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def load_file(file_location): """ Opens a given file and returns its contents. :param str file_location: The absolute path to the file :rtype: str :return: The contents of the file """ with open(file_location, 'r') as file_contents: contents = file_contents.read() return conte...
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def upperLeftOrigin( largeSize, smallSize ): """ The upper left coordinate (tuple) of a small rectangle in a larger rectangle (centered) """ origin = tuple( map( lambda x: int( ( (x[0]-x[1])/2 ) ), zip( largeSize, smallSize )) ) return origin
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def is_square_inside(row, col, rows, cols): """Check if row and col is square inside grid having rows and cols.""" return row not in (0, rows - 1) and col not in (0, cols - 1)
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def clean_repository_clone_url( repository_clone_url ): """Return a URL that can be used to clone a tool shed repository, eliminating the protocol and user if either exists.""" if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: # http:/...
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def add(n1, n2): """Adds the 2 given numbers""" return n1 + n2
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import torch def kl_reverse(logu: torch.Tensor) -> torch.Tensor: """ Log-space Csiszar function for reverse KL-divergence D_f(p,q) = KL(q||p). Also known as the exclusive KL-divergence and negative ELBO, minimizing results in zero-forcing / mode-seeking behavior. Args: logu (torch.Tensor...
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import numbers def is_number(item): """Check if the item is a number.""" return isinstance(item, numbers.Number)
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def xml_attr_or_element(xml_node, name): """ Attempt to get the value of name from the xml_node. This could be an attribute or a child element. """ attr_val = xml_node.get(name, None) if attr_val is not None: return attr_val.encode('utf-8').strip() for child in xml_node.getchildren()...
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def get_coinbase_candle_url(url, timestamp_from, pagination_id): """Get Coinbase candle URL.""" start = timestamp_from.replace(tzinfo=None).isoformat() url += f"&start={start}" if pagination_id: url += f"&end={pagination_id}" return url
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def subplot_index(nrow, ncol, k, kmin=1): """Return the i, j index for the k-th subplot.""" i = 1 + (k - kmin) // ncol j = 1 + (k - kmin) % ncol if i > nrow: raise ValueError('k = %d exceeds number of rows' % k) return i, j
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def _split_keys(keypath, separator): """ Splits keys using the given separator: eg. 'item.subitem[1]' -> ['item', 'subitem[1]']. """ if separator: return keypath.split(separator) return [keypath]
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def spacify(string, spaces=2): """Add spaces to the beginning of each line in a multi-line string.""" return spaces * " " + (spaces * " ").join(string.splitlines(True))
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def frohner_cor_3rd_order(sig1,sig2,sig3,n1,n2,n3): """ Takes cross-sections [barns] and atom densities [atoms/barn] for three thicknesses of the same sample, and returns extrapolated cross section according to Frohner. Parameters ---------- sig1 : array_like Cross section of the ...
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def split_and_filter(intermediate_str, splitter): """ Split string with given splitter - practically either one of "," or "/'". Then filter ones that includes "https" in the split pickles :param intermediate_str : string that in the middle of parsing :param splitter :return: chunk of string(s) a...
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def count_ref_alleles(variant, *traits): """Count reference allels for a variant Parameters ---------- variant : a Variant as from funcgenom the variant for which alleles should be counted *traits : str the traits for which alleles should be counted Returns -------...
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import random def random_in_range(a: int, b: int) -> int: """ Return a random number r with a <= r <= b. """ return random.randint(a, b)
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def about(template): """ Attach a template to a step which can be used to generate documentation about the step. """ def decorator(step_function): step_function._about_template = template return step_function return decorator
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import torch def _extend_batch_dim(t: torch.Tensor, new_batch_dim: int) -> torch.Tensor: """ Given a tensor `t` of shape [B x D1 x D2 x ...] we output the same tensor repeated along the batch dimension ([new_batch_dim x D1 x D2 x ...]). """ num_non_batch_dims = len(t.shape[1:]) repeat_shape = ...
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def split_component_chars(address_parts): """ :param address_parts: list of the form [(<address_part_1>, <address_part_1_label>), .... ] returns [(<char_0>, <address_comp_for_char_0), (<char_1>, <address_comp_for_char_1),.., (<char_n-1>, <address_comp_for_char_n-1)] """ char_arr = [] for addres...
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def adjacency_matrix(edges): """ Convert a directed graph to an adjacency matrix. Note: The distance from a node to itself is 0 and distance from a node to an unconnected node is defined to be infinite. Parameters ---------- edges : list of tuples list of dependencies between n...
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def estimate_Cn(P=1013, T=273.15, Ct=1e-4): """Use Weng et al to estimate Cn from meteorological data. Parameters ---------- P : `float` atmospheric pressure in hPa T : `float` temperature in Kelvin Ct : `float` atmospheric struction constant of temperature, typically 10...
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def _card(item): """Handle card entries Returns: title (append " - Card" to the name, username (Card brand), password (card number), url (none), notes (including all card info) """ notes = item.get('notes', "") or "" # Add car...
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def get_natural_num(msg): """ Get a valid natural number from the user! :param msg: message asking for a natural number :return: a positive integer converted from the user enter. """ valid_enter = False while not valid_enter: given_number = input(msg).strip() i...
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import types def copy_function(old_func, updated_module): """Copies a function, updating it's globals to point to updated_module.""" new_func = types.FunctionType(old_func.__code__, updated_module.__dict__, name=old_func.__name__, argdefs=old_func._...
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def get_recipes_from_dict(input_dict: dict) -> dict: """Get recipes from dict Attributes: input_dict (dict): ISO_639_1 language code Returns: recipes (dict): collection of recipes for input language """ if not isinstance(input_dict, dict): raise TypeError("Input is not typ...
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def lerp(a,b,t): """ Linear interpolation between from @a to @b as @t goes between 0 an 1. """ return (1-t)*a + t*b
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def generate_annotation_dict(annotation_file): """ Creates a dictionary where the key is a file name and the value is a list containing the - start time - end time - bird class. for each annotation in that file. """ annotation_dict = dict() for line i...
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def extract_jasmine_summary(line): """ Example SUCCESS karma summary line: PhantomJS 2.1.1 (Linux 0.0.0): Executed 1 of 1 SUCCESS (0.205 secs / 0.001 secs) Exmaple FAIL karma summary line: PhantomJS 2.1.1 (Linux 0.0.0): Executed 1 of 1 (1 FAILED) ERROR (0.21 secs / 0.001 secs) """ # get tota...
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def degrees_of_freedom(s1, s2, n1, n2): """ Compute the number of degrees of freedom using the Satterhwaite Formula @param s1 The unbiased sample variance of the first sample @param s2 The unbiased sample variance of the second sample @param n1 Thu number of observations in the first sample @pa...
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def get_range_to_list(range_str): """ Takes a range string (e.g. 123-125) and return the list """ start = int(range_str.split('-')[0]) end = int(range_str.split('-')[1]) if start > end: print("Your range string is wrong, the start is larger than the end!", range_str) return range(sta...
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def annealing_epsilon(episode: int, min_e: float, max_e: float, target_episode: int) -> float: """Return an linearly annealed epsilon Epsilon will decrease over time until it reaches `target_episode` (epsilon) | max_e ---|\ | \ | \ | \ mi...
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def extractYoloInfo(yolo_output_format_data): """ Extract box, objectness, class from yolo output format data """ box = yolo_output_format_data[..., :6] conf = yolo_output_format_data[..., 6:7] category = yolo_output_format_data[..., 7:] return box, conf, category
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def replace_umlauts(s: str) -> str: """ Replace special symbols with the letters with umlauts (ä, ö and ü) :param s: string with the special symbols (::) :return: edited string """ out = s.replace('A::', 'Ä').replace('O::', 'Ö').replace('U::', 'Ü').replace('a::', 'ä').replace('o::', 'ö') \ ...
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import torch import math def sample_random_lightdirs(num_rays, num_samples, upper_only=False): """Randomly sample directions in the unit sphere. Args: num_rays: int or tensor shape dimension. Number of rays. num_samples: int or tensor shape dimension. Number of samples per ray. upper_...
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def date_handler(obj): """make datetime object json serializable. Notes ----- Taken from here: https://tinyurl.com/yd84fqlw """ if hasattr(obj, 'isoformat'): return obj.isoformat() else: raise TypeError
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import base64 import struct def tiny_id(page_id): """Return *tiny link* ID for the given page ID.""" return base64.b64encode(struct.pack('<L', int(page_id)).rstrip(b'\0'), altchars=b'_-').rstrip(b'=').decode('ascii')
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def gen_all_holds(hand): """ Generate all possible choices of dice from hand to hold. hand: sorted full yahtzee hand Returns a set of tuples, where each tuple is sorted dice to hold """ # start off with the original hand in set set_holds = set([(hand)]) # now iterate with all...
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def langstring(value: str, language: str = "x-none") -> dict: """Langstring.""" return { "langstring": { "lang": language, "#text": value, } }
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def absModuleToDist(magApp, magAbs): """ Convert apparent and absolute magnitude into distance. Parameters ---------- magApp : float Apparent magnitude of object. magAbs : float Absolute magnitude of object. Returns ------- Distance : float The distance resu...
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import base64 def decoded_anycli(**kwargs): """ Return the decoded return from AnyCLI request - Do not print anything :param kwargs: keyword value: value to display :return: return the result of AnyCLI in UTF-8 :Example: result = cli(url=base_url, auth=s, command="show vlan") deco...
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import tqdm def generate_formula_dict(materials_store, query=None): """ Function that generates a nested dictionary of structures keyed first by formula and then by task_id using mongo aggregation pipelines Args: materials_store (Store): store of materials Returns: Nested dic...
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def shape_extent_to_header(shape, extent, nan_value=-9999): """ Create a header dict with shape and extent of an array """ ncols = shape[1] nrows = shape[0] xllcorner = extent[0] yllcorner = extent[2] cellsize_x = (extent[1]-extent[0])/ncols cellsize_y = (extent[3]-extent[2])/nrows i...
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import logging def logged(class_): """Class-level decorator to insert logging. This assures that a class has a ``.log`` member. :: @logged class Something: def __init__(self, args): self.log(f"init with {args}") """ class_.log= logging.get...
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import math def _generate_resolution_shells(low, high): """Generate 9 evenly spaced in reciprocal space resolution shells from low to high resolution, e.g. in 1/d^2.""" dmin = (1.0 / high) * (1.0 / high) dmax = (1.0 / low) * (1.0 / low) diff = (dmin - dmax) / 8.0 shells = [1.0 / math.sqrt(dm...
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def get_page_url(skin_name, page_mappings, page_id): """ Returns the page_url for the given page_id and skin_name """ fallback = '/' if page_id is not None: return page_mappings[page_id].get('path', '/') return fallback
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def abort_multipart_upload(resource, bucket_name, object_name, upload_id): """Abort in-progress multipart upload""" mpupload = resource.MultipartUpload(bucket_name, object_name, upload_id) return mpupload.abort()
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def double(n): """ Takes a number n and doubles it """ return n * 2
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import random def random_sources(xSize, ySize, zSize, number): """ returns a list of random positions in the grid where the sources of nutrients (blood vessels) will be """ src = [] for _ in range(number): x = random.randint(0, xSize-1) y = random.randint(0, ySize-1) z = random.ran...
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def sort_terms(node, parent_children, hierarchy): """Recursively create a list of nodes grouped by category.""" for c in parent_children.get(node, []): hierarchy.append(c) sort_terms(c, parent_children, hierarchy) return hierarchy
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def sequence_accuracy_score(y_true, y_pred): """ Return sequence accuracy score. Match is counted only when two sequences are equal. """ total = len(y_true) if not total: return 0 matches = sum(1 for yseq_true, yseq_pred in zip(y_true, y_pred) if yseq_true == yseq_...
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def load_content(sentence_file): """Load input file with sentences to build LSH. Args: sentence_file (str): Path to input with txt file with sentences to Build LSH. Returns: dict: Dict with strings and version of string in lower case and without comma. """ sentences = {} with ...
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def rare_last_digit(first): """Given a leading digit, first, return all possible last digits of a rare number""" if first == 2: return (2,) elif first == 4: return (0,) elif first == 6: return (0,5) elif first == 8: return (2,3,7,8) else: raise ValueError...
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def fermat_number(n: int) -> int: """ https://en.wikipedia.org/wiki/Fermat_number https://oeis.org/A000215 >>> [fermat_number(i) for i in range(5)] [3, 5, 17, 257, 65537] """ return 3 if n == 0 else (2 << ((2 << (n - 1)) - 1)) + 1
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def get_id_ctx(node): """Gets the id and attribute of a node, or returns a default.""" nid = getattr(node, "id", None) if nid is None: return (None, None) return (nid, node.ctx)
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import torch def get_meshgrid_samples(lower, upper, mesh_size: tuple, dtype) ->\ torch.Tensor: """ Often we want to get the mesh samples in a box lower <= x <= upper. This returns a torch tensor of size (prod(mesh_size), sample_dim), where each row is a sample in the meshgrid. """ samp...
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from functools import reduce def getattrs(o, *attrs, **kwargs): """ >>> getattrs((), '__iter__', '__name__', 'strip')('_') 'iter' >>> getattrs((), 'foo', 'bar', default=0) 0 """ if 'default' in kwargs: default = kwargs['default'] c = o for attr in attrs: ...
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def calc_mean_score(movies): """Helper method to calculate mean of list of Movie namedtuples, round the mean to 1 decimal place""" ratings = [m.score for m in movies] mean = sum(ratings) / max(1, len(ratings)) return round(mean, 1)
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import re def is_regex(regex, invert=False): """Test that value matches the given regex. The regular expression is searched against the value, so a match in the middle of the value will succeed. To specifically match the beginning or the whole regex, use anchor characters. If invert is true, th...
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def build_varint(val): """Build a protobuf varint for the given value""" data = [] while val > 127: data.append((val & 127) | 128) val >>= 7 data.append(val) return bytes(data)
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def MAKEFOURCC(ch0: str, ch1: str, ch2: str, ch3: str) -> int: """Implementation of Window's `MAKEFOURCC`. This is simply just returning the bytes of the joined characters. `MAKEFOURCC(*"DX10")` can also be implemented by `Bytes(b"DX10")`. Args: ch0 (str): First char ch1 (str): Second ...
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def get_present_types(robots): """Get unique set of types present in given list""" return {type_char for robot in robots for type_char in robot.type_chars}
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def SFRfromLFIR(LFIR): """ Kennicut 1998 To get Star formation rate from LFIR (8-1000um) LFIR in erg s-1 SFR in Msun /year """ SFR = 4.5E-44 * LFIR return SFR
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def points_from_x0y0x1y1(xyxy): """ Constructs a polygon representation from a rectangle described as a list [x0, y0, x1, y1] """ [x0, y0, x1, y1] = xyxy return "%s,%s %s,%s %s,%s %s,%s" % ( x0, y0, x1, y0, x1, y1, x0, y1 )
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def get_basic_track_info(track): """ Given a track object, return a dictionary of track name, artist name, album name, track uri, and track id. """ # Remember that artist and album artist have different entries in the # spotify track object. name = track["name"] artist = track['artists'...
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from datetime import datetime def temporal_filter(record_date_time, time_or_period, op): """ Helper function to perform temporal filters on feature set :param record_date_time: datetime field value of a feature :type record_date_time: :class:`datetime.datetime` :param time_or_period: the time ins...
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def perform_variants_query(job, **kwargs): """Query for variants. :param job: API to interact with the owner of the variants. :type job: :class:`cibyl.sources.zuul.transactions.JobResponse` :param kwargs: See :func:`handle_query`. :return: List of retrieved variants. :rtype: list[:class:`cibyl....
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from unittest.mock import patch def method_mock(cls, method_name, request): """ Return a mock for method *method_name* on *cls* where the patch is reversed after pytest uses it. """ _patch = patch.object(cls, method_name) request.addfinalizer(_patch.stop) return _patch.start()
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def _return_xarray_system_ids(xarrs: dict): """ Return the system ids for the given xarray object Parameters ---------- xarrs Dataset or DataArray that we want the sectors from Returns ------- list system identifiers as string within a list """ return list(xarr...
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def sub(a, b): """Subtracts b from a and stores the result in a.""" return "{b} {a} ?+1\n".format(a=a, b=b)
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def factory(name, Base, Deriveds): """Find the base or derived class by registered name. Parameters ---------- Base: class Start the lookup here. Deriveds: iterable of (name, class) A list of derived classes with their names. Returns ------- class """ Derived =...
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def find_expired(bucket_items, now): """ If there are no expired items in the bucket returns empty list >>> bucket_items = [('k1', 1), ('k2', 2), ('k3', 3)] >>> find_expired(bucket_items, 0) [] >>> bucket_items [('k1', 1), ('k2', 2), ('k3', 3)] Expired items are returned in the lis...
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import typing def empty_iterable() -> typing.Iterable: """ Return an empty iterable, i.e., an empty list. :return: an iterable :Example: >>> from flpy.iterators import empty_iterable >>> empty_iterable() [] """ return list()
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def feature_selection(data, features): """ Choose which features to use for training. :param data: preprocessed dataset :param features: list of features to use :return: data with selected features """ return data[features]
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from typing import Optional import yaml def get_repo_version(filename: str, repo: str) -> Optional[str]: """Return the version (i.e., rev) of a repo Args: filename (str): .pre-commit-config.yaml repo (str): repo URL Returns: Optional[str]: the version of the repo """ wit...
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def recast_to_supercell(z, z_min, z_max): """Gets the position of the particle at ``z`` within the simulation supercell with boundaries ``z_min`` y ``z_max``. If the particle is outside the supercell, it returns the position of its closest image. :param z: :param z_min: :param z_max: :retur...
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def b2str(data): """Convert bytes into string type.""" try: return data.decode("utf-8") except UnicodeDecodeError: pass try: return data.decode("utf-8-sig") except UnicodeDecodeError: pass try: return data.decode("ascii") except UnicodeDecodeError: ...
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def get_cookie_date(date): """ Return a date string in a format suitable for cookies (https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Date) :param date: datetime object :return: date string in cookie format """ return date.strftime("%a, %d %b %Y %H:%M:%S GMT")
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def valuedict(keys, value, default): """ Build value dictionary from a list of keys and a value. Parameters ---------- keys: list The list of keys value: {dict, int, float, str, None} A value or the already formed dictionary default: {int, float, str} A defa...
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def dep_graph_parser_parenthesis(edge_str): """Given a string representing a dependency edge in the 'parenthesis' format, return a tuple of (parent_index, edge_label, child_index). Args: edge_str: a string representation of an edge in the dependency tree, in the format edge_label(parent_wor...
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import math def intersection_angle(m1, m2): """ Computes intersection angle between two slopes. """ return math.degrees(math.atan((m2-m1) / (1+m1*m2)))
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import html def formatTitle(title): """ The formatTitle function formats titles extracted from the scraped HTML code. """ title = html.unescape(title) if(len(title) > 40): return title[:40] + "..." return title
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import unicodedata def has_alphanum(s): """ Return True if s has at least one alphanumeric character in any language. See https://en.wikipedia.org/wiki/Unicode_character_property#General_Category """ for c in s: category = unicodedata.category(c)[0] if category == 'L' or ca...
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def is_remote(path): """Determine whether a file is in a remote location (which can be handled) based on prefix of connection string.""" for token in ["s3://", "http://", "https://"]: # add if path.startswith(token): return True return False
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def route_distance(route): """ returns the distance traveled for a given tour route - sequence of nodes traveled, does not include start node at the end of the route """ dist = 0 prev = route[-1] for node in route: dist += node.euclidean_dist(prev) prev = node return dist
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def update_datapackage(datapackage, mappings): """Update the field names and delete the `maps_to` properties.""" for i, resource in enumerate(datapackage['resources']): fields = [] for field in resource['schema']['fields']: fiscal_key = mappings[i][field['name']] if fi...
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def mel_to_hz(mel): """From Young et al. "The HTK book", Chapter 5.4.""" return 700.0 * (10.0**(mel / 2595.0) - 1.0)
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def generate_resource_link(pid, resource_path, static=False, title=None): """ Returns a valid html link to a public resource within an autogenerated instance. Args: pid: the problem id resource_path: the resource path static: boolean whether or not it is a static resource ti...
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def complex_to_xy(complex_point): """turns complex point (x+yj) into cartesian point [x,y]""" xy_point = [complex_point.real, complex_point.imag] return xy_point
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def addr(arr): """ Get address of numpy array's data """ return arr.__array_interface__['data'][0]
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def zipper(sequence): """Given a sequence return a list that has the same length as the original sequence, but each element is now a list with an integer and the original element of the sequence.""" n = len(sequence) rn = range(n) data = zip(rn,sequence) return data
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def stitch_frame(frames, _): """ Stitching for single frame. Simply returns the frame of the first index in the frames list. """ return frames[0]
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def demandNameItem(listDb,phrase2,mot): """ put database name of all items in string to insert in database listDb: list with datbase name of all items phrase2: string with database name of all items mot: database name of an item return a string with database name of all items separated with ',' ...
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def replace_text_comment(comments, new_text): """Replace "# text = " comment (if any) with one using new_text instead.""" new_text = new_text.replace('\n', ' ') # newlines cannot be represented new_text = new_text.strip(' ') new_comments, replaced = [], False for comment in comments: if c...
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def height(tree): """Return the height of tree.""" if tree.is_empty(): return 0 else: return 1+ max(height(tree.left_child()),\ height(tree.right_child()))
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def max_power_rule(mod, g, tmp): """ **Constraint Name**: DAC_Max_Power_Constraint **Enforced Over**: DAC_OPR_TMPS Power consumption cannot exceed capacity. """ return ( mod.DAC_Consume_Power_MW[g, tmp] <= mod.Capacity_MW[g, mod.period[tmp]] * mod.Availability_Derate[g, tmp] ...
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import requests def get_mc_uuid(username): """Gets the Minecraft UUID for a username""" url = f"https://api.mojang.com/users/profiles/minecraft/{username}" res = requests.get(url) if res.status_code == 204: raise ValueError("Users must have a valid MC username") else: return res.js...
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def annualize_metric(metric: float, holding_periods: int = 1) -> float: """ Annualize metric of arbitrary periodicity :param metric: Metric to analyze :param holding_periods: :return: Annualized metric """ days_per_year = 365 trans_ratio = days_per_year / holding_periods return (1...
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def read_gold_conll2003(gold_file): """ Reads in the gold annotation from a file in CoNLL 2003 format. Returns: - gold: a String list containing one sequence tag per token. E.g. [B-Kochschritt, L-Kochschritt, U-Zutat, O] - lines: a list list containing the original line spli...
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def get_bsj(seq, bsj): """Return transformed sequence of given BSJ""" return seq[bsj:] + seq[:bsj]
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import re def parse_year(inp, option='raise'): """ Attempt to parse a year out of a string. Parameters ---------- inp : str String from which year is to be parsed option : str Return option: - "bool" will return True if year is found, else False. - Return yea...
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