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from typing import List import base64 def ToBase64(array: List[int]) -> bytes: """Convert array of bytes to base64 string.""" return base64.standard_b64encode(bytes(array))
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from typing import Optional import re import string def get_dart_well_index(coordinate: Optional[str]) -> Optional[int]: """Determines a well index from a coordinate; otherwise returns None. Well indices are determined by evaluating the row position, then column position. E.g. A04 -> 4, B04 -> 16. Argume...
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def make_season(year): """ :param year string of year (e.g. 2012, 2013) :return season valid string of season used by the API. \ (e.g. 2015-16, 2012-13) """ next_yr = str(year+1)[-2:] return '{0}-{1}'.format(year, next_yr)
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def simulateAndPlot(r, **kwargs): """ Simulate with r.simulate with given arguments and plot with tellurium. :returns: simulation result :rtype: NamedArray """ s = r.simulate(**kwargs) r.plot(s) return s
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def add_http_parameters(url: str, params: dict) -> str: """ Adds HTTP parameters to url. :param url: url address :param params: http parameters :return: url with added http parameters """ result: str = url + "?" params_added: int = 0 for param in params: result += param + "=...
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import random def shuffle(s): """Return a randomly shuffled version of string s.""" s = list(s) random.shuffle(s) return "".join(s)
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def sefl(c, f, f0): """ Semi-empirical normalized force limit. Parameters ---------- c : scalar Constant based on experience, typically around 1.5 f : scalar Frequency of interest, typically lower end of band. f0 : scalar Fundamental frequency in direction of interes...
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import math def total_delay_seconds(media_info, args): """Computes the total seconds to skip (beginning + ending). """ start_delay_seconds = math.floor(media_info.duration_seconds * args.start_delay_percent / 100) end_delay_seconds = math.floor(media_info.duration_seconds * args.end_delay_percent / 10...
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def dict_slice(Dict, *keys): """Returns a shallow copy of the subset of a given dict (or a dict-like object) with a given set of keys. The return object is a dict. No keys may be missing from Dict. Example: if d = {'abc': 12, 'def': 7, 'ghi': 32, 'jkl': 98 } then dict_slice(d, 'abc', 'ghi') will yield {'ab...
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def assertion_with_name(name): """Returns a control assertion by name.""" all_control_assertions = ["Confidentiality", "Integrity", "Availability", "Security", "Privacy"] return next(assertion for assertion in all_control_assertions if assertion == name.title())
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from typing import Iterable def all_indices(it: Iterable, item: object) -> Iterable[int]: """ All indices of item in it """ return (i for i, x in enumerate(it) if x == item)
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from typing import List def construct_service_principal_names(services: List[str], hostnames: List[str]) -> List[str]: """ Given a list of services and hostnames, construct the kerberos server principle names for them. """ spns = [] for serv in services: for hostname in hostnames: spns...
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def remove_padding(X,pad_value): """Convience function used to remove padding from inputs which have been padded during batch generation""" return X[X!=pad_value]
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def html_movie_embed_wmp(moviefile, width=400, height=400): """Return HTML text for embedding a movie file (Windows Media Player code).""" text = """ <object id="MediaPlayer1" width="180" height="200" classid="CLSID:22D6F312-B0F6-11D0-94AB-0080C74C7E95" codebase="https://activex.microsoft.com/activex/contro...
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def intersection(r1, r2): """ Helper method to obtain intersection of two rectangles r1 = [x1,y1,w1,h1] r2 = [x2,y2,w2,h2] returns [x,y,w,h] """ assert len(r1) == 4 and len(r2) == 4, "Rectangles should be defined as [x,y,w,h]" rOut = [0, 0, 0, 0] rOut[0] = max(r1[0], r2[0]) rOut...
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import torch def detection_collate(batch): """ Collate data of different batch, it is because the boxes and gt_classes have changeable length. This function will pad the boxes and gt_classes with zero. Arguments: batch -- list of tuple (im, boxes, gt_classes) im_data -- tensor of shape (3, H...
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def get_json_patch(object_kind: str, index: int, image_name: str): """ Gives different JSONPatches as a `dict`, depending on the `object_kind`. The JSONPatch replaces the image at index `index` with `image_name`. """ if object_kind == "Pod": return { "op": "replace", ...
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def combine_costs(df, func): """ Given df: a dataset with multiple cost values for each rollout/search, func: a function from series of costs to one value (perhaps e.g. "min"), returns a dataset with only one cost for each rollout/search. """ return ( df.groupby( [ ...
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def unique_timestamps(timestamps): """ Remove duplicate timestamps. """ return list(set(timestamps))
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def arr_to_dict(arr): """ takes in an numpy array or list of lists (tuple of tuples) and returns a dictionary with indices, values Example arr_to_dict([['a','b'],['c','#']]) == {(0, 0): 'a', (0, 1): 'b', (1, 0): 'c', (1, 1): '#'} """ d = {} if isinstance(arr, str): pr...
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import re def get_num(name): """ If a test case name contains a number, just return the number. Useful for sorting. """ result = re.search(r"\d+", name) if result: return int(result.group(0)) else: return 0
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def standardize_template_names(t): """Standardize names of templates for matching purposes.""" return t.strip().lower().replace(" ", "_")
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import ast def _is_celery_dict_task_definition(dict_: ast.Dict) -> bool: """ determine whether the Dict is a Celery task definition """ celery_task_dict_target_keys = {"task", "schedule"} # We are looking for the `task` and `schedule` keys that all celery tasks # configured via a Dict have ...
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def getIndex(header, item): """Get index of variable """ for i, elem in enumerate(header): if elem.lower() == item.lower(): return i return None
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def redact_config_dict(data): """ This function redacts secret values in the configuration dict. This prevents that logging prints plain api keys. """ for key, value in data.items(): # Redact the secret values if key == "api_key" and data[key]: data[key] = "<REDACTED>" ...
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def parse_line(line): """ parse the integers from: #1196 @ 349,741: 17x17 """ coords, dimensions = line.split(' @ ')[1].split(': ') coords = coords.split(',') x, y = int(coords[0]) + 1, 0 - (int(coords[1]) + 1) dimensions = dimensions.split('x') x_length, y_length = int(dimensions[0]...
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import json def _error_message(msg=None): """ Helper function to convert error messages into the JSON format. """ return json.dumps({"error": msg})
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def partial(func, *pargs, **pkwargs): """ Performs partial application on `func` :param func: function to apply :param pargs: default positional parameters :param pkwargs: default keyword parameters :return: Proxy functor """ def comp(*cargs, **ckwargs): # Concatenate positiona...
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def obsfateverb(successorset, markers): """ Return the verb summarizing the successorset and potentially using information from the markers """ if not successorset: verb = 'pruned' elif len(successorset) == 1: verb = 'rewritten' else: verb = 'split' return verb
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def _is_parent_pathway(shortest_path, targets): """Returns true if ShortestPath is a parent pathway, false if not. A ShortestPath object is the parent of a branch if its terminal residue is the only surface exposed residue in the path. For example, if targets=[A,B,C] and the pathway is [H,I,C], then th...
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def get_ratings_tuple(entry): """ Parse a line in the ratings dataset Args: entry (str): a line in the ratings dataset in the form of UserID::MovieID::Rating::Timestamp Returns: tuple: (UserID, MovieID, Rating) """ items = entry.split('::') return int(items[0]), int(items[1]), fl...
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import io import tokenize def _decode_source(source_bytes): """ Decode bytes representing source code and return the string. Universal newline support is used in the decoding. Based on CPython's implementation of the same functionality: https://github.com/python/cpython/blob/3.9/Lib/importlib/_bootstr...
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import math def scanette_status(intval, floatval): """Convert Event status value into Scanette status/result field. Scanette result values are sometimes int, sometimes float, sometimes "?". """ if intval == floatval: return intval if math.isnan(floatval): return "?" return flo...
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def determine_axes(f, *vars): """ Determine the axes along which the FT should be performed. """ if len(vars) != len(f.shape): raise TypeError('The number of variables has to match the dimension of ' '`f`. Use `None` for axis with respect to which no ' ...
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def to_lower(string): """The lower case version of a string""" return string.lower()
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def _GetValueAndIndexForMin(data_array): """Helper function to get both min and argmin of a given array. Args: data_array: (list) array with the values. Returns: (tuple) containing min(data_array) and argmin(data_array). """ value_min = min(data_array) ind_min = data_array.index(value_min) retu...
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def runs(runs: list) -> dict: """Generate Github runs like dict.""" return {"total_count": len(runs), "workflow_runs": runs}
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def _get_prop(properties: list, key: str): """ Get a property from list of properties. :param properties: The list of properties to filter on :param key: The property key :return: """ result = list(filter(lambda prop: prop["name"] == key, properties)) if len(result) == 0: raise...
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def milliseconds_to_nanoseconds(value): """Convert from ms to ns (used for pg_stat* conversion to metrics with units in ns)""" return value * 1000000
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def jcentury_to_jday(juliancentury: float) -> float: """Convert a Julian Century number to a Julian Day""" return (juliancentury * 36525.0) + 2451545.0
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import inspect def get_func_parameter_names(func): """Gets the list of parameter names of a function.""" signature = inspect.signature(func) return list(signature.parameters.keys())
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def parse_tests(input_file): """ Parses test commands from an input file. Extracts one command per line. """ res = [] for l in open(input_file).readlines(): res.append(l.strip()) return res
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import torch def calculate_gradient_penalty(D, real_samples, fake_samples): """Calculates the gradient penalty loss""" # Random weight for interpolation between real and fake samples eta = torch.rand((real_samples.size(0), 1, 1, 1), device=real_samples.device) # Get random interpolation between real a...
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def atleast_ndim(x, ndim): """Reshapes a tensor so that it has at least n dimensions.""" if x is None: return None return x.view(list(x.shape) + [1] * (ndim - x.ndim))
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def auto_pad_width( pad_width, shape, combine=None): """ Ensure pad_width value(s) to be consisting of integer. Args: pad_width (float|int|iterable[float|int]): Size of the padding to use. This is useful for mitigating border effects. If iterable, a v...
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from typing import Dict def recursive_merge(a: Dict, b: Dict, path=None) -> Dict: """ Recursively merges dictionaries Mostly taken from user `andrew cooke` on [stackoverflow](https://stackoverflow.com/a/7205107) """ path = path or [] out = a.copy() for k in b: if k in a: if isinstance(a[k], dict) and isins...
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def strip_and_split(s): """strip trailing \x00 and split on \x00 Useful for parsing output of git commands with -z flag. """ return s.strip("\x00").split("\x00")
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import hashlib def get_file_hash(path: str) -> str: """Return the hash used for caching. This incorporates the file contents as well as its path. """ md5 = hashlib.md5() with open(path, 'rb') as infile: md5.update(infile.read()) md5.update(path.encode()) return md5.hexdigest()
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from collections import defaultdict from fnmatch import fnmatch def groupkeys(keys, patterns): """Groups the given set of keys using the given patterns. It runs through the patterns sequentially, removing those from keys. Returns a dict with {pattern: [matching keys]}. Unmatches keys are added with No...
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def main(args=None): """Sample main app.""" return 0
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def before_send_to_sentry(event, hint): """Edit event properties before logging to Sentry Docs: https://docs.sentry.io/error-reporting/configuration/filtering/?platform=python#before-send """ # Report a general logger name (`ingest_pipeline`) to Sentry, # rather than the function-specific logger na...
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def set(list, index, item): """ Return a list with the item at the specified index replaced with the given item. If the index is out of bounds, return the list unmodified. """ if list == () or index < 0: return list else: head, tail = list if index == 0: retu...
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import json def ConvertToHtmlString(trace_result): """Convert a trace result to the format to be output into HTML. If the trace result is a dictionary or list, JSON-encode it. If the trace result is a string, leave it unchanged. """ if isinstance(trace_result, dict) or isinstance(trace_result, list): r...
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from typing import Any import numbers def is_number(thing: Any) -> bool: """ A function that returns whether the given value is a number, either integer or floating point. Note that this will return ``False`` for the value, ``True``, which is different from normal Python. :param thing: the value...
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from typing import List def smooth_data(scalars: List[float], weight: float) -> List[float]: """Tensorboard smoothing function to smooth noisy training data :param scalars: data points to smooth :type scalars: List[float] :param weight: Exponential Moving Average weight in 0-1 :type weight: float...
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def clean_col_names(df): """ cleans up the column names in the mta dataframe :param df: mta dataframe :return: mta dataframe with cleaned columns """ df = df.copy() before = 'EXITS ' df.rename(columns={before: 'EXITS', "C/A":...
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def decode2string(index2token, indices, end_token="END_TOKEN", remove_END_TOKEN=False): """ Decode a list of indices to string. Args: index2token: a dictionary that maps indices to tokens indices: a list of indices that correspond to tokens remove_END_TOKEN: boolean indicating whethe...
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def slqs(x_entr, y_entr): """ Computes SLQS score from two entropy values. :param x_entr: entropy value of x :param y_entr: entropy value of y :return: SLQS score """ score = 1 - (x_entr/y_entr) if y_entr != 0.0 else -1.0 return score
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def num_to_data_len(num): """ Convert a permutation number to the length of data it represents """ # Strip off the leading 1 that was added to make the math work data = int(bin(num)[3:], 2) # Convert from the integer form back to a string data = hex(data)[2:] # Return the length of the d...
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def normalize_labels(labels): """ Normalize labels to probabilities""" s = sum(labels.values()) normalized = {} for k, v in labels.iteritems(): if s > 0: normalized[k] = v / s else: normalized[k] = v return normalized
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def partition(f, xs): """ Works similar to filter, except it returns a two-item tuple where the first item is the sequence of items that passed the filter and the second is a sequence of items that didn't pass the filter """ t = type(xs) true = filter(f, xs) false = [x for x in xs if x n...
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def _vpd(es, ea): """Vapor pressure deficit Parameters ---------- es : ee.Image or ee.Number Saturated vapor pressure [kPa]. ea : ee.Image or ee.Number Actual vapor pressure [kPa]. Returns ------- ee.Image or ee.Number Vapor pressure deficit [kPa]. """ ...
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def has_marker(obj, marker_name): """Determine whether a task function has a certain marker.""" return any(marker.name == marker_name for marker in getattr(obj, "pytaskmark", []))
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def kib(num): """Return number of bytes for num KiB""" return num * 1024
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import gzip def opengz(file, mode="r"): """ Transparently open a gzipped or non-gzipped file for reading or writing. :param file: Path of file to open for writing. :param mode: Same mode options as python's default open. :return: A open file handle. """ assert mode in ['r', 'rb', 'a', 'ab...
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import cmath import math def qft(mem): """Apply quantum Fourier transform to the first t qubits.""" new_amplitudes = [] N = 2**mem.t # Calculate root of unity in two steps, as complex exponentiation is # expensive. w__ = cmath.exp(2 * math.pi * 1j / N) for k, _ in enumerate(mem): ...
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import torch def get_pair_dist(a, b): """calculate pair distances between two sets of points Parameters ---------- a,b : pytorch tensors of shape [batch,nres,3] store Cartesian coordinates of two sets of atoms Returns ------- dist : pytorch tensor of shape [batch,nres,nres] ...
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def isolatedfile_to_state(filename): """For a '.isolate' file, returns the path to the saved '.state' file.""" return filename + '.state'
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def convert_numeric_in(value): """ Convert any Decimal values into floats. """ return float(value)
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def sigmoid_poly(x): """A Chebyshev polynomial approximation of the sigmoid function.""" w0 = 0.5 w1 = 0.2159198015 w3 = -0.0082176259 w5 = 0.0001825597 w7 = -0.0000018848 w9 = 0.0000000072 x1 = x x2 = (x1 * x) x3 = (x2 * x) x5 = (x2 * x3) x7 = (x2 * x5) x9 = (x2 * ...
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def flatten_pipes_dict(pipes_dict : dict) -> list: """ Convert the standard pipes dictionary into a list """ pipes_list = [] for ck in pipes_dict.values(): for mk in ck.values(): pipes_list += list(mk.values()) return pipes_list
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import importlib def get_backend(module, backend_class, channel, appname): """Get a pubsub object. e.g.: `get_backend('backends', 'PubNubBackend')`""" mod = importlib.import_module(module) return getattr(mod, backend_class)(channel, appname)
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def format_string(code: str, pattern: str) -> str: """Format a single pattern line.""" fmt = ' ' * 8 + "'{}': '{}'" code_len = len(code) pattern_len = len(pattern) if pattern_len > 63 - code_len: index = pattern_len // 2 result = fmt.format(code, pattern[:index]) + '\n' resul...
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def format_header_for_list_commands(base_header: str, rows_count: int, page: int, page_size: int, limit: int) -> str: """ Retrieve the header of the readable output for list commands. Format the header according to the pagination use case: 'Manual Pagination' or 'Auto...
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def Invoke(frontend, implementation): """Applies implementation on frontend.""" return implementation(frontend)
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import re def extract_variable(filename, variable): # type: (str, str) -> str """Extract the version number from a python file that contains the '__version__' variable.""" with open(filename, "r", encoding="utf8") as stream: search_refind = r'{} = ["\'](\d+\.\d+\.\d+)["\']'.format(variable) v...
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import binascii def reverseHex(data): """ Flip byte order in the given data(hex string). """ b = bytearray(binascii.unhexlify(data)) b.reverse() return binascii.hexlify(b)
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def does_period_contain_data(period: str) -> bool: """Does the given period contain data or simulation? If the period is 6 characters long, then it's data. Args: period: Run period to be checked. Returns: True if the period contains data. """ if len(period) == 6: return...
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def generate_pascal_row(row): """Generate the successive row in Pascal's triangle. While there are many iterative approaches, we can zip together offsets of the given row to generate pairs of elements, which we sum to form the final data structure. For example, if row = [1, 4, 6, 4, 1], then ...
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def decaying(start, stop, decay): """Yield an infinite series of linearly decaying values.""" def clip(value): return max(value, stop) if (start > stop) else min(value, stop) nr_upd = 1. while True: yield clip(start * 1./(1. + decay * nr_upd)) nr_upd += 1
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def str2dict(dict_string): """ Convert a string of key=value pairs to a dictionary. Format is 'KEY=value KEY=other value KEY=and some more values' For example: str2dict('key1 = 1 key2 = a b c key3=23.4) returns the dictionary {'key1':'1' , 'key2':'a b c', 'key3':'23.4'} """ string_bits = dic...
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from typing import List def _sampling_from_alias( alias: List[int], probs: List[float], first_random: float, second_random: float, ) -> int: """ This is aligned with the original node2vec implementation w/ 2 random numbers. :param alias: the pre-calculated alias list :param probs: the...
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def is_csv_callback(query): """ Callback to identify if the button pressed was from the csv function :param query: the button pressed :return: if the button pressed relates to the csv """ return "," in query.data
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from typing import Dict from typing import Any def suffix_dict_keys(in_dict: Dict[str, Any], suffix: str) -> Dict[str, Any]: """Adds the given suffix to all dictionary keys.""" return {key + suffix: value for key, value in in_dict.items()}
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def tag(*tags): """Decorator to add tags to a test class or method.""" def decorator(obj): setattr(obj, 'tags', set(tags)) return obj return decorator
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def _sub_space(m): """Helper function: given a regexp match, return a string of spaces that's the same length as the matched string.""" return ' '*(m.end()-m.start())
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import math def humanise_bytes(num_bytes, si=False): """ Make a human-readable string for a number of bytes >>> humanise_bytes(689275) '673.1 KB' Taken from https://programming.guide/worlds-most-copied-so-snippet.html :param int num_bytes: :param int si: Whether to use SI units. Defaul...
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def get_name(node_name): """ Omit any parenting information from the provided node name. :param str node_name: :return: Name :rtype: str """ return node_name.rsplit("|", 1)[-1]
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def group(genes, entities): """ create lists for each gene relations :param genes: :param entities: :return: """ genes_relations = [] for gen in genes: genes_relations.append(list(filter(lambda x: x[0] == gen, entities))) return genes_relations
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def _GetElemByName(name, from_list): """Gets an element from the given list by its name field. Raises an error if it doesn't find exactly one match. """ elems = [e for e in from_list if e.name == name] if len(elems) != 1: raise ValueError('Expected 1 item named %s, found %d' % (name, len(elems))) retur...
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def get_box_points(box): """ Takes in box points of form ((x1,y1), (x2, y2)) and converts it to form [x1, y1, x2, y2]. """ box_points = [] x1, y1 = box[0] x2, y2 = box[1] box_points.append(x1) box_points.append(y1) box_points.append(x2) box_points.append(y2) return box_p...
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def expand_leaf_to_label(leaf_label): """ Expand a leaf node label into flat structure. """ labels = [] parts = list(filter(None, leaf_label.split('/'))) for i, _ in enumerate(parts): labels.append('/' + '/'.join(parts[0:i+1])) return labels
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from pathlib import Path from typing import List def _list_files(d: Path) -> List[Path]: """ Recursively list files in a dir and its sub dirs """ if d.is_file(): return [d] else: sub_dirs = [d for d in d.iterdir() if d.is_dir()] files = [f for f in d.iterdir() if f.is_file()] ...
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def list_all_subclasses(superclass): """ Get a list of all subclasses defined for a given superclass """ # sorted for determinism return sorted( # any class object in python has a meta-function for its subclasses [cls for cls in superclass.__subclasses__()], # sort based on ...
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def test_even(value): """Return true if the variable is even.""" return value % 2 == 0
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def bool2yn(b): """Helper function, returns \"yes\" if *b* is True, \"no\" if *b* is False.""" return ["no", "yes"][b]
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def intervals_frac_overlap(iv1, iv2): """ Given two intervals, calculates the fraction of iv1 covered by iv2 """ return iv1.overlap_size(iv2.begin, iv2.end) / iv1.length()
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def xy_to_xyz(x, y): """Convert `xyY` to `xyz`.""" return [x / y, 1, (1 - x - y) / y]
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import re def parse_size_to_KB(size_string: str) -> float: """Given a size string with various unit, convert to KB in float: wrk binary unit reference https://github.com/wg/wrk/blob/master/src/units.c#L29-L33 Example: "200.56KB" -> 200.56 "50MB" -> 51200 "...
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def get_file_text(path): """ Returns file text by path""" file_io = open(path, "r") text = file_io.read() file_io.close() return text
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