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from datetime import datetime def _slurm_time_trans(timestr, _format="%Y-%m-%dT%H:%M:%S"): """ Fault tolerant time string translate to time obj and time stamps :param timestr: str. :param _format: Optional[str]. Default as "%Y-%m-%dT%H:%M:%S" used in sacct output :return: Tuple[Datetime, float]. ...
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from typing import Tuple def get_transfer_distance( client, start, end, mode='driving', ) -> Tuple[int, int]: """Get the distance and duration of a transfer. Args: client (Client): A googlemaps API client. start (string): The starting point, either lat,long as a...
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def get_size_string(size): """Return string representation of bytes""" # byte conversion numbers mbyte = 1024 ** 2 gbyte = 1024 ** 3 tbyte = 1024 ** 4 pbyte = 1024 ** 5 # convert to float size = float(size) # get string if size / pbyte > 1: result = '{:.1f} PB'.format(...
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import json def dump_json(file, array): """Dumps a dict to a JSON file""" with open(file, 'w') as f: return json.dump(array, f)
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def editTransSplits(splits, minTransLen): """ Called by transOrigin(), this function takes the splits that could be combined to create the current peptide, and sorts them in the required order for the rest of the algorithm to work. We want the longest split to be first in each pair, and we want the tupl...
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def is_test_name(name): """ Returns whether the given name should be collected as a test. Parameters ---------- name : `str` The test's name. Returns ------- is_test_name : `bool` """ if name == 'test': return True if name.startswith('test_'): ...
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def is_triangular(number: int) -> bool: """ Returns True if number is a triangular number: can be written as (s+1)*s/2 https://oeis.org/A000217 """ t = 0 i = 0 while t < number: i += 1 t += i if t == number: return True return False
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from datetime import datetime def _ms_to_iso8601(milliseconds): """Convert ms to ISO8601""" return datetime.fromtimestamp(int(milliseconds)).isoformat()
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from typing import Tuple import re import fnmatch def compile_patterns(patterns: Tuple[str, ...], flags=re.IGNORECASE, use_regex=False): """Compile regular expression (or glob) patterns with `re.compile`.""" if use_regex: return re.compile("|".join(patterns), flags=flags) return re.compile( ...
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def trim_dataset(mat, batch_size): """ trims dataset to a size that's divisible by BATCH_SIZE """ no_of_rows_drop = mat.shape[0]%batch_size if(no_of_rows_drop > 0): return mat[:-no_of_rows_drop] else: return mat
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def get_url_at_page_number(url: str, counter: int) -> str: """Retrieves the link to the next result page of a query.""" # All result pages will start out like this root_url = "https://www.hearthstonetopdecks.com/cards/" # Fhe first page of the query is followed by a string # describing your query o...
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def read_solver_outputs(solver, folder): """read solver iteration outputs from file.""" with open(folder / (solver + "_iter_outputs.txt"), "r", encoding="utf-8") as f: contents = f.readlines() return contents
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import io def image_data(img, format, **save_options): """Save a PIL Image instance and return its byte contents""" fp = io.BytesIO() img.save(fp, format, **save_options) fp.seek(0) return fp.read()
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def f(x, r): """ Implement the right-hand-side of the differential equation x' = r * x - x / (1 + x) """ return r * x - x / (1 + x**2)
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def convert_to_dict(passport: str) -> dict: """Convert a single passport row from the input into a dict.""" passport_dict = {} passport_split = passport[1:].split(" ") for field in passport_split: field_value = field.split(":") passport_dict[field_value[0]] = field_value[1] ret...
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def parse_list(list_str): """Parse comma-separated list""" if list_str.strip(): return [t.strip() for t in list_str.split(',') if t.strip()] else: return []
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def check_possible_win(piece, win, board_state): """Returns a bool depending on if a win with a given piece is on the board""" # Check if the given piece has the winning combination on board for square in win: if "{}{}".format(piece, square) not in board_state: return False ...
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import re import requests def isbn(bot, trigger): """Look up a book by its ISBN.""" if not re.match( r"((978[\--– ])?[0-9][0-9\--– ]{10}[\--– ][0-9xX])|((978)?[0-9]{9}[0-9Xx])", trigger.group(2)): return bot.reply("I need a valid ISBN.") isbn_sanitized = trigger.group(2).repla...
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import re def split_problematic_endpoints_line(line): """ If the line of host contains more than one ":", for example: 10.99.184.69:900010.37.170.125:9006 this splits the line and return a list of correct endpoints Args: ``line``: the problemtic line which contains more than one endpoint ...
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def get_max_label_map_index(label_map): """Get maximum index in label map. Args: label_map: a StringIntLabelMapProto Returns: an integer """ return max([item.id for item in label_map.item])
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def list_unique(items): """ Given a list, return a new list with the unique items in order from the original list """ uniq = set() return [i for i in items if str(i) not in uniq and (uniq.add(str(i)) or True)]
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import torch def tile_and_concat(tensor: torch.Tensor, vector: torch.Tensor) -> torch.Tensor: """Merge 1D and 2D tensor (use to aggregate feature maps and representation and compute local mutual information estimation) Args: tensor (torch.Tensor): 2D tensor (feature maps) vector (torch.Te...
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def get_response_content(content_items): """ :param content_items: {} :return: { "content":[ citem1,citem2,...] } """ result = {} c = [] for item in content_items: c.append(item) result['content'] = c return result
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import json def get_config(server, path="connection.config"): """ Static method to get the configuration for the server connection :param server: name of server to connect to :type server: String :param path: path of the configuration file :type path: String :return: hostname, port :r...
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def trimBytes(bs): """ Trims trailing zeros in a byte string """ n = bs.find(b'\0') if n != -1: return bs[:n] return bs
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def get_function_names(module, prefix): """Get function names with a certain prefix from a module.""" return [fun for fun in dir(module) if fun.startswith(prefix)]
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def be16_to_native(data, signed=False) -> int: """ Unpacks a bytes-like object respecting big-endianness of outside world and returns an int according to signed. Args: data: bytes-like object. The data to be unpacked & converted signed (bool): Whether or not `data` is signed """ return ...
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def nonZeroMean(arr): """Takes the mean of an array not counting None or 0 values.""" total = 0 count = 0 for x in arr: if x is not None and x != 0: total, count = total + x, count + 1 count = 1 if count == 0 else count return round(total / count, 2)
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def calc_zeta_induced_quasisteady(E, x): """ Induced zeta potential (quasi-steady limit) """ zeta_induced_quasisteady = E*x return zeta_induced_quasisteady
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def get_entity_by_type_and_id(entity_type, entity_id): """Return the datastore object with the given type and id if it exists.""" if not entity_id or not str(entity_id).isdigit() or int(entity_id) == 0: return None return entity_type.get_by_id(int(entity_id))
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def GetNodeText(node): """Returns the node text after stripping whitespace.""" return node.text.strip() if node.text else ''
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def load_patients_ids(ids_file_path): """Loads patient ids from a file in which ids are separated by a new line """ with open(ids_file_path) as file: lines = file.readlines() patients_ids = [line.strip() for line in lines] return patients_ids
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def _get_variance(color_count: dict, average: float) -> float: """ Compute the variance :param color_count: Number of each color in the tile :param average: Average pixel color in the tile :return: Variance """ variance = 0.0 for pixel in color_count: a = pixel - average ...
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def is_valid_password(password): """ Validates password complexity - min length 6 - min one upper case - min one lower case - min one special char :param password: the password in question """ upper = lower = special = False for char in password: if not upper and char.i...
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def clean_record_id(seq_record): """ cleans up the record ID if there is a "/" :return: a str with clean id """ if "/" in seq_record.id: clean_id = str(seq_record.id) clean_id = clean_id.split('/')[0] else: clean_id = seq_record.id return clean_id
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import math def dist(p1, p2): """ Calculates the euclidean distance between two cartesian points given as tuples :param p1: Point 1 as a tuple :param p2: Point 2 as a tuple :return: Distance between points 1 and 2 """ return math.sqrt((p1[0] - p2[0])**2 + (p1[1] - p2[1])**2)
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def tuples_to_spans(tree): """ Returns list of spans, that are (start, size). """ result = [] def helper(tr, pos=0): if isinstance(tr, str): return 1 size = 0 for x in tr: subsize = helper(x, pos=pos+size) size += subsize result.a...
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def untabify(text, width): """Replace tabs with spaces in text.""" def next_stop(p): return width * ((p + width) // width) def pad(p): return ' ' * (next_stop(p) - p) out = list(text) pos = 0 for cur, c in enumerate(out): if c == '\t': out[cur] = pad(pos) ...
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def split_filters(name): """ Examples: >>> split_filters("a.b.c") ('a.b.c', []) >>> split_filters("a.b.c|upper|strict") ('a.b.c', ['upper', 'strict']) >>> split_filters("|upper|strict") ('', ['upper', 'strict']) >>> split_filters("") ('', []) "...
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from typing import Tuple def get_fields_for_plot(cloudnet_file_type: str) -> Tuple[list, int]: """Return list of variables and maximum altitude for Cloudnet quicklooks. Args: cloudnet_file_type (str): Name of Cloudnet file type, e.g., 'classification'. Returns: tuple: 2-element tuple con...
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def qsize(queue): """Get the (approximate) queue size where available. Parameters ---------- queue : :class:`queue.Queue` Input queue. Returns ------- int Queue size, -1 if `qsize` method isn't implemented (OS X). """ try: return queue.qsize() except No...
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def pad(f_bytes, mod_len): """ Pads the file bytes to the nearest multiple of mod_len """ return f_bytes + (b'0' * (mod_len - len(f_bytes) % mod_len))
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def swap_bytes(data_str): """Accepts string with hex, returns integer with order swapped for CAN.""" a = int(data_str, 16) return ((a & 0xff) << 24) + ((a & 0xff00) << 8) + ((a & 0x00ff0000) >> 8) + ((a & 0xff000000) >> 24)
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def set_config_var(from_file, from_env, default): """ Set a configuration value based on the hierarchy of: default => file => env :param from_file: value from the configuration file :param from_env: value from the environment :param default: default configuration value :return: value to...
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import six def isstring(obj): """Python 2/3 compatible string check""" return isinstance(obj, six.string_types)
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def ids_from_sentence(vocabulary, sentence): """ Convenience method, for converting a sequence of words to ids. :param vocabulary: Language, object of the language to use the look up of. :param sentence: string, a tokenized sequence of words. :return: list, containing the ids (int) of the sentence i...
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def area_over_choked_area( mach, gamma=1.4 ): """ Gives A/A^* (where A^* is "A-star"), the ratio of cross-sectional flow area to the cross-sectional flow area that would result in choked (M=1) flow. Applicable to 1D isentropic nozzle flow. Args: mach: Mach number [-] ga...
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def split_training_test(document_pairs): """ Given a list of things, split them into training and test. Returns a pair of lists: training, test. Simplest split: every 10th thing is in the test set. """ training = [] test = [] for i, pair in enumerate(document_pairs): if i % 10 =...
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def from_disk(session, schema, path, depth=0, extension=None): """Return a DataFrame object from files read. Arguments: session -- SparkSession object schema -- data types for each column path -- location where files are stored Keyword arguments: depth -- depth of directory tr...
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import random def gen_rand_seq(length): """ Generate a random DNA sequence of defined length Parameters ---------- length : int Returns --------- seq : string Random DNA sequence """ nt = ['A','T','C','G'] #nucleotides seq = ''.join(random.choice(nt) for...
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def vhost_delete_controller(client, ctrlr): """Delete vhost controller from configuration. Args: ctrlr: controller name to remove """ params = {'ctrlr': ctrlr} return client.call('vhost_delete_controller', params)
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from pathlib import Path import yaml def get_fhir_version_from_sushi_config(base_path: Path) -> str: """ Get the FHIR version from the SUSHI config file. :param base_path: Path to the SUSHI config file :return: FHIR version string """ conf_filename = base_path / "sushi-config.yaml" if not...
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def _list_product(lst): """Computes product of element of the list.""" result = 1 for item in lst: result *= item return result
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import json def json_to_dict(filename): """ Simplify json loading """ with open(filename, "rb") as json_file: object = json.load(json_file) return(object)
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def produced_files(nhosts, jobid, njobtasks): """ Associates file (to be written) to each job ID :param nhosts: total number of hosts :param jobid: job ID :param njobtasks: N of tasks per job :return: hosts_files: list of files (and associated host) for this jobID """ return [( ...
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def _auth_post(self, url, body, return_response=False, **kwargs): """Synchronous POST request. Used as standard over async currently. If return_response == True, the response object is returned rather than its .json() output. Any additional kwargs are forwarded onto the requests.post(). """ r =...
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def Getp2(M_0, M_1, M_2): """ Consider a two-body decay :math:`M_0\\rightarrow M_1M_2`. In the rest frame of :math:`M_0`, the momentum of :math:`M_1` and :math:`M_2` are definite. :param M_0: The invariant mass of :math:`M_0` :param M_1: The invariant mass of :math:`M_1` :param M_2: The invaria...
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def get_id_key(entity_name): """Get entity id key. Follows the simple convention that *id_key* is the *entity_name* followed by '_id'. Args: entity_name (str): entity_name Return: id_key (str) .. code-block:: python >>> from utils.db import get_id_key >>> ent...
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def plot_grid(flood, grid): """ Plot grid over flood image. Parameters ---------- flood : GeoDataFrame grid : GeoDataFrame """ ax = grid.plot(color='yellow'); return flood.plot(ax=ax, color='black', alpha=0.5);
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from typing import IO def _isatty(stream: IO) -> bool: """Returns ``True`` if the stream is part of a tty. Borrowed from ``click._compat``.""" # noinspection PyBroadException try: return stream.isatty() except Exception: return False
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import re def search_matches(match_list, search_list, ignore_list=None): """ Return list of football matches that match search """ if ignore_list is None: ignore_list = [] search = re.compile('|'.join(search_list)) my_matches = [m for m in match_list if search.search(m['fixture'])] ...
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import ntpath def win_to_cygwin_path(path): """ Converts a Windows path to a Cygwin path. :param path: Windows path to convert. Must be an absolute path. :type path: str :returns: Cygwin path. :rtype: str :raises ValueError: Cannot convert the path. """ drive, path = ntp...
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def get_related_model(model, relation_field_name): """ Get the related model of the (presumed) relation field with the given name on the given model. :param type model: The model class to inspect the field on. :param str relation_field_name: The field name of the (presumed) relation ...
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def _decode(encoded): """Decode a string into utf-8 :param encoded: Encoded string :type encoded: string :return: Decoded string :rtype: string """ if not encoded: return "" decoded = encoded.decode('utf-8') if decoded.endswith('\n'): decoded = decoded[:-1] retur...
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import csv def rd_csv(fname): """ read rows from csv file as list of dicts """ with open(fname) as fin: rdr = csv.DictReader(fin) return [dict(row) for row in rdr]
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import torch def rgba_to_rgb(rgba: torch.Tensor): """ Converts tensor from 3 channels into 4. Multiplies first 3 channels with the last channel. [... 4 H W] -> [... 3 H W] """ return rgba[..., :-1, :, :] * rgba[..., -1:, :, :]
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def ensure_string(data): """Ensure the data are decoded to a string if they are bytes. Parameters ---------- data : str or bytes """ if isinstance(data, str): return data elif isinstance(data, bytes): return data.decode("ascii", "replace") else: raise TypeError(f...
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def get_oldest(fromlist): """ get_oldest(fromlist) where fromlist is a list of DataObjects Get the oldest timestamp out of all the timestamps in the DataObject list. """ oldest_timestamp = fromlist[0].data[0][1] #take the first timestamp from the first DataObject in the fromlist list for obj in fromlist: ...
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import textwrap def fill(text, width): """Wraps each paragraph in text (a string) so every line is at most width characters long, and returns a single string containing the wrapped paragraph. """ width = int(width) paras = text.replace("\r\n","\n").replace("\r","\n").split("\n\n") wrapped ...
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def create_labels(sizes): """create labels starting at 0 with specified sizes sizes must be a tuple """ labels = [] for i, size in enumerate(sizes): labels += size*[i] return(labels)
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def filtered(alert, rules): """Determine if an alert meets an exclusion rule :param alert: The alert to test :param rules: An array of exclusion rules to test against :returns: Boolean - True if the alert should be dropped """ return any(rule(alert) for rule in rules)
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def build_like(operator="AND", **kwargs): """Generates an SQL WHERE string. Will replace None's with IS NULL's. Keyword Args: Containing SQL search string Eg: ``{"foo": "x", "bar": None}`` Returns: Tuple containing string that can be used after LIKE in SQL statement, ...
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def merge_dicts(*dicts): """return dict created by updating each dict in sequence, last key wins""" result = {} for d in dicts: result.update(d) return result
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import time def get_current_timestamp() -> float: """ 获取当前时间戳 :return: """ return time.time()
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def _all_done(fs, download_results): """ Checks if all futures are ready or done """ if download_results: return all([f.done for f in fs]) else: return all([f.success or f.done for f in fs])
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import random import string def random_string(length=6): """Return a random upper-case string of given length. :param length: length of string to return. """ return ''.join(random.choice(string.ascii_uppercase) for _ in range(length))
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def subj_object_provider(subj_name, subj_dict): """ Convenience function version of the subject_dict, to be turned into a nipype node. Parameters ---------- subj_name : str subject ID subj_dict : dict Dictionary of explore.hf subject objects Returns ------- subj...
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def generate_symbol(registers, polynomials, K): """Convolutionally encode one bit of data, output the encoded symbol""" # NOTE: EXPECTS registers FORMAT SUCH THAT LEFTMOST BIT IS MOST RECENT xor = 0 symbol = '' # for each symbol bit for p in polynomials: xor = 0 # for each memory stage for k in...
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def trailing_whitespace(editor, item): """ Pylint method to fix trailing-whitespace error """ line_no = item.line_no repaired_line = editor.lines[line_no].rstrip() loc = (line_no, line_no + 1) editor.replace_range(loc, [repaired_line]) return (line_no, 0)
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import requests def get_dois(issn, from_year, to_year): """ Returns a list of DOIs for a particular timeframe. """ dois = [] url = f"https://api.crossref.org/journals/{issn}/works?rows=500&filter=from-pub-date:{from_year}-01-01,until-pub-date:{to_year}-01-01&mailto=team@ourresearch.org" r = re...
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def _get_exported_include_tree(dep): """ Generate the exported thrift source includes target use for the given thrift library target. """ return dep + "-thrift-includes"
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def attribute_lca_map(tree, leaf_graph): """ Lowest common ancestor of `i` and `j` for each edge :math:`(i, j)` of the leaf graph of the given tree. Complexity: :math:`\mathcal{O}(n\log(n)) + \mathcal{O}(m)` where :math:`n` is the number of nodes in `tree` and :math:`m` is the number of edges in :attr:...
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import random def _loader(uris_data: list, target: int, original: int) -> list: """ Given a target load size, sample from the URIs list to generate the load required""" if target > original: load = _loader(uris_data, target - original, original) target = original else: load = [] ...
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async def check_archon(command, spectro: str): """Check the archon CCD status""" # Check that the configuration of archon controller has been loaded. archon_cmd = await (await command.actor.send_command("archon", "status")) if archon_cmd.status.did_fail: return "Failed getting status from the co...
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def to_tf(input): """ Transform to tensorflow order of dimensions with channel last. :param input: np array :return: channels last """ return input.transpose(0, 2, 3, 1)
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def get_character(context, character_name): """ Get character from context :param context: context :param character_name: name of character :type character_name: string .. versionadded:: 0.8 """ characters = [x for x in context.characters if x.name == character_name] ...
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import itertools def get_nonredun_dict_key_pairs(in_dict): """Take a dict and return a list of all unique two-key combinations of keys of the dict. """ # Don't modify the dict if there is only one key. if len(in_dict.keys()) == 1: return in_dict # Copy the input dict. in_dict2 = i...
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from typing import List import csv from io import StringIO def split_token(token: str) -> List[str]: """ Splits tokens separated by ";". If the resulting values have semicolons, the values must be quoted. >>> split_token('"foo";"bar;far"') ['foo', 'bar;far'] """ stream = csv.reader(Strin...
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def _format_column(column, places=4): """ Given a column from the table, converts it to a nicely formatted string and returns it. The column can be float, int, bool or a string. Strings are returned untouched. """ if isinstance(column, float): column = ("%%.%dg" % places) % column e...
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def sign(a) : """Helper returning the sign of a """ return (a>0) - (a<0)
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def gen_unknown_filter(skip_unknown = False): """ Generation of a SPARQL Filter clause to exclude unknown edge type Produces something like FILTER( ?controlType = "ACTIVATION"^^xsd:string || ?controlType = "INHIBITION"^^xsd:string) """ if skip_unknown == True: return 'FILTER( ?contr...
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def build_kwargs(registry_id): """ Builds a kwargs dict which may contain the optional registryId. :param registry_id: Optional string containing the registryId. :return: kwargs dict with registryId, if given """ if not registry_id: return dict() else: return dict(registryId...
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def rindex_list(elem, l): """Return the index of the rightmost element in list.""" return len(l) - list(reversed(l)).index(elem) - 1
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def convertToClass(predictions): """ Given a set of network outputs, returns class predictions by thresholding them. """ return (predictions >= 0.5) * 1
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import json def jsonify(topic, msg): """ json encode the message and prepend the topic """ return topic + ' ' + json.dumps({'message':msg})
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import torch def earth_mover_distance(input: torch.Tensor, target: torch.Tensor, r: float = 2): """ Batch Earth Mover's Distance implementation. Args: input: B x num_classes target: B x num_classes r: float, to penalize the Euclidean distance between the CDFs Returns: """...
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import pickle def read_pickled_file(filename): """ Returns the contents of `filename` if it exists and can be parsed by pickle. Returns `None` if file cannot be read. """ try: with open(filename, 'rb') as f: return pickle.load(f) except: return None
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import random def rand100() -> int: """Returns a random integer within [0, 100).""" return random.randrange(0, 100)
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def _insertion_cost(distances, previous_node, next_node, inserted_node): """Calculates insertion costs of inserting a node into a tour. Args: distances: A distance matrix. previous_node: The node before the inserted node. Can be a vector. next_node: The node after the inserted node. Can be a vector. ...
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def convert_size(free, total, mode): """ Takes free and total size and coverts them based on conversion mode free - returns free total - returns total used - returns difference between total and free pfree - returns free as percentage of total pused - returns used as percentage of total ...
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