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def find_nodes_with_degree(graph, degree): """ Find nodes with degree N in a graph and return a list """ degrees = graph.degree() nodes = list() for node in degrees: if degrees[node] == degree: nodes.append(node) return nodes
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from textwrap import dedent import traceback def format_exception_trace(exception: BaseException) -> str: """ Formats the traceback part of an exception as it would appear when printed by Python's exception handler. Args: exception: The exception to format Returns: A string, usually ...
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def auto_intercept(with_intercept, default): """A more concise way to handle the default behavior of with_intercept""" if with_intercept == "auto": return default return with_intercept
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def sum_forces(forces): """Returns the summed vector of a dictionary of forces""" return sum(forces.values())
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def safe_index(l, e): """ Return index of element e in list l. If e is not present, return the last index """ try: return l.index(e) except: return len(l) - 1
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def format_timedelta(time_delta): """ Convert a datetime.timedelta to str format example output: "0h:0m:18s" Parameters ---------- time_delta: datatime.timedelta Returns ------- str: formatted timedelta """ d = {} d["hours"], rem = divmod(time_delta.seconds, 3600) ...
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def title_string(in_str): """ Converts a string to title case Title case means that the first character of every word is capitalized, otherwise lowercase Parameters ---------- in_str: str The string to convert to title case Returns ------- str The input string...
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def find_start_end(grid): """ Finds the source and destination block indexes from the list. Args grid: <list> the world grid blocks represented as a list of blocks (see Tutorial.pdf) Returns start: <int> source block index in the list end: <int> destination block index...
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def validate_boolean(value, label): """Validates that the given value is a boolean.""" if not isinstance(value, bool): raise ValueError('Invalid type for {0}: {1}.'.format(label, value)) return value
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def get_export_type(export_type): """Convert template type to the right filename.""" return { "css": "colors.css", "dmenu": "colors-wal-dmenu.h", "dwm": "colors-wal-dwm.h", "st": "colors-wal-st.h", "tabbed": "colors-wal-tabbed.h", "gtk2": "colors-gtk2.rc", ...
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def make_get_tensors_fn(output_tensors): """Create a function that outputs a collection of tensors from the dataset.""" def _get_fn(data): """Get tensors by name.""" return {tensor_name: data[tensor_name] for tensor_name in output_tensors} return _get_fn
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def check_condition_status(job, condition_type): """ Determines if a generic job has a condition type: Complete(Success) or Failure """ conditions = job.status.conditions if conditions: for condition in conditions: if condition.type == condition_type and condition.status == "True...
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import torch def one_hot(args, indices): """ Returns a one-hot tensor. This is a PyTorch equivalent of Tensorflow's tf.one_hot. """ encoded_indicate = torch.zeros(args.train_n_way*args.train_n_query, args.train_n_way).cuda() index = indices.long().view(-1,1) encoded_indicate = encoded_indi...
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def gradient(x, y, w): """MSE gradient.""" y_hat = x @ w error = y - y_hat gradient = -(1.0 / len(x)) * 2 * x.T @ error mse = (error ** 2).mean() return gradient, mse
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def _rm_cfg_key(cfg, name): """ Remove key from config and return the updated config. """ if name in cfg: del cfg[name] return cfg
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def _is_valid_age(user_age): """ Determines if the age is valid. Args: user_age: Age to test. Returns: bool: If the age is valid. """ if type(user_age) != int: return False elif user_age < 0: return False return True
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def merge_list(*_list: list): """Combines multiple lists into a new one. Parameters ---------- *_list : list It contains all of the lists inside it. Returns ------- merged_list : list Returns the Merged list. """ merged_list = [] for list in _list: merg...
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def _get_chromosome_dirs(input_directory): """Collect chromosome directories""" dirs = [] for d in input_directory.iterdir(): if not d.is_dir(): continue # Just in case user re-runs and # does not delete output files elif d.name == 'logs': continue ...
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import math def circ_in(t): """Circular in. A quarter of a circle. :math:`f(t) = \sqrt{1 - t^2}`""" return 1 - math.sqrt(1 - t * t)
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import json def parse_event(event): """ :param event: event object received by lambda :return: tuple containing message and metadata from an event object """ metadata = {} message = json.loads(event['Records'][0]['Sns']['Message']) if 'NotificationMetadata' in message.keys(): metad...
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def _get_pid_from_file(fn): """Get the PID from the given file""" with open(fn) as pid_file: pid = int(pid_file.read().strip()) return pid
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from typing import OrderedDict import csv def get_fields(csv_file, fields): """Return a dictionary mapping each name in `fields` to the sequence of values seen for that field in the given file. """ result = OrderedDict() for field in fields: result[field] = [] with open(csv_file) ...
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def retain_reference(journal_reference, min_size=3, required_fields=["author","title"]): """ Determine whether the input reference should be retained, and thus resolved, or skipped. This allows to skip erroneously extracted references, partial ones, etc. :param journal_reference: the input reference (e...
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def first_non_consecutive(arr): """ Finds the first element within an array that is not consecutive. :param arr: An array of ints. :return: the first element not consecutive, otherwise None. """ for i, j in enumerate(arr): if j != arr[0] + i: return j return None
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def get_digits(value: float) -> int: """ Get number of digits after decimal point. """ value_str: str = str(value) if "e-" in value_str: _, buf = value_str.split("e-") return int(buf) elif "." in value_str: _, buf = value_str.split(".") return len(buf) else: ...
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def translate(atms, vec): """Translate a list of atoms :param atms: The list of atoms, given as a pair of the symbol and the coordinate in numpy array. :param vec: A numpy array giving the translation vector. """ return [ (i[0], i[1] + vec) for i in atms ]
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import pickle import glob def get_num_examples(data_dir, mode): """ Get the number of examples in directory. :param data_dir: str - data directory :param mode: str - `training`, `test` or `validate` (must match folder names) :return: int - number of examples """ with open('{}/labels.pickle...
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def parse_ft_line(line, vocab_to_idx=None, lbl_to_idx=None): """Convert line from fastText format to list of labels and tokens. If vocab_to_idx and/or lbl_to_idx provided, tokens are converted to integer indices. """ line = line.strip().split() labels = [w for w in line if w.startswith('__label__')...
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import typing import pathlib def parse_requirements_file (filename: str) -> typing.List: """read and parse a Python `requirements.txt` file, returning as a list of str""" with pathlib.Path(filename).open() as f: # pylint: disable=C0103 return [ l.strip().replace(" ", "") for l in f.readlines() ]
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def get_node(value): """Return new node with value.""" return { 'value': value, 'next': None, 'prev': None, }
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def check_dataset_groups(dataset, groups): """Check that all groups given are actually contained in the dataset. """ dataset_groups = {d.group for d in dataset} return set(groups) == dataset_groups
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def aggregate_shares(df): """Compute share types by year and field.""" return (df.groupby(["Year", "types", "field"]).size() .reset_index() .rename(columns={0: "count"}))
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def SymbolTypeToHuman(type): """Convert a symbol type as printed by nm into a human-readable name.""" return {'b': 'bss', 'd': 'data', 'r': 'read-only data', 't': 'code', 'w': 'weak symbol', 'v': 'weak symbol'}[type]
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import math def num_action_type_bits(num_actions): """For a table with `num_actions` different actions that can be performed, return the number of bits to do a straightforward encoding of these as separate unique ids.""" assert(num_actions >= 0) if num_actions == 0: return 0 return int...
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def _split(f, children): """ Given a function that returns true or false and a list. Return a two lists all items f(child) == True is in list 1 and all items not in the list are in list 2. """ l1 = [] l2 = [] for child in children: if f(child): l1.append(child) ...
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def parse_messages(buf): """ Parses for messages in the buffer *buf*. It is assumed that the buffer contains the start character for a message, but that it may contain only part of the rest of the message. NOTE: only understands lengthless messages for now. Returns an array of messages, and th...
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def precprint(prec_type, prec_cap, p): """ String describing the precision mode on a p-adic ring or field. EXAMPLES:: sage: from sage.rings.padics.misc import precprint sage: precprint('capped-rel', 12, 2) 'with capped relative precision 12' sage: precprint('capped-abs', 11...
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def read_file(filename): """ Read whole file to list of stripped strings :param filename: filepath :return: list of strings """ with open(filename) as f: lines = f.readlines() return map(str.rstrip, lines)
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def fits_column_format(format): """Convert a FITS column format to a human-readable form. Parameters ---------- format : :class:`str` A FITS-style format string. Returns ------- :class:`str` A human-readable version of the format string. Examples -------- >>> f...
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from pathlib import Path def strip_build_dir(build_dir, node): """Small util function for making args match the graph paths.""" return str(Path(node).relative_to(build_dir))
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def quotify(string): """Return the string with quotes >>> quotify("some string") '"some string"' """ return f'"{string}"'
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def link_cmd(path, link): """Returns link creation command.""" return ['ln', '-sfn', path, link]
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def locate_zephyr_base(checkout, version): """Locate the path to the Zephyr RTOS in a ChromiumOS checkout. Args: checkout: The path to the ChromiumOS checkout. version: The requested zephyr version, as a tuple of integers. Returns: The path to the Zephyr source. """ return ...
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def valid_number(phone_number): """Valid a cellphone number. :param phone_number: Cellphone number. :type phone_number: str :returns: true if it's a valid cellphone number. :rtype: bool """ phone_number = phone_number.replace(" ", "") if len(phone_number) != 10: return False ...
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def bool_from(obj, default=False): """ Returns: True if obj is not None and its string representation is not 0 or False (case-insensitive). If obj is None, 'default' is used. """ return str(obj).lower() not in ('0', 'false') if obj is not None else bool(default)
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def edges_to_adj_list(edges): """ Transforms a set of edges in an adjacency list (represented as a dictiornary) For UNDIRECTED graphs, i.e. if v2 in adj_list[v1], then v1 in adj_list[v2] INPUT: - edges : a set or list of edges OUTPUT: - adj_list: a dictionary with the vertices as ...
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def format_sec_to_dhm(sec): """Format seconds to days, hours, minutes. Args: sec: float or int Number of seconds in a period of time. Returns: str Period of time represented as a string on the form ``0d\:00h\:00m``. """ rem_int, s_int = divmod(int(sec), 60) rem_int, m_int,...
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def area_tr(base_t,height_t): """Calculates the area of a triangle with given base and height :Input: The base and height of the triangle (float, >=0) :Returns: The area of the triangle (float).""" if base_t < 0: raise ValueError("The base must be >= 0.") if height_...
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import six def ensure_unicode(val): """Ensure that a a given value is a unicode string. If ``val`` is a :py:data:`six.binary_type <binary type>`, assume it's UTF-8 and decode it. :param val: A :py:data:`six.binary_type <binary>` or :py:data:`six.text_type <text>` type. :rtype: :py:class:`...
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def is_super(node): """return True if the node is referencing the "super" builtin function """ if getattr(node, 'name', None) == 'super' and \ node.root().name == '__builtin__': return True return False
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def correct_capitalization(token, pronoun): """ If the original pronoun was capitalized, capitalize the new pronoun. """ if token.text[0].isupper(): pronoun = pronoun.capitalize() return pronoun
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def cache_get_langs(sql): """Get the list of languages from tooltip database.""" return [row[0] for row in sql.execute( "SELECT DISTINCT lang FROM vars").fetchall()]
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def ellipsis(text, length, cutoff='[...]'): """ shortens text with a [...] at the end """ return text if len(text) <= length else \ text[:length - len(text) - len(cutoff)] + cutoff
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def get_clean_path_option(a_string): """ Typically install flags are shown as 'flag:PATH=value', so this function splits the two, and removes the :PATH portion. This function returns a tuple consisting of the install flag and the default value that is set for it. """ option, default = a_string....
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def trim_leading_lines(lines): """ Trim leading blank lines. """ lines = list(lines) while lines and not lines[0]: lines.pop(0) return lines
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def parse_bim_line(line): """ Parse a bim line. Format should be: chromosome SNP_name 0 location allele_1 allele_2. allele_1 != allele_2. Parameters ---------- line: str bim line to parse. Returns: tuple Dictionary entry with SNP name as key. """ elems = line.transl...
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import torch def interpolate_irreg_grid(interpfunc, pos): """Interpolate the funtion Args: interpfunc (callable): function to interpolate the data points pos (torch.tensor): positions of the walkers Nbatch x 3*Nelec Returns: torch.tensor: interpolated values of the function eval...
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def _log_probability_picklable(theta, instance, name): """ Method for multiprocessing to work with class instance methods (making it pickleable). """ return getattr(instance, name)(theta)
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import requests def get_test_quote(backend, headers, amount, buy_sell="buy", pair="XUS_USD") -> str: """Creates a test quote and returns its id""" quote_payload = {"action": buy_sell, "amount": amount, "currency_pair": pair} quote_res = requests.post( f"{backend}/api/account/quotes", headers=heade...
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from pathlib import Path from typing import Optional import filecmp def files_are_identical(src_path: Path, dst_path: Path, content: Optional[str]) -> bool: """Tell whether two files are identical. Arguments: src_path: Source file. dst_path: Destination file. content: File contents. ...
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def single_type_count(clothes_list, type): """ Returns an integer value of the number of a given type of clothing in a list. Args: clothes_list (list): List of clothing objects to count from type (str): Clothing type to count Returns: type_count (int): Number of garments of the...
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def remember_umbrella(weather_arg: str) -> bool: """Remember umbrella Checks current weather data text from :meth:`get_weather` for keywords indicating rain. Args: weather_arg: String containing current weather text of specified city. Returns: True if any of the rain keywords are foun...
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import torch def mse(target, predicted): """Mean Squared Error""" return torch.mean((target - predicted)**2)
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def _build_merge_vcf_command_str(raw_vcf_path_list): """Generate command string to merge vcf files into single multisample vcf.""" command = " ".join([ 'bcftools merge', " ".join(raw_vcf_path_list) ]) return command
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def roi_reorder(sectors, new_order): """ Given a roi with dimensions RxWxH where R are rois, reorder the roi order. Parameters ---------- sectors : 3D array numpy array with dimensions RxHxW where R=roi, H=height, W=width new_order : list list of indices in correct o...
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def regularise_periapse_time(raw, period): """ Change the periapse time so it would be between 0 and the period """ res = raw if res < 0: res += period if res > period: res -= period return res
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def get_next_item(iterable): """Gets the next item of an iterable. If the iterable is exhausted, returns None.""" try: x = iterable.next() except StopIteration: x = None except AttributeError: x = None return x
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import six import binascii def _uvarint(buf): """Reads a varint from a bytes buffer and returns the value and # bytes""" x = 0 s = 0 for i, b_str in enumerate(buf): if six.PY3: b = b_str else: b = int(binascii.b2a_hex(b_str), 16) if b < 0x80: ...
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def _ensure_exists(path): """Return the path after ensuring it exists.""" if not path.exists(): raise RuntimeError(f"The path {path} does not exist!") return path
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def row_divisibles(row): """Find two items in a list of integers that are divisible""" row = list(row) row_max = max(row) for i in sorted(row): for multiplier in range(2, int(row_max/i) + 1): if i * multiplier in row: return (i, i * multiplier)
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def load_plugin_names(settings): """ Generate a unique name for a plugin based on the class name module name and path >>> settings = {'PLUGINS': ['a', 'b.c', 'a.c']} >>> load_plugin_names(settings) ['a', 'c', 'a.c'] """ seen = set() def generate_name(path, maxsplit=0, splits=None):...
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def test_function_with_fancy_docstring(arg): """Function with a fancy docstring. Args: arg: An argument. Returns: arg: the input, and arg: the input, again. @compatibility(numpy) NumPy has nothing as awesome as this function. @end_compatibility @compatibility(theano) Theano has nothing a...
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def parse_etraveler_response(rsp, validate): """ Convert the response from an eTraveler clientAPI query to a key,value pair Parameters ---------- rsp : return type from eTraveler.clientAPI.connection.Connection.getHardwareHierarchy which is an array of dicts information about the 'c...
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import re def keyword_score(title, desc, keywords): """Return match score for column title:desc given keyword list. Args: title: str of column title desc: str of column description keywords: list of keywords to match Returns: int of weighted keyword matches """ score = 0 title_words = s...
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import sqlite3 def get_columns(cursor, table): """Returns list of column names used in table.""" cursor.execute('PRAGMA table_info({0})'.format(table)) columns = [x[1] for x in cursor] if not columns: raise sqlite3.ProgrammingError('no such table: {0}'.format(table)) return columns
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import re def _extract_id(id_string): """Extracts the numeric ID from the representation of the subject or object ID that appears as an attribute of the svo element in the Medscan XML document. Parameters ---------- id_string : str The ID representation that appears in the svo element...
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def format_vdu_interfaces(interfaces_list): """ Convert the list of VDU interfaces in a dict using the name of the interfaces as keys Args: interfaces_list (list): The list of VDU net interfaces. Each item is a dict. Returns: dict: The interfaces as dict { "user": { ...
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import requests import json def cts_brenda_to_kegg(brenda_name, max_requests=3): """ Returns the KEGG id of a compound, from the name on BRENDA. """ cts_response = requests.get('http://cts.fiehnlab.ucdavis.edu/' 'service/convert/Chemical%20Name/' ...
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import math def human_filesize(filesize): """Display the filesize in a human-readable unit.""" if filesize > 0: names = [" ", "k", "M", "G", "T", "P", "E"] exponent = math.floor(math.log(filesize, 1000)) digits = filesize / math.pow(1000, exponent) prefix = names[exponent] ...
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def ele_types(eles): """ Returns a list of unique types in eles """ return list(set([e['type'] for e in eles] ))
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def pcp(pred, target, dist_func, threshold, reduce=True): """ Computes the percentage of correct predictions (PCP) between pred and target. Args: pred(np.ndarray): array of predicted data. target(np.ndarray): array of target data. dist_func(function): function to use to compute ...
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def parcellate_hemisphere(roiname: str): """ Parcellation Region's name into its related hemisphere Parameters ---------- roiname : str [description] Returns ------- [type] [description] """ if roiname.endswith("_L"): return "Left" elif roiname.endswi...
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def s3_url(row): """ Create S3 URL for object from S3 bucket and key """ return f's3://{row["Bucket"]}/{row["Key"]}'
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def time_average(a, C, emin, emax, eref=1): """ Average output of events with energies in the range [emin, emax] for a power-law of the form f = C*e**-a to the flare energy distribution, where f is the cumulative frequency of flares with energies greater than e. If the power law is for flare equi...
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def executor_type(request) -> str: """Test fixture which yields an executor type.""" return request.param
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def mask_list(l, mask): """Returns the values of the specified list that are True in the specified mask.""" return [v for i, v in enumerate(l) if mask[i]]
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def word_overlap(left_words, right_words): """Returns the Jaccard similarity between two sets. Note ---- The topics are considered sets of words, and not distributions. Parameters ---------- left_words : set The set of words for first topic right_words : set The set of...
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def convert(lines): """Convert compiled .ui file from PySide2 to Qt.py Arguments: lines (list): Each line of of .ui file Usage: >> with open("myui.py") as f: .. lines = convert(f.readlines()) """ def parse(line): line = line.replace("from PySide2 import", "from ...
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def load_grid(filename): """ reads the file and saves the content as a 2d list :param filename: str - absolute path if the file is not part of the project :return: list of lists - 2d grid """ return [list(line.rstrip('\n')) for line in open(filename)]
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from typing import Tuple def get_word_from_cursor(s: str, pos: int) -> Tuple[str, int, int]: """ Return the word from a string on a given cursor. :param s: String :param pos: Position to check the string :return: Word, position start, position end """ assert 0 <= pos < len(s) pos += 1...
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def total_return_nb(total_profit, init_cash): """Get total return per column/group.""" return total_profit / init_cash
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from io import BytesIO def bytes_to_bytesio(bytestream): """Convert a bytestring to a BytesIO ready to be decoded.""" fp = BytesIO() fp.write(bytestream) fp.seek(0) return fp
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def post_list_mentions(db, usernick, limit=50): """Return a list of posts that mention usernick, ordered by date db is a database connection (as returned by COMP249Db()) return at most limit posts (default 50) Returns a list of tuples (id, timestamp, usernick, avatar, content) """ cursor = db....
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def maskLandsatclouds(image): """ Function to mask out clouds from Landsat images args: Landsat image returns: Cloud masked image """ orig = image qa = image.select('pixel_qa') #cloudsShadowBitMask = 1 << 3 cloudsBitMask = 1 << 4 mask = qa.bitwiseAnd(clo...
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import configparser def configurations(path): """Parses and reads the configuration file named found at path. Returns a configparser Object.""" # create config parsing object config = configparser.ConfigParser() # read config config.read(path) return config
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def ensure_list_or_tuple(obj): """ Takes some object and wraps it in a list - i.e. [obj] - unless the object is already a list or a tuple instance. In that case, simply returns 'obj' Args: obj: Any object Returns: [obj] if obj is not a list or tuple, else obj """ return [ob...
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def sizeFormat(sizeInBytes): """ Format a number of bytes (int) into the right unit for human readable display. """ size = float(sizeInBytes) if sizeInBytes < 1024: return "%.0fB" % (size) if sizeInBytes < 1024 ** 2: return "%.3fKb" % (size / 1024) if sizeInBytes < 1024 *...
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def get_precipitation_forecast(points): """Get the precipitation forecast from forecast data. Parameters ---------- points : list of dicts The forecast raw data. Returns ------- precipitation_forecast : dict of list of dicts The precipitation forecast grouped by time resolu...
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import pathlib def absolute_path(*paths): """Given a path relative to this project's top-level directory, returns the full path in the OS. Args: paths: A list of folders/files. These will be joined in order with "/" or "\" depending on platform. Returns: The full absolute ...
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import requests def status_crawler(LEETCODE_SESSION: str, question_name: str) -> bool: """Check if question solved Args: LEETCODE_SESSION (str): User's LeetCode session. question_name (str): LeetCode question name. Returns: bool: Solved or not. """ cookies = {"LEETCODE_SE...
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