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def makeup(_x, n): """ Increase the length of _x to be n by duplicating some elements :param _x: input length :param n: output size :return: list of length n with all original and additional duplicate elements from _x """ x = [] for i in range(n): x.append(_x[i % len(_x)]) re...
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from pathlib import Path def temp_paths_1(tmp_path_factory): """ Makes temporary directories, for testing bak_to_git_1, and populates them with test files. Returns pathlib.Path objects for each. """ temp_path: Path = tmp_path_factory.mktemp("baktogit1") bak_path = temp_path / "_0_bak" bak_...
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def _adjugate(M, method="berkowitz"): """Returns the adjugate, or classical adjoint, of a matrix. That is, the transpose of the matrix of cofactors. https://en.wikipedia.org/wiki/Adjugate Parameters ========== method : string, optional Method to use to find the cofactors, can be "bar...
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def boundary(graph, subgraph): """ Get the nodes in the subgraph that have neighbors in the graph but not in the subgraph. This is useful for conditionally styling nodes at the boundary of a subgraph. For example: :: boundary = nxv.boundary(graph, subgraph) style = nxv.Style(node=lamb...
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def hh_mm(time_struct, twelve_hour=True): """ Given a time.struct_time, return a string as H:MM or HH:MM, either 12- or 24-hour style depending on twelve_hour flag. """ postfix = "" if twelve_hour: if time_struct.tm_hour > 12: hour_string = str(time_struct.tm_hour - 12) # 13-...
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from typing import Iterable from typing import Callable def indexOf(items: Iterable, match: Callable, *args): """Returns the index of the first item for which the `match` function returns True.""" for idx, item in enumerate(items): if match(item, *args): return idx
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def merge_two_dicts(x, y): """ Merges 2 dictionary. Overrides values from x with values from y, if key is the same. Needed for Python < 3.5 See: https://stackoverflow.com/a/26853961 :param x: :param y: :return: """ z = x.copy() # start with x's keys and values z.update(y)...
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def count_lines(input_filepath): """Count number of non-empty lines in file.""" counter = 0 with open(input_filepath, 'r', encoding='utf-8') as input_str: for line in input_str: if line.strip(): counter += 1 return counter
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def get_metal_bonds(mol, metal_atoms): """ Return a list of bonds in molecule that contain metal atoms. """ metal_bonds = [] ids_to_metals = [] for bond in mol.get_bonds(): if bond.get_atom1() in metal_atoms: metal_bonds.append(bond) ids_to_metals.append(bond.ge...
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def speed_section_bot(speed_limit_bot, D_bot, D): """ Calculates the section speed of vapor at the bottom Parameters ---------- speed_limit_bot: float The limit speed of the vapor at the bottom of column, [m/s] D_bot : float The calculating bottom diameter of column, [m] D :...
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def minutes_to_seconds(minutes: str) -> int: """ Converts minutes to seconds Arguments: minutes: The number of minutes to be converted to seconds. Returns: The number of seconds. """ return int(minutes)*60
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def make_allowed_registries(registry_list): """ turns a list of wildcard registries to allowedRegistriesForImport json setting """ return { "allowedRegistriesForImport": [ {'domainName': reg} if isinstance(reg, str) else reg for reg in registry_list ] }
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def is_one_to_one(d): """ (dict of {str: int}) -> bool Return True if and only if no two of d's keys map to the same value. >>> is_one_to_one({'a': 1, 'b': 2, 'c': 3}) True >>> is_one_to_one({'a': 1, 'b': 2, 'c': 1}) False >>> is_one_to_one({}) True """ values = [] ...
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def crop_from_right(sequence_string, crop_length): """ return a sequence string without last crop_length characters drops values at end ie chops off right side if crop_length > length sequence_string --> returns "" if crop_length <= 0 returns string """ if (crop_length <= 0): return ...
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from functools import reduce from operator import mul def _geom_mean(growth_list, weights): """Computes weighted geometric mean.""" weighted = [g**w for g, w in zip(growth_list, weights)] gmean = reduce(mul, weighted)**(1 / sum(weights)) return gmean
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def get_tensor_name(subgraph, tensor_idx): """Get the tensor name. Parameters ---------- subgraph: tflite.Subgraph.Subgraph tensor: tensor index in subgraph Returns ------- tensor name in UTF-8 encoding """ return subgraph.Tensors(tensor_idx).Name().decode(...
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def firstEmail(m, d): """ Engage stores emails and phone numbers in the 'contacts' section of a supporter record. This function finds the first email. If there's not an email record, then we'll return a None. Parameters: m dict supporter record d string default value ...
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def warc_datetime_str(date): """Amendedment to warctools' function to fix non-ISO8601 output.""" iso = date.isoformat() if "." in iso: iso = iso[:iso.find(".")] if "+" in iso: iso = iso[:iso.find("+")] return iso + "Z"
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def exists_key_in_dicts_list(dict_list, key): """From a list of dicts, checks if a certain key is in one of the dicts in the list. See also https://stackoverflow.com/questions/14790980/how-can-i-check-if-key-exists-in-list-of-dicts-in-python Parameters ---------- dict_list: list A list of...
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import hashlib def numeric_hash(string, digest_size=4): """ Returns an integer hash of a string. Args: string: str -- String to hash digest_size: int -- Size of the digest in bytes. Max is 16. Returns: int """ return int(hashlib.md5(string.encode("utf-8")).hexdigest()[...
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def generate_parameterized_path( test_rate=0, random=False, n_negative=100, by_user=False ): """Generate parameterized path. Encode parameters into path to differentiate different split parameters. Args: by_user (bool): split by user. test_rate (float): percentage of the test data. ...
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def convert_to_list(value): """ Creates a list argument from command line. Arguments: value : The keyword argument from command line Returns: None if the string none is found list if the string is space seperated values is found """ if value == 'None': return No...
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def instrument_to_insCode(instrument): """Given a pretty_midi.Instrument object, returns a concise string code representing its program number & its is_drum parameter. Parameters ---------- instrument : pretty_midi.Instrument object of pretty_midi.Instrument class. Returns ------- ...
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def construct_package_url(base_url, dist, arch, sha256): """ Construct a package URL for a debian package using the 'by-hash' path. See: https://wiki.debian.org/DebianRepository/Format#indices_acquisition_via_hashsums_.28by-hash.29 Example: http://us.archive.ubuntu.com/ubuntu/dists/bionic/by-hash/SHA25...
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import importlib def get_trainer(name, **trainer_args): """ Factory function for retrieving a trainer. """ module = importlib.import_module('.' + name, 'mldas.trainers') return module.get_trainer(**trainer_args)
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import re def is_docker() -> bool: """ Look into cgroup to detect if we are in container """ path = "/proc/self/cgroup" try: with open(path, encoding="utf-8") as file: for line in file: if re.match(r"\d+:[\w=]+:/docker(-[ce]e)?/\w+", line): r...
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def JD2epochJulian(JD): #--------------------------------------------------------------------- """ Convert a Julian date to a Julian epoch :param JD: Julian date :type JD: Floating point number :Returns: Julian epoch :Reference: Standards Of Fundamental Astronomy, http://www.iau-sofa.rl.ac.u...
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def is_midnight(dt): """ Determines if given datetime object is set to midnight. """ return dt.hour == 0 and dt.minute == 0 and dt.second == 0
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def set_outputs_key_for_list_recipient_and_sender(args): """ This function checks which argument used and returns it for the outputs prefix. Args: args: The recipient list or the sender list. Returns: The recipient list or the sender list, depending on what was used. """ return a...
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def split_tokenize(text): """Splits tokens based on whitespace after adding whitespace around punctuation. """ return (text.replace('.', ' . ').replace('. . .', '...') .replace(',', ' , ').replace(';', ' ; ').replace(':', ' : ') .replace('!', ' ! ').replace('?', ' ? ').replace('(...
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import re def _remove_prefix_username(text: str) -> str: """removes twitter style usernames at the start of the tweet""" p_text = text while re.search(r'^@[a-zA-Z0-9_]{1,15}', p_text): p_text = re.sub(r'^@[a-zA-Z0-9_]{1,15}\s*', '', p_text) return p_text
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def title(fields, __): """ Assign a title to the document. This is metadata only; nothing is added to the body text. """ return [], {'title': fields[0]}
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def _filter_files(adir, filenames, filecnt, file_type, ffilter): """ Filter files by file type(filter function) then returns matching files and cumulated count. """ rfiles = ffilter(adir, filenames) filecnt += len(rfiles) return rfiles, filecnt
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def get_datapoints(target_rps=500, rps_min=50, rps_max=20000, increment=50, exponent=0.5): """Get a distribution around target_rps from rps_min to rps_max with increasing distance between individual measurements.""" rps = [rps_min, target_rps, rps_max] for inc in sorted(set([increment * round(2 ** (i * expo...
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def get_query(string, pos=1): """Get query parameter of a URL.""" try: return string.split("?")[pos] except IndexError: if pos == 1: return "" else: return string
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def is_user(request): """Check if the incoming request is from the appropriate_user.""" return request.authenticated_userid == request.matchdict['username']
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import re def remove_bars(string): """Return argument without square brackets ('[' and ']').""" return re.sub(r"[\[\]]", "", string)
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def delta_total_seconds(td): """Equivalent to timedelta.total_seconds() available in Python 2.7. """ microseconds, seconds, days = td.microseconds, td.seconds, td.days return (microseconds + (seconds + days * 24 * 3600) * 10 ** 6) / 10 ** 6
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def is_ttt(soup): """Check if stage is team time trial.""" stage_info = soup.select("h2 span.blue")[0].text return "TTT" in stage_info
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def get_trimmed_path(location, num_segments=2): """ Return a trimmed relative path given a location keeping only the ``num_segments`` trailing path segments. For example:: >>> assert get_trimmed_path(None) == None >>> assert get_trimmed_path('a/b/c') == 'b/c' >>> assert get_trimmed_path('/b...
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from pathlib import Path def as_jupyter_path(path): """ Paths in Jupyter are delimited by / (even on Windows) and don't have trailing leading slashes. This function takes a platform-dependent path and converts it to a valid jupyter path Notes ----- https://jupyter-notebook.readthedocs.io/...
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from datetime import datetime def get_today() -> str: """ Get todays date. """ return str(datetime.today().date())
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def format_response(response_collection): """Re-format responses to a dict""" return { "code": response_collection[0]['code'], "message": "%s created" % response_collection[0]['resource'], "status": response_collection[0]['status'], "payload": response_collection }
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def check_permutations(s_one, s_two): """ Question 2: Given two strings, write a method to decide if one is a permutation of the other. """ if len(s_one) != len(s_two): return False h_table = {} for index, char in enumerate(s_two): h_table[char] = index for char in set(...
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from typing import IO from typing import Tuple import base64 import click def read_public_key(f: IO[str]) -> Tuple[str, str, str, str]: """ Read a public SSH key. This function does some basic verification to see if the content looks like a public key. """ data = f.read() try: kin...
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def is_none(value): """ is value None""" return value is None
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from typing import OrderedDict def digest_node_line(line): """Return OrderedDict of relevant line parts.""" line = line.strip() d = OrderedDict() d["num"], fields = line.split('[') fields = fields.replace('rounded,dashed', 'rounded-dashed') fields = fields.rstrip('];').split(',') fields[-...
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def read_full_superlinks(filename): """Read the full superlinks input file and create a dictionary with superlink number as the key and a list of Measures Estimation links that make it up as the value""" superlinks = {} with open(filename) as in_f: for line in in_f: row = line.split(','...
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def atomic_prop(entry, molTuple): """Return true if atom fits F5 (atomic property) entry, False otherwise""" molecule, atomIndex = molTuple #determine atom properties propList = [] nonRing = True for count, ring in enumerate(molecule.ringList): if atomIndex in ring: nonR...
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def enum_constraint(value, enum): """Test value in predefined set constraint.""" if str(value).lower() in enum: return True return False
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def required_padding(address, alignment): """ Return how many padding bytes are needed to align address """ rest = address % alignment if rest: # We need padding bytes: return alignment - rest return 0
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import torch def greedy_decoding(arc_f): """greedy_decoding Arguments: arc_f: a tensor in shape of (n, l+1, l+1) length of the sentence is l and index 0 is <root> Output: arc_pred: a tensor in shape of (n, l), indicating the head words """ f_arc = arc_f[:, 1:, :] #...
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def get_connection_info(file_name): """ Get connection details from config file Args: file_name: name of file on disk including path (relative or absolute) Returns: a dictionary containing connection details """ # Initial empty dictionary to store connection details connecti...
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def lossAttack(model, images, labels, Loss): """ Computes the loss value for a batch of samples. model: instance of a nn.Module subclass images: pytorch tensor with dimensions [batch,channels,width,height] labels: pytorch tensor of shape [batch] containing the integer labels of the samples loss: cal...
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def euclidean_distance(preference_space, person1, person2): """ Return euclidean distance measure @ https://en.wikipedia.org/wiki/Euclidean_distance Args -------------- preference_space (dict) keys are users while values are dictionary of items and ratings ie. preference_space={'userA:{'item1':'rati...
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def get_feature_filename( feature_extractor_name, h_stride, v_stride, feature_height, fov): """Returns a filename given feature map parameters.""" return "features_{}_h-{}_v-{}_height-{}_fov-{}.sstable@100".format( feature_extractor_name, h_stride, v_stride, feature_height, fov)
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import re def strip_punct( text ): """Remove punctuation and numbers. Remove select punctuation marks and numbers from a text and replaces them with a space. Non-permanent changes for evaluation purposes only. Uses the :mod:`re` library. Args: text (str): Content to be evaluated...
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def user_directory_path(instance, filename: str) -> str: """ Helper function to store images in `[...]/user_pk/filename`. Parameters ---------- instance: :class:`models.Model` The Model instance to get the PrimaryKey. filename: :class:`str` The filename to store. """ # ...
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def get_from_power_tuple(power_tuple, index): """ Extracts an exponent from an exponent tuple that may have been canonicalized to be shorter than the expected length, by removing extra zeroes. """ if index >= len(power_tuple): return 0 else: return power_tuple[index]
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import json import random def get_substitutions(subs_json): """Randomly pull phrase variations from the substitutions file.""" with open(subs_json) as subs_file: raw_subs = json.loads(subs_file.read()) return { k : random.choice(raw_subs[k]) for k in raw_subs }
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def is_mono(t): """ Returns True if all values of _t_ are equal and False otherwise. """ for i in t: if i != t[0]: return False return True
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def clamp(x: float, minval: float, maxval: float) -> float: """ Clamp value """ if x >= maxval: return maxval elif x <= minval: return minval return x
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import random def roll_d66(num): """ D66 roller, which is a 36-result table where one D6 is the 1s digit and the other is the 10s """ result = 0 rolled_die = 6 for _ in range(0, num): result += random.randint(1, rolled_die)*10 result += random.randint(1, rolled_die) re...
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import multiprocessing def get_cores() -> int: """ Get numbers of available cores. """ return multiprocessing.cpu_count()
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from pathlib import Path def format_output(output, runtype="prod", q1v4=False, bal=False, exp_v_unexp=False): """ format_output(output) Returns output path with subdirectory added based on the arguments. Required args: - output (Path): base output path Optional args: ...
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from typing import Callable from typing import Any import inspect def fn_ends_with_pass(fn: Callable[..., Any]): """ Check that function end with pass statement (probably does nothing in any way). Mainly used to filter callbacks with empty on_{event} methods. Args: fn (Callable[..., Any])...
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import json def deduplicate_results(results): """ Removes duplicates from all SPARQL queries to various Virtuoso instances Args: results: List of results which may contain duplicates Returns: Deduplicated list of results """ deduped = set() for result in results: deduped...
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def extract_species_strings(species, characteristics, species_string_dict): """ Extract the species strings from the species_string_dict based on the meta-species and characteristics given Parameters: species (meta-species object) = Instance of the meta-species to obtain the species str...
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def convert_to_unix_line_endings(source): """Converts all line endings in source to be unix line endings.""" return source.replace('\r\n', '\n').replace('\r', '\n')
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import inspect def get_python_function_arguments(f): """ Helper to get the parameter names and annotations of a Python function. Examples: """ # Note that we only return non-optional arguments (we assume that any optional args are not specified). # This allows to, e.g., accept max(a, b, *more,...
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def get_attribute(attribute_list, name): """Finds name in attribute_list and returns a AttributeValue or None.""" attribute_value = None for attr in attribute_list: if attr.name.text == name and not attr.is_default: assert attribute_value is None, 'Duplicate attribute "{}".'.format(name) attribute...
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from typing import List from typing import Pattern import re def combine_multiple_regexes(regexes: List[str]) -> Pattern[str]: """Combine multiple regular expressions in a single pattern. Parameters ---------- regexes: List[str] A list of regular expressions. Returns ------- Patt...
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def _FindRuleForRegister(cfi_row, reg): """Returns the postfix expression as string for a given register. Breakpad CFI row format specifies rules for unwinding each register in postfix expression form separated by space. Each rule starts with register name and a colon. Eg: "CFI R1: <rule> R2: <rule>". """ ...
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def gauss_fill(std): """Gaussian fill helper to reduce verbosity.""" return ('GaussianFill', {'std': std})
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from pathlib import Path def _tdep(target, dep): """Make a target name into a '.wants/requires' dir as a Path type.""" return Path(target + "." + dep)
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def is_real_number(obj): """Yield whether an object is a real number""" return isinstance(obj, float) or isinstance(obj, int)
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import re def tag_to_label(tag: str) -> str: """Return the spaced and lowercased label for the given camelCase tag.""" return re.sub(r'(?<!^)(?=[A-Z])', ' ', tag).lower()
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def copy_file(ctx, src_file, dest_path, sibling = None): """ Copy a file to a new path destination Args: ctx: the <ctx> object src_file: the source file <File> dest_path: the destination path of the file sibling: a file to use as a sibling to declare_file <File> Returns...
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from typing import Tuple import torch def prior(topics: int) -> Tuple[torch.Tensor, torch.Tensor]: """ Prior for the model. :param topics: number of topics :return: mean and variance tensors """ a = torch.Tensor(1, topics).float().fill_(1.0) mean = a.log().t() - a.log().mean(1) var = ...
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def _get_pin_cw(pincount, loc): """Helper function to locate pin number for cw_dual. Args: pincount: Total number of pins loc: Starting location Returns: pin_number: Starting pin number """ pins_per_side = pincount // 2 if loc == "top_left": return 0 elif lo...
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def merge_lists(*args): """Merge an arbitrary number of lists into a single list and dedupe it Args: *args: Two or more lists Returns: A deduped merged list of all the provided lists as a single list """ out = {} for contacts in filter(None, args): for contact in conta...
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def average(avg_list): """Averages all values in the list.""" if len(avg_list) == 0: return 0 avg = sum(avg_list) / len(avg_list) return avg
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from typing import Union from typing import Dict from typing import List from typing import Any def _func_minimum( target_attr: Union[ Dict[Union[float, int], Union[float, int]], List[Union[float, int]] ], *_: Any, ) -> Union[float, int]: """Function for returning the minimum element of a list...
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def percent_nan(data_series): """ For data_series, calculate what proportion of rows are NaN. @param data_series: data to check for NaNs @type data_series: Series @return: A number representing the proportion of data in data_series that is NaN @rtype: Float """ nan_count = data_series.is...
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def builtin_2nip(a, b, c, d): """Modify the stack: ( a b c d -- c d ).""" return (c, d)
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import math def calculateDistance(coordinate1, coordinate2) -> float: """Calculates the distance between two 2D coordinates. Args: coordinate1 (list): x, y coordinates. coordinate2 (list): x, y coordinates. Returns: float: Distance between coordinates. """ deltaX = math.fabs(coordinate1[...
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from typing import OrderedDict def get_questions_from_manifest_by_id(content_manifest): """Returns an OrderedDict of all questions in a content manifest, {question.id: question, ...}""" questions = OrderedDict() for section in content_manifest.sections: for question in section.questions: ...
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def lists_overlap(l1, l2): """ This functions return whether two lists overlap :param l1: list 1 :type l1: list :param l2: list 2 :type l2: list :return: whether the list overlap. If TRUE, then the list overlap :rtype: bool """ intersection_set = set(l1).intersection(set(l2)) ...
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import re def remove_zero_padded_dates(date_string): """Mimic %-d on unsupported platforms by trimming zero-padding For example: January 01 2018 Becomes: January 1 2018 The regex finds a space or a hyphen followed by a zero-padded digit, and replaces with the symbol (space or hyp...
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def FindMatch(matrix, seq1, x, seq2, y, options, max_advance=10, min_match=3): """advance on sequence2 from position y until you find a minimum match of min_match residues. returns the offset in y. If no match is found, an offset of 0 is returned. """ # for z in range(0,10): # print seq1.asCha...
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def xrd_from_atto(atto_amount: int) -> float: """ Converts an amount of Atto to their XRD equivalent Args: atto_amount (int): The amount of atto to get in XRD. Returns: float: The equivalent amount of XRD. """ return atto_amount / (10**18)
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import dataclasses def field(pytree_node=True, serialize=True, cache=False, **kwargs): """Mark a field of a dataclass to be: Args: pytree_node: a leaf node in the pytree representation of this dataclass. If False this must be hashable serialize: If True the node is included in the...
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def flatten_list(l): """Flatten a multidimensinoal list to a 1 dimensional list. Parameters: l (list): The list that you want to flatten. Returns: list: ! dimensional list. """ try: return flatten_list(l[0]) + (flatten_list(l[1:]) if len(l) > 1 else []) if type(l) is list else [l] ...
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def split_type_line(type_line): """Splits the comment with the type annotation into parts for argument and return types. For example, for an input of: # type: (Tensor, torch.Tensor) -> Tuple[Tensor, Tensor] This function will return: ("(Tensor, torch.Tensor)", "Tuple[Tensor, Tensor]") ...
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def get_field_description(field, description_keyword='description'): """ Gets field description if available, using the description_keyword""" return getattr(field, description_keyword, '')
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def valid_chrom(arg): """Check if a string represents a valid chromosome""" arg = arg.lower() if arg[:3] == 'chr': return True if arg.isdigit() or arg in ('x', 'y', 'mt'): return True if arg[:8] == 'scaffold' or arg[:2] == 'gl' or arg[:3] == 'par': return True return Fals...
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def read_predictions_from_file(filename): """ Reader for the gold file and the template output file. Return values are four arrays with article ids, labels (or ? in the case of a template file), begin of a fragment, end of a fragment. """ articles_id, span_starts, span_ends, gold_labels ...
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def any_match(record, patterns): """Check record for match with any of the patterns :param record: record string to search for patterns :param patterns: list of regexes :return: True of record matched with any of the patterns; False otherwise """ return any(map(lambda x: x.search(record), patter...
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def char2note(char): """Convert a char to a midi note number wih the followung syntax. First the note ('a', 'b' , etc..) then the number of the note, and finally it's accentuation ('-', '=', '+').""" if char == 's': # Return a silence return 0, 0, 0 notes = {'a': 69, 'b': 71, 'c': 60, 'd': ...
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def _convert_terms_to_spin_blocks(terms, n_orbitals: int, n_spin_components: int): """ See explanation in from_openfermion in conversion between conventions of netket and openfermion. Args: terms: the operator terms in tuple tree format n_orbitals: number of orbitals n_spin_comp...
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