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def colon_based_id_to_vep_id(colon_id): """Converts a colon-based identifier to VEP compatible one. Example: '15:7237571:C:T' → '15 7237571 . C T'""" id_fields = colon_id.split(':') assert len(id_fields) == 4, 'Invalid colon-based identifier supplied (should contain exactly 4 fields)' return '{} {} . {} {}'.format(*id_fields)
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def filter_file_paths_by_extension(file_paths, ext='csv'): """ Filters out file paths that do not have an appropriate extension. :param file_paths: list of file path strings :param ext: valid extension """ valid_file_paths = [] for file_path in file_paths: ext = ".%s" % ext if ext[0] != '.' else ext if not file_path.endswith(ext): continue valid_file_paths.append(file_path) return valid_file_paths
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import time def dateTimeNow(str_sign=''): """ .. _dateTimeNow : Return the system date and time as a string. Return format: 'yyyy-mm-dd, HH:MM:SS' + str_sign Parameters ---------- str_sign : str A sign to append to the 'yyyy-mm-dd, HH:MM:SS'. Returns ------- str_date_time : str Formatted system date time string in 'yyyy-mm-dd, HH:MM:SS' + str_sign. Examples -------- >>> dateTimeNow(':') '2017-11-20, 15:14:42:' """ str_date_time = time.strftime('%Y-%m-%d, %H:%M:%S', time.gmtime()) str_date_time = str_date_time + str_sign return str_date_time
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def variable_name_to_option_name(variable: str): """ Convert a variable name like `ec2_user` to the Click option name it gets mapped to, like `--ec2-user`. """ return '--' + variable.replace('_', '-')
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def rrl(n,dn=1,amu=1.007825,Z=1): """ compute Radio Recomb Line freqs in GHz from Brown, Lockman & Knapp ARAA 1978 16 445 UPDATED: Gordon & Sorochenko 2009, eqn A6 Parameters ---------- n : int The number of the lower level of the recombination line (H1a is Lyman alpha, for example) dn : int The delta-N of the transition. alpha=1, beta=2, etc. amu : float The mass of the central atom Z : int The ionization parameter for the atom. Z=1 is neutral, Z=2 is singly ionized, etc. For hydrogen, only z=1 makes sense, since ionized hydrogen has no electrons and therefore cannot have recombination lines. Returns ------- frequency in GHz """ nu = 3.289842e6*(1-5.48593e-4/amu)*(1/float(n)**2 - 1/float(n+dn)**2) nu = 3.28984196e6 * Z**2 * (amu-5.48579911e-4*(Z+1))/(amu-5.48579911e-4*Z) * (1/float(n)**2 - 1/float(n+dn)**2) return nu
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def record_has(inrec, fieldvals): """Accept a record, and a dictionary of field values. The format is {'field_name': set([val1, val2])}. If any field in the record has a matching value, the function returns True. Otherwise, returns False. """ retval = False for field in fieldvals: if isinstance(inrec[field], str): set1 = {inrec[field]} else: set1 = set(inrec[field]) if (set1 & fieldvals[field]): retval = True break return retval
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def force_string(val=None): """Force a string representation of an object Args: val: object to parse into a string Returns: str: String representation """ if val is None: return '' if isinstance(val, list): newval = [str(x) for x in val] return ';'.join(newval) if isinstance(val, str): return val else: return str(val)
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def id_is_int(patient_id): """ Check if patient id is integer Check if the patient's id is a integer Args: patient_id (int): id number of the patient Returns: True or str: indicate if the input patient id is an integer """ try: int(patient_id) return True except ValueError: return "Please use an integer or a numeric string containing " \ "an ID number but without any letter"
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import math def sqroot(x): """ Finds the square root of the number passed in """ return math.sqrt(x)
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def get_relative_error_success_count(relative_errors, threshold=0.05): """Return the count of the errors below a threshold""" return len(list(filter(lambda x: x <= threshold, relative_errors)))
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import math def land_cost(starting_land: int, ending_land: int, *, multiplier: float = 1, policy: bool = False) -> float: """ Calculate the cost to purchase or sell land. :param starting_land: A starting land amount. :param ending_land: The desired land amount. :param multiplier: A multiplier to adjust the ending result by. :param policy: If the land policy is being used. :return: The cost to purchase or sell land. """ def unit_cost(amount: int): return (.002*(amount-20)*(amount-20))+50 difference = ending_land - starting_land cost = 0 if difference < 0: return 50 * difference if difference > 500 and difference % 500 != 0: delta = difference % 500 cost += round(unit_cost(starting_land), 2) * delta starting_land += delta difference -= delta for _ in range(math.floor(difference // 500)): cost += round(unit_cost(starting_land), 2) * 500 starting_land += 500 difference -= 500 if difference: cost += (round(unit_cost(starting_land), 2) * difference) if policy: cost = cost * 0.95 return cost * multiplier
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def skipped_iter(data, skip_criteria): """Utility function that returns an iterator where data items are skipped according to some provided criteria. Parameters: ----------- data - list of data items skip_criteria - lambda or function that takes an item and determines whether or not to skip. Returns: -------- a data item iter starting at the first unskipped item. """ iterator = iter(data) # Skip past any sensor data that was recorded prior to min time. # if min_time: item = next(iterator) i = 0 while skip_criteria(item): item = next(iterator) i = i + 1 return iter(data[i:])
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def pprint(ast): """pretty print an Abstract Syntax Tree""" def red(string): # format a string to be printed in red return '\033[31m' + string + '\033[0m' def print_rec(ast, i): # recursively print the AST if ast[0] == "symb" or ast[0] == 'value': print(" "*i + str(ast[1])) elif ast[0] == "non": print(" "*i + red(ast[0])) print_rec(ast[1], i+1) else: print(" "*i + red(ast[0])) print_rec(ast[1], i+1) print_rec(ast[2], i+1) print_rec(ast, 0)
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from datetime import datetime def get_datetime(ts): """datetime from epoch timestamp""" if ts: return datetime.fromtimestamp(int(int(ts)/1000))
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def getattrs(value, attrs): """Helper function that extracts a list of attributes from `value` object in a `dict`/mapping of (attr, value[attr]). Args: value (object): Any Python object upon which `getattr` can act. attrs (iterable): Any iterable containing attribute names for extract. Returns: `dict` of attr -> val mappings. Example: >>> getattrs(complex(2,3), ['imag', 'real']) {'imag': 3.0, 'real': 2.0} """ return dict([(attr, getattr(value, attr)) for attr in attrs])
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def tileSizePixels() -> int: """ Tile height and width in pixels. """ return 256
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def GetFullPartitionSize(partition, metadata): """Get the size of the partition including metadata/reserved space in bytes. The partition only has to be bigger for raw NAND devices. Formula: - Add UBI per-block metadata (2 pages) if partition is UBI - Round up to erase block size - Add UBI per-partition metadata (4 blocks) if partition is UBI - Add reserved erase blocks """ erase_block_size = metadata.get('erase_block_size', 0) size = partition['bytes'] if erase_block_size == 0: return size # See "Flash space overhead" in # http://www.linux-mtd.infradead.org/doc/ubi.html # for overhead calculations. is_ubi = partition.get('format') == 'ubi' reserved_erase_blocks = partition.get('reserved_erase_blocks', 0) page_size = metadata.get('page_size', 0) if is_ubi: ubi_block_size = erase_block_size - 2 * page_size erase_blocks = (size + ubi_block_size - 1) // ubi_block_size size += erase_blocks * 2 * page_size erase_blocks = (size + erase_block_size - 1) // erase_block_size size = erase_blocks * erase_block_size if is_ubi: size += erase_block_size * 4 size += reserved_erase_blocks * erase_block_size return size
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def stats_box(points): """ Returns the extrema and dimensions for a box enclosing the points Args: points (list): a list of points in [(x1, y1),(x2, y2),(xN, yN)] form Returns: min_x (float): minimum x coordinate min_y (float): minimum y coordinate max_x (float): maximum x coordinate max_y (float): maximum y coordinate width (float): width across x-coordinates height (float): width across y-coordinates Example Returns:: min_x, min_y, max_x, max_y, width, height = stats_box(points) """ x_coordinates = [] y_coordinates = [] for x_coordinate, y_coordinate in points: x_coordinates.append(x_coordinate) y_coordinates.append(y_coordinate) min_x = min(x_coordinates) max_x = max(x_coordinates) min_y = min(y_coordinates) max_y = max(y_coordinates) return min_x, min_y, max_x, max_y, abs(max_x - min_x), abs(max_y - min_y)
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import torch def dmae(x, y): """ dMAE(x,y) = sign(x-y) """ return torch.sign(x-y)
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def get_experiment_run_name( mode: str, msg: int, msg_unit: str, freq: int, ) -> str: """ Get name of data file for a specific run. :param mode: the mode :param msg: the msg size :param msg_unit: the msg unit prefix :param freq: the publishing frequency :return: the file name for that specific run """ assert mode in ('base', 'trace') # use '_s' suffix file because that's the one that contains the latency data (subscriber) return f'1-{mode}_Array{msg}{msg_unit}_{freq}hz_s'
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def env_exists(env_variable: str) -> bool: """Validates if env variable was provided and is not an empty string. Args: env_variable: str, name of the env variable Returns: True: if env provide and not an empty string False: if env not provided or an empty string """ if env_variable is not None and env_variable != '': return True return False
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def midpoint2(x1: float, y1: float, x2: float, y2: float) -> complex: """ Returns the Midpoint between two numbers on a line""" x = (x1 + x2) / 2 y = (y1 + y2) / 2 return complex(x, y)
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from typing import List from typing import Any def difference(list1: List[Any], list2: List[Any]) -> List: """ Extend list with unique values of second lists. Parameters ---------- list1: List[Any] List of values of any type. list2: List[Any] List of values of any type. Returns ------- List The first list without elements from the second list. """ return [x for x in list1 if x not in list2]
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import yaml def YamlWrite(structured_data, dumper): """Wrap yaml.dump to make calling convention consistent.""" return yaml.dump(structured_data, default_flow_style=False, Dumper=dumper)
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import time def _get_timestamp_ms(when): """Converts a datetime.datetime to integer milliseconds since the epoch. Requires special handling to preserve microseconds. Args: when: A datetime.datetime instance. Returns: Integer time since the epoch in milliseconds. If the supplied 'when' is None, the return value will be None. """ if when is None: return None ms_since_epoch = float(time.mktime(when.utctimetuple()) * 1000.0) ms_since_epoch += when.microsecond / 1000.0 return int(ms_since_epoch)
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from typing import Mapping from typing import Any from typing import Dict def with_key_prefix(d: Mapping[str, Any], key_prefix: str) -> Dict[str, Any]: """Returns {key_prefix+k: v for k, v in d.items()}.""" return {key_prefix+k: v for k, v in d.items()}
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import copy def _convert_jsonschema_to_list_of_parameters(obj, in_="query"): """ Swagger is only _based_ on JSONSchema. Query string and header parameters are represented as list, not as an object. This converts a JSONSchema object (as return by the converters) to a list of parameters suitable for swagger. :param dict obj: :param str in_: 'query' or 'header' :rtype: list[dict] """ parameters = [] assert obj["type"] == "object" required = obj.get("required", []) for name, prop in sorted(obj["properties"].items(), key=lambda i: i[0]): parameter = copy.deepcopy(prop) parameter["required"] = name in required parameter["in"] = in_ parameter["name"] = name parameters.append(parameter) return parameters
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import torch def averaged_std(outputs): """ Computes averaged standard deviation across list of tensors with the similar size Step 1: Std across members of ensemble Step 2: Average Across all datapoints Step 3: Average Across all item """ #print("Outputs ", outputs) outputs = torch.stack(outputs) #print("Stacked outputs ", outputs) step1 = torch.std(outputs, dim=0) step2 = torch.mean(step1, dim=0) step3 = torch.mean(step2, dim=0) #print("step 3 is ", step3) return step3.tolist()
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def getSubjectName(inputname): """Determine first column subject name for output file """ if len(inputname.split('.')) == 2: return inputname.split('.')[0]
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def put_item_request_param(item): """ Creates a PutItem request used as an argument to Table.put_item() :param item: The item to put in DynamoDB :return: PutItem request """ return { 'Item': item, 'ReturnConsumedCapacity': 'TOTAL' }
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import asyncio async def async_run_command(command): """Run an async command and return stdout and stderr.""" process = await asyncio.create_subprocess_shell( command, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE ) stdout, stderr = await process.communicate() stdout, stderr = stdout.decode(), stderr.decode() return stdout, stderr
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def greedy_approach(U, N, dist): """ Compute travel cost in the greedy approach, i.e., each user travels to the nearest POI. Parameters ---------- U: array List of users. N: dict Dictionary of nearest POI. dist: array Pairwise distance. Returns ------- total_cost: int Total travel cost. """ total_dist = 0 for u in U: total_dist += dist[u][N[u]] return total_dist
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import sqlite3 def suggest_options(field, query, **kwargs): """ Sample plugin that enables CloudBolt interface to provide a form field that autocompletes as the user is typing, but that fetches matching options by invoking this action asynchronously. Use this if the set of options is so large that the normal `get_options_list` (which renders all options into the page) performs poorly. Note: This is just an example of one way such an action might be used, by querying a local SQLite database. It could also fetch options from an external API. Args: query: the word the user has typed Returns: list of tuples representing dropdown options ("value", "Visible label")] """ # Limit the results to something reasonable, for a responsive user experience; # this action is called as the user is typing and results should be returned # as quickly as possible, but also not too many. max_results = 50 # Query an SQLite database table for matching email addresses. conn = sqlite3.connect('/var/opt/cloudbolt/proserv/ldap_users.db') c = conn.cursor() emails = c.execute( 'SELECT email FROM users WHERE email LIKE ? ORDER BY email LIMIT ?', ('%{}%'.format(query), max_results) ) # Use the SQLite query result here, before closing the DB connection. It # materializes the cursor and avoids Python exception. options = [(email, email) for email in emails] conn.close() return options
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def as_list(maybe_element): """helps to regularize input into list of element. No matter what is input, will output a list for your iteration. **Basic Examples:** >>> assert as_list("string") == ["string"] >>> assert as_list(["string", "string"]) == ["string", "string"] >>> assert as_list(("string", "string")) == ["string", "string"] >>> assert as_list([["string", "string"]]) == ["string", "string"] **An Application Example:** >>> def func(*args): >>> return as_list(args) >>> >>> assert func("a", "b") == ["a", "b"] >>> assert func(["a", "b"]) == ["a", "b"] """ if type(maybe_element) == list: maybe_stacked = maybe_element if 1 == len(maybe_stacked) and type(maybe_stacked[0]) == list: mustbe_list = maybe_stacked[0] else: mustbe_list = maybe_stacked elif type(maybe_element) == tuple: maybe_stacked = maybe_element if 1 == len(maybe_stacked) and type(maybe_stacked[0]) == list: mustbe_list = maybe_stacked[0] else: mustbe_list = list(maybe_stacked) else: mustbe_list = [maybe_element] return mustbe_list
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def filter_error_ppm(df, err_range=0.5): """ Filter based on error range of - err_range to + err_range """ df = df[df['Error_ppm'].between(-err_range, err_range)] return df
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def get_query_file_type(query_file): """Takes an input query file and determines whether it is a FASTA file or an HMM file. Returns either "FASTA" or "HMM". """ file_type = None with open(query_file) as infh: first_line = infh.readline().strip() if first_line.startswith('>'): file_type = 'FASTA' elif first_line.startswith('HMM'): file_type = 'HMM' # Check that it worked. assert file_type is not None, """Error: Input file type could not be determined: %s""" % query_file # Return file type. return file_type
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def split_record(line, separator=';'): """Split `line` to a list of fields and a comment >>> split_record('0000..0009 ; XXX # some value') (['0000..0009', 'XXX'], 'some value') """ try: i = line.index('#') except ValueError: record_line = line comment = '' else: record_line = line[:i] comment = line[i+1:] fields = [x.strip() for x in record_line.split(separator)] comment = comment.strip() return fields, comment
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def has_station(train, look_for_station): """Check if this `train` stops at the given station (by the station name). Returns the index of this station within train["stations"], or if the train does not stop returns -1. """ for idx, stoptime in enumerate(train["stations"]): if stoptime["sta"] == look_for_station: return idx return -1
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def standardise_cell_values(pd_df, dict_of_nonstandard_standard): """ Maps non-standard values e.g. "Males" to standard values like "M". Mapping is carried out on a column-specific basis. """ df = (pd_df.replace (to_replace=dict_of_nonstandard_standard, value=None)) return df
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def all_subclasses(cls): """ Given a class `cls`, this recursive function returns a list with all subclasses, subclasses of subclasses, and so on. """ subclasses = cls.__subclasses__() return subclasses + [g for s in subclasses for g in all_subclasses(s)]
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def df_html_display(df): """Apply some HTML/CSS display options for the input DataFrame.""" config_df = df.style return config_df.render()
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import unicodedata def is_number(target_str): """ determine whether the word is number Args: target_str (str): target string """ try: float(target_str) return True except ValueError: pass try: unicodedata.numeric(target_str) return True except (TypeError, ValueError): pass return False
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def ComputeErrorRate(error_count, truth_count): """Returns a sanitized percent error rate from the raw counts. Prevents div by 0 and clips return to 100%. Args: error_count: Number of errors. truth_count: Number to divide by. Returns: 100.0 * error_count / truth_count clipped to 100. """ if truth_count == 0: truth_count = 1 error_count = 1 elif error_count > truth_count: error_count = truth_count return error_count * 100.0 / truth_count
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import requests def check_valid_site(url, print_status=False): """ Checks if a passed URL is valid. If the status code from the site isn't 200, than it isn't valid. :param url: a url to check :param print_status: Print if the passed site is valid or not :return: True(site is valid) or False(site isn't valid; 404) """ try: request = requests.get(url) status_code = request.status_code if status_code == 200: # return request.status_code == 200 could be used, if print_status: print(url, "was a valid site") return True else: if print_status: print(url, "was not a valid status, here's the status code:", status_code) return False except: print("It broke on", url)
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from datetime import datetime def col2datetime(df, col, datestr='%m/%d/%Y %H:%M'): """ Converts date strings in a DataFrame to datetime objects Args: df - a pandas DataFrame col - the column name in df that contains the date strings datestr - a string that encodes the formatting of the datetime strings see python's documentation for datetime to see how these strings are formatted Returns: The DataFrame with all date strings in df[col] converted to datetime objects """ for idx in df.index: d = df[col][idx] df[col][idx] = datetime.strptime(d, datestr) return df
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def testmodels(app_models_env): """ Pytest fixture that deletes existing records in any models in app_models_env.models (an OrderedDict used to access the models). Returns the OrderedDict, with all models emptied. """ testmodels = app_models_env.models for model in testmodels.values(): if hasattr(model, 'objects') and len(model.objects.all()): model.objects.all().delete() return testmodels
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def _select_option(options: dict): """ Present a dictionary of options to the user for selection """ for ix, (k, v) in enumerate(options.items()): print(f'[{str(ix)}] {k}') choice = input("Choose an option by number or name: ") print('') try: choice = int(choice) # treat the input as if it was an integer choice = list(options.keys())[choice] except ValueError: # otherwise assume it was a key value pass return options[choice], choice
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def removeChannelDuplicates(queue, channel): """ Remove settings that apply to the current channel. This way when you move the slider and generate 100 events only the last one gets acted on, but pending events for other channels are not lost. """ final_queue = [] for item in queue: if (item[0] == channel): continue final_queue.append(item) return final_queue
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from typing import Counter def count_passwords(r_start: int, r_end: int): """ Calculate the number of passwrods that meet the predefined criteria """ counter = 0 for i in range(r_start, r_end): numbers = str(i) prev = numbers[0] if len(numbers) != 6: continue increasing, similar_digits = True, set() for x in numbers[1:]: if prev > x: increasing = False break if prev == x: similar_digits.add(x) prev = x histogram = Counter(numbers) proper_similar_digits = any( [histogram[x] == 2 for x in similar_digits]) if increasing and proper_similar_digits: counter += 1 return counter
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import torch def perplexity(y_hat, ground_true): """Perplexity per single example :param y_hat: tensor of probabilities of shape (num_steps, num_classes) :param ground_true: tensor of ground true labels of shape (num_steps,) :return: a perplexity as a scalar """ row_indices = list(range(len(ground_true))) col_indices = ground_true probabilities = y_hat[row_indices, col_indices] n = len(ground_true) return torch.exp(-torch.log(probabilities).sum() / n).item()
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import importlib def load_component(component, name, class_name): """Load and return component network from file.""" imported = importlib.import_module( '.'.join(('musegan.presets', component, name))) return getattr(imported, class_name)
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def calc_static_stress_drop(Mw, fc, phase='S', v=3.5, use_brune=False): """ Calculate static stress drop from moment/corner_freq relation Note the brune model (instantaneous slip) gives stress drops ~ 8 x lower than the Madariaga values for fcP, fcS :param Mw: moment magnitude :type Mw: float :param fc: corner frequency [Hz] :type fc: float :param phase: P or S phase :type phase: string :param v: P or S velocity [km/s] at source :type v: float :param use_brune: If true --> use Brune's original scaling :type use_brune: boolean :returns: static stress drop [MPa] :rtype: float """ if use_brune: # Use Brune scaling c = .375 else: # Use Madariaga scaling if phase == 'S': c = .21 else: c = .32 v *= 1e5 # cm/s a = c * v / fc # radius of circular fault from corner freq logM0 = 3/2 * Mw + 9.1 # in N-m M0 = 10**logM0 * 1e7 # dyn-cm stress_drop = 7./16. * M0 * (1/a) ** 3 # in dyn/cm^2 stress_drop /= 10. # convert to Pa=N/m^2 #print("calc_stress_drop: Mw:%.2f M0:%g [%s] fc:%.2f a:%.1f MPa:%.1f" % (Mw, M0, corner_phase, fc, a, stress_drop/1e6)) return stress_drop / 1e6
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from pathlib import Path def get_full_path(path: str) -> str: """Resolve all implicit and relative path components to give an absolute path to a file or directory""" return str(Path(path).resolve().absolute())
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import jinja2 def create_synapse_hoc( syn_mech_args, syn_hoc_dir, template_path, gid, dt, synapses_template_name="hoc_synapses", ): """Returns a string containing the synapse hoc. Args: syn_mech_args (dict): synapse-related configuration syn_hoc_dir (str): path to directory containing synapse-related data template_path (str): path to the template to fill in gid (int): cell ID dt (float): timestep (ms) synapses_template_name (str): template name of the synapse class Returns: str: hoc script with the synapse class template """ # load template with open(template_path, "r", encoding="utf-8") as template_file: template = template_file.read() template = jinja2.Template(template) # edit template return template.render( TEMPLATENAME=synapses_template_name, GID=gid, SEED=syn_mech_args["seed"], rng_settings_mode=syn_mech_args["rng_settings_mode"], syn_dir=syn_hoc_dir, syn_conf_file=syn_mech_args["syn_conf_file"], syn_data_file=syn_mech_args["syn_data_file"], dt=dt, )
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def job_dfn_list_dict(job_dict): """A job definition list represented as a dictionary.""" return {"jobs": [job_dict]}
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import pytz def add_timezone(time_record): """ Add a default America/New_York timezone info to a datetime object. Args: time_record: Datetime object. Returns: Datetime object with a timezone if time_record did not have tzinfo, otherwise return time_record itself. """ if time_record.tzname() is None: return time_record.replace(tzinfo=pytz.timezone('America/New_York')) return time_record
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def farenheit(ctemp): """ Convert celcius to farenheit.""" return round(9.0/5.0 * ctemp + 32)
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import logging def bad_request(err): """Return a custom 400 error.""" logging.warning(err) return 'The browser (or proxy) sent a request that this server could not understand.', 400
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from functools import reduce def _calculate_in_and_out(arr): """ Calculate n_in and n_out. Args: arr (Array): Input array. Returns: Tuple, a tuple with two elements, the first element is `n_in` and the second element is `n_out`. """ dim = len(arr.shape) if dim < 2: raise ValueError("If initialize data with xavier uniform, the dimension of data must be greater than 1.") n_in = arr.shape[1] n_out = arr.shape[0] if dim > 2: counter = reduce(lambda x, y: x * y, arr.shape[2:]) n_in *= counter n_out *= counter return n_in, n_out
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def total_demand(user_demand, population, area, parameters): """ Estimate total demand based on: - population (raw number) - smartphone penetration (percentage) - market share (percentage) - user demand (Mbps) - area (km^2) E.g.:: 100 population * (80% / 100) penetration * (25% / 100) market share = 20 users 20 users * 0.01 Mbps user demand = 0.2 total user throughput 0.2 Mbps total user throughput during the busy hour / 1 km² area = 0.2 Mbps/km² area demand """ penetration = parameters['penetration_percentage'] market_share = parameters['market_share_percentage'] users = population * (penetration / 100) * market_share user_throughput = users * user_demand demand_per_kmsq = user_throughput / area return demand_per_kmsq
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def adjacent(L): """Recherche l'ensemble des éléments consécutifs d'une listes d'entiers. Cette fonction prend en argument une liste d'entiers et retourne une liste de listes contenant tous les couples d'indices dont les valeurs dans `L` sont consécutives selon l'ordre numétique. Une liste vide est retournée si aucun élément de `L` n'est consécutif. Parameters ---------- L : list `L` est une liste d'entiers. Returns ------- adj : array_like `adj` est une liste de listes contenant tous les couples d'indice de `L` dont les valeurs sont consécutives. Examples -------- >>> L1 = [3,4,1,2] >>> adjacent(L1) [[0, 1], [2, 3]] >>> L2 = [1,2,3,4] >>> adjacent(L2) [[0, 1], [1, 2], [2, 3]] >>> L3 = [2,4,1,3] >>> adjacent(L3) [] """ assert(type(L[0])== int) adj=[] for i in range(len(L)-1): if L[i]==L[i+1]+1 : adj.append([i, i+1]) elif L[i]==L[i+1]-1: adj.append([i,i+1]) return adj
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def make_lilypond_template(tonic: str, scale_type: str) -> str: """ Make template of Lilypond text file. :param tonic: tonic pitch class represented by letter (like C or A#) :param scale_type: type of scale (e.g., 'major', 'natural_minor', or 'harmonic_minor') :return: template """ raw_template = ( "\\version \"2.18.2\"\n" "\\layout {{{{\n" " indent = #0\n" "}}}}\n" "\\new StaffGroup <<\n" " \\new Staff <<\n" " \\clef treble\n" " \\time 4/4\n" " \\key {} \\{}\n" " {{{{{{}}}}}}\n" " \\\\\n" " {{{{{{}}}}}}\n" " >>\n" ">>" ) tonic = tonic.replace('#', 'is').replace('b', 'es').lower() scale_type = scale_type.split('_')[-1] template = raw_template.format(tonic, scale_type) return template
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def jacobian(theta, event, parameters_to_fit): """ Calculate chi^2 gradient (also called Jacobian). """ for (key, val) in enumerate(parameters_to_fit): setattr(event.model.parameters, val, theta[key]) return event.chi2_gradient(parameters_to_fit)
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def _find_bboxes_in_rect(bboxes, left, bottom, right, top): """ Given a list of polygon bounding boxes and a rectangle defined by left/bottom/right/top, this function returns those polygons which overlap the rectangle. Parameters ---------- bboxes : list List of all polygon bboxes. left : int or float The x-coordinate of the lefthand boundary. bottom : int or float The y-coordinate of the bottom boundary. right : int or float The x-coordinate of the righthand boundary. top : int or float The y-coordinate of the top boundary. Returns ------- result : list List of all polygon bboxes that overlap with the defined rectangle. """ result = (bboxes[:, 0] <= right) & (bboxes[:, 2] >= left) & \ (bboxes[:, 1] <= top) & (bboxes[:, 3] >= bottom) return result
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def sort_range_list(range_list, *, descending=True): """Sorts the given list of ranges based on range size. Descending by default.""" def compare_range(iterable): return abs(iterable[1] - iterable[0]) + 1 range_list.sort(key=compare_range, reverse=descending) # Can't return sort() directly, would return None, return range_list
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def valid_python(name): """ Converts all illegal characters for python object names to underscore. Also adds underscore prefix if the name starts with a number. :param name: input string :type name: str :return: corrected string :rtype: str """ __illegal = str.maketrans(' `~!@#$%^&*()-+=[]\{\}|\\;:\'",.<>/?', '_' * 34) if name[0].isdigit(): name = '_'+name return name.translate(__illegal)
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import re def remove_site_number(site): """Some sites are numbered in the VPR arch definitions. This happens for e.g. SLICE0. This function removes trailing numbers from the name""" number = re.search(r'\d+$', site) if number is not None: site = site[:-len(str(number.group()))] return site
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def wt_av(x, xw, y, yw): """ Calculate a weighted average """ return (x*xw+y*yw)/(xw+yw)
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import errno def retry_io_command(base_cmd, *argv): """PEP475: Retry syscalls if EINTR signal received. https://www.python.org/dev/peps/pep-0475/ Certain system calls can be interrupted by signal 4 (EINTR) for no good reason. Per PEP475, these signals should be ignored. This is implemented by default at the lowest level in py3, but we have to account for it in py2. :param base_cmd: The syscall to wrap. :param argv: Arguments to the syscall. :return: The return value from invoking the syscall. """ while True: try: return base_cmd(*argv) except EnvironmentError as enve: if enve.errno != errno.EINTR: raise
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from pathlib import Path from typing import IO def openConfig(path: Path, mode: str) -> IO[str]: """Open the SoftFab configuration file.""" return open(path / 'softfab.ini', encoding='utf-8', mode=mode)
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def chromoAgeRHK(log10RHKprime): """ Calculate the chromospheric age according to Donahue 1998. Donahue 1998 (ASPC 154, 1235) give a relation between chromospheric activity as measured by the R'HK index and the age of late-type stars (Eq. 1). As the level of stellar activity undergoes continuous change, Donahue cautions that individual measurements of the activity level yield notoriously poor age estimates. As an example, the spread in chromospheric solar age resulting from the 11 yr activity cycle is given, which amounts to about 2.5 Ga. This gives an idea of the accuracy of the estimates. Parameters ---------- log10RHKprime : float Chromospheric activity index log10(R'HK). Returns ------- Age : float Stellar age [Ga]. """ RHK = 10.0**log10RHKprime R5 = 1e5*RHK logAge = 10.725 - 1.334*R5 + 0.4085*R5**2 - 0.0522*R5**3 age = 10.0**logAge / 1e9 return age
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def has_column(bind, table, column): """Return True/False whether the column exists on the table in the database.""" stmt = "SELECT column_name FROM information_schema.columns WHERE table_name='{table}' and column_name='{column}';".format(table=table, column=column) result = bind.execute(stmt) return result and result.scalar()
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def mapVal(x, in_min, in_max, out_min, out_max): """ Maps a value that is between in_min and in_max to a value between out_min and out_max @param in_min The minimum value that the input value could be @param in_max The maximum value that the input value could be @param out_min The minimum value that the output value could be @param out_max The maximum value that the output value could be @return A scaled value based on a given input """ return int( (x - in_min) * (out_max - out_min) / (in_max - in_min) + out_min )
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def text_to_dict(text): """parse multilines text containing simple 'key=value' lines and return a dict of {'key': 'value'}. When the same key is encountered multiple time, value is turned into a list containing all values. >>> d = text_to_dict('''multiple=1 ... multiple= 2 ... single =3 ... ''') >>> d['single'] '3' >>> d['multiple'] ['1', '2'] """ res = {} if not text: return res for line in text.splitlines(): line = line.strip() if line and not line.startswith('#'): key, value = [w.strip() for w in line.split('=', 1)] if key in res: try: res[key].append(value) except AttributeError: res[key] = [res[key], value] else: res[key] = value return res
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import torch def make_creep_tests(stress, temperature, rate, hold_times, nsteps_load, nsteps_hold, logspace = False): """ Produce creep test input (time,stress,temperature) given tensor inputs for the target stress, target temperature, loading rate Args: stress: 1D tensor of target stresses temperature: 1D tensor of target temperature rate: 1D tensor of target rates hold_times: 1D tensor of hold times nsteps_load: number of time steps to load up the sample nsteps_hold: number of time steps to hold the sample logspace (optional): log space the hold time steps """ nbatch = stress.shape[0] nsteps = nsteps_load + nsteps_hold stresses = torch.zeros(nsteps, nbatch) times = torch.zeros_like(stresses) temperatures = torch.zeros_like(stresses) for i, (s,t,lr,T) in enumerate(zip(stress,hold_times,rate,temperature)): stresses[:nsteps_load,i] = torch.linspace(0, s, nsteps_load) stresses[nsteps_load:,i] = s times[:nsteps_load,i] = torch.linspace(0, s / lr, nsteps_load) temperatures[:,i] = T if logspace: times[nsteps_load:,i] = torch.logspace(torch.log10(times[nsteps_load-1,i]), torch.log10(t), nsteps_hold+1)[1:] else: times[nsteps_load:,i] = torch.linspace(times[nsteps_load-1,i], t, nsteps_hold+1)[1:] return times, stresses, temperatures
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def convert_single_linear_to_srgb(color_value): """ Changes as single RGB color in linear to SRGB color space :param color_value:float, single color value in 0-1 range (for example red channel) :return:float, new color converted to SRGB """ a = 0.055 if color_value <= 0.0031308: return color_value * 12.92 return (1 + a) * pow(color_value, 1 / 2.4) - a
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def equal_frame_and_index_content(df1, df2): """ Checks whether the passed dataframes have the same content and index values. This ignores index type, so a dataframe with RangeIndex(start=0, stop=3, step=1) will be considered equal to Int64Index([0, 1, 2], dtype='int64', name='index') """ return df1.equals(df2) and list(df1.index) == list(df2.index)
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def day_in_week(adate, offset = 1): """ Returns the day of the week as an integer where Sunday = 1, Monday = 2, ..., Saturday = 7 """ return ((adate.weekday() + offset) % 7) + 1
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def effective_axial_force(H, delta_P, A_i, v, A_s, E, alpha, delta_T): """ Returns the effective axial force of a totally restrained pipe in the linear elastic stress range based on thick wall stress formulation. DNVGL-ST-F101 Equation (4.10) """ return H - delta_P * A_i * (1 - 2 * v) - A_s * E * alpha * delta_T
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def sanitize(value: object) -> object: """ Default sanitize. """ return value
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def load_country_tz(filename, winter=True): """ Load the list of country timzones from a csv file Parameters ---------- filename: String Path to the csv file containing the timezone information winter: bool (defaut to True) Wether the winter time or the summertime is considered Returns ------- dict(str : int) A dictionary mapping the iso3 country codes to the corresponding timezone (hours offset from UTC) """ ctz = dict() with open(filename) as f: for line in f: words = line.split(";") if len(words[0].strip()) == 3: ctz[words[0].strip()] = int(words[2]) if not winter: ctz[words[0].strip()] += int(words[3]) return ctz
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import re def formatCommandLine(command_line): """Format a command line for printing in output""" return " ".join(map(lambda s: (' ' in s or '\n' in s) and '"' + re.sub("\\s+", " ", s) + '"' or s, command_line))
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def longest_common_substring(a, b): """Return the longest common substring between a and b. Args: a (str): A word or non-word string. b (str): A word or non-word string. Returns: res (str): The longest common substring found between a and b. """ memo = {} if a and b: for i in range(len(a)): if a[i] == b[i]: if i == 0 or memo[i - 1] == 0: memo[i] = a[i] else: memo[i] = memo[i - 1] + a[i] else: memo[i] = 0 return memo[max(memo)]
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import math def get_experience_for_level(level: int) -> int: """Gets the total experience needed for a specific level. :param level: The desired level. :return: The total experience needed for the level.""" return int(math.ceil((50 * math.pow(level, 3) / 3) - 100 * math.pow(level, 2) + 850 * level / 3 - 200))
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def compute_score_for_nervous_system(glasgow_coma_scale: int) -> int: """ Computes score based on Glasgow Coma Scale, see paper by Teasdale et al.: https://doi.org/10.1016/S0140-6736(74)91639-0 """ if glasgow_coma_scale < 6: return 4 if glasgow_coma_scale < 10: return 3 if glasgow_coma_scale < 13: return 2 if glasgow_coma_scale < 15: return 1 return 0
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def is_project_delegate(user, project): """Return if a user is owner of the project.""" return project.delegate == user
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import six def parse_methods(root, methods=None): """Parses methods from the given Discovery document. Args: root (dict): A Discovery document. When called recursively, this is a resource within a Discovery document. methods (dict): A mapping of method ID to Discovery method. Do not set, this is used to collect method IDs while recursing. Returns: dict: A mapping of method ID to method. """ if methods is None: methods = {} for method in six.itervalues(root.get('methods', {})): id_ = method['id'] methods[id_] = method for resource in six.itervalues(root.get('resources', {})): parse_methods(resource, methods) return methods
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import re def remove_special_chars(sentences, remove_digits = False): """Given a list of sentences, remove all special characters from those sentences and return the updated sentences. Method gives the option to remove digits.""" # used to isolate special characters that might be next to a character. isolate_pattern = re.compile(r'([{.(-)!}]|-)') special_char_pattern = re.compile(r'[^0-9a-zA-Z\s]+|\[|\]' if not remove_digits else r'[^-a-zA-Z\s]+|\[|\]') updated_sents = [] for sentence in sentences: sentence = isolate_pattern.sub(" \\1 ", sentence) sentence = special_char_pattern.sub("", sentence) updated_sents.append(sentence) return updated_sents
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def is_reference_target(resource, rtype, label): """ Return true if the resource has this rtype with this label """ prop = resource.props.references.get(rtype, False) if prop: return label in prop
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def make_time_unit_str(dtobj): """ Return a time unit string from a datetime object. """ return "seconds since " + dtobj.strftime("%Y-%m-%dT%H:%M:%SZ")
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import random def get_random_sample(population: tuple, k: int) -> list: """Returns a k length list of unique elements from population""" return random.sample(population, k)
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def wavelength (wn): """ wavelength in m given the wavenumber in 1/m """ return 1./wn
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def replace_multiple(y, xs, rep): """Match multiple strings to replace in sequence.""" for x in xs[1:]: y = y.replace(x, rep) return y
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from urllib.parse import urlparse, parse_qsl, urlunparse, urlencode def url_mod(url: str, new_params: dict) -> str: """ Modifies existing URL by setting/overriding specified query string parameters. Note: Does not support multiple querystring parameters with identical name. :param url: Base URL/path to modify :param new_params: Querystring parameters to set/override (dict) :return: New URL/path """ res = urlparse(url) query_params = dict(parse_qsl(res.query)) for k, v in new_params.items(): if v is None: query_params[str(k)] = '' else: query_params[str(k)] = str(v) parts = list(res) parts[4] = urlencode(query_params) return urlunparse(parts)
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import re def _strip_color(string: str) -> str: """Strip ANSI color escape sequences. See https://stackoverflow.com/questions/14693701/ """ return re.sub(r"(?:\x1B[@-_]|[\x80-\x9F])[0-?]*[ -/]*[@-~]", "", string)
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from typing import List def parse_blocks(lines: List) -> List: """ Parse list of blocks into singular data structure Args: lines (List): list of cleaned lines Returns: List of dictionaries, each dictionary a layer in the darknet """ blocks = [] block = {} for line in lines: if line[0] == "[": if len(block): blocks.append(block) block = {} block['arch'] = line[1:-1].rstrip() else: k,v = line.split("=") block[k.rstrip()] = v.lstrip() blocks.append(block) return blocks
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def _GetNestedKeyFromManifest(manifest, *keys): """Get the value of a key path from a dict. Args: manifest: the dict representation of a manifest *keys: an ordered list of items in the nested key Returns: The value of the nested key in the manifest. None, if the nested key does not exist. """ for key in keys: if not isinstance(manifest, dict): return None try: manifest = manifest[key] except KeyError: return None return manifest
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def flip_horiz_tile(s): """Flip a tile horizontally, return str repr.""" new_los = [] for line in s.split("\n"): new_los.append(str.join('', reversed(line))) return str.join("\n", new_los)
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def is_nan(builder, val): """ Return a condition testing whether *val* is a NaN. """ return builder.fcmp_unordered('uno', val, val)
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def get_info_cls(value, base_class='col-md-7'): """Return info element class""" c = base_class if value == '': c += ' text-muted' return c
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