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import re def replace_talents(talent_string, data): """Replaces the talents variable with the talent string given""" if "talents=" in data: data = re.sub( r'talents=.*', "talents={}".format(talent_string), data, 1) else: data.replace( "spec=shadow", "spec=shadow\nta...
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def shift_scale_loc(grid,loc): """ This fuction takes a location which is an array then backtransforms the shift and scaling applied to it in the process of estimation. """ loc_copy = loc.copy() if grid.dim == 2: loc_copy[0] = loc_copy[0]/grid.b0-grid.shifts[0] loc_copy[1] = loc_copy...
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import torch from typing import Tuple def get_pair_embedding( pair_info: torch.Tensor, embedding: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]: """ We are working with N pairs, the k'th pair is (a_k,b_k). Args: - pair_info: (N,6) array representing (bi,hi,wi, bj,hj,wj) ...
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def check_api(): """Test route to check if service is up and running Returns: str: message to indicate service status """ return "Sentiment Analysis API is up & running!"
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def varyansHesapla(dizi,ortalama): """Karmaşıklığı O(n)""" varyansdegeri = 0 for i in range(len(dizi)): varyansdegeri += (ortalama - dizi[i]) ** 2 return varyansdegeri / len(dizi)
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def join_array_dispatcher(*args, **kwargs): """Dispatcher for functions where first argument is a sequence.""" try: return args[0][0] except (TypeError, ValueError): # user passed an empty sequence, or something non-iterable # try to infer backend from first argument as fallback ...
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def TabSpacer(number_spaces, string): """Configuration indentation utility function.""" blank_space = ' ' return (blank_space * number_spaces) + string
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import os def get_icon_path(file_name): """ Get an icon path based on file name. All paths in the XBMLANGPATH variable processed to see if the provided icon can be found. :param str file_name: :return: Icon path :rtype: str/None """ for directory in os.environ["XBMLANGPATH"].split(os....
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def iroot(a, b): """Function to calculate a-th integer root from b. Example: iroot(2, 4) == 2 Parameters: a: int Root power b: int Number to calculate root from Returns: result: int Integer a-th root of b """ if b < 2: ...
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def get_values_matching_key(doc, key): """ Returns iterator of values in 'doc' with the matching 'key'. """ def _get_values(doc, key): if doc is not None: if key in doc: yield doc[key] for z in doc.items(): v = z[1] if isi...
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def lmap(f, x): """list(map(f, x)). Converts a map into a list containing (key,value) pairs.""" return list(map(f, x))
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def posix_get_last_error(space): """ posix_errno - Alias of posix_get_last_error """ """ posix_get_last_error - Retrieve the error number set by the last posix function that failed """ return space.newint(space.get_errno())
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import ast def redis_hgetall(duthost, db_id, key): """ Get all field name and values for a given key in given redis dataabse :param duthost: DUT host object :param db_id: ID of redis database :param key: Redis Key :return: A dictionary, key is field name, value is field value """ cmd =...
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def angle2NDE(angle): """ Converts an angle in degrees from an East due North coordinate system to a North due East coordinate system Calling this function again will convert it back, since: x = angle2NDE(angle2NDE(x)) Arguments: angle: [float] angle to be converted in degrees. Returns: ...
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def get_hostlist_by_range(hoststring, prefix='', width=0): """Convert string with host IDs into list of hosts. Example: Cobalt RM would have host template as 'nid%05d' get_hostlist_by_range('1-3,5', prefix='nid', width=5) => ['nid00001', 'nid00002', 'nid00003', 'nid00005'] "...
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def fib(n): """ Finding the Fibonacci sequence with seeds of 0 and 1 The sequence is 0,1,1,2,3,5,8,13,..., where the recursive relation is fib(n) = fib(n-1) + fib(n-2) :param n: the index, starting from 0 :return: the sequence """ n = n//1 if n>=1 else 0 # ensure n is non-negative integer if n>1: ...
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def delta_encode_values(df, total, scale=100): """Convert a dataframe from acres to delta-encoded integer scalar values, where original values are first scaled. This can be used to express percent where scale = 100. Values are packed into a caret-delimited string with 0 values omitted, e.g., '<bas...
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def celsius2kelvin(celsius): """ Convert temperature in degrees Celsius to degrees Kelvin. :param celsius: Degrees Celsius :return: Degrees Kelvin :rtype: float """ return celsius + 273.15
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def quick_FASTA_reader(file): """Simple FASTA reader, returning a list of string tuples. The single argument 'file' should be the filename of a FASTA format file. This function will open and read in the entire file, constructing a list of all the records, each held as a tuple of strings (the sequence n...
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def compare_svg( current, previous, up_color="default", down_color="default", neutral_color="default", ): """Compare current and previous value and return an SVG based on the result.""" colors = { "good": "#5e9732", "bad": "#c41230", "neutral": "#fdc010", "def...
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def create_variable(df, name, label, label_map, default_value=0): """ Create a new variable (column) in the specified dataframe. The label of this variable will be appended the global label map. Parameters ---------- df : pandas DataFrame dataframe to add variable/column to name...
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from typing import List def parse_dns(dns: bytes) -> List[bytes]: """Parse the output of grab_dns, returning a list of parsed values that we would like to search. :param dns: Output of grab_dns :type dns: bytes :return: A list of parsed values (Record Name, CNAME, A (HOST)) :rtype: List[bytes] ...
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def get_reference_columns(): """ return a test reference data column definition """ return { 'wavelength': { 'description': 'wavelength', 'required_column': True, 'unit': 'nm', 'type': 'float32', 'required_range': {'unit': 'nm', 'min':...
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import argparse def parse_args(): """ Parses arguments from the command line. """ parser = argparse.ArgumentParser(description='Extracts epitope annotations from mmCIF files.') # Arguments parser.add_argument('pdb_dir', help='Path to directory with mmCIF files.') parser.add_argument(...
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import re def normalise(s): """ Tokenize on parenthesis, punctuation, spaces and American units followed by a slash. We sometimes give American units and metric units for baking recipes. For example: * 2 tablespoons/30 mililiters milk or cream * 2 1/2 cups/300 grams all-purpose flour ...
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import re def fix_empty_methods(source): """ Appends 'pass' to empty methods/functions (i.e. where there was nothing but a docstring before we removed it =). Example: .. code-block:: python # Note: This triple-single-quote inside a triple-double-quote is also a # pyminifier self...
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def __deserialize_primitive(data, klass): """ Deserializes string to primitive type. """ try: return klass(data) except UnicodeEncodeError: return data # This might have to be marked as unicode somehow except TypeError: return data
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import collections def _sort_almost_sorted(almost_sorted_deque, key): """ Sort a deque like that where only the first element is potentially unsorted and should probably be last and the rest of the deque is sorted in descending order. :param collections.deque almost_sorted_deque: The deque of size n...
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import os def guess_realpath(path): """Checks for a file in a path, or in a local path""" basename = os.path.basename(path) # first test the path if os.path.isfile(basename): # try locally return os.path.realpath(basename) elif os.path.isfile(path): # good, it exists return os.pat...
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def _is_newer(path, ref): """ Tests whether path is newer than ref where ref is either another path or a date. >>> Path('/usr/bin/python').is_newer(0) True """ mtime = path.stat().st_mtime try: return mtime > ref except TypeError: try: return mtime > ref.timestamp exc...
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def disagreement_priority(info_dict, acc_bar=0.5): """ Everyone node points at the most different member that is not itself. Triggers if accuracies are high enough. """ refs = [] acc_list = info_dict["accuracy"] disagree_dict = info_dict["disagreement_rate"] for i in range(0, len(acc_lis...
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import torch def mix_irrep_cplx(w, z): """ Mix SO3part with complex weights. """ wr, wi = w.unbind(-1) zr, zi = z.unbind(-1) real = torch.matmul(wr, zr) - torch.matmul(wi, zi) imag = torch.matmul(wr, zi) + torch.matmul(wi, zr) return torch.stack([real, imag], -1)
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def mean_of_list(vals): """ avg value of a list :param vals: :return: """ return sum(vals)/float(len(vals)) if vals else 0
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def poi_vs_all(true_pep_iz, prep_result): """ true_pep_iz refers to the full set of all peptides. This function returns remapped values of true_pep_iz such that each peptide that is from a POI keeps its true_pep_i whereas all other peptides are remapped to class 0, ie "OTHER" """ df = prep...
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def is_collection_summary_editable(collection_summary, user_id=None): """Checks if a given user may edit an collection by checking the given domain object. """ return user_id is not None and ( user_id in collection_summary.editor_ids or user_id in collection_summary.owner_ids or ...
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import os def add_suffix(fullname, suffix): """ Add suffix to a full file name. """ name, ext = os.path.splitext(fullname) return name + '_' + suffix + ext
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def format_trade_flow(amount, unit, from_location, to_location, activity_type, flow_object, time, counter, mapping_dict): """ Model trade using a separate `transport activity <https://schema.org/TransferAction>`__. We need two ``flow`` instances for each trade: one is the production flow in the originating coun...
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import argparse import os def parse_user_arguments(*args, **kwds): """ Parses the arguments of the program """ parser = argparse.ArgumentParser( description = "Filter network", epilog = "@oliva's lab 2017") parser.add_argument('-n','--network_file',dest='network_file',action ...
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from typing import Dict from typing import Any import yaml import os def load_yaml_settings(yaml_file: str) -> Dict[str, Any]: """ Loads a standard YAML settings file. Any entry marked with a "$" sign is an environment variable. Parameters ---------- yaml_file Filename or full path to ...
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def count_less(count, a): """is a[0] shorter than a[1]?""" if len(a[0]) < len(a[1]): return count + 1 return count
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import json def dumps( data ): """Serializes the incoming object as a json string""" return json.dumps( data )
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def _check_filetype(filetype): """Checks that the filetype is compatible before trying to process it.""" return 'Mach-O' in filetype and 'ARM64' in filetype
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def is_required(param): """ :param param: :return: """ if "?" in param: return False else: return True
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def load(fl, normalise=False): """ load airfoil args: fl (str): filename kwargs: normalise (bool): flag determining whether the airfoil is normalised to unit length returns: [(x,y),...] airfoil point coordinates """ d = [] print("loading airfoil %s" % ...
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from pathlib import Path def is_filelike(obj): """Filename or file object? """ if isinstance(obj, (bytes, str, Path)): return False res = True for a in ("read", "tell", "seek"): res = res and hasattr(obj, a) if not res: raise ValueError("Invalid object passed as file") ...
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def _check_ncluster_nquestions(n_questions, n_pairs, n_clusters): """ Args: n_questions (int): n_clusters (int): n_pairs (int): Returns: boolean """ if n_questions > n_pairs: return False elif n_questions * n_clusters > n_pairs: return False ...
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def validate4(s,a): """validate4(s, a): for loop with generator and (l in a)""" for x in ((l in a) for l in s): if not x: return False return True
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def ids_from_names(ctx, names): """Given a list of string trait names, returns a dict, keyed by those string names, of the corresponding internal integer trait ID. :raises: ValueError when names is empty. :param ctx: designer_family.context.RequestContext object :param names: list of string trait ...
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def optparse_main(interface_object, local_argv): """Construct and execute an interface object""" optparse_cmd = interface_object() result = optparse_cmd(local_argv[1:]) return 0
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def list_uniq(seq, key=None): """ Removes duplicate elements from a list while preserving the order of the rest. >>> uniq([9,0,2,1,0]) [9, 0, 2, 1] The value of the optional `key` parameter should be a function that takes a single argument and returns a key to test the uniqueness. ...
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def neighbor_equality(w1, w2): """ Test if the neighbor sets are equal between two weights objects Parameters ---------- w1 : W instance of spatial weights class W w2 : W instance of spatial weights class W Returns ------- Boolean Notes ----- Only se...
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def _check_convert_version(tup): """create a PEP 386 pseudo-format conformant string from tuple tup""" ret_val = str(tup[0]) # first is always digit next_sep = "." # separator for next extension, can be "" or "." nr_digits = 0 # nr of adjacent digits in rest, to verify post_dev = False # are we ...
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def echo(sample: str): """ Sample GET request Returns: Echos back whatever was sent """ return sample
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import numpy as np def to_numpy_matrix(G, edge_sign = 1.0, not_edge_sign = 0.0): """ Returns the graph adjacency matrix as a NumPy matrix. Parameters ---------- edge_sign : float Sign for the position of matrix where there is an edge not_edge_sign : float Sign for the pos...
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def unpack_numpy(var, count, dtype, buff): """ create numpy deserialization code """ return var + " = numpy.frombuffer(%s, dtype=%s, count=%s)"%(buff, dtype, count)
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def role_edit(id=None): """ 编辑角色 """ return 'role/edit'
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def _cdp_split_single_times_read_aligns(split_alignment_dict, pos): """ Dict. of times a read aligns to all references {read: times aligned} """ srna_align_counts = {} for aligned_sRNAs in list(split_alignment_dict.values())[pos]: for aligned_sRNA, count in aligned_sRNAs.items(): ...
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def clean_location_text(text: str) -> str: """ Clean location before using fuzzy string match """ text = text.replace("แขวง", " ") text = text.replace("เขต", " ") text = text.replace("อำเภอ", " ") text = text.replace("ตำบล", " ") text = text.replace("ต.", " ") text = text.replace("ตฺ...
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def count_str(string): """ Build a dict of letter frequency for a string. :param string: :return: New dictionary. """ tt = {} for ch in string: tt[ch] = string.count(ch) return tt
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def svg_from_file(pathname): """ Read SVG string from a file """ f = open(pathname, 'r') svg = f.read() f.close() return(svg)
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import imghdr def detect_format_from_data(data): """Try to detect the format of the given binary data and return None if it fails.""" fmt = None try: if b'<svg' in data[:500]: fmt = 'svg' elif data.startswith(b'%PDF'): fmt = 'pdf' elif data.startswith(b'%!PS...
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def atom_to_csv(self): """Return Atom as a comma-separated string of its properties.""" return f"{self.chain},{self.atomid},{self.resid},{self.icode},{self.name}"
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import os from shutil import copyfile import shlex import subprocess def convert_to_wav(filename, output, sr=22050): """Convert a file to 16-bit 22050hz wav.""" base, ext = os.path.splitext(filename) if filename == output: backup = f"{base}-backup{ext}" copyfile(filename, backup) f...
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def drag_force(c_d,A,rho,v): """ Calculate drag force given c_d,A,rho,v: rho -> density of fluid A -> Frontal area c_d -> Drag coefficient v -> Velocity of bicycle """ return 0.5*c_d*rho*A*v**2
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import time def try_until(func, count=1, sleep=0.5): """ Tries to execute the specified function a number of times. @param func callable to execute @param count number of times to try (default 1) @param sleep seconds to sleep after failed attempts, if any (defaul...
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def docker_mem_used(container_id): """ Bytes of memory used from the docker container. Note: If you have problems with this command you have to enable memory control group. For this you have to add the following kernel parameters: `cgroup_enable=memory swapaccount=1`. See: https://docs.docker.com/e...
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import six def create_mashup_dict(image_meta): """ Returns a dictionary-like mashup of the image core properties and the image custom properties from given image metadata. :param image_meta: metadata of image with core and custom properties """ def get_items(): for key, value in six....
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def preprocess_data(df, target_map): """ General element-wise cleanup of full data set :return: df, cleaned data """ # Strip whitespace object_cols = df.select_dtypes(include=['object']).columns for col in object_cols: df[col] = df[col].apply(lambda x: str.strip(x)) # map targe...
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import click import configparser def get_token(config_auth): """ Extract token from auth config and do the checks config_auth: ConfigParser with loaded configuration of auth """ if config_auth is None: click.secho('Auth configuration not supplied!', err=True) exit(1) try: ...
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def convert_list_to_tuple(shp): """Check the type of the shape, if is list, convert to tuple""" if not isinstance(shp, (list, tuple)): raise ValueError(f"The shape variable should be a list or tuple, but got {type(shp)}") if isinstance(shp, list): shp = tuple(shp) return shp
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def _align_mask(value, mask): """ Alignment mask """ return ((value)+(mask))&~(mask)
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def get_wind_degrees(value): """ Returns the wind direction in degrees from a dict containing degrees and direction """ try: new_value = float(value['degrees']) except (TypeError, KeyError): return value return new_value
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def load_pretrained_word2vec(infile): """Load the pre-trained word2vec from file.""" if isinstance(infile, str): infile = open(infile) word2vec_list = {} for idx, line in enumerate(infile): if idx == 0: vocab_size, dim = line.strip().split() else: tks = l...
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import random def freq_mask(spec, F=30, num_masks=1, replace_with_zero=False): """ https://ai.googleblog.com/2019/04/specaugment-new-data-augmentation.html """ cloned = spec.copy() num_mel_channels = cloned.shape[0] #H for i in range(0, num_masks): f = random.randrange(0, ...
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import os def string_from_file(value): """ Read a string from a file or return the string unchanged. If the string begins with '@', the remainder of the string will be treated as a path to the file to be read. Precede the '@' with a '\' to treat it as a literal. """ assert isinstance(va...
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def strip_hash_bookmark_from_url(url): """Strip the hash bookmark from a string url""" return (url or '').split('#')[0]
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import subprocess def find_git_root(): """ Returns a string containing the absolut path to the tiscamera directory. Assumes a git checkout has been done. """ repo_dir = subprocess.Popen(['git', 'rev-parse', '--show-toplevel'], stdout=subprocess.PIPE).communicate()[0...
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def get_adjacents(i, j, matrix): """given a matrix and a couple of indices finds indexes of points adjacent to given input Args: i ([int]): [index of row] j ([int]): [index of column] matrix ([numpy array]): [matrix of measurements] Returns: [list]: [list of adjacent in...
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def get_conditions(xml_data_model, tag_name='nodeset', conditions='relevant', max_str=10): """ Get the conditional tag values that should be met before the tag under consideration should be checked :param xml_data_model: data model list read from ODK config (read_odk_data_model) :param tag_name: column ...
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from typing import Optional def get_fullname(namespace: Optional[str], name: str) -> str: """ Constructs a fullname from a namespace and a name. """ if namespace: return namespace + "." + name else: return name
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import os def xonsh_data_dir(env): """Ensures and returns the $XONSH_DATA_DIR""" xdd = os.path.expanduser(os.path.join(env.get('XDG_DATA_HOME'), 'xonsh')) os.makedirs(xdd, exist_ok=True) return xdd
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def to_sense_key(syn): """ Returns the sense key for the given synset. @param syn - Synset @return Corresponding sense key as string """ return syn.lemmas()[0].key()
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def generate_exploit() -> str: """This function returns the payload that will print `hacked`. Our payload should cause `run.py` to print out `hacked`. Warnings: 1. `run.py` should print `hacked`, and the testing will be case *sensitive* 2. This time, `run.py` must NOT crash Returns: ...
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def source2id(source_words, vocab): """ 将源文转化成id :param source_words: :param vocab: :return: """ ids = [] oovs = [] unk_id = vocab.UNK for w in source_words: i = vocab[w] if i == unk_id: if w not in oovs: oovs.append(w) oov_...
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from collections import Counter def fix_dup_names(names): """ :param names: :return: """ names_upper = [x.upper() for x in names] dup_names = {item: 0 for item, count in Counter(names_upper).items() if count > 1} renamed_names = [] for name in names_upper: if...
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import re def parse_logs(response): """ Parses the travis log. :params response: text from the ci log :return: dict that contains error information """ start = "FAILURE: Build failed with an exception." end = "BUILD FAILED" # capture the substring between two strings capture_error ...
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import os def make_dir(path_of_new_dir): """ Makes a directory at the given path. (> str) """ try: os.makedirs(path_of_new_dir) return path_of_new_dir except: return 'Error while making the new folder'
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def range_tag(value, min_value=0): """ tag that return a range """ if value: return range(min_value, value) return range(min_value)
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def can_import(name): """Attempt to __import__ the specified package/module, returning True when succeeding, otherwise False""" try: __import__(name) return True except ImportError: return False
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import os def postgres_uri() -> str: """Connection URI for PostgreSQL database.""" value = os.environ.get("POSTGRES_URI") if value: return value raise EnvironmentError('Required environment variable "POSTGRES_URI" is missing')
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import os import glob import shutil def _prepare_camera_detection(dataset_dir, camera_output_dir, id_): """Copy camera detection.""" camera_detection_path = os.path.join(dataset_dir, "detections", "camera") camera_new_path = os.path.join(camera_output_dir, f"{int(id_):06d}.txt") camera_old_path = list...
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def _find(root: dict, word: str) -> dict: """Find the node after following the path in a trie given by {word}. :arg root: Root of the trie. :arg word: A word. :returns: The node if found, {} otherwise. """ node = root for char in word: if char not in node: return {} ...
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import re def all_matches(iterable, pattern): """ Get all of the items that match a pattern. Args: iterable (Iterable[str]) pattern (str or regular expression) Returns: List[str] """ result = [] for string in iterable: match = re.search(pattern, string) ...
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import inspect def _methods_of(cls): """Get all callable methods of a class that don't start with underscore. :returns: a list of tuples of the form (method_name, method) """ # The idea of unbound methods exists in Python 2 and was removed in # Python 3, so "inspect.ismethod" is used here for Pyt...
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def reblock_by2(df, ntimes, c=None): """ Reblocks data according to “Error estimates on averages of correlated data”, H. Flyvbjerg, H.G. Petersen, J. Chem. Phys. 91, 461 (1989). """ newdf = df.copy() if c is not None: newdf = newdf[c] for i in range(ntimes): m = newdf.shape[0...
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def conv(x, h): """ Perform the convolution operation between two input signals. The output signal length is the sum of the lenght of both input signal minus 1.""" length = len(x) + len(h) - 1 y = [0]*length for i in range(len(y)): for j in range(len(h)): if i-j >= 0 and i-j < ...
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def diff(a1, a2, shift): """ Compute the diff after shifting array a2 by shift """ if len(a1) != len(a2): raise ValueError("Diff, input arrays must be same length, got {} and {}".format(len(a1), len(a2))) return a1[:(-shift)] - a2[shift:]
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from typing import Optional import random def make_monster_name(is_titan: Optional[bool] = False) -> str: """ Generate a normal boss's name Parameters ---------- is_titan : bool If the boss is a titan Returns ------- str The name of the boss """ # Boss is a t...
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import torch def _get_pyramid_gaussian_kernel() -> torch.Tensor: """Utility function that return a pre-computed gaussian kernel.""" return torch.tensor([ [1., 4., 6., 4., 1.], [4., 16., 24., 16., 4.], [6., 24., 36., 24., 6.], [4., 16., 24., 16., 4.], [1., 4., 6., 4., 1....
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def readme(): """Use README file as long_description""" with open('README.md') as readme_f: return readme_f.read()
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