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def _mad(x, axis=None): """Calculate median absolute deviations from the median (MAD) for an array. Parameters ---------- x : np.ndarray A 1-D or 2-D numeric array to summarize. axis : {int, tuple of int, None}, optional Axis along which MADs should be calculated. If ``None``, the M...
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def ode_plotter(name, t, ny, svars, log = False, labels = None, xlim = None, ylim = None, plim = None, labels_strict = False): """ Plots the ODE trajectories. Args: name (str): Name of the outputfile including extension (e.g. *.pdf) t (list[flt]) : time units plotted on the x-axis. ny...
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def Proxy(f): """A helper to create a proxy method in a class.""" def Wrapped(self, *args): return getattr(self, f)(*args) return Wrapped
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def french_to_english(french_text): """french to English translation""" translation= language_translator.translate(text=french_text, model_id="fr-en").get_result() english_text=translation['translations'][0]['translation'] return english_text
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import pandas from typing import Union from typing import List def calculate_metric_scores( r: pandas.Series, metrics_to_calculate: Union[str, list] = "all", ) -> List[Result]: """Calculates the metric score(s) between two images and returns a list of the results. Args: r (pandas.Series): Row con...
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def parse_results(results): """Break up multiline output from ls into a list of (name, size) tuples.""" return [(line.split()[8], int(line.split()[4])) for line in results.splitlines() if line.strip()] #return [(line.split()[1], int(line.split()[0])) for line in results.splitlines() if line.strip()]
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def use_for_variety(variety, *, read=True, write=True): """ A class wrapper to associate a specific variety with the class. Defaults to registering for both read and write widgets. Parameters ---------- variety : str The variety (e.g., 'command') read : bool, optional Use ...
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import requests def getListings(): """ :param ticker: str Returns: """ return requests.get(URL_LISTINGS, headers=headers).text
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def STALTA_picker(st, nphase=2, nsta=1e-3, nlta=4e-2, fc=50, nc=2, noise_mag=1e-25, SNR_window=5e-3): """The STA/LTA picker provides a first order good estimate of the arrival times for both the P- and S- wave. The STA/LTA picker uses :py:class:`obspy.signal.trigger.recursive_sta_lta `. :param st: ...
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def underscore_to_camel(match): """ Cast sample_data to sampleData. """ group = match.group() if len(group) == 3: return group[0] + group[2].upper() else: return group[1].upper()
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def select_tapered_estimator(debiased, direct): """Select the tapered estimator of the structure factor. Args: debiased (bool): Trigger the use of a debiased tapered estimator. direct (bool): If ``debiased`` is True, trigger the use of the direct/undirect debiased tapered estimator. Return...
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import torch def test_ae(model, dataloader, gpu, criterion): """ Computes the loss of the model, either the loss of the layer-wise AE or all the AEs in a big graph one time. :param model: the network (subclass of nn.Module) :param dataloader: a DataLoader wrapping a dataset :param gpu: (bool) if ...
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def moments(input_t, axes=None, keepdims=False): """ Returns (mean, variance) of input_t input_t Tensor axes(None) int Iterable of ints. None - all axes keepdims(False) keep reduced axes """ mean = reduce_mean(input_t, a...
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def sin(): """ Returns class instance of `Sin`. For more details, please have a look at the implementations inside `Sin`. Returns ------- Sin : Class instance implementing all 'sin' processes. """ return Sin()
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def parse_format(frm): """ Determine a struct format from a CPHD format string. Parameters ---------- frm : str Returns ------- Tuple[str, ...] """ return tuple(_map_part(el) for el in frm.strip().split(';') if len(el.strip()) > 0)
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import boto def needs_aws(test_item): """ Use as a decorator before test classes or methods to only run them if AWS usable. """ test_item = _mark_test('aws', test_item) try: # noinspection PyUnresolvedReferences except ImportError: return unittest.skip("Skipping test. " ...
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def dropout_layer(input_layer, nodropout_probability): """Dropout layer""" output = tf.nn.dropout(input_layer, nodropout_probability) return output
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def isSceneDescription(logtrack_type): """Checks if the logtrack type indicates it is a Scene Description""" return logtrack_type == LogTrackType.SCENE_DESC.value or logtrack_type == LogTrackType.SCENE_DESC2.value or \ logtrack_type == LogTrackType.SCENE_DESC3.value or logtrack_type == LogTrackType.S...
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def compile_model(context, source, dtype, fast=False): # type: (cl.Context, str, np.dtype, bool) -> cl.Program """ Build a model to run on the gpu. Returns the compiled program and its type. Raises an error if the desired precision is not available. """ dtype = np.dtype(dtype) if not a...
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def common_text(stringlist, kind='prefix'): """ For a list of strings find common prefix or suffix, returns None if no common substring of kind is not 'prefix' or 'suffix' :param stringlist: a list of strings to test :param kind: string, either 'prefix' or 'suffix' :return: """ substri...
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def _get_literal_string_prefix_len(token_string: str) -> int: """ Getting the length of the literal string prefix. Parameters ---------- token_string : str String to check. Returns ------- int Length of the literal string prefix. Examples -------- >>> examp...
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def format_view_link(body: Json) -> Json: """Format view link data. :param body: Input body. :type body: dict :return: Formatted body. :rtype: dict """ result: Json = {} if "analyzers" in body: result["analyzers"] = body["analyzers"] if "fields" in body: result["fiel...
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def local_head(venue, results): """Plot the magnitude of the local head. Plot the grid showing the relative magnitude of the estimated local head as color-coded markers. """ xtarget = np.array([row[0][0] for row in results]) ytarget = np.array([row[0][1] for row in results]) bdry = venue....
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from ..models.models import TrialMetadata from typing import Optional from typing import List def _build_trial_upload_prefixes( trial_id: Optional[str], upload_type: Optional[str] ) -> List[str]: """ Build the set of prefixes associated with the trial_id and upload_type If no trial_id is given, all tr...
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def repackage_hidden(h): """Wraps hidden states in new Variables, to detach them from their history.""" if type(h) != tuple and type(h) != list: return Variable(h.data) else: return tuple(repackage_hidden(v) for v in h)
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import warnings def _maskClouds( self, method, prob, maskCirrus, maskShadows, scaledImage, dark, cloudDist, buffer, cdi, ): """Masks clouds and shadows in an image or image collection (valid just for Surface Reflectance products). Parameters ---------- self : e...
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def next_delay(t): """Next possible pump-probe delay to the given value""" if "linear stage" in translate.mode: t = Ensemble_SAXS.next_delay(t) return t
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def get_hyperplane(point_one, point_two): """Generate a hyperplane between two points. This is achieved by finding a line that goes through the median segment between both points, that is also orthogonal to the median segment. A hyperplane in 2-dimensional space is of the form: x1 = m*x2 + b ...
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from typing import List def find_markdown(text: str, text_start: int = 0, text_end=-1, real_start: int = 0) -> (str, List[MessageEntity]): """ find nearest markdown block :param real_start: offset in plain text :param text_start: start pos in markdown text :param text_end: end pos in markdown text...
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def build_right_circular_cylinder_surface(radius, height, position, surface_num, comment): """Create a right circular cylinder in the z direction.""" surface_card = "{} RCC {} {} {} 0 0 {} {} {}".format(surface_num, position[0], position[1], round(position[2], 5), ...
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def order_nodes_from_leaves(G): """ Returns the node of G ordered from the LEAVES to the ROOTS """ return __order_nodes(G, False)
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def recursive_integration2(f, x0, x1, S, xList, tol=1e-5, recursiveLim=1e4): """ f: function of f(x) [a,b] : the interval of integration S : the previous integration result tol : the tolerance This is a subfunction of adapt_simpson. """ Sn, xListNew = myMidpointList_Integration2(f,...
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import cmath import math import itertools def _recognize_v(matrix): """ Recognizes a matrix which can be written in the following form: V = [[-sin(c/2) * exp(j*a), exp(j*(a-b)) * cos(c/2)], [exp(j*(a+b)) * cos(c/2), exp(j*a) * sin(c/2)]] Args: matrix(list): 2x2 matrix Returns: ...
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def vertices_text(text, angel_code): """Generate vertex data for a text object""" ac = angel_code o_c = ac["char"][str(ord('O'))] builtin = ac["info"]["face"] == "Bfont" scale = 0.0225 * (1.4 if builtin else 1) unit_height = o_c["height"] * scale verts = [] pos = 0 z = 0 for c...
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def list_strip_prefix(l, prefix): """Remove prefix, if it's there.""" return l[len(prefix):] if list_startswith(l, prefix) else l
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def bullets_of(id): """ Counts the number of bullets of id. """ return lookup.bullets.get(id, 0)
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def is_subcmd(opts, args): """if sys.argv[1:] does not match any getopt options, we simply assume it is a sub command to execute onecmd()""" if not opts and args: return True return False
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def sample (x, y, c=0, e=0): """ Performs logarithmic sampling on the given data. Args: x (list of float): The x-values. y (list of float): The y-values. c (int): The current offset in the data. e (int): The current exponent. Returns: pair: The sampled x and y values,...
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def set_batch_projection_args( \ args, fields=None, dataset_fields=None): """Return batch projection args dict """ batch_projection_args = set_basic_batch_args(args, args.name) if args.fields_map_ and fields is not None: if dataset_fields is None: dataset_fields = fields ...
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def FailPercent(threshold): """Tasks with FailPercent(r) will fail the DF if the task is triggered >= r percent of the total number of records in the DF Args: threshold (double): the threshold after which the DF fails. value is between 0.0 and 1.0 Returns: (DQMTaskP...
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def gauss_1(t, n, freq, pulse_delay): """ :param t: time sequence (s). :type t: list of floats :param n: time iteration index :type n: int :param freq: frequency of the sinusoid (Hz) :type freq: float :param pulse_delay: number of iteration for the delay of the signal defined in the...
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def wheel_to_variants(wheel): """Parse WHEEL file of `distribution` as per PEP427 https://www.python.org/dev/peps/pep-0427/#file-contents Arguments: wheel (str): Contents of a WHEEL file Returns: variants (dict): With keys {"platform", "os", "python"} """ variants = { ...
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def dmsp_system_3_comp_mm( c, t, f_total_in, alpha_d, alpha_c1, alpha_cp, kappa_32_d, kappa_32_c1, kappa_32_cp, vmax_34_d, vmax_34_c1, vmax_34_cp, vmax_32_d, vmax_32_c1, vmax_32_cp, transcripts_d, transcripts_c1, transcripts_cp ): """ Fu...
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from openforcefield.topology import Molecule, Topology from openforcefield.typing.engines.smirnoff import ForceField import parmed def generateSMIRNOFFStructure(oemol): """ Given an OpenEye molecule (oechem.OEMol), create an OpenMM System and use to generate a ParmEd structure using the SMIRNOFF forcefiel...
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def build_input(tfrecord_paths): """Builds the graph's input. Args: tfrecord_paths: List of paths to the input TFRecords Returns: serialized_example_tensor: The next serialized example. String scalar Tensor image_tensor: The decoded image of the example. Uint8 tensor, shape=[1, None, None,3]...
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def mean_affine(mats, shapes): """Compute a mean orientation matrix. Parameters ---------- mats : (N, dim+1, dim+1) array_like or list[(dim+1, dim+1) array_like] Input orientation matrices shapes : (N, dim) array_like or list[(dim,) array like] Input shape Returns ------- ...
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def get() -> FFCClient: """Returns the singleton Python SDK client instance, using the current configuration. To use the SDK as a singleton, first make sure you have called :func:`ffcclient.set_config()` at startup time. Then :func:`ffcclient.get()` will return the same shared :class:`ffcclient.client.FFCC...
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def prepare_deploy(id='HEAD'): """ Execute all steps which can in advance of actually switching the site live This is done to speed up activating deployments """ packaged_code, release_dir = _package_code(id) execute(deploy_package, packaged_code, release_dir) execute(install_requirements, r...
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def ShapeAnalysis_FreeBounds_SplitWires(*args): """ * Extracts closed sub-wires out of <wires> and adds them to <closed>, open wires remained after extraction are put into <open>. If <shared> is True extraction is performed only when edges share the same vertex. If <shared> is False connection is performed only w...
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def iterate(func, r, iter_num): """ function to generate the cobweb coordinates """ x = np.random.uniform(0, 1) xs = [x] ys = [x] for i in range(iter_num): xs.append(x) y = func(x, r) ys.append(y) x = y xs.append(x) ys.append(x) return xs, ys
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def start_menu(): """ Displays menu at execution start. Returns ------- name: str if provided custom environment name, else "test-env" channel_lst: lst if provided, contains additional conda-channels to install from """ print("Hello :)") #What kind of checks to add here? name = input("Please provide a na...
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def min_energy_conformer_locators(cnf_save_fs, mod_thy_info): """ Obtain the (ring-id, tors-id) filesystem locator pair and path for the conformer of a species with the lowest energy for the specified electronic structure method that currently exists in the save filesystem. :param c...
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def create_user(email='test@user.com', password='123'): """Shortcut for quick user creation""" return get_user_model().objects.create_user( email=email, password=password, first_name='Jhon', last_name='Doe' )
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def _shorten_fname(fname: str) -> str: """Reduce extraneous stuff from filenames""" fname = fname.replace(_SP, '.../site-packages') fname = fname.replace(_STD_LIB, '.../python') return fname.replace(ROOT_DIR, "napari")
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def anc_names(anc_id): """ Return formatted ANC names """ ancs = pd.read_csv('data/ancs.csv') anc_upper = 'ANC' + anc_id anc_lower = anc_upper.lower() anc_neighborhoods = ancs[ancs['anc_id'] == anc_id]['neighborhoods'].values[0] return anc_upper, anc_lower, anc_neighborhoods
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def get_psis_from_rhos(rhos, mst): """ This method is specific to MSTfit reconstructions. Note that for now I have found this method to work poorly. It seems to make the geometry more symmetric, rendering the result non-invertible. """ psis = np.zeros(rhos.shape) for i, rho in enumerate(rho...
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def probably_bool(arr): """ dumb test for bool arrays that ahve nans """ s = pd.Series(arr) counts = s.value_counts() keys = list(counts.keys()) for key in keys: if not isinstance(key, bool) and not isinstance(key, np.bool_): return False return True
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def img_dict_rgb2gray(img_dict, show=False): """ Extract a channel from the rgb image, so that a width*height*1 matrix is achieved. :param img_dict: a dictionary with 4 key/value pairs: "features", "labels", "sizes", "coords" :param channel: available channels: "GRAY" :return: a dictionary with 4 ke...
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from typing import List def exif_gps_date_fields() -> List[List[str]]: """ Date fields in EXIF GPS """ return [["GPS GPSDate", "EXIF GPS GPSDate"]]
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def _calc_power_spectrum(phase): """ Helper function to assist with memory re-allocation during FFT calculation """ fft_phase = fft2(phase) pspec = real(fft_phase) ** 2 + imag(fft_phase) ** 2 return pspec.astype(dtype=np.float32)
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from tensorflow.keras import Model from tensorflow.keras.layers import Conv2D, Flatten, Dense, MaxPool2D, BatchNormalization, ReLU import typing from datetime import datetime def prepare_model( stations: typing.Dict[typing.AnyStr, typing.Tuple[float, float, float]], target_time_offsets: typing.List[da...
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def split_segmentation_by_intersection(a, b, min_size): """Computes the intersection of two segmentations. Intersects two spatially overlapping segmentations and assigns a new ID to every unique (id1, id2) pair of overlapping voxels. If 'id2' is the largest object overlapping 'id1', their intersection retains ...
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from typing import Union from typing import List def fill_prediction_str( y: float, Y: Union[np.ndarray, None] = None, classes: Union[List[str], str, None] = None, decimals: int = 3, ) -> str: """Create a string describing the prediction Args: y (float): the prediction Y (Unio...
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def check_dtable_permission(username, workspace, dtable=None): """Check workspace/dtable access permission of a user. """ owner = workspace.owner if dtable: dtable_share = DTableShare.objects.get_by_dtable_and_to_user(dtable, username) if dtable_share: return dtable_share.pe...
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def get_calculated_attributes(df, axes=None, history=None): """ Functions to automate netCDF attribute generation from the data itself This is a wrapper for the other four functions, which could be called separately. :param df: data (Pandas DataFrame) :param axes: keys (x,y,z,t) are associated with act...
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def cron_method(handler): """ Decorator to indicate that this is a cron method and applies request.headers check """ def check_if_cron(self, *args, **kwargs): """ Check if it is executed by Cron in Staging or Production Allow run in localhost calling the url """ ...
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def fetch_urls_from_list_of_pages(urls: list, results_number: int): """Extract results_number urls from given pages. :param urls: given pages to extract urls :param results_number: number or urls to extract :return: list of urls """ all_urls = [] for url in urls: all_urls += fetch_...
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def nti(note): """ Note to index returns the index of enharmonic note names or False if not found """ return notes.get(note, False)
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def can_edit_project_fn(user, proj, file): """ Check if a user can edit a proposal. Used to show/hide editbuttons on detailproposal and for the can_edit_project decorator. :param user: user :param proj: proposal :param file: whether editing a file. This is not allowed in limited edit mode (stat...
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from pathlib import Path from bs4 import BeautifulSoup def get_exc_page_contents(html_string, current_dir_path, dig_parent_dir_path, readfile): """Extract the html contents linked to from within a exc_**.html file.""" full_current_dir_path = Path(dig_parent_dir_path) / ("." + current_dir_path) frames = B...
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def divide_by(array_list, num_workers): """Divide a list of parameters by an integer num_workers. :param array_list: :param num_workers: :return: """ for i, x in enumerate(array_list): array_list[i] /= num_workers return array_list
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def lemmatizing(text): """ input: string Lemmatize input using nltk WordNetLemmatizer (eg wolves -> wolf) output: string """ return ' '.join([wnl.lemmatize(word) for word in text.split(' ')])
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def _find_match(ele, lst): """ Find a matching element in a list. """ for _ele in lst: for match_key in _MATCH_KEYS: if _ele.get(match_key) == ele.get(match_key): return ele
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def get_grams(text, from_=1, to_=3): """ Takes text as an input and returns N-grams, which are consecutive strings of N words. :param text: Text to convert to n-grams. :param from_: The size of the smallest n-gram. :param to_: The size of the biggest n-gram. :return: Generator that returns ...
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def make_root_node(state): """ Construct the initial root node without parent nor action """ return SearchNode(state, None, None)
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def net_dashboard(request): """ Network vulnerability Dashboard. :param request: :return: """ all_openvas_data = scan_save_db.objects.all() all_nessus_data = nessus_scan_db.objects.all() all_network_data = chain(all_openvas_data, all_nessus_data ...
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import copy def merge_dicts(dict1, dict2, make_copy=True): """ Recursively merges dict2 with dict1. Otherwise if both dict1 and dict2 have a key, it is overwritten by the value in dict2. """ if make_copy: dict1 = copy.copy(dict1) for key, value in dict2.iteritems(): if isinstance(dict1.get(key), dict)...
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def confirm(prompt): """Displays the prompt, only returns true with input 'Y' or 'y'.""" confirmation = input(COLORS["yellow"] + prompt + COLORS["endc"]).lower() return confirmation == "y"
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def comments(): """ Full-page comments view. """ return make_response(render_template('comments.html', **make_context()))
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def netcdf_to_pandas(file_path: str, last_x_years: int = 30) -> pd.DataFrame: """ Parses either the air or precip weather dataset from the University of Delaware and outputs the not null data in a long format pandas dataframe. Data per month is averaged over the `last_x_years`. Parameters -----...
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def get_const_diff_ints(ints, length): """f(n) = an + b""" first = ints[0] diff = ints[1] - ints[0] return [first + diff * n for n in range(length)]
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def remove_invalid_req_args(credentials_dict, invalid_args): """ This function iterates through the invalid_args list and removes the elements in that list from credentials_dict and adds those to a new dictionary Returns: credentials_dict: Input dictionary after popping the elements in ...
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def pre_process(image, h_w_c_size, if_random_crop=True, if_flip=False, if_bright=False, if_contrast=False, if_whiten=False): """ Do preprocessing for image data. Atgs: image: tensor with shape [height,width,channal]. h_w_size: integer python list. if_random_crop: boo...
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def schulze(winning_votes: dict[tuple[str, str], int]) -> SchulzeResult: """Use Schulze method to find winners and strength of strongest path""" candidates = set(chain.from_iterable(winning_votes)) strengths = {} for a, b in permutations(candidates, 2): if winning_votes[a, b] > winning_votes[b...
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def box_config_put(node_addon, user_addon, auth, **kwargs): """View for changing a node's linked box folder.""" folder = request.json.get('selected') uid = folder['id'] path = folder['path'] node_addon.set_folder(uid, auth=auth) return { 'result': { 'folder': { ...
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def create_normal_buffer(vertices, triangles): """ Creates normal vectors for each vertex on the mesh. Qt requires each vertex to have it's own normal. :param vertices: The vertices for the mesh :param triangles: A list of the triangles that make up each face in the mesh :return: A list of the n...
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def _get_base_query(export_instance): """ Return an ESQuery object for the given export instance. Includes filters for domain, doc_type, and xmlns/case_type. """ if isinstance(export_instance, FormExportInstance): return get_form_export_base_query( export_instance.domain, ...
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def NormalizeFilePath(file_path): """Normalizes the file path. 0. Strip leading "/" or "\". 1. Convert "\", "\\", and "//" to "/" 2. Resolve ".." and "." from the file path. 3. Extract relative file path from the root src of a chromium repo checkout. eg.: //BUILD.gn -> BUILD.gn ../a/b/c.cc -> a/b...
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def fill_var(current_var: list or str or int or float or dict, new_var: any) -> list or any: """ This is another of those functions that probably already exist or what i am trying to do is not wise. Anway it either directly returns new_var if current_var is either an empty string or None. If not it creates ...
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import csv def read_csv_as_dict(path, delimiter=','): """Accepts a path, creates a file object, and returns a list of dictionaries that represent the row values. Parameters: path (str): path to file delimiter (str): delimiter that overrides the default delimiter Returns: list...
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def product_detail_view(request, id): """Product detail view and newsletter as context""" product = get_object_or_404(Product, id=id) context = { 'newsletter_form': SubscriberForm(), "product": product } return render(request, "product_detail.html", context)
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def tf_frequency_weight(t_inst, weight_type = 'linear', factor = 1.0): """ Compute a per-instruction weighting based on inverse frequency """ freqs = np.array([0.456536, 0.456536, 0.001150, 0.026873, 0.012083, 0.000129, 0.012083, 0.000129, 0.012083, 0.000129, 0.012083, 0.000129, 0.002053, 0.002053, 0.00...
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def fields_for_repeated_item(field_name, fields): """Unpack field specifications for repeated items. Given the following message: message Item { string title = 1; } message Something { repeated Item items = 1; } We support specifying sepcific field...
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def bottleneck_lstm(inputs,state,filters): """ Bottleneck lstm from: https://arxiv.org/pdf/1711.06368.pdf :param inputs: Input featuremap [B,H,W,C] :param state: Previous state [B,H,W,C] :param filters: number of output channels :return: tuple containing outp...
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def data_already_scaled(data): """ Test if data looks like it is already standardised """ return abs(np.mean(np.mean(data, axis=0))) < 0.1
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def calcRmsDistancesVsRef(groupView, refVisit, magRange, band, verbose=False): """Calculate the RMS distance of a set of matched objects over visits. Parameters ---------- groupView : lsst.afw.table.GroupView GroupView object of matched observations from MultiMatch. magRange : length-2 `astr...
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def _area_interpolate_binning( source_df, target_df, extensive_variables=None, intensive_variables=None, table=None, allocate_total=True, spatial_index="auto", ): """ Area interpolation for extensive and intensive variables. Parameters ---------- source_df : geopandas.Ge...
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import random def update_masks(pop, infectivity, risk, m, u): """ Grants masks to m proportion of the unmasked susceptible and infected population Take away masks from u proportion of the masked susceptible and infected population """ sus_m = get_indices(pop.flatten(), 'S', True) inf_m = g...
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def _get_panel_cls(value): """return the class best suited for displaying 'value'""" if _pandas_available: if isinstance(value, (pa.DataFrame, pa.Series)): return DataFramePanel if isinstance(value, dict): return DictPanel elif isinstance(value, (list, tuple, deque)): ...
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from datetime import datetime import time def get_ttl(ttl_days, start_date=datetime.datetime.today()): """Get ttl value epoch format to insert into DDB TTL field Arguments: ttl_days {int} -- Number of days to keep the record Keyword Arguments: start_date {datetime} -- Starting timestamp ...
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