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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 contents

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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://[email protected]:9009/repos/some_username/column items = repository_clone_url.split( '@' ) tmp_url = items[ 1 ] elif repository_clone_url.find( '//' ) > 0: # We have an url that includes only a protocol, something like: # http://bx.psu.edu:9009/repos/some_username/column items = repository_clone_url.split( '//' ) tmp_url = items[ 1 ] else: tmp_url = repository_clone_url return tmp_url

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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): ``p.log_prob``s evaluated at samples from q. """ return -logu

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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(): if child.tag == name: return child.text.encode('utf-8').strip() return None

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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 thinnest of the three samples. sig2 : array_like Cross section of the mid-thickness of the three samples. sig3 : array_like Cross section of the thickest of the three samples. n1 : float Atom density of the thinnest sample n2 : float Atom density of the mid-thickness sample n3 : float Atom density of the thickest sample Returns ------- sig0 : array_like The extrapolated cross section from sig1, sig2, and sig3 """ # two terms in the numerator numer1 = (n1*sig2-n2*sig1)*(n3**2-n1**2-(n1-n3)/(n1-n2)*(n2**2-n1**2)) numer2 = (n1*n2**2-n1**2*n2)*(sig3-sig2-(n1-n3)/(n1-n2)*(sig2-sig1)) denom = (n1-n2)*(n3**2-n1**2) - (n1-n3)*(n2**2-n1**2) return (numer1-numer2)/denom

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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) as a list """ intermediate_split = intermediate_str.split(splitter) intermediate_filter = [elem for elem in intermediate_split if 'https' in elem] return intermediate_filter[0]

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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 ------- int the reference allele count """ return ( ''.join(variant.traits[trait]['alleles'] for trait in traits) .replace(',', '.') .count('.') )

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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 = (new_batch_dim, *(1 for _ in range(num_non_batch_dims))) return t.repeat(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 address_part, address_part_label in address_parts: # The address part of the tuple (address_part, address_part_label) for c in address_part: char_arr.append((c, address_part_label)) return char_arr

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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 nodes in the graph [(source node, destination node, weight), ...] Returns ------- out : tuple (names, adjacency matrix) names - list of unique nodes in the graph adjacency matrix represented as list of lists """ # determine the set of unique nodes names = set() for src, dest, _ in edges: # add source and destination nodes names.add(src) names.add(dest) # convert set of names to sorted list names = sorted(names) # determine initial adjacency matrix with infinity weights matrix = [[float('Inf')] * len(names) for _ in names] for src, dest, weight in edges: # update weight in adjacency matrix matrix[names.index(src)][names.index(dest)] = weight for src in names: matrix[names.index(src)][names.index(src)] = 0 # return list of names and adjacency matrix return names, matrix

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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^-5 - 10^-2 near the surface Returns ------- `float` Cn """ return (79 * P / (T ** 2)) * Ct ** 2 * 1e-12

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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 card info to the notes notes = notes + ("\n".join([f"{i}: {j}" for i, j in item.get('card', "").items()])) return f"{item['name']} - Card", \ item.get('card', {}).get('brand', '') or "", \ item.get('card', {}).get('number', "") or "", \ "", \ notes

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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() if given_number.isdigit(): num = int(given_number) valid_enter = True return num

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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.__defaults__, closure=old_func.__closure__) new_func.__dict__.update(old_func.__dict__) new_func.__module__ = updated_module.__name__ return new_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 type dict") recipes = input_dict return recipes

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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 in open(annotation_file): file_name, start_time, end_time, bird_class = line.strip().split('\t') if file_name not in annotation_dict: annotation_dict[file_name] = list() annotation_dict[file_name].append([start_time, end_time, bird_class]) return annotation_dict

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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 totals totals = line.split(' Executed ')[1].split(' ') executed_tests, total_tests = int(totals[0]), int(totals[2]) # get failed if 'SUCCESS' in line: failed_tests = 0 else: failed_tests = int(totals[3][1:]) return { 'total_tests': total_tests, 'executed_tests': executed_tests, 'failed_tests': failed_tests, 'passed_tests': executed_tests - failed_tests }

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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 @param n2 The number of observations in the second sample """ numerator = (s1**2/n1 + s2**2/n2)**2 denominator = ((s1**2/n1)**2)/(n1-1) + ((s2**2/n2)**2)/(n2-1) degrees_of_freedom = numerator/denominator return degrees_of_freedom

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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(start, end+1)

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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 ---|\ | \ | \ | \ min_e ---|____\_______________(episode) | target_episode slope = (min_e - max_e) / (target_episode) intercept = max_e e = slope * episode + intercept Args: episode (int): Current episode min_e (float): Minimum epsilon max_e (float): Maximum epsilon target_episode (int): epsilon becomes the `min_e` at `target_episode` Returns: float: epsilon between `min_e` and `max_e` """ slope = (min_e - max_e) / (target_episode) intercept = max_e return max(min_e, slope * episode + intercept)

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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') \ .replace('u::', 'ü') return out

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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_only: bool. Whether to sample only on the upper hemisphere. Returns: lightdirs: [R, S, 3] float tensor. Random light directions sampled from the unit sphere for each sampled point. """ if upper_only: min_z = 0 else: min_z = -1 phi = torch.rand(num_rays, num_samples) * (2 * math.pi) # [R, S] cos_theta = torch.rand(num_rays, num_samples) * (1 - min_z) + min_z # [R, S] theta = torch.acos(cos_theta) # [R, S] x = torch.sin(theta) * torch.cos(phi) y = torch.sin(theta) * torch.sin(phi) z = torch.cos(theta) lightdirs = torch.cat((x[..., None], y[..., None], z[..., None]), dim=-1) # [R, S, 3] return lightdirs

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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 sub hands with one element removed for item in hand: list_hand = list(hand) list_hand.remove(item) # add to set_holds this sub hand set_holds.add(tuple(list_hand)) # also add to set_holds the recursion of this sub hand # set functionality also takes care of repeated sub hands set_holds.update(gen_all_holds(tuple(list_hand))) return set_holds

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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 resulting from the difference in apparent and absolute magnitude [pc]. """ d = 10.0**(-(magAbs - magApp) / 5.0 + 1.0) return d

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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") decoded_anycli(result) """ value = kwargs.get('value', None) return base64.b64decode(value['result_base64_encoded']).decode('utf-8')

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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 dictionary keyed by formula-mp_id with structure values. """ props = ["pretty_formula", "structure", "task_id", "magnetic_type"] results = list(materials_store.groupby("pretty_formula", properties=props, criteria=query)) formula_dict = {} for result in tqdm.tqdm(results): formula = result['_id']['pretty_formula'] task_ids = [d['task_id'] for d in result['docs']] structures = [d['structure'] for d in result['docs']] formula_dict[formula] = dict(zip(task_ids, structures)) return formula_dict

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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 if cellsize_x != cellsize_y: raise ValueError('extent produces different cellsize in x and y') cellsize = cellsize_x header = {'ncols':ncols, 'nrows':nrows, 'xllcorner':xllcorner, 'yllcorner':yllcorner, 'cellsize':cellsize, 'NODATA_value':nan_value} return header

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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.getLogger(class_.__qualname__) return class_

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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(dmax)] for j in range(8): shells.append(1.0 / math.sqrt(dmax + diff * (j + 1))) return shells

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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.randint(0, zSize-1) if (x, y, z) not in src: src.append((x,y,z)) return src

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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_pred) return matches / total

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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 open(sentence_file) as content: for line in content: line = line.strip() line_clean = line.replace(",", "") line_clean = line_clean.lower() sentences[line_clean] = line return sentences

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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(f"Invalid first digit of rare number: {first}")

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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. """ sample_dim = len(mesh_size) assert (len(upper) == sample_dim) assert (len(lower) == sample_dim) assert (len(mesh_size) == sample_dim) meshes = [] for i in range(sample_dim): meshes.append( torch.linspace(lower[i], upper[i], mesh_size[i], dtype=dtype)) mesh_tensors = torch.meshgrid(*meshes) return torch.cat( [mesh_tensors[i].reshape((-1, 1)) for i in range(sample_dim)], dim=1)

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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: try: c = getattr(c, attr) except AttributeError: return default return c else: return reduce(getattr, attrs, o)

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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, then matching the regex will cause the test to fail. """ # pylint: disable=unused-argument # args defined by test definition rex = re.compile(regex) def is_regex_test(conf, path, value): match = rex.search(value) if invert and match: return u'"{0}" matches /{1}/'.format(value, regex) if not invert and not match: return u'"{0}" does not match /{1}/'.format(value, regex) return None return is_regex_test

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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 char ch2 (str): Third char ch3 (str): Fourth char Returns: int: The integer representation of given characters. **Reference**: `Microsoft <https://goo.gl/bjtMFA>`__ """ return (ord(ch0) << 0) | (ord(ch1) << 8) | (ord(ch2) << 16) | (ord(ch3) << 24)

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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'][0]['name'] album = track['album']['name'] uri = track["uri"] track_id = track['id'] output = {"name": name, "artist": artist, "album": album, "uri": uri, "id": track_id} return output

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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 instant or time span to use as a filter :type time_or_period: :class:`datetime.datetime` or a tuple of two datetimes or a tuple of one datetime and one :class:`datetime.timedelta` :param op: the comparison operation :type op: str :return: a comparison expression result :rtype: bool """ d = datetime.strptime(record_date_time, "%Y-%m-%dT%H:%M:%SZ") result = None # perform before and after operations if op in ['BEFORE', 'AFTER']: query_date_time = datetime.strptime( time_or_period.value, "%Y-%m-%dT%H:%M:%SZ") if op == 'BEFORE': return d <= query_date_time elif op == 'AFTER': return d >= query_date_time # perform during operation elif 'DURING' in op: low, high = time_or_period low = datetime.strptime(low.value, "%Y-%m-%dT%H:%M:%SZ") high = datetime.strptime(high.value, "%Y-%m-%dT%H:%M:%SZ") result = d >= low and d <= high if 'BEFORE' in op: result = d <= high elif 'AFTER' in op: result = d >= low return result

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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.sources.zuul.transactions.VariantResponse`] """ return job.variants().get()

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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(xarrs.keys())

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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 = Base for (nm, NmCl) in Deriveds: if nm == name: Derived = NmCl break return 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 list and deleted from the bucket >>> find_expired(bucket_items, 2) ['k1'] >>> bucket_items [('k2', 2), ('k3', 3)] """ expired_keys = [] for i in range(len(bucket_items) - 1, -1, -1): key, expires = bucket_items[i] if expires < now: expired_keys.append(key) del bucket_items[i] return expired_keys

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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 """ with open(filename, "r") as stream: pre_commit_data = yaml.safe_load(stream) pre_config_repo = next( (item for item in pre_commit_data["repos"] if item["repo"] == repo), None ) if pre_config_repo: return pre_config_repo["rev"] return None

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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: :return: """ sc_size = (z_max - z_min) return z_min + (z - z_min) % sc_size

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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: return data.decode("latin-1")

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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 default value to set if no value Returns ------- dict A dictionary Notes ----- This standalone and generic function is only required by plotters. """ if isinstance(value, dict): return {key: value.get(key, default) for key in keys} else: return dict.fromkeys(keys, value or default)

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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_word-parent_index, child_word-child_index) Returns: tuple of (parent_index, edge_label, child_index) """ tokens = edge_str.split("(") label = tokens[0] tokens = tokens[1].split(", ") parent = int(tokens[0].split("-")[-1]) - 1 child = int(",".join(tokens[1:]).split("-")[-1][:-1]) - 1 return (parent, label, child)

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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 category == 'N': return True return False

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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 fiscal_key not in ('_unknown', '_ignored'): field.update({'name': fiscal_key}) del field['maps_to'] if 'translates_to' in field: del field['translates_to'] fields.append(field) resource['schema']['fields'] = fields return datapackage

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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 title: the displayed text. Defaults to the path Returns: The html link to the resource. """ return '<a target=_blank href="/api/autogen/serve/{}?static={}&pid={}">{}</a>'.format( resource_path, "true" if static else "false", pid, resource_path if not title else title )

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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 ',' """ for i in range(len(listDb)): mot = str(listDb[i]) phrase2 += mot if not i == len(listDb)-1: phrase2 += ',' return phrase2

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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 comment.startswith('# text ='): new_comments.append('# text = {}'.format(new_text)) replaced = True else: new_comments.append(comment) if not replaced: new_comments.append('# text = {}'.format(new_text)) return new_comments

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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.json().get("id")

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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 + metric) ** trans_ratio - 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 split at "\t" """ gold = [] lines = [] with open(gold_file, encoding="utf-8") as f: for line in f: if line == "\n": continue line = line.strip().split("\t") gold.append(line[3]) lines.append(line) return gold, lines

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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 year int / raise a RuntimeError otherwise Returns ------- out : int | bool Year int parsed from inp, or boolean T/F (if found and option is bool). Examples -------- >>> year_str = "NSRDB_2018.h5" >>> parse_year(year_str) 2018 >>> year_str = "NSRDB_2018.h5" >>> parse_year(year_str, option='bool') True >>> year_str = "NSRDB_TMY.h5" >>> parse_year(year_str) RuntimeError: Cannot parse year from NSRDB_TMY.h5 >>> year_str = "NSRDB_TMY.h5" >>> parse_year(year_str, option='bool') False """ # char leading year cannot be 0-9 # char trailing year can be end of str or not 0-9 regex = r".*[^0-9]([1-2][0-9]{3})($|[^0-9])" match = re.match(regex, inp) if match: out = int(match.group(1)) if 'bool' in option: out = True else: if 'bool' in option: out = False else: raise RuntimeError('Cannot parse year from {}'.format(inp)) return out

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