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def rotate_point_by_90(x, y, k, w = 1.0, h = 1.0): """ Rotate a point xy on an image by k * 90 degrees. Params: x, y: a point, (x, y). If not normalized within 0 and 1, the width and height of the image should be specified clearly. w, h: the width and height of image ...
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def list_square_to_input(list_signs,list_index_signs): """ Take the list of squares fill in by a sign and create a 9x1 array (input_layer for neural network) with values -1 for a cross, 0 if empty square and 1 for a circle. """ input_layer = [0 for k in range(9)] for i in range(len(list_sign...
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import copy def sh_curve_summer_off(sh_array, resc=0.2): """ Modifies space heating load array to be zero during non heating period from April to September Parameters ---------- sh_array : np.array (of floats) Numpy array with space heating power in Watt (for each timestep) resc :...
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def _hash(number, alphabet): """Hashes `number` using the given `alphabet` sequence.""" hashed = '' len_alphabet = len(alphabet) while True: hashed = alphabet[number % len_alphabet] + hashed number //= len_alphabet if not number: return hashed
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def get_width(n: int) -> int: """Returns width of rangoli.""" if n == 1: # basecase return 1 width = 0 for i in range(n): if i == 0: ## Middle char width += 3 elif i < n-1: ## Inter-rim chars width += 4 elif i == n-1: ## Bookend chars ...
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def has_alpha(img): """Checks if the image has an alpha channel. Args: img: an image Returns: True/False """ return img.ndim == 4
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import json def load_dict(dict_path, array_key=False): """ Args: dict_path: The path to a json dictionary array_key: If true the parser will consider the first element in a sublist at the key {_:[K,...,V],...}. Otherwise it will parse as {K:V,...} or {K:[...,V],...} Ret...
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def prepend_reserved_windows_names(parts: list): """ Prepend the first part of a file or directory name with underscore if that name part is a reserved windows name. The prepend is applied in all operating systems. Parameters ========== parts : list list of parts making up the name. p...
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def base_convert_to_ten(base: int, digits: list[int]) -> int: """ Examples: >>> digits = [0, 1, 1] >>> base_convert_to_ten(2, digits) 6 """ assert abs(base) >= 2 p = 1 n = 0 for d in digits: n += d * p p *= base return n
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def dot3(vec1, vec2): """Calculate dot product for two 3d vectors.""" return vec1[0]*vec2[0] + vec1[1]*vec2[1] + vec1[2]*vec2[2]
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import re def check_id_type(row_dict): """Determine which type of id this record holds. Varying on specific field values and lack thereof. Results: 'specimen', 'extraction', 'library', 'pool', 'Invalid' """ parent = row_dict['parent_jaxid'] sample = row_dict['sample_type'] nucleic = row_di...
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def read_labels_file(inputfile): """ Read a text file containing true and predicted labels """ labels, preds = [], [] with open(inputfile) as fin: for line in fin: line = line.strip() if line and not line.startswith('#'): y, p = line.split() la...
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def compute_in_degrees(digraph): """ Compute the in-degrees for the nodes in digraph and store them in a dictionary """ in_degrees = {} for key_i in digraph: degree = 0 for key_j in digraph: if key_i in digraph[key_j]: degree += 1 in_degrees[key_i] = degree return in_degrees
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def get_columns_of_type(df, type_): """ Generate a list of columns from a given df that match a certain type """ return list(df.select_dtypes(include=type_).columns)
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import logging def get_logger(name="urlchecker", level=logging.INFO): """ Get a default logger for the urlchecker library, meaning that we use name "urlchecker" and use the default logging level INFO Parameters: - name: the name for the logger (defaults to urlchecker) - level: the log...
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def validate_positive_int(ctx, param, value): """Check that a command line argument is a positive integer.""" if value < 1: raise ValueError("%s parameter cannot be < 1", param) if int(value) != value: raise ValueError("%s parameter must be an int, not a float", param) return value
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def stats(d_raw_materials, f_secret_points, f_total_money_collected): """ Show machine statistics Params: d_raw_materials: dict f_secret_points: int f_total_money_collected: float Returns: str """ cm_stats = 'sugar {0} tablespoons remaining\n'.format(d_raw_mater...
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def process_asa_data(rsa_data): """Process the .asa output file: atomic level SASA data.""" naccess_atom_dict = {} for line in rsa_data: full_atom_id = line[12:16] atom_id = full_atom_id.strip() chainid = line[21] resseq = int(line[22:26]) icode = line[26] res...
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def add(x, y): """Return the addition of values x & y""" return (x + y)
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def collect(msg): """ Collecting cookie from HttpMessage """ cookies = msg.getRequestHeader().getHttpCookies(); return cookies;
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def call_function_from_varnames(fn_name, input_names, output_names): """ Build c++ code to call a function using the given paramerers """ lines = '' outputs_avail = output_names is not None and len(output_names) != 0 inputs_avail = input_names is not None and len(input_names) != 0 li...
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def mul_by_const(constant, rh_coeffs): """Multiplies a constant by a list of coefficients. Parameters ---------- constant : numeric type The constant to multiply by. rh_coeffs : list The coefficients of the right hand side. Returns ------- list A list of (id, si...
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def make_valid_latex_string(s: str) -> str: """ Take a string and make it a valid latex math string by wrapping it with "$"" when necessary. Of course, strings are only wrapped with the "$" if they are not already present. Args: s: The input string. Returns: The properly formatted stri...
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import math def erfc(x): """The complementary error function.""" exp = math.exp p = 0.3275911 a1 = 0.254829592 a2 = -0.284496736 a3 = 1.421413741 a4 = -1.453152027 a5 = 1.061405429 t = 1.0 / (1.0 + p*x) erfcx = ( (a1 + (a2 + (a3 + (a4 + a5*t)*t)...
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def get_char_num(x): """ Convert signed integer to number in range 0 - 256 """ return int((256+x)%256)
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def _get_instance(resp): """ Get the one and only match for the instance list in the response. If there are more or less and one match, log errors and return None. """ instances = [i for r in resp['Reservations'] for i in r['Instances']] # return the one and only match if len(instances) == ...
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def divisor(field, data): """ Construct a divisor from the data. INPUT: - ``field`` -- function field - ``data`` -- dictionary of place and multiplicity pairs EXAMPLES:: sage: K.<x> = FunctionField(GF(2)); R.<t> = K[] sage: F.<y> = K.extension(t^3 - x^2*(x^2 + x + 1)^2) ...
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from pathlib import Path def get_config_path(base_path, vin): """Return path to settings file.""" path = Path(str(vin) + '.ini') if path.is_file(): return path path = Path(base_path) / path if path.is_file(): return path path = Path('default.ini') if path.is_file(): ...
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from typing import List import functools import operator def prod(factors: List[int]) -> int: """ Compute the product of a list of integers. """ return functools.reduce(operator.mul, factors, 1)
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import math def previous_power_of_2(n): """ Return the biggest power of 2 which is smaller than n """ return 2 ** math.floor(math.log2(n))
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import shutil def copy_sample(sample, destination): """ Copy a sample to a destination. :param sample: Sample name (str) :param destination: Destination directory (str) :rtype: Output path (str) """ output_path = "{0}/{1}".format(destination, sample) shutil.copytree("samples/{0}"...
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def repeater(fun, num_repeats): """ Returns a new function f. f should take a single input i, and return fun applied to i num_repeats times. In other words, if num_repeats is 1, f should return fun(i). If num_repeats is 2, f should return fun(fun(i)). If num_repeats is 0, f should return i. :par...
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import pathlib def extract_file_extension(file_path_or_url): """ Extract the file extension if it exists. Args: file_path_or_url: The path to the file. Type can can be anything that pathlib.Path understands. Returns: File extension without the period, i.e. ("txt" not ".txt"). None if...
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def _get_et(sel_cim_data): """Return evapotranspiration.""" return sel_cim_data.Evap_tavg
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def update_query(context, **kwargs): """Construct an URL contains only the querystring (excluding "?") by updating the current URL's querystring with the provided arguments.""" request = context['request'] query = request.GET.copy() for k, v in kwargs.items(): query[k] = v return query.urlen...
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def paths_concordance_fna(path_fixtures_base): """Paths to FASTA inputs for concordance analysis.""" return [ _ for _ in (path_fixtures_base / "concordance").iterdir() if _.is_file() and _.suffix == ".fna" ]
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def mapify_iterable(iter_of_dict, field_name): """Convert an iterable of dicts into a big dict indexed by chosen field I can't think of a better name. 'Tis catchy. """ acc = dict() for item in iter_of_dict: acc[item[field_name]] = item return acc
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def get_required_static_files(analysis_settings): """Based on config options, return a list of static data files that will be required. """ # Start with list of files that are always required static_files = ['footprint', 'vulnerability', 'damage_bin_dict'] # Check if random is required if...
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def nest_level(lst): """Calculate the nesting level of a list.""" if not isinstance(lst, list): return 0 if not lst: return 1 return max(nest_level(item) for item in lst) + 1
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def in_shape_from(output_shape): """ Returns input_shape required for a output_shape x output_shape SPD tensor Args: output_shape (int): The dimension of square tensor to produce. Returns: (int): The input shape associated from a `[output_shape, output_shape` SPD tensor. ...
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def extract_sample_name_from_sam_reader(sam_reader): """Returns the sample name as derived from the BAM file of reads. Args: sam_reader: Already opened sam_reader to use to extract the sample names from. This sam_reader will not be closed after this function returns. Returns: The sample ID annotat...
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def vmul(vect, s): """ This function returns the vector result of multiplying each entries of a vector by a scalar. Works also for flat matrices :param vect: the vector to be multiplied with the scalar value :param s: the scalar value :type vect: double or integer iterable :type s: double o...
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import re def remove_punctuation(question): """ Removes punctuation from a question. """ return re.sub(r"[?|\.|!|:|,|;]", '', question)
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def test(_method): """@test annotation for test methods.""" _method.IS_TEST_METHOD = True return _method
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def hhmm(secs): """ Format a number of seconds in hours and minutes """ hr = int(secs // 3600) mn = int((secs % 3600) / 60) return "{:02d}:{:02d}".format(hr, mn)
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import random import string def get_random_str(length): """Return random string with desired length.""" return ''.join( random.choice(string.ascii_lowercase) for i in range(length))
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from typing import List def tag(parts: List[str]) -> str: """ Get only interesting values from *parts*. - values without `=` - values starting with `text=` Source: https://sv.wiktionary.org/wiki/Mall:tagg >>> tag(["historia"]) 'historia' >>> tag(["biologi", "allmänt"]) ...
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from typing import List from typing import Set def unanimous_answers(group: List[str]) -> Set[str]: """Finds the unique answers in a given group, that anyone gave.""" answers = set.intersection(*(set(item) for item in group)) return answers
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def get_classes(y) -> int: """ Get the total number of classes. Args: y : The labels list of the data. Returns: int: Number of total classes """ return int(y.shape[1])
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import logging def update_classy_state(task, state_dict): """ Updates the task with the provided task dictionary. Args: task: ClassyTask instance to update state_dict: State dict, should be the output of a call to ClassyTask.get_classy_state(). """ logging.info("Loadin...
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def find_contributing_basins(chainids, HB_gdf): """ Given an input GeoDataFrame of HydroBasins shapefiles and a list of chainids denoting which basins are part of the chain, this function walks upstream from the upstream-most basin by following the "NEXT_DOWN" attribute until all possible basins are...
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def transform_labels_two(row): """Takes original score (label) and converts to binary classes""" label = int(row['label']) if label <= 2: return 0 else: return 1
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def FindPhase(name, phases): """Find the specified phase, or return None""" for phase in phases: if phase.name.lower() == name.lower(): return phase return None
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def rsrpad(data: bytes, block_size_bytes: int) -> bytes: """Return data padded to match the specified block_size_bytes. Arguments: data {bytes} -- Data string to pad. block_size_bytes {int} -- Block size for padding. Returns: bytes -- Padded data. The first byte of the padding...
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def _split_by_length(msg, size): """ Splits a string into a list of strings up to the given size. :: >>> _split_by_length('hello', 2) ['he', 'll', 'o'] :param str msg: string to split :param int size: number of characters to chunk into :returns: **list** with chunked string components """ r...
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def remove_chars(str_, char_list): """ removes all chars in char_list from str_ Args: str_ (str): char_list (list): Returns: str: outstr Example: >>> # ENABLE_DOCTEST >>> from utool.util_str import * # NOQA >>> str_ = '1, 2, 3, 4' >>> char_...
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import random import string def random_alpha(n=8): """Return random set of ASCII letters with length `n`.""" return "".join(random.SystemRandom().choice(string.ascii_letters) for _ in range(n))
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from datetime import datetime import pytz def set_last_update(details, *args, **kwargs): # pylint: disable=unused-argument """ Pipeline function to add extra information about when the social auth profile has been updated. Args: details (dict): dictionary of informations about the user ...
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def get_shrink_type(plugins): """Gets the type of shrinking process requested by the user, taking into account backward compatibility values :param dict plugins: the part of the manifest related to plugins :return: None (if none selected), "vmware-vdiskmanager" or "qemu-img" (tool to be used)""" sh...
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def getKfactorsFrom(output): """ Read NLLfast output and return the k-factors. """ if not output: return False else: lines = output.split('\n') il = 0 line = lines[il] process = False while not "K_NLO" in line and il < len(lines) - 2: ...
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def indexAll(inputList=None, value=None): """ find the index of a given value in a given list :param inputList: input as a list :param value: the value that targeted to index :return: the index of value lies in a list """ if not isinstance(inputList, list): raise TypeError('Input lis...
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def trim(x): """Removes (strips) whitespace from both ends of the string""" return x.strip()
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def correct_ordering_of_component_masses(mass_1, mass_2): """Ensure mass 1 always greater than mass 2.""" if mass_1 > mass_2: return mass_1, mass_2 else: return mass_2, mass_1
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def getMid(elem): """Get mid xyz coordinates given a pyNastran Element """ return elem.get_node_positions().mean(axis=0)
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from typing import Union from pathlib import Path def resource(*nodes: Union[Path, str]) -> Path: """Gets a path of a test resource file under resources/.""" return Path(Path(__file__).parent, "resources", *nodes)
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def sq_vidx(self, i, ltrip_of_idx): """Computes the index of the optimal distribution (q_vars) in the optimal solution of the Exponential Cone Programming Args: i: int ltrip_of_idx: int - length of triplet t,u,v Returns: int """ return 3*ltrip_of...
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def _format_values(val, n, e_type): """Returns a feature formated value Args: val: `str`, "num1,num2,num3,...", value to format n: `int`, number of elememts within tuples e_type: `str`, the type of each elements within tuples Returns a list of tuples of e_type values """ lst = [e_type(float(...
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def land(value): """Returns a new trampolined value that lands off the trampoline.""" return ('land', value)
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import math def hsvToRGB(h, s, v): """ Convert HSV (hue, saturation, value) color space to RGB (red, green blue) color space. **Parameters** **h** : float Hue, a number in [0, 360]. **s** : float Saturation, a number in [0, 1]. ...
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def square(a): """ Square a number Parameters: a (float): Number to square Returns: float: square of a """ return a * a
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def _unpack_player(sid, p, **_): # pylint: disable=invalid-name """Unpack a player""" return sid, p
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def figure_layout(annotations=None, title_text=None, x_label=None, y_label=None, show_legend=False): """Customize plotly figures Parameters ---------- annotations: a list of dictionaries informing the values of parameters to format annotations. x_label: str. Title fo...
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def SetCounts(setList): """Take a list of sets and return a dict that maps elements in the sets to the number of sets they appear in as ints. """ keys = set() for curSet in setList: keys.update(curSet) # Initialize the dictionary that will be used to store the counts of each element ...
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def get_root_tables(metadata): """Get all root tables (tables who are never a child table in a foreign key relation) of the dataset. Args: metadata (dict): a ``MetaData`` instance Returns: set: the root table names """ all_tables = {table['name'] for table in metadata.get_t...
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from typing import Any def table_input(name: str, label: str, subparameters: list[Any], **kwargs: Any) -> dict[str, Any]: """Allows to have a table input for SLimsGate. Args: name (String): the name of the input label (String): the label of the input subparameters (list): the list of ...
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def global_maxima(mylist): """ Returns the max index and global maxima of the list. """ maxima = -1 index = -1 for i in range(0, len(mylist), 1): distance = float(mylist[i]) if distance > maxima: maxima = distance index = i return index, maxima
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import hashlib def hash_barcode(barcode_data): """ Calculate an MD5 hash of barcode data """ hash = hashlib.md5(str(barcode_data).encode()) return str(hash.hexdigest())
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from typing import List from typing import Any from typing import Tuple import itertools def common_subsequences( dataset: List[Any], min_match_len = 3, max_match_len = 10) -> List[Tuple[int, List[Any]]]: """Catalog common sequential patterns (ie, occuring twice or more) that are of length mi...
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def read_query(name: str): """ Read in a query from a separate SQL file Retrieves a query from a separate SQL file and stores it as a string for later execution. Query files are stored in the utils/sql_queries directory Args: name: Name of the SQL file to retreive Returns: (str): ...
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def decimal_to_binary(n, i): """ Converts i to a binary list that contains n bits :param n: total number of bits (integer) :param i: number to convert (integer) :return: (list) """ return list(map(int, list(format(i, "0{0}b".format(n)))))
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def aic(log_likelihood, df): """Calculate AIC given log-likelihood and degrees of freedom.""" return -2 * log_likelihood + 2 * df
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def toggle_switch(context): """ Dependencies for toggle_switch gizmo. """ return ('tethys_gizmos/vendor/bootstrap_switch/dist/css/bootstrap3/bootstrap-switch.min.css', 'tethys_gizmos/vendor/bootstrap_switch/dist/js/bootstrap-switch.min.js')
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def string_to_number(value: str, strict: bool=False): """ Check if the value is a number and return it's true numberic rpresentation Parameters ---------- value (Any): value to convert Returns ------- Any: int, str, float """ if not isinstance(value, str): ...
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def get_bar_type_space(ax, plot_params): """ Gets the amount of space to place in between the ends of bars and labels """ # Estimate bar_type_space as a fraction of largest xlim x_width = 2 * abs(max(ax.get_xlim(), key=lambda x: abs(x))) bar_type_space = plot_params["bar_type_space_scaling"] * x...
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def moeda(n=0, moeda='R$'): """ Formata o valor com R$ e vírgula(,) :param n: valor monetário :param moeda: padrão R$ :return: valor formatado se solicitado pelo usuário """ return f'{moeda}{n:.2f}'. replace('.', ',')
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def isB(ner_tag: str): """ We store NER tags as strings, but they contain two pieces: a coarse tag type (BIO) and a label (PER), e.g. B-PER :param ner_tag: :return: """ return ner_tag.startswith("B")
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def make_choices(choices): """ Zips a list with itself for field choices. """ return list(zip(choices, choices))
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import pickle def read_usernames(username_path: str, current_username_set: set = set()) -> set: """reads usernames from a saved pickle. Also adds any locally added usernames if available. Args: username_path (str): path to the pickle file current_username_set DEFAULT -> set(): in case th...
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import copy def _format_options_dict(options): """ Format the options dictionnary to print 'False' or 'True' instead of '0' or '1'. :param options: options module dict. :return: Formatted options for Beautifultable printing :rtype: Dict. """ # Make a copy of the original options dict (To a...
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def add_qartod_ident(qartod_id, qartod_test_name): """ Adds attributes to the QARTOD functions corresponding to database fields. """ def dec(fn): fn.qartod_id = qartod_id fn.qartod_test_name = qartod_test_name return fn return dec
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def get_more_than_x(numbers, value): """ Get numbers more than x in a list """ ret = list() for i in numbers: if i >= value: ret.append(i) return ret
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def symbols_from_xyz(xyz_list): """ Takes a list of lists containing xyz file lines and the elemental symbols Parameters ---------- xyz_list: List of lists Outer list is whole xyz file, each inner list is a line of the file containing the symbol and x,y,z...
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def extract_text_before_first_compute_cell(text): """ OUTPUT: Everything in text up to the first {{{. """ i = text.find('{{{') if i == -1: return text return text[:i]
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def check_reaction(reaction_row, keep_list): """Checks a row parsed from a reaction file and checks it only contains acceptable things. Args: reaction_row (list): List parsed from a reaction file and formatted to be able to called Reaction(reaction_row) keep_list (list): list of elements that a...
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def inverse_of_relation(r): """ Function to determine the inverse of a relation :param r: a relation :return: inverse of the relation """ return [(y, x) for (x, y) in r]
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def start_end_edges_subpath_list(subpath_list): """ First/last node pairs (edges) from list of node pairs :param subpath_list: list of node pairs :return: first and last node pairs """ return subpath_list[0], subpath_list[-1]
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def is_macro(var): """returns true if given var is macro""" return var.startswith("@@{") and var.endswith("}@@")
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def value_set(d): """A set of all the values of a dict.""" return set(d.itervalues())
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from pathlib import Path from typing import Optional def get_current_version(datadir: Path) -> Optional[str]: """Retrieves current version from the app data directory, if it exists Args: datadir (Path): Path of the data directory Returns: Optional[str]: The current version, otherwise Non...
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import itertools def get_list_count(*args): """Calculates the number of elements in the list of lists passed""" return len(list(itertools.chain(*args)))
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