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def apply_split_linear(lin_module_1, lin_module_2, input1, input2, activation=None): """Returns a linear output of two inputs, run independently and summed.""" output_1 = lin_module_1(input1) output_2 = lin_module_2(input2...
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def calc_disfrac(input_df, threshold=0.5): """Take a merged IUPRed input (multiple proteins) and calculate the fraction of disordered residues according to a specific threshold for each case. A pd.GroupBy object is first generated and then the function applied. Arguments: input_df {string} ...
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import random def dummy_decision(board): """ make a random dummy move """ legal_moves = list(board.legal_moves) return random.choice(legal_moves)
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def add(a, b, c): """Take three inputs as integer and returns their sum.""" total = a+b+c return total
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def create_payment_msg(identifier, status): """Create a payment payload for the paymentToken.""" payment_msg = {'paymentToken': {'id': identifier, 'statusCode': status}} return payment_msg
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def get_coords(name, geo_coder): """ Returns the coordinates of the `name` location using the geo_coder. """ location = geo_coder(name + ', Canada') # Default to province if geocoding failed if location is None: print(f"WARNING: Failed to geocode {name}.") location = geo_coder(na...
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def reverse_and_complement(s): """Takes an RNA sequence and returns the reversed and complemented form. Presumably `s` is formed by transcribing a DNA sequence. If the same DNA sequence was transcribed in the opposite direction, you would get the RNA sequence that this function returns. """ rna...
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def traverse_get(target, *args): """ Travel down through a dict >>> traverse_get({"one": {"two": 3}}, ["one", "two"]) 3 """ current = target for level in args: current = current[level] return current
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import unicodedata def _is_punctuation(char): """ 判断字符是否为标点符号,这里包括其他除字母和数字以外的符号 :param char: char :return: bool """ cp = ord(char) if ((33 <= cp <= 47) or (58 <= cp <= 64) or (91 <= cp <= 96) or (123 <= cp <= 126)): return True cate = unicodedata.category(char) # ...
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from typing import List import random def genfrags(sequence: str, number: int, size: int) -> List[str]: """ Generate `number` fragments all of equal length: `size`, from `sequence`. Ensure that there is a fragment covering the very beginning and end of `sequence`. """ random.seed() start...
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import itertools def merge_event_pages(event_pages): """ Combines a iterable of event_pages to a single event_page. Parameters ---------- event_pages: Iterabile An iterable of event_pages Returns ------ event_page : dict """ pages = list(event_pages) if len(pages)...
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def sane_parser_name(name) -> bool: """ Checks whether given name is an acceptable parser name. Parser names must not be preceded or succeeded by a double underscore '__'! """ return name and name[:2] != '__' and name[-2:] != '__'
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def bare_name(msg_type): """ Get bare_name from <dir>/<bare_name>[x] format """ bare = msg_type if '/' in msg_type: # removing prefix bare = (msg_type.split('/'))[1] # removing suffix return bare.split('[')[0]
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def get_a_policy(base, policy_id): """Utility function that gets a Senlin policy.""" res = base.client.get_obj('policies', policy_id) return res['body']
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import socket def receive_all(conn: socket.socket, size: int) -> bytes: """Receive a given length of bytes from socket. Args: conn (socket.socket): Socket connection. size (int): Length of bytes to receive. Raises: RuntimeError: If connection closed before chunk was read, it will...
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def get_email_domain_part(address): """ Get the domain part from email ab@cd.com -> cd.com """ return address[address.find("@") + 1 :].strip().lower()
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import re def unsubscribe_user(cur, phone, confcode): """ Adds a user to the unsubscribe table Params: cur: (psycopg2.extensions.cursor) A Cursor to the database phone: (str) phone number in E.164 format confcode: (int) randome 128-bit code Returns: (str) a response m...
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def month_difference(a, b): """ Calculates difference in months between two datetime objects Args: a (pandas datetime object) latest datetime object b (pandas datetime object) earliest datetime object Returns: integer value of months between two dates """ return 12 * (a.year - ...
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def aio_rpc_request(method): """ A method decorator announcing the method to be exposed as a request handler. This decorator assumes that the first parameter (after ``self``) takes a BSONRpc/JSONRpc object reference as an argument, so that the method will have an access to make RPC callbacks on...
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def get_by_name(ast, name): """ Returns an object from the AST by giving its name. """ for token in ast.declarations: if token.name == name: return token return None
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def index_of_last_non_zero(x): """Index of last non-zero item.""" for i, a in reversed(list(enumerate(x))): if a != 0: return i return -1
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def get_enz_remnant(enz): """Get enzyme recognition site remnant sequence""" if enz.ovhg > 0: remnant = enz.site[enz.fst3:] return [remnant,remnant.replace('G','A')] else: remnant = enz.site[enz.fst5:] return [remnant,remnant.replace('C','T')]
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def Trace_finder(lines:list): """Finds traces index from data. And extract eact trace section from data Args: lines (list): A list of lines from '.ndf' file. Returns: trace_sections (list): A list of trace sections. """ trace_index = [] # segment_index = [] for line in line...
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def huffman_decoding(encoded_str, root): """Huffman decoding algorithm Args: sentence: encoded string root: root Node for Huffman Binary Tree Returns: decode_str: string decoded from the sequence """ decoded = [] node = root for e in encoded_str: if e ==...
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def flatten(lst): """ Returns a list containing the items found in sublists of lst. """ return [item for sublist in lst for item in sublist]
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def is_field_allowed(name, field_filter=None): """ Check is field name is eligible for being split. For example, '__str__' is not, but 'related__field' is. """ if field_filter in ["year", "month", "week", "day", "hour", "minute", "second"]: return False return isinstance(name, s...
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def doTest(n): """Runs a test. returns score.""" score = 0 l = list(range(1,16)) for i in l: if input("what is {} to the power of 3? ".format(i)) == str(i**3): score += 1 print("Correct.") else: print("Wrong, the correct answer is {}".format(i**3)...
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import socket import errno def connection_reset(e: Exception) -> bool: """ Return true if an error is a connection reset error. """ # For some reason we get 'error: [Errno 104] Connection reset by peer' where the # English description suggests that errno is 54 (ECONNRESET) while the actual # e...
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def count_simulation_problem_batches(n_simulation_problem_chunks, n_simulation_problems, n_simulation_problem_batches_per_chunk): """ Count batches to be generated. :param n_simulation_problem_chunks: number of chunks of simulation problems :param n_simulation_probl...
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import itertools def year_state_filter(years=(), states=()): """ Create filters to read given years and states from partitioned parquet dataset. This function was the only dependency on the pudl repo, so I copied it from pudl.outputs.epacems.py:year_state_filter A subset of an Apache Parquet dat...
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import uuid def generate_username(user, profile, client): """ Default function to generate usernames using the built in `uuid` library. """ return str(uuid.uuid4())[:30]
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from typing import Union def to_n_cpus(cpu_str: str) -> Union[int, float]: """Convert cpu string to number of cpus (e.g. '500m' -> 0.5, '2000000000n' -> 2) """ if cpu_str.endswith("n"): return int(cpu_str.strip("n")) / 1000000000 elif cpu_str.endswith("u"): return int(cpu_str.strip...
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def stationlist2filelist(slo): """ Input a stationlist object (slo). From this extract the station codes and create a list of file names that represent long period data files """ site_list = slo.getStationList() files = [] for sta in site_list: fname = "%s" % (sta.scode) file...
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def multQuatLists(q0, q1): """Multiply two quaternions that are represented as lists.""" x0, y0, z0, w0 = q0 x1, y1, z1, w1 = q1 return [ w0 * x1 + x0 * w1 + y0 * z1 - z0 * y1, w0 * y1 - x0 * z1 + y0 * w1 + z0 * x1, w0 * z1 + x0 * y1 - y0 * x1 + z0 * w1, w0 * w1 - x0 * x...
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import re def simple_preprocess(text_list:list) -> list: """Performs simple preprocessing on the list of texts Args: text_list (list): list of texts Returns: list: list of preprocessed texts in tokens format """ text_list = [x.lower() for x in text_list] text_list = [re.sub(r...
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def SfromL( L, nmax=25, epsilon= 2**(-50) ): """ Compute sequence of generalized inverses from given Schroder value L. Args: L (real): main arg, range 0.0 to 1.0 nmax (integer): default 22. Max length to allow for S. epsilon (real): smallest change in L you don't care about. Returns:...
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from typing import Iterable from typing import Any def allunique(iterable: Iterable[Any]) -> bool: """Check whether all items of an iterable are distinct. Works for either hashable or unhashable items. If all items are hashable, allunique_hashable() will be much faster. Returns True for an empty ite...
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def ceiling_cpm(cpm, ceiling = 1000): """Sets CPM to have ceiling Args: cpm (float): CPM of isoform ceiling (int, optional): Maximum. Defaults to 1000. Returns: float: new cpm constrained to ceiling """ # gtf top score is 1000 if cpm > ceiling: return ceiling ...
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def make_reveal_url(handler, content_id): """Produces a link to this reveal handler that, on success, redirects back to the given 'target' URL with a signature for the given 'content_id'.""" return handler.get_url( '/reveal', target=handler.request.path_qs, content_id=content_id)
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def image_group_object_factory(image_id, group_id): """Cook up a fake imagegroup json object from given ids.""" groupimage = { 'image_id': image_id, 'group_id': group_id } return groupimage
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def normalize_name(s): """Normalizes the name of a file. Used to avoid characters errors and/or to get the name of the dataset from a config filename. Args: s (str): The name of the file. Returns: new_s (str): The normalized name. """ if s is None: return '' s = s....
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def maxWithNone(a, b): """ Returns maximal value from two values, if any of them is None, returns other one. :param a: int, float or None value :param b: int, float or None value :return: class instance with given properties >>> maxWithNone(None, 1) 1 """ if a == None: return b ...
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def get_storage_status(dev): """Return storage status """ if dev: return dev.get_storage_status() else: return None
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def batch_submit(func, batches, client, *args, **kwargs): """ Args: func: function to call using client. batches (list): list of input(s) per batch, e.g. from split_dataframe or split_zip client (concurrent.futures.Executor, dask.distributed.Client) *args: arguments t...
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def _union(groupA, groupB): """Returns the union of groupA and groupB""" elems = set(groupA) elems.update(groupB) return list(elems)
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import yaml def load_yaml(filename): """ Load a YAML file. Parameters ---------- filename : str The name of the file to load Returns ------- dict The contents of the file. """ with open(filename) as file: return yaml.load(file, Loader=yaml.FullLoader)
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def fake_call(command, **kwargs): """ Instead of shell.call, call a command whose output equals the command. :param command: Command that will be echoed. :return: Returns a tuple of (process output code, output) """ return (0, str(command))
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def argparse_textwrap_unwrap_first_paragraph(doc): """Join by single spaces all the leading lines up to the first empty line""" index = (doc + "\n\n").index("\n\n") lines = doc[:index].splitlines() chars = " ".join(_.strip() for _ in lines) alt_doc = chars + doc[index:] return alt_doc
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from pathlib import Path def exists_fixture(filename: str) -> bool: """Check if a fixture exists.""" path = Path(Path(__file__).parent.joinpath("fixtures"), filename) return path.exists()
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def convert_xywh_to_xyxy(api_bbox): """ Converts an xywh bounding box to an xyxy bounding box. Note that this is also different from the TensorFlow Object Detection API coords format. Args: api_bbox: bbox output by the batch processing API [x_min, y_min, width_of_box, height_of_box] Re...
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def validation_error_view(error, request): """ Return Marshmallow :class:`ValidationError` as a JSON response with a proper response code. :param error: Marshmallow error instance :type error: ValidationError :param request: Pyramid request :type request: pyramid.request.Request :return:...
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def validate_option(option, min_value, max_value): """ Validates whether an option number is in the accepted interval (between min_value and max_value) """ if (option >= min_value and option <= max_value): return True else: print("\nNot a valid option!") print(f'Only numb...
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import platform import shlex def split_command_string(string): """Uses shlex.split() to split a string into a list according to the operating system """ is_posix = platform.system() != 'Windows' return shlex.split(string, posix=is_posix)
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from typing import Dict from typing import OrderedDict def build_year_scoring_dict() -> Dict: """Returns an OrderedDict that will be used to populate panelist scoring data""" score_dict = OrderedDict(Jan=0, Feb=0, Mar=0, Apr=0, May=0, Jun=0, Jul=0, Aug=0, ...
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def eval_expr(expr, dict_data): """ If expr is a string, will do a dict lookup using that string as a key. If expr is a callable, will call it on the dict. """ if callable(expr): return expr(dict_data) else: return dict_data.get(expr, None)
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import urllib3 def with_urllib3(url): """Get a streaming response for the given event feed using urllib3.""" http = urllib3.PoolManager() return http.request('GET', url, preload_content=False)
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def subpx_bias(f, pos_columns=None): """Histogram the fractional part of the x and y position. Parameters ---------- f : DataFrame pos_columns : list of column names, optional Notes ----- If subpixel accuracy is good, this should be flat. If it depressed in the middle, try using a ...
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def get_all_dict_words(dict_): """ This function gets all the word entries of the dictionary. :param dict_: Dictionary words and their definitions. :type dict_: dict :return: All the word entries. :rtype: list """ words = set([]) for k, v in dict_.items(): for lev, meaning_...
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def with_metaclass(mcls): """ For metaclass compatibility between Python 2 and 3. cf. http://stackoverflow.com/questions/22409430/portable-meta-class-between-python2-and-python3 """ def decorator(cls): body = vars(cls).copy() # clean out class body body.pop('__dict__', None)...
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def read_gene_cov_file(input_file): """Convert coverage mapping file into a dictionary data structure""" d = {} f = open(input_file, mode='rt') for line in f: words = line.strip().split('\t') gene, coverage = words[0], int(words[1]) d[gene] = coverage f.close() return d
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def filter_after_preprocess(processed_tokens, retained_dict): """ Removes any tokens not in the retained_dict from a list of processed tokens Argument(s): processed_tokens - a list of pre-processed token retained_dict - a token-frequency dictionary of tokens retained ...
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def _read_one(stream): """Read a byte from the file (as an integer) raises EOFError if the stream ends while reading bytes. """ c = stream.read(1) if c == b'': raise EOFError("Unexpected EOF while reading bytes") return ord(c)
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def mode(ary): """ mode function find the object with the biggest number of appears in the given ary :param ary: input ary (some iterable object) :return: the number with the largest appearence number """ dct = {} for value in ary: if value in dct: dct[value]+=1 ...
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def class_as_string(obj): """Return the full class of an object as string""" module = obj.__class__.__module__ if module is None or module == str.__class__.__module__: return obj.__class__.__name__ return module + '.' + obj.__class__.__name__
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def linear_tri(frags, thr): """ Triangle (pyramid) of linear increase then linear decrease weights. Args: frags (list of list): [chrom,start,end] for each fragment in a GEM Returns: lin_all (list of bed entries): bed entries in format [chrom,start,end] """ lin_all = [] n = len(...
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def _data_augmentation(text, labels, augmenter): """Use an augmentation method to expand a training set. :param text: list of input text. :param labels: list of corresponding labels. :param augmenter: textattack.augmentation.Augmenter, augmentation scheme. :return: augmented_text, augmented_labels...
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import json def conv_to_json(my_string: str): """ Converts a valid string to a JSON object. """ try: json_obj = json.loads(my_string) return json_obj except ValueError: return None
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def differential(f, x, deltax=1e-12): """ Returns the slope of the given function at the point x using the midpoint method. A deltax of 1e-12 or 1e-11 works best. """ # the following formula is the average between the slopes using # the right limit [(f(x + deltax) - f(x)) / deltax] and ...
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def get_lambda_timeout(lambda_context) -> int: """Gets the remaining lambda execution time in seconds.""" return int(lambda_context.get_remaining_time_in_millis()/1000)
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def count_words(tokens, n_words = 20): """ Count the number of comments containing each entry Parameters ---------- tokens: list a nested list containing lists of tokens or a list of spacy docs n: int The number of words to return. Defaults to 20, i.e. the top 20 words Retu...
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def split_function_name(fn): """ Given a method, return a tuple containing its fully-qualified class name and the method name. """ qualname = fn.__qualname__ if '.' in qualname: class_name, fn_name = qualname.rsplit('.', 1) class_name = '%s.%s' % (fn.__module__, class_name) e...
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def MODULE_PATH(analysis_module): """Returns the "module_path" used as a key to look up analysis in ACE.""" return '{}:{}'.format(analysis_module.__module__, analysis_module.__name__ if isinstance(analysis_module, type) else type(analysis_module).__name__)
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def R0(beta, gamma): """ R0 from model parameters. """ return beta / gamma
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def pipe_info(source, sink): """Return stream information header.""" # First line if source is None: source = '' else: source = f' from {repr(source)}' if sink is None: sink = '' else: sink = f' to {repr(sink)}' return f"{source}{sink}"
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def A11_2_d11(A11, SRM_ratio=4.04367): """ Convert Abundance to Delta notation. Default SRM_ratio is NIST951 11B/10B """ return ((A11 / (1 - A11)) / SRM_ratio - 1) * 1000
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def rule_passes(rule_regexp, product_repr): """ rule: rule(keep, drop)_A_B_C_D product: A_B_C """ #we have altered the rules to have "*" as the 4th parameter (if split by _) # so all the D's will pass return rule_regexp.match(product_repr+"_")
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def _get_category_names(category_ids: list) -> list: """ Transform the category id like '10_blogging' to a human-friendly name like 'Blogging' If no name is found for an id the input value will be returned """ categories = { "1_communication": "Social & Communication", "2_entertainment": "Entertainment", "6_...
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def getFile(file): """ Read out a file and return a list of string representing each line """ with open (file, "r") as out: return out.readlines()
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def esc(code: int) -> str: """ Converts the integer code to an ANSI escape sequence :param code: code :return: escape sequence """ return f"\033[{code}m"
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def aic(model): """Given a model, calculates an AIC score.""" k = model.num_of_params L = model.lnlikelihood() return 2*(k-L)
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def find_subset_sum(values, target): """ Find a subset of the values that sums to the target number This implements a dynamic programming approach to the subset sum problem Implementation is taken from: https://github.com/saltycrane/subset-sum/blob/master/subsetsum/stackoverflow.py @param values: L...
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def _temperature(temperature_register, farenheight=False): """Return the temperature in Celsius given the raw temperature register value. If farenheight is True, return the temperature in Farenheight. """ temp = (0xFF & (temperature_register >> 8)) + ((0x7 & (temperature_register >> 5)) / 8.0) if f...
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import inspect def get_method_arguments(method, exclude=None): """ Return the method's argument, associated with a boolean describing whether or not the given argument is required. """ signature = inspect.getfullargspec(method) args_count = len(signature.args) if signature.args else 0 ...
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def mergeinfo_ranges_to_set(mergeinfo_ranges): """Convert compact ranges representation to python set object""" result = set() for r in mergeinfo_ranges: if type(r) == int: result.add(r) else: result |= set(range(r[0], r[1]+1)) return result
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import glob def get_lines_from_file(folder_name, interface_name, file_string): """Open file with the path "folder_name/interface_name/filestring" and return its contents. """ with open(glob.glob( f"{folder_name}/{interface_name}/{file_string}")[0], "r") as file: return file.readlin...
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import torch def expand_dims(input, axis): """ Inserts a dimension of 1 into a tensor's shape. Parameters ---------- input : tensor A Tensor. axis : int 0-D (scalar). Specifies the dimension index at which to expand the shape of input. Must be in the range [-rank(input...
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def rescue_default(callback, default=""): """Call callback. If there's an exception, return default. It's convenient to use lambda to wrap the expression in order to create a callback. Only catch IndexError, AttributeError, and ValueError. """ try: return callback() except (IndexError, AttributeErro...
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def capacity_cost_rule(mod, g, p): """ The capacity cost of projects of the *gen_ret_bin* capacity type is its net capacity (pre-specified capacity or zero if retired) times the per-mw fixed cost for each of the project's operational periods. """ return mod.gen_ret_bin_fixed_cost_per_mw_yr[g, p]...
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def sample_from_bam(bam): """Extract sample name from BAM""" read_groups = bam.header["RG"] samples = set([rg["SM"] for rg in read_groups]) assert len(samples) == 1, "BAM file {} must contain a single sample".format( bam.filename ) sample, = samples # Extract single value from set r...
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from typing import List from typing import Any def is_int_array(array: List[Any]) -> bool: """Returns `True` is array contains integers or floats otherwise `False`. Examples: >>> assert not is_int_array("") >>> assert not is_int_array(None) >>> assert not is_int_array("-1") >>...
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def _cid2c(cid): """Gets just the component portion of a cid string e.g. main_page/axis_controls|x_column.value => x_column """ return cid.split("|")[-1].split(".")[0]
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import math def round_mult(val, multiple, direction='round'): """Rounds :val: to the nearest :multiple:. The argument :direction: should be either 'round', 'up', or 'down'.""" round_func = {'round': round, 'up': math.ceil, 'down': math.floor} return round_func[direction](val / multiple) * multiple
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def get_tech_installed(enduse, fuel_switches): """Read out all technologies which are specifically switched to of a specific enduse Parameter --------- enduse : str enduse fuel_switches : dict All fuel switches where a share of a fuel of an enduse is switched to a specif...
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def underscore_ip(ip): """ Takes an ipv4 adress and replaces dots with underscores. """ if (ip is None): return None return ip.replace(".", "_")
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def is_avx512_instruction_form(instruction_form): """Indicates whether the instruction form belongs to AVX512 extensions""" return instruction_form.isa_extensions and instruction_form.isa_extensions[0].name.startswith("AVX512")
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def upload_file_to_slack(slack_connection, file_name, channel_name, timestamp): """ Upload a file to Slack in a thread under the main message. All channel members will have access to the file. Only works for files <50MB. """ try: file_response = slack_connection.files_upload( ...
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def user_with_role(user, role): """ Build user representation with attached role """ return { 'id': user.id, 'username': user.username, 'email': user.email, 'role': role }
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def f(x): """Cubic function.""" return x**3
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def clean_data(df): """ :param df: DataFrame of messages and categories :return: cleaned DataFrame of messages and categories, with duplicates removed """ return df.drop_duplicates(subset='id')
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def tempo_execucao(start_time, end_time, num_el, show): """ Calcula o tempo de execução do código Parâmetros ---------- start_time: float Tempo inicial end_time: flaot Tempo final num_el: int Número de elementos d...
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