj.rotation_quaternion else: # eurler return obj.rotation_euler.to_quaternion()
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def _set_dim_0(t, d0): """Sets the 0-th dimension of the input tensor. Args: t: the input tensor, assuming the rank is at least 1. d0: an integer indicating the 0-th dimension of the input tensor. Returns: the tensor t with the 0-th dimension set. """ t_shape = t.get_shape().as_list() t_shape[...
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def check_if_bst(node, mini=float('-inf'), maxi=float('+inf')): """ Check if the given tree is Binary Search Tree (BST) Args: node: root node of the Tree. `node` arg must have `.left`, `.right` and `.data` variables mini: min value - should be omitted maxi: max value - should be omi...
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import random def random_colour(bits=24): """Returns a random 24-bit colour hex value.""" # For 24 bits, 1 << 24 == 0x1000000 # 0x1000000 - 1 = 0xFFFFFF. return random.randint(0, (1 << bits) - 1)
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import math def c_div(q, d): """ Arbitrary signed integer division with c behaviour. >>> (c_div(10, 3), c_div(-10, -3), c_div(-10, 3), c_div(10, -3)) (3, 3, -3, -3) >>> c_div(-11, 0) Traceback (most recent call last): ... ZeroDivisionError """ s = int(math.copysign(1, q) *...
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def get_all_subclasses(base_class): """ Method for getting all child classes from a parent object. Taken from: http://stackoverflow.com/questions/3862310/how-can-i-find-all-subclasses-of-a-class-given-its-name Inputs: :param class base_class: The parent class which we are looking towards. Retu...
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def parselinje( linje ): """ Dekoder en linje på formen 200, download size: 'https://www.vegvesen.no/nvdb/api/v3/veg?veglenkesekvens=0.99786547288010718%401125762' og returnerer en dictionary med følgende komponenter: { 'status' : 200, 'url' : 'https://www.vegvesen.no/nvdb/api/...
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def unpack_ipv4_bytes(byte_pattern): """ Given a list of raw bytes, parse out and return a list of IPs :param byte_pattern: The raw bytes from the DHCP option containing a list of IP addresses. The RFC specifies that an IP list will be a list of octets, with each group of 4 octets representing ...
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def stats(r): """returns the median, average, standard deviation, min and max of a sequence""" tot = sum(r) avg = tot/len(r) sdsq = sum([(i-avg)**2 for i in r]) s = list(r) s.sort() return s[len(s)//2], avg, (sdsq/(len(r)-1 or 1))**.5, min(r), max(r)
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def calc_centered_grid(cols_list, hpad=.05, vpad=.05): """Calculates a centered grid of Rectangles and their positions. Parameters ---------- cols_list : [int] List of ints. Every entry represents a row with as many channels as the value. hpad : float, optional The amount of...
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import io def stream_binary(f): """ Create a data stream from a file path (str), raw bytes, or stream. """ if isinstance(f, str): return open(f, "rb") if isinstance(f, bytes): return io.BytesIO(f) if hasattr(f, "read"): if hasattr(f, "seek"): f.seek(0) ...
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def document_features(doc_words, top_words): """ Basic features extraction from a list of words in a document (doc_words). For all words in top_words (most used in all corpus), set True/False if the word is in the document's words set. """ # transform the list of words into a set to optimize sea...
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import random def gen_a_random_probability(self): """generate a random probability obey uniform distribution Returns: float: a random probability Examples: >>> s = String() >>> s.gen_a_random_probability() 0.5 """ return random.uniform(0, 1)
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def bytes_needed(i): """ Compute the number of bytes needed to hold arbitrary-length integer i """ bn = 1 while True: i >>= 7 if i == 1: # negative sign bit return bn + 1 elif i == 0: return bn i >>= 1 bn += 1
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def format_price(price): """ formats number 12345678 -> 12 345 678 """ s_list = [] while price: s_list.append(str(price % 1000)) price /= 1000 s_list.reverse() return ' '.join(s_list).strip()
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def flatten_lists(*lists): """Flatten several lists into one list. Examples -------- >>> flatten_lists([0, 1, 2], [3, 4, 5]) [0, 1, 2, 3, 4, 5] Parameters ---------- lists : an arbitrary number of iterable collections The type of the collections is not limited to lists, ...
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def trim_variable_postfixes(scope_str): """Trims any extra numbers added to a tensorflow scope string. Necessary to align variables in graph and checkpoint Args: scope_str: Tensorflow variable scope string. Returns: Scope string with extra numbers trimmed off. """ idx = scope_str.find(':') retur...
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def closestPointOnSegment1(p = "const %(Vector)s&", a0 = "const %(Vector)s&", a1 = "const %(Vector)s&", result = "%(Vector)s&"): """Find the point on a line segment (a0,a1) closest to point (p). This version return True if the closest ...
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from typing import List def shift_list(l: List, n: int) -> List: """Return a new list based on the one given with its elements shifted n times. """ return [l[(i - n) % len(l)] for i in range(len(l))]
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