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def format_priorities(df): """ Format the work management priorities for insertion into the SQL table. """ df=df[['WellName','Corp_ID','Facility_ID', 'Area', 'Route','Latitude', 'Longitude', 'Priority', 'Priority_Level', 'Description', 'Assigned_To', 'chokeStatusCreatedBy', 'chokeStatusDate'...
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def normalize(value, dict_type=dict): """Normalize values. Recursively normalizes dict keys to be lower case, no surrounding whitespace, underscore-delimited strings.""" if isinstance(value, dict): normalized = dict_type() for k, v in value.items(): key = k.strip().lower().replac...
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import torch def gather_one(x, indices, *, dim): """ Gather with only one element along the gathered dimension """ return torch.gather(x, dim=dim, index=indices.unsqueeze(dim)).squeeze(dim)
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def bin_from_float(number: float): """Return binary from float value. >>> bin_from_float(446.15625) 0b110111110.00101 """ integer = int(number) fractional = abs(number) % 1 count = len(str(fractional)[2:]) binary = [] while (count > 0): # print(number, integer, fractional...
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def matches(character): """ Returns true if the given character matches the token. """ return lambda tokens: tokens and tokens[0] == character
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def binomial(n, k): """ Chose k objects from n. (n, k) = n!/(k!(n-k)!) Pascal's rule: (n + 1, k) = (n, k) + (n, k - 1) (k, k) = 0 """ # if k > n: # return 0 # if k == n or k == 0: # return 1 # return binomial(n - 1, k) + binomial(n - 1, k - 1) res = 1 ...
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def _get_base_href(tree): """ Return href value of a base tag """ base_hrefs = tree.xpath('//base/@href') if base_hrefs: return base_hrefs[0]
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import colorsys def hsv_to_rgb(h: float, s: float, v: float) -> int: """ Converts hue, saturation and value parts in percents to rgb int value. :param h: hue part in percents :param s: saturation part in percents :param v: value part in percents :return: int """ r, g, b = colorsys.hsv...
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def is_actor_alive(actor, time=0.5): """ wait the actor to terminate or 0.5 secondes and return its is_alive value """ actor.join(time) return actor.is_alive()
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def initializeStateFlags(*args): """return an initial state, built up by one or more state flags example from natspeak_spell: state = nsformat.initializeStateFlags(nsformat.flag_no_space_next) """ return set(args)
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import pickle def do_unpickle(filename): """Unpickles an object from a given file.""" with open(filename, "rb") as f: return pickle.load(f)
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def is_host_name_unique(yaml, hostname): """Returns True if there is at most one occurence of the given ifname amonst all host-names of TAPs.""" if not "taps" in yaml: return True host_names = [] for _tap_ifname, tap_iface in yaml["taps"].items(): host_names.append(tap_iface["host"]["nam...
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def broadcast_shape(shape, length): """Pad a shape with ones following standard Numpy broadcasting.""" n = len(shape) if n < length: return tuple([1] * (length - n) + list(shape)) else: return shape
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def children_of_model(self,model): """Returns all children of the given model This method extends the mosaik.scenario.Entity class. It returns all children of the given model of the entity. Args: model: The model of the children Returns: A list of entities. """ children =...
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def parse_line_update_success(tokens): """Parses line which logs stats for a successful write/update request.""" latency = float(tokens[2]) name = tokens[1] name_server = int(tokens[4]) local_name_server = int(tokens[5]) return latency, name, name_server, local_name_server
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import requests def get_json_resource(resource_uri): """ Get a uri which returns JSON, return Python object. Returns None if the request status code is 4xx or 5xx. :param resource_uri: uri to request :return: Python dict/object from the request JSON. """ r = requests.get(resource_uri) ...
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def _is_in_placeholders(op, func_arg_placeholders): """Checks whether any output of this op is in func_arg_placeholders.""" return op.values() and any(x.name in func_arg_placeholders for x in op.values())
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def bool_(value: bool) -> bytearray: """ Pack bool to Starbound format. :param value: bool :return: bytearray """ return bytearray([value])
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def convindicetoplanetype(listindice): """ Converts miller plane (3 indices) into plane type for recognition where indices are sorted in decreasing order ex: [1,-2,-1] -> 211 """ listpositiveinteger = [abs(elem) for elem in listindice] listpositiveinteger.sort(reverse=True) resint = (1...
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def process_inputs(data): """ Process user inputs and apply default values if parameters not specified. Parameters ---------- data : dict User input containing model parameters Returns ------- out : dict Model data in format that allows construction of the Pyomo model ...
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def nan_check(test_dataframe): """ :param test_dataframe: pandas data frame :return: bool, whether there is any missing value in the data frame. """ return test_dataframe.isnull().values.any()
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def V_d2bV_by_V_Approx(V): """ Approximate V*d^2(bV)/dV^2 for single mode fiber. This value is needed to determine the waveguide dispersion. This approximation is for the fundamental mode in the fiber and is good to 1% when 1.4<V<2.4. Approximation by Marcuse (1979) Args: V: V-p...
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def read_parallel_batches(response): """ Given a `response` from dynamoDB's get_item (after translating from dyJSON, that is, a dict where the important information, the content of a table's item, is inside the key 'Item'), return the number of parallel batches in which to split the requests. Thi...
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def calculate_probabilities(previous_probabilities): """ Calculate the probabilities for each genotype (AA, Aa, aa) based on the probabilities of the previous generation. """ probability_AA = (previous_probabilities["AA"] * 1/2 + previous_probabilities["Aa"] * 1/4 + ...
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def make_twin_ax(ax): """ Create a twin axis on an existing axis with a shared x-axis """ # align the twinx axis twin_ax = ax.twinx() # Turn twin_ax grid off. twin_ax.grid(False) # Set ax's patch invisible ax.patch.set_visible(False) # Set axtwin's patch visible and colorize it...
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import yaml def load_yaml_conf(yaml_file): """Helper function to load the configuration yaml files""" with open(yaml_file, 'r') as stream: return yaml.safe_load(stream)
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def write_out(filename,data=b""): """ write_out(path,str/bytes) like: write_out(r"c:\1.txt",data) """ result = False try: with open(filename,"wb") as f: if isinstance(data,str): f.write(data.encode("utf-8")) else: f.write(...
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import re def _rgb_txt_line(string): """Parse a line from an X11 rgb.txt file Gives a name and 3 integers (RGB values) """ regexp = re.compile( r"([ 0-9][ 0-9][ 0-9])\s+([ 0-9][ 0-9][ 0-9])\s+([ 0-9][ 0-9][ 0-9])" r"\s+([a-zA-Z0-9 ]+)\s*" ) match = regexp.match(string) if ...
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import random def nth_element(x, n): """Returns the nth order statistic of a list Note on stability: If multiple order statistics are equal, this function will return the first index of the element in the list Args: x (list): The list from which to chooise n (nonnegative int): The order statistic ...
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def strip_transient(nb): """Strip transient values that shouldn't be stored in files. This should be called in *both* read and write. """ nb.metadata.pop('orig_nbformat', None) nb.metadata.pop('orig_nbformat_minor', None) nb.metadata.pop('signature', None) for cell in nb.cells: cell...
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def _get_works(df, run, project, GEN=None): """ Get set of work values from a dataframe Parameters ---------- df : pandas.DataFrame Information generated from folding at home run : str run to collect data for (i.e. 'RUN0') project : str project to collect data for (i.e. ...
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import pathlib from typing import Tuple from typing import List from typing import Optional import re def output_files(output_dir: pathlib.Path, jobid: str) -> Tuple[List[pathlib.Path], Optional[str]]: """Gives the list of output files from an array job. Args: output_dir: The directory con...
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import re def extract_hashtags(tweets): """Extracts all hashtags included in the input tweet data Parameters ---------- tweets : array_like List of tweets Returns ------- list List of hashtags included in the tweets list Examples -------- >>> tweets_list ...
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def linear_search_iterative(array, item): """Incrementing index until item is found in the array iteratively. array: list item: str Best case running time: O(1) if the item is at the beginning of the array. Worst case running time: O(n) if the item is last in the array. """...
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import socket def parse_ip(ip): """ >>> parse_ip("192.0.2.1") == (socket.AF_INET, "192.0.2.1") True >>> parse_ip("2001:DB8::1234:5678") == (socket.AF_INET6, "2001:db8::1234:5678") True >>> parse_ip("not-an-ip") Traceback (most recent call last): ... ValueError: 'not-an-ip' is...
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def mergeOptions(defaults, options): """Returns a dictionary where options are merged into the defaults""" merged_options = defaults.copy() for key, val in options.iteritems(): if key in merged_options: merged_options[key] = val return merged_options
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def get_property_names(obj): """Return set of object property name Inspiration: https://stackoverflow.com/questions/17735520/determine-if-given-class-attribute-is-a-property-or-not-python-object """ props = set() obj_type = type(obj) for attr in dir(obj): if isinstance(getattr(obj_type...
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def sign(n): """Return sign of number (-1,0,1).""" return 1 if n>0 else -1 if n<0 else 0
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def sorted_container_nodes(containers): """Returns a sorted iterable of containers sorted by label or id (whatever is available) Arguments: containers (iterable): The the list of containers to sort Returns: iterable: The sorted set of containers """ return sorted(containers, key=la...
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import re def _strip_ansi(source): """ Remove ANSI escape codes from text. Parameters ---------- source : str Source to remove the ANSI from """ ansi_re = re.compile('\x1b\\[(.*?)([@-~])') return ansi_re.sub('', source)
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import glob def read_labels(root_path): """ Reads labels and returns them in a tuple of sorted lists """ label_list = [] map_1 = sorted(glob.glob(root_path + 'Maps1_T/Maps1_T/*.png')) map_2 = sorted(glob.glob(root_path + 'Maps2_T/Maps2_T/*.png')) map_3 = sorted(glob.glob(root_path + 'Maps3...
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import requests def is_private(username): """ Check if user is private :param username: :return: bool """ r = requests.get(f"https://www.instagram.com/{username}/?__a=1") private_status = r.json()['graphql']['user']['is_private'] return private_status
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from typing import Optional from typing import Tuple from typing import Any def top_color_and_depth(container: tuple) -> Optional[Tuple[Any, int]]: """ Returns the top color from the container, along with the number of continuous segments that are that color. """ if len(container) == 0: re...
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def cpf_has_correct_length(value): """ This function receives the Brazilian CPF and returns True if the length of CPF is 11 or False if not. :param value: A string with the number of Brazilian CPF :return: """ if len(value) != 11: return False else: return True
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import re def make_wildcard_domain(d): """ >>> make_wildcard_domain('foo-bar.example.com') ['*.example.com', 'example.com'] """ if d.count('.') == 1: without_star = d with_star = f'*.{without_star}' else: with_star = re.sub(r'^([^.]+)(?=.)', '*', d, 1) without_s...
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def lemmatize(sentence_vector): """ Function to lemmatize an array of sentences. Args: sentence_vector (array): Array containing text. Returns: numpy.array: Array containing the lemmatized words. """ return sentence_vector.progress_apply(lambda token_list: ...
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def get_billing_data(order): """Extracts order's billing address into payment-friendly billing data.""" data = {} if order.billing_address: data = { 'billing_first_name': order.billing_address.first_name, 'billing_last_name': order.billing_address.last_name, 'bill...
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def levels_to_graph(levels): """ Convert an array of levels into a unicode string graph. Each level in the levels array is an integer 0-3. Those levels will be represented in the graph by 1-4 dots each. The returned string will contain two levels per rune. """ if len(levels) % 2 == 1: ...
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def extract_data(result): """Extract plain text data.""" try: return result['data'] except KeyError: return ""
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def receive(socket, msglen, chunksize=2048): """Receive an entire message from a socket, which may be chunked. Parameters ---------- socket : socket.socket object from which to receive data msglen : int length of the entire message chunksize : int ; optional ...
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def setup(setup_method): """Decorator for declaring setup methods for test cases.""" setup_method._is_setup_method = True return setup_method
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def FRET_efficiency_from_lifetime(fret_lifetime, donor_lifetime): """Compute FRET efficiency from FRET and donor-only states lifetimes.""" return 1 - fret_lifetime / donor_lifetime
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import logging import math import collections def get_simulation_parameters(open_rocket_helper, sim, rocket_components, random_parameters, randomize=True): """Collect all global simulation parameters for export""" logging.info("Used global parameters...") options = sim.getOpt...
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def egg_drop(n: int, k: int) -> int: """ What is the minimum number of trials we need to drop eggs to determine which floors of a building are safe for dropping eggs, given n eggs and k floors? :param n: number of eggs :param k: number of floors :return: the minimum number of trials >>> egg...
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def removeSlash(p): """ If string p ends with character '/' or backslash, it is removed. """ if p.endswith('/') or p.endswith('\\'): return p[:-1] else: return p
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def get_s3_keys(prefix, s3_client, bucket='fcp-indi'): """Retrieve all keys in an S3 bucket that match the prefix and site ID Parameters ---------- prefix : string S3 prefix designating the S3 "directory" in which to search. Do not include the site ID in the prefix. s3_client : bot...
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def _has_non_ascii_characters(data_string): """ Check if provided string contains non ascii characters :param data_string: str or unicode object """ try: data_string.encode('ascii') except UnicodeEncodeError: return True return False
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def rotate_list(numbers, cursor): """Rotate list such that the current start moves to the position indicated by the cursor.""" return numbers[len(numbers) - cursor:] + numbers[:len(numbers) - cursor]
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def iter_is_empty(i): """Test for empty iterator without consuming more than first element.""" try: i.next() except StopIteration: return True return False
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def get_bbox_from_gt(gt_root): """ Get the all the supervised bounding boxes (ground truth) having `gt_root` as root folder. :param gt_root: root folder for the ground truth bounding boxes :return all_objs: all supervised bounding boxes """ all_objs = dict() all_objs_elem = gt_root.findall("./...
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def load_input(filename): """ Load input names from file """ with open(filename) as f: return [quoted[1:-1] for quoted in f.readlines()[0].split(",")]
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def get_project_folder_name(project_file_name: str) -> str: """ Get the name of a folder associated with a project. :param project_file_name: Name of the project. :return: Name of the project folder according to Simio's nomenclature. """ project_name = project_file_name.split('.')[0] folder_...
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def calc_num_metric(predicted_number, actual_number): """ How similar are 2 numbers of references? The difference between the predicted and actual numbers of references as a percentage of the actual number """ # In the case of 0 references (some documents don't have references but do # have...
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import hashlib def _compute_file_md5(filename, block_size=2 ** 20): """ Compute the md5 hash of a file, catching any errors. Adapted from http://stackoverflow.com/a/1131255/256798 :param filename: :param block_size: :return: string version of hash, or empty string if IOError. """ md...
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import itertools def one_to_one(graph, nodes): """ Return True if graph contains only one to one mappings. The directed graph should be represented as a dictionary mapping of edges for each node. Nodes should be passed a simple list. """ edges = itertools.chain.from_iterable(graph.values()) ...
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def normalize_series(series, min_max): """ Normalizes a series where all values between 0 and 1. Values can exceed 1 if they exceed the provided max in the min_max tuple. :param series: Pandas series to normalize :param min_max: Tuple of minimum and maximum value for ...
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import torch def pdist(X,Y): """ Computes the squared Euclidean distance between all pairs x in X, y in Y """ # From https://github.com/clinicalml/cfrnet/blob/master/cfr/util.py M = -2*torch.matmul(X,torch.transpose(Y,0,1)) sqx = torch.sum(X**2,1,keepdim=True) sqy = torch.sum(Y**2,1,keepdim=True) ...
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def format_coordinates_for_cql(tile_coordinates: str) -> str: """ Format the tile coordinates for the cql filter string """ cql_filter_string = ( f"POLYGON(({tile_coordinates[0][1]}+{tile_coordinates[0][0]}," f"{tile_coordinates[1][1]}+{tile_coordinates[1][0]}," f"{tile_coordinates[2][1...
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from typing import Any def force_string(s: Any) -> str: """converts an Any value into a string by forcing string formatting""" return f'{s}'
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import torch from typing import Optional def merge_features(xyz: torch.Tensor, features: Optional[torch.Tensor]) -> torch.Tensor: """Merge xyz coordinates and features to point cloud.""" if features is None: return xyz.transpose(1, 2) else: return torch.cat((xyz.transpose(1, 2), features),...
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def prob(counts, variables=None, condition=(), transform=False): """Calculate (conditional) probabilites from counts. The levels of the result series, will allways be sorted to ensure proper behavior under multiplication and addition. :param counts: a series of counts with the variables as ind...
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def _topological_sort(key_less_than_values): """Topological sort for monotonicities. Args: key_less_than_values: A defaultdict from index to a list of indices, such that for j in key_less_than_values[i] we must have output(i) <= output(j). Returns: A topologically sorted list of indices. Raises...
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def is_record(data): """ Returns whether the data is a record. A record has required ``releases`` and ``ocid`` fields. """ return 'releases' in data and 'ocid' in data
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def strage_to_intage(str_age): """Turn a string-age into an integer age""" if str_age[-1] == '+': return int(str_age[:-1]) return int(str_age)
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def hcp_coord_test(x, y, z): """Test for coordinate in HCP grid""" m = x+y+z return m % 6 == 0 and (x-m//12) % 3 == 0 and (y-m//12) % 3 == 0
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from typing import List def check_args_validate(args: List[str]): """ Function for checking the legitimacy of an option. Details are written in usage. """ if len(args) != 2 or not args[1].isdigit(): return False, 0 elif not 0 < int(args[1]) < 100: return False, 0 return Tr...
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def set_robust(robust): """Return generic name if user passes None to the robust parameter in a regression. Note: already verified that the name is valid in check_robust() if the user passed anything besides None to robust. Parameters ---------- robust : string or None O...
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def contains_npmi_metric(metrics): """Checks if the csv file contains a metric that matches the plugin requirements. Args: metrics: The metrics in the header of the csv. Returns: Whether the header contains a metric that can be used by the plugin. """ for metric in metrics: ...
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def labels_from(labels_df): """ Extracts the unique labels from the labels dataframe """ # Build list with unique labels label_list = [] for tag_str in labels_df.tags.values: labels = tag_str.split(' ') for label in labels: if label not in label_list: labe...
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import re def extract_tags_links(string): """Extract tags and links from a narration string. Args: string: A string, possibly containing tags (`#tag`) and links (`^link`). Returns: A triple (new_string, tags, links) where `new_string` is `string` stripped of tags and link...
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def _get_ids_for_cameras(cameras): """Get list of camera IDs from cameras""" return list(map(lambda camera: camera.id, cameras))
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def findIndexInList (L: list, item) -> int: """finds the index of an item in a given list""" for i in range (len (L)): if L[i] == item: return i # return -1 when unsuccessful return -1
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from typing import List from typing import Dict from typing import Any from typing import Callable from functools import reduce def pluck( keys: List[str], items: List[Dict[str, Any]], key_sep: str = ".", key_func: Callable[[str], str] = lambda k: k, ) -> List[Dict[str, Any]]: """Pluck `keys` from...
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def make_board(board_string): """Make a board from a string. For example:: >>> board = make_board(''' ... N C A N E ... O U I O P ... Z Q Z O N ... F A D P L ... E D E A Z ... ''') >>> len(board) 5 >>> board[0] ['N', 'C'...
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def EMPTY(value): """Constant validator that requires empty values (allows None).""" return not bool(value)
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def detectFileFormat(filename): """ return format name by examining the last suffix of file name """ suffixFormatDict = { 'gb': 'GenBank', 'fa': 'FASTA', 'fasta': 'FASTA', 'gff3': 'GFF3'} suffix = file...
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def createTexFile(filename): """Creates a .tex file with the filename given and returns a file Parameters: filename (string): Name of the .tex file created. Returns: file: .tex file with filename """ out_file = open(f'{filename}.tex', "w") header = "\documentclass{article}\n\\b...
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def remove_paren(token: str): """Remove ( and ) from the given token.""" return token.replace('(', '') \ .replace(')', '')
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def id_to_loc(gdf, fid): """Provides the location (coordinates) of the given feature identifier in the GeoDataFrame. Args: gdf: A GeoDataFrame containing the input points. fid: The identifier of a feature in the GeoDataFrame. Returns: An array [x, y] denoting the c...
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def groupbykey(iterable, key=None): """ Returns a list of sublists of *iterable* grouped by key: all elements x of a given sublist have the same value key(x). key(x) must return a hashable object, such that set(key(x) for x in iterable) is possible. If not given, key() is the identity func...
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import io def PIL_im_to_BytesIO(im): """ Convert pillow image to io.BytesIO object ___ im: PIL.Image ___ Output: io.BytesIO object with the image data """ output = io.BytesIO() im.save(output, format="PNG") return output
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def bytescl(img, bottom, top): """ Scale a pixel image to limits (0, 1). Keyword arguments: img -- Original pixel image. bottom -- Lower limit of img. top -- Upper limit of img. Output(s): scl_img -- Scaled image with new limits 0(min) - 1(max). """ scl_img = (((top - bott...
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from typing import OrderedDict import json def load_recording(frame_file_tuples, session_id=None, camera=None, width=None, height=None, verbose=False): """ Load all frames of a single recording and return the dict representation of the recording. :param frame_file_tuples: List of (frame index, filename) t...
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def list2p(paragraphs): """list of paragraphs to html""" return ''.join(['<p>{}</p>'.format(p) for p in paragraphs])
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def valid_transfer_value(transfer_value): """Returns True if transfer_value is valid Returns False if transfer_value is not valid """ try: int(transfer_value) except: return False return True
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import random def shuffle(l): """ Return a randomly shuffled list given an ordered list. """ final_list = [] for _ in l: final_list.append(l.pop(random.randrange(0, len(l)))) return final_list
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from typing import Tuple def parse_mode(mode: str) -> Tuple[str, bool, bool]: """Parse a mode used in open. Order is not considered at all. Binary flag (b) is ignored. Valid modes are: r, r+, w, w+, x, x+. Return a tuple (nomalized, is_read, is_write). """ mode_set = set(mode) if len...
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def filter_not_in(values, vmin=None, vmax=None): """ Handles 'not in' filters op: ['in', 'not in'] values: iterable of values vmin, vmax: the range to compare within Returns ------- True or False """ if len(values) == 0: return False if vmax is not None and vmax in ...
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from typing import Tuple def mapRange(a: Tuple[float, float], b: Tuple[float, float], s: float) -> float: """Calculate a multiplier for the extrusion value from the distance to the perimeter. Args: a (Tuple[float, float]): a tuple containing: - a1 (float): the minimum distance to the peri...
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def import_txt(file_name, two_dimensional=False, **kwargs): """ Reads control points from a text file and generates a 1-D list of control points. The following code examples illustrate importing different types of text files for curves and surfaces: .. code-block:: python # Import curve control p...
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