content
stringlengths
22
815k
id
int64
0
4.91M
def _system_message(message_contents): """ Create SYSTEM_MESSAGES_FILE file w/contents as specified. This file is displayed in the UI, and can be embedded in nginx 502 (/opt/galaxy/pkg/nginx/html/errdoc/gc2_502.html) """ # First write contents to file. if os.path.exists(SYSTEM_MESSAGES_FILE): with open(SYSTEM_MESSAGES_FILE, 'a+') as f: f.write(message_contents) # Copy message to appropriate places in nginx err_502.html pages. # possible_nginx_paths = ['/opt/galaxy/pkg/nginx/html/errdoc/gc2_502.html', # '/usr/nginx/html/errdoc/gc2_502.html']
31,500
def detected(numbers, mode): """ Returns a Boolean result indicating whether the last member in a numeric array is the max or min, depending on the setting. Arguments - numbers: an array of numbers - mode: 'max' or 'min' """ call_dict = {'min': min, 'max': max} if mode not in call_dict.keys(): print('Must specify either max or min') return return numbers[-1] == call_dict[mode](numbers)
31,501
def test_delete_multiple_status(mock_event: dict) -> None: """ Test that status effects get correctly removed when there are multiple status effects with a duration of 1 in the status effects list :param mock_event: Mock AWS lambda event dict """ # Arrange mock_event["body"]["Player1"]["action"] = "disrupt" mock_event["body"]["Player2"]["action"] = "block" mock_event["body"]["Player1"]["status_effects"] = [["disorient", 1], ["connected", 2], ["poison", 1], ["lag", 1], ["anti_area", 999]] mock_event["body"]["Player1"]["enhanced"] = True # Act # Perform a round of combat combat_result_1 = do_combat(mock_event, mock_event) combat_body_1 = json.loads(combat_result_1["body"]) # Assert Actual == Expected assert combat_body_1["Player1"]["status_effects"] == [["connected", 1], ["anti_area", 998], ["enhancement_sickness", 1]] assert combat_body_1["Player2"]["status_effects"] == [["prone", 1]]
31,502
def generator_v0( samples, cfg ) : """Taken from section 18. Generators""" num_samples = len(samples) batch_size = cfg["batch_size"] step_size = batch_size // 2 while True : samples = sklearn.utils.shuffle(samples) for offset in range( 0, num_samples, step_size ) : batch_samples = samples[offset : offset + step_size ] images = [] angles = [] for sample in batch_samples: fname = DATA_DIR + "IMG/" + sample[0].split('/')[-1] center_image = cv2.imread( fname ) center_angle = float( sample[3] ) images.append( center_image ) angles.append( center_angle ) mirrored_img = center_image[ : ,::-1, :] images.append( mirrored_img ) angles.append( -center_angle ) X_train = np.array( images ) y_train = np.array( angles ) yield X_train, y_train
31,503
def calculate_compass_bearing(point_a, point_b): """ Calculates the bearing between two points. The formulae used is the following: θ = atan2(sin(Δlong).cos(lat2), cos(lat1).sin(lat2) − sin(lat1).cos(lat2).cos(Δlong)) :Parameters: - `pointA: The tuple representing the latitude/longitude for the first point. Latitude and longitude must be in decimal degrees - `pointB: The tuple representing the latitude/longitude for the second point. Latitude and longitude must be in decimal degrees :Returns: The bearing in degrees :Returns Type: float """ # LICENSE: public domain from https://gist.github.com/jeromer/2005586 if (type(point_a) != tuple) or (type(point_b) != tuple): raise TypeError("Only tuples are supported as arguments") lat1 = math.radians(point_a[0]) lat2 = math.radians(point_b[0]) diff_long = math.radians(point_b[1] - point_a[1]) x = math.sin(diff_long) * math.cos(lat2) y = math.cos(lat1) * math.sin(lat2) - (math.sin(lat1) * math.cos(lat2) * math.cos(diff_long)) initial_bearing = math.atan2(x, y) # Now we have the initial bearing but math.atan2 return values # from -180° to + 180° which is not what we want for a compass bearing # The solution is to normalize the initial bearing as shown below initial_bearing = math.degrees(initial_bearing) compass_bearing = (initial_bearing + 360) % 360 return compass_bearing
31,504
def parse_instructions(instruction_list): """ Parses the instruction strings into a dictionary """ instruction_dict = [] for instruction in instruction_list: regex_match = re.match(r"(?P<direction>\w)(?P<value>\d*)",instruction) if regex_match: instruction_dict.append(regex_match.groupdict()) return instruction_dict
31,505
def calc_elapsed_sleep(in_num, hyp_file, fpath, savedir, export=True): """ Calculate minutes of elapsed sleep from a hypnogram file & concatenate stage 2 sleep files Parameters ---------- in_num: str patient identifier hyp_file: str (format: *.txt) file with hypnogram at 30-second intervals fpath: str path to EEG files cut by sleep stage savedir: str path to save EEG files cut by hrs elapsed sleep export: bool (default: True) whether to export blocked dataframes Returns ------- .csv files with EEG data blocked in two-hour chunks (according to Purcell et al. 2017) OR pd.dataframes blocked in two-hour chunks (according to Purcell et al. 2017) """ # calculate elapsed sleep for each 30-second time interval print('Loading hypnogram...') sleep_scores = [1, 2, 3, 4, 5] # exclude 0 and 6 for awake and record break hyp = pd.read_csv(hyp_file, header=None, index_col=[0], sep='\t', names=['time', 'score'], parse_dates=True) mins_elapsed = hyp.score.isin(sleep_scores).cumsum()/2 # get a list of all matching files glob_match = f'{fpath}/{in_num}*_s2_*' files = glob.glob(glob_match) # make list of dfs for concat print('Reading data...') data = [pd.read_csv(file, header = [0, 1], index_col = 0, parse_dates=True) for file in files] # add NaN to the end of each df data_blocked = [df.append(pd.Series(name=df.iloc[-1].name + pd.Timedelta(milliseconds=1))) for df in data] # concatenate the dfs print('Concatenating data...') s2_df = pd.concat(data_blocked).sort_index() # assign indices to hours elapsed sleep print('Assigning minutes elapsed...') idx0_2 = mins_elapsed[mins_elapsed.between(0, 120)].index idx2_4 = mins_elapsed[mins_elapsed.between(120.5, 240)].index idx4_6 = mins_elapsed[mins_elapsed.between(240.5, 360)].index idx6_8 = mins_elapsed[mins_elapsed.between(360.5, 480)].index # cut dataframe into blocks by elapsed sleep (0-2, 2-4, 4-6, 6-8) df_two = s2_df[(s2_df.index > idx0_2[0]) & (s2_df.index < idx0_2[-1])] df_four = s2_df[(s2_df.index > idx2_4[0]) & (s2_df.index < idx2_4[-1])] df_six = s2_df[(s2_df.index > idx4_6[0]) & (s2_df.index < idx4_6[-1])] df_eight = s2_df[(s2_df.index > idx6_8[0]) & (s2_df.index < idx6_8[-1])] if export: # export blocked data if not os.path.exists(savedir): print(savedir + ' does not exist. Creating directory...') os.makedirs(savedir) print('Saving files...') for df, hrs in zip([df_two, df_four, df_six, df_eight], ['0-2hrs', '2-4hrs', '4-6hrs', '6-8hrs']): date = df.index[0].strftime('%Y-%m-%d') savename = in_num + '_' + date + '_s2_' + hrs + '.csv' df.to_csv(os.path.join(savedir, savename)) print(f'Files saved to {savedir}') else: return df_two df_four df_six df_eight print('Done')
31,506
def delete_file(path): """ 删除一个目录下的所有文件 :param path: str, dir path :return: None """ for i in os.listdir(path): # 取文件或者目录的绝对路径 path_children = os.path.join(path, i) if os.path.isfile(path_children): if path_children.endswith(".h5") or path_children.endswith(".json"): os.remove(path_children) else: # 递归, 删除目录下的所有文件 delete_file(path_children)
31,507
def label(ctx, name): """Manipulate labels.""" ctx.obj['name'] = name
31,508
def valid_pairs(pairs, chain): """ Determine if the chain contains any invalid pairs (e.g. ETH_XMR) """ for primary, secondary in zip(chain[:-1], chain[1:]): if not (primary, secondary) in pairs and \ not (secondary, primary) in pairs: return False return True
31,509
def setup(sub_args, ifiles, repo_path, output_path): """Setup the pipeline for execution and creates config file from templates @param sub_args <parser.parse_args() object>: Parsed arguments for run sub-command @param repo_path <str>: Path to installation or source code and its templates @param output_path <str>: Pipeline output path, created if it does not exist @return config <dict>: Config dictionary containing metadata to run the pipeline """ # Check for mixed inputs, # inputs which are a mixture # of FastQ and BAM files mixed_inputs(ifiles) # Resolves PATH to reference file # template or a user generated # reference genome built via build # subcommand genome_config = os.path.join(repo_path,'config','genome.json') # if sub_args.genome.endswith('.json'): # Provided a custom reference genome generated by build pipline # genome_config = os.path.abspath(sub_args.genome) required = { # Base configuration file "base": os.path.join(repo_path,'config','config.json'), # Template for project-level information "project": os.path.join(repo_path,'config','containers.json'), # Template for genomic reference files # User provided argument --genome is used to select the template "genome": genome_config, # Template for tool information "tools": os.path.join(repo_path,'config', 'modules.json'), } # Create the global or master config # file for pipeline, config.json config = join_jsons(required.values()) # uses templates in config/*.json config['project'] = {} config = add_user_information(config) config = add_rawdata_information(sub_args, config, ifiles) # Resolves if an image needs to be pulled # from an OCI registry or a local SIF exists config = image_cache(sub_args, config, repo_path) # Add other runtime info for debugging config['project']['version'] = __version__ config['project']['workpath'] = os.path.abspath(sub_args.output) git_hash = git_commit_hash(repo_path) config['project']['git_commit_hash'] = git_hash # Add latest git commit hash config['project']['pipeline_path'] = repo_path # Add path to installation # Add all cli options for data provenance for opt, v in vars(sub_args).items(): if opt == 'func': # Pass over sub command's handler continue elif not isinstance(v, (list, dict)): # CLI value can be converted to a string v = str(v) config['options'][opt] = v # Save config to output directory with open(os.path.join(output_path, 'config.json'), 'w') as fh: json.dump(config, fh, indent = 4, sort_keys = True) return config
31,510
def fqname_for(obj: Any) -> str: """ Returns the fully qualified name of ``obj``. Parameters ---------- obj The class we are interested in. Returns ------- str The fully qualified name of ``obj``. """ if "<locals>" in obj.__qualname__: raise RuntimeError( "Can't get fully qualified name of locally defined object. " f"{obj.__qualname__}" ) return f"{obj.__module__}.{obj.__qualname__}"
31,511
def analyzer_zipfile(platform, monitor): """Creates the Zip file that is sent to the Guest.""" t = time.time() zip_data = io.BytesIO() zip_file = zipfile.ZipFile(zip_data, "w", zipfile.ZIP_STORED) # Select the proper analyzer's folder according to the operating # system associated with the current machine. root = cwd("analyzer", platform) root_len = len(os.path.abspath(root)) if not os.path.exists(root): log.error("No valid analyzer found at path: %s", root) raise CuckooGuestError( "No valid analyzer found for %s platform!" % platform ) # Walk through everything inside the analyzer's folder and write # them to the zip archive. for root, dirs, files in os.walk(root): archive_root = os.path.abspath(root)[root_len:] for name in files: path = os.path.join(root, name) archive_name = os.path.join(archive_root, name) zip_file.write(path, archive_name) # Include the chosen monitoring component and any additional files. if platform == "windows": dirpath = cwd("monitor", monitor) # Generally speaking we should no longer be getting symbolic links for # "latest" anymore, so in the case of a file; follow it. if os.path.isfile(dirpath): monitor = os.path.basename(open(dirpath, "rb").read().strip()) dirpath = cwd("monitor", monitor) for name in os.listdir(dirpath): zip_file.write( os.path.join(dirpath, name), os.path.join("bin", name) ) # Dump compiled "dumpmem" Yara rules for zer0m0n usage. zip_file.write(cwd("stuff", "dumpmem.yarac"), "bin/rules.yarac") zip_file.close() data = zip_data.getvalue() if time.time() - t > 10: log.warning( "It took more than 10 seconds to build the Analyzer Zip for the " "Guest. This might be a serious performance penalty. Is your " "analyzer/windows/ directory bloated with unnecessary files?" ) return data
31,512
def symbol_size(values): """ Rescale given values to reasonable symbol sizes in the plot. """ max_size = 50.0 min_size = 5.0 # Rescale max. slope = (max_size - min_size)/(values.max() - values.min()) return slope*(values - values.max()) + max_size
31,513
def test_distance_function(cosine_kmeans): """ Checks that cosine kmeans uses distance_cosine as the distance calculator. """ assert isinstance(cosine_kmeans.distance_func, type(distance_cosine))
31,514
def AddServiceAccountArg(parser): """Adds argument for specifying service account used by the workflow.""" parser.add_argument( '--service-account', help='The service account that should be used as ' 'the workflow identity. "projects/PROJECT_ID/serviceAccounts/" prefix ' 'may be skipped from the full resource name, in that case ' '"projects/-/serviceAccounts/" is prepended to the service account ID.')
31,515
def delete(id): """Soft delete a patient.""" check_patient_permission(id) patient = Patient.query.get(id) patient.deleted = datetime.datetime.now() patient.deleted_by = current_user db.session.commit() return redirect(url_for('screener.index'))
31,516
def system_temp_dir(): """ Return the global temp directory for the current user. """ temp_dir = os.getenv('SCANCODE_TMP') if not temp_dir: sc = text.python_safe_name('scancode_' + system.username) temp_dir = os.path.join(tempfile.gettempdir(), sc) create_dir(temp_dir) return temp_dir
31,517
def _pipeline_network_multiple_database(database: List[str], kernel_method: Callable, filter_network_omic: Union[List, str]) -> Union[Matrix, str]: """Process network for a multiple database.""" network = None db_norm = frozenset([db.lower().replace(' ', '_') for db in database]) if db_norm in list(PATHME_MAPPING.keys()): db_norm = PATHME_MAPPING[db_norm] kernels_db_path = os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'pathme') kernels_files_list = get_or_create_dir(kernels_db_path) for kernel in kernels_files_list: if db_norm in kernel or db_norm == kernel: network = os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'by_db', f'{db_norm}.pickle') break if not network: network = os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'by_db', f'{db_norm}.pickle') GoogleDriveDownloader.download_file_from_google_drive(file_id=DATABASE_LINKS[db_norm], dest_path=network, unzip=True) else: intersecc_db = db_norm.intersection(PATHME_DB) intersecc_db_str = '' for db_name in intersecc_db: intersecc_db_str += f'_{db_name}' if intersecc_db: kernels_db_path = os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'by_db') kernels_files_list = get_or_create_dir(kernels_db_path) for kernel_file in kernels_files_list: if intersecc_db_str == kernel_file: network = os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'by_db', f'{intersecc_db_str}.pickle') break if not network: graph_db_path = os.path.join(DEFAULT_DIFFUPATH_DIR, 'graphs', 'by_db') graphs_files_list = get_or_create_dir(graph_db_path) if graphs_files_list: for graph_file in graphs_files_list: if f'{intersecc_db_str}.pickle' == graph_file: network = os.path.join(DEFAULT_DIFFUPATH_DIR, 'graphs', 'by_db', f'{intersecc_db_str}.pickle') break if not network: graph = process_graph_from_file(GRAPH_PATH) network = get_subgraph_by_annotation_value(graph, 'database', intersecc_db ) to_pickle(network, os.path.join(DEFAULT_DIFFUPATH_DIR, 'graphs', 'by_db', f'{intersecc_db_str}.pickle')) if not filter_network_omic: click.secho(f'{EMOJI}Generating kernel from {GRAPH_PATH} {EMOJI}') network = get_kernel_from_graph(network, kernel_method) click.secho(f'{EMOJI}Kernel generated {EMOJI}') to_pickle(network, os.path.join(DEFAULT_DIFFUPATH_DIR, 'kernels', 'by_db', f'{db_norm}.pickle')) else: raise ValueError( 'Subgraph filtering by database only supported for PathMe network (KEGG, Reactome and Wikipathways).') return network
31,518
def _to_tensor(args, data): """Change data to tensor.""" if vega.is_torch_backend(): import torch data = torch.tensor(data) if args.device == "GPU": return data.cuda() else: return data elif vega.is_tf_backend(): import tensorflow as tf data = tf.convert_to_tensor(data) return data
31,519
def materialize_jupyter_deployment( config: ClusterConfig, uuid: str, definition: DeploymentDefinition) -> JupyterDeploymentImpl: # noqa """Materializes the Jupyter deployment definition. :param config: Cluster to materialize the Jupyter deployment with. :param uuid: Unique deployment id. :param definition: Deployment definition to materialize. """ jupyter_deployment = deserialize_jupyter_deployment_impl( config=config, uuid=uuid, serialized=definition.value) return jupyter_deployment
31,520
async def test_filter_matching_past_event(mock_now, hass, calendar): """Test that the matching past event is not returned.""" config = dict(CALDAV_CONFIG) config["custom_calendars"] = [ {"name": "Private", "calendar": "Private", "search": "This is a normal event"} ] assert await async_setup_component(hass, "calendar", {"calendar": config}) await hass.async_block_till_done() state = hass.states.get("calendar.private_private") assert state.name == calendar.name assert state.state == "off"
31,521
def show_M(N): """ N: int """ n = np.arange(N) k = n.reshape((N,1)) M = k*n print("M:", M)
31,522
def update_weekly_downloads(): """Update the weekly "downloads" from the users_install table.""" raise_if_reindex_in_progress() interval = datetime.datetime.today() - datetime.timedelta(days=7) counts = (Installed.objects.values('addon') .filter(created__gte=interval, addon__type=amo.ADDON_WEBAPP) .annotate(count=Count('addon'))) ts = [webapp_update_weekly_downloads.subtask(args=[chunk]) for chunk in chunked(counts, 1000)] TaskSet(ts).apply_async()
31,523
def _CreateLSTMPruneVariables(lstm_obj, input_depth, h_depth): """Function to create additional variables for pruning.""" mask = lstm_obj.add_variable( name="mask", shape=[input_depth + h_depth, 4 * h_depth], initializer=tf.ones_initializer(), trainable=False, dtype=lstm_obj.dtype) threshold = lstm_obj.add_variable( name="threshold", shape=[], initializer=tf.zeros_initializer(), trainable=False, dtype=lstm_obj.dtype) # Add old_weights, old_old_weights, gradient for gradient # based pruning. old_weight = lstm_obj.add_variable( name="old_weight", shape=[input_depth + h_depth, 4 * h_depth], initializer=tf.zeros_initializer(), trainable=False, dtype=lstm_obj.dtype) old_old_weight = lstm_obj.add_variable( name="old_old_weight", shape=[input_depth + h_depth, 4 * h_depth], initializer=tf.zeros_initializer(), trainable=False, dtype=lstm_obj.dtype) gradient = lstm_obj.add_variable( name="gradient", shape=[input_depth + h_depth, 4 * h_depth], initializer=tf.zeros_initializer(), trainable=False, dtype=lstm_obj.dtype) return mask, threshold, old_weight, old_old_weight, gradient
31,524
def get_index_fredkin_gate(N, padding = 0): """Get paramaters for log2(N) Fredkin gates Args: - N (int): dimensional of states - padding (int, optional): Defaults to 0. Returns: - list of int: params for the second and third Frekin gates """ indices = [] for i in range(0, int(np.log2(N))): indices.append(2**i + padding) return indices
31,525
def import_by_name(name): """ 动态导入 """ tmp = name.split(".") module_name = ".".join(tmp[0:-1]) obj_name = tmp[-1] module = __import__(module_name, globals(), locals(), [obj_name]) return getattr(module, obj_name)
31,526
def fyolo_vgg_voc(backbone="vgg16", num_layers=13, pretrained_base=True, pretrained=False, num_sync_bn_devices=-1, **kwargs): """FYOLO of VGG on VOC dataset Parameters ---------- backbone : str Use the imagenet pretrained backbone ("vgg11", "vgg13" or "vgg16") for initialization. num_layers : int Keep the first num_layers of pretrained darknet to build an fnet. pretrained_base : boolean Whether fetch and load pretrained weights for base network. pretrained : boolean Whether fetch and load pretrained weights for the entire network. num_sync_bn_devices : int Number of devices for training. If `num_sync_bn_devices < 2`, SyncBatchNorm is disabled. Returns ------- mxnet.gluon.HybridBlock Fully hybrid yolo3 network. """ from gluoncv.data import VOCDetection from .vgg import get_vgg_lsf pretrained_base = False if pretrained else pretrained_base base_net = get_vgg_lsf(backbone=backbone, keep_layers=num_layers, pretrained=pretrained_base, num_sync_bn_devices=num_sync_bn_devices, **kwargs) classes = VOCDetection.CLASSES # TODO @ xyutao: Implemenet vgg-based single-scale yolo.
31,527
def f1_score(y_true, y_pred): """F-measure.""" p = precision(y_true, y_pred) r = true_positive_rate(y_true, y_pred) return 2 * (p * r) / (p + r)
31,528
def hexColorToInt(rgb): """Convert rgb color string to STK integer color code.""" r = int(rgb[0:2],16) g = int(rgb[2:4],16) b = int(rgb[4:6],16) color = format(b, '02X') + format(g, '02X') + format(r, '02X') return int(color,16)
31,529
def reset_speed(): """ reset vertical speed as score achieves certain level :return: float, new vertical speed """ global y_speed # when score achieves 50 if score == 50: # ball moves faster y_speed = y_speed * 1.2 graphics.reset_vertical_velocity(dy) # when score achieves 70 elif score == 70: # ball moves faster y_speed = y_speed * 1.2 graphics.reset_vertical_velocity(dy) elif score == 120: # ball moves faster y_speed = y_speed * 1.3 graphics.reset_vertical_velocity(dy)
31,530
def test(model, X, model_type, test_type, counter=False): """Test functions.""" if model_type == 'notear-mlp': X = np.vstack(X) y = model(torch.from_numpy(X)) y = y.cpu().detach().numpy() mse = mean_squared_loss(y.shape[0], y[:, 0], X[:, 0]) elif model_type == 'notear-castle': X = np.vstack(X) y = model(torch.from_numpy(X)) y = y.cpu().detach().numpy() mse = mean_squared_loss(y.shape[0], y[:, 0], X[:, 0]) elif model_type == 'ISL': y = model.test(X) mse = mean_squared_loss(y.shape[0] * y.shape[1], y, X[:, :, 0][:, :, np.newaxis]) if not counter: if test_type == 'ID': metrics[f'{model_type}_testID_MSE'] = mse elif test_type == 'OOD': metrics[f'{model_type}_testOOD_MSE'] = mse else: if test_type == 'ID': metrics[f'{model_type}_counter_testID_MSE'] = mse elif test_type == 'OOD': metrics[f'{model_type}_counter_testOOD_MSE'] = mse return mse
31,531
def scale(): """ Returns class instance of `Scale`. For more details, please have a look at the implementations inside `Scale`. Returns ------- Scale : Class instance implementing all 'scale' processes. """ return Scale()
31,532
def imread_rgb(filename): """Read image file from filename and return rgb numpy array""" bgr = cv2.imread(filename) rgb = cv2.cvtColor(bgr, cv2.COLOR_BGR2RGB) return rgb
31,533
def insert_at_index(rootllist, newllist, index): """ Insert newllist in the llist following rootllist such that newllist is at the provided index in the resulting llist""" # At start if index == 0: newllist.child = rootllist return newllist # Walk through the list curllist = rootllist for i in range(index-1): curllist = curllist.child # Insert newllist.last().child=curllist.child curllist.child=newllist return rootllist
31,534
def _save_observables( file_name: str, file_override: bool, observable_names: List[str], observable_defs: List[Union[str, Callable]], ) -> None: """ Save observable properties into a HDF5 data file Parameters ---------- file_name: str HDF5 file name to save observables properties into file_override: bool Whether to override HDF5 file contents or not observable_names : list List of observable names observable_defs: list List of observable string-encoded or callable function definitions Returns ------- None """ observable_names = _encode_strings(observable_names) # Filter out callable definitions when saving into HDF5 file observable_defs = [d if isinstance(d, str) else EMPTY_EXPR for d in observable_defs] observable_defs = _encode_strings(observable_defs) # Append if file exists, otherwise create with h5py.File(file_name, "a") as file: if file_override: with suppress(KeyError): del file["observables"] file.create_dataset("observables/names", data=observable_names, dtype="S256") file.create_dataset("observables/definitions", data=observable_defs, dtype="S256")
31,535
def kpi_value(request, body): """kpi值接口 根据 indicator 传入参数不同请求不同的 handler""" params = { "indicator": body.indicator } handler = KpiFactory().create_handler(params["indicator"]) result = handler(params=params) return DashboardResult(content=result)
31,536
def safeReplaceOrder( references ): """ When inlining a variable, if multiple instances occur on the line, then the last reference must be replaced first. Otherwise the remaining intra-line references will be incorrect. """ def safeReplaceOrderCmp(self, other): return -cmp(self.colno, other.colno) result = list(references) result.sort(safeReplaceOrderCmp) return result
31,537
def broken_link_finder(urls: Union[str, list, tuple, set], print_to_console: bool = False, file_out = None, viewer = DEFAULT_CSV_VIEWER, open_results_when_done = True, exclude_prefixes: Iterable = EXCLUDE_LINKS_STARTING_WITH): """ Checks for broken links on a specific web page(s) as specified by the urls argument. :param urls: the url or urls to check. :param print_to_console: True / False -- print each link to console while checking. :param file_out: if not None, name of file to which to write broken link checker output :param viewer: program to use to open and view the results (csv file) :param open_results_when_done: True/False :param exclude_prefixes: list-like :return: list of sets of broken_urls, local_urls, foreign_urls, processed_urls """ start_time = time.time() working_urls: List[Any] = [] broken_urls: List[Any] = [] if type(exclude_prefixes) == str: exclude_prefixes = [exclude_prefixes] if 'mailto' not in exclude_prefixes: exclude_prefixes = list(exclude_prefixes) exclude_prefixes.append('mailto') if type(urls) == str: urls = [urls] links = [] for url in urls: lst = get_links_from_webpage(url, full_links = True, exclude_prefixes = exclude_prefixes) links += lst['urls'] # remove duplicates links = set(links) tot = len(links) cnt = 0 for link in links: if print_to_console: cnt += 1 print(f'Checking link {cnt} of {tot}: {link}') try: # TODO: should probably leverage link_check instead of repeating code. # compare the code in this function and link_check to see what's up. head = requests.head(link) success = head.ok status = "Retrieved header from: {link}" try: response = requests.get(link) success = response.ok status = "Received response from: {link}" except Exception as e: success = False status = f"{e}. Retrieved header but failed to open page: {link}" except Exception as e: success = False status = f"{e}. Failed to retrieved header from: {link}" if link.startswith('ftp:'): # get stats from ftp server stats = ez_ftp.stats(link) filename = stats.basename file_size = stats.size # filename, file_size = ftp_file_size(link) if not filename: success = False status = f"FTP file not found: {link}" if type(filename) == str: if file_size > 0: success = True status = f"FTP file found: {link}" else: success = False status = f"FTP file is empty: {link}" else: success = False status = f"{file_size}. FTP file: {link}" if success: # found a broken link working_urls.append((link, success, status)) else: broken_urls.append((link, success, status)) processed_urls = working_urls + broken_urls if file_out: df = pd.DataFrame(data = processed_urls, index = None, columns = ['link', 'success', 'header']) df.to_csv(path_or_buf = file_out, sep = ',', header = True) if open_results_when_done: # open result file in viewer text editor). view_file(filename = file_out, viewer = viewer) # Done recursive loop. Report results. stop_time = time.time() run_time = stop_time - start_time if print_to_console: print(f'\n\nChecked: {len(processed_urls)} links in {run_time} seconds') print(f'\nFound {len(broken_urls)} BROKEN LINKS: \n', broken_urls) # Return results. ReturnTuple = namedtuple('ReturnTuple', 'processed_urls broken_urls run_time') return ReturnTuple(processed_urls, broken_urls, run_time)
31,538
def test_compute_reproject_roi_issue1047(): """ `compute_reproject_roi(geobox, geobox[roi])` sometimes returns `src_roi != roi`, when `geobox` has (1) tiny pixels and (2) oddly sized `alignment`. Test this issue is resolved. """ geobox = GeoBox(3000, 3000, Affine(0.00027778, 0.0, 148.72673054908861, 0.0, -0.00027778, -34.98825802556622), "EPSG:4326") src_roi = np.s_[2800:2810, 10:30] rr = compute_reproject_roi(geobox, geobox[src_roi]) assert rr.is_st is True assert rr.roi_src == src_roi assert rr.roi_dst == np.s_[0:10, 0:20]
31,539
def clean_value(value: str) -> t.Union[int, float, str]: """Return the given value as an int or float if possible, otherwise as the original string.""" try: return int(value) except ValueError: pass try: return float(value) except ValueError: pass return value
31,540
def check_matching_unit_dimension( ureg: UnitRegistry, base_units: str, units_to_check: List[str] ) -> None: """ Check if all units_to_check have the same Dimension like the base_units If not :raise DimensionalityError """ base_unit = getattr(ureg, base_units) for unit_string in units_to_check: unit = getattr(ureg, unit_string) if unit.dimensionality != base_unit.dimensionality: raise DimensionalityError(base_unit, unit)
31,541
def sumstat(*L): """ Sums a list or a tuple L Modified from pg 80 of Web Programming in Python """ if len(L) == 1 and \ ( isinstance(L[0],types.ListType) or \ isinstance (L[0], types.TupleType) ) : L = L[0] s = 0.0 for k in L: s = s + k return s
31,542
def test_cases_by_pinned_gene_query(app, case_obj, institute_obj): """Test cases filtering by providing the gene of one of its pinned variants""" # GIVEN a test variant hitting POT1 gene (hgnc_id:17284) suspects = [] test_variant = store.variant_collection.find_one({"genes.hgnc_id": {"$in": [17284]}}) assert test_variant with app.test_client() as client: resp = client.get(url_for("auto_login")) assert resp.status_code == 200 # GIVEN a case with this variant pinned form = { "action": "ADD", } client.post( url_for( "cases.pin_variant", institute_id=institute_obj["internal_id"], case_name=case_obj["display_name"], variant_id=test_variant["_id"], ), data=form, ) updated_case = store.case_collection.find_one({"suspects": {"$in": [test_variant["_id"]]}}) assert updated_case # WHEN the case search is performed using the POT1 gene slice_query = f"pinned:POT1" resp = client.get( url_for( "overview.cases", query=slice_query, institute_id=institute_obj["internal_id"], ) ) # THEN it should return a page with the case assert resp.status_code == 200 assert case_obj["display_name"] in str(resp.data)
31,543
def halref_to_data_url(halref: str) -> str: """ Given a HAL or HAL-data document URIRef, returns the corresponding HAL-data URL halref: str HAL document URL (Most important!) https://hal.archives-ouvertes.fr/hal-02371715v2 -> https://data.archives-ouvertes.fr/document/hal-02371715v2 https://data.archives-ouvertes.fr/document/hal-02371715v2.rdf -> https://data.archives-ouvertes.fr/document/hal-02371715v2.rdf https://data.archives-ouvertes.fr/document/hal-02371715 -> https://data.archives-ouvertes.fr/document/hal-02371715 """ parsed_ref = urlparse(halref) assert "archives-ouvertes.fr" in parsed_ref.netloc, "Expected HAL (or HAL-data) document URL" if "hal.archives-ouvertes.fr" in parsed_ref.netloc: parsed_ref = parsed_ref._replace(netloc="data.archives-ouvertes.fr", path=f"/document{parsed_ref.path}") return urlunparse(parsed_ref)
31,544
def find_best_rate(): """ Input: Annual salary, semi-annual raise, cost of home Assumes: a time frame of three years (36 months), a down payment of 25% of the total cost, current savings starting from 0 and annual return of 4% Returns the best savings rate within (plus/minus) $100 of the downpayment, and bisection search else returns false if result is not possible """ annual_salary = float(input("Enter your annual salary: ")) total_cost = float(1000000) semi_annual_raise = float(0.07) monthly_salary = annual_salary/12 r = 0.04 down_payment = 0.25 * total_cost current_savings = 0 time = 36 epsilon = 100 low = 0 high = 10000 savings_rate = (low + high)//2 num = 0 while abs(current_savings - down_payment) >= epsilon: mod_annual_salary = annual_salary #The annual salary we will use to modify/ make changes current_savings = 0 portion_saved = savings_rate/10000 #Converting our floor/ int division to decimal (as a portion to save) for month in range(1, time+1): if month % 6 == 0: mod_annual_salary += (annual_salary * semi_annual_raise) monthly_salary = mod_annual_salary/12 monthly_savings = monthly_salary * portion_saved additional = monthly_savings + (current_savings * r/12) #Additional return considering monthly and current savings current_savings += additional #Bisection search if current_savings < down_payment: low = savings_rate else: high = savings_rate savings_rate = (low + high)//2 num += 1 if num > 15: #Log_2 (10000) is 13.28... it will not make sense to keep searching after this point break if num < 15: print("Best Savings Rate: {} or {}%".format(portion_saved, portion_saved*100)), print("Steps in bisection Search: {}".format(num)) return portion_saved else: return("It is not possible to pay the down payment in three years")
31,545
def export_secret_key(ctx, account_name): """print secret key of own account.""" account = get_account(ctx, account_name) data = account.export_secret_key() click.echo(data)
31,546
def q_inv(a): """Return the inverse of a quaternion.""" return [a[0], -a[1], -a[2], -a[3]]
31,547
def divide_hex_grid_flower(points, hex_radius=None): """Partitions a hexagonal grid into a flower pattern (this is what I used for the final product. Returns a list of partition indices for each point.""" if hex_radius is None: # copied from build_mirror_array() mini_hex_radius = (10 * 2.5 / 2) + 1 hex_radius = mini_hex_radius * 1.1 points = np.array(points) # Divide into quarters partition_indices = np.ones(len(points)) * -1 for i, point in enumerate(points): x, y, z = point if np.sqrt(x**2 + y**2) <= 3 * (2*hex_radius + 1) * np.sqrt(3)/2: partition_indices[i] = 0 else: θ = np.arctan2(x,y) + pi - 1e-10 partition_indices[i] = 1 + np.floor(6 * θ / (2 * pi)) return partition_indices
31,548
def fis_gauss2mf(x:float, s1:float, c1:float, s2:float, c2:float): """Split Gaussian Member Function""" t1 = 1.0 t2 = 1.0 if x < c1: t1 = fis_gaussmf(x, s1, c1) if x > c2: t2 = fis_gaussmf(x, s2, c2) return (t1 * t2)
31,549
def _is_trigonal_prism(vectors, dev_cutoff=15): """ Triangular prisms are defined by 3 vertices in a triangular pattern on two aligned planes. Unfortunately, the angles are dependent on the length and width of the prism. Need more examples to come up with a better way of detecting this shape. For now, this code is experimental. Parameters ---------- vectors : list scitbx.matrix.col dev_cutoff : float, optional Returns ------- bool """ if len(vectors) != 6: return angles = _bond_angles(vectors) a_85s, a_135s = [], [] for angle in angles: if abs(angle[-1] - 85) < abs(angle[-1] - 135): a_85s.append(angle[-1] - 85) else: a_135s.append(angle[-1] - 135) if len(a_85s) != 9 and len(a_135s) != 6: return deviation = sqrt(sum(i ** 2 for i in a_85s + a_135s) / len(angles)) if deviation < dev_cutoff: return deviation, 6 - len(vectors)
31,550
def get_sza(times, rad, mask=None): """ Fetch sza at all range cell in radar FoV rad: Radar code mask: mask metrix """ fname = "data/sim/{rad}.geolocate.data.nc.gz".format(rad=rad) os.system("gzip -d " + fname) fname = fname.replace(".gz","") data = Dataset(fname) lat, lon = data["geo_lat"], data["geo_lon"] sza = [] for d in times: sza.append(get_altitude(lat, lon, d)) sza = np.array(sza) os.system("gzip " + fname) return sza
31,551
def load_results(path): """ return a dictionary of columns can't use genfromtex because of weird format for arrays that I used :param path: :return: """ data = defaultdict(list) column_casts = { "epoch": float, "env_name": str, "game_counter": int, "game_length": int, "score_red": float, "score_green": float, "score_blue": float, "wall_time": float, "date_time": float } # load in data step_counter = 0 player_count = None with open(path, "r") as f: header = f.readline() column_names = [name.strip() for name in header.split(",")] infer_epoch = "epoch" not in column_names for line in f: row = line.split(",") for name, value, in zip(column_names, row): if name in column_casts: value = column_casts[name](value) else: value = str(value) data[name] += [value] # fix a bug with a specific version of rescue game if "stats_voted_offplayer_count" in data: data["player_count"] = data["stats_voted_offplayer_count"] if player_count is None: player_count = sum([int(x) for x in data["player_count"][0].split(" ")]) step_counter += data["game_length"][-1] * player_count # convert the team stats to single columns for i, hit in enumerate(int(x) for x in str(data["stats_player_hit"][-1]).split(" ")): if vs_order[i] not in data: data[vs_order[i]] = [] data[vs_order[i]] += [hit] # convert the team stats to single columns if "stats_player_hit_with_witness" in data: for i, hit in enumerate(int(x) for x in str(data["stats_player_hit_with_witness"][-1]).split(" ")): key = vs_order[i]+"_ww" if key not in data: data[key] = [] data[key] += [hit] # convert the team stats to single columns for stat in ["deaths", "kills", "general_shot", "general_moved", "general_hidden", "tree_harvested"]: stats_name = f"stats_{stat}" if stats_name not in data: continue for team, value in zip("RGB", (int(x) for x in str(data[stats_name][-1]).split(" "))): field_name = f"{team}_{stat}" data[field_name] += [value] # convert the team stats to single columns for stat in ["votes"]: stats_name = f"stats_{stat}" if stats_name not in data: continue for team, value in zip("RGBT", (int(x) for x in str(data[stats_name][-1]).split(" "))): field_name = f"{team}_{stat}" data[field_name] += [value] if infer_epoch: data["epoch"].append(float(step_counter)/1e6) # make epoch an into to group better data["epoch"][-1] = round(data["epoch"][-1], 1) return data
31,552
def save_tf(model, folder, filename): """Save model in Tensorflow format Args: model {graph_def} -- classification model folder {string} -- folder name filename {string} -- model filename """ filepath = os.path.join(folder, filename) sess = K.get_session() outputs = ["input_1", "dense_2/Softmax"] constant_graph = tf.graph_util.convert_variables_to_constants(sess, sess.graph.as_graph_def(), outputs) tf.train.write_graph(constant_graph,folder,filename,as_text=False) print('saved the graph definition in tensorflow format at: ', filepath)
31,553
def priority(n=0): """ Sets the priority of the plugin. Higher values indicate a higher priority. This should be used as a decorator. Returns a decorator function. :param n: priority (higher values = higher priority) :type n: int :rtype: function """ def wrapper(cls): cls._plugin_priority = n return cls return wrapper
31,554
def vecangle(u,v): """ Calculate as accurately as possible the angle between two 3-component vectors u and v. This formula comes from W. Kahan's advice in his paper "How Futile are Mindless Assessments of Roundoff in Floating-Point Computation?" (https://www.cs.berkeley.edu/~wkahan/Mindless.pdf), section 12 "Mangled Angles." θ=2 atan2(|| ||v||u−||u||v ||, || ||v||u+||u||v ||) """ modu = modvec(u) modv = modvec(v) vmodu = [modu*v[0] , modu*v[1], modu*v[2] ] umodv = [modv*u[0] , modv*u[1], modv*u[2] ] term1 = [umodv[0]-vmodu[0], umodv[1]-vmodu[1], umodv[2]-vmodu[2]] modterm1 = modvec(term1) term2 = [umodv[0]+vmodu[0], umodv[1]+vmodu[1], umodv[2]+vmodu[2]] modterm2 = modvec(term2) return (2.0*math.atan2(modterm1,modterm2))
31,555
def _setup_sensor(hass, humidity): """Set up the test sensor.""" hass.states.async_set(ENT_SENSOR, humidity)
31,556
def rm_empty_dir(path, rmed_empty_dirs): """Recursively remove empty directories under and including path.""" if not os.path.isdir(path): return fnames = os.listdir(path) if len(fnames) > 0: for fn in fnames: fpath = os.path.join(path, fn) if os.path.isdir(fpath): rm_empty_dir(fpath, rmed_empty_dirs) if len(os.listdir(path)) == 0: rmed_empty_dirs.append(str(path)) os.rmdir(path)
31,557
def sanitize_option(option): """ Format the given string by stripping the trailing parentheses eg. Auckland City (123) -> Auckland City :param option: String to be formatted :return: Substring without the trailing parentheses """ return ' '.join(option.split(' ')[:-1]).strip()
31,558
def node_values_for_tests(): """Creates a list of possible node values for parameters Returns: List[Any]: possible node values """ return [1, 3, 5, 7, "hello"]
31,559
def computeGramMatrix(A, B): """ Constructs a linear kernel matrix between A and B. We assume that each row in A and B represents a d-dimensional feature vector. Parameters: A: a (n_batch, n, d) Tensor. B: a (n_batch, m, d) Tensor. Returns: a (n_batch, n, m) Tensor. """ assert(A.dim() == 3) assert(B.dim() == 3) assert(A.size(0) == B.size(0) and A.size(2) == B.size(2)) return torch.bmm(A, B.transpose(1,2))
31,560
def parse_config(config): """Backwards compatible parsing. :param config: ConfigParser object initilized with nvp.ini. :returns: A tuple consisting of a control cluster object and a plugin_config variable. raises: In general, system exceptions are not caught but are propagated up to the user. Config parsing is still very lightweight. At some point, error handling needs to be significantly enhanced to provide user friendly error messages, clean program exists, rather than exceptions propagated to the user. """ # Extract plugin config parameters. try: failover_time = config.get('NVP', 'failover_time') except ConfigParser.NoOptionError, e: failover_time = str(DEFAULT_FAILOVER_TIME) try: concurrent_connections = config.get('NVP', 'concurrent_connections') except ConfigParser.NoOptionError, e: concurrent_connections = str(DEFAULT_CONCURRENT_CONNECTIONS) plugin_config = { 'failover_time': failover_time, 'concurrent_connections': concurrent_connections, } LOG.info('parse_config(): plugin_config == "%s"' % plugin_config) cluster = NVPCluster('cluster1') # Extract connection information. try: defined_connections = config.get('NVP', 'NVP_CONTROLLER_CONNECTIONS') for conn_key in defined_connections.split(): args = [config.get('NVP', 'DEFAULT_TZ_UUID')] args.extend(config.get('NVP', conn_key).split(':')) try: cluster.add_controller(*args) except Exception, e: LOG.fatal('Invalid connection parameters: %s' % str(e)) sys.exit(1) return cluster, plugin_config except Exception, e: LOG.info('No new style connections defined: %s' % e) # Old style controller specification. args = [config.get('NVP', k) for k in CONFIG_KEYS] try: cluster.add_controller(*args) except Exception, e: LOG.fatal('Invalid connection parameters.') sys.exit(1) return cluster, plugin_config
31,561
def example(tracker,img_path,dest,scr,disp,log,kb_obj,kb_chc): """ Describe Demonstration Example """ txt_task = ("Scientist at work in a laboratory.") img_name = "scientist.jpg" exp1(tracker,dest,img_path,img_name,txt_task,scr,disp,log,kb_obj,kb_chc) scr.clear() scr.draw_text(text= "Great work! Here's another example sentence. Press spacebar to continue.", fontsize=20) disp.fill(scr) _ =disp.show() response, t_1 = kb_obj.get_key() beep(1) txt_task = ("Man playing with a dog.") img_name = "man_dog.jpg" exp1(tracker,dest,img_path,img_name,txt_task,scr,disp,log,kb_obj,kb_chc) scr.clear() scr.draw_text(text= "Great work! This time, without the written instructions. Feel free to ask any questions. Press spacebar to continue.", fontsize=20) disp.fill(scr) _ =disp.show() response, t_1 = kb_obj.get_key() txt_task = ("The phone says 'pass me the pizza'") img_name = "phone.jpg" task(tracker,dest,img_path,img_name,txt_task,scr,disp,log,kb_obj,kb_chc) scr.clear() beep(1) scr.draw_text(text= "Great work! Press spacebar to continue.", fontsize=20) disp.fill(scr) _ =disp.show() response, t_1 = kb_obj.get_key() txt_task = ("Two young women are playing a game of cards.") img_name = "music1.jpg" task(tracker,dest,img_path,img_name,txt_task,scr,disp,log,kb_obj,kb_chc) scr.clear() beep(1) scr.draw_text(text= "Great work! Press spacebar to continue.", fontsize=20) disp.fill(scr) _ =disp.show() response, t_1 = kb_obj.get_key() txt_task = ("The president would arrive here within two hours.") img_name = "control.jpg" task(tracker,dest,img_path,img_name,txt_task,scr,disp,log,kb_obj,kb_chc)
31,562
def test_private_median(example_private_table: PrivateTable): """check private median implementation using Age in adult dataset.""" noisy_median = example_private_table.median('Age', PrivacyBudget(10000.)) check_absolute_error(noisy_median, 37., 1.) del noisy_median
31,563
def _generate_output_data_files_threaded( short_topic, output_template, plaintext_key, output_folder, encryption_json_text_output, output_iv_full, job_id, ): """Generates required historic data files from the files in the given folder using multiple threads. Keyword arguments: short_topic -- the short topic output_template -- the name and location for the output template json file plaintext_key -- the plaintext data key for encrypting the data file output_folder -- the folder to store the generated output files in encryption_json_text_output -- the encryption text output_iv_full -- the iv used to encrypt job_id -- job id for the messages """ global keys local_keys = keys output_base_content = file_helper.get_contents_of_file(output_template, False) with ThreadPoolExecutor() as executor_output: future_results_output = [] for key_number in range(0, len(local_keys)): future_results_output.append( executor_output.submit( generate_output_file, output_base_content, output_folder, local_keys[key_number], encryption_json_text_output, short_topic, plaintext_key, output_iv_full, job_id, key_number + 1, ) ) wait(future_results_output) for future in future_results_output: try: yield future.result() except Exception as ex: raise AssertionError(ex)
31,564
def deletable_proxy_user(request, onefs_client): """Get the name of an existing proxy user that it is ok to delete.""" return _deletable_proxy_user(request, onefs_client)
31,565
def get_from_module(identifier, module_params, module_name, instantiate=False, kwargs=None): """The function is stolen from keras.utils.generic_utils. """ if isinstance(identifier, six.string_types): res = module_params.get(identifier) if not res: raise Exception('Invalid ' + str(module_name) + ': ' + str(identifier)) if instantiate and not kwargs: return res() elif instantiate and kwargs: return res(**kwargs) else: return res elif type(identifier) is dict: name = identifier.pop('name') res = module_params.get(name) if res: return res(**identifier) else: raise Exception('Invalid ' + str(module_name) + ': ' + str(identifier)) return identifier
31,566
def test_mnist_model_register_and_scale_using_non_existent_handler(): """ Bug - Following code block will result in "Buggy" behaviour. If a non-existent handler is used, then ideally we should not be able to scale up workers anytime, but currently Torchserve scales up background workers. Uncomment it after the Bug is fixed """ # mnist_model_register_and_scale_using_non_existent_handler_synchronous() # mnist_model_register_and_scale_using_non_existent_handler_asynchronous()
31,567
def color_lerp(c1, c2, a): """Return the linear interpolation between two colors. ``a`` is the interpolation value, with 0 returing ``c1``, 1 returning ``c2``, and 0.5 returing a color halfway between both. Args: c1 (Union[Tuple[int, int, int], Sequence[int]]): The first color. At a=0. c2 (Union[Tuple[int, int, int], Sequence[int]]): The second color. At a=1. a (float): The interpolation value, Returns: Color: The interpolated Color. """ return Color._new_from_cdata(lib.TCOD_color_lerp(c1, c2, a))
31,568
def get_equations(points): """ Calculate affine equations of inputted points Input : 1 points : list of list ex : [[[x1, y1], [x2, y2]], [[xx1, yy1], [xx2, yy2]]] for 2 identified elements Contains coordinates of separation lines i.e. [[[start points x, y], [end points x, y]] [...], [...]] Output : 2 columns_a : list of list Contains all the a coefficients of an affine equation (y = ax + b) of all the calculated lines, in the same order as the input columns_b : list of list Contains all the b coefficients of an affine equation (y = ax + b) of the all the calculated lines, in the same order as the input""" columns_a, columns_b = [], [] # iterate throught points for k in points: # calculate the a coefficients of start and end separation lines of this element a1 = (k[0][1] - k[1][1])/(k[0][0] - k[1][0]) a2 = (k[2][1] - k[3][1])/(k[2][0] - k[3][0]) columns_a.append([a1, a2]) # then calculate the b coefficients of start and end separation lines # using the a coeff calculated before b1 = k[0][1] - a1*k[0][0] b2 = k[2][1] - a2*k[2][0] columns_b.append([b1, b2]) return (columns_a, columns_b)
31,569
def Temple_Loc(player, num): """temple location function""" player.coins -= num player.score += num player.donation += num # player = temple_bonus_check(player) for acheivements return (player)
31,570
def save_crowdin(data): """ Save crowdin `data`. """ fpath = os.path.join(REPO_ROOT, CROWDIN_FILE) with open(fpath, "w") as fh: fh.write(yaml.safe_dump(data))
31,571
def indexGenomeFile(input, output): """Index STAR genome index file `input`: Input probes fasta file `output`: SAindex file to check the completion of STAR genome index """ #print input #print output base = splitext(input)[0] base = base + ".gtf" #print base gtfFile = base outputDir = proDir + "/result/Genome" print colored("Stage 4: Creating genome index file from the probe fasta file ....", "green") print input #print cpuNum result = tasks.index_db_file(input, outputDir, cpuNum, gtfFile) return result
31,572
def assert_allclose( actual: numpy.ndarray, desired: Tuple[float, float, float], rtol: numpy.float64, atol: numpy.float64, err_msg: Literal["driver: None"], ): """ usage.scipy: 2 """ ...
31,573
def test_list_id_max_length_1_nistxml_sv_iv_list_id_max_length_2_1(mode, save_output, output_format): """ Type list/ID is restricted by facet maxLength with value 6. """ assert_bindings( schema="nistData/list/ID/Schema+Instance/NISTSchema-SV-IV-list-ID-maxLength-2.xsd", instance="nistData/list/ID/Schema+Instance/NISTXML-SV-IV-list-ID-maxLength-2-1.xml", class_name="Out", version="1.1", mode=mode, save_output=save_output, output_format=output_format, structure_style="filenames", )
31,574
def performance(origin_labels, predict_labels, deci_value, bi_or_multi=False, res=False): """evaluations used to evaluate the performance of the model. :param deci_value: decision values used for ROC and AUC. :param bi_or_multi: binary or multiple classification :param origin_labels: true values of the data set. :param predict_labels: predicted values of the data set. :param res: residue or not. """ if len(origin_labels) != len(predict_labels): raise ValueError("The number of the original labels must equal to that of the predicted labels.") if bi_or_multi is False: tp = 0.0 tn = 0.0 fp = 0.0 fn = 0.0 for i in range(len(origin_labels)): if res is True: if origin_labels[i] == 1 and predict_labels[i] == 1: tp += 1.0 elif origin_labels[i] == 1 and predict_labels[i] == 0: fn += 1.0 elif origin_labels[i] == 0 and predict_labels[i] == 1: fp += 1.0 elif origin_labels[i] == 0 and predict_labels[i] == 0: tn += 1.0 else: if origin_labels[i] == 1 and predict_labels[i] == 1: tp += 1.0 elif origin_labels[i] == 1 and predict_labels[i] == -1: fn += 1.0 elif origin_labels[i] == -1 and predict_labels[i] == 1: fp += 1.0 elif origin_labels[i] == -1 and predict_labels[i] == -1: tn += 1.0 try: sn = tp / (tp + fn) r = sn except ZeroDivisionError: sn, r = 0.0, 0.0 try: sp = tn / (fp + tn) except ZeroDivisionError: sp = 0.0 try: acc = (tp + tn) / (tp + tn + fp + fn) except ZeroDivisionError: acc = 0.0 try: mcc = (tp * tn - fp * fn) / math.sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn)) except ZeroDivisionError: mcc = 0.0 try: auc = roc_auc_score(origin_labels, deci_value) except ValueError: # modify in 2020/9/13 auc = 0.0 try: p = tp / (tp + fp) except ZeroDivisionError: p = 0.0 try: f1 = 2 * p * r / (p + r) except ZeroDivisionError: f1 = 0.0 balance_acc = (sn + sp) / 2 return acc, mcc, auc, balance_acc, sn, sp, p, r, f1 else: correct_labels = 0.0 for elem in zip(origin_labels, predict_labels): if elem[0] == elem[1]: correct_labels += 1.0 acc = correct_labels / len(origin_labels) return acc
31,575
def group_emoves(emoves, props): """Elementary moves with the same scale ratio can be combined. All emoves are from the same group, so they share the same transformation distance. We can combine all emoves that also share the same scale ratio.""" # group the emoves by ratio emoves.sort(key=lambda x: x.n_sources/x.n_targets) emovemap = {ratio: list(emove) for ratio, emove in groupby(emoves, key=lambda x: x.n_sources/x.n_targets)} ratios = list(emovemap.keys()) # consider non-scales first -> ratio of 1 first if props.low_scale_first: ratios.sort(key=lambda x: abs(log2(x))) for ratio in ratios: if ratio < 1: continue ratio_emoves = emovemap[ratio] # we generate the a list of possible allocations to the emoves, that work to form a possible pair line_gen = _group_emoves_lines(ratio_emoves, ratio) exhaust_gen = _group_emoves_exhaust(ratio_emoves, 0, set(), props) if props.exhaustive and props.line: gen = chain(line_gen, exhaust_gen) elif props.exhaustive: gen = exhaust_gen else: gen = line_gen # generate the actual pair out of the emove allocation for emove_alloc in gen: if emove_alloc is None: continue up, down = set(), set() for (emove, sources, targets) in emove_alloc: (lx, ly, lneg), (hx, hy, hneg) = emove.move up |= {A(nr, lx, ly, lneg) for nr in sources} down |= {A(nr, hx, hy, hneg) for nr in targets} yield (up, down)
31,576
def rotkehlchen_instance( uninitialized_rotkehlchen, database, blockchain, accountant, start_with_logged_in_user, start_with_valid_premium, function_scope_messages_aggregator, db_password, rotki_premium_credentials, accounting_data_dir, username, etherscan, ): """A partially mocked rotkehlchen instance""" initialize_mock_rotkehlchen_instance( rotki=uninitialized_rotkehlchen, start_with_logged_in_user=start_with_logged_in_user, start_with_valid_premium=start_with_valid_premium, msg_aggregator=function_scope_messages_aggregator, accountant=accountant, blockchain=blockchain, db_password=db_password, rotki_premium_credentials=rotki_premium_credentials, data_dir=accounting_data_dir, database=database, username=username, etherscan=etherscan, ) return uninitialized_rotkehlchen
31,577
def enable_dashboard(cls, config): """Method to enable the dashboard module. if user bootstrap with skip-dashboard option then enabling the dashboard module. Args: cls (CephAdmin object) : cephadm instance object. config (Dict): Key/value pairs passed from the test suite. Example:: args: username: admin123 password: admin@123 """ user = config.get("username") pwd = config.get("password") # To create password text file temp_file = tempfile.NamedTemporaryFile(suffix=".txt") passwd_file = cls.installer.node.remote_file( sudo=True, file_name=temp_file.name, file_mode="w" ) passwd_file.write(pwd) passwd_file.flush() # To enable dashboard module DASHBOARD_ENABLE_COMMANDS = [ "ceph mgr module enable dashboard", "ceph dashboard create-self-signed-cert", ] for cmd in DASHBOARD_ENABLE_COMMANDS: out, err = cls.shell(args=[cmd]) LOG.info("STDOUT:\n %s" % out) LOG.error("STDERR:\n %s" % err) # command to create username and password to access dashboard as administrator cmd = [ "ceph", "dashboard", "ac-user-create", user, "-i", temp_file.name, "administrator", ] out, err = cls.shell( args=cmd, base_cmd_args={"mount": "/tmp:/tmp"}, ) LOG.info("STDOUT:\n %s" % out) LOG.error("STDERR:\n %s" % err) validate_enable_dashboard(cls, user, pwd)
31,578
def store_inspection_outputs_df(backend, annotation_iterators, code_reference, return_value, operator_context): """ Stores the inspection annotations for the rows in the dataframe and the inspection annotations for the DAG operators in a map """ dag_node_identifier = DagNodeIdentifier(operator_context.operator, code_reference, backend.code_reference_to_description.get(code_reference)) annotations_df = build_annotation_df_from_iters(backend.inspections, annotation_iterators) annotations_df['mlinspect_index'] = range(1, len(annotations_df) + 1) inspection_outputs = {} for inspection in backend.inspections: inspection_outputs[inspection] = inspection.get_operator_annotation_after_visit() backend.dag_node_identifier_to_inspection_output[dag_node_identifier] = inspection_outputs return_value = MlinspectDataFrame(return_value) return_value.annotations = annotations_df return_value.backend = backend if "mlinspect_index" in return_value.columns: return_value = return_value.drop("mlinspect_index", axis=1) elif "mlinspect_index_x" in return_value.columns: return_value = return_value.drop(["mlinspect_index_x", "mlinspect_index_y"], axis=1) assert "mlinspect_index" not in return_value.columns assert isinstance(return_value, MlinspectDataFrame) return return_value
31,579
def picard_bedtointervallist(bed, refdict, out_path, no_header_out_path): """Starts a Picard BedToIntervalList process that writes to out_path""" cmd = f'{GATK_PATH} BedToIntervalList -SD "{refdict}" --INPUT "{bed}" --OUTPUT "{out_path}"' run_ext_process(cmd, shell=True) # Some GATK-Picard modules do not currently report an accurate exit # status this is indended to catch errors with this GATK command if not os.path.exists(out_path): msg = f'Expected output ({out_path}) not found for command: {cmd}' raise ChildProcessError(msg) cmd = f'grep -v "@" "{out_path}" > {no_header_out_path}' run_ext_process(cmd, shell=True) if not os.path.exists(no_header_out_path): msg = f'Expected output ({no_header_out_path}) not found for command: {cmd}' raise ChildProcessError(msg)
31,580
def breadth_first_search(g, s): """ Breadth First Search. Based on CLR book. For each node, it calculates a distance (from starting vertex s), and the parent node. @param g: input graph, assume all unvisited @type g: Graph @param s: starting vertex name """ # g.reset() node_s = g[s] # get Node from name node_s.color = 1 # set to GRAY node_s.distance = 0 node_s.parent = None queue = deque() # create queue and add S to queue queue.append(node_s) while queue: node_v = queue.popleft() # remove first element of queue for node_w in node_v.child: # for each edge (v, w) if not node_w.color: # if color is WHITE node_w.color = 1 # set color to GRAY node_w.distance = node_v.distance + 1 node_w.parent = node_v queue.append(node_w) # add to queue at the end node_v.color = 2
31,581
def draw_overlay(image, overlay, alpha): """Draws an overlay over an image at a specified alpha. :param image: The base image. :param overlay: The overlay image. :param alpha: The opacity, from 0 to 1. :type image: ndarray :type overlay: ndarray :type alpha: float """ cv2.addWeighted(overlay, alpha, image, 1 - alpha, 0, image)
31,582
def switched (decorator): """decorator transform for switched decorations. adds start_fun and stop_fun methods to class to control fun""" @simple_decorator def new_decorator (fun): event = new_event() def inner_fun (self, *args): if args: event.wait() if threads_alive(): return fun(self, *args) def new_fun (self, *args): setattr(self, 'start_%s' % fun.__name__, event.set) setattr(self, 'stop_%s' % fun.__name__, event.clear) decorator(inner_fun)(self, *args) return new_fun return new_decorator
31,583
def logistic_embedding0(k=1, dataset='epinions'): """using random embedding to train logistic Keyword Arguments: k {int} -- [folder] (default: {1}) dataset {str} -- [dataset] (default: {'epinions'}) Returns: [type] -- [pos_ratio, accuracy, f1_score0, f1_score1, f1_score2, auc_score] """ print('random embeddings') embeddings = np.random.rand(DATASET_NUM_DIC[dataset], EMBEDDING_SIZE) pos_ratio, accuracy, f1_score0, f1_score1, f1_score2, auc_score = common_logistic(dataset, k, embeddings, 'random') return pos_ratio, accuracy, f1_score0, f1_score1, f1_score2, auc_score
31,584
def process_plus_glosses(word): """ Find all glosses with a plus inside. They correspond to one-phoneme affix sequences that are expressed by the same letter due to orthographic requirements. Replace the glosses and the morphemes. """ return rxPartsGloss.sub(process_plus_glosses_ana, word)
31,585
def replication(): """ 1) Connect to the PostgreSQL database server 2) Create and start logical replication with Postgres Server. 3) Call the Pub/sub function to push to Pub/Sub """ conn = None try: # read connection parameters dsn = config() # connect to the PostgreSQL server print('Connecting to the PostgreSQL database...') conn = psycopg2.connect(dsn, connection_factory=psycopg2.extras.LogicalReplicationConnection) print('Connection created') # create a cursor cur = conn.cursor() # replication slot name replication_slot = 'postgres_replication' try: # Start replication slot if available cur.start_replication(slot_name=replication_slot, decode=True) except psycopg2.ProgrammingError: # Create replication slot only the first time, with wal2json decoding. cur.create_replication_slot(replication_slot, output_plugin='wal2json') cur.start_replication(slot_name=replication_slot, decode=True) print('calling streaming') democonsumer = DemoConsumer() print("Starting streaming, press Control-C to end...", file=sys.stderr) try: #consuming the stream msgs. cur.consume_stream(democonsumer) except KeyboardInterrupt: cur.close() conn.close() print("The slot " + replication_slot + "still exists. Drop it by running following command on Postgres: " "SELECT pg_drop_replication_slot('" + replication_slot + "'); if no longer needed.", file=sys.stderr) print("WARNING: Transaction logs will accumulate in pg_xlog " "until the slot is dropped.", file=sys.stderr) # close the communication with the PostgreSQL cur.close() except (Exception, psycopg2.DatabaseError) as error: print(error) finally: if conn is not None: conn.close() print('Database connection closed.')
31,586
def check_in_the_past(value: datetime) -> datetime: """ Validate that a timestamp is in the past. """ assert value.tzinfo == timezone.utc, "date must be an explicit UTC timestamp" assert value < datetime.now(timezone.utc), "date must be in the past" return value
31,587
def fixture(filename): """ Get the handle / path to the test data folder. """ return os.path.join(fixtures_dir, filename)
31,588
def character_count_helper(results: Dict) -> int: """ Helper Function that computes character count for ocr results on a single image Parameters ---------- results: Dict (OCR results from a clapperboard instance) Returns ------- Int Number of words computed from OCR results """ count = 0 for element in results: words_list = element["text"].split(" ") for word in words_list: count += len(word) return count
31,589
def from_pickle(input_path): """Read from pickle file.""" with open(input_path, 'rb') as f: unpickler = pickle.Unpickler(f) return unpickler.load()
31,590
def PromptForRegion(available_regions=constants.SUPPORTED_REGION): """Prompt for region from list of available regions. This method is referenced by the declaritive iam commands as a fallthrough for getting the region. Args: available_regions: list of the available regions to choose from Returns: The region specified by the user, str """ if console_io.CanPrompt(): all_regions = list(available_regions) idx = console_io.PromptChoice( all_regions, message='Please specify a region:\n', cancel_option=True) region = all_regions[idx] log.status.Print('To make this the default region, run ' '`gcloud config set ai/region {}`.\n'.format(region)) return region
31,591
def update(x, new_x): """Update the value of `x` to `new_x`. # Arguments x: A `Variable`. new_x: A tensor of same shape as `x`. # Returns The variable `x` updated. """ return tf.assign(x, new_x)
31,592
def r1r2_to_bp(r1,r2,pl=0.01, pu=0.25): """ Convert uniform samling of r1 and r2 to impact parameter b and and radius ratio p following Espinoza 2018, https://iopscience.iop.org/article/10.3847/2515-5172/aaef38/meta Paramters: ----------- r1, r2: float; uniform parameters in from u(0,1) pl, pu: float; lower and upper limits of the radius ratio Return: ------- b, p: tuple; impact parameter and radius ratio """ assert np.all(0<r1) and np.all(r1<=1) and np.all(0<r2) and np.all(r2<=1), f"r1 and r2 needs to be u(0,1) but r1={r1}, r2={r2}" Ar = (pu-pl)/(2+pu+pl) if np.all(r1 > Ar): b = (1+pl) * (1 + (r1-1)/(1-Ar) ) p = (1-r2)*pl + r2*pu elif np.all(r1 <= Ar): q1 = r1/Ar b = (1+pl) + q1**0.5 * r2*(pu-pl) p = pu + (pl-pu)* q1**0.5*(1-r2) return b, p
31,593
def is_utc_today(utc): """ Returns true if the UTC is today :param utc: :return: """ current_time = datetime.datetime.utcnow() day_start = current_time - datetime.timedelta(hours=current_time.hour, minutes=current_time.minute, seconds=current_time.second) day_start_utc = unix_time(day_start) return (utc - day_start_utc) >= 0
31,594
def test_run_completed(mock_job, mock_queue, mock_driver): """Test run function for a successful run.""" # Setup def mock_render(*args, **kwargs): return class MockStorage: def __init__(self): pass def load(self, *args, **kwargs): return 'blah' def save(self, *args, **kwargs): return True # Execute render.run( sleep=5, job_queue=mock_queue, job=mock_job, render=mock_render, storage=MockStorage(), driver=mock_driver, ) # Verify assert mock_job.status is StatusEnum.complete
31,595
async def get_telegram_id(phone_number, user_mode=False): """ Tries to get a telegram ID for the passed in phone number. """ async with start_bot_client() as bot: if user_mode: # just leaving this code here in case it proves useful. # It only works if you use a user, not a bot. # more details: https://stackoverflow.com/a/51196276/8207 # https://tl.telethon.dev/methods/contacts/import_contacts.html#examples contact = InputPhoneContact(client_id=0, phone=phone_number, first_name="a", last_name="") result = await bot(ImportContactsRequest([contact])) print(result) else: # this only works if you have already messaged the contact, so only will allow looking # up "known" users. # more details: https://stackoverflow.com/a/41696457/8207 room_id = settings.MPACT_CONTACT_LOOKUP_ROOM_ID or GroupChat.objects.all()[0].id print('room id', room_id) receiver = await bot.get_entity(PeerChat(room_id)) msg_inst = await bot.send_file( receiver, InputMediaContact( phone_number=phone_number, first_name='Jane', last_name='Doe', vcard='', )) # "unknown" users return "0" instead of the actual ID return msg_inst.media.user_id if msg_inst.media.user_id != 0 else None
31,596
def QuadRemesh(thisMesh, parameters, multiple=False): """ Quad remesh this mesh. """ url = "rhino/geometry/mesh/quadremesh-mesh_quadremeshparameters" if multiple: url += "?multiple=true" args = [thisMesh, parameters] if multiple: args = list(zip(thisMesh, parameters)) response = Util.ComputeFetch(url, args) response = Util.DecodeToCommonObject(response) return response
31,597
def part_2_helper(): """PART TWO This simply runs the script multiple times and multiplies the results together """ slope_1 = sled_down_hill(1, 1) slope_2 = sled_down_hill(1, 3) slope_3 = sled_down_hill(1, 5) slope_4 = sled_down_hill(1, 7) slope_5 = sled_down_hill(2, 1) return slope_1 * slope_2 * slope_3 * slope_4 * slope_5
31,598
def test_shuffle_each_shard(): """Test that shuffle_each_shard works.""" n_samples = 100 n_tasks = 10 n_features = 10 X = np.random.rand(n_samples, n_features) y = np.random.randint(2, size=(n_samples, n_tasks)) w = np.random.randint(2, size=(n_samples, n_tasks)) ids = np.arange(n_samples) dataset = dc.data.DiskDataset.from_numpy(X, y, w, ids) dataset.reshard(shard_size=10) dataset.shuffle_each_shard() X_s, y_s, w_s, ids_s = (dataset.X, dataset.y, dataset.w, dataset.ids) assert X_s.shape == X.shape assert y_s.shape == y.shape assert ids_s.shape == ids.shape assert w_s.shape == w.shape assert not (ids_s == ids).all() # The ids should now store the performed permutation. Check that the # original dataset is recoverable. for i in range(n_samples): np.testing.assert_array_equal(X_s[i], X[ids_s[i]]) np.testing.assert_array_equal(y_s[i], y[ids_s[i]]) np.testing.assert_array_equal(w_s[i], w[ids_s[i]]) np.testing.assert_array_equal(ids_s[i], ids[ids_s[i]])
31,599