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import yaml def read_yaml(yaml_file): """ Read a YAML file Parameters ---------- yaml_file : str or PathLike Path to the YAML file. Returns ------- content : dict Dictionary with the content of the YAML file. """ with open(yaml_file, "r") as f: content...
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def sanitize(text): """Escapes characters that have a special meaning in latex.""" text = text.replace('\\', '\\textbackslash{}') for c in '$%^{}#_&': text = text.replace(c, '\\' + c) # Allow some more line breaks to happen. text = text.replace('/', '\\slash{}') text = text.replace('='...
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from typing import Counter def ngram_counter(list_of_token, n=2): """ Function for converting a list of ordered tokens into n-grams. | Argument | | list_of_token: a list of ordered tokens to be processed. | | Parameter | | n: number of continuous tokens to group | | Output | | dictionary of count of ngrams...
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def Dmap(tree): """ Butcher's function D(t). Represents differentiation. Defined by D(t)=0 except for D('T')=1. """ return 1*(tree=='T')
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def findElementRecursively(obj, elem_name): """Recursively find hierarchy of element in nested object""" if not hasattr(obj, "__dict__"): # object has no named fields return None elif elem_name in obj.__dict__.keys(): # required hierarchy was reached return obj else: # hierarchy is ye...
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def ratio(num, den): """ Returns the ratio of integers `num` and `den`. """ try: return float(num) / float(den) except ZeroDivisionError: return 0.0
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import yaml def save_yaml(val): """ Save data to yaml string :param val: Value or struct to save :type val: None | int | float | str | unicode | list | dict :return: The yamlified string :rtype: str | unicode """ return yaml.dump(val)
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import math def getHeading(lat_diff, long_diff): """Return directional heading (0=North) given lat and long diffs Args: lat_diff: (float) difference in latitude long_diff: (float) difference in longitude Returns: The heading value """ angleEast = int(math.atan2(lat_diff, ...
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def linear_search(numbers: list, item: int) -> int: """ Algorithm that implement linear search Parameters ---------- numbers : list The numbers list item : int The element to search Returns ------- index int The index of element. Return -1 if element not ...
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def get_all(qradarAppliance, check_mode=False, force=False): """ Retrieves a list of all server hosts in the deployment """ return qradarAppliance.invoke_get("Get server hosts", "/system/servers")
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def _compute_ngrams_py(word, min_n, max_n): """Get the list of all possible ngrams for a given word. Parameters ---------- word : str The word whose ngrams need to be computed. min_n : int Minimum character length of the ngrams. max_n : int Maximum character length of the...
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import textwrap import pprint def pprint_msg(dic, prefix=' '): """ Give logger.info a string for neatly printing a dictionary. Usage: logger.info(pprint_msg(arbitrary_object)) """ return "\n" + textwrap.indent(pprint.pformat(dic), prefix=prefix)
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def to_pair(seq): """ Convert a FastaEntry object to a simple header/sequence pair """ return (seq.header, seq.seq)
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def complete_sentence(learn, start_phrase, n_words=30, n_samples=3, temp=.75): """Generate text from a given input. This is a decent way to get a glimpse of how a language model is doing. Parameters ---------- learn: fastai Learner start_phrase: str The prompt (start of a sentence) that...
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import torch def _get_relation_types(dataset,): """ Classify relations into 1-N, M-1, 1-1, M-N Bordes, Antoine, et al. "Translating embeddings for modeling multi-relational data." Advances in neural information processing systems. 2013. :return: dictionary mapping from int -> {1-N, M-1, 1-1,...
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def getdistribfunc(distrib, funcname): """ Returns the distrib.funcname function for recognized funcnames """ if ( funcname == "cdf" ): return distrib.cdf elif ( funcname == "isf" ): return distrib.isf elif ( funcname == "pdf" ): return distrib.pdf elif ( funcname == ...
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def replace_simple_tags(string, from_tag="italic", to_tag="i", to_open_tag=None): """ Replace tags such as <italic> to <i> This does not validate markup """ if to_open_tag: string = string.replace("<" + from_tag + ">", to_open_tag) elif to_tag: string = string.replace("<" + from_...
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from typing import Dict from typing import Any from pathlib import Path def get_history_dir(config: Dict[str, Any]) -> Path: """ Return the directory where all the runs are stored. :param config: config file :return: path to folder """ folder = config["history_data_dir"] return folder
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def get_table_schema(conn, table): """Get column name and type of given table Args: conn: a database connection, this function will leave it open table: table name or db.table Returns: Tuple of (field_name, field_type) tuples """ return conn.get_table_schema(table)
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def _extract_region(host): """Extract region from Amazon S3 host.""" tokens = host.split(".") token = tokens[1] # If token is "dualstack", then region might be in next token. if token == "dualstack": token = tokens[2] # If token is equal to "amazonaws", region is not passed in the hos...
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def filter_none(lst): """Removes None elements from the list.""" lst = [el for el in lst if el is not None] return lst
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import operator def _sortPullRequests(pull_requests): """ Helper function from _formatPullRequests(). Sort a list of pull requests by pull request number and then by comment creation date. GIVEN: pull_requests (list) -- nested list of pull_requests and their comments RETURN: new_pull...
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def pad(base, fill, count, right = False): """Pad base string with given fill until count, on either left or right.""" while len(base) < count: if right: base += fill else: base = fill + base return base
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def _named_idx(idx): """ Converts 0 to x, 1 to y, 2 to z, or raises an exception. """ if idx < 0 or idx > 2: raise ValueError('idx must be between 0 and 2, got %d' % idx) return ('x', 'y', 'z')[idx]
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def create_gcp_connector(api, configuration, api_version, api_exception, name, service_account): """ Creates a GCP connector. :param api The Deep Security API exports. :param configuration The configuration object to pass to the API client. :param api_version The API version to use....
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def addChildNode(node, name, obj=None): """ Use this to build paths to your plugin's endpoints. :param node: The parent node to add the child node to. :param name: The name of the child node in the URL path. :type name: str :param obj: The object to place at this new node, or None if this child...
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def create_blob_client(blob_service_client, container_name, blob_file): """ Create a blob-specific client :param blob_service_client: type: azure.storage.blob.BlobServiceClient :param container_name: type str: Name of the container of interest :param blob_file: type iterable from azure.storage.blob....
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def _pattern_common(**params): """ Do common preprocessing steps for pattern_match and pattern_count. Not really useful on its own. Args: data (list): values. params (kwargs): pattern (str or list): the pattern to be sought in data (obligatory) metric (str): 'id...
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def __is_utf8(rule_string): """ Takes the string of the rule and parses it to check if there are only utf-8 characters present. :param rule_string: the string representation of the yara rule :return: true if there are only utf-8 characters in the string """ try: rule_string.encode('utf-8...
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def deepcopy_nested_dict(nested_dict_to_deepcopy: dict): """ Deepcopy of a nested dictionary of two levels, e.g. {k1:{...}, k2:{...}, ..., kN:{...}} :param nested_dict_to_deepcopy: The nested dictionary to return a deepcopy of :return: A deepcopy of a nested dictionary """ # Copy the upper level...
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def CalcMetricMatrix(inData, metricFunc): """ generates a metric matrix **Arguments** - inData is assumed to be a list of clusters (or anything with a GetPosition() method) - metricFunc is the function to be used to generate the matrix **Returns** the metric matrix as a Numeric arr...
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import re def is_email_valid(email): """ Checks if a certain email address follows the given conventional pattern of username@domain.extension :param email: given email address :return: True if the given email address is valid, False otherwise :rtype: bool """ return ( True ...
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def hmean(iterable): """ Returns the harmonic mean of the given list of values. """ a = iterable if isinstance(iterable, list) else list(iterable) return float(len(a)) / sum(1.0 / x for x in a)
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def get_long_description(path): """Return contents of file.""" with open(path) as fh: return fh.read()
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import collections def get_rare_char_info(char_to_lang_map, shared_lang_threshold): """Returns a tuple of: - a set of 'rare_chars' (those used threshold langs or fewer), - a mapping from each locale with rare chars to a set of its rare chars""" rare_chars = set() locs_with_rare_chars = collections.de...
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def welcome_prompt(name): """Prompts the user with the game opening banner. If the player chooses to begin, the method returns True. Any other input will return False. Parameters: name -- the variable for storing the player's name in""" print("Welcome, Traveler.") name = input("What do ...
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def binary_to_decimal(number): """ Converts a binary-number to decimal-number """ return int(number, 2)
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def comment(commentstr=''): """Insert comment.""" return '<!-- ' + commentstr.replace('--','') + ' -->'
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import torch def _add_rician_noise(dat, noise_prct=0.1): """Adds rician noise to a tensor as: dat = dat + n_real + i*n_img, where n_real, n_img ~ N(0, std**2) dat = magnitude(dat) Parameters ---------- dat : tensor Input data noise_prct : float, default=0.1 Amount of noise...
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import copy def _enforce_hierarchy(dupe_dict, values, hierarchy): """ Enforce a general hierarchy of which structures to keep, based on the list of values and their importance. Parameters: dupe_dict (dict): the dictionary keyed by the index of unique structures that holds lists of dup...
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import string def to_constant(s: str) -> str: """Returns a new str in CONSTANT_CASE, given any str. Examples: >>> to_constant('to_constant') 'TO_CONSTANT' >>> to_constant('Meals, Entrees, and Side Dishes') 'MEALS_ENTREES_AND_SIDE_DISHES' >>> to_constant('American India...
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def list_strings(string1='', string2='', string3='', string4=''): """ Put strings in a list. Parameters ---------- string1 : string string2 : string string3 : string string4 : string Returns ------- string_list : list of strings Examples -------- >>> from mindb...
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def column_parser(text_column): """ Returns a parser which parses a row of a csv file containing labeled data, extracting the label and the text This parser assumes the label is the zeroth element of the row, and the text is the 'text_column' element """ def f(row): return int(row[0]), row[text_co...
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def in_commands(substr, commands): """ Test that a string is in the command list """ return any(substr in cmd[1] for cmd in commands)
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def compare(name, first, second, bfr): """ Ensure correct open is paired with correct close """ o = bfr[first.begin:first.end] c = bfr[second.begin:second.end] match = False if o == "if" and c == "fi": match = True elif o in ["select", "for", "while", "until"] and c == "done": ...
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def make_mongo_url(user, pwd, url, db): """ makes the mongo url string :param user: user :param pwd: password :param url: url :param db: db :return: mongo url string """ return "mongodb://" + user + ":" + pwd + "@" + url + "/" + db
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def get_commit_statuses(api, urn, ref): """ Returns combined commit statuses It uses aggregated status endpoint: https://developer.github.com/v3/repos/statuses/#get-the-combined-status-for-a-specific-ref ref can be an sha, tag or a branch name (e.g. "master") """ path = "/repos/{urn}/commits...
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def get_resolwe(*resources): """Return resolwe object used in given resources. Raise an error if there is more than one. """ resolwes = {res_obj.resolwe for res_obj in resources} if len(resolwes) != 1: raise TypeError('All input objects must be from the same `Resolwe` connection.') ret...
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def rgb24_to_rgb16(red, green, blue): """ Convert 24-bit RGB color components to a 16-bit RGB color. :param red: The RED component in the RGB color. :type red: int :param green: The GREEN component in the RGB color. :type green: int :param blue: The BLUE component in the RGB color. :typ...
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async def resolve_delete_user(_root, info, id): """Resolver function for deleting a user object""" user = await info.context["registry"].get(id) await info.context["registry"].delete(user.id) return True
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import string def _consume_whitespace(line, start=0): """return index of next non whitespace character returns length of string if it can't find anything """ for i, c in enumerate(line[start:]): if c not in string.whitespace: return i+start return len(line)
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import pickle def load_worker(worker_file): """Load worker from file.""" with open(worker_file, 'rb') as f: worker = pickle.load(f) return worker
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def is_even(num): """ Check for number is even. """ return num % 2 == 0
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def get_strictness_label(strictness): """Get the alert box/label coloring based on strictness.""" levels = dict( low='info', medium='warning', high='danger', veryhigh='danger', ) if strictness not in levels: return 'default' return levels[strictness]
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def reset_params_skorch(regressor): """ Simple helper function that manually resets the parameters in each layer of a skorch regressor model. Parameters ---------- regressor : skorch.NeuralNetRegressor The neural net regressor (wrapped PyTorch model) that parameters must be res...
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def Ttr(x): """Equation for the triple point of ammonia-water mixture Parameters ---------- x : float Mole fraction of ammonia in mixture [mol/mol] Returns ------- Ttr : float Triple point temperature [K] Raises ------ NotImplementedError : If input isn't in li...
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def concatenate_list_data(char_list): """ DESCRIPTION: List concatenation of characters to produce words. INPUT: Translated character list OUTPUT: A single element that represents a word """ result = '' for element in char_list: result += str(element) return result
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def options( request ): """Return the command-line options.""" return request.config.option
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from typing import Generator import re def split_lines(string: str) -> Generator[str, None, None]: """ Splits string into lines, skipping empty; surrounding spaces are removed. """ return ( x.group(0).strip() for x in re.finditer(r".*(?:$|\n)", string) if len(x.group(0).strip()...
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def flatten_list(lst): """ Flattens a list of lists :param lst: list """ flatten = [] for item in lst: if isinstance(item, list): flatten.extend(item) else: flatten.append(item) return flatten
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def file_to_class_name(f_name: str) -> str: """ Take the file name of a scan and return the name of it as a class: snake to camel case """ return "".join(word.title() for word in f_name.split('_'))
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def get_coords(object_, points): """Return coordinates for an object which is somewhere in a list of points.""" return next(coords for coords, maybe_this_object in points if maybe_this_object == object_)
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def inter_over_union(interval_1, interval_2): """Intersection over union for two intervals.""" a, b = interval_1 c, d = interval_2 intersection = max(0, min(b, d) - max(a, c)) if intersection > 0: union = max(b, d) - min(a, c) else: union = (b - a) + (d - c) return intersecti...
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import colorsys def rgb_to_hs(rgbstr): """ Convert RGB color to (hue, saturation) """ r, g, b = bytes.fromhex(rgbstr[1:]) h, s, v = colorsys.rgb_to_hsv(r, g, b) s2 = 0.5+(255-v)/512 return {'hue':h, 'saturation':s2}
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def requires(filename): """Returns a list of all pip requirements :param filename: the Pip requirement file (usually 'requirements.txt') :return: list of modules :rtype: list """ modules = [] with open(filename, 'r') as pipreq: for line in pipreq: line = line.strip() ...
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def get_wdl_boolean_string(boolean): """ WDL expects `true` or `false` strings for `read_boolean`, Python `str` doesn't work """ return str(boolean).lower()
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def Lipinski(calc, exp, low, high): """ Input: listLike calculated and experimental data you want to compare float low and high limits for the test returns: number of correctly predicted values (in or outside range) number of false positives number of false negatives """ correct = 0 ...
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def S(Lt, l): """ Calculates the S coefficient Parameters ---------- Lt : float The length way of liquid, [m] l : float The length way of liquid of one slot mix, [m] Returns ------- Lt : float The S coefficient, [dismensionless] References ---------- ...
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def _flatten_serializer_errors_to_list(serializer_errors): """ Flatten DRF Serializer validation errors to a list with one field per item. """ field_errors = [] for field_name, details in serializer_errors.items(): details_string = ','.join([str(detail) for detail in details]) field_...
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def test_tosolr_index_update_errors(basic_exporter_class, record_sets, new_exporter, setattr_model_instance, assert_records_are_indexed, assert_records_are_not_indexed): """ When updating indexes via a To...
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def _build_summary(top_sentences, all_sents, max_len, sents_to_add=None): """ Auxillary function for summary building. Attempts to fit as many sentences into a summary as possible. Specifically, tries to add each sentence to the summary, starting from the best one and making ...
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def get_machine_from_parent(self): """Search in the parent to find the machine Parameters ---------- self : OP An OP object Returns ------- machine : Machine Machine from the parent (or None) """ parent = self.parent while parent is not None and not hasattr(par...
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def type_check(what, of_type, msg=None, allow_none=False): """Verify that object 'what' is of type 'of_type' and if not the case, raise a TypeError. :param what: the object to check :param of_type: the type (or tuple of types) to compare to :param msg: if specified, allows to customize the message that...
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def enable_explore_tab(bio_network, enrichment=None): """Disables Explore tab if there is no network to explore.""" return False if bio_network and enrichment else True
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def finddefault(f): """return the default value given a format""" if f.count('A'): default="UNKNOWN" elif f.count('I'): default=-999 else: default=-999.99 return default
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def produce_can_h(can_entry): """generate code for a can info entry (row of csv file)""" field_name = can_entry["Field Name"].lower() can_id = can_entry["CAN ID"] py_str = "\n" py_str += f"// {can_entry['Field Name']}\n" py_str += f"// Type: {can_entry['Format']}\n" py_str += f"// Sender: {c...
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import typing import multiprocessing def enumerate_cpu_counts() -> typing.List[int]: """This program prints the number of CPU counts to benchmark on this machine. We remove some percentage of CPU cores off the top for system / background processing. With the CPUs that remain, we generate a list of evenly...
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def is_visible(lat, lon, domain_boundaries, cross_dateline) -> bool: """Check if a point (city) is inside the domain. Args: lat float latitude of city lon float longitude of city domain_boundaries list lon/lat range of domain cro...
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def merge_dicts(idict): """ Merge an iterator over dictionaries into a single dict """ return {k:v for d in idict for k,v in d.items()}
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def merge_dicts(dict1: dict, dict2: dict) -> dict: """ Merges two dictionaries into one dictionary. :type dict1: ``dict`` :param dict1: The first dictionary. :type dict2: ``dict`` :param dict2: The second dictionary. :return: The merged dictionary. :rtype: ``dict`...
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def all_keys_in_dict(in_dict, keys): """ Check that all keys are present in a dictionary. Args: in_dict (dict): Input dict. keys (list): Keys that must be present in ``in_dict``. Returns: True if all ``keys`` are in ``in_dict``, False otherwise. >>> all...
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import itertools import six def iterate_allocations(path, alloc): """Generate (path, alloc) tuples for the leaves of the allocation tree.""" if not alloc.sub_allocations: return iter([('/'.join(path), alloc)]) else: def _chain(acc, item): """Chains allocation iterators.""" ...
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def _make_singular_filter(filter_name: str, filter_val): """Create a elasticsearch filter for a single filter_name, filter_val pair. Note filter_val can be a list and an OR will be applied Args: filter_name (str): Name of filter filter_val (str | str[]): Value of filter Retur...
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def map_transcript_id2gene_symbol(maf_df): """Create and return a mapping from transcript_id to gene_symbol. Assume that each transcript_id uniquely maps to a gene_symbol.""" transcript_id2gene_symbol = dict() for index, row in maf_df.iterrows(): gene_symbol = row['Gene_Symbol'] # e.g. 'AFF2...
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def real_project_name(project_name): """ Used to let Mezzanine run from its project template directory, in which case "{{ project_name }}" won't have been replaced by a real project name. """ if project_name == "{{ project_name }}": return "project_name" return project_name
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import re def clean_value(value): """ Clean the value of any newline expressions and then convert it to a float :param value: A string representation of a value from the body of the table :type value: str :return: A float representation of a value from the body of the table :rtype: float ...
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import math def ipart(x): """Return integer part of given number.""" return math.modf(x)[1]
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from typing import OrderedDict def prep_json_entry(entry): """Properly format and return a json object """ json_obj = OrderedDict() json_obj["vocabulary"] = entry["vocabulary"] json_obj["variant_of"] = entry["variant_of"] json_obj["pronunciation"] = entry["pronunciation"] json_obj["meanin...
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def calculate_input_vector_length(user_count, computer_count, auth_type_count, logon_type_count): """ Return model input vector length with user, computer, auth_type, logon_type one-hot encoded. """ return 3 + 2 * user_count + 2 * computer_count + auth_type_count + logon_type_count
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def get_mean_intensities(conn, image, the_c, shape_id): """ Get the mean pixel intensities of an roi in a time series image :param conn: The BlitzGateway :param image: The image :param the_c: The channel index :param shape_id: The ROI shape id :return: List of mean intensity values (one for ...
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import requests def get_metadata_value(key): """ Fetch the key from the metadata server """ url = 'http://metadata/computeMetadata/v1/instance/' + key headers = {'content-type': 'application/json', 'Metadata-Flavor': 'Google'} r = requests.get(url, headers=headers) return r.text
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def add_to_list(existing_list, inp_list): """ Add input list to an existing list. The existing "list" and input "list" are checked to see if they are list instances, and if not configured to be a lists. The existing list is extended with the input list. :param existing_list: Existing list, which n...
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import math def partie_entiere(x): # Utilité ? Concept de la partie entière difficile au lycée pour les nombres négatifs. Faire une fonction pour prendre la partie sans la virgule ? """ Renvoie la partie entiere du nombre ``x``, c'est a dire le plus grand entier inferieur au reel ``x``. Arguments: ...
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def PadLeft(s, Len, Padding = '0'): """Pads s on the left with Padding to length Len. s: a string. Len: an integer. Padding: a string.""" while len(s) < Len: s = Padding + s return s
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def convertArrayInTupleList(array): """ Convert an array (or a list) of element in a list of tuple where each element is a tuple with two sequential element of the original array/list Parameters ---------- array : numpy array/list Returns ------- tuple_list. List of tuple Given...
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def get_color_from_color_code(color_code): """Converts a color code to a color name. Args: color_code (list): color code Returns: str: color name """ if color_code[0]: return 'red' elif color_code[1]: return 'green' elif color_code[2]: return 'blue' ...
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def all_a_in_b(a, b): """Return true if all elements *s* of <a> also exist in <b>.""" return all(s in b for s in a)
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from typing import Iterable from typing import Deque import collections def rotate_copy(iterable: Iterable, n: int) -> Deque: """Return a deque of iterable with it's content rotated n places to the right. iterable: An iterable to rotate n: The number of places to rotate the iterable (negative values rota...
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def _beam_fit_fn_2(z, d0, Theta): """Fitting function for d0 and Theta.""" return d0**2 + (Theta*z)**2
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import difflib def get_name_similarity(string1, string2): """ Return a score between 0 and 100 of the strings' similarity, based on difflib's string similarity algorithm returning an integer between 0 (no match) and 100 (perfect). 70 or more seems to be a confident enough match """ # Based on http...
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