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def create_output(whole_exome_indel_list, whole_exome_snp_list, coding_exons_indel_list, coding_exons_snp_list): """ This function creates the output file. :param whole_exome_indel_list: A list the values for a single output line. :type whole_exome_indel_list: list :param whole_exome_snp_list: A li...
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def get_offset(sample_time): """ Find simple offsett values. During the sample time of this function the BBB with the magnetometer on should be rotated along all axis. sample_time is in seconds """ start = time.clock() mag_samples = [] mag_max = [0,0,0] mag_min = [0,0,0] ...
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def get_zips(directory: str) -> list: """ Return a the ZIP from a specified directory after running some sanity checks """ zips = {} for file in [os.path.join(dp, file) for dp, dn, fn in os.walk(directory) for file in fn]: if file.split('.')[-1] != 'zip': continue ...
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def get_multimode_2d_dist(num_modes: int = 1, scale: float = 1.0): """Get a multimodal distribution of Gaussians.""" angles = jnp.linspace(0, jnp.pi * 2, num_modes + 1) angles = angles[:-1] x, y = jnp.cos(angles) * scale / 2., jnp.sin(angles) * scale / 2. loc = jnp.array([x, y]).T scale = jnp.ones((num_mode...
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def residual_squared_error(data_1, data_2): """ Calculation the residual squared error between two arrays. Parameters ---------- data: numpy array Data calc: numpy array Calculated values Return ------ rse: float residual squared error """ RSS = np....
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def by_index(pot): """ Build a new potential where the keys of the potential dictionary correspond to the indices along values of n-dimensional grids, rather than, possibly, the coordinate values of the grids themselves. Key Transformation: ((grid_val_i, grid_val_j, ...)_i,) -> ((i,...
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def current_user(): """Получить текущего пользователя или отредактировать профиль""" user = get_user_from_request() if request.method == "POST": json = request.get_json() user.email = json.get("email", user.email) user.name = json.get("name", user.name) user.about = sanitiz...
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def writelines_infile(filename,lines): """Writelines in the specific file""" with open(filename,"w") as file: file.writelines(lines)
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def test_impossible_traveler_det_distance_bad_dest_coords(mocker): """ Given: Coordinations lists to calculate distances between, when the two are different When: Calculating impossible traveler distances Then Raise an error """ with pytest.raises(ValueError) as e: ...
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async def async_union_polygons(bal_name, geom_list): """union a set of polygons & return the resulting multipolygon""" start_time = datetime.now() big_poly = unary_union(geom_list) print(f"\t - {bal_name} : set of polygons unioned: {datetime.now() - start_time}") return big_poly
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async def test_websocket_get_triggers(hass, hass_ws_client, device_reg, entity_reg): """Test we get the expected triggers from a light through websocket.""" await async_setup_component(hass, "device_automation", {}) config_entry = MockConfigEntry(domain="test", data={}) config_entry.add_to_hass(hass) ...
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def _error_text(because: str, text: str, backend: usertypes.Backend) -> str: """Get an error text for the given information.""" other_backend, other_setting = _other_backend(backend) if other_backend == usertypes.Backend.QtWebKit: warning = ("<i>Note that QtWebKit hasn't been updated since " ...
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def COUNT(condition: pd.DataFrame, n: int): """the number of days fits the 'condition' in the past n days Args: condition (pd.DataFrame): dataframe index by date time(level 0) and asset(level 1), containing bool values n (int): the number of past days """ return condition.rollin...
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def Mat33_nrow(): """Mat33_nrow() -> int""" return _simbody.Mat33_nrow()
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def test_build_instru23(): """USE_PL=0 PL_OVERLOAD_NEW_DELETE=0""" build_target("testprogram", test_build_instru23.__doc__)
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def isstruct(ob): """ isstruct(ob) Returns whether the given object is an SSDF struct. """ if hasattr(ob, '__is_ssdf_struct__'): return bool(ob.__is_ssdf_struct__) else: return False
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def where_between(field_name, start_date, end_date): """ Return the bit of query for the dates interval. """ str = """ {0} between date_format('{1}', '%%Y-%%c-%%d %%H:%%i:%%S') and date_format('{2}', '%%Y-%%c-%%d 23:%%i:%%S') """ .format( field_name, ...
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def to_console_formatted_string(data: dict) -> str: """...""" def make_line(key: str) -> str: if key.startswith('__cauldron_'): return '' data_class = getattr(data[key], '__class__', data[key]) data_type = getattr(data_class, '__name__', type(data[key])) value = '{...
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def cluster_instance_get_info_ajax(request, c_id): """ get cluster instance status """ dic = {"res": True, "info":None, "err":None} instance_id = request.GET.get("instance_id") require_vnc = request.GET.get("require_vnc") if require_vnc == "true": require_vnc = True else: require_vnc = False if instance_id...
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def timeit(verbose=False): """ Time functions via decoration. Optionally output time to stdout. Parameters: ----------- verbose : bool Example Usage: >>> @timeit(verbose=True) >>> def foo(*args, **kwargs): pass """ def _timeit(f): @wraps(f) def wrapper(*args, **...
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async def _iter_reference_values( client: redis.ResourceClient, index: redis.ResourceIndex, key: _RedisKeyT, *, window_size: int = DEFAULT_WINDOW_SIZE, match: typing.Optional[str] = None, ) -> typing.AsyncIterator[typing.Iterator[typing.Optional[bytes]]]: """Asynchronously iterate over slice...
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def signal_period(peaks, sampling_rate=1000, desired_length=None, interpolation_order="cubic"): """Calculate signal period from a series of peaks. Parameters ---------- peaks : list, array, DataFrame, Series or dict The samples at which the peaks occur. If an array is passed i...
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def model_co_group_by_key_tuple(email_list, phone_list, output_path): """Applying a CoGroupByKey Transform to a tuple. URL: https://cloud.google.com/dataflow/model/group-by-key """ import google.cloud.dataflow as df from google.cloud.dataflow.utils.options import PipelineOptions p = df.Pipeline(options=Pip...
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def get_recommendation(anime_name, cosine_sim, clean_anime, anime_index): """ Getting pairwise similarity scores for all anime in the data frame. The function returns the top 10 most similar anime to the given query. """ idx = anime_index[anime_name] sim_scores = list(enumerate(cosine_sim[idx]))...
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def get_nwb_metadata(experiment_id): """ Collects metadata based on the experiment id and converts the weight to a float. This is needed for further export to nwb_converter. This function also validates, that all metadata is nwb compatible. :param experiment_id: The experiment id given by the us...
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def string_to_value_error_mark(string: str) -> Tuple[float, Union[float, None], str]: """ Convert string to float and error. Parameters ---------- string : str DESCRIPTION. Returns ------- value : float Value. error : float Error. """ value, error, ...
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def _children_with_tags(element, tags): """Returns child elements of the given element whose tag is in a given list. Args: element: an ElementTree.Element. tags: a list of strings that are the tags to look for in child elements. Returns: an iterable of ElementTree.Element instances, which are the ch...
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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 in HPARAM_FLAGS ]) if FLAGS.experiment_type == '...
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def align_with_known_width(val, width: int, lowerBitCntToAlign: int): """ Does same as :func:`~.align` just with the known width of val """ return val & (mask(width - lowerBitCntToAlign) << lowerBitCntToAlign)
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def get_email_from_request(request): """Use cpg-utils to extract user from already-authenticated request headers.""" user = get_user_from_headers(request.headers) if not user: raise web.HTTPForbidden(reason='Invalid authorization header') return user
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def test_get_authorization_header(authorizer): """ Get authorization header, confirms expected value """ assert authorizer.get_authorization_header() == "Bearer " + TOKEN
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def get_kernels(params: List[Tuple[str, int, int, int, int]]) -> List[np.ndarray]: """ Create list of kernels :param params: list of tuples with following format ("kernel name", angle, multiplier, rotation angle) :return: list of kernels """ kernels = [] # type: List[np.ndarray] for param i...
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def forward_propagation(propagation_start_node, func, x): """A forward propagation starting at the `propagation_start_node` and wrapping the all the composition operations along the way. Parameters ---------- propagation_start_node : Node The node where the gradient function (or anything si...
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def main(): """ Main function of the script. """ args = parse_args() if args.version: print("{v}".format(v=__version__)) return 0 config = ConfigFile(args.config_file, CONFIG_FILE_SCHEMA) if args.help_config: print(config.help()) return 0 if args.conf...
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def read_entities(): """ find list of entities :return: """ intents = Entity.objects.only('name','id') return build_response.sent_json(intents.to_json())
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def available(unit, item) -> bool: """ If any hook reports false, then it is false """ for skill in unit.skills: for component in skill.components: if component.defines('available'): if component.ignore_conditional or condition(skill, unit): if not...
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def step_impl(context, easting, northing, index): """ :type context: behave.runner.Context :param easting: The easting value from the trajectory at index. :type easting: float :param northing: The northing value for the trajectory at index. :type northing: float :param index: The index of th...
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def cleanArray(arr): """Clean an array or list from unsupported objects for plotting. Objects are replaced by None, which is then converted to NaN. """ try: return np.asarray(arr, float) except ValueError: return np.array([x if isinstance(x, number_types) else None ...
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def translate_node_in_object_space(node, translation_list, **kwargs): """ Translates given node with the given translation vector :param node: str :param translation_list: list(float, float, float) """ raise NotImplementedError()
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def test_datetime(snapshot): """Simple test with datetime""" expect = datetime.datetime(2017, 11, 19) snapshot.assert_match(expect)
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def parse_args(): """Main function for parsing args. Utilizes the 'check_config' function from the config module to ensure an API key has been passed. If not, user is prompted to conduct initial configuration for pwea. If a valid configuration is found (there is currently no validity check for ...
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def test_tcp_server_ssl(sdc_builder, sdc_executor): """Runs a test using the TCP server origin pipeline with Enable TLS set and asserts that the file is received""" expected_msg = get_expected_message(TCP_SSL_FILE_PATH) # Start TCP server pipeline. pipeline_builder = sdc_builder.get_pipeline_builder() ...
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def check_in_federated_context(): """Checks if the current context is a `tff.program.FederatedContext`.""" context_stack = get_context_stack.get_context_stack() if not isinstance(context_stack.current, FederatedContext): raise ValueError( 'Expected the current context to be a `tff.program.FederatedCon...
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def _ensure_args(G, source, method, directed, return_predecessors, unweighted, overwrite, indices): """ Ensures the args passed in are usable for the API api_name and returns the args with proper defaults if not specified, or raises TypeError or ValueError if incorrectly specified. ...
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def read_siemens_scil_b0(): """ Load Siemens 1.5T b0 image form the scil b0 dataset. Returns ------- img : obj, Nifti1Image """ file = pjoin(dipy_home, 'datasets_multi-site_all_companies', '1.5T', 'Siemens', 'b0.nii.gz'...
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def twin_primes(): """ Twin Primes: Primes that are two more or less than another prime\n OEIS A001097 """ P = primes() a,b,c = next(P),next(P),next(P) while True: if b-2 == a or b+2 == c: yield b a,b,c = b,c,next(P)
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def gdpcleaner(gdpdata: pd.DataFrame): """ Author: Gabe Fairbrother Remove spurious columns, Rename relevant columns, Remove NaNs Parameters ---------- gdpdata: DataFrame a loaded dataframe based on a downloaded Open Government GDP at basic prices dataset (https://open.canada.ca/en/open...
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def sort_with_num(path): """Extract leading numbers in a file name for numerical sorting.""" fname = path.name nums = re.match('^\d+', fname) if nums: return int(nums[0]) else: return 0
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def ship_new(name): """Creates a new ship.""" click.echo(f"Created ship {name}")
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def test_get_representative_trip_for_route(request): """ Tests that parameters are read """ print("\n--Starting:", request.node.name) transit_network = Transit.load_all_gtfs_feeds( path = os.path.join(root_dir, "data", "external", "gtfs", "2015"), roadway_network= roadway_network, ...
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def prob8(cur: sqlite3.Cursor) -> pd.DataFrame: """Give a list of the services which connect the stops 'Craiglockhart' and 'Tollcross'. Parameters ---------- cur (sqlite3.Cursor) : The cursor for the database we're accessing. Returns ------- (pd.DataFrame) : Table with the ...
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def get_command(name): """ return command represented by name """ _rc = COMMANDS[name]() return _rc
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def start_adash(self): """Start Adash in background inside VM.""" adash_start_command = ( "./adash-linux-x86_64 --bindhost 0.0.0.0 -bindport 8081 -notoken &" ) with When( "Connect to VM and run the Adash in background", description=f"{adash_start_command}", ): ba...
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def _str_struct(a): """converts the structure to a string for logging purposes.""" shape_dtype = lambda x: (jnp.asarray(x).shape, str(jnp.asarray(x).dtype)) return str(jax.tree_map(shape_dtype, a))
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def get_moved_files(dir_path: str) -> Set: """ 获取要移动的文件(夹),包括: - 文件夹 - 损坏的图片 - 非图像文件 - 重复的图片 """ removed_files = set() file_map = {} for file in os.listdir(dir_path): file_path = os.path.join(dir_path, file) # 过滤文件 if os.path.isfile(file_pa...
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def delete_interface_address( api_client, interface_id, address_id, **kwargs ): # noqa: E501 """delete_interface_address # noqa: E501 Delete interface address details # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_re...
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async def set_promo(message: types.Message, state: FSMContext): """ Команда /setpromo """ arg = message.get_args() if not arg: return await message.answer(_("Укажите аргумент: промокод. Например: <pre>/set_promo my-promo-code</pre>"), parse_mode="HTML") ...
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def plot_waterfall(*sigObjs, step=10, xLim:list=None, Pmin=20, Pmax=None, tmin=0, tmax=None, azim=-72, elev=14, cmap='jet', winPlot=False, waterfallPlot=True, fill=True, lines=False, alpha=1, figsize=(20, 8), winAlpha=0, removeGridLines=Fal...
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def write_output( payload: Union[dict, List[dict]], out_handle: TextIO, fmt: str = "json", compact: bool = False, indent: int = 4, ) -> None: """Writes the given dictionary as JSON or YAML to the output handle. :param payload: Payload to write. :param out_handle: Output handle. :par...
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def play_game(game): """Run the checkers game This is the entry function that runs the entire game. """ game.show_rules() game.get_player_names() while True: curr_player = game.black_name if game.blacks_turn else \ game.white_name # Prompt for player input mo...
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def test_pytest_really_fails(): """Make sure pytest fails due to incorrect expected output in the .md. Generate a pytest that will assert. """ simulator_status = verify.one_example( "phmdoctest tests/unexpected_output.md --outfile discarded.py", want_file_name=None, pytest_optio...
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def indices(input_file): """ Parse the index file or target file and return a list of values. :return: """ index_list = [] line_num = 0 index_file = list(csv.reader(open(input_file), delimiter='\t')) for line in index_file: line_num += 1 col_count = len(line) if...
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def parse_arguments(): """ Parse the arguments from the user """ parser = argparse.ArgumentParser( description="omeClust visualization script.\n", formatter_class=argparse.RawTextHelpFormatter) parser.add_argument( "adist", help="the input file D*N, Rows: D feature...
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def checkSequences(numl, rowlen, seqlen): """In a square of numbers, represented by the list with the given row length, look for the top product with length of seqlen""" listl=len(numl) collen=math.ceil(listl/rowlen) seqind=seqlen-1 log.debug("List length, collen: %d, %d", listl, collen) ...
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def has_same_facts(ruler_intervals1, ruler_intervals2, D): """ Check whether the two same-pattern ruler lists have the same facts at each corresponding ruler-interval Args: ruler_intervals1: a list of ruler-intervals ruler_intervals2: a list of ruler-intervals D: contain all relation...
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def listenInput(username): """Listens user input and returns formatted messages (PeerMessage) using generators.""" print('Starting listening user input...') while (True): msgToSend = input() if (len(msgToSend) == 0): continue timeStr = datetime.datetime.now().strftime('%...
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def named_keywords_params_func2(name, age, *info, qq, **kwargs): """ #如果函数定义中已经有了一个可变参数,后面跟着的命名关键字参数就不再需要一个特殊分隔符*了 """ print(name, age, *info, qq, kwargs)
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def make_example_scripts_docs(spth, npth, rpth): """ Generate rst docs from example scripts. Arguments `spth`, `npth`, and `rpth` are the top-level scripts directory, the top-level notebooks directory, and the top-level output directory within the docs respectively. """ # Ensure that outpu...
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def main(): """ """ undet = argument_parse() print 'Start\t|\tCheck incorrect index' fq_list = split_fastq(undet) print 'Process\t|\tAnalysis undetermined data' combined_df = multi_process(fq_list) sorted_combined_df = combined_df.sort_values( by='count', ascending=F...
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def ruleset_delete(p_engine, p_username, rulesetname, envname): """ Delete ruleset from Masking engine param1: p_engine: engine name from configuration param2: rulesetname: ruleset name return 0 if added, non 0 for error """ return ruleset_worker(p_engine=p_engine, p_username=p_username, ru...
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def tree_gzw(flag, width, mbl='-', xmin='-', xmax='-', ymin='-', ymax='-', logpath=None, outdir=None, shellscript=None): """ | Phase unwrapping tree generation (GZW algorithm) | Copyright 2008, Gamma Remote Sensing, v3.6 5-Sep-2008 clw/uw Parameters ---------- flag: (input) phase unwrap...
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def upload_to_bucket(client, src_path, dest_bucket_name, dest_path): """Upload a file or a directory (recursively) from local file system to specified bucket. Args: client: Google Cloud storage client object to ask resources. src_path: Path to the local file or directory you want to send ...
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def config_from_file(file_name): """Load and return json from file.""" with open(file_name) as config_file: config = ujson.load(config_file) return config
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def setMinGap(typeID, minGap): """setMinGap(string, double) -> None Sets the offset (gap to front vehicle if halting) of vehicles of this type. """ traci._sendDoubleCmd(tc.CMD_SET_VEHICLETYPE_VARIABLE, tc.VAR_MINGAP, typeID, minGap)
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def build_yaml_object( dataset_id: str, table_id: str, config: dict, schema: dict, metadata: dict = dict(), columns_schema: dict = dict(), partition_columns: list = list(), ): """Build a dataset_config.yaml or table_config.yaml Args: dataset_id (str): The dataset id. ...
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def read_candidate_data_list(file, path=IEDC_paths.candidates): """ Will read a candidate file and return its data. :param file: Filename of the file to process :param path: Path of the file :return: Dictionary of dataframes for metadata, classifications, and data """ # make it a proper pat...
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def make_cumulative(frame, filedate, unit): """Create a cumulative graph of cases over time""" gb = frame.groupby("Accurate_Episode_Date").agg(patients=("Row_ID", "count")) gb = gb.resample("D").last().fillna(0).reset_index() max_date = gb["Accurate_Episode_Date"].max().strftime("%Y-%m-%d") gb["cumu...
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def most_common(l): """ Helper function. :l: List of strings. :returns: most common string. """ # another way to get max of list? #from collections import Counter #data = Counter(your_list_in_here) #data.most_common() # Returns all unique items and their counts #data.most_...
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def reduce_avg(reduce_target, lengths, dim): """ Args: reduce_target : shape(d_0, d_1,..,d_dim, .., d_k) lengths : shape(d0, .., d_(dim-1)) dim : which dimension to average, should be a python number """ shape_of_lengths = lengths.get_shape() shape_of_target = reduce_target.g...
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def _near_mod_2pi(e, t, atol=_DEFAULT_ATOL): """Returns whether a value, e, translated by t, is equal to 0 mod 2 * pi.""" return _near_mod_n(e, t, n=2 * np.pi, atol=atol)
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def create_test_votes_data(votes_table): """ Populates a votes table with test data :param votes_table: table object """ votes_table.put_item( Item={ "User": "user_1", "TopicKey": "project_a/topic_aaa", "ProjectName": "project_a", "Topic": "top...
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def create_returns_similarity(strategy: QFSeries, benchmark: QFSeries, mean_normalization: bool = True, std_normalization: bool = True, frequency: Frequency = None) -> KDEChart: """ Creates a new returns similarity chart. The frequency is determined by the specified returns series....
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def info(path): """ Debug sideload status. """ _echo_table("System Info:", [system_info()]) _echo_table("Word Installation:", [office_installation("word")]) net_shares = get_net_shares() _echo_table("Net Shares:", net_shares) title = rf"HKEY_CURRENT_USER\{SUBKEY_OFFICE}\{OFFICE_SUBKEY...
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def apply_colormap_on_image(org_im, activation, colormap_name='viridis', alpha=.4, thresh=30): """ Apply heatmap on image Args: org_img (PIL img): Original image activation_map (numpy arr): Activation map (grayscale) 0-255 colormap_name (str): Name of the colormap """ imp...
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def player_stats(cli, nick, chan, rest): """Gets the stats for the given player and role or a list of role totals if no role is given.""" if (chan != nick and var.LAST_PSTATS and var.PSTATS_RATE_LIMIT and var.LAST_PSTATS + timedelta(seconds=var.PSTATS_RATE_LIMIT) > datetime.now()): ...
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def _cli(): """ command line interface :return: """ parser = generate_parser() args = parser.parse_args() return interface(args.bids_dir, args.output_dir, args.aseg, args.subject_list, args.session_list, ...
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def run_experiment(parpath, subjname, run_id): """ Main function to run total experient. For each new participant, a new run sequence will be generated and saved into the output pickle file. run_num selected from 1-8. """ if not os.path.isfile(pjoin(parpath, 'RecordStimuli', subjname...
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def statusize(): """Posts a status from the web.""" db = get_session(current_app) user_id = session.get('user_id') if not user_id: return forbidden('You must be logged in to statusize!') user = db.query(User).get(user_id) message = request.form.get('message', '') if not message: ...
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def savedata(): """ This function will put data in output file if given. """ # for item in tldSorting(finalset): # print(termcolor.colored(item, color='green', attrs=['bold'])) # if ipv4list: # print(termcolor.colored("\nGot Some IPv4 addresses:\n", # ...
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def urlsafe_b64decode_nopadding(val): """Deal with unpadded urlsafe base64.""" # Yes, it accepts extra = characters. return base64.urlsafe_b64decode(str(val) + '===')
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def _subimg_bbox(img, subimage, xc, yc): """ Find the x/y bounding-box pixel coordinates in ``img`` needed to add ``subimage``, centered at ``(xc, yc)``, to ``img``. Returns ``None`` if the ``subimage`` would extend past the ``img`` boundary. """ ys, xs = subimage.shape y, x = img.shap...
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def draw_rectangle(faces, img): """ Draws the box and text around the intruder's face Keyword arguments: faces -- frames that have faces detected img -- the frame itself, this is what we are drawing on. """ for (x, y, w, h) in faces: cv2.rectangle(img, (x, y), (x + w, y + h), (0, 0, 255...
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def _ToDatetimeObject(date_str): """Converts a string into datetime object. Args: date_str: (str) A date and optional time for the oldest article allowed. This should be in ISO 8601 format. (yyyy-mm-dd) Returns: datetime.datetime Object. Raises: ValueError: Invalid date for...
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def select_most_uncertain_patch(x_image_pl, y_label_pl, fb_pred, ed_pred, fb_prob_mean_bald, kernel_window, stride_size, already_select_image_index, previously_selected_binary_mask, num_most_uncert_patch, method): """This function is used to acquire th...
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def submit_extraction(connector, host, key, datasetid, extractorname): """Submit dataset for extraction by given extractor. Keyword arguments: connector -- connector information, used to get missing parameters and send status updates host -- the clowder host, including http and port, should end with a ...
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def fix_sys_path(): # XXX - MarkH had the bright idea *after* writing this that we should # ensure the CVS version of SpamBayes is *not* used to resolve SB imports. # This would allow us to effectively test the distutils setup script, so # any modules or files missing from the installed version raise er...
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def fcmp(x, y, precision): """fcmp(x, y, precision) -> -1, 0, or 1""" if math.fabs(x-y) < precision: return 0 elif x < y: return -1 return 1
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def destroy_nodes(cluster): """Call deleteinstance on all nodes in cluster.""" for z in cluster.keys(): for node in cluster[z]: print "...deleting node %s in zone %s" % (node['name'], node['zone']) _ = subprocess.call(["gcutil", "--service_version=%s" % API_VE...
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def parse_vcf_line(line): """ Args: line (str): line in VCF file obj. Returns: parsed_line_lst (lst): with tuple elem (chr, pos, ref, alt) Example: deletion pos 123456789012 reference ATTAGTAGATGT deletion ATTA---GATGT VCF: ...
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def new_auth(): """ Performs the new authentication song and dance. Waves the dead chicken in the air in just the right way. @see: https://api-portal.digikey.com/node/188 """ magic_code = invoke_auth_magic_one() invoke_auth_magic_two(magic_code) return
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