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def clean_texmath(txt): """ clean tex math string, preserving control sequences (incluing \n, so also '\nu') inside $ $, while allowing \n and \t to be meaningful in the text string """ s = "%s " % txt out = [] i = 0 while i < len(s)-1: if s[i] == '\\' and s[i+1] in ('n', 't'...
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import math def days_frac_to_dhms(days_frac): """Convert a day float to integer days, hours, minutes and seconds. Returns a tuple (days, hours, minutes, seconds). >>> days_frac_to_dhms(2.5305) (2, 12, 43, 55) """ days = math.floor(days_frac) hms_frac = days_frac - days hours = ma...
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def yes_or_no(question): """ a utility tool to ask the user yes/no question Parameters ---------- question : str the text for the question Returns ------- value : bool True or False """ while True: answer = input(question + ' (y/n): ').lower().strip() ...
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import os def resource_path(path: str) -> str: """ return the absolute path for a file """ return os.path.join(os.path.abspath(os.path.dirname(__file__)), path)
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def keyboard_data_signals_an_interrupt( keyboard_data, stop_signal_chars=frozenset(['\x03', '\x04', '\x1b']) ): """The function returns a positive stop signal (1) if the character is in the `stop_signal_chars` set. By default, the `stop_signal_chars` contains: * \x03: (ascii 3 - End of Text) * \...
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def vep_csq(): """Returns the CSQ entry of a VEP-annotated variant - Has the same fields as vep_csq_header""" # Note that this has both MANE_SELECT and MANE_PLUS_CLINCAL set for testing purposes, but that # will never happen in real CSQ entries csq_entry = """C|synonymous_variant|LOW|SCN5A|6331|Transcri...
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import os def scan_project_names(projects_dir): """Scan and return project list from directory.""" projects = [] for root, dirs, files in os.walk(projects_dir): for file in files: if file == 'Dockerfile': projects.append(os.path.basename(root)) return sorted(projects)
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def clean_prior_names(df, **kwargs): """ :param df: a pandas data frame containing experimental results :return: a pandas data frame containing the same results but with cleaner prior names """ df = df.replace('mle', 'MLE') df = df.replace('standard', 'Standard') df = df.replace('vamp', 'VAM...
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def get_metric(mod, obs, fun, dim='time', verbose=False): """Calculate a metric along a dimension. Metrics implemented: name * correlation > corr * mse > mse * rmse > rmse * mean percentage error > mpe * stan...
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import json import requests def get_public_ip(): """Fetch public IP of hosting server with the help of httpbin API""" return json.loads(requests.get('http://httpbin.org/ip').text)['origin']
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def remove_spaces(st): """ Removes spaces from a string :param st: (str) input string with spaces :return: (str) string without any spaces """ return st.replace(' ', '')
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def usage(): """Returns usage string. May be different on what's installed in this Sakai Instances""" return ''' turnitin runtests - runs tests turnitin runtest testname - run a single named test turnitin showtests - show all available tests turnitin viewasnn siteid taskid - view the info...
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import itertools def Powerset(iterable): """powerset([1,2,3]) --> () (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3).""" s = list(iterable) return itertools.chain.from_iterable(itertools.combinations(s, r) for r in range(len(s)+1))
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def update_leases(transform, persistence_service): """ Update the leases configuration in the persistence service. :param transform: A function to execute on the currently configured leases to manipulate their state. :param persistence_service: The persistence service to which the updat...
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def fib(n: int) -> int: """Fibonacci numbers with naive recursion >>> fib(20) 6765 >>> fib(1) 1 """ if n == 0: return 0 if n == 1: return 1 return fib(n-1) + fib(n-2)
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import subprocess def get_hostname() -> str: """Get the hostname from the command line utility `hostname` :return: (str) of the hostname """ p = subprocess.Popen(["hostname"], stdout=subprocess.PIPE, stderr=subprocess.PIPE) return p.communicate()[0].rstrip().decode("utf-...
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def pkg_key(pkg, type_): """ generate a package key for a given type string Generates a compatible "package key" for a unsanitized package name ``pkg`` of a specific key ``type``. The package string is "cleaned" to replaces select characters (such as dashes) with underscores and becomes uppercase. ...
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import re def generate_node_id(node, data): """Generate a node ID from the node label, extracts data from: [$ID]. Return the extracted node ID and the label, without the ID part, so it can be the expression if one isn't specified in the description.""" pat = r"\[(?P<node_id>\w+)\]" m = re.search(...
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import argparse def parse_args(): """ Parses the command-line arguments. """ parser = argparse.ArgumentParser(description='Submits data to the real-time streaming endpoint.') parser.add_argument('-k', '--key', required=True, help='YOUR_DEEPGRAM_API_KEY (authorization)') parser.add_argument('input'...
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from typing import Counter def most_repeated_values(query_list): """[Get most repeated values for each key in list of objects] Args: query_list ([list]): [List of dictionaries containing query results from three different APIs. Dict Keys are 'deductible', 'stop_loss', 'oop_max'] ...
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def get_translation_suggestions(vocabulary_article, translation_suggestions): """Returns XML with translate suggestions""" res = [] if len(vocabulary_article['def']) != 0: for article in vocabulary_article['def']: for translation in article['tr']: if 'ts' in article.keys(...
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def normalize(msg): """ Normalizes the plain text removing all invalid characters and spaces :param msg: Plain text to be normalized :return: the normalized message without invalid chars """ return "".join([let.lower() for let in msg if let.isalpha() or let.isdigit()])
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import json def load_json(filename): """Load dictionary from JSON file.""" with open(filename, 'r') as f: mybooks = json.load(f) return(mybooks)
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def update_nested_dictionary(old, new): """ Update dictionary with the values from other dictionary. Recursively update any nested dictionaries if both old and new values are dictionaries. :param old: Old dictionary that will be updated :type old: dict :param new: New dictionary that contains t...
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def fisbHexErrsToStr(hexErrs): """ Given an list containing error entries for each FIS-B block, return a string representing the errors. This will appear as a comment in either the result string, or the failed error message. Args: hexErrs (list): List of 6 items, one for each FIS-B block. Each entry ...
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def wing(Sw,bw,cw,Nwr,t_cw,Nwer,nult,GW): """ Compute weight of human-powered aircraft wing Assumptions: All of this is from AIAA 89-2048, units are in kg. These weight estimates are from the MIT Daedalus and are valid for very lightweight carbon fiber composite structures. This may n...
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def _spline_to_path_list(spline, height, replace_with_prev=False): """Converts SplineSet to a list of tokenized commands in svg path.""" path = [] prev_xy = [] for line in spline.splitlines(): if not line: continue tokens = line.split(' ') cmd = tokens[-2] if ...
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import argparse import os def parse_args(argv): """Parse input arguments""" parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('exp_name', type=str, help='id of experiment. Ex: exp0') ...
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import codecs def get_nationality(nation): """Test id a word is a nationality adjective""" with codecs.open("nationalities.txt", "r", "utf-8") as f: nationalities = {} for x in f.readlines(): nationalities[x.strip().lower().split(',')[1]] = x.strip().lower().split(',')[0] res...
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import numpy as np from typing import Collection from typing import Dict def symbol_counts_dist(texts: Collection[str], symbols: str = "`~!@#$%^&*)(-_+=|\\}{][:;><,.?" ) -> Dict[str, Dict[int, int]]: """Count distribution of symbols in strings.""" return { ...
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import os def is_elf_binary(bin_path): """Return true if the binary is valid ELF.""" if not os.access(bin_path, os.X_OK): return False if os.path.islink(bin_path) or os.path.isdir(bin_path): return False with open(bin_path, 'rb') as f: if f.read(4)[1:].decode('ascii') != 'ELF': return False ...
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def read_lines(file_name): """ Read lines from given file and return as list """ with open(file_name, 'r') as fobj: lines = fobj.readlines() return lines
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def defaults_add(dictionary, defaults): """if a value has not been defined in the dictionary add it from defaults""" if dictionary: for key in defaults.keys(): if not key in dictionary.keys(): dictionary[key] = defaults[key] return dictionary else: return ...
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def count_frequency(my_list): """ count the frequency of elements in a list using a dictionary Args: my_list (list): List Returns: dict: Dictionary containing unique item and frequency Example:: >> my_list = ["happy", "neutral", "happy"] >> count_frequency...
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def _ensure_list(item): """ Ensures that the given item is a list. :param item: :return: """ if item is None: return [] if isinstance(item, list): return item if isinstance(item, tuple): return list(item) return [item]
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import ast async def literal_eval(str_to_eval: str): """ Evaluate the input using ast.literal_eval() Parameters ---------- str_to_eval : str A string to be evaluated. Returns ------- dict A dict containing python literal. Examples -------- The following ...
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import glob import os def iterate_dictionary(path): """iterates through all kinds of files in a directory by using the glob package and leaves directories alone""" if path[-1] != "/": path += "/" files_only = list(filter(lambda obj: os.path.isfile(obj), glob.glob(path + "*"))) retu...
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from typing import Dict import subprocess def get_pip_requirements() -> Dict[str, str]: """This assumes it was generated with pip freeze, i.e, all lines are ==""" output = subprocess.check_output("pip freeze", shell=True, text=True) cleaned_packages: Dict[str, str] = {} for row in output.split("\n"): ...
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from typing import Tuple def asn1_get_value(der: bytes, indices: Tuple[int, int, int]) -> bytes: """get value""" ixs, ixf, ixl = indices return der[ixf : ixl + 1]
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def add_neighbours(cluster_index, Adj, check, factor=0.5): """ Creates a list of nodes which are densely connected between each other. Parameters ---------- cluster_index : Node index of nodes belonging to a densely connected cluster Adj : Adjacency matrix of the graph check : Temp arra...
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from pathlib import Path def guess_array_type(raw_data: Path) -> str: """ Guess array type, just like its name suggested """ raw_data = Path(raw_data) if not raw_data.exists(): raise FileNotFoundError(f"Could not find: {str(raw_data)}") array_type = None for file in raw_data.iterd...
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import torch def sequence_loss(flow_preds, flow_gt, valid_flow_mask, gamma=0.8, max_flow=400): """Loss function defined over sequence of flow predictions""" if gamma > 1: raise ValueError(f"Gamma should be < 1, got {gamma}.") # exlude invalid pixels and extremely large diplacements flow_norm...
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def floodFill(pos, data, dataArray): """ checks how much room there is if snake does a move used so snake doesn't run into a corner returns free space """ count = 0 try: if dataArray[pos["y"]][pos["x"]] == 1 or pos["x"] not in range (0, data["board"]["width"]) or pos["y"] not in range(0, data["board"]["height"...
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def header_exists(header_name, headers): """Check that a header is present.""" return header_name.lower() in (k.lower() for (k, _) in headers)
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def pre_process_expressions(expressions, variable_templates): """ This one is pretty simple - pass in a list of expressions which contain references to templates and pass a dictionary of the templates themselves. Strings will only be evaluated which are prepended with $. Parameters ---------- ...
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import torch def neigh_square(position_diff: torch.Tensor, sigma: torch.Tensor) -> torch.Tensor: """ Square-shaped neighborhood scaling function based on center-wise diff `position_diff` and radius `sigma`. Parameters ---------- position_diff : torch.Tensor The positional difference aroun...
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def join_strings(strings, glue=" AND "): """ Returns the non-empty strings joined together with the specified glue. @param glue separator used as glue between strings @return (joined string, number of strings actually used) """ strings = list(filter(None, strings)) return glue.joi...
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import argparse def get_parser(): """ Get parser. :return: parser :rtype: argparse.ArgumentParser """ parser = argparse.ArgumentParser('Evaluate predicted occupancy grids and LTSDFs.') parser.add_argument('--predictions', type=str, help='Predictions HDF5 file.') parser.add_argument('...
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import bz2 def task_compress_bz2(): """bz2 compression (C)""" with open(__file__, "rb") as f: arg = f.read(3000) * 2 def compress(s): bz2.compress(s) return compress, (arg, )
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def custom(datacells, ncells, value): """Calculate percent of total""" x = float(datacells.GetUnformattedValueAt(ncells-1,2)) # total return float(value) / x
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def shape(x): """Change str to List[int] >>> shape('3,5') [3, 5] >>> shape(' [3, 5] ') [3, 5] """ # x: ' [3, 5] ' -> '3, 5' x = x.strip() if x[0] == '[': x = x[1:] if x[-1] == ']': x = x[:-1] return list(map(int, x.split(',')))
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def Node(k: int, v: str, l: dict, r: dict) -> dict: """ Crée un arbre binaire avec un noeud de clé k, de valeur v, de fils gauche l et de fils droit r.""" return {"Node": (k, v, l, r)}
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def determineWhatIsDeleted(ref, alt): """Must take the deletion from the ends. """ altIdx = ref.find(alt) if altIdx == 0: # the tail is deleted # AGGTCTG to A # TCCTACACCTACT to TCCTACA so TCCTACA(CCTACT) (want) endDelIdx = altIdx + len(alt) return ref[endDelIdx:]...
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import glob import os def get_files(directory, pattern = "*.gz", full_path = True): """ Returns the files in the specified directory. :param directory: the directory to scan :param pattern: the file extension, default '*.gz'. :param full_path: if True the full path to the files is retured, otherw...
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def max_value(tab): """ Brief: computes the max with positiv value Args: tab: a liste of numeric value exepcts at least one positive valus, raise expection Return: the max value Raises : ValueError if no positive value is found """ if not(isinstance(tab, list)): rai...
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def calc(x, y, serial): """ Find the fuel cell's rack ID, which is its X coordinate plus 10. Begin with a power level of the rack ID times the Y coordinate. Increase the power level by the value of the grid serial number (your puzzle input). Set the power level to itself multiplied by the rack I...
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def swap_chunk(chunk_orig): """Swap byte endianness of the given chunk. Returns: swapped chunk """ chunk = bytearray(chunk_orig) # align to 4 bytes and pad with 0x0 chunk_len = len(chunk) pad_len = chunk_len % 4 if pad_len > 0: chunk += b'\x00' * (4 - pad_len) chun...
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def _cut_title(fixed_front, variable, fixed_rear, MAX_LENGTH=240): """Return the given title smartly cut""" fixed_length = len(fixed_front) + len(fixed_rear) available_length = MAX_LENGTH - fixed_length chunked = variable.split() part = 1 while len(variable) > available_length: variable ...
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def sdfGetTitle(mol): """ sdfGetTitle() returns the title of molecule mol """ molblock = mol["molblock"] if not molblock: return None first_eol_pos = molblock.find('\n') return molblock[0:first_eol_pos]
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def make_snapshots(frame, ignore): """Extract a subset of atoms from a given frame.""" snapshot = { 'header': 'Removed.', 'box': frame['box'], 'residunr': [], 'residuname': [], 'atomname': [], 'atomnr': [], 'x': [], 'y': [], 'z': [], } ...
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def getFluctuationFrame( dataFrame, valueKeys, collectByKeys, averageOverKeys=None, ): """Routine for computing the collective average and standard deviation information for specified keys in a data frame. Computes the mean and standard deviations for the 'valueKeys' over all keys no collected ...
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def comp_sym(self): """Compute the symmetry factor of the lamination Parameters ---------- self : LamHole A LamHole object Returns ------- sym : int Number of symmetries of the Lamination is_antisym : bool True if an anti-symmetry is possible after the symmetrie...
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def measure(function, xs, ys, popt, weights): """ measure the quality of a fit """ m = 0 n = 0 for x in xs: try: if len(popt) == 2: m += (ys[n] - function(x, popt[0], popt[1]))**2 * weights[n] elif len(popt) == 3: m += (ys[n] - func...
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def find_schema_links(resource_type, schemas): """ returns a dict with schema and paths pointing to resource_type e.g. find_schema_links("person", schemas) should return: { "software": [ [ "contributors", "foreignKey" ] ] },...
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def cg(A, b, x, imax=50, eps=1e-6): """ A, b, x : matrix, rhs, solution imax : maximum allowed iterations eps : tolerance for convergence """ # allocate work vectors r = b.duplicate() d = b.duplicate() q = b.duplicate() # initialization i = 0 A.mult(x, r) r....
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import os def get_times(file): """ Return a tuple of (atime, mtime) for the given file. """ stat_info = os.stat(file) return (stat_info[7], stat_info[8])
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import sys import shlex def invocation(): """reconstructs the invocation for this python program""" cmdargs = [sys.executable] + sys.argv[:] invocation = " ".join(shlex.quote(s) for s in cmdargs) return invocation
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import json def compare(df): """ If the category of UEID is present in the segment file, it is considered as normal(0) otherwise, the sample is considered as anomaly. """ with open("ad/ue_seg.json", "r") as json_data: segment = json.loads(json_data.read()) anomaly = [] for i in d...
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def mean_gare(data): """ Affiche le barycentre des données. :param DataFrame data: Tableau de données numériques. :return: * **b** (*pd.core.Series.Series*) - Le vecteur aux coordonnées moyennes. :example: .. code:: python >>> import asltam as atm >>> # aff...
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from typing import Optional import os def auto_detect_content_type(filename: Optional[str]) -> Optional[str]: """Auto detects the content type based on the filename. Args: filename : A filename to use to auto detect the content type. Returns: The content type of the file. None if the con...
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def clone_aiida_structure (s): """ A cloned structure is not quite ready to store more atoms. This function fixes it """ t=s.clone() t._internal_kind_tags={} return t
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import sys def isatty(): """ Wrapper for isatty I use this for monkeypatching input detection in the add method. Its not nice. It works. Its mine <3 """ return sys.stdin.isatty()
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def calculate_difference(dsm_array, dtm): """Calculate the difference between the dsm and dtm""" dtm_array = dtm.read(1, masked = True) difference = dsm_array - dtm_array difference.data[difference < 0] = 0 # We set to 0 anything that might have been negative return difference
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def norm_colname(colname): """Given an arbitrary column name, translate to a SQL-normalized column name a la CARTO's Import API will translate to Examples * 'Field: 2' -> 'field_2' * '2 Items' -> '_2_items' Args: colname (str): Column name that will be SQL normalized Return...
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def destination_mac(source_list): """Returns the destination MAC address, byte 0 - byte 5""" output = "" for i in range(6): output += source_list[i] + " " return output[:-1]
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def build_vo_from_dn(user_dn): """ Generate an 'anonymous' VO from the user_dn """ components = filter(lambda c: len(c) == 2, map(lambda c: tuple(c.split('=')), user_dn.split('/'))) domain = [] uname = '' for key, value in components: if key.upper() == 'CN' and not uname: ...
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from typing import Iterable from typing import Any def composed_to_string(seq: Iterable[Any]) -> str: """Test helper to convert a sql query to a string for comparison. Works for queries built with postgres.sql.Composable objects. From https://github.com/psycopg/psycopg2/issues/747#issuecomment-662857306 ...
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def makesafe(s): """Makes the given string "safe" by replacing spaces and lower-casing (less aggressive)""" def rep(c): if c.isalnum(): return c.lower() else: return '_' ret = ''.join([rep(c) for c in s]) return ret
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from glob import glob import os import stat def get_searched_ids(root_directories): """Export the inode numbers of the selected directories.""" inode_to_path = {} inodes = "{" total_dirs = 0 for root_directory in root_directories.split(','): searched_dirs = glob(root_directory, recursive=T...
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def _get_empty_lines(text): """Get number of empty lines before and after code.""" before = len(text) - len(text.lstrip('\n')) after = len(text) - len(text.strip('\n')) - before return before, after
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import re def unescape(in_s): """ :param in_s: Input string """ return re.sub(r"\\(.)", r"\1", in_s)
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def _get_db_table_for_model(model): """ Return table name in database server for passed model. """ return model._meta.db_table
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def INT_ICART(a, b, c): """Given a, b, and c, return a cartesian offset. #define INT_ICART(a, b, c) (((((((a)+(b)+(c)+1)<<1)-(a))*((a)+1))>>1)-(b)-1) """ return ((((((a + b + c + 1) << 1) - a) * (a + 1)) >> 1) - b - 1)
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async def root() -> dict: """Get root.""" return {"message": "Welcome:)"}
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def run_process(cls_instance, message): """ 运行一个子进程 :param MultiProcessExecutor cls_instance: 运行实例 :param Message message: 消息 :return: 执行结果 :rtype: dict """ return cls_instance.message_handler(message)
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def pixels_voisins(y, x): """ Calcul les 4 voisins du point aux coordonnees (y,x) Retourne les voisins a droite gauche bas haut """ vecteur = [(0, 1), (0, -1), (1, 0), (-1, 0)] voisins = [] for v in vecteur: voisins.append((v[0] + y, v[1] + x)) return voisins
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def walk(path, container): """ Recurse over the ActBlue JSON object, and get the values that we need, based on the settings file. Returns a single value for each path. """ if not container or isinstance(container, str): return None key = path[0] if len(path) == 1: if key...
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def feature_diff(features_a, features_b): """Compute features_a - features_b :param features_a: :param features_b: :return: """ keys = set(features_a.keys() + features_b.keys()) diff = dict() for k in keys: v_a = features_a.get(k, 0.0) v_b = features_b.get(k, 0.0) ...
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def sparse_mimmax(A, B, type="mim"): """Return the element-wise mimimum/maximum of sparse matrices `A` and `B`. Parameters ---------- A: The first sparse matrix B: The second sparse matrix type: The type of calculation, either mimimum or maximum....
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import argparse def parse_command_line(): """Parse the utility's command-line arguments.""" parser = argparse.ArgumentParser(description='Read an AFP file or files and output an ASCII representation') parser.add_argument( 'afp_files', metavar='afp-file', nargs='+', help='an...
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from typing import List def find_missing_element(numbers: List[int]) -> int: """ Finds the missing element in a list of numbers :param numbers of numbers :return missing element :rtype: int """ missing_element = len(numbers) + 1 for index, number in enumerate(numbers): missi...
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import os def rebase(path_to_rebase, base): """ Rebase the parameter (a list or a single string) """ if base is None or base == "" or base == ".": return path_to_rebase path_list = path_to_rebase if isinstance(path_to_rebase, list) else [path_to_rebase] rebased_paths = [] for path in p...
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import os def _is_astropy_source(path=None): """ Returns whether the source for this module is directly in an astropy source distribution or checkout. """ # If this __init__.py file is in ./astropy/ then import is within a source # dir .astropy-root is a file distributed with the source, but ...
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def format_literal(raw): """Format a literal into a safe format. This is used to format the flont:Literal IRI. """ return "_" + raw.replace(" ", "_")
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def make_PEM_filename(cert_id: str) -> str: """Create a filename for PEM certificate""" return cert_id + '.pem'
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def is_in_list(num, lst): """ >>> is_in_list(4, [1, 2, 3, 4, 5]) True >>> is_in_list(6, [1, 2, 3, 4, 5]) False >>> is_in_list(5, [5, 4, 3, 2, 1]) True """ if not lst: return False else: return lst[0] == num or is_in_list(num, lst[1:])
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def get_investigation_data(investigation_response): """Get investigation raw response and returns the investigation info for context and human readable. Args: investigation_response: The investigation raw response Returns: dict. Investigation's info """ investigation_data = { ...
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def wraps(wrapped, fun, namestr="{fun}", docstr="{doc}", **kwargs): """ Like functools.wraps, but with finer-grained control over the name and docstring of the resulting function. """ try: name = getattr(wrapped, "__name__", "<unnamed function>") doc = getattr(wrapped, "__doc__", "") or "" fun.__d...
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import re def keyvault_name(name: str) -> bool: """Validate the name of the keyvault. Args: name (str): Name of the keyvault. Returns: bool: True or False depending on the name validity. """ regex = "^[a-zA-Z0-9-]{3,24}$" pattern = re.compile(regex) return pattern.match(...
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def misses_cost(a: set, b: set): """ Misses cost measures the proportion of non-sensitive itemsets hidden by the sanitisation process; this indicates the number of itemsets which are consistent across the original and sanitised database. Given a transactional database D and an associated sanitised data...
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