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def filter_to_sentry(event, hint): """filter_to_sentry is used for filtering what to return or manipulating the exception before sending it off to Sentry (sentry.io) The 'extra' keyword is part of the LogRecord object's dictionary and is where the flag for sending to Sentry is set. Example use case: current_app.logger.error( err_formatted, exc_info=ex, extra={'to_sentry': True}) """ # By default, we send to sentry to_sentry = event['extra'].get('to_sentry', True) if to_sentry: return event return None
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def _capture_callback(x): """Validate the passed options for capturing output.""" if x in [None, "None", "none"]: x = None elif x in ["fd", "no", "sys", "tee-sys"]: pass else: raise ValueError("'capture' can only be one of ['fd', 'no', 'sys', 'tee-sys'].") return x
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def get_new_sol_file(test_nr): """ Get name of new solution file """ return "test/{0}-new.sol".format(test_nr)
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import re def unwrap_wrapped_text(text): """ Unwraps multi-line strings, but keeps paragraphs separated by two or more newlines separated by newlines. """ result = [] _re_indentation = re.compile(r'^[ \t]*|[ \t]*$', re.MULTILINE) for paragraph in re.split(r'\n{2,}', text): paragraph = _re_indentation.sub('', paragraph) result.append(re.sub(r'\n', ' ', paragraph)) return '\n'.join(result)
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def test_hindcast_verify_brier_logical(hindcast_recon_1d_ym): """Test that a probabilistic score requiring a binary observations and probability initialized inputs gives the same results whether passing logical as kwarg or mapping logical before for hindcast.verify().""" he = hindcast_recon_1d_ym def logical(ds): return ds > 0.5 brier_logical_passed_as_kwarg = he.verify( metric="brier_score", comparison="m2o", logical=logical, dim="member", alignment="same_verif", ) brier_logical_mapped_before_and_member_mean = ( he.map(logical) .mean("member") .verify(metric="brier_score", comparison="e2o", dim=[], alignment="same_verif") ) brier_logical_mapped_before_no_member_mean = he.map(logical).verify( metric="brier_score", comparison="m2o", dim="member", alignment="same_verif" ) assert ( brier_logical_mapped_before_and_member_mean == brier_logical_passed_as_kwarg ).all() assert ( brier_logical_mapped_before_no_member_mean == brier_logical_passed_as_kwarg ).all()
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import re def could_be_content_page(url: str) -> bool: """ Try to guess if the link is a content page. It's not a perfect check, but it can identify URLs that are obviously not content. """ url = url.lower().rstrip('/') if url.endswith('/signin') or url.endswith('/login') or \ url.endswith('/login-page') or url.endswith('/logout'): return False if url.endswith('/my-account') or url.endswith('/my-wishlist'): return False if re.search('/(lost|forgot)[_-]password$', url): return False if url.endswith('/search') or url.endswith('/archive'): return False if url.endswith('/privacy-policy') or url.endswith('/cookie-policy') or \ url.endswith('/terms-conditions'): return False if url.endswith('/tos') or re.search('/terms[_-]of[_-](service|use)$', url): return False # Yei, it might be a content page return True
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def collide_rect(sprite1, sprite2): """ **pyj2d.sprite.collide_rect** Check if the rects of the two sprites intersect. Can be used as spritecollide callback function. """ return sprite1.rect.intersects(sprite2.rect)
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def compute_image_data_statistics(data_loader): """ Return the channel wise mean and std deviation for images loaded by `data_loader` (loads WebDataset defined in `datasets.py`) """ mean = 0. std = 0. n_samples = 0. for images, bboxes, labels in data_loader: batch_samples = images.size(0) images = images.view(batch_samples, images.size(1), -1) mean += images.mean(2).sum(0) std += images.std(2).sum(0) n_samples += batch_samples mean /= n_samples std /= n_samples return mean, std
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def int_to_roman(n): """ Convert an integer to its standard Roman Numeral representation """ V = [1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1] S = ["M", "CM", "D", "CD", "C", "XC", "L", "XL", "X", "IX", "V", "IV", "I"] out = "" for val,sym in zip(V,S): while n >= val: out += sym n -= val return out
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def _get_module_ver_hash(prov): """Get module commit hash, falling back to semantic version, and finally 'UNKNOWN'""" ver = None subacts = prov[0].get('subactions') if subacts: ver = subacts[0].get('commit') if not ver: ver = prov[0].get('service_ver', 'UNKNOWN') return ver
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def get_nominal_conc(df, species): """ Get the nominal hector concentration for a given species Parameters ---------- df : Pandas DataFrame DataFrame containing output from a nominal hector run species : str Species to retrieve output for Return ------ species_df : Pandas DataFrame Pandas DataFrame containing hector concentration output for the given species """ species = species.upper() # Ensure string is all uppercase # ensure correct string for atmospheric co2 concentration if (species == 'CO2'): species = 'Ca' species_df = df.loc[df['variable'] == species] return species_df
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def gpib_control_ren(library, session, mode): """Controls the state of the GPIB Remote Enable (REN) interface line, and optionally the remote/local state of the device. Corresponds to viGpibControlREN function of the VISA library. :param library: the visa library wrapped by ctypes. :param session: Unique logical identifier to a session. :param mode: Specifies the state of the REN line and optionally the device remote/local state. (Constants.GPIB_REN*) :return: return value of the library call. :rtype: :class:`pyvisa.constants.StatusCode` """ return library.viGpibControlREN(session, mode)
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def truncate(string: str, width: int, ending: str = "...") -> str: """Truncate string to be no longer than provided width. When truncated, add add `ending` to shortened string as indication of truncation. Parameters ---------- string: str String to be truncated. width: int Maximum amount of characters before truncation. ending: str, optional Indication string of truncation. Returns ------- Truncated string. """ if not len(string) > width: return string length = width - len(ending) return string[:length] + ending
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def split_ver_str(ver_str): """Split version string into numeric components. Return list of components as numbers additionally checking that all components are correct (i.e. can be converted to numbers). """ ver_list = [] for c in ver_str.split('.')[0:3]: if not c.isdecimal(): raise RuntimeError("Malformed version string '{}'. " "Component '{}' is not an integer." .format(ver_str, c)) ver_list.append(int(c)) return ver_list
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import torch def get_first_idx(numel_per_tensor): """Returns the first indices of each tensor in the :ref:`packed tensor <packed>`. See :ref:`first_idx definition <packed_first_idx>` for more information. Args: numel_per_tensor (torch.LongTensor): The number of elements (vertices, faces, points...) in each unbatched tensor, as a 1D tensor. Returns: (torch.LongTensor): first indices for each unbatched tensor in the packed tensor, and the last index + 1, as 1D tensor. Example: >>> numel_per_tensor = torch.LongTensor([2, 3, 5]) >>> get_first_idx(numel_per_tensor) tensor([ 0, 2, 5, 10]) """ output = torch.zeros((numel_per_tensor.shape[0] + 1,), dtype=torch.long, device=numel_per_tensor.device) torch.cumsum(numel_per_tensor, dim=0, out=output[1:]) return output
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def shipping_charge(method, basket, postcode): """ Template tag for calculating the shipping charge for a given shipping method and basket, and injecting it into the template context. """ return method.calculate(basket, postcode)
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import re def _re_compile(regex): """Compile a string to regex, I and UNICODE.""" return re.compile(regex, re.I | re.UNICODE)
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from io import StringIO def df_to_csv_string(df): """Converts pandas DataFrame to a CSV string.""" out = StringIO() df.to_csv(out, encoding='utf-8') return out.getvalue()
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def left_shift(number, n): """ Left shift on 10 base number. Parameters ---------- number : integer the number to be shift n : integer the number of digit to shift Returns ------- shifted number : integer the number left shifted by n digit Examples -------- >>> left_shift(152, 1) 15 >>> left_shift(14589, 3) 14 """ return number // 10 ** n
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import math def calculate_distance(location1, location2): """ Calculates the distance between two pairs of lat, long coordinates using the Haversine formula Inputs: location1 - [lat, lon] array with first location location2 - [lat, lon] array with second location Outputs: distance - in kilometers """ lat1 = math.radians(abs(location1[0])) lon1 = math.radians(abs(location1[1])) lat2 = math.radians(abs(location2[0])) lon2 = math.radians(abs(location2[1])) # haversine formula dlon = lon2 - lon1 dlat = lat2 - lat1 a = math.sin(dlat/2)**2 + math.cos(lat1) * math.cos(lat2) * math.sin(dlon/2)**2 c = 2 * math.asin(math.sqrt(a)) # Radius of earth in kilometers r = 6371.0 return c * r
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import re def rmsp(s): """Replace multiple spaces with one. """ return re.sub(r"\ +", ' ', s.strip())
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def ir(some_value): """ Rounds and casts to int Useful for pixel values that cannot be floats Parameters ---------- some_value : float numeric value Returns -------- Rounded integer Raises ------ ValueError for non scalar types """ return int(round(some_value))
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def decibels_to_amplitude_ratio(decibels): """The ratio between two amplitudes given a decibel change""" return 2 ** (decibels/10)
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import requests def get_stock_data(symbol, token): """Send a request to the API with the symbol and token. Return the stock data we want: Symbol, Company Name, Current Price""" url = f"https://cloud.iexapis.com/stable/stock/{symbol}/quote?token={token}" response = requests.get(url) if response.status_code != 200: print(response.text) return None all_stock_data = response.json() name = all_stock_data["companyName"] symbol = all_stock_data["symbol"] current_price = all_stock_data["latestPrice"] stock_data = {"name": name, "symbol": symbol, "current_price": current_price} return stock_data
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def handle_exhibition_desc(company: str, desc: str) -> str: """ Handles exhibition description special formatting needs. Returns the updated description. :param company: company name :param desc: company description """ if company.lower() == "mathworks": desc = desc.replace(" o ", "\n- ") if company.lower() == "simulation and data lab neuroscience": desc = desc.replace("\n•", "\n- ") return desc
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import click def soft_nprocs(soft, nprocs): """Reduce the number of ranks to the largest acceptable soft value""" # If no soft specification given, use -n value if not soft: return nprocs # Filter to values between 1 and nprocs try: return max([x for x in soft if 0 < x <= nprocs]) except ValueError: # pylint: disable=raise-missing-from raise click.UsageError("No soft values found between 1 and %d" % nprocs)
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def _IsOverlapping(alert_entity, start, end): """Whether |alert_entity| overlaps with |start| and |end| revision range.""" return (alert_entity.start_revision <= end and alert_entity.end_revision >= start)
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import torch def GTA_prop_to_hot(img, n_classes: int, width: int, height: int): """ This function turns the output of the network (given in probability format) into the most likely onehot encoded output. Args: img (tensor): The tensor with probabilities. n_classes (int): Amount of classes in the onehot encoded format. width (int): Size width of the given tensor. height (int): Size height of the given tensor. Returns: Tensor: In onehot encoded format. """ mat = torch.argmax(img, dim=1) map = torch.zeros((n_classes, height, width), dtype=torch.uint8) for r in range(height): for c in range(width): map[mat[0][r][c]][r][c] = 1 return map
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import math def polar2cart(r, x0, y0, theta): """Changes polar coordinates to cartesian coordinate system. :param r: Radius :param x0: x coordinate of the origin :param y0: y coordinate of the origin :param theta: Angle :return: Cartesian coordinates :rtype: tuple (int, int) """ x = int(x0 + r * math.cos(theta)) y = int(y0 + r * math.sin(theta)) return x, y
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def binary_search(query, array): """ Determine whether the query is in an sorted array. Return the index of the query if it is present in the array. If the query is not in the array, return -1 >>> binary_search(4, [1, 2, 3, 4, 5, 6, 7, 8, 9]) 3 >>> binary_search(8, [1, 2, 3, 4, 5, 6, 7, 8, 9]) 7 >>> binary_search(10, [1, 2, 3, 4, 5, 6, 7, 8, 9]) -1 """ lo, hi = 0, len(array) - 1 while lo <= hi: mid = (lo + hi) // 2 if query < array[mid]: hi = mid - 1 elif query > array[mid]: lo = mid + 1 else: return mid return -1
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import torch def calculate_output_dim(net, input_shape): """Calculates the resulting output shape for a given input shape and network. Args: net (torch.nn.Module): The network which you want to calculate the output dimension for. input_shape (int | tuple[int]): The shape of the input being fed into the :obj:`net`. Batch dimension should not be included. Returns: The shape of the output of a network given an input shape. Batch dimension is not included. """ if isinstance(input_shape, int): input_shape = (input_shape,) placeholder = torch.zeros((0,) + tuple(input_shape)) output = net(placeholder) return output.size()[1:]
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def markdown_escape_filter(text): """Escape special characters in Markdown.""" return text.replace("\\", "\\\\").replace("`", "\\`").replace( "*", "\\*").replace("_", "\\_").replace("{", "\\{").replace( "}", "\\}").replace("[", "\\[").replace("]", "\\]").replace( "(", "\\(").replace(")", "\\)").replace("#", "\\#").replace( "+", "\\+").replace("-", "\\-").replace(".", "\\.").replace( "!", "\\!").replace("|", "\\|")
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def thousands_separator(value): """ 千位分隔符 例如传入 1000000000,返回 1,000,000,000 :param value: 需要转换的数字 :return: 格式化后的字符串 """ return '{:,}'.format(value)
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from typing import List import math def equal_split(s: str, width: int) -> List[str]: """ Split the string, each split has length `width` except the last one. """ num = int(math.ceil(len(s) / width)) # python3 return [s[i * width: (i + 1) * width] for i in range(num)]
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def prob1(l): """Accept a list 'l' of numbers as input and return a list with the minimum, maximum, and average of the original list. """ ans = [] ans.append(min(l)) ans.append(max(l)) ans.append(float(sum(l))/len(l)) return ans
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def get_ns_name(uri): """ Get the namespace (the namespace is placed before the first '#' character or the last '/' character) """ hash_index = uri.find('#') index = hash_index if hash_index != -1 else uri.rfind('/') namespace = uri[0: index + 1] return namespace
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import struct def pack_date(date): """ Packs a date (assumed to be UTC) as a struct with of 16-bit, unsigned `year` (big endian), 1 byte `month`, and 1 byte `day`. """ return struct.pack("!HBB", date.year, date.month, date.day)
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from typing import Set def allocate_mid(mids: Set[str]) -> str: """ Allocate a MID which has not been used yet. """ i = 0 while True: mid = str(i) if mid not in mids: mids.add(mid) return mid i += 1
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def _xor(a,b): """Return true iff exactly one of and b are true. Used to check some conditions.""" return bool(a) ^ bool(b)
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from typing import Any from typing import get_args from typing import get_origin from typing import Literal def is_str_literal(hint: Any) -> bool: """Check if a type hint is Literal[str].""" args = get_args(hint) origin = get_origin(hint) if origin is not Literal: return False if not len(args) == 1: return False return isinstance(args[0], str)
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def get_pitch_at_time(genotype, time): """given genotype and durk time point, returns pitch being played at that durk point and whether or not pitch ends perfectly on time Args: genotype ((int, int)[]): genotype of chromosome, which is list of (pitch, dur) time (int): time point in durks Returns: (int, bool): (pitch, end_on_time) where pitch is [1,21] and end_on_time represents whether or not the pitch ends perfectly at the time point time. """ pitch = -9999 dur_running_total = 0 end_on_time = False for i, (ed, dur) in enumerate(genotype): dur_running_total += dur if dur_running_total > time: pitch = ed break elif dur_running_total == time: pitch = ed end_on_time = True break return (pitch, end_on_time)
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def _get_source_files(commands): """Return a list of all source files in the compilation.""" return list(commands.keys())
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def dnode(period): """ Orbit nodal precession on each rev. Orbits below GEO move (drift) Westerly while orbits above GEO move Easterly. Orbits at GEO are stationary, 0 deg drift. Use siderial day rotation for better accuracy. Arg: period [sec] Return: node precession (dn) [deg] """ return 360 - 360/(23*3600+56*60+4)*period
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def process_search_term(lookup): """ Removes any whitespace from the search string, and replaces them with the appropriate character to pass as a URL :param lookup: :return: lookup """ lookup = lookup.replace(" ", "+") return lookup
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import torch def check_gpu(gpu): """ Fuction takes one argument as boolean and provides support for gpu or cpu selection and print out the current device being used. Command Line Arguments: 1. GPU as True value that enables GPU support and use cuda for calculation, and False to enable CPU. Function returns device and print out the device being used, either for trianing or inference. """ # If gpu is True gpu is enabled and print out "\nGPU is availabe...". if the gpu didn't exist device switchs to cpu and print out "\nDevice didn't find GPU, using CPU instead" if gpu: device = torch.device("cuda" if torch.cuda.is_available() else "cpu") if torch.cuda.is_available(): print("\nGPU is availabe...") else: print("\nDevice didn't find GPU, using CPU instead") else: print("\nCPU is availabe...") return torch.device("cpu") return device
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import csv import re def load_peptides(input_file, peptide_column, column_separator): """ Parses the input file and extracts all peptides occuring within the file. Peptide strings are cleaned (only valid characters retained) and returned as a set. :param input_file: The file to parse :param peptide_column: The column header to extract the peptides from. :param column_separator: The separator used for the columns :return: A set of strings representing the peptides. """ with open(input_file, "r") as input_stream: csv_reader = csv.DictReader(input_stream, delimiter=column_separator) peptides = set() for row in csv_reader: if peptide_column not in row: raise Exception("Specified peptide column '" + peptide_column + "' not found in input file.") sequence = row[peptide_column] clean_sequence = re.sub("[^A-Z]", "", sequence) peptides.add(clean_sequence) return peptides
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def input_prompt(prompt): """ Get user input """ return input(prompt)
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from typing import List def alphabetical_binary_search(sorted_list: List, search_name: str) -> int: """Alphabetical binary search (for study purpuses) Args: sorted_list (List): A list of names (must be ordered) search_name (str): name to search Returns: int: found index or -1 """ lowest_index = 0 highest_index = len(sorted_list) - 1 intermediate_index = highest_index // 2 while lowest_index <= highest_index: name = sorted_list[intermediate_index] if search_name == name: return intermediate_index if name > search_name: highest_index = intermediate_index - 1 if name < search_name: lowest_index = intermediate_index + 1 intermediate_index = (lowest_index + highest_index) // 2 return -1
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import torch def compute_loss(inputs, outputs, criterion, edge_criterion): """Compute loss automatically based on what the model output dict contains. 'doc_logits' -> document-label CE loss 'para_logits' -> paragraph-label CE loss 'pare_edge_weights' -> additional edge CE loss """ if 'para_logits' in outputs: loss = criterion(outputs['para_logits'], inputs['para_label']) loss *= (inputs['para_lengths'] != 0).to(torch.float) loss = loss.sum() else: loss = criterion(outputs['doc_logits'], inputs['label']).sum() if 'para_edge_weights' in outputs: edge_loss_lambda = 0.1 edge_loss = edge_criterion(outputs['para_edge_weights'], 1 - inputs['para_label']) edge_loss *= (inputs['para_lengths'] != 0).to(torch.float) loss += edge_loss_lambda * edge_loss.sum() return loss
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import base64 def decode_base64(input_string: str) -> bytes: """Decode an unpadded standard or urlsafe base64 string to bytes.""" input_bytes = input_string.encode("ascii") input_len = len(input_bytes) padding = b"=" * (3 - ((input_len + 3) % 4)) # Passing altchars here allows decoding both standard and urlsafe base64 output_bytes = base64.b64decode(input_bytes + padding, altchars=b"-_") return output_bytes
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def normalize_extension(extension): """ Normalize extension Converts given extension to canonical format for storage :param extension: original extension :return: normalized extension """ extension = extension.lower() exts = dict() exts['jpg'] = ['jpeg','jpe','jif','jfif','jfi''jp2','j2k','jpx','jpf','jpm'] exts['tif'] = ['tiff'] exts['tar.gz'] = ['tgz'] for canonical, variants in exts.items(): if extension in variants: extension = canonical break return extension
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def parseTrackLog(line): """Parse trackLog line and return important fields: db, year, month, hgsid, and a list of tracks""" #### Sample line being processed #### # [Sun Mar 05 04:11:27 2017] [error] [client ###.###.###.##] trackLog 0 hg38 hgsid_### cytoBandIdeo:1,cloneEndCTD:2 #### splitLine = line.strip().split('trackLog') prefix = splitLine[0].split() month = prefix[1] year = prefix[4].replace("]","") suffix = splitLine[1].split() db = suffix[1] hgsid = suffix[2] if len(suffix) > 3: activeTracks = suffix[3] tracks = activeTracks.split(",") else: tracks = [] return db, year, month, hgsid, tracks
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import re def getWords(text): """From a text input as a string, get the words separated by a space and return it as a list of strings""" return re.compile('\w+').findall(text)
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def sqdist(point1, point2, rotmat): """ This routine calculates the anisotropic distance between two points given the coordinates of each point and a definition of the anisotropy. This method only consider a single anisotropy senario. Parameters ---------- point1 : tuple Coordinates of first point (x1,y1,z1) point2 : tuple Coordinates of second point (x2,y2,z2) rotmat : 3*3 ndarray matrix of rotation for this structure Returns ------- sqdist : scalar The squared distance accounting for the anisotropy and the rotation of coordinates (if any). """ dx = point1[0] - point2[0] dy = point1[1] - point2[1] dz = point1[2] - point2[2] sqdist = 0.0 for i in range(3): cont = rotmat[i, 0] * dx + \ rotmat[i, 1] * dy + \ rotmat[i, 2] * dz sqdist += cont * cont return sqdist
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def _is_path_within_scope(scope, fullpath): """Check whether the given `fullpath` is within the given `scope`""" if scope == '/': return fullpath is not None fullpath = fullpath.lstrip('/') if fullpath else '' scope = scope.strip('/') return (fullpath + '/').startswith(scope + '/')
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def age_interp(request): """Fixture for age_interp flag.""" return request.param
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def avoids(word, forbidden): """ Predicate that asks whether word avoids letters in the forbidden string """ # Feels like there should be a more efficient way to do this using # set intersection, but I'll just check the word character by character for letter in forbidden: if word.find(letter)!=-1: return False return True
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def get_vocabulary(path_to_vocab): """ Return a list of prefixes defining the vocabulary. """ vocab = [] with open(path_to_vocab) as f: for line in f: line = line.rstrip() vocab.append(line) return vocab
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def b_delta(rewards,states,alpha): """ Implements the Resorla-Wagner (delta) learning rule. V_intial is 0. Note: Null (0 or '0') states are silently skipped. Returns two dictionaries containing value and RPE timecourses, for each state. """ # Init s_names = set(states) V_dict = {} RPE_dict = {} for s in s_names: V_dict[s] = [0.] RPE_dict[s] = [] for r,s in zip(rewards,states): ## Skip terminal states if (s == 0) | (s == '0'): continue V = V_dict[s][-1] ## the Delta rule: RPE = r - V V_new = V + alpha * RPE ## Store and shift V_new to ## V for next iter V_dict[s].append(V_new) ## Store RPE RPE_dict[s].append(RPE) return V_dict, RPE_dict
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def get_weight_shapes(num_inputs, layer_sizes, num_outputs): """ adapted from original tf_model.get_weight_shapes() to convert from method to function """ weight_shapes = [] input_size = num_inputs for i, layer in enumerate(layer_sizes): weight_shapes.append((input_size, layer)) weight_shapes.append((layer,)) input_size = layer weight_shapes.append((input_size, num_outputs)) weight_shapes.append((num_outputs,)) return weight_shapes
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import warnings def format_channel_id(ch): """ Function for formatting an `idelib.dataset.Channel` or `SubChannel` for display. Renders as only the channel and subchannel IDs (the other information is shown in the rest of the table). :param ch: The `idelib.dataset.Channel` or `idelib.dataset.SubChannel` to format. :return: A formatted "channel.subchannel" string. """ try: if ch.parent: return f"{ch.parent.id}.{ch.id}" else: return f"{ch.id}.*" except (AttributeError, TypeError, ValueError) as err: warnings.warn(f"format_channel_id({ch!r}) raised {type(err).__name__}: {err}") return str(ch)
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def _IsBold(weight): """Is this weight considered bold? Per Dave C, only 700 will be considered bold. Args: weight: Font weight. Returns: True if weight is considered bold, otherwise False. """ return weight == 700
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def add_attributes(rsrc_id, manifest): """Add additional attributes to the manifest.""" proid = rsrc_id[0:rsrc_id.find('.')] environment = 'prod' updated = { 'proid': proid, 'environment': environment } updated.update(manifest) return updated
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def setup_walkers(cfg_emcee, params, level=0.1): """Initialize walkers for emcee. Parameters ---------- cfg_emcee: dict Configuration parameters for emcee. params: asap.Parameter object Object for model parameters. level: float, optional Returns ------- ini_positions: numpy array with (N_walker, N_param) shape Initial positions of all walkers. """ # Initialize the walkers if cfg_emcee['ini_prior']: # Use the prior distributions for initial positions of walkers. return params.sample(nsamples=cfg_emcee['burnin_n_walker']) return params.perturb(nsamples=cfg_emcee['burnin_n_walker'], level=level)
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def pack_4_4(x: int, y: int) -> int: """Pack two 4-bit values into an 8-bit value. x and y must be in range 0..15 inclusive. Result is in range 0..255 inclusive. """ assert 0 <= x <= 15 assert 0 <= y <= 15 return (x << 4) | y
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def _GetLibMetadata(layer): """ Return a dictionary of library-specific data found in layer.""" globalPrim = layer.GetPrimAtPath('/GLOBAL') if not globalPrim: raise Exception("Code generation requires a \"/GLOBAL\" prim with " "customData to define at least libraryName. GLOBAL prim not found.") if not globalPrim.customData: raise Exception("customData is either empty or not defined on /GLOBAL " "prim. At least \"libraryName\" entries in customData are required " "for code generation.") # Return a copy of customData to avoid accessing an invalid map proxy during # template rendering. return dict(globalPrim.customData)
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def build_system_info(platform=None, platform_type=None, accel_type=None, cpu_cores=None, cpu_type=None, cpu_sockets=None): """Information about the system the test was executed on. Args: platform (str): Higher level platform, e.g. aws, gce, or workstation. platform_type (str): Type of platform, DGX-1, p3.8xlarge, or z420. accel_type (str, optional): Type of accelerator, e.g. K80 or P100. cpu_cores (int, optional): Number of physical cpu cores. cpu_type (str, optional): Type of cpu. cpu_sockets (int, optional): Number of sockets Returns: `dict` with system info. """ system_info = {} if platform: system_info['platform'] = platform if platform_type: system_info['platform_type'] = platform_type if accel_type: system_info['accel_type'] = accel_type if cpu_cores: system_info['cpu_cores'] = cpu_cores if cpu_type: system_info['cpu_type'] = cpu_type if cpu_type: system_info['cpu_sockets'] = cpu_sockets return system_info
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import re def strip_spaces(string): """Remove white-space from a string Parameters ---------- string: str Returns ------- str """ pattern = re.compile(r'\s+') return re.sub(pattern, '', string)
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def hexint_parser(arg: str) -> int: """Parse a hexadecimal starting with 0x into an integer.""" if not arg.startswith("0x"): raise Exception("Received non-hex integer where hex expected") return int(arg, 16)
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def orbtell(orb): """Query current connection read-head position""" return orb.tell()
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import random def random_bbox(config): """Generate a random tlhw with configuration. Args: config: Config should have configuration including IMG_SHAPES, VERTICAL_MARGIN, HEIGHT, HORIZONTAL_MARGIN, WIDTH. Returns: tuple: (top, left, height, width) """ img_shape = config.IMG_SHAPES img_height = img_shape[0] img_width = img_shape[1] maxt = img_height - config.VERTICAL_MARGIN - config.HEIGHT maxl = img_width - config.HORIZONTAL_MARGIN - config.WIDTH t = int(random.uniform(config.VERTICAL_MARGIN, maxt)) l = int(random.uniform(config.HORIZONTAL_MARGIN, maxl)) h = config.HEIGHT w = config.WIDTH return t, l, h, w
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from datetime import datetime def from_epoch(seconds): """Given seconds since epoch, return a datetime object Args: seconds: Seconds since epoch Returns: datetime representation of seconds since epoch """ return datetime.utcfromtimestamp(float(seconds))
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def _word_feats(words): """ NLTK word feature generator for the NaiveBayesClassifier """ return dict([(word, True) for word in words])
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def build_machine(network=None, machine_type=None, preemptible=None, service_account=None, boot_disk_size_gb=None, disks=None, accelerators=None, labels=None, cpu_platform=None, nvidia_driver_version=None, enable_stackdriver_monitoring=None): """Build a VirtualMachine object for a Pipeline request. Args: network (dict): Network details for the pipeline to run in. machine_type (str): GCE Machine Type string for the pipeline. preemptible (bool): Use a preemptible VM for the job. service_account (dict): Service account configuration for the VM. boot_disk_size_gb (int): Boot disk size in GB. disks (list[dict]): List of disks to mount. accelerators (list[dict]): List of accelerators to attach to the VM. labels (dict[string, string]): Labels for the VM. cpu_platform (str): The CPU platform to request. nvidia_driver_version (str): The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator. enable_stackdriver_monitoring (bool): Enable stackdriver monitoring on the VM. Returns: An object representing a VirtualMachine. """ return { 'network': network, 'machineType': machine_type, 'preemptible': preemptible, 'serviceAccount': service_account, 'bootDiskSizeGb': boot_disk_size_gb, 'disks': disks, 'accelerators': accelerators, 'labels': labels, 'cpuPlatform': cpu_platform, 'nvidiaDriverVersion': nvidia_driver_version, 'enableStackdriverMonitoring': enable_stackdriver_monitoring, }
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def copy_event_attributes(ev1, ev2): """Copy all attributes from one roxar event to another. Args: ev1: roxar event to copy into ev2: roxar event to copy attributes from Returns: An updated version of ev1. Unaltered if the two events are not of same type. """ if ev1.type == ev2.type: for key in ev1.attribute_keys: ev1[key] = ev2[key] return ev1
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def group_by(object_list, key_function): """ Return dictionary of objects grouped by keys returned by `key_function` for each element in `object_list`. `object_list` does not need to be sorted. >>> group_by([1, 2, 3, 4, 5], lambda x: x % 2) {0: [2, 4], 1: [1, 3, 5]} """ groups = dict() for obj in object_list: key = key_function(obj) if key not in groups: groups[key] = list() groups[key].append(obj) return groups
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def mass_hpa_tail_boom( length_tail_boom, dynamic_pressure_at_manuever_speed, mean_tail_surface_area, ): """ Finds the mass of a tail boom structure of a human powered aircraft (HPA), following Juan Cruz's correlations in http://journals.sfu.ca/ts/index.php/ts/article/viewFile/760/718 Assumes a tubular tail boom of high modules (E > 228 GPa) graphite/epoxy :param length_tail_boom: length of the tail boom [m]. Calculated as distance from the wing 1/4 chord to the furthest tail surface. :param dynamic_pressure_at_manuever_speed: dynamic pressure at maneuvering speed [Pa] :param mean_tail_surface_area: mean of the areas of the tail surfaces (elevator, rudder) :return: mass of the tail boom [m] """ l = length_tail_boom q = dynamic_pressure_at_manuever_speed area = mean_tail_surface_area w_tb = (l * 1.14e-1 + l ** 2 * 1.96e-2) * (1 + ((q * area) / 78.5 - 1) / 2) return w_tb
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def find_first2(l, pred1, pred2): """ Find first occurrence in list satisfying two-step predicate. :param l: list. :param pred1: predicate on the list elements. :param pred2: predicate on two list elements. :return: index of first occurrence in list satisfying pred2(l[index-1], l[index]) or pred1(l[0]) if only one elment in the list; length of the list if not found. """ length = len(l) index = length if length > 0: if length == 1: if pred1(l[0]): index = 0 else: index = 1 else: for i in range(1, length): if pred2(l[i-1], l[i]): index = i break return index
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from datetime import datetime def meta_from_pid(product_id): """Extract metadata contained in a Landsat Product Identifier.""" meta = {} parts = product_id.split("_") meta["product_id"] = product_id meta["sensor"], meta["correction"] = parts[0], parts[1] meta["path"], meta["row"] = int(parts[2][:3]), int(parts[2][3:]) meta["acquisition_date"] = datetime.strptime(parts[3], "%Y%m%d") meta["processing_date"] = datetime.strptime(parts[4], "%Y%m%d") meta["collection"], meta["tier"] = int(parts[5]), parts[6] return meta
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import requests def check_status(datum): """Check that both the url and image link are valid URLs and that the image link isn't just a redirect. """ if requests.get(datum["url"], verify=False).status_code != 200: return False get_ = requests.get(datum["image"], verify=False) if get_.status_code != 200: return False if get_.url != datum["image"]: return False return True
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def recursive_find_xml_element( xmlnode, name, _nodes=None ): """ recursively finds all XML sub-elements with the name 'name', such as for nd in recursive_find_xml_element( xmlnode, 'TestList' ): pass """ if _nodes == None: _nodes = [] for nd in xmlnode: if nd.tag == name: _nodes.append( nd ) recursive_find_xml_element( nd, name, _nodes ) return _nodes
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from typing import Callable from typing import Union import torch from typing import Dict from typing import List from typing import Tuple from typing import Set from typing import Any def _apply_to_tensors( fn: Callable, container: Union[torch.Tensor, Dict, List, Tuple, Set] ) -> Any: """Recursively apply to all tensor in different kinds of container types.""" def apply(x: Union[torch.Tensor, Dict, List, Tuple, Set]) -> Any: if torch.is_tensor(x): return fn(x) elif isinstance(x, dict): return {key: apply(value) for key, value in x.items()} elif isinstance(x, (list, tuple, set)): return type(x)(apply(el) for el in x) else: return x return apply(container)
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def r10s(factor: float = 1) -> float: """ The horizontal screw spacing on the mounting rails of a 10-inch half rack. """ return 236.525 * factor
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import yaml def read_experiment_config(config_file): """ Read experiment configuration yml file for setting up the optimization. yml file contains the list of parameters, and whether each parameter is a fixed parameter or a range parameter. Fixed parameters have a value specified, and range parameters have a range specified. Parameters ---------- config_file : str File path for the experiment configuration file Returns ------- loaded_configs: dict """ # Load the experiment config yml file with open(config_file, "r") as yml_config: loaded_configs = yaml.safe_load(yml_config) # Format parameters for Ax experiment for param in loaded_configs.get("parameters", {}).keys(): loaded_configs["parameters"][param][ "name" ] = param # Add "name" attribute for each parameter # Parameters from dictionary to list loaded_configs["search_space_parameters"] = list(loaded_configs.get("parameters", {}).values()) return loaded_configs
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def unknown_labels(dim): """ The labels for the "unknown" basis. Just returns an empty list. Parameters ---------- dim : int Dimension Returns ------- list """ return []
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import torch from typing import Sequence from typing import cast def project_point_cloud_to_map( xyz_points: torch.Tensor, bin_axis: str, bins: Sequence[float], map_size: int, resolution_in_cm: int, flip_row_col: bool, ): """Bins an input point cloud into a map tensor with the bins equaling the channels. This code has been adapted from https://github.com/devendrachaplot/Neural-SLAM. # Parameters xyz_points : (x,y,z) pointcloud(s) as a torch.Tensor of shape (... x height x width x 3). All operations are vectorized across the `...` dimensions. bin_axis : Either "x", "y", or "z", the axis which should be binned by the values in `bins`. If you have generated your point clouds with any of the other functions in the `point_cloud_utils` module you almost certainly want this to be "y" as this is the default upwards dimension. bins: The values by which to bin along `bin_axis`, see the `bins` parameter of `np.digitize` for more info. map_size : The axes not specified by `bin_axis` will be be divided by `resolution_in_cm / 100` and then rounded to the nearest integer. They are then expected to have their values within the interval [0, ..., map_size - 1]. resolution_in_cm: The resolution_in_cm, in cm, of the map output from this function. Every grid square of the map corresponds to a (`resolution_in_cm`x`resolution_in_cm`) square in space. flip_row_col: Should the rows/cols of the map be flipped? See the 'Returns' section below for more info. # Returns A collection of maps of shape (... x map_size x map_size x (len(bins)+1)), note that bin_axis has been moved to the last index of this returned map, the other two axes stay in their original order unless `flip_row_col` has been called in which case they are reversed (useful as often rows should correspond to y or z instead of x). """ bin_dim = ["x", "y", "z"].index(bin_axis) start_shape = xyz_points.shape xyz_points = xyz_points.reshape([-1, *start_shape[-3:]]) num_clouds, h, w, _ = xyz_points.shape if not flip_row_col: new_order = [i for i in [0, 1, 2] if i != bin_dim] + [bin_dim] else: new_order = [i for i in [2, 1, 0] if i != bin_dim] + [bin_dim] uvw_points = cast( torch.Tensor, torch.stack([xyz_points[..., i] for i in new_order], dim=-1) ) num_bins = len(bins) + 1 isnotnan = ~torch.isnan(xyz_points[..., 0]) uvw_points_binned: torch.Tensor = torch.cat( ( torch.round(100 * uvw_points[..., :-1] / resolution_in_cm).long(), torch.bucketize( uvw_points[..., -1:].contiguous(), boundaries=uvw_points.new(bins) ), ), dim=-1, ) maxes = ( xyz_points.new() .long() .new([map_size, map_size, num_bins]) .reshape((1, 1, 1, 3)) ) isvalid = torch.logical_and( torch.logical_and( (uvw_points_binned >= 0).all(-1), (uvw_points_binned < maxes).all(-1), ), isnotnan, ) uvw_points_binned_with_index_mat = torch.cat( ( torch.repeat_interleave( torch.arange(0, num_clouds).to(xyz_points.device), h * w ).reshape(-1, 1), uvw_points_binned.reshape(-1, 3), ), dim=1, ) uvw_points_binned_with_index_mat[~isvalid.reshape(-1), :] = 0 ind = ( uvw_points_binned_with_index_mat[:, 0] * (map_size * map_size * num_bins) + uvw_points_binned_with_index_mat[:, 1] * (map_size * num_bins) + uvw_points_binned_with_index_mat[:, 2] * num_bins + uvw_points_binned_with_index_mat[:, 3] ) ind[~isvalid.reshape(-1)] = 0 count = torch.bincount( ind.view(-1), isvalid.view(-1).long(), minlength=num_clouds * map_size * map_size * num_bins, ) return count.view(*start_shape[:-3], map_size, map_size, num_bins)
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def check_sorted(a): """Determines if list is sorted.""" for i, val in enumerate(a): if i > 0 and val < a[i-1]: return False return True
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def extract_properties_values_from_json(data, keys): """Extracts properties values from the JSON data. .. note:: Each of key/value pairs into JSON conventionally referred to as a "property". More information about this convention follow `JSON Schema documentation <https://json-schema.org/understanding-json-schema/reference/object.html>`_. Passing ``data`` argument for an example: .. code-block:: python data = { 'verb': 'GET', 'endpoint': 'users', 'host': 'http://localhost:8080' ... } along with ``keys`` argument for an example: .. code-block:: python keys = ('verb', 'endpoint', 'host') Iterating over ``keys`` parameter values and extracts the property value of ``data`` parameter by key with the exact same value. Result: .. code-block:: python ('GET', 'users, 'http://localhost:8080') :param dict data: An arbitrary data. :param tuple|list|set keys: Iterable with values of type `str`. :returns: Packaged values. :rtype: `tuple` """ return tuple(data[key] for key in keys if key in data)
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def tcl_str(string: str = '') -> str: """ Returns Tcl string surrounded by {} :param string: Python string. """ return ' {' + string + '} '
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from datetime import datetime def create_identifier(hint: str = '') -> str: """ Can be used to create unique names for files by exploiting the uniqueness of the current date. Be aware that if two identifiers are created during the same second they are equal! Follows the form YYYY_MM_DD__hh_mm_ss. :return: YYYY_MM_DD__hh_mm_ss_{hint} """ now = datetime.now() dt_string = now.strftime("%Y_%m_%d__%H_%M_%S") return f"{dt_string}_{hint}" if hint else dt_string
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from typing import List def sieve(n: int) -> List[int]: """ A simple implementation of the http://en.wikipedia.org/wiki/Sieve_of_Eratosthenes :param n: Maximum value to search up to, not included. :return: List of primes upto but not including n. """ all_numbers = [True] * n for i in range(2, int(n ** 0.5 + 1)): if all_numbers[i]: for f in range(i * i, n, i): all_numbers[f] = False primes = [] for i in range(2, n): if all_numbers[i]: primes.append(i) return primes
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def isValidID(id: str) -> bool: """ Check for valid ID. """ #return len(id) > 0 and '/' not in id # pi might be "" return id is not None and '/' not in id
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import math def vershik_kerov_logan_shepp(n): """ Returns asymptotic value of ℓn for large n. For a permutation σ∈Sn, let ℓ(σ) denote the maximal length of an increasing subsequence in σ. Define ℓn = (1/n!) * ∑(σ∈Sn) ℓ(σ), the average value of ℓ(σ) for a σ chosen uniformly at random from Sn. Parameters ---------- n : int denotes n in vershik equation as stated above return : float returns float number denoting asymptotic value of ℓn. """ if(n != int(n)): raise ValueError( "n must be integer" ) return 2 * math.sqrt(n)
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def flip_corner(corner: tuple) -> tuple: """ Flip a tuple of a variable amount of sides :param corner: tuple with number of sides :return: flipped clock-wise tuple """ fliped_sides: list[str] = list() for s in corner: if s == 'N': fliped_sides.append('W') elif s == 'E': fliped_sides.append('S') elif s == 'S': fliped_sides.append('E') elif s == 'W': fliped_sides.append('N') return tuple(fliped_sides)
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def format_import(names): """Format an import line""" parts = [] for _, name, asname in names: if asname is None: parts.append(name) else: parts.append(name + " as " + asname) line = "import " + ", ".join(parts) + "\n" return line
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def count_leading_spaces(string: str) -> int: """ Count the number of spaces in a string before any other character. :param string: input string :return: number of spaces """ return len(string) - len(string.lstrip(" "))
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def replace_special_quotes(html_str: str): """ replace special quotes with html entities """ # special quotes html_str = html_str.replace('“', '&ldquo;') html_str = html_str.replace('”', '&rdquo;') html_str = html_str.replace('’', '&rsquo;') html_str = html_str.replace('‘', '&lsquo;') html_str = html_str.replace('„', '&sbquo;') html_str = html_str.replace('‚', '&obquo;') html_str = html_str.replace('‹', '&usbquo;') html_str = html_str.replace('›', '&ensquo;') return html_str
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def bash_array(lst): """Converts python array [a, b, c] to bash array (a b c)""" contents = ' '.join(str(x) for x in lst) return '({:s})'.format(contents)
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import re def get_length(s): """ Determine the length of the string from it's name which is prepended as: "foobar%d" % N """ x = re.search("[\d]+$", s) # there can be only one or no match here n = 0 if x : n = int(x.group(0)) return n
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from typing import Optional import re def _try_parse_port(port_str: str) -> Optional[int]: """Tries to extract the port number from `port_str`.""" if port_str and re.match(r"^[0-9]{1,5}$", port_str): return int(port_str) return None
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