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def _generate_new_prefix(current_prefix, class_name): """ Generate the new prefix to be used when handling nested configurations. Examples: >>> _generate_new_prefix("", "config_group_1") "CONFIG_GROUP_1" >>> _generate_new_prefix("my_app", "another_config_group") "MY_APP_ANOTHER_CONFIG_GROU...
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from typing import Dict from typing import Any import zlib import base64 def _serialize_bytes(data: bytes, compress: bool = True) -> Dict[str, Any]: """Serialize binary data. Args: data: Data to be serialized. compress: Whether to compress the serialized data. Returns: The serial...
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import re def parse_cuda_device_id(device: str) -> int: """Parse cuda device index from a string. Args: device (str): The typical style of string specifying cuda device, e.g.: 'cuda:0'. Returns: int: The parsed device id, defaults to `0`. """ match_result = re.match('...
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import math def combination_num(n, r): """Combination formula to calculate the maximum amount of different combinations "n choose r" :param n (int) : n distict objects r (int) : sample of r elements :return Returns result of combination calculation""" if n < r: rai...
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def msi(b8a, b11): """ Moisture Stress Index (Rock, Williams, and Vogelmann, 1985). .. math:: MSI = b11 / b8a :param b8a: NIR narrow. :type b8a: numpy.ndarray or float :param b11: SWIR 1. :type b11: numpy.ndarray or float :returns MSI: Index value .. Tip:: Rock, B.N., Wi...
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def flatten_list(l): """Flatten a 2D list""" return sum(l, [])
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def make_unpack_map(node): """ Make a mapping of unpack values for a template instance. Parameters ---------- node : TemplateInstanceNode The compiler node for the template instantiation. Returns ------- result : dict A dict mapping unpack name to compiler node for the temp...
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import inspect def string_annotation(typ, default): """ Construct a string representation of a type annotation. Parameters ---------- typ : type Type to turn into a string default : any Default value (if any) of the type Returns ------- str String version ...
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def get_thing_types(tx): """ Get all schema types, excluding those for implicit attribute relations and base types Args: tx: Grakn transaction Returns: Grakn types """ schema_concepts = tx.query( "match $x sub thing; " "not {$x sub @has-attribute;}; " "no...
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def _last_char(word): """Get last alphanumeric character of word. :param word: word to get the last letter of. """ for i in range(len(word)): if word[len(word)-1-i].isalpha() or word[len(word)-1-i].isdigit(): return len(word) - 1 - i return -1
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import re def normalize_docstring(docstring): """ Normalizes whitespace in the given string. >>> normalize_docstring('This is\ta docstring.') 'This is a docstring.' """ return re.sub(r"[\r\n\t ]+", " ", docstring).strip()
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def make_hash(args): """Generate a unique hash for the experience""" if "killing" in args: return "%(network)s-m=%(method)s-d=%(directivity)s-k=%(killing)s" % args else: return "%(network)s-m=%(method)s-d=%(directivity)s" % args
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def get_long_be(s): """Convert a 4-char value to integer.""" return (ord(s[0])<<24) | (ord(s[1])<<16) | (ord(s[2])<<8) | ord(s[3])
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from typing import OrderedDict def parse_attributes(attribute_str): """ Parse attribute field of GFF3 file :param attribute_str: attribute field as string :return: dict with the values for each attribute as key """ attributes = attribute_str.split(';') output = OrderedDict() for attr...
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import re def formula_to_composition(formula): """ Breaks a molecular formula into its constituent elements. Returns a dictionary of element keys and an integer formula """ # Ignore the first value in the split, because it will be blank from # trying to split on the first element symbol. ...
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def summarize(seq,field_name,func=None,msg=None): """ Compute a summary of a given field (eg. count of different values). Resulting dictionary is either passed to `func`, or printed on screen (if `func is None`). :param seq: Datastream :param field_name: Field name to summarize :param func: Func...
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def _total_query(db): """ Query # of lead art elements """ result = db.query(""" select count(distinct(lead_art_url)) as count from seamus """) value = list(result).pop() return value['count']
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import re def strip_text(text, pattern='.* ?- ?(.*) (Abc Iview)?.*'): """ Strips text matching the pattern from the string. Args: text (str): the string to clean pattern (str): the regex pattern for matching the text to remove. This pattern needs to define a single capture tha...
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def _otus_abundant(freq_counts, rare_threshold): """Count number of abundant OTUs.""" return freq_counts[rare_threshold + 1:].sum()
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def check_sequence_names_unique(sequence): """ Checks that the names of entities are all unique """ entity_names = [x['name'] for x in sequence] result = len(entity_names) == len(set(entity_names)) if not result: return { 'result': False, 'message': "All names of ...
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def std_chr_name(chrom_str): """Standardize chromosome name so it starts with 'chr'""" if chrom_str.startswith("chr"): return chrom_str else: if chrom_str.startswith("Chr"): return "chr" + chrom_str[3:] else: return "chr" + chrom_str
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def new_source(resource_id, text, offset, length): """ Create a new SADFace source (Python dict) using the supplied resource ID (a source always refers to an existing resource object) and identifying a section of text in the resource as well as an offset & segment length for locating the text in the or...
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import base64 def from_base64(data): """ Utility function to base64 decode. :param data: The data to decode. :return: The decoded data. """ return base64.b64decode(data)
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from typing import List def insertion_sort(array: List[float]): """ Iterate through each number of the array starting from index 1 and check if it's bigger than the previous ones. If a bigger one is found, shift the number to the left. This algorithm runs faster than selection sort in best case sc...
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import struct def keytag(dnskey): """ Given a dns.rdtypes.ANY.DNSKEY, compute and return its keytag. See rfc2535 section 4.1.6 for details. """ if dnskey.algorithm == 1: a = ord(dnskey.key[-3]) << 8 b = ord(dnskey.key[-2]) return a + b else: header = struct...
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from typing import List from typing import Optional from pathlib import Path def determine_package_relevance(dep_src_paths: List[str], src_paths: Optional[List[str]] = None) -> bool: """Determine if the package is relevant to the given source paths. A package is relevant if any of...
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def xy_sequencer(start_x, start_y, stroke_height, stroke_spacing, n_strokes, both_directions=True): """ xy_sequencer generates a list of tuples specifying the x,y coordinates of the path that the LU20 sampler must follow. This path has two forms. The first form, where both_directions=True ...
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from typing import List def oc_n_project(project: str) -> List: """ Construct['oc', '-n', '<project name>'] """ return ['oc', '-n', project]
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def create_nd_array(shape): """create n-dimensional array filled with 0""" if len(shape) == 0: return 0 res = [] for _ in range(shape[0]): res.append(create_nd_array(shape[1:])) return res
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import math def _edge_lengths(points): """ Compute edge lengths from ordered points Assumes points are in order. Returns ------- list[float, ..] """ if len(points) != 4: raise ValueError('Expected 4 points instead of {}'.format(len(points))) lengths = [] for i in range...
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def create_multiplicative_function(multiplier): """ return multiplication by a fixed value as a function :param multiplier: float value that the returned function multiplies by :return: function function that can multiply by the multiplier parameter when called """ return lambda...
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def safe_get(collection, key, default=None): """Get values from a collection without raising errors""" try: return collection.get(key, default) except TypeError: pass try: return collection[key] except (IndexError, TypeError): pass return default
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def get_bench_name(func): """ Get a benchmark name, based on it's function (strip the `bench_` part.) """ return func.__name__.partition('_')[-1]
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def list_length(data): """Report the list length""" return len(data)
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def flip_dim2(ndarray): """ Flip x coordinate for training data :param ndarray: 4d array :return: flipped 4d array """ return ndarray[:, :, ::-1, ...]
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import random def random_string(size): """Return a random string of size size.""" l = [chr(random.randrange(256)) for i in range(size)] return "".join(l)
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def determine_filetype(filename): """ Return the filetype of a given file by examining the first few bytes. Adapted from pyart.io.auto_read.py script by : https://arm-doe.github.io/pyart/ The following filetypes are detected: * 'csv' * 'txt' * 'excel' * 'NETCDF3' * 'NETCDF4' ...
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def check_json_keys(json_dict): """ Checks if all required keys are set :param json_dict: dict parsed from json :return: True if required key are set """ required_keys = ["command", "runtime", "weight", "actual_stretch", "graph_information"] required_graph_information = ["nodes", "edges", "d...
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def make_nonterminal(label, children): """returns a tree node with root node label and children""" return [label]+children
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def goodbye_world() -> str: """Creates a command to print "Goodbye World".""" return 'echo "Goodbye Cruel World"'
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def count_first_choices(tally): """ Return dict giving count of all first choices in tally dictionary. Args: tally (dictionary): dictionary mapping ballots to nonnegative reals. Returns: (dict): dictionary mapping all choices that occur at least once as a first ...
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def placeholder2ix(placeholder): """ Extracts index from placeholder, e.g., #₂ => 2 """ return int(placeholder[1:])
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def percentage_string(val): """ Returns a percentage-formatted string for a value, e.g. 0.9234 becomes 92.34% """ return '{:,.2%}'.format(val)
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def matches_filter(finding, request): """ Filters: * /scans/0/kb/?name= returns only vulnerabilities which contain the specified string in the vulnerability name. (contains) * /scans/0/kb/?url= returns only vulnerabilities for a specific URL (startswith) If more than o...
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import torch def compute_jacobian_on_map(x, y, forward_transform, eps=0.01): """ Computes the differentials dx/du, dy/du, dx/dv, dy/dv for the given projection function) using central differences. For spherical projections, (lon, lat = u, v) Returns (x.shape[0], x.shape[1], 2, 2) """ # Compute d...
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def pp_num(num): """ pretty prints number with commas """ s = '%d' % num groups = [] while s and s[-1].isdigit(): groups.append(s[-3:]) s = s[:-3] return s + ','.join(reversed(groups))
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def calculate_winner(rules: dict, left_attack: str, right_attack: str) -> str: """ Function to calculate the winner of combat Left player has priority and goes first :param rules: Dictionary of current rules :param left_attack: Attack type of priority player :param right_attack: Attack type of ...
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def split_epochs(epochs): """Savely split up one epochs file into two with adequate channel names.""" epochs_1 = epochs.copy().pick_channels([ch for ch in epochs.ch_names if ch[:4] == "sub1"], ordered=True) epochs_2 = epochs.copy().pick_channels([ch for ch in epoc...
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import math def sqrt_bins(arr): """ Uses a rule of thumb to calculate the appropriate number of bins for an array. :param arr: An array containing numbers. :returns: An integer to serve as the number of bins. """ return int(math.sqrt(len(arr)))
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def select_countries(df, select_years=[str(x) for x in range(2005, 2019)], threshold=12, values='value'): """ Extract a list of countries that has sufficient data for the selected years. Args: df: (DataFrame) Created by "extract_data". select_years...
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from typing import Any def key_by_val(dictionary: dict, value: Any, ) -> Any: """ A helper function for getting a key from a dictionary corresponding to a certain value. Does not check for value unicity. Args: dictionary (dict): The dictionary. value: The...
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import math def RastFunc(vardim, x, bound): """ Rastrigin function """ s = 10 * 25 for i in range(1, vardim + 1): s = s + x[i - 1] ** 2 - 10 * math.cos(2 * math.pi * x[i - 1]) return s
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import math def regular_poly_circumrad(n_sides, side_length): """Circumradius of a regular polygon.""" return side_length / (2 * math.sin(math.pi / n_sides))
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def get_gerrit_patch_from_parameters_action(action): """For the given action dictionary, return the Gerrit patch URL if present, else return None.""" for param in action['parameters']: if param['name'] == 'GERRIT_CHANGE_URL': return param['value'] return None
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def not_none(passed, default): """Returns `passed` if not None, else `default` is returned""" return passed if passed is not None else default
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import json def retrieve_ldap_password(secrets_manager_client, logger, ldap_password_secret_name): """ Retrieve LDAP service account password from secrets manager Expected password format: { "PASSWORD": "service_account_password" } Returns: str: plaintext ldap password ""...
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def merge_verifyta_args(cfg_dict): """ Concatenate and format a string of verifyta arguments given by the .yaml configuration file. """ args = "" for k, v in cfg_dict.items(): if (v != None): args += " --" + k + " " + str(v) else: args += " --" + k ret...
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import pytz def get_country_code(request): """ Country code based on ISO 3166-1 (http://en.wikipedia.org/wiki/ISO_3166-1) :param request: Request Object :return: ISO Code of the country """ if 'X-AppEngine-Country' in request.headers: if request.headers['X-AppEngine-Country'] in pytz.c...
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from typing import Iterable import six def is_non_string_iterable(arg): """Return True if arg is an iterable, but not a string.""" return ( isinstance(arg, Iterable) and not isinstance(arg, six.string_types) )
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def extract_measurement_names(data_file_src: str) -> list[str]: """Extract the row name (first column) from the provided plaintext data file.""" data_lines = data_file_src.splitlines() return [row.split(",")[0] for row in data_lines]
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from datetime import datetime def parse_timestamp(time_str): """ There are three datetime string formats in eMammal, and some have an empty field. Args: time_str: text in the tag ImageDateTime Returns: datetime object, error (None if no error) """ if time_str == '' or tim...
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import random def random_product(*args, **kwargs): """random_product(*args, repeat = 1) -> tuple Arguments: args: One or more iterables repeat(int): Number of times to repeat `args`. Returns: A random element from ``itertools.product(*args, repeat = repeat)``. Examples: >>...
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def airtovac(wave): """ Convert air-based wavelengths to vacuum Parameters: ---------- wave: ndarray Wavelengths Returns: ---------- wavelenght: ndarray Wavelength array corrected to vacuum wavelengths """ # Assume AA wavelength = wave # Standard conversion for...
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def is_structure(structure): """Check if an object is a structure that javelin can understand. ase.atoms with have cell, get_scaled_positions and get_atomic_numbers attributes diffpy.structure with have lattice, xyz, and element attributes """ return (((hasattr(structure, 'cell') or hasattr(structu...
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def dimensions(bound): """ Get the width and height of a bound :param bound: a bound tuple :return: a tuple containing the width and height of the ``bound`` i.e ``(width, height)`` """ return bound[2] - bound[0], bound[3] - bound[1]
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def Dup(x, **unused_kwargs): """Duplicate (copy) the first element on the stack.""" if isinstance(x, list): return [x[0]] + x if isinstance(x, tuple): return tuple([x[0]] + list(x)) return [x, x]
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def str_to_felt(text): """Convert from string to felt.""" b_text = bytes(text, "ascii") return int.from_bytes(b_text, "big")
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def check_int(integer, name): """Verify that an object is an integer, or coercible to one. Parameters ---------- integer : int The integer to check. name : str The name to print in the error message if it fails. """ if isinstance(integer, int): return integer # ...
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def get_dicts_from_list(list_of_dicts, list_of_key_values, key='id'): """ Returns list of dictionaries with keys: @prm{key} equal to one from list @prm{list_of_key_values} from a list of dictionaries: @prm{list_of_dicts}. """ ret = [] for dictionary in list_of_dicts: if dictionary.get(ke...
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def get_types(input_types, args, kwargs): """Extract the types of args, kwargs, optional kwargs and output. Parameters ---------- input_types : list List of inputs' input_types, including for optional inputs. args : tuple Args of a function. kwargs : dict Kwargs of a fun...
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def prep_for_jinja(images): """ Prepares svg `images` for jinja rendering Parameters ---------- images : list-of-str Returns ------- outputs : list-of-tuple """ outputs = [] for im in images: with open(im, 'r') as src: content = src.read() outpu...
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import operator def _validate_int(k, name, minimum=None): """ Validate a scalar integer. This functon can be used to validate an argument to a function that expects the value to be an integer. It uses `operator.index` to validate the value (so, for example, k=2.0 results in a TypeError). ...
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def rebuild_params(values, keys): """ Build parameter dictionary from flattened values and ordered parameter names. For example, given the following: values = np.array([1., 5., .2, .5, 50., .1, 3, 3]), keys = [("Rt_fac", ["mu", "gamma", "b-a"]), ("R_fac", ["mu", "gamma", "b-a"]), ("consts", ...
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def getItemDict(node, recursive=True): """From a Houdini item, get the contents :param node: Node to get a content dict from :type node: hou.Node() :param recursive: In recursive mode, this will recurse on all sub-children items :type recursive: bool :return: A dictionary containing information...
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def append_wrapper(list): """ Returns a decorator that appends its argument to 'list' """ def decorator(x): list.append(x) return x return decorator
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def send_and_exhaust(iterator, arg, default): """Send a single value to a coroutine, exhaust it, and return the final element or a default value if it was empty.""" # Python's coroutine syntax is still a bit rough when you want to do # slightly more complex stuff. Watch this logic closely. output = ...
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import inspect def get_mismatching_default_values(f1, f2, mapping=None): """Check that two functions have the same default values for shared parameters.""" # Additional mappings from f1 parameters to f2 parameters may be provided if mapping is None: mapping = {} params1 = inspect.signature(f1...
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from functools import reduce def get_earliest_trade(trades): """ Gets the earliest trade from a list of trades. """ return reduce(lambda trade_a, trade_b: trade_a if trade_a.timestamp < trade_b.timestamp else trade_b, trades)
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def connection_gsm(gsm_client, network_apn, network_user, network_password): """ This function waits for the network to be available and opens a gprs connection Args: gsm_client (GsmClient): An object of the GsmClient class network_apn (string): The network apn network_u...
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def delete_images_json(ibs, image_uuid_list): """ REST: Method: DELETE URL: /api/image/json/ Args: image_uuid_list (list of str) : list of image UUIDs to be delete from IBEIS """ gid_list = ibs.get_image_gids_from_uuid(image_uuid_list) ibs.delete_images(gid_list) ret...
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from bs4 import BeautifulSoup def parse_response_error(html_text: str) -> str: """Parse HTML error response :param html_text: HTML error message. :return: Parsed error message. """ message = '' html = BeautifulSoup(markup=html_text, features="html.parser") if html.p: ...
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def int_representation(entity): """Returns a unique integer representation of a string (entity).""" return int.from_bytes(entity.encode(), "little")
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def get_labels(ss): """Return two labels from a string containing "-" or two words starting with a capital. For example, the input string may be 'G-X', 'GX', 'Gamma-X', 'GammaX'. The output is always: ('G', 'X') or ('Gamma', 'X'). """ if '-' in list(ss): labels = ss.split('-') else: ...
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import configparser def _open_reg_file(file_path): """ Open file at given path and return as config option.""" config = configparser.ConfigParser() config.read_file(open(file_path)) return config
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def getProjectNameFromFile(f: str) -> str: """ Helper funcion that obtains a project name from a project file name """ f=f.replace("\\","/") # e.g. LondonMaeCompany_ldpproto_fe04304 -> LondonMaeCompany/ldpproto projectName = '/'.join(f.split("/")[1].replace("_","/").split("/")[:-1]) #pri...
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import secrets def randomHex(len: int): """Returns a random hex string at the given length.""" byteArray = [] for foo in range(len): byteArray.append(secrets.randbelow(255).to_bytes(1, "little")) return b"".join(byteArray).hex()
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import re def extract_jobs_flags(mflags): """Extracts make job flags from a list of other make flags, i.e. -j8 -l8 :param mflags: string of space separated make arguments :type mflags: str :returns: space separated list of make jobs flags :rtype: str """ regex = r'(?:^|\s)(-?(?:j|l)(?:\s*...
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def template_check(template_id_hex): """Checks the template hex vlad and returns the template name corresponding to it Parameters ---------- template_id_hex: hex str of template id The template id retrieved from the parsed RAP packet Returns ------- The corresponding templat...
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def chunk_string_increment(string, n): """ string: 'aabbccdd' n: 2 returns ['aa', 'aabb', 'aabbcc', 'aabbccdd'] """ # chunks = ['aa', 'bb', 'cc', 'dd'] chunks = [string[i:i+n] for i in range(0, len(string), n)] result = [] step = 1 # for index, e in enumerate(chunks): # ...
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def stream_resampling(stream, sampling_rate=100.0): """ To resample the input seismic data. Parameters ---------- stream : obspy stream input seismic data. sampling_rate : float required sampling rate in Hz, default is 100 Hz. Returns ------- stream : obspy stream ...
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def slice_pagination(page_range, current_page): """Slices paginator.page_range to limit which page links are displayed The logic for which page numbers are shown is based on Google Search's pagination. Examples: When current_page is within the first four pages 1 [2] 3 4 5 6 7 8 When ...
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from datetime import datetime def get_age(year_of_birth): """ Returns the age of the person. """ return datetime.now().year - year_of_birth
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def get_diff(throw, target): """ Determines the difference between a throw and a target E.g. between '111344' and '111144' Here, the difference is 1, dice to keep is '11144', to remove is '3' """ diff = 0 remove = [] keep = [] for i, j in zip(throw, target): if i != j: ...
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import decimal import calendar def dt_to_decimal(utc): """Datetime to Decimal. Some databases don't store microseconds in datetime so we always store as Decimal unixtime. """ if utc is None: return None decimal.getcontext().prec = 30 return (decimal.Decimal(str(calendar.timegm(ut...
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from typing import Optional def int_range_to_string( begin_optional: Optional[int] = None, end_optional: Optional[int] = None, unit: Optional[str] = None, default_begin_value: str = "", default_end_value: str = "", ) -> Optional[str]: """ Change range int to string for TFDS. Parameter...
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def prot_domains(ips_result): """ Reads the tsv output of an InterProScan run and returns a dict with gene name and minimal E-value found for any domain for any application for the protein. """ res = {} with open(ips_result) as f: for line in f: fields = line.split('\t') ...
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import math def comb(n,k): """Return the number of ways to choose k items from n items without repetition and without order. """ return math.factorial(n) / (math.factorial(k) * math.factorial(n-k))
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import torch def moments_log(log_probs, log_levels, bias_levels, log_squared_levels, bias_squared_levels): """ Compute mean and variance of a probability tensor. Note: the probability is represented in log-space. Arguments: ---------- log_probs: an (N+1)-th order tensor of ...
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def lookup(dlist, lkey, lvalue, rkey=None): """ Use a known key:value pair to lookup a dictionary in a list of dictionaries. Return the dictonary or None. If rkey is provided, return the value referenced by rkey or None. If more than one dict matches, raise an error. args: dlist: lo...
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import wave import click def validate_wave(ctx, param, value): """ Validate the wave file by trying to open it and checking that its got a single channel. :param ctx:<class 'click.core.Context'> :param param:<class 'click.core.Option'> :param value:str :return:<cla...
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