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from typing import List def load_actions(action_file: str) -> List[str]: """ Load unique actions from an action file """ return load_uniq_lines(action_file)
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def get_formula(name, sbml_model, params, assignment_rules, replacements): """ get a string representation for a function definition with parameters already replaced @param name: function name @type name: str @param sbml_model: libsbml model @type sbml_model: libsbml.model @param params: par...
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def ConvertFile(filename_in, filename_out, loglevel='INFO'): """ Converts an ANSYS input file to a python pyansys script. Parameters ---------- filename_in : str Filename of the ansys input file to read in. filename_out : str Filename of the python script to write a translation...
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from typing import Optional def get_metadata_saml(idp_id: Optional[str] = None, opts: Optional[pulumi.InvokeOptions] = None) -> AwaitableGetMetadataSamlResult: """ Use this data source to retrieve SAML IdP metadata from Okta. ## Example Usage ```python import pulumi imp...
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from typing import Dict def _average_latency(row: Dict): """ Calculate average latency for Performance Analyzer single test """ avg_sum_fields = [ "Client Send", "Network+Server Send/Recv", "Server Queue", "Server Compute", "Server Compute Input", "Serve...
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from typing import Dict from typing import Any import json import re def load_dict_from_string(string: str) -> Dict[str, Any]: """Convert string to JSON string, convert to a dictionary, and return.""" logger.debug('Loading Dictionary from string: "{}"'.format(string)) json_string = jsonify_string(string)...
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def _(expr, assumptions): """ Integer**Integer -> !Prime """ if expr.is_number: return _PrimePredicate_number(expr, assumptions) if ask(Q.integer(expr.exp), assumptions) and \ ask(Q.integer(expr.base), assumptions): return False
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import tqdm import torch def train(model, trainLoader, optimizer, loss_function, device, trainParams): """ Function to train the model for one iteration. (Generally, one iteration = one epoch, but here it is one step). It also computes the training loss, CER and WER. The CTC decode scheme is always 'gree...
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def reorder(A, B): """Change coefficient order from y**2 xy x**2 to x**2 xy y**2 in both A and B. Parameters ---------- A : array polynomial coefficients B : array polynomial coefficients Returns ------- A2, B2: numpy arrays coefficients with changed order ...
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import functools import collections def collate_revs(old, new, key=lambda x: x, merge=lambda old, new: new): """ Given revision sets old and new, each containing a series of revisions of some set of objects, collate them based on these rules: - all items from each set are yielded in stable order ...
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from typing import Tuple from typing import List def load_conversation( filename: str, dictionary: corpora.Dictionary, with_symbol: bool=True ) -> (Tuple[List[int], List[int]]): """対話コーパスをロードする。 Args: filename (str): コーパスファイル コーパスファイルの一行は 何 が 好き です か ?,Python ...
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def close_incons_reduction(incons: list): """ Two step: 0. under the same backends pair 1. the same input, choose largest.(done before) * 2. different inputs with small distance. Do not update(not used) """ def is_duplicate(t: tuple, li: list): """unique inconsistency""" for...
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def mf2tojf2(mf2): """I'm going to have to recurse here""" jf2={} items = mf2.get("items",[]) jf2=flattenProperties(items,isOuter=True) #print jf2 return jf2
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def import_all(filename): """ Imports file contents from user with parameters from nueral net and later calculations currently not robust to missing or incorrect arguments from file currently does not convert values to int; done in later functions inputs: filename - name of input file, curre...
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from typing import Union from pathlib import Path from typing import Dict from typing import Tuple from typing import Any def fill_database(path: Union[str, Path], settings: SettingsConfig, inputs: MeasurementInputs, alchemy: Alchemy, parent_location_id: int, sex_id: int, child_pri...
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def ydhms2dt(year,doy,hh,mm,ss): """ ydhms2dt Take a year, day-of-year, etc and convert it into a date time object Usage: dto = ydhms2dt(year,day,hh,mm,ss) Input: year - 4 digit integer doy - 3 digit, or less integer, (1 <= doy <= 366) hh - 2 digit, or less int, (0 <= hh <...
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def create_test_db(verbosity=1, autoclobber=False): """ Creates a test database, prompting the user for confirmation if the database already exists. Returns the name of the test database created. """ # If the database backend wants to create the test DB itself, let it creation_module = get_creat...
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import _ctypes def key_import(data, key_type=KEY_TYPE.SYMMETRIC, password=b''): """Imports a key or key generation parameters.""" key = _ctypes.c_void_p() _lib.yaca_key_import(key_type.value, _ctypes.c_char_p(password), data, len(data), _ctypes.byref(key)) return Key(key)
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def test_training_arguments_timestamp(monkeypatch, grim_config): """Test TrainingWrapperArguments correctly applies a timestamp.""" def mock_return(): return '2019-06-29_17-13-41' monkeypatch.setattr(grimagents.common, "get_timestamp", mock_return) grim_config['--timestamp'] = True argume...
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def to_vsizip(zipfn, relpth): """ Create path from zip file """ return "/vsizip/{}/{}".format(zipfn, relpth)
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import sys def readMashDBParams(dbPrefix, kmers, sketch_sizes, mash_exec = 'mash'): """Get kmers lengths and sketch sizes from existing database Calls :func:`~getKmersFromReferenceDatabase` and :func:`~getSketchSize` Uses passed values if db missing Args: dbPrefix (str) Prefix fo...
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import fastr def crossval(config, label_data, image_features, param_grid=None, use_fastr=False, fastr_plugin=None, tempsave=False, fixedsplits=None, ensemble={'Use': False}, outputfolder=None, modus='singlelabel'): """ Constructs multiple individual classifi...
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def flw3i8e(ex, ey, ez, ep, D, eq=None): """ Compute element stiffness (conductivity) matrix for 8 node isoparametric field element. Parameters: ex = [x1,x2,x3,...,x8] ey = [y1,y2,y3,...,y8] element coordinates ez = [z1,z2,z3,...,z8] ep = [ir] ...
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def cidr_to_netmask(value): """ Converts a CIDR prefix-length to a network mask. Examples: >>> "{{ '24'|cidr_to_netmask }}" -> "255.255.255.0" """ return str(netaddr.IPNetwork("1.1.1.1/{}".format(value)).netmask)
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def rgb_to_name(rgb_triplet: IntTuple, spec: str = CSS3) -> str: """ Convert a 3-tuple of integers, suitable for use in an ``rgb()`` color triplet, to its corresponding normalized color name, if any such name exists. The optional keyword argument ``spec`` determines which specification's list o...
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def get_rr_Lix(N, Fmat, psd, x): """ Given a rank-reduced decomposition of the Cholesky factor L, calculate L^{-1}x where x is some vector. This way, we don't have to built L, which saves memory and computational time. @param N: Vector with the elements of the diagonal matrix N @param Fma...
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def ParameterSet_Create(*args): """ Create() -> ParameterSet ParameterSet_Create(std::string const & publicID) -> ParameterSet """ return _DataModel.ParameterSet_Create(*args)
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def generate_html_from_cli_args(cli_dict_for_command): """ Turn the dict into an html representation of the cli args and options. :param cli_dict_for_command: :return str: """ # def arg_md(opt, long_opt, default, help): # return f"*) {opt}, {long_opt}, {help}\n" text = "" # ev...
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def conical_sigma_Mach_walldeflection(Mach, deflection, gamma=defg._gamma): """computes shock angle sigma from upstream Mach number and wall deflection Args: Mach: param deflection: gamma: Default value = defg._gamma) deflection: Returns: """ def local_def(sig): """inte...
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def get_hashrate_info(results, miner, algo): """ Get Hashrate Information for a particular Miner and Algo Returns: dict """ # do the lookup hashrate_info = results.get_hashrate_info(miner, algo) if hashrate_info is None: logger.warning("Model/Algo combination does not ex...
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import hashlib def verify_verification_code(doctype, document_name, verification_code): """This method verfies the user verification code by fetching the originally sent code by the system from cache. Args: doctype (str): Name of the DocType. document_name (str): Name of the document of the D...
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def orient1(ppos, apos, bpos): """ ORIENT1 return orientation of PP wrt. the line [PA, PB]. """ #---------------------------------------------- calc. det(S) smat = np.empty( (2, 2, ppos.shape[0]), dtype=ppos.dtype) smat[0, 0, :] = \ apos[:, 0] - ppos[:, 0] smat[0, 1, :] = \ ...
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def get_storm_data(storm_path): """ Obtain raster grid of the storm with rasterio Arguments: *storm_path* (string) -- path to location of storm """ with rio.open(storm_path) as src: # Read as numpy array array = src.read(1) array = np.array(array,dtype='flo...
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import functools def wrap_with_spectral_norm(module_class, sn_kwargs=None, pow_iter_collection=None): """Returns a constructor for the inner class with spectral normalization. This function accepts a Sonnet AbstractModule class as argument (the class, *no...
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def ask_daemon_sync(view, ask_type, ask_kwargs, location=None): """Jedi sync request shortcut. :type view: sublime.View :type ask_type: str :type ask_kwargs: dict or None :type location: type of (int, int) or None """ daemon = _get_daemon(view) return daemon.request( ask_type, ...
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import logging import time def _etl_epacems(etl_params, datapkg_dir, pudl_settings, ds_kwargs): """Extract, transform and load CSVs for EPA CEMS. Args: etl_params (dict): ETL parameters required by this data source. datapkg_dir (path-like): The location of the directory for this p...
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def GetNvccOptions(argv): """Collect the -nvcc_options values from argv. Args: argv: A list of strings, possibly the argv passed to main(). Returns: 1. The string that can be passed directly to nvcc. 2. The leftover options. """ parser = ArgumentParser() parser.add_argument('-nvcc_options', n...
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import json def show_node(request, name='', path='', revision=''): """ View for show_node page, which provides context for show_node.html Shows description for yang modules. :param request: Array with arguments from webpage data submition. :param module: Takes first argument from url if request do...
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def compute_F1(TP, TN, FP, FN): """ Return the F1 score """ numer = 2 * TP denom = 2 * TP + FN + FP F1 = numer/denom Acc = 100. * (TP + TN) / (TP + TN + FP + FN) return F1, Acc
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def name_full_data(): """Full name data.""" return { "name": "Doe, John", "given_name": "John", "family_name": "Doe", "identifiers": [ { "identifier": "0000-0001-8135-3489", "scheme": "orcid" }, { "identifier...
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def platypus(in_file, data): """Filter Platypus calls, removing Q20 filter and replacing with depth and quality based filter. Platypus uses its own VCF nomenclature: TC == DP, FR == AF Platypus gVCF output appears to have an 0/1 index problem so the reference block regions are 1 base outside regions o...
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def delete(i): """ Input: { See 'rm' function } Output: { See 'rm' function } """ return rm(i)
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import logging def _get_remote_image_id(s3_object) -> str: """ Get the image id of the docker cache which is represented by the S3 object :param s3_object: S3 object :return: Image id as string or None if object does not exist """ try: if S3_METADATA_IMAGE_ID_KEY in s3_object.metadata:...
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def test_circuit_str(default_compilation_configuration): """Test function for `__str__` method of `Circuit`""" def f(x): return x + 42 x = hnp.EncryptedScalar(hnp.UnsignedInteger(3)) inputset = range(2 ** 3) circuit = hnp.compile_numpy_function(f, {"x": x}, inputset, default_compilation_c...
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def add_game(): """Adds game to database""" check_admin() add_game = True form = GameForm() # Checks if form is valid if form.validate_on_submit(): game = Game(name=form.name.data) try: db.session.add(game) db.session.commit() flash('Game suc...
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def requires_moderation(page): """Returns True if page requires moderation """ return bool(page.get_moderator_queryset().count())
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from typing import Optional def _get_node_info( node: NodeObject, current_path: str, node_type: str, label: Optional[str] = None, is_leaf: bool = True ) -> NodeInfo: """ Utility method for generating a NodeInfo from a NodeObject :param node: NodeObject to convert in...
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def get_peers(): """Retrieve PeerIds and SSIDs for peers that are ready for OOB transfer""" query = 'SELECT Ssid, PeerId from EphemeralState WHERE PeerState=1' data = exec_query(query, db_path_peer) return data
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from bs4 import BeautifulSoup def get_html_text(html): """ Return the raw text of an ad """ if html: doc = BeautifulSoup(html, "html.parser") return doc.get_text(" ") return ""
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def valid_parentheses(string): """ Takes a string of parentheses, and determines if the order of the parentheses is valid. :param string: a string of parentheses and characters. :return: true if the string is valid, and false if it's invalid. """ stack = [] for x in string: if x == "...
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import os import ctypes def find_microbit(): """ Returns a path on the filesystem that represents the plugged in BBC micro:bit that is to be flashed. If no micro:bit is found, it returns None. Works on Linux, OSX and Windows. Will raise a NotImplementedError exception if run on any other oper...
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def in_2core_graph_slow(cats: ArrayLike) -> BoolArray: """ Parameters ---------- cats: {DataFrame, ndarray} Array containing the category codes of pandas categoricals (nobs, ncats) Returns ------- retain : ndarray Boolean array that marks non-singleton entries as Tru...
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def has_form_encoded_header(header_lines): """Return if list includes form encoded header""" for line in header_lines: if ":" in line: (header, value) = line.split(":", 1) if header.lower() == "content-type" \ and "x-www-form-urlencoded" in value: ...
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from pathlib import Path def get_best_checkpoint_path(path: Path) -> Path: """ Given a path and checkpoint, formats a path based on the checkpoint file name format. :param path to checkpoint folder """ return path / LAST_CHECKPOINT_FILE_NAME_WITH_SUFFIX
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def storage_charge_rule(model, technology, timepoint): """ Storage cannot charge at a higher rate than implied by its total installed power capacity. Charge and discharge rate limits are currently the same. """ return model.Charge[technology, timepoint] + model.Provide_Power[technology, timepoint] <...
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def blck_void(preprocessor: Preprocessor, args: str, contents: str) -> str: """The void block, processes commands inside it but prints nothing""" if args.strip() != "": preprocessor.send_warning("extra-arguments", "the void block takes no arguments") preprocessor.context.update(preprocessor.current_position.end, "...
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import typing def resize_image(image: np.ndarray, width: typing.Optional[int] = None, height: typing.Optional[int] = None, interpolation=cv2.INTER_AREA): """ Resize image using given width or/and height value(s). If both values are passed, aspect ratio is...
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def attr(*args, **kwargs): """Decorator that adds attributes to classes or functions for use with unit tests runner. """ def wrapped(element): for name in args: setattr(element, name, True) for name, value in kwargs.items(): setattr(element, name, value) r...
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def convert_units(table_name, value, value_unit, targets): """ Converts a given value in a unit to a set of target units. @param table_name Name of table units are contained in @param value Value to convert @param value_unit Unit value is currently in @param targets List of units to convert to ...
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import os def find_vital_library_path(use_cache=True): """ Discover the path to a VITAL C interface library based on the directory structure this file is in, and then to system directories in the LD_LIBRARY_PATH. :param use_cache: Store and use the cached path, preventing redundant search...
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def hex2binary(hex_num): """ converts from hexadecimal to binary """ hex1 = h[hex_num[0]] hex2 = h[hex_num[1]] return str(hex1) + str(hex2)
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def nn(value: int) -> int: """Casts value to closest non negative value""" return 0 if value < 0 else value
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def resolve_vcf_counts_data(vcf_data, maf_data, matched_normal_sample_id, tumor_sample_data_col): """ Resolves VCF allele counts data. """ vcf_alleles = [vcf_data["REF"]] vcf_alleles.extend(vcf_data["ALT"].split(",")) tumor_sample_format_data = vcf_data["MAPPED_TUMOR_FORMAT_DATA"] normal_sample_for...
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def example_profile_metadata_target(): """Generates an example profile metadata document. >>> root = example_profile_metadata_target() >>> print_tree(root) <?xml version='1.0' encoding='UTF-8'?> <Profile xmlns="http://soap.sforce.com/2006/04/metadata"> <classAccesses> <apexClass>ARTra...
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def separate(expr, deep=False): """Rewrite or separate a power of product to a product of powers but without any expanding, ie. rewriting products to summations. >>> from sympy import * >>> x, y, z = symbols('x', 'y', 'z') >>> separate((x*y)**2) x**2*y**2 >>> separate((x...
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import os def get_sub_dirs(path: str): """Get sub-directories contained in a specified directory Args: path (str): path to directory Returns: str: lists of absolute paths str: list of dir names """ try: dirs = os.walk(path).next()[1] except AttributeError: ...
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def app_base(request): """ This should render the required HTML to start the Angular application. It is the only entry point for the pyramid UI via Angular :param request: A pyramid request object, default for a view :return: A dictionary of variables to be rendered into the template """ de...
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from typing import List import re def check_lists(document: Document, args: Args) -> List[Issue]: """Check that markdown lists items: - Are preceded by a blank line. - Are not left empty. - End with a period if they're a list of sentences. - End without a period if they're a list of items.""" ...
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def transform_one(mt, vardp_outlier=100_000) -> Table: """transforms a gvcf into a form suitable for combining The input to this should be some result of either :func:`.import_vcf` or :func:`.import_vcfs` with `array_elements_required=False`. There is a strong assumption that this function will be cal...
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def volume_rebalance(volume: str) -> Result: """ # This function doesn't do anything yet. It is a place holder because # volume_rebalance is a long running command and I haven't decided how to # poll for completion yet # Usage: volume rebalance <VOLNAME> fix-layout start | start # [force]|stop|...
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import json def get_droplet_ip(): """get droplet ip from cache.""" cached_droplet_info_file = 'droplet_info.json' with open(cached_droplet_info_file, 'r') as info_f: droplet_info = json.load(info_f) return droplet_info['networks']['v4'][0]['ip_address']
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def country_converter(text_input, abbreviations_okay=True): """ Function that detects a country name in a given word. :param text_input: Any string. :param abbreviations_okay: means it's okay to check the list for abbreviations, like MX or GB. :return: """ # Set default values country_...
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def lat_long_to_idx(gt, lon, lat): """ Take a geotransform and calculate the array indexes for the given lat,long. :param gt: GDAL geotransform (e.g. gdal.Open(x).GetGeoTransform()). :type gt: GDAL Geotransform tuple. :param lon: Longitude. :type lon: float :param la...
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def bugs_mapper(bugs, package): """ Update package bug tracker and support email and return package. https://docs.npmjs.com/files/package.json#bugs The url to your project's issue tracker and / or the email address to which issues should be reported. { "url" : "https://github.com/owner/project/i...
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def BSMlambda(delta: float, S: float, V: float) -> float: """Not really a greek, but rather an expression of leverage. Arguments --------- delta : float BSM delta of the option V : float Spot price of the option S : float Spot price of the underlying Returns...
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import pwd def uid_to_name(uid): """ Find the username associated with a user ID. :param uid: The user ID (an integer). :returns: The username (a string) or :data:`None` if :func:`pwd.getpwuid()` fails to locate a user for the given ID. """ try: return pwd.getpwuid(uid)....
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def fit_poly(data, error_func, degree = 3): """ Fit a polynomial to given data, using supplied error function. Parameters ---------- data: 2D array where each row is a point (X0, Y) error_func: function that computes the error between a polynomial and observed data degree: polynomial degree ...
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def find_skyrmion_center_2d(fun, point_up=False): """ Find the centre the skyrmion, suppose only one skyrmion and only works for 2d mesh. `fun` accept a dolfin function. `point_up` : the core of skyrmion, points up or points down. """ V = fun.function_space() mesh = V.mesh() c...
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import time def test(num_games, opponent, silent): """ Test running a number of games """ def autoplayer_creator(state): """ Create a normal autoplayer instance """ return AutoPlayer(state) def minimax_creator(state): """ Create a minimax autoplayer instance """ return Au...
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import webbrowser def pseudo_beaker(UserId: str, SessionId: str, replay=True, scope=True, browser=None, OrgId: str=None, is_staging: bool=True) -> dict: """ Mimic the Beaker admin tool in opening up one or both of session replay and Scope tools for a given User Id and Session Id. Option to specify a ...
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def table_parse(table): """ """ data = [] rows = table.find_all('tr') for row in rows: cols = row.find_all('td') cols = [ele.text.strip() for ele in cols] data.append([ele for ele in cols if ele]) return data
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import pandas import numpy def scan_mv_preprocessing_fill_pivot_nan(df): """ Value imputation. Impute missing data in pivot table. Parameters ---------- df : dataframe Pivot table data with potentially missing values. Returns ------- df : dataframe Pivot table da...
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def image_show(request,item_container): """ zeigt die Beschreibung der Datei an """ app_name = 'image' vars = get_item_vars_show(request, item_container, app_name) file_path = DOWNLOAD_PATH + item_container.container.path file_name = file_path + item_container.item.name width, height = get_image_size(file_n...
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import logging import collections import functools def train_and_eval(): """Train and evaluate StackOver NWP task.""" logging.info('Show FLAGS for debugging:') for f in HPARAM_FLAGS: logging.info('%s=%s', f, FLAGS[f].value) hparam_dict = collections.OrderedDict([ (name, FLAGS[name].value) for name ...
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def common_kwargs(cfg, bin_count, pointing): """Creates a prepfold-friendly dictionary of common arguments to pass to prepfold""" name = generate_prep_name(cfg, bin_count, pointing) prep_kwargs = {} if cfg["run_ops"]["mask"]: prep_kwargs["-mask"] = cfg["run_ops"]["mask"] prep_kwargs["-o"] = ...
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def quatMultiply(q1,q2): """Returns a quaternion that is a composition of two quaternions Parameters ---------- q1: 1 x 4 numpy array representing a quaternion q2: 1 x 4 numpy array representing a quatnernion Returns ------- qM: 1 x 4 numpy array rep...
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def expandingPrediction(input_list, multiple=5): """ :param input_list: :param multiple: :return: """ expanded_list = [] for prediction in input_list: for i in range(multiple): expanded_list.append(prediction) return expanded_list
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def pages_siblings_menu(context, page, url='/'): """Get the parent page of the given page and render a nested list of its child pages. Good for rendering a secondary menu. :param page: the page where to start the menu from. :param url: not used anymore. """ lang = context.get('lang', pages_sett...
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def aes(img, mask=None, canny_edges=None, canny_sigma=2): """Calculate the Average Edge Strength Reference: Aksoy, M., Forman, C., Straka, M., Çukur, T., Hornegger, J., & Bammer, R. (2012). Hybrid prospective and retrospective head motion correction to mitigate cross-calibration errors. Magnetic ...
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def projection(basis, vectors): """ The vectors live in a k dimensional space S and the columns of the basis are vectors of the same space spanning a subspace of S. Gives a representation of the projection of vector into the space spanned by basis in term of the basis. :param basis: an n-by-k array...
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import json import os def _build_execution_context(worker_index, ports): """ Create execution context for the model. :param worker_index: The index of this worker in a distributed setting. :param ports: A list of port numbers that will be used in setting up the servers. :return: The generated exec...
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import numpy def grab(sequence, random = numpy.random): """ Return a randomly-selected element from the sequence. """ return sequence[random.randint(len(sequence))]
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def csl_url_args_retriever(): """Returns the style and locale passed as URL args for CSL export.""" style = resource_requestctx.args.get("style") locale = resource_requestctx.args.get("locale") return style, locale
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import glob import os def list_available_filter(): """ List all available filter responses Returns ------- filter_dict : dict Dictionary of filter names containing lists of available instruments """ filter_list = glob(FILTER_DIR + '*_*.dat') filter_dict = {} for filter_fi...
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import random def select_parents(population, m): """Select randomly parents for the new population from sorted by fitness function existing population.""" fitness_population = sorted( population, key=lambda child: fitness_function(child, m), reverse=True) # ordered_population =...
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def rsqrt(x: Tensor): """Computes reciprocal of square root of x element-wise. Args: x: input tensor Returns: output tensor Examples: >>> x = tf.constant([2., 0., -2.]) >>> rsqrt(x) <Tensor: shape=(3,), dtype=float32, numpy=array([0.707, inf, nan], dtype=f...
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def averageObjPeg(objpegpts, planet, catalog=None, sceneid='NO_POL'): """ Average peg points. """ logger.info('Combining individual peg points: %s' % sceneid) peg = stdproc.orbit.pegManipulator.averagePeg([gp.getPeg() for gp in objpegpts], planet) pegheights = [gp.getAverageHeight() for gp in ob...
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def _bytes_chr_py2(i): """ Returns a byte string of length 1 whose ordinal value is i in Python 2. Do not call directly, use bytes_chr instead. """ return chr(i)
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from typing import Any def convert(parser: Any) -> c2gtypes.ParserRep: """Convert getopt to a dict. Args: parser (Any): docopt parser Returns: c2gtypes.ParserRep: dictionary representing parser object """ return {"parser_description": "", "widgets": extract(parser)}
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def redirect_vurlkey(request, vurlkey, *args, **kwargs): """redirect_vurlkey(vurlkey) looks up the Vurl with base58-encoded index VURLKEY and issues a redirect to the target URL""" v = Vurl.get_with_vurlkey(vurlkey.encode('utf-8')) return v.http_response()
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