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from typing import List def _hostnames() -> List[str]: """Returns all host names from the ansible inventory.""" return sorted(_ANSIBLE_RUNNER.get_hosts())
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def seabass_to_pandas(path): """SeaBASS to Pandas DataFrame converter Parameters ---------- path : str path to an FCHECKed SeaBASS file Returns ------- pandas.DataFrame """ sb = readSB(path) dataframe = pd.DataFrame.from_dict(sb.data) return dataframe
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def countVisits(item, value=None): """This function takes a pandas.Series of item tags, and an optional string for a specific tag and returns a numpy.ndarray of the same size as the input, which contains either 1) a running count of unique transitions of item, if no target tag is given, or 2) a running ...
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import numpy as np import torch from pathlib import Path def test_run_inference(ml_runner_with_container: MLRunner, tmp_path: Path) -> None: """ Test that run_inference gets called as expected. """ def _expected_files_exist() -> bool: output_dir = ml_runner_with_container.container.outputs_fol...
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def gen_accel_table(table_def): """generate an acceleration table""" table = [] for i in range(1001): table.append(0) for limit_def in table_def: range_start, range_end, limit = limit_def for i in range(range_start, range_end + 1): table[i] = limit return table
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from typing import Tuple import torch def dataset_constructor( config: ml_collections.ConfigDict, ) -> Tuple[ torch.utils.data.Dataset, torch.utils.data.Dataset, torch.utils.data.Dataset ]: """ Create datasets loaders for the chosen datasets :return: Tuple (training_set, validation_set, test_set) ...
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def ensemble_log_params(m, params, hess=None, steps=scipy.inf, max_run_hours=scipy.inf, temperature=1.0, step_scale=1.0, sing_val_cutoff=0, seeds=None, recalc_hess_alg = False, recalc_func=None, save...
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import os def issue_config_exists(repo_path): """ returns True if the issue template config.yml file exists in the repo_path """ path_to_config = repo_path + "/.github/ISSUE_TEMPLATE/config.yml" return os.path.exists(path_to_config)
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import os def _read(fd): """Default read function.""" return os.read(fd, 1024)
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def get_metrics(actual_classes, pred_classes): """ Function to calculate performance metrics for the classifier For each class, the following is calculated TP: True positives = samples that were correctly put into the class TN: True negatives = samples that were correctly not put into the class ...
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import dateutil def extract_tika_meta(meta): """Extracts and normalizes metadata from Apache Tika. Returns a dict with the following keys set: - content-type - author - date-created - date-modified - original-tika-meta The dates are encoded in the ISO format.""" ...
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def __gen_pause_flow(testbed_config, src_port_id, flow_name, pause_prio_list, flow_dur_sec): """ Generate the configuration for a PFC pause storm Args: testbed_config (obj): L2/L3 config of a T0 testbed src_...
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def parse_str_to_bio(str, dia_act): """ parse str to BIO format """ intent = parse_intent(dia_act) w_arr, bio_arr = parse_slots(str, dia_act) bio_arr[-1] = intent return ' '.join(w_arr), ' '.join(bio_arr), intent
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def train_early_stop( update_fn, validation_fn, optimizer, state, max_epochs=1e4, **early_stop_args ): """Run update_fn until given validation metric validation_fn increases. """ logger = Logger() check_early_stop = mask_scheduler(**early_stop_args) for epoch in jnp.arange(max_epochs): (...
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from typing import List def get_povm_object_names() -> List[str]: """Return the list of valid povm-related object names. Returns ------- List[str] the list of valid povm-related object names. """ names = ["pure_state_vectors", "matrices", "vectors", "povm"] return names
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def choose(a,b): """ n Choose r function """ a = op.abs(round(a)) b = op.abs(round(b)) if(b > a): a, b = b, a return factorial(a) / (factorial(b) * factorial(a-b))
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from typing import List import torch from typing import Optional def pad_and_stack_list_of_tensors(lst_embeddings: List[torch.Tensor], max_sequence_length: Optional[int] = None, return_sequence_length: bool = False): """ it takes the list of embeddings as the input, then appl...
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from typing import List def bq_solid_for_queries(sql_queries): """ Executes BigQuery SQL queries. Expects a BQ client to be provisioned in resources as context.resources.bigquery. """ sql_queries = check.list_param(sql_queries, 'sql queries', of_type=str) @solid( input_defs=[InputDe...
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def mock_accession_unreplicated( mocker: MockerFixture, mock_accession_gc_backend, mock_metadata, lab: str, award: str, ) -> Accession: """ Mocked accession instance with dummy __init__ that doesn't do anything and pre-baked assembly property. @properties must be patched before instantia...
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from typing import Optional def get_prepared_statement(statement_name: Optional[str] = None, work_group: Optional[str] = None, opts: Optional[pulumi.InvokeOptions] = None) -> AwaitableGetPreparedStatementResult: """ Resource schema for AWS::Athena::Prepare...
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def handle_col(element, box, _get_image_from_uri, _base_url): """Handle the ``span`` attribute.""" if isinstance(box, boxes.TableColumnBox): integer_attribute(element, box, 'span') if box.span > 1: # Generate multiple boxes # http://lists.w3.org/Archives/Public/www-style/...
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def get_dotted_field(input_dict: dict, accessor_string: str) -> dict: """Gets data from a dictionary using a dotted accessor-string. Parameters ---------- input_dict : dict A nested dictionary. accessor_string : str The value in the nested dict. Returns ------- dict ...
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import re def separa_frases(sentenca): """[A funcao recebe uma sentenca e devolve uma lista das frases dentro da sentenca] Arguments: sentenca {[str]} -- [recebe uma frase] Returns: [lista] -- [lista das frases contidas na sentença] """ return re.split(r'[,:;]+', sentenca)
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import pathlib import json import importlib def read_datasets(path=None, filename="datasets.json"): """Read the serialized (JSON) dataset list """ if path is None: path = _MODULE_DIR else: path = pathlib.Path(path) with open(path / filename, 'r') as fr: ds = json.load(fr) ...
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def as_actor(input, actor) : """Takes input and actor, and returns [as <$actor>]$input[endas].""" if " " in actor : repla = "<%s>"%actor else : repla = actor return "[as %s]%s[endas]" % (repla, input)
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def error_403(request): """View rendered when encountering a 403 error.""" return error_view(request, 403, _("Forbidden"), _("You are not allowed to acces to the resource %(res)s.") % {"res": request.path})
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def _format_param(name, optimizer, param): """Return correctly formatted lr/momentum for each param group.""" if isinstance(param, (list, tuple)): if len(param) != len(optimizer.param_groups): raise ValueError("expected {} values for {}, got {}".format( len(optimizer.param_gr...
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def as_binary_vector(labels, num_classes): """ Construct binary label vector given a list of label indices. Args: labels (list): The input label list. num_classes (int): Number of classes of the label vector. Returns: labels (numpy array): the resulting binary vector. """ ...
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def evaluation_lda(model, data, dictionary, corpus): """ Compute coherence score and perplexity. params: model: lda model data: list of lists (tokenized) dictionary corpus returns: coherence score, perplexity score """ coherence_model_lda = CoherenceModel(model=model, texts=data, di...
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def get_map_with_square(map_info, square): """ build string of the map with its top left bigger square without obstacle full """ map_string = "" x_indices = list(range(square["x"], square["x"] + square["size"])) y_indices = list(range(square["y"], square["y"] + square["size"])) M = map_i...
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def bgr_colormap(): """ In cdict, the first column is interpolated between 0.0 & 1.0 - this indicates the value to be plotted the second column specifies how interpolation should be done from below the third column specifies how interpolation should be done from above if the second column does not equal the t...
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def autovalidation_from_docstring(): """ Test validation using JsonSchema The default payload is invalid, try it, then change the age to a valid integer and try again --- tags: - officer parameters: - name: body in: body required: true schema: i...
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import requests def get_vlan_groups(url, headers): """ Get dictionary of existing vlan groups """ vlan_groups = [] api_url = f"{url}/api/ipam/vlan-groups/" response = requests.request("GET", api_url, headers=headers) all_vlan_groups = response.json()["results"] for vlan_group in all_vl...
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def getLastReading(session: Session) -> Reading: """ Finds the last reading associated with the session NB: Always returns a Reading, because every Session has at least 1 Reading Args: session (Session): A Session object representing the session record in the database Returns: date...
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def process_outlier(data, population_set): """ Parameters ---------- data population_set Returns ------- """ content = list() for date in set(map(lambda x: x['date'], data)): tmp_item = { "date": date, "value": list() } for val...
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import six def valid_http(http_success=HTTPOk, # type: Union[Type[HTTPSuccessful], Type[HTTPRedirection]] http_kwargs=None, # type: Optional[ParamsType] detail="", # type: Optional[Str] content=None, # typ...
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def operating_cf(cf_df): """Checks if the latest reported OCF (Cashflow) is positive. Explanation of OCF: https://www.investopedia.com/terms/o/operatingcashflow.asp cf_df = Cashflow Statement of the specified company """ cf = cf_df.iloc[cf_df.index.get_loc("Total Cash From Operating Activities"...
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from io import StringIO def generate_performance_scores(query_dataset, target_variable, candidate_datasets, params): """Generates all the performance scores. """ performance_scores = list() # params algorithm = params['regression_algorithm'] cluster_execution = params['cluster'] hdfs_add...
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import cmath import math def correct_sparameters_twelve_term(sparameters_complex,twelve_term_correction,reciprocal=True): """Applies the twelve term correction to sparameters and returns a new sparameter list. The sparameters should be a list of [frequency, S11, S21, S12, S22] where S terms are complex number...
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def api_activity_logs(request): """Test utility.""" auth = get_auth(request) obj = ActivityLogs(auth=auth) check_apiobj(authobj=auth, apiobj=obj) return obj
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def RNAshapes_parser(lines=None,order=True): """ Returns a list containing tuples of (sequence,pairs object,energy) for every sequence [[Seq,Pairs,Ene],[Seq,Pairs,Ene],...] Structures will be ordered by the structure energy by default, of ordered isnt desired set order to False """ resu...
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from typing import Callable from typing import Optional from typing import Union from typing import Dict from typing import Any def get_case_strategy( # pylint: disable=too-many-locals draw: Callable, operation: APIOperation, hooks: Optional[HookDispatcher] = None, data_generation_method: DataGenerat...
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def type_from_value(value, visitor=None, node=None): """Given a Value from resolving an annotation, return the type.""" ctx = _Context(visitor, node) return _type_from_value(value, ctx)
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def _accesslen(data) -> int: """This was inspired by the `default_collate` function. https://github.com/pytorch/pytorch/blob/master/torch/utils/data/_utils/ """ if isinstance(data, (tuple, list)): item = data[0] if not isinstance(item, (float, int, str)): return len(item) ...
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def createSkill(request, volunteer_id): """ Method to create skills and interests :param request: :param volunteer_id: :return: """ if request.method == 'POST': volunteer = Volunteer_User_Add_Ons.objects.get(pk=volunteer_id) skills = request.POST.getlist('skills') in...
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def analyticJacobian(robot : object, dq = 0.001, symbolic = False): """Using Homogeneous Transformation Matrices, this function computes Analytic Jacobian Matrix of a serial robot given joints positions in radians. Serial robot's kinematic parameters have to be set before using this function Args: robot (Seria...
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def test_sharedmethod_reuse_on_subclasses(): """ Regression test for an issue where sharedmethod would bind to one class for all time, causing the same method not to work properly on other subclasses of that class. It has the same problem when the same sharedmethod is called on different instan...
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import os import inspect def get_subtask_spec_factory_classes(): """Return dictionary with all factory classes defined in files in this directory. This file is excluded from the search.""" this_file = os.path.split(__file__)[-1] directory = os.path.dirname(__file__) exclude = [this_file, "subtask...
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def triu_indices_from(arr, k=0): """ Returns the indices for the upper-triangle of `arr`. Args: arr (Union[Tensor, list, tuple]): 2-dimensional array. k (int, optional): Diagonal offset, default is 0. Returns: triu_indices_from, tuple of 2 tensor, shape(N) Indices for t...
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def is_debug(): """Return true if xylem is set to debug console output.""" global _debug return _debug
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def func(var): """Function""" return var + 1
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def flanking_regions_fasta_deletion(genome, dataframe, flanking_region_size): """ Makes batch processing possible, pulls down small region of genome for which to design primers around. This is based on the chromosome and position of input file. Each Fasta record will contain: >Sample_Gene_chr:...
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import functools def numpy_episodes( train_dir, test_dir, shape, loader, preprocess_fn=None, scan_every=10, num_chunks=None, **kwargs): """Read sequences stored as compressed Numpy files as a TensorFlow dataset. Args: train_dir: Directory containing NPZ files of the training dataset. test...
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def fft_convolve(ts, query): """ Computes the sliding dot product for query over the time series using the quicker FFT convolution approach. Parameters ---------- ts : array_like The time series. query : array_like The query. Returns ------- array_like - The sli...
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from typing import List from typing import Optional def _add_merge_gvcfs_job( b: hb.Batch, gvcfs: List[hb.ResourceGroup], output_gvcf_path: Optional[str], sample_name: str, ) -> Job: """ Combine by-interval GVCFs into a single sample GVCF file """ job_name = f'Merge {len(gvcfs)} GVCFs...
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def register_permission(name, codename, ctypes=None): """Registers a permission to the framework. Returns the permission if the registration was successfully, otherwise False. **Parameters:** name The unique name of the permission. This is displayed to the customer. codename The u...
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def calculate_outliers(tile_urls, num_outliers, cache, nprocs): """ Fetch tiles and calculate the outlier tiles per layer. The number of outliers is per layer - the largest N. Cache, if true, uses a local disk cache for the tiles. This can be very useful if re-running percentile calculations. ...
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import random def load_trigger_dataset( fname, templatizer, limit=None, train=False, preprocessor_key=None, priming_dataset=None, max_priming_examples=64, ): """ Loads a MLM classification dataset. Parameters ========== fname : str The filename. templatizer...
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def pmu2bids(physio_files, verbose=False): """ Function to read a list of Siemens PMU physio files and save them as a BIDS physiological recording. Parameters ---------- physio_files : list of str list of paths to files with a Siemens PMU recording verbose : bool verbose fla...
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def add_chain(length): """Adds a chain to the network so that""" chained_works = [] chain = utils.generate_chain(length) for i in range(len(chain)-1): agent_id = get_random_agent().properties(ns.KEY_AGENT_ID).value().next() work_id = g.create_work().properties(ns.KEY_WORK_ID).value().nex...
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from vartools.result import re_fit_data import sys def re_fit(file_name, top_c, bot_c): """ re-fits a prepared oocyte file (-t and -b flags for top and bot constraints)""" if top_c == "True": top_c = True elif top_c == "False": top_c = False else: sys.exit("Invalid option: " + ...
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def convert_graph_to_db_format(input_graph: nx.Graph, with_weights=False, cast_to_directed=False): """Converts a given graph into a DB format, which consists of two or three lists 1. **Index list:** a list where the i-th position contains the index of the beginning of the list of adjacent nodes (in the se...
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def auxiliary_subfields(): """Factory associated with AuxSubfieldsPoroelasticity. """ return AuxSubfieldsPoroelasticity()
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def cassandra_get_unit_data(): """ Basing function to obtain units from db and return as dict :return: dictionary of units """ kpi_dict = {} cassandra_cluster = Cluster() session = cassandra_cluster.connect('pb2') query = session.prepare('SELECT * FROM kpi_units') query_data = sessio...
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def read_cfg_float(cfgp, section, key, default): """ Read float from a config file Args: cfgp: Config parser section: [section] of the config file key: Key to be read default: Value if couldn't be read Returns: Resulting float """ if cfgp.has_option(section, key...
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def random(website): """ 随机获取cookies :param website:查询网站给 如:weibo :return:随机获取的cookies """ g = get_conn() cookies = getattr(g, website + '_cookies').random() return cookies
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import requests def get_pid(referral_data): """ Example getting PID using the same token used to query AD NOTE! to get PID the referral information must exist in the BETA(UAT) instance of TOMS """ referral_uid = referral_data['referral_uid'] url = "https://api.beta.genomics.nhs.uk/reidentific...
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from typing import Union from pathlib import Path from typing import Tuple from typing import List from datetime import datetime def open_events( fname: Union[Path, str], leap_sec: float, get_frame_rate: bool = False ) -> Tuple[ List[float], List[float], List[float], List[datetime], Union[List[float], None] ]...
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def intdags_permutations(draw, min_size:int=1, max_size:int=10): """ Produce instances of a same DAG. Instances are not nesessarily topologically sorted """ return draw(lists(permutations(draw(intdags())), min_size=min_size, max_size=max_size))
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def getConfiguredGraphClass(doer): """ In this class method, we must return a configured graph class """ # if options.bReified: # DU_GRAPH = Graph_MultiSinglePageXml_Segmenter_Separator_DOM if options.bSeparator: DU_GRAPH = ConjugateSegmenterGraph_MultiSinglePageXml_Separator els...
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def find_amped_polys_for_syntheticidle(qubit_filter, idleStr, model, singleQfiducials=None, prepLbl=None, effectLbls=None, initJ=None, initJrank=None, wrtParams=None, algorithm="greedy", require_all_amped=True, ...
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def _seed(x, deg=5, seeds=None): """Seed the greedy algorithm with (deg+1) evenly spaced indices""" if seeds is None: f = lambda m, n: [ii*n//m + n//(2*m) for ii in range(m)] indices = np.sort(np.hstack([[0, len(x)-1], f(deg-1, len(x))])) else: indices = seeds errors = [] return indices, errors
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def get_ref(cube): """Gets the 8 reflection symmetries of a nd numpy array""" L = [] L.append(cube[:,:,:]) L.append(cube[:,:,::-1]) L.append(cube[:,::-1,:]) L.append(cube[::-1,:,:]) L.append(cube[:,::-1,::-1]) L.append(cube[::-1,:,::-1]) L.append(cube[::-1,::-1,:]) L.append(cube[...
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from typing import Collection from typing import Tuple from typing import Optional from typing import Mapping def get_relation_functionality( mapped_triples: Collection[Tuple[int, int, int]], add_labels: bool = True, label_to_id: Optional[Mapping[str, int]] = None, ) -> pd.DataFrame: """Calculate rela...
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import json def df_to_vega_lite(df, path=None): """ Export a pandas.DataFrame to a vega-lite data JSON. Params ------ df : pandas.DataFrame dataframe to convert to JSON path : None or str if None, return the JSON str. Else write JSON to the file specified by path. ...
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def _is_json_mimetype(mimetype): """Returns 'True' if a given mimetype implies JSON data.""" return any( [ mimetype == "application/json", mimetype.startswith("application/") and mimetype.endswith("+json"), ] )
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from datetime import datetime def make_request(action, data, token): """Make request based on passed arguments and timestamp.""" return { 'action': action, 'time': datetime.now().timestamp(), 'data': data, 'token': token }
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def get_stats_historical_prices(timestamp, horizon): """ We assume here that the price is a random variable following a normal distribution. We compute the mean and covariance of the price distribution. """ hist_prices_df = pd.read_csv(HISTORICAL_PRICES_CSV) hist_prices_df["timestamp"] = pd.to_d...
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def _unflattify(values, shape): """ Unflattifies parameter values. :param values: The flattened array of values that are to be unflattified :type values: torch.Tensor :param shape: The shape of the parameter prior :type shape: torch.Size :rtype: torch.Tensor """ if len(shape) < 1 or...
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def theme_cmd(data, buffer, args): """Callback for /theme command.""" if args == '': weechat.command('', '/help ' + SCRIPT_COMMAND) return weechat.WEECHAT_RC_OK argv = args.strip().split(' ', 1) if len(argv) == 0: return weechat.WEECHAT_RC_OK if argv[0] in ('install',): ...
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def get_unique_chemical_names(reagents): """Get the unique chemical species names in a list of reagents. The concentrations of these species define the vector space in which we sample possible experiments :param reagents: a list of perovskitereagent objects :return: a list of the unique chemical names...
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def get_sorted_keys(dict_to_sort): """Gets the keys from a dict and sorts them in ascending order. Assumes keys are of the form Ni, where N is a letter and i is an integer. Args: dict_to_sort (dict): dict whose keys need sorting Returns: list: list of sorted keys from dict_to_sort ...
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def model_3d(psrs, psd='powerlaw', noisedict=None, components=30, gamma_common=None, upper_limit=False, bayesephem=False, wideband=False): """ Reads in list of enterprise Pulsar instance and returns a PTA instantiated with model 3D from the analysis paper: per pulsar: ...
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def max_votes(x): """ Return the maximum occurrence of predicted class. Notes ----- If number of class 0 prediction is equal to number of class 1 predictions, NO_VOTE will be returned. E.g. Num_preds_0 = 25, Num_preds_1 = 25, Num_preds_NO_VOTE = 0, ...
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def misclassification_error(y_true: np.ndarray, y_pred: np.ndarray, normalize: bool = True) -> float: """ Calculate misclassification loss Parameters ---------- y_true: ndarray of shape (n_samples, ) True response values y_pred: ndarray of shape (n_samples, ) Predicted response ...
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from scipy.stats import uniform def dunif(x, minimum=0,maximum=1): """ Calculates the point estimate of the uniform distribution """ result=uniform.pdf(x=x,loc=minimum,scale=maximum-minimum) return result
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def _generate_upsert_sql(mon_loc): """ Generate SQL to insert/update. """ mon_loc_db = [(k, _manipulate_values(v, k in TIME_COLUMNS)) for k, v in mon_loc.items()] all_columns = ','.join(col for (col, _) in mon_loc_db) all_values = ','.join(value for (_, value) in mon_loc_db) update_query = '...
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import functools def filtered_qs(func): """ #TODO: zrobić, obsługę funkcji z argumentami :param func: :return: """ @functools.wraps(func) def wrapped(self, *args, **kwargs): ret_qs = func(self) return ret_qs.filter(*args, **kwargs) return wrapped
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def dict2obj(d): """Given a dictionary, return an object with the keys mapped to attributes and the values mapped to attribute values. This is recursive, so nested dictionaries are nested objects.""" top = type('dict2obj', (object,), d) seqs = tuple, list, set, frozenset for k, v in d.items(): ...
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def customized_algorithm_plot(experiment_name='finite_simple_sanity', data_path=_DEFAULT_DATA_PATH): """Simple plot of average instantaneous regret by agent, per timestep. Args: experiment_name: string = name of experiment config. data_path: string = where to look for the files. Returns: p: ggplot p...
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def _get_log_time_scale(units): """Retrieves the ``log10()`` of the scale factor for a given time unit. Args: units (str): String specifying the units (one of ``'fs'``, ``'ps'``, ``'ns'``, ``'us'``, ``'ms'``, ``'sec'``). Returns: The ``log10()`` of the scale factor for the time...
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def resolvermatch(request): """Add the name of the currently resolved pattern to the RequestContext""" match = resolve(request.path) if match: return {'resolved': match} else: return {}
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def selection_sort(arr: list) -> list: """ Main sorting function. Using "find_smallest" function as part of the algorythm. :param arr: list to sort :return: sorted list """ new_arr = [] for index in range(len(arr)): smallest = find_smallest(arr) new_arr.append(arr.pop(sma...
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def get_primary_monitor(): """ Returns the primary monitor. Wrapper for: GLFWmonitor* glfwGetPrimaryMonitor(void); """ return _glfw.glfwGetPrimaryMonitor()
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def query_people_and_institutions(rc, names): """Get the people and institutions names.""" people, institutions = [], [] for person_name in names: person_found = fuzzy_retrieval(all_docs_from_collection( rc.client, "people"), ["name", "aka", "_id"], person_name, c...
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from typing import Union from typing import Tuple def add_device(overlay_id) -> Union[str, Tuple[str, int]]: """ Add device to an overlay. """ manager = get_manager() api_key = header_api_key(request) if not manager.api_key_is_valid(api_key): return jsonify(error="Not authorized"), 403...
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from math import sin, cos def pvtol(t, x, u, params={}): """Reduced planar vertical takeoff and landing dynamics""" m = params.get('m', 4.) # kg, system mass J = params.get('J', 0.0475) # kg m^2, system inertia r = params.get('r', 0.25) # m, thrust offset g = params.get('g', 9.8) # m/...
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from typing import List from typing import Any from typing import Callable def route( path: str, methods: List[str], **kwargs: Any ) -> Callable[[AnyCallable], AnyCallable]: """General purpose route definition. Requires you to pass an array of HTTP methods like GET, POST, PUT, etc. The remaining kwargs a...
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import wx def canHaveGui(): """Return ``True`` if a display is available, ``False`` otherwise. """ # We cache this because calling the # IsDisplayAvailable function will cause the # application to steal focus under OSX! try: return wx.App.IsDisplayAvailable() except ImportError: ...
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def syntactic_analysis(input_fd): """ Realiza análisis léxico-gráfico y sintáctico de un programa Tiger. @type input_fd: C{file} @param input_fd: Descriptor de fichero del programa Tiger al cual se le debe realizar el análisis sintáctico. @rtype: C{LanguageNode} @return: Como ...
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