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import builtins def any(iterable, pred): """Returns True if ANY element in the given iterable is True for the given pred function""" return builtins.any(pred(x) for x in iterable)
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def tri_ravel(l, m1, m2): """Ravel indices for the 'stack of triangles' ordering.""" # m1 must be >= m2 if m1 < m2 or m1 > l or m2 > l or m1 < 0 or m2 < 0: raise ValueError("Invalid indices") base = l * (l + 1) * (l + 2) // 6 offset = (l - m1) * (l + 3 + m1) // 2 + m2 ind = base + offset...
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def _create_dictionary(sequences): """ Create id/token mappings for sequences. :param sequences: list of token sequences :return: mappings from id to token, and token to id """ tokens = {} for s in sequences: for token in s: tokens[token] = tokens.get(token, 0) + 1 s...
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def lower_bound(arr, value, first, last): """Find the lower bound of the value in the array lower bound: the first element in arr that is larger than or equal to value Args: arr : input array value : target value first : starting point of the search, inclusi...
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import lzma import json def raw_numpy_to_object(numpy_bytes_array): """Convert numpy array to a Python object. Args: numpy_bytes_array: a numpy array of bytes. Returns: Return a Python object. """ return json.loads( lzma.decompress(numpy_bytes_array.tobytes()).decode('ut...
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def repeated(pattern, sep, least=1, most=None): """ Returns a pattern that matches a sequence of strings that match ``pattern`` separated by strings that match ``sep``. For example, for matching a sequence of ``'{key}={value}'`` pairs separated by ``'&'``, where key and value contains only lowercas...
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def norm_rows(X, stats=None): """ Normalize the rows of the data. X is an M-by-N array to normalize. It is modified in-place. The data is not returned. If stats is given it must be a sequence of 2 M-length arrays for the min and max statistics to normalize by instead of calculating them fr...
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def createboard(rows,columns): """ Creates a string given rows and columns desired that can be converted into a matrix through numpy >>> createboard(5,4) '0,0,0,0,0; 0,0,0,0,0; 0,0,0,0,0; 0,0,0,0,0' >>> createboard(3,7) '0,0,0; 0,0,0; 0,0,0; 0,0,0; 0,0,0; 0,0,0; 0,0,0' """ row_size ...
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def make_histogram(s): """Make a map from letters to number of times they appear in s. s: string Returns: map from letter to frequency """ hist = {} for x in s: hist[x] = hist.get(x, 0) + 1 return hist
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def omp_get_team_size(level : int): """ The omp_get_team_size routine returns, for a given nested level of the current thread, the size of the thread team to which the ancestor or the current thread belongs. Parameters ---------- level : int """ return 1
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import os def get_version(): """Get version number of the package from version.py without importing core module.""" package_dir = os.path.abspath(os.path.dirname(__file__)) version_file = os.path.join(package_dir, 'src/seqdiag/__init__.py') namespace = {} with open(version_file, 'r') as f: ...
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def invert_color(color): """ Инвертировать цвет (выдать комплиментарный по RGB) """ return tuple(255 - i for i in color)
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import time def profile(func): """profile execution time of provided function""" func_start = time.time() func() func_end = time.time() func_delta = func_end - func_start label = str(func).split()[4].split('.')[2] return f"'{label}' passed in {func_delta:.2f}s"
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import textwrap import tempfile import subprocess import sys def interpret_bash_array(pkgbuild, array_name): """Return the Bash array array_name in the file at path pkgbuild. Returns: A list of strings, or an empty string if the array is not defined in the PKGBUILD, or None if there was a pro...
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import types def rebuild_code_object(co, code=None, constants=None, filename=None): """Rebuild the code object.""" code = code or co.co_code constants = tuple(constants or co.co_consts) filename = filename or co.co_filename params = [co.co_argcount, co.co_kwonlyargcount, co.co_nlocal...
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from sympy import Function def _functions(expr, x): """ Find the types of functions in expr, to estimate the complexity. """ return set(e.func for e in expr.atoms(Function) if x in e.free_symbols)
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import time def time2int(time_struct, format24=False): """Convert time, passed in as a time.struct_time object, to an integer with hours in the hundreds place and minutes in the units place. Returns 24 hour format if format24 is True, 12 hour format (default) otherwise. """ if not isinstance(time_...
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def error_response(message): """ Construct error response for API containing given error message. Return a dictionary. """ return {"error": message}
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import os def sort_dir(dir_name, sub_split=-3, param_split=-1): """ :param dir_name: Full directory name to be sorted :param sub_split: Location of subID to split in sorting :param param_split: Location of parameter to split in sorting :return: Sorted directory according to first (subID) and third...
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def make_boulder (fasta, primer3_input_DIR, exclude_list=[], output_file_name="", sequence_targets=[]): """ create a boulder record file in primer3_input_DIR from a given fasta STRING. SEQUENCE_ID is the fasta header, usually the genomic re...
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def price(company): """Get historical price data. Used in class TestPrice. """ return company.historical('2021-8-3', '2021-8-10')
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from io import StringIO def s3(mocker): """Patch Boto3 S3 Calls""" s3_patch = mocker.patch('boto3.client') s3_patch.return_value.get_object.return_value = { 'Body': StringIO(u"foo: bar"), } return s3_patch
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def unit_width_to_available_footprint(unit_width): """Convert a key width in standard keyboard units to the width of the kicad footprint to use""" if unit_width < 1.25: return "1.00" elif unit_width < 1.5: return "1.25" elif unit_width < 1.75: return "1.50" elif unit_w...
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def export_fasta(dic): """Export a dictionary.""" fasta = "" for (k, v) in dic.iteritems(): fasta += ">%s\n%s\n" % (k, v) return fasta
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def Slope(pt1, pt2): """ Calculates the slope of the line connecting 2 points. :param `pt1`: an instance of `wx.Point`; :param `pt2`: another instance of `wx.Point`. """ y = float(pt2.y - pt1.y) x = float(pt2.x - pt1.x) if x: return y/x else: return None
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def is_sorted(items): """Return a boolean indicating whether given items are in sorted order. DONE: Running time: O(n), because the worst-case scenario would require iterating through the entire array once. DONE: Memory usage: O(1), because the input array is modified in-place (if at all).""" # DON...
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def get_works_with_xml(pages): """ Arguments: pages: result of `get_wiki_content_for_pages` """ ret = [] for page in pages: if "{{XML}}" in page["content"]: ret.append(page) return ret
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import mpmath def cdf(x, dfn, dfd): """ Cumulative distribution function of the F distribution. `dfn` and `dfd` are the numerator and denominator degrees of freedom, resp. """ if x <= 0: return mpmath.mp.zero with mpmath.mp.extradps(5): x = mpmath.mp.mpf(x) dfn = mpmat...
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def shift(cube, axis, n=1, cval=0): """Returns a cube with the axis shifted. Ex. cp.shift(nodo_ejemplo,index_para_ejemplo,1) """ return cube.shift(axis,n,cval)
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import os def alias_dict(fname): """ Aliases hard to read accessions to easier to read names: NC_045512 wuhan-hu-1 MN996532 raTG13 """ if not fname or not os.path.isfile(fname): return dict() stream = open(fname) lines = map(lambda x: x.strip(), stream) lines = filter(la...
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def is_iter(obj): """ Checks if an object behaves iterably. Args: obj (any): Entity to check for iterability. Returns: is_iterable (bool): If `obj` is iterable or not. Notes: Strings are *not* accepted as iterable (although they are actually iterable), since string...
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def _make_rows(data, headers, defaults={}): """ extract the values from the data based on the headers data is a list of dicts headers is a list of keys defaults is a dict, where the keys are from the headers list returns the data in a list or rows (tabulate data format) """ ...
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def sampling(array, interval=1, offset=0): """ Down-sample the input signal with certain interval. input: array: numpy array. The input temporal signal. 1d or with multiple dimensions interval: int. The interval to sample EEG signal. Default is 1, which means NO down-sampling is applied ...
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def stat_float_times(newvalue=False): """Determine whether :class:`stat_result` represents time stamps as float objects. If *newvalue* is ``True``, future calls to :func:`~os.stat` return floats, if it is ``False``, future calls return ints. If *newvalue* is omitted, return the current setting....
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def acquire_page_list_urls_books(soup): """ Take a BeautifulSoup content of a category page. Return a list of the urls of the books in the first page for a unique category. """ page_list_partial_urls_books = map( lambda x: x.a['href'][8:], soup.find_all('h3'), ) page_list_urls_books = map( lambda x: f"ht...
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def LUT_match(data, lut, idi, idj, mod09): """look up table""" p_aot1 = data[idi][idj] # band 3 p_sur = mod09[idi][idj] # mod09 min_d = 100 aod_v = 0 for i in lut: p_aot2 = i[2] + (i[1] * p_sur) / (1 - i[0] * p_sur) _delta = abs(p_aot2 - p_aot1) if _delta < min_d:...
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def _convert_to_dict(caps_str: str) -> dict: """ Parses the VCP capabilities string to a dictionary. Non continuous capabilities will include an array of all supported values. Returns: Dict with all capabilities in hex Example: Expected string "04 14(05 06) 16" is converted to:...
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import torch def pck(x, x_gt, perm_mat, dist_threshs, ns): """ Percentage of Correct Keypoints evaluation metric. :param x: candidate coordinates :param x_gt: ground truth coordinates :param perm_mat: permutation matrix or doubly stochastic matrix indicating correspondence :param dist_threshs:...
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import os def change_ext(original_file, new_ext): """Changes extensions @returns (new_filename, original_ext)""" base, original_ext = os.path.splitext(original_file) new_filename = '{}.{}'.format(base, new_ext) return new_filename, original_ext
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def get_line_end( is_last_line: bool, ) -> str: """ Get the characters needed for the end of a row of a TeX table being created by one of the functions below. Note that for some TeX-related reason, we can't put the \\ on the last line. Args: is_last_line: Whether this is the last line o...
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def db2xml(db, rootnode = None, rownode = None, fields = None, expressions = None, primary = False): """convert a database view to XML""" return db.xml( rootnode, rownode, fields, expressions, primary )
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def change_log_level_console(logger, new_level): """Change the minimum level that will be logged to the console Parameters ---------- logger : logger object As created by "init_root_logger" method new_level : int New minimum level to log to console """ logger.handlers[1].se...
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import requests def graph_query(url, proxies, headers, operation='query', payload={}): """Perform a query.""" try: response = requests.post(url, headers=headers, cookies=None, verify=False, allow_re...
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def writeLabels(label): """Format text to be output by LaTeX.""" return label.replace('_', r'\_')
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def get_public_translation(instance, language_slug): """ This tag returns the most recent public translation of the requested content object in the requested language. :param instance: The content object instance :type instance: ~integreat_cms.cms.models.pages.page.Page, ~integreat_cms.cms.models.event...
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def is_cjk(character): """ Borrowed from the nltk https://github.com/alvations/nltk/blob/79eed6ddea0d0a2c212c1060b477fc268fec4d4b/nltk/tokenize/util.py """ return any( [ start <= ord(character) <= end for start, end in [ (4352, 4607), ...
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def openappend(file): """Open as append if exists, write if not.""" try: output = open(file, 'a') except Exception: try: output = open(file, 'w') except Exception: return 'error' return output
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def ext_checker(fname, ext): """Replaces the extension of fname with ext, or adds ext to fname if fname doesn't already have an extension.""" ext_begin = -len(fname) for ind in range(1, len(fname) + 1): if fname[-ind] == ".": ext_begin = ind break return fname[:-ext_b...
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def click(pos): """ clicks on the board squares :return: mouse position in 2D board Array form """ rect = (113,113,525,525) x = pos[0] y = pos[1] if rect[0] < x < rect[0] + rect[2]: if rect[1] < y < rect[1] + rect[3]: divX = x - rect[0] divY = y - rec...
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def get_primes(number): """ 得到小于num的质数 :param number: :return: """ w = [True] * number li_number = [] for i in range(2, number): if w[i]: w[i * i::i] = [False] * (len(range(i * i, number, i))) li_number.append(i) return li_number
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def _air_check( game_data ): """ Below-min breath is called exhaustion. Knowing when to breathe is important. """ for p in range( 2 ): c = game_data[str(p)]['calm'] # Punish will if calm is below zero if c < 0: game_data[str(p)]['calm'] = 0 game_data[str(p)]['will'] += c # Treat Air as maximum Calm ...
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def backward_sorted_array(len_arr): """ Function generates a backward array of size 2 ** n of integers. """ array = [] for i in range(len_arr): array.append(len_arr-i) return array
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def asa_scp_handler(ssh_conn, cmd='ssh scopy enable', mode='enable'): """Enable/disable SCP on Cisco ASA.""" if mode == 'disable': cmd = 'no ' + cmd return ssh_conn.send_config_set([cmd])
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def project_client(rubicon_client): """Setup an instance of rubicon configured to log to memory with a default project and clean it up afterwards. """ rubicon = rubicon_client project_name = "Test Project" project = rubicon.get_or_create_project( project_name, description="In memory pro...
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def progress(status_code): """Translate PROGRESS status codes from GnuPG to messages.""" lookup = { 'pk_dsa': 'DSA key generation', 'pk_elg': 'Elgamal key generation', 'primegen': 'Prime generation', 'need_entropy': 'Waiting for new entropy in the RNG', 'tick': 'Generic t...
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import re def ir_parsing(text): """Parsing IR data to detect solvent,units and spectrum values. param text:IR data block return:a dictionary that include all the information about solvent, units and IR spectrum values """ IR_Spectroscopy = {"solvent": None, "units": None, "spectrum": {}} spectrum...
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def YELLOW(obj): """Format an object into string of yellow color in console. Args: obj: the object to be formatted. Returns: None """ return '\x1b[1;33m' + str(obj) + '\x1b[0m'
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def per_target(imgs): """Arrange samples per target. Args: imgs (list): List of (_, target) tuples. Returns: dict: key (target), value (list of data with this target) """ res = {} for index in range(len(imgs)): _, target = imgs[index] if target not...
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from datetime import datetime import time def uptime(since): """Turn an date and time into an uptime value. The returned value is a number of seconds from the provided value to the current time. The date/time provided is expected to be a local time using the following format: 2017-01-10 16:32:21. ...
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def interpret_word_seg_results(char_seq, label_seq): """Transform model output into user-friendly contents. Example: In CWS, convert <BMES> labeling into segmented text. :param char_seq: list of string, :param label_seq: list of string, the same length as char_seq Each entry is one of ('B',...
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def _set_model_dict(resource_type_name, properties_target, prefix, created_at, updated_at): """return a model dict set with the passed in key values""" model_dict = {'name': resource_type_name, 'properties_target': properties_target, 'prefix': prefix, ...
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def get_location_from_event(event): """ Append the coordinates of the event in a list of locations for the GMaps marker locations """ location = {} coordinates = event["_embedded"]["venues"][0]["location"] location["lng"] = float(coordinates["longitude"]) location["lat"] = float(coordina...
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def kw_pop(*args,**kwargs): """ Treatment of kwargs. Eliminate from kwargs the tuple in args. """ arg=kwargs.copy() key,default=args if key in arg: return arg,arg.pop(key) else: return arg,default
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import json def getCustomResponse(responseData, url, params): """convert requests lib response data to my custom response dictionary Args: responseData (Response): response class returned from requests lib url (String): requests uri params (Dict): params used Returns: ...
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import random import json def makeSurveyJson (transaction) : """Generates a problem description matching the survey definition in the working database.""" durations = ["overnight","overnight+", "days", "4-8hours", "minutes", ">1hour", "hours", "1-2hours"] problem_types = [ 'full', 'absent'...
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import os def filter_audio(f): """ Return only pydub supported audio """ ext = os.path.splitext(os.path.basename(f))[1][1:] if ext in ['mp3', 'wav', 'raw', 'ogg', 'aif']: return f
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def drop_duplicate_psites(df): """ remove duplicate phosphosites. Retain site with maximum intensity across samples """ df2 = df.copy() samples = [s for s in df2.columns.tolist() if 'sum' in s] df2['max_int'] = df2[samples].sum(axis=1) df2 = df2.sort_values('max_int').drop_duplicates(['identifier'],...
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import importlib def try_import(path, keys=None, _as=True): """Try to import from a module. Parameters ---------- path : str Path to module or variable in a module keys : str or list[str], optional Keys to load from the module _as : bool, defualt=True If False, perform...
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def normalize_path_for_settings(path, escape_drive_sep=False): """ Normalize a path for a settings file in case backslashes are treated as escape characters :param path: The path to process (string or pathlib.Path) :param escape_drive_sep: Option to escape any ':' driver separator (wi...
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def round_robin(w) -> bool: """Implements a round-robin association strategy where iots are associated their ssid modulo number of APs. Return: Returns true on successful association. False otherwise. """ m = len(w.aps) i = 0 for device in w.iots: if device.do_associate(w.aps[i%m]) == False: return False...
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def create_property_type(data): """Create whole/naked property feature.""" data['Tipo_proprietà'] = (data['Tipo proprietà'] .str.lower() .str.extract('(intera proprietà|nuda' 'proprietà|multiproprietà)', ...
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import numpy def computeMicrocanonicalRateCoefficients(network, T=1000): """ Compute all of the microcanonical rate coefficients k(E) for the given network. """ Elist = network.autoGenerateEnergyGrains(Tmax=2000, grainSize=0.5*4184, Ngrains=250) # Determine the values of some counters Ngr...
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def convert_oct_set(oct_set, og_names): """ Maps an OCT set on the preprocessed graph to their original vertices. """ try: return list(map(lambda x: og_names[x], oct_set)) except Exception: print('Error: OCT set', oct_set) print('Error: og_names', og_names) print('Pro...
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def check_dict_is_contained_in_another(filter_data: dict, data: dict) -> bool: """ Check if a dict is contained in another one. * Works with nested dicts by using _dot notation_ in the filter_data keys so a filter with `{"base_key.sub_key": "value"}` will look for dicts containing `...
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import pkgutil def list_skeletons(): """List available skeletons for generating conda recipes from external sources. The returned list is generally the names of supported repositories (pypi, cran, etc.)""" modules = pkgutil.iter_modules(['conda_build/skeletons']) files = [] for _, name, _ in modu...
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def inside_bounding_box(bb_minlat, bb_minlon, bb_maxlat, bb_maxlon, start_lat, start_lon, end_lat, end_lon): """ Check if two given sets of coordinates (start_lat, start_lon) and (end_lat, end_lon) are within a bounding box (bb_minlat, bb_minlon, bb_maxlat, bb_maxlon) Examples: >>> inside_bounding_...
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import sys def is_pytest(): """This tells if the current process is started by pytest.""" for one_arg in sys.argv: if one_arg.find("pytest") >= 0: return True return False
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def time_representation(hours, minutes, seconds): """Conversion of readable to internal time representation. Parameters ---------- hours : float or array, shape (n_steps,) Hours since start minutes : float or array, shape (n_steps,) Minutes since start seconds : float or array...
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import typing def get_destination_for_notebook(relative_path: str) -> typing.Any: """ Get the destination for a notebook. The destination can be of a type of your choice, but it must be serializable with itsdangerous. It will be used by the other methods defining local behavior to determine where...
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def _update_change_dec(func): """ Decorator to track property changes in class. Apply @property.setter after @_update_change_dec :param func: function object to decorate :return: decorated function """ def _wrapper(self, val): self._changed = True func(self, val) return _wr...
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def generate_properties_test(dataset, abs_path): """ :param dataset: :param abs_path: :return: """ return dataset.to_dict()
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def colorclose(color, hsva_expected): """ Compares HSV values which are stored as 16-bit integers. """ hsva_actual = color.getHsvF() return all(abs(a-b) <= 2**(-16) for (a,b) in zip(hsva_actual, hsva_expected))
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def nice_pypy_mem(mem: str) -> str: """Improves formatting of the memory statistics produced by pypy's garbage collector (which are provided as strings)""" return mem.replace("KB", " KiB").replace("MB", " MiB").replace("GB", " GiB")
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def swap_short_telos_group_number(row): """ swaps all group 1 patients to group 2 & all group 2 patients to group 1 this is done purely for visualization reasons and has no impact whatsoever on interpretation of results; just swapping #s for interpretability """ if row == 1: row = 2 ...
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def _float_to_int(x: float) -> int: """ Symbolic tracing helper to substitute for inbuilt `int`. Hint: Inbuilt `int` can't accept an argument of type `Proxy` """ return int(x)
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def calculate_board_dim(img_mat, start_pos): """ Calculates the length of one side of the board (all info we need to find specific tiles) """ x, y = start_pos dim = 0 # size of one side of the chess board while img_mat[x, y, 0] != 0 and img_mat[x, y, 1] != 0 and img_mat[x, y, 0] != 0: d...
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def update(data): """Update the data in place to remove deprecated properties. Args: data (dict): dictionary to be updated Returns: True if data was changed, False otherwise """ changed = False for cfg_object in data.values(): externals = [] paths = cfg_object.p...
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def digit_facorials(): """Find the sum of all numbers which are equal to the sum of the factorial of their digits. """ final_list = [] facts = [1, 1, 2, 6, 24, 120, 720, 5040, 40320, 362880] for x in range(3, 2500000): string = str(x) total = 0 for i in string: t...
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def cut_levels(nodes, level): """ For cutting the nav_extender levels if you have a from_level in the navigation. """ result = [] if nodes: if nodes[0].level == level: return nodes for node in nodes: result += cut_levels(node.childrens, level) return result
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import os import json def bids_load_prot_dict(prot_dict_json): """ Read protocol translations from JSON file in DICOM directory :param prot_dict_json: string JSON protocol translation dictionary filename :return: """ if os.path.isfile(prot_dict_json): # Read JSON protocol tr...
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def find_cont_substring(l1, l2, n): """Dynamic programming algorithm to find continuous, uninterrupted substrings in two increasing lists. Given two lists, finds the position in the first one which is proceeded by n elements from the first list, not interrupted by the second. For example, find...
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import torch def layernorm(x): """ :param x: (B, K, L) or (B, K, C, H, W) (function adapted from: https://github.com/MichaelKevinKelly/IODINE) """ if len(x.size()) == 3: layer_mean = x.mean(dim=2, keepdim=True) layer_std = x.std(dim=2, keepdim=True) elif len(x.size()) == 5: ...
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def add_fdcuk_meta_data(df, filepath): """ Accepts a dataframe and a filepath parses the filepath to get strings representing nation, league, and season writes this data to the dataframe Returns the changed dataframe """ season = filepath.stem str_filepath = str(filepath) str_fil...
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def can_link_to(person, contact, model): """ Determines whether or not the specified person can form a social network link to the specified contact. :param person: The person wanting to link. :param contact: The contact to determine link eligibility. :param model: The model to use. """ ...
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def tail(): """ Returns a string that will cover up bleeding output when printing in place """ return " \r"
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def should_show_entry_state(entry, current_api_id): """Returns wether or not entry state should be shown. :param entry: Contentful entry. :param current_api_id: Current API selected. :return: True/False """ return ( current_api_id == 'cpa' and ( entry.__dict__.get('...
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def undefined_context(): """Fixture. Populate context variable for future tests.""" return { 'cookiecutter': {'project_slug': 'testproject', 'github_username': 'hackebrot'} }
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def getCodons(sequence, gap_chars="-."): """get codons in sequence.""" codons, codon = [], [] full_codons, full_codon = [], [] for x in range(len(sequence)): c = sequence[x] full_codon.append(c) if c not in gap_chars: codon.append(c) if len(codon) % 3 == 0: ...
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def up(f): """Perform computation rounding down.""" return f()
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def read_results(bq): """ Read results """ return [row for row in bq.readResult()]
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