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def sumevenfib(N): """ N is a positive number This function will add up all even fibonacci numbers that do not exceed N We use the convention that F_0 = 0, F_1 = 1,...,F_3 = 2 Note that F_3k is the subsequence of even Fibonacci numbers """ F1 = 1 F0 = 0 S = 0 while F0 <= N: S += F0 F3 = 2*F1 + F0 F1 =...
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import collections def _append_cell_contents(notebook): """Appends prior cell contents to a later cell dependent on labels This function will iterate through a notebook and grab all cells that have a label and add them to any cell that references that label (i.e., has the label in its ref_labels list). Each ...
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def change_op(instructions, i, new_op): """ Return a copy of the `instructions` where the operation at index `i` is changed to `new_op` """ # Store the value of the argument at index `i` in the instructions _, arg = instructions[i] # Make a copy of the instructions list modified = instructio...
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def _intersection(A,B): """ A simple function to find an intersection between two arrays. @type A: List @param A: First List @type B: List @param B: Second List @rtype: List @return: List of Intersections """ intersection = [] for i in A: if i in B: ...
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def compound_score(text, sia): """ This function computes VADER's compound score of some text Arguments: text : (string) sia: nltk.SentimentIntensityAnalyzer() object Returns: float between -1 and 1 """ return sia.polarity_scores(text)['compound']
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def recursively_split_version_string(input_version: str, output_version: list = []): """ Splits a version/tag string into a list with integers and strings i.e. "8.0.0.RC10" --> [8, '.', 0, '.', 0, '.RC', 10] Input: input_version (str): a version or tag i.e. "8.0.0.RC10" output_versio...
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import types import importlib def import_pickle() -> types.ModuleType: """ Returns cPickle module if available, returns imported pickle module otherwise """ try: pickle = importlib.import_module('cPickle') except ImportError: pickle = importlib.import_module('pickle') return pickle
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def clean_euler_path(eulerian_path: list) -> list: """Cleans a Eulerian path so that each edge (not directed) appears only once in the list. If a edge appears more than once, only the first occurrence is kept. Arguments: eulerian_path {list} -- Eulerian path Returns: list -- cleaned Euleri...
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def frame_idx(fname): """Get frame index from filename: `name0001.asc` returns 1""" return int(fname[-8:-4])
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import pickle def load_calib(filename): """ Loads calibration parameters from '.pkl' file. Parameters ---------- filename : str Path to load file, must be '.pkl' extension Returns ------- calib_params : dict Parameters for undistorting images. """ # read python dict back from the file pk...
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import re def get_molecular_barcode(record, molecular_barcode_pattern): """Return the molecular barcode in the record name. Parameters ---------- record : screed record screed record containing the molecular barcode molecular_barcode_pattern: regex pattern ...
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def int_to_bytes(x): """Changes an unsigned integer into bytes.""" return x.to_bytes((x.bit_length() + 7) // 8, 'big')
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import uuid def get_uuid(data): """Compute a UUID for data. :param data: byte array """ return str(uuid.uuid3(uuid.NAMESPACE_URL, data))
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def ssqrange(charge, sz, nsingle): """ Make a list giving all possible :math:`S^{2}` values for given charge and :math:`S_{z}`. Parameters ---------- charge : int Value of the charge. sz : int Value of sz. nsingle : int Number of single particle states. Returns ...
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def split(iterable, **split_options): """Perform a split on iterable. This method is highly inspired in the `iter` global method (in conjunction with its __iter__ counterpart method) for iterable classes. :param iterable: An iterable, which will typically be a Storage<Collection> :param split_opti...
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def scale_vector(vector, scale): """Scale a 3D vector's components by scale.""" return vector[0] * scale, vector[1] * scale, vector[2] * scale
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def lr_lambda(epoch, base=0.99, exponent=0.05): """Multiplier used for learning rate scheduling. Parameters ---------- epoch: int base: float exponent: float Returns ------- multiplier: float """ return base ** (exponent * epoch)
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import string def isValidMapKey(key): """Returns ``True`` if the given string is a valid key for use as a colour map or lookup table identifier, ``False`` otherwise. A valid key comprises lower case letters, numbers, underscores and hyphens. """ valid = string.ascii_lowercase + string.digits + '_...
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def factory_class_name(model_class_name): """Return factory class name from model class""" return model_class_name + 'Factory'
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import pathlib import json import re def check_markers(test_mode=False): """Validate markers in PinNames.h files""" mbed_os_root = pathlib.Path(__file__).absolute().parents[3] errors = [] with ( mbed_os_root.joinpath("targets", "targets.json") ).open() as targets_json_file: targe...
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def _group_counts_to_group_sizes(params, group_counts): """Convert numbers of groups to sizes of groups.""" _, out_channels, _ = params group_sizes = [out_channels // count for count in group_counts] return group_sizes
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def __read_sequence_ids(data): """ Reads SequenceIDs.txt (file included in OrthoFinder Output) and parses it to a dict :param data: list of lines in SequenceIDs.txt :return: dict with key: OrthoFinder ID en value: the proper name """ output = {} for l in data: if l.strip() != '': ...
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def snap_value(input, snap_value): """ Returns snap value given an input and a base snap value :param input: float :param snap_value: float :return: float """ return round((float(input) / snap_value)) * snap_value
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from pathlib import Path def fixture(name: str): """ Construct an absolute path to the fixture directory """ return str(Path(Path(__file__).parent.absolute(), 'fixtures', name))
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from datetime import datetime def parseDate(timestamp): """Parses an EXIF date.""" return datetime.strptime(timestamp, '%Y:%m:%d %H:%M:%S')
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import torch def one_hot_vector(length, index, device=torch.device('cpu')): """ Create a one-hot-vector of a specific length with a 1 in the given index. Args: length: Total length of the vector. index: Index of the 1 in the vector. device: Torch device (GPU or CPU) to load the ve...
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def get_minutes(seconds): """Convert seconds to minutes.""" return seconds // 60
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import math def sumlog(v1, v2): """Returns the sum of two logspaced values in logspace.""" if v1 < v2: v1, v2 = v2, v1 return math.log(1 + math.exp(v2 - v1)) + v1
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import requests def _get_bin_count(fpath, delimiter=',', encoding='ISO-8859-1'): """ Gets the number of bins in the file. :param fpath: A path or url for the file (if a url it must include `http`, and if a file path it must not contain `http`). :type fpath: string :param del...
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def is_auxiliary_relation(token1, token2): """Return True if `token1` is an auxiliary dependent of `token2`.""" return ( (token1.upos == "AUX") and (token1.deprel in ["aux", "aux:pass"]) and (token2.upos == "VERB") and (token1.head == token2.id) )
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from datetime import datetime def convert_string_date_to_datetime(now_str: str) -> datetime: """ Converts string of the format yyyy-dd-yy-hh-mm-ss to datetime format. :param now_str: str. String of the format yyyy-dd-yy-hh-mm-ss. """ numbers = [int(string_number) for string_number in now_str.split...
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def toCategorical(df): """ This function change object datatype in pandas.DataFrame into category datatype. Parameters ---------- df : pandas.DataFrame with train or test DataFrame. Returns ------- df : pandas.DataFrame with new datatypes. """ columns=['availability','g...
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def seperate_list(all_list, pred): """Given a predicate, seperate a list into a true and false list. Arguments: all_list {list} -- all items pred {function} -- predicate function """ true_list = [] false_list = [] for item in all_list: if pred(item): true_l...
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def count_parameters(model): """ Compute the number of trainable parameters of the model. :param model: type nn.Module :return: number of parameters, type int """ return sum(p.numel() for p in model.parameters() if p.requires_grad)
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from typing import Any from typing import Dict from typing import OrderedDict def convert_dict_to_ordered_dict(qconfig_dict: Any) -> Dict[str, Dict[Any, Any]]: """ Convert dict in qconfig_dict to ordered dict """ # convert a qconfig list for a type to OrderedDict def _convert_to_ordered_dict(key, qcon...
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def checkEmblFile(filin): """Check EMBL annotation file given by user""" line = filin.readline() # TEST 'ID' if line[0:2] != 'ID': return 1 else: return 0
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import math def calc_distance(asteroid1, asteroid2): """Calculates the distance between two asteroids""" x1, y1 = asteroid1 x2, y2 = asteroid2 dx = x2 - x1 dy = y2 - y1 return math.sqrt(dx * dx + dy * dy)
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def gzipOA(directory=None, cmdverbose : int =0, add_check : bool = True, unzip_text : bool = False): """ Create script to compress all oa files in a directory with gzip """ if directory is not None: cmd = 'cd %s\n' % directory else: cmd = '' if cmdverbose>=2: cmd += 'echo ...
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def get_record_count(hook, database, table): """ gets the row count for a specific table """ query = '''SELECT t.row_count as record_count FROM "{}".information_schema.tables t WHERE t.table_name = '{}';'''.format(database, table) return hook.get_records(query).pop()[0]
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import fnmatch def fpath_has_ext(fname, exts, case_sensitive=False): """returns true if the filename has any of the given extensions""" fname_ = fname.lower() if not case_sensitive else fname if case_sensitive: ext_pats = ['*' + ext for ext in exts] else: ext_pats = ['*' + ext.lower() ...
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def area_triangle(base: float, height: float) -> float: """ Calculate the area of a triangle given the base and height. >>> area_triangle(10, 10) 50.0 >>> area_triangle(-1, -2) Traceback (most recent call last): ... ValueError: area_triangle() only accepts non-negative values >>...
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import math def get_3d_pos_from_x_orientation(x_orientation, norm=1): """ Get a 3d position x, y, z for a specific x orientation in degrees Args: - (float) orientation around x axis - (float) norm to rescale output vector Return: - (float) x position [0; 1] * norm - (f...
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import math def invertedCantorParingFunction(z): """ @see http://en.wikipedia.org/wiki/Pairing_function >>> invertedCantorParingFunction(0) (0, 0) >>> invertedCantorParingFunction(1) (1, 0) >>> invertedCantorParingFunction(2) (0, 1) >>> invertedCantorParingFunction(3) (2, 0) ...
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def extract_data(source:str): """Read list of newline delineated ints from text file.""" with open(source, "r") as f: data = f.readlines() data = [int(el) for el in data if el != "/n"] return data
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def yes_no_dialog(prompt: str) -> bool: """Return true/false based on prompt string and Y/y or N/n response.""" while True: print() print(prompt) print() s = input("Y/n to confirm, N/n to reject >") if s in ("Y", "y"): return True if s in ("N", "n"):...
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def getHuffmanCoding( tree, prefix="", code = {} ): """ Projde rekurzivně předaný strom a ohodnotí jednotlivé znaky dle pravidel Huffmanova kódování. To znamená, že hrana jdoucí od svého rodiče nalevo, má ohodnocení 0 a hrana napravo ohodnocení 1. Ohodnocení samotného vrcholu je tvořen posloupn...
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from typing import Dict from typing import OrderedDict def _scores_to_ranks( *, scores: Dict, reverse: bool = False ) -> Dict[str, float]: """ Go from a score (a scalar) to a rank (integer). If two scalars are the same then they will have the same rank. Takes a dictionary where the keys are the p...
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def get_resource(requests, reference): """ Fetches a resource. ``reference`` must be a relative reference. e.g. "Patient/12345" """ response = requests.get(endpoint=reference, raise_for_status=True) return response.json()
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def printTime(t): """ Takes time in seconds, and print in the output in human friendly format (DD:hh:mm:ss) """ t = round(t) if t < 60: return ("%d seconds" %t), (0, 0, 0, t) else: m = int(t/60) s = t%60 if (m < 60) & (m > 1): return ("%d minutes, %d s...
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import re def sanitizeTitle(title): """Sanitizes the passed title string to allow the file to be saved on windows without introducing illegal characters""" matches = re.findall(r"[^/\\:*?\"<>|]+", title) fullstring = "" for match in matches: fullstring += match return fullstring
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def get_alias(dataset): """Get alias for dataset. Parameters ---------- dataset : dict Dataset metadata. Returns ------- str Alias. """ alias = f"{dataset['project']} dataset {dataset['dataset']}" additional_info = [] for key in ('mip', 'exp', 'ensemble'): ...
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import bz2 def compress(data): """ Helper function to compress data (using bz2) """ c = bz2.BZ2Compressor() a = c.compress(data) b = c.flush() return a+b
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import six def lowercase_value(value): """ Lowercase the provided value. In case of a list, all the string item values are lowercases and in case of a dictionary, all of the string keys and values are lowercased. """ if isinstance(value, six.string_types): result = value.lower() e...
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def are_checksums_equal(checksum_a_pyxb, checksum_b_pyxb): """Determine if checksums are equal. Args: checksum_a_pyxb, checksum_b_pyxb: PyXB Checksum objects to compare. Returns: bool - ``True``: The checksums contain the same hexadecimal values calculated with the same algorithm. Ide...
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def unify_str_list(strlist): """ Remove duplicates and sort list of strings :param strlist: list of strings :return: sorted unique list """ return sorted(set(strlist))
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def get_header(cursor): """ Given a cursor object, returns the appropriate header (column names) """ header = [] for i in cursor.description: s = i[0] if "." in s: s = s[s.find(".")+1:] header.append(s) return header
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def get_other_player(player): """ Get the other player. """ return "X" if player == "O" else "O"
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def sep_nondummies(data): """ Finds the features that are: 1. have nominal values 2. have more than 2 distinct values so it needs to be dummified Args: data: DataFrame containing the dataset Returns: nominal: Array-like structure that contains the nominal features ...
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def PortToTag(switch, port): """Returns the tag for a port.""" return 'switches.%s.%d' % (switch, port)
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def _compose_attribute_file(attributes): """Make the contents of an osg attributes file""" def islist(var): return isinstance(var, list) variable_string = "" export_string = "" # keep a list of array variables array_vars = {} keys = sorted(attributes.keys()) for key in keys: ...
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from typing import Optional from typing import Dict from typing import Any import json def input_dictionary_to_parameter(input_dict: Optional[Dict[str, Any]]) -> str: """Convert json input dict to encoded parameter string. This function is required due to the limitation on YAML component definition that YAML d...
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def valid_int(param, allow_zero=False, allow_negative=False): """Validate that param is an integer, raise an exception if not""" pt = param try: # a very permissive integer typecheck pt += 1 except TypeError: raise TypeError( "Expected integer but found argument of type '{}'...
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def version_to_string(version, parts=3): """ Convert an n-part version number encoded as a hexadecimal value to a string. version is the version number. Returns the string. """ part_list = [str((version >> 16) & 0xff)] if parts > 1: part_list.append(str((version >> 8) & 0xff)) i...
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from pathlib import Path from typing import Tuple def create_alignment_job_directory_structure(output_directory: Path) -> Tuple[Path, Path, Path]: """Create directory structure for a tilt-series alignment job.""" stacks_directory = output_directory / 'stacks' stacks_directory.mkdir(parents=True, exist_ok=...
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import struct import pickle def indexed_pickler_load_keys(path): """ Return the list of keys in the indexed pickle """ with open(path, "rb") as f: index_len = struct.unpack("Q", f.read(8))[0] return pickle.loads(f.read(index_len)).keys()
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import re def convert_to_filename(sample_name): """ Convert to a valid filename. Removes leading/trailing whitespace, converts internal spaces to underscores. Allows only alphanumeric, dashes, underscores, unicode. """ return re.sub(r"(?u)[^-\w]", "", sample_name.strip().replace(" ", "_"))
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import math def get_rgba_from_triplet(incolour: list, alpha=1, as_string=False): """ Convert the input colour triplet (list) to a Plotly rgba(r,g,b,a) string if `as_string` is True. If `False` it will return the list of 3 integer RGB values. E.g. [0.9677975592919913, 0.44127456009157356, 0.535...
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def build_factorized(factorized: dict) -> int: """ Build integer from its factorized form, (reverse function of factorization) :param factorized: factorized integer dict :return: integer """ num = 1 for factor in factorized: num *= factor ** factorized[factor] return int(num)
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import re def check_hgt(value): """ hgt (Height) - a number followed by either cm or in: - If cm, the number must be at least 150 and at most 193. - If in, the number must be at least 59 and at most 76. """ pattern = r"^([0-9]{2,3})(cm|in)$" match = re.match(pattern, value) if match: ...
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from typing import List def get_available_executors() -> List[str]: """ Get all the available executors that can be provided to `run_notebook` and `run_notebooks`. """ return [ 'simple_executor', 'pandas_miner', 'plotly_miner', 'mpl_seaborn_viz_miner', ]
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import re def convert_numerical(s): """ try to convert a string tu numerical :param str s: input string :return: >>> convert_numerical('-1') -1 >>> convert_numerical('-2.0') -2.0 >>> convert_numerical('.1') 0.1 >>> convert_numerical('-0.') -0.0 >>> convert_numerical('...
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def truncate_string(string, truncation, message = ''): """ Truncate a string to a given length. Optionally add a message at the end explaining the truncation :param string: A string :param truncation: An int :param message: A message, e.g. '...<truncated>' :return: A new string no longer th...
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def _(x): """Identity function for string extraction.""" return x
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def take(l,n): """ Return the first n elements from iterable l.""" itr = iter(l) results = [] for i in range(n): results.append(next(itr)) return results
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from typing import Union def cpf_format(cpf: Union[int, str, float]) -> str: """ Format CPF. Args: cpf (Union[int, str, float]): CPF Returns: str: Formated CPF "***.***.***-**" """ try: if type(cpf) == float: cpf = int(cpf) cpf_cleaned = int(''.joi...
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def contains(value, arg): """ Checks insensitive if a substring is found inside a string Args: value (str): The string arg (str): The substring Returns: bool: True if string contains substring, False otherwise """ value = value.upper() arg = arg.upper() if arg in va...
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import click def common_cv_options(f): """CV-specific CLI options.""" f = click.option('--folds', type=int, default=5, help='Number of folds in CV.')(f) f = click.option('--replicates', type=int, default=10, help='Number of replicates for CV.')(f) f = click.option('--threads', type=int, default=1, hel...
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from pathlib import Path from typing import Dict from typing import Any import json def load_json(path: Path) -> Dict[str, Any]: """Load a JSON file to create a dictionary.""" with path.open() as f: return json.load(f)
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def _show_consistency(field, message, is_consistent): """ If `is_consistent` is false, make `field` RED with tooltip caption `message` & return 1. Otherwise reset colour and tooltip caption of `field` to default values, and return 0. """ if is_consistent is True: field.setStyleSheet(...
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import math def ceil_log2(num): """ Return integer ceil value of log2(num) """ return int(math.ceil(math.log(int(num), 2) ) )
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def prior_transform(self, unit_coords, priors, prior_args=[]): """An example of one way to use the `Prior` objects below to go from unit cube to parameter space, for nested sampling. This takes and returns a list instead of an array, to accomodate possible vector parameters. Thus one will need somethi...
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def is_control_gate(op_type: str) -> bool: """Get whether a gate type includes a control (q)bit.""" return op_type in { "CX", "CY", "CZ", "CH", "CRx", "CRy", "CRz", "CU1", "CU3", "CV", "CVdg", "CSx", "CSXdg",...
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import requests def get_value(sensor_id): """Get value from Luftdaten-API""" url = f"https://api.luftdaten.info/v1/sensor/{sensor_id}/" r = requests.get(url, headers={"Host": "api.luftdaten.info"}) if not r.json(): return None value = r.json()[-1]["sensordatavalues"][0]["value"] retu...
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import math def EvalExponentialPdf(x, lam): """Computes the exponential PDF. x: value lam: parameter lambda in events per unit time returns: float probability density """ return lam * math.exp(-lam * x)
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def service_model(service): """Produce the model for a service""" return { 'name': service.name, 'admin': service.admin, 'url': service.url, 'prefix': service.server.base_url if service.server else '', 'command': service.command, 'pid': service.proc.pid if service...
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from pathlib import Path def scanfolder_glob(folder): """ scan folder for mp3 files :param folder: root folder of mp3 files :return: list of mp3 files """ found_files = Path(folder).glob('**/*.mp3') return found_files
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import re def _get_base_key(key): """Extracts the base key from the provided key. Earth Engine exports `TFRecords` containing each data variable with its corresponding variable name. In the case of time sequences, the name of the data variable is of the form `variable_1, variable_2, ..., variable_n`, where...
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import click from pathlib import Path def _cbk_opt_inventory(ctx: click.Context, param, value): """callback for inventory option to read into list of strings""" try: return Path(value).read_text().splitlines() except Exception as exc: ctx.fail(f"Unable to load inventory file '{value}': {st...
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def _get_leaf(node): """ Gets innermost definition of Typedef or Struct-/UnionMember. Other nodes pass through. """ while getattr(node, 'definition', None): node = node.definition return node
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import pkg_resources def pkg_req(text): """ :param str|None text: Text to parse :return pkg_resources.Requirement|None: Corresponding parsed requirement, if valid """ if text: try: return pkg_resources.Requirement(text) except Exception: return None
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def backends_mapping(custom_backend): """ Create 2 separate backends: - path to Backend 1: "/echo" - path to Backend 2: "/quotes" """ return {"/echo": custom_backend("echo"), "/quotes": custom_backend("quotes")}
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def crud_url_name(model, action, prefix=None): """ Returns url name for given model and action. """ if prefix is None: prefix = "" app_label = model._meta.app_label model_lower = model.__name__.lower() return '%s%s_%s_%s' % (prefix, app_label, model_lower, action)
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import logging def split_list(source_list, splitter_algo: str, splitter_args, randomizer): """ Removes a set of items from the source list and returns them in a new list based on the splitter algorithm and splitter_args; :param source_list: The source list to split. It is MODIFIED. :param splitte...
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def geoIsPointInPoly(loc, poly): """ Determine if a point is inside a polygon. Points that are along the perimeter of the polygon (including vertices) are considered to be "inside". Parameters ---------- loc: list The coordinate of the point, in [lat, lon] format poly: list of lists The polygon to check if ...
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def q2mat(q): """ Generate a left rotation matrix from a normalized quaternion Parameters q: The normalized quaternion (list) Returns u: The rotation matrix (2-dimensional list) """ u = [] for i in range(3): u.append([]) for j in range(3...
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def obj_to_dict(obj): """ Converts an :py:obj:`object` to a :py:obj:`dict` by taking the object's properties and variables and their values and putting them into a dict. Private and dunder (``__``) properties are ignored. The use case for this is to enable passing of an object's data across the...
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def selected_list(element): """ Given an element dict, return a list of the indexes. """ if 'selected' in element: return element['selected'] return [int(idx.strip()) for idx in element['value'].split(',')]
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def check_inputs(input1, input2): """ Checks the inputs given to ensure that input1 is a list of just numbers, input2 is a number, and input2 is within input1. Raises an exception if any of the conditions are not true. >>> check_inputs([1, 2.0, 3.0, 4], 4) 'Input validated' >>> check_i...
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import struct def format_oath_code(response: bytes, digits: int = 6) -> str: """Formats an OATH code from a hash response.""" offs = response[-1] & 0xF code = struct.unpack_from(">I", response[offs:])[0] & 0x7FFFFFFF return ("%%0%dd" % digits) % (code % 10 ** digits)
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def select_candidates(candidate_data, number): """ Select top candidates from candidate dataframe, based off of lowest bandgap. """ candidate_data = candidate_data.sort_values('bandgap_pred', ascending=True) top_candidates = candidate_data.head(number) return top_candidates
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