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def dpv(vec1, vec2)->float: """Dot product of two vectors""" product = 0. for idx, val in enumerate(vec1): product += val * vec2[idx] return product
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def is_proxy(obj): """ Return True if `obj` is an array proxy """ try: return obj.is_proxy except AttributeError: return False
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def is_palindrome(n, base=10): """ Is the given number n a palindrome in the given base? """ if base == 10: n_str = str(n) elif base == 2: n_str = "{0:b}".format(n) else: raise RuntimeError("Only 2 and 10 bases supported") for i in range(len(n_str) // 2): if n_str[i] != n_str[-1 - i]: return False return True
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def extract_best_aligns(aligns_df): """Extracts alignments with highest score from the provided alignments dataframe. """ mask = aligns_df.groupby('seq_index').agg({'score': 'idxmax'}) # get /!\ FIRST /!\ index of max align score for each sequence aligns_df_best = aligns_df.loc[mask['score']].reset_index(drop=True) return aligns_df_best
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def bitstring_readable(data, batch_size, model_output=None, whole_batch=False): """Produce a human readable representation of the sequences in data. Args: data: data to be visualised batch_size: size of batch model_output: optional model output tensor to visualize alongside data. whole_batch: whether to visualise the whole batch. Only the first sample will be visualized if False Returns: A string used to visualise the data batch """ def _readable(datum): return '+' + ' '.join(['-' if x == 0 else '%d' % x for x in datum]) + '+' obs_batch = data.observations targ_batch = data.target iterate_over = range(batch_size) if whole_batch else range(1) batch_strings = [] for batch_index in iterate_over: obs = obs_batch[batch_index, :, :] targ = targ_batch[batch_index, :, :] readable_obs = 'Observations:\n' + '\n'.join([_readable(obs_vector) for obs_vector in obs]) readable_targ = 'Targets:\n' + '\n'.join([_readable(targ_vector) for targ_vector in targ]) strings = [readable_obs, readable_targ] if model_output is not None: output = model_output[batch_index, :, :] strings.append('Model Output:\n' + '\n'.join([_readable(output_vec) for output_vec in output])) batch_strings.append('\n\n'.join(strings)) return '\n' + '\n\n\n\n'.join(batch_strings)
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def large_dollar_volume_stocks(df, price_column, volume_column, top_percent): """ Get the stocks with the largest dollar volume stocks. Parameters ---------- df : DataFrame Stock prices with dates and ticker symbols price_column : str The column with the price data in `df` volume_column : str The column with the volume in `df` top_percent : float The top x percent to consider largest in the stock universe Returns ------- large_dollar_volume_stocks_symbols : List of str List of of large dollar volume stock symbols """ dollar_traded = df.groupby('ticker').apply(lambda row: sum(row[volume_column] * row[price_column])) return dollar_traded.sort_values().tail(int(len(dollar_traded) * top_percent)).index.values.tolist()
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import math def prob_no_match(n): """analytical result using integers - python can handle arb large numbers""" return math.factorial(n)*math.comb(365,n)/(365**n)
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from typing import Mapping def _recursive_update(d, u): """Recursively update a nested dict with another.""" # https://stackoverflow.com/a/3233356/1595060 for k, v in u.items(): if isinstance(v, Mapping): d[k] = _recursive_update(d.get(k, {}), v) else: d[k] = v return d
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def test_data_dir(name): """ Decorator allowing to customize test data directory for a test. The specified name will be used only as the last component of the path following the directory corresponding to the test class (by default test name itself is used for this purpose). Example:: @test_data_dir('common_test_data') def test_scenario(): ... """ def decorator(f): f._test_data_dir = name return f return decorator
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def group_by_key(dict_list, key): """ >>> data = [ ... {'a': 1, 'b': 2}, ... {'a': 1, 'b': 3} ... ] >>> group_by_key(data, 'a') {1: [{'a': 1, 'b': 2}, {'a': 1, 'b': 3}]} """ grouped = {} for d in dict_list: group_key = d.get(key) grouped.setdefault(group_key, []) grouped[group_key].append(d) return grouped
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def buffer_to_offset(buffer): """ Convert a byte buffer into an integer offset according to ArcGIS packing scheme: (buffer[0] & 0xff) + (buffer[1] & 0xff) * 2 ** 8 + (buffer[2] & 0xff) * 2 ** 16 + (buffer[3] & 0xff) * 2 ** 24 ... Parameters ---------- buffer: list[bytes] byte buffer Returns ------- int: offset """ return sum(((v & 0xFF) * 2 ** (i * 8) for i, v in enumerate(buffer)))
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def line(display=False): """To make easy separations while printing in console""" if display == True: return print("____________________________________________________________\n")
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def group_edge_pairs(edges): """ Group pairs of forward and reverse edges between nodes as tuples in a list together with single directed edges if any :param edges: list of edges :type edges: :py:list :return: paired edges :rtype: :py:list """ pairs = [] done = [] for e in edges: if e in done: continue reverse_e = e[::-1] if reverse_e in edges: pairs.append((e, reverse_e)) done.append(reverse_e) else: pairs.append(e) done.append(e) return pairs
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def calculate_xy_coords(image_size, screen_size): """Calculates x and y coordinates used to display image centered on screen. Args: image_size as tuple (int width in pixels, int height in pixels). screen_size as tuple (int width in pixels, int height in pixels). Returns: tuple (int x coordinate, int y coordinate). """ image_width, image_height = image_size screen_width, screen_height = screen_size x = (screen_width - image_width) / 2 y = (screen_height - image_height) / 2 return (x, y)
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def args_env(args): """ Create a dictionary of enumerated arguments. """ return {str(i): str(v) for i, v in enumerate(args)}
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def can_merge(a, b): """ Test if two cubes may be merged into a single cube (their bounding box) :param a: cube a, tuple of tuple ((min coords), (max coords)) :param b: cube b, tuple of tuple ((min coords), (max coords)) :return: bool, if cubes can be merged """ c = 0 # Count the number of continued dimensions for i, j, k, l in zip(a[0], a[1], b[0], b[1]): x = i == k and j == l # If this dimension matches exactly y = i == l or j == k # If one cube continues the other z = y and (c == 0) # If we are the first dimension to be continued if not x and not z: return False if y: # Increment the continued dimension count c += 1 return True
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from typing import List def get_function_contents_by_name(lines: List[str], name: str): """ Extracts a function from `lines` of segmented source code with the name `name`. Args: lines (`List[str]`): Source code of a script seperated by line. name (`str`): The name of the function to extract. Should be either `training_function` or `main` """ if name != "training_function" and name != "main": raise ValueError(f"Incorrect function name passed: {name}, choose either 'main' or 'training_function'") good_lines, found_start = [], False for line in lines: if not found_start and f"def {name}" in line: found_start = True good_lines.append(line) continue if found_start: if name == "training_function" and "def main" in line: return good_lines if name == "main" and "if __name__" in line: return good_lines good_lines.append(line)
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from functools import reduce from operator import add def determine_breadth(iterable): """ Determines the breadth of the addable contents of the iterable """ return reduce(add, iterable)
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def get_announcement(message, reminder_offset): """ Generates the announcement message :param str message: Message about the event :param number reminder_offset: Minutes in which event is about to happen """ pos = message.find(":") if pos == -1: activity = message.strip() message = f"{activity} in {reminder_offset} minutes." else: activity = message[pos + 1 :].strip() person = message[0:pos].strip() message = f"Hello {person}, you have {activity} in {reminder_offset} minutes." return message
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def get_concordance(text, keyword, idx, window): """ For a given keyword (and its position in an article), return the concordance of words (before and after) using a window. :param text: text :type text: string :param keyword: keyword :type keyword: str or unicode :param idx: keyword index (position) in list of article's words :type idx: int :window: number of words to the right and left :type: int :return: concordance :rtype: list(str or unicode) """ text_list= text.split() text_size = len(text_list) if idx >= window: start_idx = idx - window else: start_idx = 0 if idx + window >= text_size: end_idx = text_size else: end_idx = idx + window + 1 concordance_words = [] for word in text_list[start_idx:end_idx]: concordance_words.append(word) return concordance_words
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import json def retrieve(corpus_path, labels_path="", edges_path=""): """ Retrieve corpus and labels of a custom dataset given their path Parameters ---------- corpus_path : path of the corpus labels_path : path of the labels document Returns ------- result : dictionary with corpus and optionally labels of the corpus """ result = {} corpus = [] labels = [] with open(corpus_path) as file_input: for line in file_input: corpus.append(str(line)) result["corpus"] = corpus if len(labels_path) > 1: with open(labels_path) as file_input: for label in file_input: labels.append(json.loads(label)) result["doc_labels"] = labels if len(edges_path) > 1: doc_ids = {} tmp_edges = [] with open(edges_path) as file_input: for line in file_input: neighbours = str(line) neighbours = neighbours[2:len(neighbours)-3] doc_ids[neighbours.split()[0]] = True tmp_edges.append(neighbours) edges_list = [] for edges in tmp_edges: tmp_element = "" for edge in edges.split(): if edge in doc_ids: tmp_element = tmp_element + edge + " " edges_list.append(tmp_element[0:len(tmp_element)-1]) result["edges"] = edges_list return result
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def removesuffix(s: str, suffix:str) -> str: """Removes the suffix from s.""" if s.endswith(suffix): return s[:-len(suffix)] return s
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def remove_prepended_comment(orig_df): """ remove the '#' prepend to the first column name Note: if there is no comment, this won't do anything (idempotency). """ input_df = orig_df.copy() first_col = input_df.columns[0] return input_df.rename(columns={first_col: first_col.replace('#', "")})
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def get_ordinal_string(n): """ Return the ordinal representation of a positive integer (e.g. 1 -> "1st") Code by CTT @ http://stackoverflow.com/a/739301 """ if 10 <= n % 100 < 20: return str(n) + 'th' else: return str(n) + {1 : 'st', 2 : 'nd', 3 : 'rd'}.get(n % 10, "th")
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def _is_file_external(f): """Returns True if the given file is an external file.""" return f.owner.workspace_root != ""
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def nombre_joueurs_annee(annee,liste): """ Fonction qui en paramètre prend une année (int) et la liste des joueurs sous forme de liste de dictionnaires et qui retourne le nombre de joueurs ayant joués l'année donnée """ compteur = 0 for enreg in liste : if int(enreg['Année']) == annee: compteur += 1 return compteur
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def AuthorToJSON(author): """ Converts an Author object into a JSON-compatible dictionary. Returns None on failure. """ if not author: return None try: json_dict = { "type":"author", "id":author.url, "host":author.host, "displayName":author.username, "url":author.url, "github":author.github } return json_dict except: return None
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import requests def basic_auth_request(method, url, token=None, payload=None, params=None): """ make a request using basic authorization :param method: [GET, POST, PUT, DELETE ...] :param url: :param token: basic authentication token :param payload: post body :param params: Dictionary or bytes to be sent in the query string :return: """ request_kwargs = {} if token is not None: request_kwargs["headers"] = {"Authorization": "Basic {0}".format(token)} if payload is not None: request_kwargs["json"] = payload if params is not None: request_kwargs["params"] = params return requests.request(method, url, **request_kwargs)
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def probability_in_subspace(wavefunc: dict, subspace: list) -> float: """ Calculates the probability that the wavefunction 'wavefunc' lies in 'subspace' Note: This only works for subspaces aligned with the comp. basis. :param wavefunc: dict, contains complex amplitudes of the wavefunction in computational basis states :param subspace: list, list containing the computational basis vectors which span the subspace :return: float """ assert isinstance(wavefunc, dict), 'Please provide your state as a dict.' assert isinstance(subspace, list), 'Please provide subspace as a list of str.' # Deal with empty subspace: if not subspace: return 0 assert isinstance(subspace[0], str), 'Please provide subspace as a list of str.' assert len(wavefunc) >= len(subspace) subspace_prob = 0. # add up probabilities for all basisvectors in the subspace for basisvector in subspace: basisvector_prob = abs(wavefunc[basisvector]) ** 2 subspace_prob += basisvector_prob return subspace_prob
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def is_sublist(l1, l2, pos=False): """ Check if l1 is a sublist of l2 (it contains all elements from l1 in the same order). if pos is True, return position where sublist starts, not a boolean value """ if l1 == []: return 0 if pos else True elif l1 == l2: return 0 if pos else True elif len(l1) > len(l2): return -1 if pos else False for i in range(len(l2)): if l2[i] == l1[0]: n = 1 while (n < len(l1)) and (i + n < len(l2)) and (l2[i + n] == l1[n]): n += 1 if n == len(l1): return i if pos else True return -1 if pos else False
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import typing def asBool(key: str, value: typing.Union[str, bool, int]) -> bool: """ Coerce a key to boolean Parameters ---------- key : str Name of this setting. Used in error reporting value : string or bool or int Trivial for booleans. If integer, return the corresponding value **only** for values of ``1`` and ``0``. If a string, values of ``{"1", "yes", "y", "true"}`` denote True, values of ``{"0", "no", "n", "false"}`` denote False. Strings are case-insensitive Raises ------ TypeError If the conversion fails """ if isinstance(value, bool): return value elif isinstance(value, int): if value == 0: return False if value == 1: return True raise ValueError( f"Could not coerce {key}={value} to boolean. Integers " "must be zero or one" ) elif isinstance(value, str): if value.lower() in {"1", "yes", "y", "true"}: return True if value.lower() in {"0", "no", "n", "false"}: return False raise ValueError( f"Could not coerce {key}={value} to boolean. Strings must be " "0 1 y n yes no true false" ) raise TypeError(f"Could not coerce {key}={value} to boolean")
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def _NormalizePath(path): """Returns the normalized path of the given one. Normalization include: * Convert '\\' to '/' * Convert '\\\\' to '/' * Resolve '../' and './' Example: '..\\a/../b/./c/test.cc' --> 'b/c/test.cc' """ path = path.replace('\\', '/') path = path.replace('//', '/') filtered_parts = [] for part in path.split('/'): if part == '..': if filtered_parts: filtered_parts.pop() elif part == '.': continue else: filtered_parts.append(part) return '/'.join(filtered_parts)
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def _softmax_output_grad(ans, x, y): """Gradient function for softmax output.""" def grad(_0): #pylint: disable= missing-docstring N = x.shape[0] return (ans - y) / N return grad
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def gst_value_from_inclusive(amount, gst_rate): """Calculate GST component from a GST inclusive total. GST amount calculated as amount - (1 + gst_rate)). Args: amount (float): GST inclusive amount gst_rate (float): GST rate to apply. Returns: gst_component (float): Calculated GST component. """ return amount - (amount / (1 + gst_rate))
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import pytz def compare_dates(date_a, date_b): """ Compares two dates with offset-aware format. Args: date_a: The first date to compare date_b: The second date to compare Returns: - if the date_b is greater than date_a = =1 - if the date_a is greater than date_b = 1 - otherwise = 0 """ try: date_a_offset_aware = pytz.UTC.localize(date_a) except ValueError: date_a_offset_aware = date_a try: date_b_offset_aware = pytz.UTC.localize(date_b) except ValueError: date_b_offset_aware = date_b if date_a_offset_aware > date_b_offset_aware: return 1 elif date_b_offset_aware > date_a_offset_aware: return -1 else: return 0
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def read_msr_line(line, tstat_switch, msr_id_switch): """ Function to read msr components from a single line in adj file :param line: Msr line in adj file :param tstat_switch: True/False switch for presence of tstats :param msr_id_switch: True/False switch for presence of msr_ids :return: Dictionary of components """ msr_type = line[:1] stn1 = line[2:22].strip() stn2 = line[22:42].strip() if stn2 == '': stn2 = None stn3 = line[42:62].strip() if stn3 == '': stn3 = None if msr_type == 'D': if msr_id_switch: items = line.split() cluster_id = items[-1].strip() msr_id = items[-2] else: msr_id = None cluster_id = None msr_components = { 'msr_type': msr_type, 'stn1': stn1, 'stn2': stn2, 'stn3': stn3, 'msr_id': msr_id, 'cluster_id': cluster_id } return msr_components else: if line[62:65].strip() == '*': ignore = True else: ignore = False cardinal = line[65:67].strip() msr = line[67:86].strip() adj = line[86:105].strip() cor = line[105:117].strip() msr_sd = line[117:130].strip() adj_sd = line[130:143].strip() cor_sd = line[143:156].strip() nstat = line[156:167].strip() if tstat_switch: tstat = line[167:178].strip() pelzer = line[178:190].strip() pre_adj_cor = line[190:204].strip() outlier = line[204:216] if msr_id_switch: msr_id = line[216:226].strip() cluster_id = line[226:236].strip() else: msr_id = None cluster_id = None else: tstat = None pelzer = line[167:178].strip() pre_adj_cor = line[180:193].strip() outlier = line[204:205] if msr_id_switch: msr_id = line[205:216].strip() cluster_id = line[216:226].strip() else: msr_id = None cluster_id = None msr_components = { 'msr_type': msr_type, 'stn1': stn1, 'stn2': stn2, 'stn3': stn3, 'ignore': ignore, 'cardinal': cardinal, 'msr': msr, 'adj': adj, 'cor': cor, 'msr_sd': msr_sd, 'adj_sd': adj_sd, 'cor_sd': cor_sd, 'nstat': nstat, 'tstat': tstat, 'pelzer': pelzer, 'pre_adj_cor': pre_adj_cor, 'outlier': outlier, 'msr_id': msr_id, 'cluster_id': cluster_id } return msr_components
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def PrintSourceMatrix(S,params): """Auxiliary function to print the source matrix (S)""" dim = params["dim"] # Spatial dimensions print("The source term matrix is:\n") for i in range (0,dim+2): for j in range (0,dim+2): print("S[",i,",",j,"]=",S[i,j],"\n") return 0
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def get_special_tokens(vocab_size): """Gets the ids of the four special tokens. The four special tokens are: pad: padding token oov: out of vocabulary bos: begin of sentence eos: end of sentence Args: vocab_size: The vocabulary size. Returns: The four-tuple (pad, oov, bos, eos). """ pad = 0 oov = vocab_size + 1 bos = vocab_size + 2 eos = vocab_size + 3 return pad, oov, bos, eos
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def calculate_tcp_checksum(message): """ Calculate the TCP checksum @param message: payload + TCP headers + pseudoheader @return: 16-bit TCP checksum value """ cs = 0 for i in range(0, len(message), 2): w = (ord(message[i])<<8 + ord(message[i+1])) cs = cs + w cs = (cs>>16) + (cs & 0xffff) cs = ~cs & 0xffff return cs
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import time def ControlRate(t_last_call, max_rate): """ Limits rate at which this function is called by sleeping. Returns the time of invocation. """ p = 1.0 / max_rate t_current = time.time() dt = t_current - t_last_call if dt < p: time.sleep(p - dt) return t_current
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import itertools def GetLatencyEvents(process, timeline_range): """Get LatencyInfo trace events from the process's trace buffer that are within the timeline_range. Input events dump their LatencyInfo into trace buffer as async trace event of name starting with "InputLatency". Non-input events with name starting with "Latency". The trace event has a member 'data' containing its latency history. """ latency_events = [] if not process: return latency_events for event in itertools.chain( process.IterAllAsyncSlicesStartsWithName('InputLatency'), process.IterAllAsyncSlicesStartsWithName('Latency')): if event.start >= timeline_range.min and event.end <= timeline_range.max: for ss in event.sub_slices: if 'data' in ss.args: latency_events.append(ss) return latency_events
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def splitlines(text): """Split text into lines.""" return text.splitlines()
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from typing import List def format_row(columns: List[str], widths: List[int]) -> str: """Format one row of the table. This may go into multiple lines if any of the columns were wrapped.""" row = "" had_values = True lineno = 0 while had_values: had_values = False line = "" for (i, c) in enumerate(columns): collines = c.split("\n") if len(collines) > lineno: had_values = True line += "| " + collines[lineno] + " " else: line += "|" + " " * (2 + widths[i]) if had_values: row += line + "|\n" lineno += 1 return row[0:-1]
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import ast def _combine_side_inputs(side_input_shapes='', side_input_types='', side_input_names=''): """Zips the side inputs together. Args: side_input_shapes: forward-slash-separated list of comma-separated lists describing input shapes. side_input_types: comma-separated list of the types of the inputs. side_input_names: comma-separated list of the names of the inputs. Returns: a zipped list of side input tuples. """ side_input_shapes = [ ast.literal_eval('[' + x + ']') for x in side_input_shapes.split('/') ] side_input_types = eval('[' + side_input_types + ']') # pylint: disable=eval-used side_input_names = side_input_names.split(',') return zip(side_input_shapes, side_input_types, side_input_names)
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def dict_sample_list(a_dict, n_sample = 4): """Sample dictionary data using even spacing - returns a list for printing""" data_len = len(a_dict) header = ['Printing {} entries evenly sampled from {} combinations:\n'.format(n_sample, data_len)] return header + ['** {} ** \n{}'.format(k,repr(a_dict[k])) for k in list(a_dict.keys())[1:-1:data_len // n_sample]]
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def _bbox(pts): """Find the AABB bounding box for a set of points""" x, y = pts[0] ax, ay, bx, by = x, y, x, y for i in range(1, len(pts)): x, y = pts[i] ax = x if x < ax else ax ay = y if y < ay else ay bx = x if x > bx else bx by = y if y > by else by return ax, ay, bx, by
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def get_x(path, width): """Gets the x value from the image filename""" return (float(int(path.split("_")[1])) - width/2) / (width/2)
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def hasCycle(head): """ Use two pointers(one slow, one fast) to traverse the list. Two pointers are bound to meet if there is a cycle; otherwise, fast pointer will reach the end eventually. """ slow = head fast = head while fast and fast.next: # note the condition slow = slow.next fast = fast.next.next if slow == fast: return True return False
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import string import random def generate_identifier(size = 16, chars = string.ascii_uppercase + string.digits): """ Generates a random identifier (may be used as password) with the provided constrains of length and character ranges. This function may be used in the generation of random based keys for both passwords and api keys. @type size: int @param size: The size (in number of characters) to be used in the generation of the random identifier. @type chars: List @param chars: The list containing the characters to be used in the generation of the random identifier. @rtype: String @return: The randomly generated identifier obeying to the provided constrains. """ return "".join(random.choice(chars) for _index in range(size))
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import re def tokenize(text): """Tokenize the text (i.e., insert spaces around all tokens)""" toks = re.sub(r'([?.!;,:-]+)(?![0-9])', r' \1 ', text) # enforce space around all punct # most common contractions toks = re.sub(r'([\'’´])(s|m|d|ll|re|ve)\s', r' \1\2 ', toks) # I'm, I've etc. toks = re.sub(r'(n[\'’´]t\s)', r' \1 ', toks) # do n't # other contractions, as implemented in Treex toks = re.sub(r' ([Cc])annot\s', r' \1an not ', toks) toks = re.sub(r' ([Dd])\'ye\s', r' \1\' ye ', toks) toks = re.sub(r' ([Gg])imme\s', r' \1im me ', toks) toks = re.sub(r' ([Gg])onna\s', r' \1on na ', toks) toks = re.sub(r' ([Gg])otta\s', r' \1ot ta ', toks) toks = re.sub(r' ([Ll])emme\s', r' \1em me ', toks) toks = re.sub(r' ([Mm])ore\'n\s', r' \1ore \'n ', toks) toks = re.sub(r' \'([Tt])is\s', r' \'\1 is ', toks) toks = re.sub(r' \'([Tt])was\s', r' \'\1 was ', toks) toks = re.sub(r' ([Ww])anna\s', r' \1an na ', toks) # clean extra space toks = re.sub(r'\s+', ' ', toks) return toks
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def truncate(s, amount) -> str: """Return a string that is no longer than the amount specified.""" if len(s) > amount: return s[:amount - 3] + "..." return s
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def parse_strling_info_for_locus(strling_genotype_df, locus_chrom, locus_start, locus_end, margin=700): """Extract info related to a specific locus from the STRling genotype table. See https://strling.readthedocs.io/en/latest/outputs.html for more details. Args: strling_genotype_df (pd.DataFrame): parsed STRling genotype table locus_chrom (str): locus chromosome locus_start (int): locus start coord locus_end (int): locus end coord margin (int): when looking for matching STRling results, include calls this many base pairs away from the locus. This should be approximately the fragment-length or slightly larger (700 is a reasonable value for Illumina short read data). """ locus_chrom = locus_chrom.replace("chr", "") strling_results_for_locus = strling_genotype_df[ (strling_genotype_df.chrom.str.replace("chr", "") == locus_chrom) & (strling_genotype_df.start_1based < locus_end + margin) & (strling_genotype_df.end_1based > locus_start - margin) ] """ Example row: {'allele1_est': 0.0, 'allele2_est': 22.09, 'anchored_reads': 8, 'chrom': 'chr4', 'depth': 32.0, 'expected_spanning_pairs': 57.83, 'left': 39348477, 'left_clips': 5, 'repeatunit': 'AAGGG', 'right': 39348477, 'right_clips': 0, 'spanning_pairs': 0, 'spanning_pairs_pctl': 0.0, 'spanning_reads': 0, 'sum_str_counts': 265, 'unplaced_pairs': 0} """ return [row.to_dict() for _, row in strling_results_for_locus.iterrows()]
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import random def random_choice(sequence): """Return a random element from the non-empty sequence.""" return random.SystemRandom().choice(sequence)
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def __slice_scov__(cov, dep, given): """ Slices a covariance matrix keeping only the covariances between the variables indicated by the array of indices of the independent variables. :param cov: Covariance matrix. :param dep: Index of dependent variable. :param given: Array of indices of independent variables. :return: A |given| x |given| matrix of covariance. """ row_selector = [x for x in range(cov.shape[0]) if x in given and x != dep] col_selector = [x for x in range(cov.shape[1]) if x in given and x != dep] v = cov[row_selector, :] v = v[:, col_selector] return v
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def drawBorder(grid: list) -> list: """Draw a border around the maze""" for i, x in enumerate(grid): # Left and Right border x[0] = x[len(grid)-1] = (20,20,20) grid[i] = x grid[0] = grid[len(grid)-1] = [(20,20,20) for x in range(len(grid))] # Top and Bottom border return grid
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def iterkeys(obj, **kwargs): """Iterate over dict keys in Python 2 & 3.""" return (obj.iterkeys(**kwargs) if hasattr(obj, 'iterkeys') else iter(obj.keys(**kwargs)))
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def join_string_lists(**kwargs) -> dict: """Convert named lists of strings to one dict with comma-separated strings. :param kwargs: Lists of strings :return: Converted dict. Example: >>> join_string_lists(foo=["a", "b", "c"], bar=["a", "b"], foobar=None) {"foo": "a,b,c", "bar": "a,b"} """ return {k: ",".join(v) for k, v in kwargs.items() if v}
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def num2char(numpair, key): """Takes in a numpair like '34', and returns the character in row 3 (actually 4th row) and column 4 (actually 5th column) of the key""" row_num = int(numpair[0]) column_num = int(numpair[1]) return(key[row_num][column_num])
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def closest_number(val, num_list): """ Return closest element to val in num_list. Parameters ---------- val: integer, float, value to find closest element from num_list. num_list: list, list from which to find the closest element. Returns ------- A element of num_list. """ return min(num_list, key=lambda x: abs(x-val))
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def nid(x): """Return the address of an array data, used to check whether two arrays refer to the same data in memory.""" return x.__array_interface__['data'][0]
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def build_file_list(path): """ Build a list a list of files (and directories) by iterating recursively over the given path :param path: The path to iterate over :type path: pathlib.Path :return: A tuple of directories and files :rtype: tuple(list, list) """ dirs = [] files = [] for x in path.iterdir(): try: if x.is_symlink(): continue elif x.is_dir(): dirs.append(x) new_dirs, new_files = build_file_list(x) dirs.extend(new_dirs) files.extend(new_files) elif x.is_file(): files.append(x) except PermissionError: continue return dirs, files
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def get_timeout(run_type): """Get timeout for a each run type - daily, hourly etc :param run_type: Run type :type run_type: str :return: Number of seconds the tool allowed to wait until other instances finish :rtype: int """ timeouts = { 'hourly': 3600 / 2, 'daily': 24 * 3600 / 2, 'weekly': 7 * 24 * 3600 / 2, 'monthly': 30 * 24 * 3600 / 2, 'yearly': 365 * 24 * 3600 / 2 } return timeouts[run_type]
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def default_key(rarity: float) -> float: """The default function that converts rarity to drop rate (1/x) Parameters ---------- rarity : float the rarity of the item Returns ------- float the drop rate of the item """ return 1 / rarity
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import pkg_resources import yaml def get_metadata(package_name): """ Return runner related metadata for the provided runner package name. :rtype: ``list`` of ``dict`` """ file_path = pkg_resources.resource_filename(package_name, 'runner.yaml') with open(file_path, 'r') as fp: content = fp.read() metadata = yaml.safe_load(content) return metadata
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import json def jsonifyer(someDict): """Provides standardization of pretty json Args: someDict (dict): Any JSON compatible dictionary Returns: JSON string """ return json.dumps(someDict, sort_keys=True, indent=4, separators=(',', ': '))
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def not_equal(x, y): """Element-wise `(x != y)`.""" return x != y
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def _build_technical_detail( target: str, header: str, method: str, uri: str, param: str, attack: str, evidence: str) -> str: """Build the technical detail markdown content.""" return f"""{header} * Target: {target} ```http {method} {uri} {param} {attack} {evidence} ``` """
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def getallis(l,match): """ get all indices of match pattern in list """ return [i for i, x in enumerate(l) if x == match]
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def move_bounding_rect(rect, delta_x, delta_y): """ Move bounding rect x,y by some delta_x, delta_y . """ x, y, w, h = rect return (x+delta_x, y+delta_y, w, h)
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def hits_to_dict(hits_df): """ Given a hits_df, return a dict of sample id -> list of hits """ sample_to_clones = {} for sample, sub_hits_df in hits_df.groupby("sample_id"): sample_to_clones[sample] = sub_hits_df[ ["clone1", "clone2"] ].stack().unique() return sample_to_clones
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def count(lbls, wntarget): """ Count the number of line transitions with wavenumber smaller than wntarget. Parameters ---------- lbls: List of lbl objects wntarget: Float The target wavenumber. Returns ------- nwave: Integer The number of transitions with wavenumber smaller than wntarget. """ nwave = 0 for lbl in lbls: nwave += lbl.bs(wntarget, 0, lbl.nlines-1) return nwave
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import random def init_centroids(data:list, k): """ Can be intialiazed in several ways. One of them is picking K random samples from the data :param data: :return: """ return random.sample(data, k)
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def doc_to_text(doc, sent_delim='\n'): """ Convert document object to original text represention. Assumes parser offsets map to original document offsets :param doc: :param sent_delim: :return: """ text = [] for sent in doc.sentences: offsets = map(int, sent.stable_id.split(":")[-2:]) char_start, char_end = offsets text.append({"text": sent.text, "char_start": char_start, "char_end": char_end}) s = "" for i in range(len(text) - 1): gap = text[i + 1]['char_start'] - text[i]['char_end'] s += text[i]['text'] + (sent_delim * gap) return s
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def middle_truncate(value, size): """ Truncates a string to the given size placing the ellipsis in the middle. """ size = int(size) if len(value) > size: if size > 3: start = (size - 3) / 2 end = (size - 3) - start return value[:start] + u'\u2026' + value[-end:] else: return value[:size] + u'\u2026' else: return value
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def get_doc_str(fun): """Get the doc string for a function and return a default if none is found.""" if fun.__doc__: return '\n'.join([line.strip() for line in fun.__doc__.split('\n')]) else: return 'No documentation provided for %s()' % fun.__name__
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def is_feature_extractor_model(model_config): """ If the model is a feature extractor model: - evaluation model is on - trunk is frozen - number of features specified for features extraction > 0 """ return ( model_config.FEATURE_EVAL_SETTINGS.EVAL_MODE_ON and ( model_config.FEATURE_EVAL_SETTINGS.FREEZE_TRUNK_ONLY or model_config.FEATURE_EVAL_SETTINGS.FREEZE_TRUNK_AND_HEAD ) and len(model_config.FEATURE_EVAL_SETTINGS.LINEAR_EVAL_FEAT_POOL_OPS_MAP) > 0 )
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import ntpath import posixpath def to_posix(path): """ Return a path using the posix path separator given a path that may contain posix or windows separators, converting "\\" to "/". NB: this path will still be valid in the windows explorer (except for a UNC or share name). It will be a valid path everywhere in Python. It will not be valid for windows command line operations. """ return path.replace(ntpath.sep, posixpath.sep)
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def append_form_control(value): """A filter for adding bootstrap classes to form fields.""" return value.replace( '<input', '<input class="form-control"' ).replace( '<textarea', '<textarea class="form-control"' ).replace( '<select', '<select class="form-control"' )
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def prefixed(strlist, prefix): """ Filter a list to values starting with the prefix string :param strlist: a list of strings :param prefix: str :return: a subset of the original list to values only beginning with the prefix string """ return [g for g in strlist if str(g).startswith(prefix)]
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def zone_origin(zone_object): """ Return coordinates of a zone Args: zone_object (EpBunch): zone element in zone list Returns: Coordinates [X, Y, Z] of the zone in a list """ return [zone_object.X_Origin, zone_object.Y_Origin, zone_object.Z_Origin]
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def to_string(obj, last_comma=False): """Convert to string in one line. Args: obj(list, tuple or dict): a list, tuple or dict to convert. last_comma(bool): add a comma at last. Returns: (str) string. Example: >>> to_string([1, 2, 3, 4], last_comma=True) >>> # 1, 2, 3, 4, >>> to_string({'a': 2,'b': 4}) >>> # a=2, b=4 """ s = '' if type(obj) == list or type(obj) == tuple: for i, data in enumerate(obj): s += str(data) if last_comma or i != len(obj)-1: s += ', ' elif type(obj) == dict: for i, data in enumerate(obj.items()): k, v = data s += '%s=%s' % (str(k), str(v)) if last_comma or i != len(obj)-1: s += ', ' else: s = str(obj) return s
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def find_inner(obj, find_key): """ Recursively search through the data structure to find objects keyed by find_key. """ results = [] if not hasattr(obj, "__iter__"): # not a sequence type - return nothing # this excludes strings return results if isinstance(obj, dict): # a dict - check each key for key, prop in obj.items(): if key == find_key: results.extend(prop) elif isinstance(prop, dict): results.extend(find_inner(prop, find_key)) elif isinstance(obj, list): # a list / tuple - check each item for i in obj: results.extend(find_inner(i, find_key)) return results
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def split_lindblad_paramtype(typ): """ Splits a Lindblad-gate parameteriation type into a base-type (e.g. "H+S") and an evolution-type string. Parameters ---------- typ : str The parameterization type, e.g. "H+S terms". Returns ------- base_type : str The "base-parameterization" part of `typ`. evotype : str The evolution type corresponding to `typ`. """ bTyp = typ.split()[0] # "base" type evostr = " ".join(typ.split()[1:]) if evostr == "": evotype = "densitymx" elif evostr == "terms": evotype = "svterm" elif evostr == "clifford terms": evotype = "cterm" else: raise ValueError("Unrecognized evotype in `typ`=%s" % typ) return bTyp, evotype
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def clean_side_panel(sidepanel): """ Cleans the SidePanel data and stores it in a dict. Parameter: sidepanel: html-sidepanel extracted using bs4 Returns: data: dict of extracted data """ data = dict() for x in sidepanel: x = x.text.strip().replace('\n', '') index = x.find(':') if index == -1: continue y, x = x[:index], x[index+1:].strip() data[y] = x return data
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import itertools def normalize_padding(padding, rank): """ normalized format of padding should have length equal to rank+2 And the order should follow the order of dimension ex. Conv2d (rank=2) it's normalized format length:2+2 ==>(left, right,top bottom) Args: padding (None, int, tuple): rank (int): Returns: the normalized format of padding Examples: >>> normalize_padding(((1,0),(1,0)),2) (1, 0, 1, 0) >>> normalize_padding((1,0),2) (0, 0, 1, 1) """ if padding is None: padding = (0,) * (2 * rank) elif isinstance(padding, int): padding = (padding,) * (2 * rank) elif isinstance(padding, (list, tuple)) and len(padding) == 1: padding = padding * (2 * rank) elif isinstance(padding, (list, tuple)) and len(padding) == rank and isinstance(padding[0], int): # rank=2 (1,1)=>(1,1,1,1) (1,0)=>(0,0,1,1) reversed_padding = list(padding) reversed_padding.reverse() return_padding = [] for i in range(rank): return_padding.append(reversed_padding[i]) return_padding.append(reversed_padding[i]) padding = tuple(return_padding) elif isinstance(padding, (list, tuple)) and len(padding) == rank and isinstance(padding[0], (list, tuple)): # rank=2 ((1,0),(1,0)=>(1,0,1,0) padding = tuple(list(itertools.chain(*list(padding)))) elif isinstance(padding, (list, tuple)) and len(padding) == 2 * rank and isinstance(padding[0], int): padding = padding return padding
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def null_input_op_fn(x): """This function does no transformation on the inputs, used as default.""" return x
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import math def float_iszero(distance: float, threshold: float = 1e-05) -> bool: """ Computes if a distance is close to zero modulo an epsilon. :param distance: distance to evaluate :param threshold: the epsilon value :return: true or false if the condition is met """ return math.isclose(distance, 0.0, rel_tol=threshold, abs_tol=threshold)
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def get_main_domain_name(url_str) -> str: """get url domain texts Args: url_str (str): url string Returns: str: domain name of url """ domain_name = url_str.split("/")[2] main_domain_name = domain_name.split(".")[-2] return main_domain_name
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def get_flights_sorted_price(flights, reverse=False): """Return a list of flights sorted by price. Args: flights (list): list of flights, each flight is represented by a dictionary. reverse (bool, optional): defines the sorting order, by default to False - ascending, if True sort in descending order. Returns: list: a list of flights sorted by price. """ return sorted( flights, key=lambda flight: float(flight['Price']['TicketPrice']), reverse=reverse, )
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def remove_non_ascii(text: str) -> str: """ Removes non ascii characters :param text: Text to be cleaned :return: Clean text """ return ''.join(char for char in text if ord(char) < 128)
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def get_allowed_tokens_from_config(config, module='main'): """Return a list of allowed auth tokens from the application config""" env_variable_name = "" if module == "main": env_variable_name = 'DM_ANTIVIRUS_API_AUTH_TOKENS' elif module == 'callbacks': # though SNS uses the "Basic" auth scheme, we can treat the payload section of the header as a single opaque # token set in DM_ANTIVIRUS_API_CALLBACK_AUTH_TOKENS like any normal "Bearer" tokens. env_variable_name = 'DM_ANTIVIRUS_API_CALLBACK_AUTH_TOKENS' return [token for token in config.get(env_variable_name, '').split(':') if token]
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import torch def load_checkpoint(checkpoint_file, model, model_opt): """ Loads a checkpoint including model state and running loss for continued training """ if checkpoint_file is not None: checkpoint = torch.load(checkpoint_file) state_dict = checkpoint["state_dict"] start_iter = checkpoint['iter'] running_loss = checkpoint['running_loss'] opt_state_dict = checkpoint['optimizer'] model_opt.load_state_dict(opt_state_dict) for state in model_opt.state.values(): for key, value in state.items(): if isinstance(value, torch.Tensor): state[key] = value.cuda() model.load_state_dict(state_dict) else: start_iter = 1 running_loss = 0 return start_iter, running_loss
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def new_session(graph, expire_on_commit=False): """ Create a new session. """ return graph.sessionmaker(expire_on_commit=expire_on_commit)
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def unique_column_name(df, name): """ Generate a column name that is not already present in the dataframe. """ i = 1 newname = name while newname in list(df): i += 1 newname = '%s_%d' % (name, i) return newname
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import typing def is_unpackable(obj: typing.Any): """ Checks if the given object is unpackable or not (if you can use **obj or not) """ return all(hasattr(obj, attr) for attr in ('keys', '__getitem__'))
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def replace_user_in_file_path(file_name, user): """Replace user name in give file path Args: file_name (str): Path to file user (str): New user to replace with Returns: str: New file path """ file_items = [x.strip() for x in file_name.strip().split('/') if len(x.strip())] file_items[1] = user return "/" + '/'.join(file_items).strip()
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def dictget(d, l): """ Lookup item in nested dict using a list of keys, or None if non-existent d: nested dict l: list of keys, or None """ try: dl0 = d[l[0]] except (KeyError, TypeError): return None if len(l) == 1: return dl0 return dictget(dl0, l[1:])
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def y_intersection(line_slope, intercept, x_value): """ Finds the y value of the line (y = mx + b) at point x and returns the point This basically solves y = mx + b :param line_slope: slope of the line (m) :param intercept: the intercept of the line (b) :param x_value: the value to be used (substituted with x) :return: the y value """ return x_value, line_slope * x_value + intercept
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def jaccard_distance(label1, label2): """Jaccard distance metric""" union_len = len(label1 | label2) intersection_len = len(label1 & label2) return (union_len - intersection_len) / float(union_len)
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def create_id(fname: str, lname: str) -> str: """Create a player ID from a first name and last name. String format: <first 5 characters of last name><first 2 characters of first name><01> The last two integer digits allow for the prevention of ID conflicts. To increment by an integer n, use add_n(player_id, n) NOTE: spaces, periods, and apostrophes are omitted """ fname = fname.lower() # remove spaces, periods, and apostrophes lname = lname.lower().replace(" ", "").replace(".", "").replace("'", "") if len(lname) > 5: lname = lname[0:5] if len(fname) > 2: fname = fname[0:2] return "{}{}01".format(lname, fname)
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