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def clean_headers_server(header): """ Only allows through headers which are safe to pass to the client """ valid = ['content-length', 'content-type', 'x-roll-ntime', 'x-reject-reason', 'noncerange'] for name, value in header.items(): if name.lower() not in valid: de...
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def S_find_range_values(_data_list): """ Returns smallest and largest values in the one dimensional dataset """ return (min(_data_list), max(_data_list))
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def delta(a, b): """ Function that returns the Kronecker delta delta(a, b). Returns 1 if a = b and 0 otherwise. """ if a==b: return 1 else: return 0
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def is_coach(user): """ Returns True if the user is a coach, False otherwise. """ try: user.coach return True except: return False
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def __format_datetime_input(datetime_input, language): """Formats the specified datetime input. Args: datetime_input (dict): A datetime input configuration to format. language (dict): A language configuration used to help format the input configuration. Returns: dict: A formatted d...
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def create_name_simu_and_info(index, prm): """Create name_simu and info key""" prm['name_simu'] = prm['name_simu'] + "_" + str(index) prm['info'] = 'date_' + prm['date'] + '_name_simu_' + prm['name_simu'] + '_model_' + prm['model'] return (prm)
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def all_of(*conditions): """Returns True if all of the conditions match""" def check(): for c in conditions: if not c(): return False return True return check
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def model_y(ec, params): """ Simple model of a kinematic trajectory. Args: ec (`dict`): dictionary with a key 't' leading to a float value params (`dict`): dictionary with keys 'v0' and 'g' leading to float values Returns: float: y-value at the given time assuming the given par...
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def get_value(component, name): """ Get a variable from a component """ variable = component.variables[name] vr = [variable.valueReference] if variable.type == 'Real': return component.fmu.getReal(vr)[0] elif variable.type in ['Integer', 'Enumeration']: return component.fmu.getInte...
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def PO2_Calc(KO2, tO2, Kr, I, qO2): """ Calculate PO2. :param KO2: oxygen valve constant [kmol.s^(-1).atm^(-1)] :type KO2 : float :param tO2: oxygen time constant [s] :type tO2 : float :param Kr: modeling constant [kmol.s^(-1).A^(-1)] :type Kr : float :param I: cell load current [A]...
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def cast_date(dcm_date): """ Cast DICOM date string (YYYYMMDD) into ElasticSearch pre-defined strict_date format (yyyy-MM-dd) """ return dcm_date[:4] + '-' + dcm_date[4:6] + '-' + dcm_date[6:]
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def _union_lists(l1, l2): """ Returns the union of two lists as a new list. """ return l1 + [x for x in l2 if x not in l1]
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import imp def __import__(name, path): """ Imports a module that is outside of python path. Modified from Python Library Reference. Arguments: - name: module name (file name without '.py') - path: directory where the module resides, relative to the directory of the calling functi...
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import socket def isAvailable(port, family=socket.AF_INET, sockType=socket.SOCK_STREAM): """Return True if the specified socket is available, False otherwise """ s = socket.socket(family, sockType) try: s.connect(("localhost", port)) s.close() return False except Exception:...
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def make_stdout(data): """Returns a valid log output with given data as message.""" return ' 1553110400.424 5583 5658 D Tag: %s' % data
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def snapshot(path, compression="AUTO", reader_func=None, shard_func=None): """API to persist the output of the input dataset. The snapshot API allows users to transparently persist the output of their preprocessing pipeline to disk, and materialize the pre-processed data on a different training run. This AP...
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def get_exposure_value(tags): """Extracts exposure value from given tags """ if tags and "EXIF ExposureTime" in tags: exposure = tags["EXIF ExposureTime"] exposure = eval(str(exposure)) return exposure return None
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def get_kappa(searchers: dict): """Retrieve kappa from each searcher and return as list""" kappa_list = [] for s_id in searchers.keys(): s = searchers[s_id] kappa_list.append(s.kappa) return kappa_list
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import string def first_int(s): """Return the first integer in a string, or None""" # This technique appears to be faster than the re-based method # by almost an order of magnitude. Prefer it ret = '' for c in s: if c in string.digits: ret += c else: break...
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def chunk(seq, size): """Return generator that yields chunks of length `size` from `seq`.""" return (seq[pos:pos + size] for pos in range(0, len(seq), size))
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def get_msg_data(msg): """Get message data.""" return msg["data"]
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def is_box_in_zones(box, zones): """Determine if an object bounding box is within a list of zones""" for zone in zones: # print('alwaysai.py: is_box_in_zones: zone: {}'.format(box, zone)) if zone.box is None: # zone.box = edgeiq.BoundingBox(zone.start_x, zone.start_y, zone.end_x, zon...
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def check_for_border(m_index_list, m_borders): """ Checks for the borders of membrane regions, from M indices. Parameters ---------- m_indices : list List of membrane region indices, extracted from the flatfile, (e.g. IIIMMMMMMMMMOOOO for Inside, Membrane and Outside), giving the list o...
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def remove_dupes(L): """ Given list L of words, return set of unique words """ return list(set(L))
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def get_markdown_title(markdown_src): """ Get the title of a Markdown document. The title in this case is considered to be a H1 that occurs before any other content in the document. The procedure is then to iterate through the lines, stopping at the first non-whitespace content. If it is a title, re...
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from typing import Set def digit_rotations(n: int) -> Set[int]: """Finds all unique digit rotations of a positive integer in base 10. Args: n: A positive integer value. Returns: A set of all distinct integers that result from rotating the base-10 digits of ``n``. A rotation is gi...
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def get_ycbcr_bands(image): """Returns a tuple of the 3 bands (Y, Cb, Cr).""" color_transformed = image.convert(mode='YCbCr') return color_transformed.split()
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from datetime import datetime def _get_timezone_name(timezone): """ Returns the name of ``timezone``. """ try: # for pytz timezones return timezone.zone except AttributeError: # for regular tzinfo objects local_now = datetime.now(timezone) return timezone.tz...
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def AvgPoolSequence(attn_mask, feats, e=1e-12): """ The function will average pool the input features 'feats' in the second to rightmost dimension, taking into account the provided mask 'attn_mask'. Inputs: attn_mask (torch.Tensor): [batch_size, ...x(N), 1] Mask indicating ...
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def find_all_connecting(graph, start, end): """Return the set of all nodes along all paths between start and end. The start and end nodes are included in the set if they're connected. """ if start == end: return set() Gsucc = graph.succ Gpred = graph.pred fwdset = set() bac...
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def Binom(n, k, d={}): """Compute the binomial coefficient "n choose k". Args: n: number of trials k: number of successes d: map from (n,k) tuples to cached results Returns: int """ if k == 0: return 1 if n == 0: return 0 try: return d[n, k]...
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def get_by_pickup(state,b1): """Generate a pickup subtask.""" if state.is_true("clear", [b1]): return [('pickup_task',b1)] return False
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from pathlib import Path def path_to_string(value): """Convert paths to strings.""" if isinstance(value, Path): value = str(value) elif isinstance(value, list) and len(value) and isinstance(value[0], Path): value = [str(val) for val in value] return value
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def setCopy( set ): """(shallow) copy a set""" return set[:]
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def find_centroid(gdf): """Find the centroid of polygons, even when in a geographic CRS If the crs is geographic (uses lat/lon) then it is converted to a projection before calculating the centroid. The projected CRS used here is: <Projected CRS: EPSG:2163> Name: US National Atlas Equal Area ...
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def _get_dihedral_rb_torsion_key(dihedral, epsilon_conversion_factor): """Get the dihedral_type key for a Ryckaert-Bellemans (RB) dihedrals/torsions Parameters ---------- dihedral : parmed.topologyobjects.Dihedral The dihedral information from the parmed.topologyobjects.Angle epsilon_conver...
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def noop(x): """No-operation/identity function.""" return x
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def probs_out_of_counts(array_counts): """ function that takes an array-like object (e.g. a list) with counts and calculates the corresponding probabilities """ sum_count = array_counts.sum() factor = 100/sum_count array_probs = [] for i in array_counts: array_probs.append(i*fac...
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def user(rel): """Add relationship category prefix for user resources. Parameters ---------- rel: string Link relationship identifier Returns ------- string """ return 'users:{}'.format(rel)
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def get_selected_action(body): """Get selected value from an action event""" if body["actions"] is not None and len(body["actions"]) > 0: return body["actions"][0]["selected_option"]["value"]
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def lbyl_convert(text): """ >>> lbyl_convert("123") 123 >>> lbyl_convert("-5") """ if text.isdigit(): num= int(text) else: num= None return num
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def find_connected_vertices_to(graph, vertice): """Given a graph and a vertice, find all other vertices that are connected to it""" visited = [] # if the visitation order to vertices isn't relevant, a set is better for performance purposes def dfs(node): """Actual DFS algorithm""" visited...
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def build_dataset_attributes_json_object(output_files, container_name, num_files, num_multi_page, percentage_multi_page): """ :param output_files: The files to output :param container_name: The storage container name :param num_files: The number of files process...
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def match_any(iterable, predicate): """Returns True if at least one item in the iterable matches the predicate.""" for x in iterable: if predicate(x): return True return False
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def get_province(project_object): """ Return province of project in lowercase """ try: return project_object['province'].lower().strip() except: return 'unknown'
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def create_cfg_test_daemon( run_dir, receptor_f, ligand_f, *ignore, **everythinelse): """ Create HADDOCK3 configuration file that only generates the topology. This function is usefull to use test the benchmark daemon. """ cfg_str = \ f""" run_dir = {str(run_d...
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def layout_items(layout): """ Returns the items from the given layout and returns them :param layout: QLayout, layout to retrieve items from :return: list(QWidgetItem) """ return [layout.itemAt(i) for i in range(layout.count())]
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import math def text_center(text, width, padchar=" "): """ Center `text` in a string of width `width` padded on both sides by varying lengths of `padchar`. """ tlen = len(text) out = "" if tlen > width: # Append "..." to signify a continuation. out = "..."+text[(-1*width)+2...
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def Q_distcooler(P_mass, Cp, t_coolwater_exit, tp): """ Calculates the heat load of distilliat cooler. Parameters ---------- W_mass : float The mass flow rate of distilliat, [kg/s] Cp : float The heat capacity of distilliat, [J/(kg * degrees C)] t_coolwater_exit: float ...
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def status(prog_comp, obs_comp): """ Compute weighting factor representative of observation and program status. - 1.0 if observation and program have not been observed - 1.5 if program has been partially observed - 2.0 if observation has been partially observed Parameters ------...
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def _apply_decreasing_rate(value: float, rate: float) -> float: """ Apply a decreasing rate to a value :param value: current value :param rate: per second :return: updated value """ return value - (60 * rate)
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def round_float_math(number: float) -> int: """ Unified rounding in all python versions. Parameters: ---------- number : float Input number. Returns: ------- int Output rounded number. """ if abs(round(number) - number) == 0.5: return int(2.0 * round(0.5...
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import torch def log_sum_exp(x): """ Compute log(sum(exp(x), 1)) in a numerically stable way. Assumes x is 2d. """ max_score, _ = x.max(1) return max_score + torch.log(torch.sum(torch.exp(x - max_score[:, None]), 1))
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def get_num_bins(args): """ Gets the number of bins that will be used in this analysis. """ n_maf = 2 if args.maf_bins_2 else 5 n_ld = args.num_ld_bins return n_maf * n_ld
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from typing import Dict from typing import Any def get_asset_custom_context_for_whois(resp: Dict[str, Any], whois_content: Dict[str, Any]) -> Dict[str, Any]: """ Modifying the lists fetched from whois details of response to comma separated strings. :param resp: Response fetched from the API call :par...
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import math def expected_unanchored_L2_discrepancy(num_points, dimension): """Expected value for unanchored L2 discrepancy of random uniform points. Note that this is the square root of :math:`\\mathrm{E}(T^2)`, i.e. ``sqrt(1.0 / n * (6 ** -d) * (1 - 2 ** -d))``. For details see [Morokoff1994]_. ...
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def anagram1(S1,S2): """ Checks if the two strings are anagram or not""" S1 = S1.replace(' ', '').lower() S2 = S2.replace(' ', '').lower() if len(S1) != len(S2): return False # Edge case check count = {} for x in S1: if x in count: count[x] += 1 else: ...
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import json def load_speeddial(file_path): """ Load the bookmark entries from Vivaldi's speed dial and return as dictionary """ # read bookmark file with open(file_path, encoding="UTF-8") as jfile: bookmarks = json.load(jfile) # access speed dial speeddial = bookmarks["roots"]...
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from typing import Union from pathlib import Path from typing import List def readfile(contents: Union[str, Path]) -> List[str]: """ Takes a file path or the contents of a file and attemts to split it into lines. Parameters ---------- contents: Union[str, Path] Returns ------- List[str] The lines in the f...
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def parse_CPC2_output(path): """Returns sequence IDs lists of cds and non-coding sequences. To to passed into fasta subset.""" with open(path, "r") as f: contents= f.read().split("\n") cds=[] ncds=[] for line in contents: if line.split("\t")[-1] == "noncoding": ncds+=[lin...
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import statistics def fitness(population, goal): """Measure population fitness based on an attribute mean vs target.""" ave = statistics.mean(population) return ave / goal
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def vni_row_name(network_type): """Determine name of row for VNI in allocations table. :param network_type: Network type to determine row name for. :type network_type: str :returns: Row name :rtype: str :raises: ValueError """ if network_type in ('gre',): return '{}_id'.format(n...
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def are_equal_trees(t1, t2): """True if t1 and t2 has the same shape and the same contents. False otherwise""" if t1.is_empty() and t2.is_empty(): return True elif t1.is_empty() or t2.is_empty(): return False else: return t1.root_element() == t2.root_element()\ and...
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def _is_builtin(obj): """Check if an object need not be converted.""" return isinstance(obj, (float, int, str, bool))
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def day_days(d1, d2): """ Returns total amount of days between days d1 and d2. """ return d2 - d1
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def sort_dict(d: dict, number: bool = False) -> dict: """Sort a dict by keys""" if number: return dict(sorted(d.items(), key=lambda item: int(item[0]))) else: return dict(sorted(d.items(), key=lambda item: item[0]))
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def combined_prefix(cluster_bin_index, isoform_type, sample_name): """Return i{cluster_bin_index}_{isoform_type}_{sample_name}""" assert isoform_type in ["HQ", "LQ", "ICE"] return "i{i}_{t}_{s}".format(i=cluster_bin_index, t=isoform_type, s=sample_name)
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def adder_function_json(args): """Dummy function to execute returning a dict.""" loc, scale = args return {'result': loc + scale}
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import requests import json def png2latex(input_path, output_path): """ Calls the EqDecoder pipeline with a PNG image and returns JSON containing the tokenized latex output from OpenNMT. Args: input_path: [String] -- in the form: /path/to/input/<filename>.png output_path: [String] -- ...
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def slugify(name) -> str: """Return a slugified version of the name.""" return f'#{name.lower().replace(" ", "-").replace("(", "").replace(")", "")}'
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def get_last_date_of_a_month(date): """ Given date, returns the last day of the same month as date. i.e. if given 15 Jan it would return 31 Jan. """ start_month = date.month next_try = date while next_try.shift(days=1).month == start_month: next_try = next_try.shift(days=1) retur...
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def _ensure_value(namespace, name, value): """Force empty namespace attribute to specified value.""" if getattr(namespace, name, None) is None: setattr(namespace, name, value) return getattr(namespace, name)
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def calc_sides(tile: list) -> list: """Compute the sides of each tile, returned in a N W S E order.""" return [ tile[0], "".join([line[-1] for line in tile]), "".join(reversed(tile[-1])), "".join([line[0] for line in reversed(tile)]), ]
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def is_leaf_node(dt, node_index): """Checks if node at node_index is a leaf node to a DecisionTree Args: dt (sklearn.DecisionTree): decision tree to be examined node_index (int): index of node in dt Returns: bool : whether node at index is a leaf node in dt """ return (dt.c...
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def count_chars(text: str, char_to_count: str) -> int: """Count the number of times that 'char_to_count' is found in the 'text'.""" count = 0 for char in text: if char == char_to_count: count += 1 return count
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def openconfig_to_cisco_af(value): """Translate openconfig AF name to Cisco AFI name.""" if ":" in value: value = value.split(":")[1] mapd = { 'IPV4_UNICAST': "ipv4 unicast", 'IPV6_UNICAST': "ipv6 unicast", 'IPV4_LABELED_UNICAST': "ipv4 unic...
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import hashlib def hash256(s: bytes) -> bytes: """ two rounds of sha256 :param s: data :return: hashed data """ return hashlib.sha256(hashlib.sha256(s).digest()).digest()
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def sizeof_fmt(num, suffix='B', longsuffix=True, usespace=True, base=1024): """ Returns a string representation of the size ``num``. - Examples: >>> sizeof_fmt(1020) '1020 B' >>> sizeof_fmt(1024) '1 KiB' >>> sizeof_fmt(12011993) '11.5 MiB' >>> sizeof_fmt(123456789) '117.7 MiB' ...
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def getType(item) : """Attempt to determine what type of value a string represents""" item = item.strip() if not item : return "NULL" if item[0] == "$": return "$" if item.strip("0123456789,.") : return "STR" return "NUM"
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def PyDateTime_GET_YEAR(space, w_obj): """Return the year, as a positive int. """ return space.int_w(space.getattr(w_obj, space.newtext("year")))
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def remove_indices(indices, inds_to_be_rm): """ Convert some bound indices to free ones. The conversion goes as: inds_to_be_rm[i] -> -1 - i Args: indices ([int]): list in which the conversion is to be done inds_to_be_rm ([int]): list of the indices to be made free in order Return:...
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import torch def gaussian_kernel(x, sigma=4): """Gaussian distance kernel. Args: x (Tensor): difference between two input features. sigma (float): standard deviation of the gaussian kernel. Returns: The Gaussian kernel for features `x` and standard deviation `sigma`. """ return torch.exp(- (x ...
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import requests def get_user_data(username): """ Downloads the content of a user profile. :param username: The user whose profile to retrieve. :return: html of the user profile """ address = 'http://archiveofourown.org/users/' + username + '/profile' r = requests.get(address) return r....
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def _word_wrap(string, max_length=0): """wrap long strings to be no longer than max_length.""" if max_length <= 0: return string return '\n'.join([string[i:i + max_length] for i in range(0, len(string), max_length)])
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def getArraySize(arr): """ Return size in bytes of numpy array """ nbytes = arr.dtype.itemsize for n in arr.shape: nbytes *= n return nbytes
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import math def cone(individual, position, height, width): """The cone peak function to be used with scenario 2 and 3. :math:`f(\mathbf{x}) = h - w \sqrt{\sum_{i=1}^N (x_i - p_i)^2}` """ value = 0.0 for x, p in zip(individual, position): value += (x - p)**2 return height - wi...
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def get_file_contents(filename): """Returns file content as string.""" with open(filename, 'r') as srcfile: return srcfile.read()
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from typing import Iterable def count(data: Iterable) -> dict: """Counts number of occurrences for each item in list.""" return {el: list(data).count(el) for el in set(data)}
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def add_suffix_to_file_name(file_name, suffix=None): """Adds the specified suffix, if any, either to the end of the specified file_name; or, if the file_name has an "extension" starting with a dot ('.'), then just in front of the dot. """ result = file_name if suffix: ext_index = str(fil...
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import re def remove_urls(text): """Remove urls from a string""" clean = re.compile('https?://\S+?(?=~)') return re.sub(clean, '~', text)
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from base64 import urlsafe_b64encode def encode_payload(payload: str) -> str: """ Encode payload with URL-safe base64url. """ result: bytes = urlsafe_b64encode(payload.encode()) return result.decode()
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def settings_name(value): """Makes a capitalized name from an option flag.""" return value.lstrip('-').replace('-', '_').upper()
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def get_package_version_key(pkg_name, pkg_version): """Return unique key combining package name and version.""" return pkg_name + '@' + pkg_version
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def diff_action(diff): """Return 'add', 'replace', or 'delete' based on action represented by difference tuple `d`. Append "_rule" if the change is a Selector. """ if "replace" in diff[-1]: result = "replace" elif "add" in diff[-1]: result = "add" elif "delete" in diff[-1]: ...
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def known_devtypes() -> list: """Returns the list of known dev types""" return(['cumulus', 'eos', 'iosxe', 'iosxr', 'ios', 'junos-mx', 'junos-qfx', 'junos-qfx10k', 'junos-ex', 'junos-es', 'linux', 'nxos', 'sonic', 'panos'])
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def serialize_addresses(multipart_address): """Get the addresses from the address segment of a multipart message. :param multipart_address: A list representing the address part of a multipart message (including an empty delimiter). :returns: The list of non-empty addresses. """ return [x fo...
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def _region_by_region_type(all_forecasts): """Pick out all regions represented in all_forecasts. Order by region_type (A regions first) and descending region_id.""" regions_and_type_dict = {} for f in all_forecasts: if f.region_type_name not in regions_and_type_dict.keys(): regions_...
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def _convert_counts_logits_to_mean_disp(total_count, logits): """NB parameterizations conversion - Copied over from scVI :param total_count: Number of failures until the experiment is stopped. :param logits: success logits. :return: the mean and inverse overdispersion of the NB distribution. """ ...
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def shift_rows(state): """ Section 5.1.2: ShiftRows() Transformation !!! FUN FACT ALERT !!! Rotating a row by one position to the left is equivalent to polynomial multiplication by {01}x^3 + {00}x^2 + {00}x^1 + {00}x^0, modulo x^4 + 1 >>> shift_rows(b"ABCDefghIJKLmnop") bytearray(b'AfKpeJoDInChmBgL')...
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def sidak(alpha_orig, p_values): """ Sidak correction. en.wikipedia.org/wiki/%C5%A0id%C3%A1k_correction Parameters ---------- alpha_orig : float alpha value before correction p_values: list[float] p values resulting from all the tests Returns ------- alpha_corr...
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