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import csv def get_ycoordinates(filename): """Transforms CSV file of Y coordinates (new line seperated) to list""" with open(filename) as o: y = [float(item) for sublist in csv.reader(o) for item in sublist] return y
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def node_weight(G, u): """ Computes the weighted degree of a node :param G: networkx.Graph Graph containing the node u :param u: node Node of which the degree will be computed :return: w: double Degree of u """ w = 0 for v in G[u].keys(): w = w + G[u][v]['weight'] return w
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def compare_balance_with_zero(balance): """ :param balance: a double with the value of the balance in after a year. :return: 0 if the balance is equal to zero or nearly equal, 1 if the balance is greater than zero and -1 if the balance is lower than zero. """ if 0.05 >= balance >= -0.05: return 0 elif balance > 0.05: return 1 else: return -1
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def get_subseq(df, perc_start, perc_end): """Get a subsequence from a dataframe Args: df (pd.DataFrame): Pandas DataFrame perc_start (int): Starting percentage of the subsequence perc_end (int): Ending percentage of the subsequence Returns: subseq (pd.DataFrame): The requested subsequence """ start = int(len(df) * perc_start/100) end = int(len(df) * perc_end/100) df = df.iloc[start:end] return df
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import math def line_angle(p1, p2): """ Return the angle of the line that goes from p1 to p2 Clockwise in pygame window Counter clockwise in xy-space """ angle = math.atan2((p1[1]-p2[1]), (p1[0]-p2[0])) * 180.0/math.pi return (angle + 360) % 360
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def create_profile_name_from_role_arn( role_arn, account_alias, profile_name_format ): """Create a profile name for a give role ARN and account alias.""" profile_name = role_arn.split("role/")[-1].replace("/", "-") if profile_name_format == "RoleName-AccountAlias": return f"{profile_name}-{account_alias}" return profile_name
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def GetPDBAtomNames(mol): """Extracts PDB atoms names""" names = {} for i, atom in enumerate(mol.GetAtoms()): name = atom.GetPDBResidueInfo().GetName() names[name.strip()] = i return names
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def splitParents(parents): """Splits the input string into at most 3 parts: - father's first name - mother's first name - mother's last name. The input is in the format: "{father_first_name},{mother_first_name} {mother_last_name}" """ split = parents.split(',', 1) if len(split) == 1: father = '' mother = parents else: father = split[0].strip() mother = split[1].strip() motherSplit = mother.rsplit(' ', 1) if not father: return motherSplit return [father] + motherSplit
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def _merge_tables(d1, d2): """ Merge dictionaries Args: d1 (dict): first dict to merge d2 (dict): second dict to merge """ for key, l in d2.items(): if key in d1: for item in l: if item not in d1[key]: d1[key].append(item) else: d1[key] = l return d1
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def unpad(data, length): """ PKCS #7-style unpadding with the given block length """ assert length < 256 assert length > 0 padlen = ord(data[-1]) assert padlen <= length assert padlen > 0 assert data[-padlen:] == padlen * chr(padlen) return data[:-padlen]
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import torch def dis_primal( input_view: torch.Tensor, param: torch.Tensor, n_sample: int, ) -> torch.Tensor: """Computes distortion penalty for the primal formulation. Let n be the number of samples in the view of interest and p the number of features. In the primal formulation, the 'param' matrix is the p*low_dim model parameter and input_view corresponds to the input data, of shape n*p. The distortion penalty can be written as distortion = ||input_view*input_view.T - input_view*param*param.T*input_view.T||_2. The distortion is computed as is when n < p. However, if n > p, we compute the following formulation: distortion = torch.sqrt(Tr((I - param*param.T)*input_view.T*input_view *(I - param*param.T)*input_view.T*input_view)) to avoid computing terms that are O(n**2) in memory or runtime. Arguments: input_view: torch.Tensor, one of the two views. param: torch.Tensor, model parameters. n_sample: int, sample size of entire dataset. Returns: distortion_value: torch.Tensor, scalar value. """ n_sample, p_feature = input_view.shape if n_sample < p_feature: inner_prod = torch.matmul(input_view, input_view.t()) tmp = torch.matmul(torch.matmul( torch.matmul(input_view, param), param.t()), input_view.t()) tmp = (inner_prod - tmp)**2 distortion_value = torch.sqrt(torch.sum(tmp)) else: gram = torch.matmul(input_view.t(), input_view) tmp = torch.matmul(param, torch.matmul(param.t(), gram)) prod = gram - tmp distortion_value = torch.sqrt(torch.trace(torch.matmul(prod, prod))) return distortion_value
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def fill_dict (feed_dict, placeholders, data): """Feeds a dictionary of data into a dictionary of placeholders.""" for k in data: feed_dict[placeholders[k]] = data[k] return feed_dict
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def compare_dates(converted_creation_date, rotation_date): """ Compares createTime date to x (default 90) days ago. Args: converted_creation_date - The datatime formatted creation date of our API key. rotation_date - datetime formatted "rotation_period" days ago (default 90). Example: 2020-09-18 13:38:52.943663 """ # If the createTime value for our key # is over x days (default 90) # Return true to key_analysis function if converted_creation_date < rotation_date: return True else: return False
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def _deg_ord_idx(deg, order): """Get the index into S_in or S_out given a degree and order.""" # The -1 here is because we typically exclude the degree=0 term return deg * deg + deg + order - 1
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def linkify_phone(value): """ Render a telephone number as a hyperlink. """ if value is None: return None return f"tel:{value}"
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def _convert_unit(size_string): """ Convert given string to size in megabytes :param string size_string: Size with unit :returns integer: Converted size from given unit :rtype integer: """ size, unit = size_string.split(' ') if 'M' in unit: return int(float(size)) elif 'G' in unit: return int(float(size)) * 1024 elif 'T' in unit: return int(float(size)) * 1024 * 1024
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import pathlib def find_component(path: pathlib.PurePath): """ Extracts the likely component name of a CSV file based on the path to it :param path: path to a CSV file :return: likely component to use """ # pylint: disable=no-else-return if path.parent.name.isnumeric(): # Probably a version directory return path.parents[1].name else: return path.parent.name
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from typing import List def create_cave(depth: int, tx: int, ty: int) -> List[List[int]]: """ Creates the cave according to the cave generation rules. Since the cave is essentially infinite a constant size padding is applied around the target coordinates to make the pathfinding feasible. Note that there needs to be a padding because the optimal path can overshoot the target. The padding size for this input was found simply by starting with a very large value and progressively decreasing it until a value small enough was found which produces the correct pathfinding result but is still relatively quick to compute. """ PADDING = 50 cave = [[0] * (tx + PADDING) for _ in range(ty + PADDING)] for y in range(ty + PADDING): for x in range(tx + PADDING): index = None if y == 0 and x == 0: index = 0 elif y == 0: index = x * 16807 elif x == 0: index = y * 48271 elif y == ty and x == tx: index = 0 if index is None: cave[y][x] = (cave[y-1][x] * cave[y][x-1] + depth) % 20183 else: cave[y][x] = (index + depth) % 20183 return cave
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import logging def logging_setup(logging_handler, logging_level) -> logging.Logger: """ Init logger object for logging in rubrik-sdk For more info - https://docs.python.org/3/library/logging.html Args: logging_level(int): Log level logging_handler (Handler): Handler to log Returns: logging.Logger: logger object """ logger = logging.getLogger('rubrik-sdk') logger.setLevel(logging_level) logger.addHandler(logging_handler) return logger
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import re def extract_template(pattern): """Extracts a 'template' of a url pattern given a pattern returns a string Example: input: '^home/city (-(?P<city_name>bristol|bath|cardiff|swindon|oxford|reading))?$' output: 'home/city(-{})?' """ pattern = pattern.strip('$^') pattern = re.sub(r'\(\?P.+?\)', '{}', pattern) return pattern
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def add_a_half(rectangle): """Adds 0.5 to a rectangle (2x2 coordinates)""" return [(x + 0.5, y + 0.5) for x, y in rectangle]
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from pydantic import BaseModel # noqa: E0611 def is_base_model_type(type_): """ Whether ``type_`` is a subclass of ``BaseModel``. """ if not isinstance(type_, type): return False return issubclass(type_, BaseModel)
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def extract_2d_info(img_meta, tensor): """Extract image augmentation information from img_meta. Args: img_meta(dict): Meta info regarding data transformation. tensor(torch.Tensor): Input tensor used to create new ones. Returns: (int, int, int, int, torch.Tensor, bool, torch.Tensor): The extracted information. """ img_shape = img_meta['img_shape'] ori_shape = img_meta['ori_shape'] img_h, img_w, _ = img_shape ori_h, ori_w, _ = ori_shape img_scale_factor = ( tensor.new_tensor(img_meta['scale_factor'][:2]) if 'scale_factor' in img_meta else tensor.new_tensor([1.0, 1.0])) img_flip = img_meta['flip'] if 'flip' in img_meta else False img_crop_offset = ( tensor.new_tensor(img_meta['img_crop_offset']) if 'img_crop_offset' in img_meta else tensor.new_tensor([0.0, 0.0])) return (img_h, img_w, ori_h, ori_w, img_scale_factor, img_flip, img_crop_offset)
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import math import random def train_test(data, val_ratio=0.2, test_ratio=0.2, shuffle=True, seed=42): """Split a list into training and test sets, with specified ratio. By default, the data is shuffled with a fixed random seed. The data is not mutated. :param data: list of data objects :param val_ratio: ratio of data to take for validation set :param test_ratio: ratio of data to take for test set :param shuffle: if true, the data is shuffled before being split :param seed: random seed for the shuffle :returns: triple of lists (training set, validation set, test set) """ n = len(data) k_val = math.floor((1 - val_ratio - test_ratio) * n) k_test = math.floor((1 - test_ratio) * n) if shuffle: random.seed(42) data_shuffled = random.sample(data, k=n) else: data_shuffled = data return data_shuffled[:k_val], data_shuffled[k_val:k_test], data_shuffled[k_test:]
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def set_difference(set_a, set_b): """ compare two sets and return the items which are in set_b but not in set_a """ diff = set_b - set_a return diff
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import re def split_dump_pattern(pattern): """Split a comma separated string of patterns, into a list of patterns. :param pattern: A comma separated string of patterns. """ regex = re.compile('\s*,\s*') return regex.split(pattern)
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def get_branch_list(nodes, exit_index): """Computes the branch list for the control flow graph. Args: nodes: A list of control_flow.ControlFlowNodes. exit_index: The index of the exit node. Returns: A Python list representing the branch options available from each node. Each entry in the list corresponds to a node in the control flow graph, with the final entry corresponding to the exit node (not present in the cfg). Each entry is a 2-tuple indicating the next node reached by the True and False branch respectively (these may be the same.) The exit node leads to itself along both branches. """ indexes_by_id = { id(node): index for index, node in enumerate(nodes) } indexes_by_id[id(None)] = exit_index branches = [] for node in nodes: node_branches = node.branches if node_branches: branches.append([indexes_by_id[id(node_branches[True])], indexes_by_id[id(node_branches[False])]]) else: try: next_node = next(iter(node.next)) next_index = indexes_by_id[id(next_node)] except StopIteration: next_index = exit_index branches.append([next_index, next_index]) # Finally we add branches from the exit node to itself. # Omit this if running on BasicBlocks rather than ControlFlowNodes, because # ControlFlowGraphs have an exit BasicBlock, but no exit ControlFlowNodes. branches.append([exit_index, exit_index]) return branches
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def convert_names_to_highlevel(names, low_level_names, high_level_names): """ Converts group names from a low level to high level API This is useful for example when you want to return ``db.groups()`` for the :py:mod:`bob.bio.base`. Your instance of the database should already have ``low_level_names`` and ``high_level_names`` initialized. """ if names is None: return None mapping = dict(zip(low_level_names, high_level_names)) if isinstance(names, str): return mapping.get(names) return [mapping[g] for g in names]
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def get_load_config_timestamp(pefile_object): """ Retrieves the timestamp from the Load Configuration directory. :param pefile.PE pefile_object: pefile object. :return: Recovered timestamps from PE load config (if any). None if there aren't. :rtype: int """ timestamp = 0 if hasattr(pefile_object, 'DIRECTORY_ENTRY_LOAD_CONFIG'): loadconfigdata = pefile_object.DIRECTORY_ENTRY_LOAD_CONFIG timestamp = getattr(loadconfigdata.struct, 'TimeDateStamp', 0) return timestamp
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def soft_timing(Nframes, time, fpsmin=10, fpsmax=20): """determines time & fps; aims for target time, but forces fpsmin < fps < fpsmax. example usage: target 3 seconds, but force 10 < fps < 25: import QOL.animations as aqol for i in range(50): code_that_makes_plot_number_i() aqol.saveframe('moviename') plt.close() aqol.movie('moviename', **soft_timing(3, 10, 25)) returns dict(time=time, fps=fps) """ if time > Nframes/fpsmin: #makes sure the movie doesnt go too slow. (time, fps) = (None, fpsmin) elif time < Nframes/fpsmax: #makes sure the movie doesnt go too fast. (time, fps) = (None, fpsmax) else: #makes the movie <time> duration if it will have fpsmin < fps < fpsmax. (time, fps) = (time, 1) #fps will be ignored in aqol.movie since time is not None. return dict(time=time, fps=fps)
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import ast def has_docstring(node): """Retuns true if given function or method has a docstring. """ docstring = ast.get_docstring(node) if docstring is not None: return not docstring.startswith('mys-embedded-c++') else: return False
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import json def encode_pretty_printed_json(json_object): """Encodes the JSON object dict as human readable ascii bytes.""" return json.dumps( json_object, ensure_ascii=True, indent=4, sort_keys=True, ).encode("ascii")
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def format_field(relation_name, field): """Util for formatting relation name and field into sql syntax.""" return "%s.%s" % (relation_name, field)
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def validate_initial_digits(credit_card_number: str) -> bool: """ Function to validate initial digits of a given credit card number. >>> valid = "4111111111111111 41111111111111 34 35 37 412345 523456 634567" >>> all(validate_initial_digits(cc) for cc in valid.split()) True >>> invalid = "14 25 76 32323 36111111111111" >>> all(validate_initial_digits(cc) is False for cc in invalid.split()) True """ return credit_card_number.startswith(("34", "35", "37", "4", "5", "6"))
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def j2k(j, E, nu, plane_stress=True): """ Convert fracture Parameters ---------- j: float (in N/mm) E: float Young's modulus in GPa. nu: float Poisson's ratio plane_stress: bool True for plane stress (default) or False for plane strain condition. Returns ------- K : float Units are MPa m^0.5. """ if plane_stress: E = E / (1 - nu ** 2) return (j * E) ** 0.5
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import gzip def openGzipOrText(fPath,encoding=None) : """Opens a file for reading as text, uncompressing it on read if the path ends in .gz""" if str(fPath).lower().endswith('.gz') : return gzip.open(fPath,'rt',encoding=encoding) else : return open(fPath,'rt',encoding=encoding)
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def get_parent_technique_id(sub_tid): """Given a sub-technique id, return parent""" return sub_tid.split(".")[0]
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def lineStartingWith(string, lines): """ Searches through the specified list of strings and returns the first line starting with the specified search string, or None if not found """ for line in lines: if line.startswith(string): return line else: return None
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from pathlib import Path def _get_file_from_folder(folder: Path, suffix: str) -> Path: """Gets this first file in a folder with the specified suffix Args: folder (Path): folder to search for files suffix (str): suffix for file to search for Returns: Path: path to file """ return list(Path(folder).glob("*" + suffix))[0]
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import copy def _normalize_barcodes(items): """Normalize barcode specification methods into individual items. """ split_items = [] for item in items: if item.has_key("multiplex"): for multi in item["multiplex"]: base = copy.deepcopy(item) base["description"] += ": {0}".format(multi["name"]) del multi["name"] del base["multiplex"] base.update(multi) split_items.append(base) elif item.has_key("barcode"): item.update(item["barcode"]) del item["barcode"] split_items.append(item) else: item["barcode_id"] = None split_items.append(item) return split_items
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def __to_float(num): """ Try to convert 'num' to float, return 'num' if it's not possible, else return converted :code:`num`. """ try: float(num) return float(num) except ValueError: return num
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def calc_minutes(hhmm): """Convert 'HH:MM' to minutes""" return int(hhmm[:2]) * 60 + int(hhmm[3:])
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def is_stop_word(word, nlp): """ Check if a word is a stop word. :param word: word :param nlp: spacy model :return: boolean """ return nlp(word)[0].is_stop
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def format_80(s): """ Split string that is longer than 80 characters to several lines Args: s (str) Returns: ss (str): formatted string """ i = 0 ss = '' for x in s: ss += x i += 1 if i == 80: i = 0 ss += ' \ \n' return ss
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def check_panagram( input_str: str = "The quick brown fox jumps over the lazy dog", ) -> bool: """ A Panagram String contains all the alphabets at least once. >>> check_panagram("The quick brown fox jumps over the lazy dog") True >>> check_panagram("My name is Unknown") False >>> check_panagram("The quick brown fox jumps over the la_y dog") False """ frequency = set() input_str = input_str.replace( " ", "" ) # Replacing all the Whitespaces in our sentence for alpha in input_str: if "a" <= alpha.lower() <= "z": frequency.add(alpha.lower()) return True if len(frequency) == 26 else False
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def df_query_with_ratio(df_in, query, ratio_name='ratio'): """ This function calls the .query() method on a DataFrame and additionally computes the ratio of resulting rows over the original number of rows. The result is a tuple with the filtered dataframe as first element and the filter ratio as second element. """ df_out = df_in.query(query) ratio = df_out.shape[0] / df_in.shape[0] print('{} = {:.2f} %'.format(ratio_name, 100 * ratio)) return df_out, ratio
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import torch def cthw2tlbr(boxes): """ Convert center/size format `boxes` to top/left bottom/right corners. :param boxes: bounding boxes :return: bounding boxes """ top_left = boxes[..., :2] - boxes[..., 2:]/2 bot_right = boxes[..., :2] + boxes[..., 2:]/2 return torch.cat([top_left, bot_right], dim=-1)
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def get_location_by_offset(filename, offset): """ This function returns the line and column number in the given file which is located at the given offset (i.e. number of characters including new line characters). """ with open(filename, encoding='utf-8', errors='ignore') as f: for row, line in enumerate(f, 1): length = len(line) if length < offset: offset -= length else: return row, offset + 1
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def scale_to_percent(val, min, max): """ Utility function to scale a given value to a percentage within a range """ current = val # first, ensure that current is within our defined min/max if val < min: current = min elif current > max: current = max # now, we scale it to b/t 0 and 1 scaled = (current-min)/(max - min) return scaled * 100
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def get_node_exec_options(profile_string, exec_node_id): """ Return a list with all of the ExecOption strings for the given exec node id. """ results = [] matched_node = False id_string = "(id={0})".format(exec_node_id) for line in profile_string.splitlines(): if matched_node and line.strip().startswith("ExecOption:"): results.append(line.strip()) matched_node = False if id_string in line: # Check for the ExecOption string on the next line. matched_node = True return results
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def leaf_2(key): """Returns the key value of the leaf""" return key
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def denormalize_images(imgs_norm): """ De normalize images for plotting """ imgs = (imgs_norm + 0.5) * 255.0 return imgs
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def drop_zombies(feed): """ In the given Feed, drop stops with no stop times, trips with no stop times, shapes with no trips, routes with no trips, and services with no trips, in that order. Return the resulting Feed. """ feed = feed.copy() # Drop stops of location type 0 that lack stop times ids = feed.stop_times['stop_id'].unique() f = feed.stops cond = f['stop_id'].isin(ids) if 'location_type' in f.columns: cond |= f['location_type'] != 0 feed.stops = f[cond].copy() # Drop trips with no stop times ids = feed.stop_times['trip_id'].unique() f = feed.trips feed.trips = f[f['trip_id'].isin(ids)] # Drop shapes with no trips ids = feed.trips['shape_id'].unique() f = feed.shapes if f is not None: feed.shapes = f[f['shape_id'].isin(ids)] # Drop routes with no trips ids = feed.trips['route_id'].unique() f = feed.routes feed.routes = f[f['route_id'].isin(ids)] # Drop services with no trips ids = feed.trips['service_id'].unique() if feed.calendar is not None: f = feed.calendar feed.calendar = f[f['service_id'].isin(ids)] if feed.calendar_dates is not None: f = feed.calendar_dates feed.calendar_dates = f[f['service_id'].isin(ids)] return feed
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def mock_get(pipeline, allowDiskUse): # pylint: disable=W0613,C0103 """ Return mocked mongodb docs. """ return [ {'_id': 'dummy_id_A', 'value': 'dummy_value_A'}, {'_id': 'dummy_id_B', 'value': 'dummy_value_B'}, ]
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def roce(net_income, preferred_dividends, average_common_equity): """Computes return on common equity. Parameters ---------- net_income : int or float Net income preferred_dividends : int or float Preferred dividends average_common_equity : int or float Average common equity Returns ------- out : int or float Return on common equity """ return (net_income - preferred_dividends) / average_common_equity
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def _is_int_in_range(value, start, end): """Try to convert value to int and check if it lies within range 'start' to 'end'. :param value: value to verify :param start: start number of range :param end: end number of range :returns: bool """ try: val = int(value) except (ValueError, TypeError): return False return (start <= val <= end)
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def isstdiofilename(pat): """True if the given pat looks like a filename denoting stdin/stdout""" return not pat or pat == b'-'
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import bisect def _RevisionState(test_results_log, revision): """Check the state of tests at a given SVN revision. Considers tests as having passed at a revision if they passed at revisons both before and after. Args: test_results_log: A test results log dictionary from GetTestResultsLog(). revision: The revision to check at. Returns: 'passed', 'failed', or 'unknown' """ assert isinstance(revision, int), 'The revision must be an integer' keys = sorted(test_results_log.keys()) # Return passed if the exact revision passed on Android. if revision in test_results_log: return 'passed' if test_results_log[revision] else 'failed' # Tests were not run on this exact revision on Android. index = bisect.bisect_right(keys, revision) # Tests have not yet run on Android at or above this revision. if index == len(test_results_log): return 'unknown' # No log exists for any prior revision, assume it failed. if index == 0: return 'failed' # Return passed if the revisions on both sides passed. if test_results_log[keys[index]] and test_results_log[keys[index - 1]]: return 'passed' return 'failed'
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def dmlab_level_label(level) -> str: """Returns the label for a DMLab level.""" return level.replace('_', ' ').title()
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from typing import Dict from typing import List from typing import Tuple def get_raw_dependency_information_from_dep_file(dep_file: str) -> Dict[str, List[Tuple[str, str]]]: """return RAW dependency information contained in dep_file in the form of a dictionary. Format: {source_line: [(sink_line, var_name)] :param dep_file: path to dependency file :return: RAW dictionary """ raw_dependencies: Dict[str, List[Tuple[str, str]]] = dict() with open(dep_file) as f: for line in f.readlines(): line = line.replace("\n", "") # format of dependency entries in _dep.txt-file: # sourceLine NOM RAW sinkLine|variable if " NOM " not in line: continue split_line = line.split(" NOM ") source_line = split_line[0] # split entries entries = [] current_entry = "" for word in split_line[1].split(" "): word = word.replace(" ", "") if word == "RAW" or word == "WAR" or word == "WAW" or word == "INIT": if len(current_entry) > 0: entries.append(current_entry) current_entry = "" if len(current_entry) > 0: current_entry += " " + word else: current_entry += word if len(current_entry) > 0: entries.append(current_entry) if source_line not in raw_dependencies: raw_dependencies[source_line] = [] for entry in entries: # filter for RAW dependencies split_entry = entry.split(" ") if split_entry[0] != "RAW": continue split_sink_line_var = split_entry[1].split("|") sink_line = split_sink_line_var[0] var_name = split_sink_line_var[1].replace(".addr", "") raw_dependencies[source_line].append((sink_line, var_name)) return raw_dependencies
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def flag(s): """Turn 'flag_name' into `--flag-name`.""" return '--' + str(s).replace('_', '-')
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def pmi(financedamount, pmirate): """Return annual private mortgage insurance cost. :param financedamount: Amount of money borrowed. :type financedamount: double :param pmirate: Rate charged when loan-to-value > 80%. :type pmirate: double :return: double """ return financedamount * pmirate
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def get_relevant_files(session_data: dict): """ Generates the pipeline's "starting node" Parameters ---------- session_data : dict A dictionary with the locations of all necessary session's data Returns ------- str,str The "starting" node for processing """ return session_data.get("dwi"), session_data.get("fmap")
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def _last_index(x, default_dim): """Returns the last dimension's index or default_dim if x has no shape.""" if x.get_shape().ndims is not None: return len(x.get_shape()) - 1 else: return default_dim
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def qsize(queue): """Return the (approximate) queue size where available; -1 where not (OS X).""" try: return queue.qsize() except NotImplementedError: # OS X doesn't support qsize return -1
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def layer_point_to_map(map_layer, point): """Convert a pair of coordinates from layer projection to map projection.""" return [point[0] / map_layer.data.tilewidth, point[1] / map_layer.data.tileheight]
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def prodigal_gene_start(rec_description: str) -> int: """Get a gene start index from a Prodigal FASTA header Examples -------- Given the following Prodigal FASTA output header, parse the gene start index (i.e. 197) >>> prodigal_gene_start("k141_2229_1 # 197 # 379 # 1 # ID=4_1;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.437") 197 Parameters ---------- rec_description : str SeqRecord description of Prodigal FASTA header Returns ------- int Gene start index """ return int(rec_description.split('#')[1].strip())
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def ini_conf_to_bool(value): """ Depending INI file interpreter, False values are simple parsed as string, so use this function to consider them as boolean :param value: value of ini parameter :return: bollean value """ if value in ('False', 'false', '0', 'off', 'no'): return False return bool(value)
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def has_cloned_parent(c, p): """Return True if p has a cloned parent within the @rst tree.""" root = c.rstCommands.root p = p.parent() while p and p != root: if p.isCloned(): return True p.moveToParent() return False
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import re def get_depth_of_exec_function(backtrace): """ >>> get_depth_of_exec_function(["#1 0x00007f29e6eb7df5 in standard_ExecutorRun (queryDesc=0x562aad346d38,"]) 1 >>> get_depth_of_exec_function(["#27 0x00007f29e6eb7df5 in pgss_ExecutorRun (queryDesc=0x562aad346d38,"]) 27 >>> get_depth_of_exec_function(["#13 0x00007f29e6eb7df5 in explain_ExecutorRun (queryDesc=0x562aad346d38,"]) 13 >>> get_depth_of_exec_function(["#4 0x00007f29e6eb7df5 in ExecEvalNot (notclause=<optimized out>,"]) 4 >>> get_depth_of_exec_function(["#5 0x00007f29e6eb7df5 in ExecProcNode (node=node@entry=0x562aad157358,)"]) 5 >>> get_depth_of_exec_function(["#12 0x00007f29e6eb7df5 in ExecutePlan (dest=0x562aad15e290,"]) 12 >>> get_depth_of_exec_function(["#21 standard_ExecutorRun (queryDesc=0x562aad0b46f8, direction=<optimized out>,"]) 21 >>> bt = ["#0 palloc0 (size=size@entry=328)", \ "#1 0x0000562aac6c9970 in InstrAlloc (n=n@entry=1, instrument_options=4)", \ "#2 0x0000562aac6bdddb in ExecInitNode (node=node@entry=0x562aad49e818,"] >>> get_depth_of_exec_function(bt) 2 """ exec_regexp = re.compile(r"#([0-9]+) .*Exec[a-zA-Z]+ \(") for frame in backtrace: m = exec_regexp.search(frame) if m: return int(m.group(1)) return None
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def read_weights_file(weights_file): """ Given a tab separated file with leaf names for a phylogenetic tree in column one and multipliers for that leaf's branch length in column two, will create a dictionary with leaf names as keys and multipliers as values :param weights_file: Path to a tab-separated text file described above. :return: dictionary with leaf names as keys and multipliers as values """ weights = dict() with open(weights_file) as f: for line in f: stripped_line = line.rstrip() x = stripped_line.split('\t') if len(x) != 2 and stripped_line != '': raise RuntimeError('One of the lines in your weights file ({}) is not formatted correctly. ' 'Correct format is leafname\tweight, tab-separated. ' 'Offending line was: {}'.format(weights_file, stripped_line)) elif len(x) == 2: try: weight = float(x[1]) except ValueError: raise ValueError('The second column in your weights file ({}) must be a number. Please fix the ' 'following line: {}'.format(weights_file, stripped_line)) weights[x[0]] = weight return weights
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def modelSpin(model, nodes): """ Determines and reports spin state of nodes. Args: model: an instance of a Model object. nodes: a dictionary of node objects. Returns: state: a list of node spins for the model, either -1 or +1. """ state = [] for e in nodes: state.append(nodes[e].getSpin()) state = ['+' if x > 0 else '-' for x in state] return state
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def engineer_data(data): """ Returns modified version of data with left and right aggregate features while dropping weight and distance features :param data: data to work with :return: modified dataframe """ data['left'] = data['left_weight'] * data['left_distance'] data['right'] = data['right_weight'] * data['right_distance'] data = data.drop(['left_weight', 'left_distance', 'right_weight', 'right_distance'], axis=1) return data
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def convert_8_int_to_tuple(int_date): """ Converts an 8-digit integer date (e.g. 20161231) to a date tuple (Y,M,D). """ return (int(str(int_date)[0:4]), int(str(int_date)[4:6]), int(str(int_date)[6:8]))
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def clean(iterator) -> list: """ Takes an iterator of strings and removes those that consist that str.strip considers to consist entirely of whitespace. """ iterator = map(str.strip, iterator) return list(filter(bool, iterator))
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import json def load_js(fname): """ Parameters ---------- fname: str Returns ------- obj content of the json file, generally dict """ with open(fname,"r") as f: jsdict = json.load(f) return jsdict
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from pathlib import Path def default_path_factory(refname: str, ispkg: bool) -> Path: """Default path factory for markdown.""" path = Path(*refname.split(".")) if ispkg: filepath = path / "index.md" else: filepath = path.with_suffix(".md") return filepath
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def loadtxt(filename): """Read list fo strings from file""" txt = [] with open(filename, 'r') as f: for l in f: txt.append(l.strip()) return txt
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import torch def deltaE(lab1, lab2): """Delta E (CIE 1976). lab1: Bx3xHxW lab2: Bx3xHxW return: Bx1xHxW >>> lab1 = torch.tensor([100., 75., 50.]).view(1, 3, 1, 1) >>> lab2 = torch.tensor([50., 50., 100.]).view(1, 3, 1, 1) >>> deltaE(lab1, lab2).item() 75.0 """ return torch.norm(lab1 - lab2, 2, 1, keepdim=True)
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def derivative_relu(relu_output): """ Compute derivative of ReLu function """ relu_output[relu_output <= 0] = 0 relu_output[relu_output > 0] = 1 return relu_output
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import torch def pdist2(x, y): """ Compute distance between each pair of row vectors in x and y Args: x: tensor of shape n*p y: tensor of shape m*p Returns: dist: tensor of shape n*m """ p = x.shape[1] n = x.shape[0] m = y.shape[0] xtile = torch.cat([x] * m, dim=1).view(-1, p) ytile = torch.cat([y] * n, dim=0) dist = torch.pairwise_distance(xtile, ytile) return dist.view(n, m)
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def s2ca(s): """Takes a string of cipher texts and returns it as an array of cipher texts""" cypher_array = [] for i in range(int((len(s))/314)): cypher_array.append(s[i:i+314]) return cypher_array
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def is_dict(value): """ is value a dict""" return isinstance(value, dict)
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def _kernel_seq(inputs, estimator): """ Wrapper around a function that computes anything on two sequences and returns a dict While it is written as a general purpose kernel for anything, here it is used for causal discovery and estimation from CCM based methods. The function unpacks inputs into an index element and a sequence pair and runs the estimator function on the sequence pair, returning various estimates in a dict Parameters ---------- inputs : tuple Tuple of two elements - (a, b) where a is an index, b is a tuple of two. a can be produced manually or more typically using enumerate; b holds the two sequences usually passed in by zip-ping larger iterables or itertools' product/combinations. a, the index, is passed to keep track of order in case of asynchronous execution Should look like this: (index, (sequence_x, sequence_y) estimator : function A function that can compute something on two arrays and return a dict. Preferably one that can compute something meaningful, like causal discovery Returns ------- out : dict Estimates obtained by running estimator on inputs. """ # Unpack inputs idx, seqs = inputs # Unpack sequences idx_x, idx_y, seq_x, seq_y = seqs # Initialize dictionary of output estimates with index out = {"index_pair": idx, "index_x": idx_x, "index_y": idx_y} # Execute the estimator function on the sequence pair out.update(estimator(seq_x, seq_y)) # Some feedback to console # print(".", end="") return out
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def _lookup_response_str(status_code): """ Simple function to return a response string for a Ping StatusCode :param status_code: int: :return: str: Response string """ status_msg = {0: 'Success', 11001: 'Buffer Too Small', 11002: 'Dest Net Unreachable', 11003: 'Dest Host Unreachable', 11004: 'Dest Protocol Unreachable', 11005: 'Dest Port Unreachable', 11006: 'No Resources', 11007: 'Bad Option', 11008: 'Hardware Error', 11009: 'Packet Too Big', 11010: 'Timed Out', 11011: 'Bad Request', 11012: 'Bad Route', 11013: 'TTL Expired Transit', 11014: 'TTL Expired Reassembly', 11015: 'Parameter Problem', 11016: 'Source Quench', 11017: 'Option Too Big', 11018: 'Bad Destination', 11032: 'Negotiating IPSEC', 11050: 'General Failure'} return status_msg.get(status_code, 'Unknown StatusCode')
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def __create_python_code_block(message): """Create a python code block""" return f"```python\n{message}```"
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def label_map(value): """ Function that determines the diagnosis according to the Glucose level of an entry. The three possible diagnosis are: Hypoglycemia, hyperglycemia and normal :param value: Glucose level :return: Diagnosis (String) """ hypoglycemia_threshold = 70 hyperglycemia_threshold = 180 severe_hyperglycemia_threshold = 240 if value < hypoglycemia_threshold: return 'Hypoglycemia' elif value > hyperglycemia_threshold: if value > severe_hyperglycemia_threshold: return 'Severe_Hyperglycemia' else: return 'Hyperglycemia' else: return 'In_Range'
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def getSizeOfVST(vst): """ Description: Return the size of the vector space of an vst variable. Look for the first existing vector of the vst and get its size. NB: Used only to not have to pass the size of the vst as a parameter. """ size = 0 for key in vst: if vst[key] is not None: #size = vst[key].size size = len(vst[key]) break return size
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def within_bounds( x: float, y: float, min_x: float, min_y: float, max_x: float, max_y: float ): """ Are x and y within the bounds. >>> within_bounds(1, 1, 0, 0, 2, 2) True """ return (min_x <= x <= max_x) and (min_y <= y <= max_y)
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def validate_sp(sp): """Validate seasonal periodicity. Parameters ---------- sp : int Seasonal periodicity Returns ------- sp : int Validated seasonal periodicity """ if sp is None: return sp else: if not isinstance(sp, int) and (sp >= 0): raise ValueError(f"Seasonal periodicity (sp) has to be a positive integer, but found: " f"{sp} of type: {type(sp)}") return sp
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def integrate(func, interval=None, rects=100000): """ Returns the result of the integral from the inclusive interval (a, b) using a Riemann sum approximation """ if interval is None or not isinstance(interval, tuple): interval = eval(input('Interval (a, b): ')) a, b = interval if a > b: print('note: the calculated area will be negative') if b - a > rects: rects = b - a area = 0 x = a dx = (b - a) / rects for n in range(rects): try: area += func(x) * dx except Exception as e: print('Error:', e) x += dx return area
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def log_hide(message): """Hide security sensitive information from log messages""" if type(message) != dict: return message if "token" in message: message["token"] = "xxxxxxxx-xxxx-xx" if "AccessToken" in message: message["AccessToken"] = "xxxxxxxx-xxxx-xx" return message
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def extractLabels(data, label_column): """ Extracts the labels from the data Arguments: data {Dict/List of times series} -- Time series label_column {str} -- Name of the column to extract """ if isinstance(data, dict): labels = {d: data[d][label_column] for d in data} data = {d: data[d][[c for c in data[d].columns if c != label_column]] for d in data} else: labels = data[label_column] data = data[[c for c in data.columns if c != label_column]] return data, labels
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from functools import reduce def product(nums): """ Like sum, but for product. """ return reduce(lambda x,y:x*y,nums)
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def get_published_templateid(context): """ Return the template id, as of the PUBLISHED variable, or None """ request = context.REQUEST if request.has_key('PUBLISHED'): return request['PUBLISHED'].__name__ return None
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def CalcTimeStep(CFL, diff, conv, dX, dY, Dimension, Model): """Return the time step size in the numerical approximation. Call Signature: CalcTimeStep(CFL, diff, conv, dX, dY, Dimension, Model) Parameters ---------- CFL: float In this program, CFL is treated as the diffusion number for diffusion equations, and Courant number for the convection equations. Caution: This is not a true numerical definition of CFL though. diff: float Physics specific coefficient in the diffusion model. For example, kinematic viscosity or thermal diffusivity. conv: float Physics specific coefficient in the convection model. For example, speed of sound in the first-order linear wave eq. dX: float Grid step size along X-axis. dY: float Grid step size along Y-axis. Value required for 2D applications. Dimension: str Dimension of the domain. Allowed inputs are "1D" or "2D". Model: str Model of the governing equation. To see available options for this parameter, type the following command on your terminal python fetchoption.py "model" Returns ------- TimeStep: float Time step in the model equation. """ print("Calculating time step size for the simulation: Completed.") # ************** DIFFUSION EQN. ****************** if Model.upper() == "DIFFUSION": dX2 = dX*dX if Dimension.upper() == "1D": TimeStep = CFL*dX2/diff return TimeStep elif Dimension.upper() == "2D": dY2 = dY*dY TimeStep = CFL*(1.0/((1/dX2) + (1/dY2)))/diff return TimeStep # ************** FIRST-ORDER WAVE EQN. ***************** elif Model.upper() == "FO_WAVE": if Dimension.upper() == "1D": TimeStep = CFL*dX/conv return TimeStep # ************** BURGERS EQN. ***************** elif Model.upper() == "INV_BURGERS": if Dimension.upper() == "1D": TimeStep = CFL*dX return TimeStep elif Model.upper() == "VISC_BURGERS": if Dimension.upper() == "1D": dX2 = dX*dX TimeStep = CFL*dX2 return TimeStep
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import math def smooth(x): """ smooth value x by using a cosinus wave (0.0 <= x <= 1.0) """ return (-math.cos(math.pi * x) + 1) / 2
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import ast def matches(value, pattern): """Check whether `value` matches `pattern`. Parameters ---------- value : ast.AST pattern : ast.AST Returns ------- matched : bool """ # types must match exactly if type(value) != type(pattern): return False # primitive value, such as None, True, False etc if not isinstance(value, ast.AST) and not isinstance(pattern, ast.AST): return value == pattern fields = [ (field, getattr(pattern, field)) for field in pattern._fields if hasattr(pattern, field) ] for field_name, field_value in fields: if not matches(getattr(value, field_name), field_value): return False return True
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def int_to_base36(integer: int) -> str: """Convert an integer to a base36 string.""" char_set = "0123456789abcdefghijklmnopqrstuvwxyz" if integer < 0: raise ValueError("Negative base36 conversion input.") if integer < 36: return char_set[integer] b36 = "" while integer != 0: integer, index = divmod(integer, 36) b36 = char_set[index] + b36 return b36
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def _fit_estimator(clf, X, y): """Helper to fit estimator""" return clf.fit(X, y)
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