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import re def split_lines(source): """ Split selection lines in a version-agnostic way. Python grammar only treats \r, \n, and \r\n as newlines. But splitlines() in Python 3 has a much larger list: for example, it also includes \v, \f. As such, this function will split lines across all Python ver...
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def ema(df, window, targetcol='weightedAverage', colname='ema', **kwargs): """ Calculates Expodential Moving Average on a 'targetcol' in a pandas dataframe """ df[colname] = df[targetcol].ewm( span=window, min_periods=kwargs.get('min_periods', 1), adjust=kwargs.get('adjust', True), ...
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def filter_fiona_metadata(dct): """Include only valid Fiona keywords for opening a feature collection""" valid_keys = {"crs", "driver", "schema", "layer", "vfs"} return {k: v for k, v in dct.items() if k in valid_keys}
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import json def backup_luks2_token(module, device, token_id): """Backup LUKS2 token, as we may need to restore the metadata. Return: <backup> <error>""" args = ["cryptsetup", "token", "export", "--token-id", token_id, device] ret, token, err = module.run_command(args) if ret != 0: return ...
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def _geny(xx, func): """ Generates an array containing y-values corresponding to given x-coordinates by using a function y = f(x). Args: xx (1darray): Array containing the x-values for which matching y-values shall be computed. func (callable object): The function used to ge...
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def isbool(s): """ Checks whether the string ``s`` represents a boolean. The string requires Python capitalization (e.g. 'True', not 'true'). :param s: the candidate string to test :type s: ``str`` :return: True if s is the string representation of a boolean :rtype: ``bool``...
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from typing import Dict from typing import Any def is_compatible(assignment1: Dict[str, Any], assignment2: Dict[str, Any]): """ Check if two (potentially partial) assignments are compatible. Compatible means that there is no disagreement on variable assignment. :param assignment1: a dict var ->val ...
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def SetFieldValue(regValue, lsb, fsize, fieldValue): """ An internal utility function to assign a field value to a register value. Perform range check on fieldValue using fsize. :type regValue: ``int`` or ``long`` :param regValue: The value of the register to parse :type lsb: ``int`` :par...
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import re def clean_regex_string(s: str) -> str: """Converts regex string pattern for a path into OpenAPI format. Example:: >>s = '^toy\\/^(?P<toyId>[a-zA-Z0-9-_]+)\\/details' >>clean_regex_string(s) 'toy/{toyId}/details' """ s = s.replace("^", "").replace("\\", "") rege...
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def check_nulls(df): """ Takes a data frame and returns a sorted list of the number of null values each column has. """ return(df.isnull().sum().sort_values())
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import mimetypes def get_mimetype(url): """ Guess based on the file extension. Args: url (text): Web url that was linked to by a reddit submission. Returns: modified_url (text): The url (or filename) that will be used when constructing the command to run. content_...
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import random def generate_chunks(total, min_val, max_val, num_chunks=-1): """ Randomly generate a list of integers l such that sum(l) = total and for each x in l, min_val <= x <= max_val. If num_chunks > 0, it is guaranteed that the list contains exactly num_chunks elements. """ if num_chunks <=...
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from typing import Union from typing import List import torch from typing import Tuple def exact_match_rate( real_start: Union[List[List[torch.Tensor]], torch.Tensor], real_end: Union[List[List[torch.Tensor]], torch.Tensor], pred_start: torch.Tensor, pred_end: torch.Tensor ) -> Tuple[i...
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def allowed_file(filename): """Returns `True` if file extension is `.tar`""" return '.' in filename and filename.rsplit('.', 1)[1] in ['tar']
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import colorsys def get_hue(image): """Return the most common hue of the image.""" hues = [0 for x in range(256)] # Iterate each pixel. Count each hue value in `hues`. for pixel in image.getdata(): # Ignore greyscale pixels. if pixel[0] == pixel[1] and pixel[1] == pixel[2]: ...
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def split(s, delimiter=','): """Split a string on given delimiter or newlines and return the results stripped of whitespace""" return [ item.strip() for item in s.replace(delimiter, '\n').splitlines() if item.strip() ]
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import pickle def stop_idx_in_route(stop_times_file, FOLDER): """ This function saves a dictionary to provide easy access to index of a stop in a route. Args: stop_times_file (pandas.dataframe): stop_times.txt file in GTFS. FOLDER (str): path to network folder. Returns: idx_by_...
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def find_key_in_list(key, key_list): """ Look for the right corresponding key in a list. key has to start with an given key from the list and the longest key will be returned. Parameters ---------- key : str Given key. key_list : list of str Valid keys to be checked aga...
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def get_suffix_base64(raw_base64): """ get suffix and base code :param raw_base64: data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAA :return: png, iVBORw0KGgoAAAANSUhEUgAA """ parts = raw_base64.split(',', 1) code = parts[1] splits = parts[0].split(';')[0].split('data:')[1].split('/') s...
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from typing import List def make_squares(arr: List[int]) -> List[int]: """ Time Complexity: O(len(arr)) Space Complexity: O(len(arr)) :param arr: input array :return: new array containing squares of all the number of the input array in the sorted order """ n = len(arr) p1 = 0 p2 =...
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def read_taxonomies_to_design_for(fn): """Read different taxonomies to design for. The columns must be, in order: 1) a taxonomic (e.g., species) ID from NCBI 2) a segment label, or 'None' if unsegmented Args: fn: path to TSV file, where each row corresponds to a taxonomy Retur...
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import re def identify_hypers(df_fit): """Identify hyperparameters. Arguments: df_fit: A pd.DataFrame of model fit data. Returns: hypers: A list of strings. """ hypers = [] for col_name in list(df_fit.columns): if re.match(r'hyp_*.', col_name): hypers.app...
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import binascii def _pack_mac(mac_address): """Pack a mac_address into binary.""" return binascii.unhexlify(mac_address.replace(':', ''))
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from datetime import datetime def monthlyVector(startyr,endyr,startmth,endmth): """ Returns two datetime vectors with start and end dates at the start and end of months """ month=[] year=[] m0 = startmth y0 = startyr while m0 <= endmth or y0 <= endyr: month.append(m0) ...
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from typing import List def make_low_rcp_list(predicted_temps_dict: dict) -> List[float]: """Return a list of RCP 2.6 temperature values """ low_rcp_list = [] for year in list(predicted_temps_dict.keys()): low_rcp_list.append(predicted_temps_dict[year]['RCP 2.6']) return low_rcp_list
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def is_dunder(val: str) -> bool: """Returns True if a __dunder__ name, False otherwise.""" return (len(val) > 4 and val[:2] == val[-2:] == '__' and val[2] != '_' and val[-3] != '_')
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import tempfile def build_ansible_inventory(config=None, fw_ip=None): """ Build a basic ini-style Ansible inventory file. Parameters: config (dict): Optional dictionary representing the current configuration file (used in production mode). fw_ip (string): Optional firewall IP address (use...
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import re def replace(s, pattern, replacement): """Replaces occurrences of a match string in a given string and returns the new string. The match string can be a regex expression. Args: s (str): the string to modify pattern (str): the search expression replacemen...
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def populate_table(conn, sql, rows): """ insert multiple rows of data into a table :param conn: Connection object :param sql: INSERT INTO statement :param rows: the data as a list of rows :return: lastrowid """ cur = conn.cursor() cur.executemany(sql, rows) conn.commit() return c...
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def is_solved(neighbours, colors): """Checks for all countries, if all their neighbours have another color. :param neighbours: A dict with country as keys, list of neighbours as values :param colors: A list indicating which country has which color. First element in this list corresponds to color of fir...
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async def is_record(value): """ Checks whether a value is a Record ID or a list of Record IDs Args: value (``obj``): any value retrieved from an airtable record field. Returns: (``bool``): True if value is Record ID or a list of Record IDs """ if isinstance(value, list) and valu...
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def TransToRp(T): """Converts a homogeneous transformation matrix into a rotation matrix and position vector :param T: A homogeneous transformation matrix :return R: The corresponding rotation matrix, :return p: The corresponding position vector. Example Input: T = np.array([[1, 0, 0, 0...
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def host_available(compute_host): """:returns: `True` if compute host is enabled in nova, `False` otherwise""" return compute_host.state == 'up' and compute_host.status == 'enabled'
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def recurPower(base, exp): """ base: int or float. exp: int >= 0 returns: int or float, base^exp """ if exp == 0: return 1 else: return base * recurPower(base, exp-1)
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import base64 def b64_decode(data): """Decodes standard unpadded base64 encoded string.""" mod = len(data) % 4 if mod: data += '=' * (4 - mod) return base64.b64decode(data)
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import json def load_features(features_path): """ Reading the features from disk. :param features_path: Location of feature JSON. :return features: Feature hash table. """ features = json.load(open(features_path)) features = {str(k): [str(val) for val in v] for k,v in features.items()} ...
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import math def factor(n): """Simple factorization function. Makes sure to only try each number once.""" factors = [] for i in range(2, int(math.sqrt(n)) + 1): if i not in factors and not n % i: factors.append(i) factors.append(n / i) return factors
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import torch import math def bucket_values( distances: torch.Tensor, num_identity_buckets: int = 4, num_total_buckets: int = 10 ) -> torch.Tensor: """ Places the given values (designed for distances) into `num_total_buckets`semi-logscale buckets, with `num_identity_buckets` of these capturing single v...
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def _indexing(x, indices): """ :param x: array from which indices has to be fetched :param indices: indices to be fetched :return: sub-array from given array and indices """ # np array indexing if hasattr(x, 'shape'): return x[indices] # list indexing return [x[idx] for...
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def strtime(time): """Takes a number of seconds; returns a formatted duration string""" years, days, hours, mins = 0, 0, 0, 0 timestr = "" if time > 31536000: years = int(time / 31536000) time = time - (31536000 * years) if time > 86400: days = int(time / 86400) time ...
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def gen(x): """ Return the generator of ``x``. EXAMPLES:: sage: R.<x> = QQ[]; R Univariate Polynomial Ring in x over Rational Field sage: gen(R) x sage: gen(GF(7)) 1 sage: A = AbelianGroup(1, [23]) sage: gen(A) f """ return x....
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def expToTrain(exp,start=None): """Converts a bunch of individual domain values to lists, because each domain value must be iterable for training data.""" x_train = [] for data in exp[start:,0]: x_train.append([data, ]) return x_train
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def calculate_segment_name(host_name, recorder): """ Returns the segment name based on recorder configuration and input host name. This is a helper generally used in web framework middleware where a host name is available from incoming request's headers. """ if recorder.dynamic_naming: r...
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def stations_by_river(stations): """takes list of station objects returns dictionary of format {river: list of stations on this river}""" stations_by_river_dictionary = {} # if station is in dictionary, add to to appropriate list, else create new key and item for object in stations: ...
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def get_status(i2c_hat): """Gets the I2C-HAT status word. The exported robotframework keyword is 'Get Status'. Args: i2c_hat (I2CHat): board Returns: int: The status word """ return i2c_hat.status.value
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def popcount(x): """ count the number of high bits in the integer `x`. Taken from https://en.wikipedia.org/wiki/Hamming_weight """ # put count of each 2 bits into those 2 bits x -= (x >> 1) & 0x5555555555555555 # put count of each 4 bits into those 4 bits x = (x & 0x3333333333333333) +...
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import time import torch def record_ddp_fit_model_stats(trainer, model, use_cuda): """Helper to calculate wall clock time for fit + max allocated memory. Args: trainer: The trainer object. model: The model to fit. use_cuda: Whether to sync CUDA kernels. Returns: Max Memor...
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def get_transfer_indicator(filename, transferred, total, spaces=50): """Returns progress indicator for byte stream transfer.""" if not total: return "{}, ?".format(filename) transferred = min(transferred, total) spaces_filled = int(spaces * transferred / total) return "{}, [{}] {}kB".format(...
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def fix_lon(lon): """ :returns: a valid longitude in the range -180 <= lon < 180 >>> fix_lon(11) 11 >>> fix_lon(181) -179 >>> fix_lon(-182) 178 """ return (lon + 180) % 360 - 180
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import logging def load_files_serial(feature_files, load_function, **kwargs): """ Function for loading the feature files serially. :param feature_files: The collection of feature files to load. :param load_function: The function to use for loading the feature files. :param kwargs: keyword argument...
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def _extract_one_stim_dur(stim_durs): """ In case of multiple photostim durations - pick the shortest duration In case of no photostim durations - return the default of 0.5s """ default_stim_dur = 0.5 if len(stim_durs) == 0: return default_stim_dur elif len(stim_durs) > 1: pr...
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def read_images(cursor): """Returns the ID, recorded datetime and image content of all Testbed images.""" cursor.execute('SELECT id, recorded, testbed_image FROM observations WHERE ' 'testbed_image IS NOT NULL ORDER BY id ASC') return cursor.fetchall()
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def is_url(output_location: str) -> bool: """Returns True if the output location is a URL.""" return output_location.startswith(('http://', 'https://'))
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def get_rgb_channel(image, channel): """ Converts an image to RGB and extracts a single channel """ return image[:, :, channel.value]
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def is_valid_key(key: str) -> bool: """Check if an exiftool key is valid and interesting.""" # https://exiftool.org/TagNames/Extra.html file_keys = ( 'FileName', 'Directory', 'FileSize', 'FileModifyDate', 'FileAccessDate', 'FileInodeChangeDate', 'FilePermissions', 'FileType', 'FileType', ...
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def deduplicate_list_of_periods(periods): """ Deduplicates a list of ``Period`` objects, ensuring no two ``Period``s have the same id`` """ known_ids = [] result = [] for period in periods: if period.id not in known_ids: known_ids.append(period.id) result.app...
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def get_input_shapes_map(input_tensors): """Gets a map of input names to shapes. Args: input_tensors: List of input tensor tuples `(name, shape, type)`. Returns: {string : list of integers}. """ input_arrays = [tensor[0] for tensor in input_tensors] input_shapes_list = [] for _, shape, _ in inp...
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def load_moves(filename): """Load a list of moves from a file, ignoring whitespace.""" with open(filename) as f: return [line.strip() for line in f if line.strip()]
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def _zbc_to_hgvs(i): """Convert zero-based coordinate to hgvs (1 based, missing zero)""" if i >= 0: i += 1 return i
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def decode(state): """ decodes the taxi env state (int in [0,500) ) to: (taxirow, taxicol, passloc, destidx) tuple :param state: int in [0,500) :return: (taxirow, taxicol, passloc, destidx) tuple """ destidx = state % 4 state = state // 4 passloc = state % 5 state = state // 5 ...
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def _has_text(string: str) -> bool: """Returns True if a string has non whitespace text.""" string_without_whitespace = string.strip() return len(string_without_whitespace) > 0
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import base64 def deserialise_job_command(command): """Deserialise job commands received through REST API.""" return base64.b64decode(command).decode("utf-8")
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def extract(seq, f): """ Extract items from a possibly nested sequence. All items of the possibly nested sequence ``seq`` for which the callback ``f`` returns ``True`` are returned in a list. """ try: it = iter(seq) except TypeError: return [] items = [] for item in ...
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import random def getRescind() -> str: """ Returns: A random message ending for rescinding a user """ options=[ "YOU ARE JUST BEGGING FOR RESCINDITAS, AREN'T YOU?", "swiggity swind, catch this rescind!", "rescinded, enjoy ...
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def get_word_from_derewo_line(line): """Processor for individual line from DeReWo textfile. Args: line: Single line from DeReWo text file Returns: Lowercase word, None if invalid """ line = line.split() # skip words with whitespace if len(line) > 2: return None ...
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def dotND(v1, v2): """Returns dot product of two nD vectors (same as itemwise multiplication followed by summation).""" return sum(vv1 * vv2 for vv1, vv2 in zip(v1, v2))
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def experiment_type_from_filename(filename): """ Get the experiment type based on filename. It is assumed that the filename is compliant with '<some_path>/measurements_<experiment_type>_summary.csv' :param filename: A string representing the file name. It can be either full or relative pat...
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import re def _collapse_impacted_interfaces(text): """Removes impacted interfaces details, leaving just the summary count.""" return re.sub( r"^( *)([^ ]* impacted interfaces?):\n(?:^\1 .*\n)*", r"\1\2\n", text, flags=re.MULTILINE)
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def get_groups_per_chain(chains, ligands, waters): """Takes lists of chains, ligands and waters, and returns the chain counts that should go in the .mmtf file. :param list chains: the chains to pack. :param list ligands: the ligands to pack. :param list waters: the waters to pack. :rtype: ``lis...
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from typing import Dict def is_grpc_enabled(server_config: Dict) -> bool: """ Checks if the API has the grpc protocol enabled (cortex.yaml). Args: server_config: API configuration. """ return server_config["protobuf_path"] is not None
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def get_matched_rule(command, rules, settings): """Returns first matched rule for command.""" for rule in rules: if rule.match(command, settings): return rule
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def s2m(seconds: float) -> float: """Convert seconds to minutes.""" return round(seconds / 60, 1)
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import re def process_field_cancelled_value(value): """This method processes the value in field. It checks for the value 'CANCELED' or 'CANCELLED' in the <value> tag under the parent <field> tag. """ value = value.strip().lower() cancel_match = re.findall(r'cancel[led$]*', value, re.I)...
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def get_expiry_date(obj): """ A custom field to show the expiry date in the Moderation Request Admin Changelist in djangocms-moderation. :param obj: A Moderation Request object supplied from the admin view table row :return: The expiry date from the matching moderation request object """ ve...
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def get_lists_diff(py_list1, py_list2): """ Get elements of py_list1 which are not in py_list2. """ return list(set(py_list1) - set(py_list2))
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def pad_left(orig, pad, new_length): """ Pad a string on the left side. Returns a padded version of the original string. Caveat: The max length of the pad string is 1 character. If the passed in pad is more than 1 character, the original string is returned. """ if len(p...
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def center(u): """Compute the center between edges.""" return 0.5 * (u[1:] + u[:-1])
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def is_valid_uuid (uuid): """ is_valid_uuid (uuid) -> bool returns True if uuid is a valid 128-bit UUID. valid UUIDs are always strings taking one of the following forms: XXXX XXXXXXXX XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX where each X is a hexadecimal digit (case insensitive) """ ...
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def position_to_index(v, nelx, nely): """ Convert a position vector to the index of the element containing it """ return int(v[0]) + int(v[1])*nelx
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def fdr(ps,alpha=0.05): """Given a list of p-values and a desired significance alpha, find the adjusted q-value such that a p-value less than q is expected to be significant at alpha, via the Benjamini-Hochberg method (appropriate for independent tests). """ ps = sorted(ps) m = len(ps) k...
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import sympy def expr_to_json(expr): """ Converts a Sympy expression to a json-compatible tree-structure. """ if isinstance(expr, sympy.Mul): return {"type": "Mul", "args": [expr_to_json(arg) for arg in expr.args]} elif isinstance(expr, sympy.Add): return {"type": "Add", "args": [e...
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import torch from typing import Tuple def _extract_sizes( h: torch.Tensor, r: torch.Tensor, t: torch.Tensor, ) -> Tuple[int, int, int, int, int]: """Extract size dimensions from head/relation/tail representations.""" num_heads, num_relations, num_tails = [xx.shape[i] for i, xx in enumerate((h, r, ...
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def get_false_times(obs_pair_hash, variable): """ Get the timepoints where the variable is false. Parameters: obs_pair_hash: the dictionary containing all observations by time unit as a tuple (case, variable). variable: the observation to look for. Returns: A list with all ...
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import decimal def big_int_cube_root(x): """Return the cube root of the given number. This works with integers that would cause OverflowErrors when trying to calculate the cube root the more straightforward way (x ** (1/3)). It seems to reliably return the result with enough precision that cubing it ...
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def problem_2_5(node): """ Given a circular linked list, implement an algorithm which returns the node at the beginning of the loop. DEFINITION Circular linked list: A (corrupt) linked list in which a node’s next pointer points to an earlier node, so as to make a loop in the linked list. EXAMPL...
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import hashlib def _sha512(data): """ Creates the string of sha512 hashed to the passed in data. Args: data (bytes): The data to be hashed Returns: type: str The sha512 hashed data in string of hex values. """ return hashlib.sha512(data).hexdigest()
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def show_most_common_entities(entity_dict, n=5): """Format information on entity count in a string Args: entity_dict (dictionary): entities and their attributes n (int, optional): only the n most common occurrences are used. Defaults to 5. Return: string: formatted output string ...
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def html_movie_embed_qt(moviefile, width=400, height=400): """Return HTML for embedding a moviefile (QuickTime code).""" text = """ <object classid="clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B" codebase="https://www.apple.com/qtactivex/qtplugin.cab" width="%(width)s" height="%(height)s" > <param name="src" value...
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def get_number_digits(number: int) -> int: """Gets the number of digits in a number. Parameters ---------- number : int The number. Returns ------- int The number of digits. """ return len(str(number))
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import re def process(text): """ Remove the leading " * " prefixes from a Purpose, Returns, or Throws multiiline block of text that we've just pulled out of the function header. Convert <text> to `text` (Markdown code). """ text = re.sub(r'^ \*[ \t]+(\S)', r'\1', text, flags=re.MULT...
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def close(scope): """ Closes the existing connection with the remote host. This function is rarely used, as normally Exscript closes the connection automatically when the script has completed. """ conn = scope.get('__connection__') conn.close(1) scope.define(__response__=conn.response) ...
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def query_long_descr(database, dict_name): """Return long description for a given dictionary.""" curs = database.cursor() sql = ''' SELECT DI_LONG_DESCR FROM DICTIONARIES WHERE DI_DICT=? ''' curs.execute(sql, (dict_name,)) results = list(curs) if len(results) == 0...
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def db2lin(data): """ Convert from logarithm to linear units Parameters ---------- data: single value or an array Returns ------- returns the data converted to linear """ return 10**(data/10.)
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def is_not_none(value): """Helper function returning whether ``value is not None``""" return value is not None
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import torch def mapk(output, target, k=3): """ Computes the mean average precision at k. Parameters ---------- output (torch.Tensor): A Tensor of predicted elements. Shape: (N,C) where C = number of classes, N = batch size target (torch.int): A Tensor of elements t...
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def Check_VCF_Paths(tp_vcf_path, fp_vcf_path): """Checks to make sure there are equal numbers of tp and fp vcfs Parameters ---------- tp_vcf_path : str comma seperated list of TP vcf paths fp_vcf_path : str comma seperated list of FP vcf paths Returns ------- list ...
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def get_nearest_neighbours(p, N, i): """Return the nearest N neighbours to a given point, i Args: p (DataFrame): vertices dataframe N (int): integer for number of nearest neighbours to return i (int): loc within dataframe p Returns: a tuple of locs of the nearest neighbours...
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def mean(values): """ Computes the mean of a list of values. This is primarily included to reduce dependency on external math libraries like numpy in the core algorithm. :param values: a list of numbers :type values: list :return: the mean of the list of values :rtype: float >>> m...
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def sqlquote( value ): """Naive SQL quoting All values except NULL are returned as SQL strings in single quotes, with any embedded quotes doubled. """ if value is None or value=="": return 'NULL' return "'{}'".format(str(value).replace( "'", "''" ))
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from typing import Tuple from typing import List def parse_path(path_string: str) -> Tuple[str, List[str]]: """ Inputs: path_string: a string containing drive_name a colon and one or more folders like: 'my_drive:folder1/folder2' returns a tuple of the drive_name, folder_list ...
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