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def postprocess(output, length_1, length_2): """Post process the output of the inferred alignment.""" score, paths, sw_params = tf.nest.map_structure( functools.partial(tf.squeeze, axis=0), output) # Stacks SW params, flipping sign of gap penalties for convenience. substitution_scores, gap_open, gap_exten...
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def test_stackedblocks_with_params(): """ Test StackedBlocks when all layers have trainable params """ aes = [Autoencoder(100, 50, 'tanh', 'tanh'), Autoencoder(50, 10, 'tanh', 'tanh')] sb = StackedBlocks(aes) _params = set([p for l in sb._layers for p in l._params]) assert sb._p...
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def cli(): """命令集""" pass
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def select_random_word() -> str: """Selects a random word from the lexicon.""" next_word = lexicon.sample(RandomWordSelectStrategy()) print(f"Chose: {next_word}!") return next_word
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def edit_profile(request, username=None): """Edit user profile.""" # If a username is specified, we are editing somebody else's profile. user = None if username: username = username.replace(" ", "+") if username != request.user.username: try: user = User.obje...
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def split_at_pattern(text, pattern): """ Split a string where a pattern begins """ obj = regex.search(pattern, text) if obj: start = obj.start() return text[0:start], text[start:] else: return text, ""
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def store_deepdeps(roots:List[Ref])->List[Ref]: """ Return an exhaustive list of dependencies for the `roots` references. References themselves are also included """ frontier=set(roots) processed=set() while frontier: ref = frontier.get() #FIXME processed.add(ref) for dep in store_deps(ref): ...
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def focal_lossIII(prediction_tensor, target_tensor, weights, gamma=2., epsilon=0.00001, ): """Compute loss function. This function was adapted from the Tensorflow issues section on GitHub. Args: prediction_tens...
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def grouper(iterable: Iterable[_T], n: int) -> Generator[Iterable[_T], None, None]: """ given a iterable, yield that iterable back in chunks of size n. last item will be any size. """ for i in range(math.ceil(len(iterable) / n)): yield iterable[i * n : i * n + n]
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def stack_lag_h5_maker(f, f2, buffer=2, shift_to_the_right_by=0): """ Parameters ---------- f : h5 file with SINGLE FRAMES this is ment to be a test program. if used long term I will change this part f2 : buffer : shift_to_the_right_by : Returns ------- """ h5c = image_too...
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def draw_vertical_bar(info:pd.Series)->plt.Figure: """Dibuja un vertical bar chart basado en un analisis previamente hecho Args: info (pd.Series): Los datos a graficar Returns: [plt.Figure]: La figura armada """ plt.bar(info.index, height=info) return plt.gcf()
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def bash_live( command: str, cwd: str = None, exception: Type[Exception] = Exception, prefix: str = "", logfile = None ) -> None: """Run a command in bash shell in live mode to fetch output when it is available :param command: the command to run :param cwd: directory where to run the command (defaults to curren...
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def set_seed_iftrue(condition, seed=10): """ Fix the seed for random test. Parameters ---------- seed : int Random seed passed to np.random.seed Returns ------- decorator : function Decorator which, when applied to a function, sets the random seed before running t...
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def get_current_utc_time(): """Return string representation of current time in UTC.""" utcnow = datetime.datetime.utcnow() return str(utcnow.timestamp())
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def _split_extension_test(ctx): """Unit tests for paths.split_extension.""" env = unittest.begin(ctx) # Try some degenerate cases. asserts.equals(env, ("", ""), paths.split_extension("")) asserts.equals(env, ("/", ""), paths.split_extension("/")) asserts.equals(env, ("foo", ""), paths.split_ext...
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def get_cluster_details(): """ Gets the credentials from the config file """ config = configparser.ConfigParser() config.read_file(open('dwh.cfg')) KEY = config.get('AWS','KEY') SECRET = config.get('AWS','SECRET') DWH_CLUSTER_TYPE = config.g...
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def get_publication_comments(project, publication_id): """ List all comments for the given publication """ connection = db_engine.connect() publications = get_table("publication") publication_comments = get_table("publication_comment") statement = select([publications.c.publication_comment_i...
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def parse_genapp_customer(genapp_record: Dict) -> Optional[X12Demographics]: """ Parses a GenApp Customer from a JSON response to a X12Demographics model :param genapp_record: The GenApp Customer record :return: The X12Demographics model for the customer record """ no_match_found = genapp_record...
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def test_mlflow_metrics_dataset_saved_and_logged(tmp_path, tracking_uri, data, prefix): """Check if MlflowMetricsDataSet can be saved in catalog when filepath is given, and if logged in mlflow. """ mlflow.set_tracking_uri(tracking_uri.as_uri()) mlflow_client = MlflowClient(tracking_uri=tracking_uri....
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def download_and_install(args: argparse.Namespace, url: str): """Download the asset and install it Args: args (Namespace): CLI arguments url (str): The asset download URL""" with tempfile.TemporaryFile() as zip_file_w: download_to_file(zip_file_w, url) with zipfile.ZipFile(zip_file_w, mode="r") a...
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def cons (l,v): """ Add the value :code:`v` at the begining of the list :code:`l`. :param l: The list, possibly empty. :type l: dict :param v: The value to be added. :type v: Any UC: not compatible with iterators """ if l["head"] == None: l["head"] = l["tail"] = __new_cell ...
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def configure_master(): """ Configures the master node after rpm install """ common.setup_user() common.setup_common_configurations() __setup_master_specific_conf_files() __setup_hawq_user_profile() __create_local_dirs()
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def assert_(val: bool, msg: Literal["1.5.1"]): """ usage.scipy: 1 """ ...
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def make_dirs(directory: Union[str, Path], mode: int = 0o777) -> bool: """Wrapper around os.makedirs to make it suitable for using in a multithreaded/multiprocessing enviroment: Unlike the regular function, this wrapper does not throw an exception if the directory already exists, which may happen if ano...
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def get_best_shift(img): """ DESCRIPTION: Calculate the center of mass of the input image and return the best shift amount to center an image on the character. INPUT: Image OUTPUT: Calculated shift amount for x and y directions """ # Calculate the center of mass through scipy center_y, c...
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def patch_copyfile(): """ Used to monkey patch shutil.copyfile() """ if shutil.copyfile != copyfile: shutil._orig_copyfile = shutil.copyfile shutil.copyfile = copyfile
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def main(): """ The main function to execute upon call. Returns ------- int returns integer 0 for safe executions. """ print("Program to check positive, negative, or zero input.") temp = check_number_sign() return 0
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def read_openPMD_params( filename ): """ Extract the time and some openPMD parameters from a file Parameter --------- filename: string The path to the file from which parameters should be extracted Returns ------- A tuple with: - A float corresponding to the time of this it...
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def save_pcap_task(files, save_dir, session_threshold): """ This method takes all files in a list (full path names) and uses the method save_pcap that converts a pcap to h5 format :param files: :param session_threshold: :return: """ for fullname in files: print('Currently saving file...
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def class_to_val(raw_scores): """ Finds the highest softmax for each class :param raw_scores: tensor (batch, verts, classes) :return: highest class (batch, verts) """ cls = torch.argmax(raw_scores, dim=2) val = (cls + 0.5) / DEEPCONTACT_NUM_BINS return val
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def map_arg(**maps): """ Apply a mapping on certains argument before calling the original function. Args: maps (dict): {key: map_func} """ def deco(func): @functools.wraps(func) def wrapper(*args, **kwargs): argmap = inspect.getcallargs(func, *args, **kwargs) ...
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def installIfNeeded(moduleName, nameOnPip=None, notes="", log=print): """ Installs a Python library using pip, if it isn't already installed. """ from pkgutil import iter_modules # Check if the module is installed if moduleName not in [tuple_[1] for tuple_ in iter_modules()]: log("Installing " ...
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def test_can_load_established_ontologies(ontology_uri): """ Test that we can load some commonly used ontologies. """ ontology = Ontology.load(ontology_uri) assert_that(ontology.__terms__, is_not(empty()))
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def create_spark_session(): """Create an apache spark session on AWS""" spark = SparkSession \ .builder \ .config("spark.jars.packages", "org.apache.hadoop:hadoop-aws:2.7.0") \ .getOrCreate() return spark
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def evaluate(model, dataset): """ Evaluates model on all dataset images. Assumes all images have corresponding pose labels. """ loc_err_acc = [] loc_encoded_err_acc = [] ori_err_acc = [] ori_encoded_err_acc = [] distances_acc = [] esa_scores_acc = [] # Variance used only for prob. ...
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def clean_catalog(ukidss_catalog, clean_band='K_1', badclass=-9999, maxerrbits=41, minerrbits=0, maxpperrbits=60): """ Attempt to remove 'bad' entries in a catalog. Parameters ---------- ukidss_catalog : `~astropy.io.fits.BinTableHDU` A FITS binary table instance from the ...
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def setmask(arr, x1=None, x2=None): """setmask(arr, x1, x2) arr = 1D arr x1 = lower value x2 = upper value by default it returns a mask that is the full range of arr returns ======= mask, x1, x2 if input x1 and x2 are out of bounds then it sets x1 and x2 to the boundry of arr...
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def test_ensure_config(configuration): """This is just to make sure the autouse fixture is doing what I expect.""" assert get_configuration() == configuration
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def test_local_normalized_cross_correlation(): """ Testing computed local normalized cross correlation function between images using image.local_normalized_cross_correlation by comparing to precomputed. """ tensor_true = np.array(range(24)).reshape((2, 1, 2, 3, 2)) tensor_pred = 0.6 * np.ones((2, 1,...
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def get_tree(splits): """Convert a dict keyed by splits into the equivalent tree. The dict values should be dicts appropriate for the params input to TreeBuilder.create_edge. """ Edge = TreeBuilder().create_edge # Create a star from the tips tips = [] the_rest = [] for split, params...
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def create_hash(secret: str, url: str) -> str: """Create a hash of the secret and url.""" s = f'{secret}{url}' return str(hashlib.md5(s.encode()).hexdigest()[0:8])
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def load_defaults(db): """ Adds default jurisdiction types: * control_group * tier * cluster Adds default configuration for each of the three jurisdiction types Adds default userdata templates """ pd = PROVISIONER_DEFAULTS # jurisdiction types for jt in PROVISIONER_DEF...
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def check_pii_annotations_yml(repo_path, all_results): """ TODO(jinder) """ all_results[module_dict_key][".pii_annotations.yml"] = file_exists( repo_path, ".pii_annotations.yml" )
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def get_model_name(model): """Obtains the model name for a Scikit-Learn, ML Studio estimator Obtains the model name for Scikit-Learn estimators, ML Studio estimators, and GridSearchCV and RandomSearchCV objects Parameters ---------- model : BaseEstimator, GridSearchCV, RandomSearchCV ...
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def create_script_to_chars(): """Returns a mapping from script to defined characters, based on script and extensions, for all scripts.""" load_data() result = collections.defaultdict(set) for cp in _defined_characters: if cp in _script_data: result[_script_data[cp]].add(cp) ...
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def get_filter(): """ Вывод товаров на странице каталогов :return: context """ price = dict() seller = Seller.objects.values('title', 'title_en').all() price['max'] = math.ceil(seller.aggregate(max=Max('catalog__price')).get('max')) price['min'] = math.floor(seller.aggregate(min=Min('ca...
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def email_weekly_orders_csv(current_menu_meal_totals): """ Emails all the current admins an email containing every users current order. Email contains a csv file as well. Returns total emails sent and the email for every admin. """ all_orders = get_all_users_orders() user_login_url = get_log...
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def ConvTranspose(out_chan: int, filter_shape: Sequence[int], strides: Optional[Sequence[int]] = None, padding: str = Padding.VALID.name, W_std: float = 1.0, b_std: Optional[float] = None, dimension_numbers: Opti...
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def wait_for_result_is_none(method, timeout, wait_msg=None): """Calls the method until the return value is None.""" count = 0 end_time = time.time() + timeout while True: try: result = method() if result is None: return True except: pa...
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def restoreLastState(): """ Restores the most recently pushed clipboard state, but does not remove it from the archive stack. Replaces current clipboard contents. Returns nothing. Stack must not be empty. """ # Preconditions: assert( len( _archiveStack ) > 0 ) state = _archiv...
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def connect(db_uri): """Connect to a database to record deployments. :param db_uri: Database URI to connect to :return: SQLAlchemy session for interacting with this database """ engine = create_engine(db_uri, convert_unicode=True) session = scoped_session(sessionmaker(autocommit=False, autoflus...
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def final_run_could_be_extended(values, end_idx): """Heuristically see if the value run at end_idx could be extended Returns true if there is a run at end_idx, if end_idx is not the last value, and if the value after end_idx could be part of a run. To keep this constant-time, we aren't checking if the...
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def request_nodes_http(url: str) -> None: """Request the status over HTTP :param url: the base URL """ nodes = HttpClient(url).request_cluster_hw_status() rows = [] for node in nodes: for gpu in node['gpus']: rows.append(_gpu2row(gpu, node['host'])) print_table(rows)
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def merge_filename(filename, pat, sep): """ Apply a merging pattern to a filename. Sections of the base filename are kept according to the provided pattern. Args: filename: The filename to merge. pat: The merging pattern to use. sep: String separating filename sections. Re...
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def test_parse_user_data_raise_missing_variable() -> None: """Test parse_user_data.""" with pytest.raises(MissingVariable): parse_user_data({"name": "tom"}, "name: ${name}, last: $last and $$", "test")
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async def fetch_geoloc_web(ip: IPAddress) -> Optional[Geolocation]: """Fetch geolocation data based on ip (using ip-api).""" url = f"http://ip-api.com/line/{ip}" async with http.get(url) as resp: if not resp or resp.status != 200: log("Failed to get geoloc data: request failed.", Ansi.L...
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def task_query(job_key=None, hosts=None, job_keys=None): """Creates TaskQuery optionally scoped by a job(s) or hosts. Arguments: job_key -- AuroraJobKey to scope the query by. hosts -- list of hostnames to scope the query by. job_keys -- list of AuroraJobKeys to scope the query by. """ return TaskQuery( ...
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def reset_selection(): """Deselect all selected nodes """ clear_selection_recursive()
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def previous_scheduled_day(date, first_trading_day, is_scheduled_day_hook): """ Returns the previous session date in the calendar before the provided date. Parameters ---------- date : Timestamp The date whose previous date is needed. Returns ------- Timestamp The previ...
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def preorder_elements(t): """通过生成器遍历二叉树,先根序遍历""" stack = [] while t is not None or stack: while t is not None: yield t.data stack.append(t.right) t = t.left t = stack.pop()
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def measure_distance_euclidean(point1, point2): """Return euclidean distance between two shapely Points as float.""" if (type(point1) != Point) or (type(point2) != Point): raise TypeError("Only Points are supported as arguments, got {} and {}".format(point1, point2)) return point1.distance(point2)
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def bootstrap(app_id, service_name): """ # generate a demo app """ from rest_arch import __version__ app_slug = package_name = app_id.split('.')[1] mapping = dict(app_id=app_id, service=service_name, package=package_name, app_slug=app_slug...
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def _unpack_asf_image(data): """Unpack image data from a WM/Picture tag. Return a tuple containing the MIME type, the raw image data, a type indicator, and the image's description. This function is treated as "untrusted" and could throw all manner of exceptions (out-of-bounds, etc.). We should clea...
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def dicenet_w3d2(**kwargs): """ DiCENet x1.5 model from 'DiCENet: Dimension-wise Convolutions for Efficient Networks,' https://arxiv.org/abs/1906.03516. Parameters: ---------- pretrained : bool, default False Whether to load the pretrained weights for model. root : str, default '~/....
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def patch_vertices(vertices,pole, width): """ find 'vertices' within the cone of 'width' degrees around 'pole' """ return [i for i,v in enumerate(vertices) if np.abs(np.dot(v,pole)) > np.abs(np.cos(np.pi*width/180))]
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def test_frame_dropna(): """ Tests whether the monkey patching of ('pandas.core.frame', 'dropna') works """ test_code = cleandoc(""" import pandas as pd df = pd.DataFrame([0, 2, 4, 5, None], columns=['A']) assert len(df) == 5 df = df.dropna() assert len(d...
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def plot_gcam_reclassified(gcam_df, landclass, start_yr=2015, through_yr=2100, interval=5): """Plot GCAM landclass allocation over a time period reclassified to Demeter land cover types.""" yrs = [str(i) for i in range(start_yr, through_yr + interval, interval)] lc_mapping = gcam_to_demeter_lc_map() ...
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def train(model): """Train the model.""" # Training dataset. dataset_train = CarlaDataset() dataset_train.load_carla(args.dataset, "train") dataset_train.prepare() # Validation dataset dataset_val = CarlaDataset() dataset_val.load_carla(args.dataset, "val") dataset_val.prepare() ...
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def test_dataset_add_with_copy(tmpdir, runner, project, client): """Test adding data to dataset with copy.""" import os import stat # create a dataset result = runner.invoke(cli, ["dataset", "create", "my-dataset"]) assert 0 == result.exit_code assert "OK" in result.output paths = [] ...
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def get_sigmas_index(indices): """Takes a tuple and gives back a length-16 array with a single 1. Parameters ---------- indices: a tuple of two integers, each one between 0 and 3. Examples -------- >>> get_sigmas_index((1, 0)) array([ 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0...
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def test_histogram1D_to_from_existing_histogram(logging_mixin: Any) -> None: """ Test passing a Histogram1D to ``from_existing_histogram``. It should return the same object. """ h_input = histogram.Histogram1D( bin_edges=np.array([0, 1, 2]), y=np.array([2.3, 5.4]), errors_squared=np.arra...
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def authenticated(): """Utility function checking if the current user is logged in or not.""" fas_user = None try: fas_user = flask.g.fas_user except (RuntimeError, AttributeError): pass return fas_user is not None
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def _get_or_create_workspace(auth, subscription_id, resource_group_name, workspace_name, location): """ Gets or creates a workspace. :param auth: :type auth: azureml.core.authentication.AbstractAuthentication :param subscription_id: :type subscription_id: str :param resource_group_nam...
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def backup_file(directory, filename): """ Backup a given file by appending .bk to the end """ origfile = join(directory, filename) backupfile = origfile + '.bk' if exists(backupfile): os.remove(backupfile) if exists(origfile): os.rename(origfile, backupfile)
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def add_calculated_fields(*, current_item: Dict[str, Any], initial_status, current_status, position_list, lap_list, total, charging_proces...
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def nusmv(ctx, model, trace, outfile): """Generates a nuSMV encoding of the model. If the trace is given then it's incorporated into the model. """ dawnet = getTraceModel(model, trace) dawnetnusmv.process_model(dawnet, outfile=outfile if outfile else sys.stdout, solve=c...
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def test_allow_unverified_option(httpsserver): """Ensure that we allow unverified servers if the user passes a flag.""" api = Api(domain=httpsserver.url, verify=False) api.login('test@test.com', 'test') api.logout() api.refresh_token() # Also ensure that the RestResource works as well res...
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def check_if_all_passed(statuses): # type: (Dict[str, str]) -> bool """ Check if all items in supplied `statuses` dict passed parsing and conversion. :param statuses: dictionary init info statuses (files/nodes to their status) :type statuses: dict :return: boolean indicating if all files and no...
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def get_database_connection(): """Returns a connection to Redis DB or creates a new one if it does not already exist.""" global _database try: return _database except NameError: config = get_config() _database = redis.Redis(host=config['redis_db_address'], ...
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def _get_config(**kwargs): """ Return configuration """ config = { "filter_id_regex": [".*!doc_skip"], "filter_function_regex": [], "replace_text_regex": {}, "proccesser": "highstate_doc.proccesser_markdown", "max_render_file_size": 10000, "note": None, ...
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def describe_environment_managed_actions(EnvironmentName=None, EnvironmentId=None, Status=None): """ Lists an environment's upcoming and in-progress managed actions. See also: AWS API Documentation :example: response = client.describe_environment_managed_actions( EnvironmentName='strin...
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def get_neon_core_root(): """ Determines the root of the available/active Neon Core. Should be the immediate parent directory of 'neon_core' dir Returns: Path to the core directory containing 'neon_core' """ site = sysconfig.get_paths()['platlib'] if exists(join(site, 'neon_core')): ...
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def signal_framing( signal: Union[torch.Tensor, ComplexTensor], frame_length: int, frame_step: int, bdelay: int, do_padding: bool = False, pad_value: int = 0, indices: List = None, ) -> Union[torch.Tensor, ComplexTensor]: """Expand `signal` into several frames, with each frame of length ...
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def test_abstract_classes(): """很多时候我们会觉得mongoengine.Document提供的方法不够多, 我们会想要自定义 一些方法。为了减少冗余代码, 我们想要将通用的方法以继承的方式实现。这时, 我们 需要建立一个新的Document的基类, 然后用户的类都从这个基类继承而来。 具体做法如下: Ref: http://docs.mongoengine.org/guide/defining-documents.html?#abstract-classes """ class ExtendedDocument(Document): ...
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def evaluate_conditional(string: str, fields: Dict[str, str]) -> bool: """ Evaluates a conditional from $string on a Anki card template using the field values $fields. """ field_name = get_field_name(string) if field_name not in fields: logger.warning("Field '{}' from conditional '{}' not define...
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def has_all_channels(stream, channels, starttime, endtime): """Check whether all channels have any data within time range. Parameters ---------- stream: obspy.core.Stream The input stream we want to make certain has data channels: array_like The list of channels that we want to have...
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def world_xyzn_im_to_pts(world_xyz, world_n): """Makes a 10K long XYZN pointcloud from an XYZ image and a normal image.""" # world im + world normals -> world points+normals is_valid = np.logical_not(np.all(world_xyz == 0.0, axis=-1)) world_xyzn = np.concatenate([world_xyz, world_n], axis=-1) world_xyzn...
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def clean_email_default(email, allowed_domains): """ Clean email address and check if it has allowed domain :param email: emailadress in string :param allowed_domains: FQDN of allowed domain of mail :return: cleaned lowercase email addresss string or ValidationError """ email = email.strip(...
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def GetSourceImages(local_dir, pro): """Downloads the various sources that we need. Of note: Because Express does not include ATL, there's an additional download of the 7.1 WDK which is the latest publically accessible source for ATL. When |pro| this is not necessary (and CHROME_HEADLESS always implies Pro). ...
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def add_binary_prefix(value: float) -> str: """ Function that converts a number to his version with Binary prefix @input value (an integer) @example: >>> add_binary_prefix(65536) '64.0 kilo' """ for prefix in BinaryUnit: numerical_part = value / (2**prefix.value) if numer...
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def status_statement(current, final, count, chr=None): """ Print progress statements for long processes :param current: current iteration number :param final: total number of iterations :param count: number of print statements total :param chr: print chromosome information of current progress ...
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def exhibit_type(elem): """Returns the exhibit type of the file.""" val = attr_val(elem, 'exhibitType') if val is None: return 'EX-101' return val
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def get_mailboxes_v2(): """ Get all mailboxes - including unverified mailboxes Output: - mailboxes: list of mailbox dict """ user = g.user mailboxes = [] for mailbox in Mailbox.query.filter_by(user_id=user.id): mailboxes.append(mailbox) return ( jsonify(mailboxe...
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def angle_to_direction(input_angle, full=False, level=3): """Convert the meteorological angle to directional text. Works for angles greater than or equal to 360 (360 -> N | 405 -> NE) and rounds to the nearest angle (355 -> N | 404 -> NNE) Parameters ---------- input_angle : numeric or array-l...
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def decode_packets(data, error_callback=None, check_crc=True, resync=True): """ Generator function to decode packets from a bitstream The bitstream may be presented as either a bitarray, a file object or a socket """ if isinstance(data, bitarray): logger.debug('decoding packets fro...
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def test_get_object_self_and_multiple_admins( client_admin_factory, employee_factory, request_factory, ): """ The employee should be able to fetch their own record if their are multiple admins for the client company. Regression test for GH-113. https://github.com/comp523-jarvis/timetra...
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def test_can_crud_url(): """ Tests that full get/set/delete functionality is available for the url property """ path = "path" d = DatasetFile(path) url = "http://mysite.com" assert d.url is None d.url = url assert d.url is url del(d.url) assert d.url is None
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def met_setup_fixture(): """Patch Met Éireann setup entry.""" with patch( "homeassistant.components.met_eireann.async_setup_entry", return_value=True ): yield
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def asset(ses, ticker_sym): """ function that returns a single asset object given for a given ticker """ return _assets_response_handle(_get_assets_json( ses, ticker=ticker_sym), ticker=ticker_sym)
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def test_truth(): """This test checks whether running the same config twice produces the same cosmos sampler properties """ # The config dict to write some images to a MEDS file i_run = 0 seed = 1234 pixel_scale = 0.26 g1,g2 = 0.01, 0. stamp_size=32 nobj=100 n_per_obj=1 ...
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