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def _remove_whitespace(s, regex=_RE_WHITESPACE): return regex.sub(' ', s.strip())
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replace extra whitespace inside of a string with a single space .
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def read_gitfile(f): cs = f.read() if (not cs.startswith('gitdir: ')): raise ValueError("Expected file to start with 'gitdir: '") return cs[len('gitdir: '):].rstrip('\n')
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read a .
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def set_project_type_handler(project_type, project_type_handler): global PROJECT_TYPES PROJECT_TYPES[project_type] = project_type_handler
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set a project type handler for the given project_type .
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@not_implemented_for('directed') @not_implemented_for('multigraph') def modularity_matrix(G, nodelist=None, weight=None): if (nodelist is None): nodelist = list(G) A = nx.to_scipy_sparse_matrix(G, nodelist=nodelist, weight=weight, format='csr') k = A.sum(axis=1) m = (k.sum() * 0.5) X = ((k * k.transpose()) / (2 * m)) return (A - X)
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return the modularity matrix of g .
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def temp_install(html=False, del_module=None): if html: Checker = LHTMLOutputChecker else: Checker = LXMLOutputChecker frame = _find_doctest_frame() dt_self = frame.f_locals['self'] checker = Checker() old_checker = dt_self._checker dt_self._checker = checker if _IS_PYTHON_3: check_func = frame.f_locals['check'].__func__ checker_check_func = checker.check_output.__func__ else: check_func = frame.f_locals['check'].im_func checker_check_func = checker.check_output.im_func doctest.etree = etree _RestoreChecker(dt_self, old_checker, checker, check_func, checker_check_func, del_module)
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temporary install for convenience .
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@register.filter() def getlist(value, arg): return value.getlist(arg)
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return all values of a querydict key .
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def _gf_pow_pnm1d2(f, n, g, b, p, K): f = gf_rem(f, g, p, K) h = f r = f for i in range(1, n): h = gf_frobenius_map(h, g, b, p, K) r = gf_mul(r, h, p, K) r = gf_rem(r, g, p, K) res = gf_pow_mod(r, ((p - 1) // 2), g, p, K) return res
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utility function for gf_edf_zassenhaus compute f**( // 2) in gf(p)[x]/(g) f**( // 2) = (f*f**p* .
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def asanyarray(a, dtype=None): return cupy.asarray(a, dtype)
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converts an object to array .
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def _concatenate_coils(coils): rmags = np.concatenate([coil['rmag'] for coil in coils]) cosmags = np.concatenate([coil['cosmag'] for coil in coils]) ws = np.concatenate([coil['w'] for coil in coils]) n_int = np.array([len(coil['rmag']) for coil in coils]) if (n_int[(-1)] == 0): raise RuntimeError('not supported') bins = np.repeat(np.arange(len(n_int)), n_int) return (rmags, cosmags, ws, bins)
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helper to concatenate meg coil parameters .
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def bulk_upload(): s3.stylesheets.append('plugins/fileuploader.css') return dict()
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custom view to allow bulk uploading of photos @todo: allow creation of a gis feature layer to view on the map @todo: allow uploading of associated gpx track for timestamp correlation .
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def MakeFreshResponse(): reference = json.loads(kVerifyResponseRenewedExpired) new = {'status': 0, 'receipt': reference['receipt']} new['receipt']['expires_date'] = (1000.0 * (time.time() + datetime.timedelta(days=28).total_seconds())) return json.dumps(new)
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returns a response for a subscription which has an expiration date in the future .
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@ckan.logic.validate(ckan.logic.schema.job_clear_schema) def job_clear(context, data_dict): _check_access(u'job_clear', context, data_dict) queues = data_dict.get(u'queues') if queues: queues = [jobs.get_queue(q) for q in queues] else: queues = jobs.get_all_queues() names = [jobs.remove_queue_name_prefix(queue.name) for queue in queues] for (queue, name) in zip(queues, names): queue.empty() log.info(u'Cleared background job queue "{}"'.format(name)) return names
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clear background jobs .
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@snippet def sink_pubsub(client, to_delete): topic = _sink_pubsub_setup(client) to_delete.append(topic) SINK_NAME = ('robots-pubsub-%d' % (_millis(),)) FILTER = 'logName:apache-access AND textPayload:robot' UPDATED_FILTER = 'textPayload:robot' DESTINATION = ('pubsub.googleapis.com/%s' % (topic.full_name,)) sink = client.sink(SINK_NAME, filter_=FILTER, destination=DESTINATION) assert (not sink.exists()) sink.create() assert sink.exists() to_delete.insert(0, sink) for sink in client.list_sinks(): do_something_with(sink) existing_sink = client.sink(SINK_NAME) existing_sink.reload() assert (existing_sink.filter_ == FILTER) assert (existing_sink.destination == DESTINATION) existing_sink.filter_ = UPDATED_FILTER existing_sink.update() existing_sink.reload() assert (existing_sink.filter_ == UPDATED_FILTER) sink.delete() to_delete.pop(0)
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sink log entries to pubsub .
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@gen.engine def _Run(callback): job_set = options.options.job_set assert (job_set in kJobSets.keys()), ('--job_set must be one of %r' % kJobSets.keys()) jobs = kJobSets[job_set] client = db_client.DBClient.Instance() job = Job(client, job_set) got_lock = (yield gen.Task(job.AcquireLock)) if (not got_lock): logging.warning('Failed to acquire job lock: exiting.') callback() return try: for (title, args) in jobs: logging.info(('[%s] running %s' % (title, ' '.join(args)))) proc = process.Subprocess(args, io_loop=ioloop.IOLoop.instance()) code = (yield gen.Task(proc.set_exit_callback)) logging.info(('[%s] finished with code: %r' % (title, code))) except: logging.error(traceback.format_exc()) finally: (yield gen.Task(job.ReleaseLock)) callback()
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grab the lock and run all commands an subprocesess .
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@synchronized(DIR_LOCK) def get_unique_path(dirpath, n=0, create_dir=True): if (not check_mount(dirpath)): return dirpath path = dirpath if n: path = ('%s.%s' % (dirpath, n)) if (not os.path.exists(path)): if create_dir: return create_dirs(path) else: return path else: return get_unique_path(dirpath, n=(n + 1), create_dir=create_dir)
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determine a unique folder or filename .
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def process_args(args, defaults, description): parser = argparse.ArgumentParser(description=description) parser.add_argument('-r', '--rom', dest='rom', default=defaults.ROM, help='ROM to run (default: %(default)s)') parser.add_argument('-e', '--epochs', dest='epochs', type=int, default=defaults.EPOCHS, help='Number of training epochs (default: %(default)s)') parser.add_argument('-s', '--steps-per-epoch', dest='steps_per_epoch', type=int, default=defaults.STEPS_PER_EPOCH, help='Number of steps per epoch (default: %(default)s)') parser.add_argument('-t', '--test-length', dest='steps_per_test', type=int, default=defaults.STEPS_PER_TEST, help='Number of steps per test (default: %(default)s)') parser.add_argument('--display-screen', dest='display_screen', action='store_true', default=False, help='Show the game screen.') parser.add_argument('--experiment-prefix', dest='experiment_prefix', default=None, help='Experiment name prefix (default is the name of the game)') parser.add_argument('--frame-skip', dest='frame_skip', default=defaults.FRAME_SKIP, type=int, help='Every how many frames to process (default: %(default)s)') parser.add_argument('--repeat-action-probability', dest='repeat_action_probability', default=defaults.REPEAT_ACTION_PROBABILITY, type=float, help=('Probability that action choice will be ' + 'ignored (default: %(default)s)')) parser.add_argument('--update-rule', dest='update_rule', type=str, default=defaults.UPDATE_RULE, help=('deepmind_rmsprop|rmsprop|sgd ' + '(default: %(default)s)')) parser.add_argument('--batch-accumulator', dest='batch_accumulator', type=str, default=defaults.BATCH_ACCUMULATOR, help='sum|mean (default: %(default)s)') parser.add_argument('--learning-rate', dest='learning_rate', type=float, default=defaults.LEARNING_RATE, help='Learning rate (default: %(default)s)') parser.add_argument('--rms-decay', dest='rms_decay', type=float, default=defaults.RMS_DECAY, help='Decay rate for rms_prop (default: %(default)s)') parser.add_argument('--rms-epsilon', dest='rms_epsilon', type=float, default=defaults.RMS_EPSILON, help=('Denominator epsilson for rms_prop ' + '(default: %(default)s)')) parser.add_argument('--momentum', type=float, default=defaults.MOMENTUM, help=('Momentum term for Nesterov momentum. ' + '(default: %(default)s)')) parser.add_argument('--clip-delta', dest='clip_delta', type=float, default=defaults.CLIP_DELTA, help=('Max absolute value for Q-update delta value. ' + '(default: %(default)s)')) parser.add_argument('--discount', type=float, default=defaults.DISCOUNT, help='Discount rate') parser.add_argument('--epsilon-start', dest='epsilon_start', type=float, default=defaults.EPSILON_START, help=('Starting value for epsilon. ' + '(default: %(default)s)')) parser.add_argument('--epsilon-min', dest='epsilon_min', type=float, default=defaults.EPSILON_MIN, help='Minimum epsilon. (default: %(default)s)') parser.add_argument('--epsilon-decay', dest='epsilon_decay', type=float, default=defaults.EPSILON_DECAY, help=('Number of steps to minimum epsilon. ' + '(default: %(default)s)')) parser.add_argument('--phi-length', dest='phi_length', type=int, default=defaults.PHI_LENGTH, help=('Number of recent frames used to represent ' + 'state. (default: %(default)s)')) parser.add_argument('--max-history', dest='replay_memory_size', type=int, default=defaults.REPLAY_MEMORY_SIZE, help=('Maximum number of steps stored in replay ' + 'memory. (default: %(default)s)')) parser.add_argument('--batch-size', dest='batch_size', type=int, default=defaults.BATCH_SIZE, help='Batch size. (default: %(default)s)') parser.add_argument('--network-type', dest='network_type', type=str, default=defaults.NETWORK_TYPE, help=('nips_cuda|nips_dnn|nature_cuda|nature_dnn' + '|linear (default: %(default)s)')) parser.add_argument('--freeze-interval', dest='freeze_interval', type=int, default=defaults.FREEZE_INTERVAL, help=('Interval between target freezes. ' + '(default: %(default)s)')) parser.add_argument('--update-frequency', dest='update_frequency', type=int, default=defaults.UPDATE_FREQUENCY, help=('Number of actions before each SGD update. ' + '(default: %(default)s)')) parser.add_argument('--replay-start-size', dest='replay_start_size', type=int, default=defaults.REPLAY_START_SIZE, help=('Number of random steps before training. ' + '(default: %(default)s)')) parser.add_argument('--resize-method', dest='resize_method', type=str, default=defaults.RESIZE_METHOD, help='crop|scale (default: %(default)s)') parser.add_argument('--nn-file', dest='nn_file', type=str, default=None, help='Pickle file containing trained net.') parser.add_argument('--death-ends-episode', dest='death_ends_episode', type=str, default=defaults.DEATH_ENDS_EPISODE, help='true|false (default: %(default)s)') parser.add_argument('--max-start-nullops', dest='max_start_nullops', type=int, default=defaults.MAX_START_NULLOPS, help=('Maximum number of null-ops at the start ' + 'of games. (default: %(default)s)')) parser.add_argument('--deterministic', dest='deterministic', type=bool, default=defaults.DETERMINISTIC, help=('Whether to use deterministic parameters ' + 'for learning. (default: %(default)s)')) parser.add_argument('--cudnn_deterministic', dest='cudnn_deterministic', type=bool, default=defaults.CUDNN_DETERMINISTIC, help=('Whether to use deterministic backprop. ' + '(default: %(default)s)')) parameters = parser.parse_args(args) if (parameters.experiment_prefix is None): name = os.path.splitext(os.path.basename(parameters.rom))[0] parameters.experiment_prefix = name if (parameters.death_ends_episode == 'true'): parameters.death_ends_episode = True elif (parameters.death_ends_episode == 'false'): parameters.death_ends_episode = False else: raise ValueError('--death-ends-episode must be true or false') if (parameters.freeze_interval > 0): parameters.freeze_interval = (parameters.freeze_interval // parameters.update_frequency) return parameters
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take a list of string arguments parsed via pyparsing and evaluate the special variables .
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def take_action(name=None, call=None, command=None, data=None, method='GET', location=DEFAULT_LOCATION): caller = inspect.stack()[1][3] if (call != 'action'): raise SaltCloudSystemExit('This action must be called with -a or --action.') if data: data = json.dumps(data) ret = [] try: ret = query(command=command, data=data, method=method, location=location) log.info('Success {0} for node {1}'.format(caller, name)) except Exception as exc: if ('InvalidState' in str(exc)): ret = [200, {}] else: log.error('Failed to invoke {0} node {1}: {2}'.format(caller, name, exc), exc_info_on_loglevel=logging.DEBUG) ret = [100, {}] return ret
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take action call used by start .
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def decomposeGlyph(font, glyphName): glyph = font[glyphName] deepCopyContours(font, glyph, glyph, (0, 0), (1, 1)) glyph.clearComponents()
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moves the components of a glyph to its outline .
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def cross_entropy_bernoulli(mat, p, target=None, tiny=1e-10): if (not target): target = mat if isinstance(p, CUDAMatrix): err_code = _cudamat.compute_cross_entropy_bernoulli(mat.p_mat, p.p_mat, target.p_mat, ct.c_float(tiny)) else: raise ValueError, 'Value must be of type CUDAMatrix.' if err_code: raise generate_exception(err_code) return target
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compute -mat*log(p) - .
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def patch(target, new=DEFAULT, spec=None, create=False, spec_set=None, autospec=None, new_callable=None, **kwargs): (getter, attribute) = _get_target(target) return _patch(getter, attribute, new, spec, create, spec_set, autospec, new_callable, kwargs)
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monkey-patch the djangousermixin class .
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def load_module_sections(trans): module_sections = {} module_sections['inputs'] = {'name': 'inputs', 'title': 'Inputs', 'modules': [{'name': 'data_input', 'title': 'Input Dataset', 'description': 'Input dataset'}, {'name': 'data_collection_input', 'title': 'Input Dataset Collection', 'description': 'Input dataset collection'}]} if trans.app.config.enable_beta_workflow_modules: module_sections['experimental'] = {'name': 'experimental', 'title': 'Experimental', 'modules': [{'name': 'pause', 'title': 'Pause Workflow for Dataset Review', 'description': 'Pause for Review'}, {'name': 'parameter_input', 'title': 'Parameter Input', 'description': 'Simple inputs used for workflow logic'}]} return module_sections
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get abstract description of the workflow modules this galaxy instance is configured with .
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@register.tag def ifhasperm(parser, token): return PermissionComparisonNode.handle_token(parser, token)
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this function provides functionality for the ifhasperm template tag syntax:: {% ifhasperm permission_label .
train
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def geocode_r(): vars = request.post_vars lat = vars.get('lat', None) lon = vars.get('lon', None) results = gis.geocode_r(lat, lon) results = json.dumps(results, separators=SEPARATORS) response.headers['Content-Type'] = 'application/json' return results
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reverse-geocode a location - designed to be called via ajax post looks up lx in our own database @todo: if not found then calls out to 3rd party services .
train
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def network_entry(is_metal, interface, bridge=None, net_type=None, net_mtu=None): if is_metal: _network = dict() else: _network = {'interface': interface} if bridge: _network['bridge'] = bridge if net_type: _network['type'] = net_type if net_mtu: _network['mtu'] = net_mtu return _network
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return a network entry for a container .
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def prepare_path_for_serialization(path): return [(unicode(path_item.usage_key), path_item.display_name) for path_item in path]
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return the data from a list of pathitems ready for serialization to json .
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@transaction.atomic def override_field_for_ccx(ccx, block, name, value): field = block.fields[name] value_json = field.to_json(value) serialized_value = json.dumps(value_json) override_has_changes = False clean_ccx_key = _clean_ccx_key(block.location) override = get_override_for_ccx(ccx, block, (name + '_instance')) if override: override_has_changes = (serialized_value != override.value) if (not override): (override, created) = CcxFieldOverride.objects.get_or_create(ccx=ccx, location=block.location, field=name, defaults={'value': serialized_value}) if created: _get_overrides_for_ccx(ccx).setdefault(clean_ccx_key, {})[(name + '_id')] = override.id else: override_has_changes = (serialized_value != override.value) if override_has_changes: override.value = serialized_value override.save() _get_overrides_for_ccx(ccx).setdefault(clean_ccx_key, {})[name] = value_json _get_overrides_for_ccx(ccx).setdefault(clean_ccx_key, {})[(name + '_instance')] = override
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overrides a field for the ccx .
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def test_uninstall_as_egg(script, data): to_install = data.packages.join('FSPkg') result = script.pip('install', to_install, '--egg', expect_error=True) fspkg_folder = (script.site_packages / 'fspkg') egg_folder = ((script.site_packages / 'FSPkg-0.1.dev0-py%s.egg') % pyversion) assert (fspkg_folder not in result.files_created), str(result.stdout) assert (egg_folder in result.files_created), str(result) result2 = script.pip('uninstall', 'FSPkg', '-y') assert_all_changes(result, result2, [(script.venv / 'build'), 'cache', (script.site_packages / 'easy-install.pth')])
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test uninstall package installed as egg .
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def multinomial_logpmf(x, n, p): return ((gammaln((n + 1.0)) - np.sum(gammaln((x + 1.0)))) + np.sum((x * np.log(p))))
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log pmf of multinomial .
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@status('Fixing whitespace', info=(lambda x: ('%s files' % x))) def normalize_whitespace(file_paths): reindent.makebackup = False result = map(reindent.check, (x for x in file_paths if x.endswith('.py'))) return sum(result)
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make sure that the whitespace for .
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@library.filter def selector_content_find(document, selector): content = '' try: page = pq(document.rendered_html) except ValueError: pass try: content = page.find(selector).text() except SelectorSyntaxError: pass return content
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provided a selector .
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def check_or_raise_extra(value, message=u'WAMP message invalid'): if (type(value) != dict): raise ProtocolError(u'{0}: invalid type {1}'.format(message, type(value))) for k in value.keys(): if (type(k) != six.text_type): raise ProtocolError(u"{0}: invalid type {1} for key '{2}'".format(message, type(k), k)) return value
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check a value for being a valid wamp extra dictionary .
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def enable_pretty_logging(options=None, logger=None): if (options is None): import tornado.options options = tornado.options.options if ((options.logging is None) or (options.logging.lower() == 'none')): return if (logger is None): logger = logging.getLogger() logger.setLevel(getattr(logging, options.logging.upper())) if options.log_file_prefix: rotate_mode = options.log_rotate_mode if (rotate_mode == 'size'): channel = logging.handlers.RotatingFileHandler(filename=options.log_file_prefix, maxBytes=options.log_file_max_size, backupCount=options.log_file_num_backups) elif (rotate_mode == 'time'): channel = logging.handlers.TimedRotatingFileHandler(filename=options.log_file_prefix, when=options.log_rotate_when, interval=options.log_rotate_interval, backupCount=options.log_file_num_backups) else: error_message = ('The value of log_rotate_mode option should be ' + ('"size" or "time", not "%s".' % rotate_mode)) raise ValueError(error_message) channel.setFormatter(LogFormatter(color=False)) logger.addHandler(channel) if (options.log_to_stderr or ((options.log_to_stderr is None) and (not logger.handlers))): channel = logging.StreamHandler() channel.setFormatter(LogFormatter()) logger.addHandler(channel)
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turns on formatted logging output as configured .
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def memoize_in_request_cache(request_cache_attr_name=None): def _decorator(func): 'Outer method decorator.' @functools.wraps(func) def _wrapper(self, *args, **kwargs): '\n Wraps a method to memoize results.\n ' request_cache = getattr(self, request_cache_attr_name, None) if request_cache: cache_key = '&'.join([hashvalue(arg) for arg in args]) if (cache_key in request_cache.data.setdefault(func.__name__, {})): return request_cache.data[func.__name__][cache_key] result = func(self, *args, **kwargs) request_cache.data[func.__name__][cache_key] = result return result else: return func(self, *args, **kwargs) return _wrapper return _decorator
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memoize a method calls results in the request_cache if theres one .
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def StartTcpServer(context, identity=None, address=None, console=False, **kwargs): from twisted.internet import reactor address = (address or ('', Defaults.Port)) framer = ModbusSocketFramer factory = ModbusServerFactory(context, framer, identity, **kwargs) if console: from pymodbus.internal.ptwisted import InstallManagementConsole InstallManagementConsole({'factory': factory}) _logger.info(('Starting Modbus TCP Server on %s:%s' % address)) reactor.listenTCP(address[1], factory, interface=address[0]) reactor.run()
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a factory to start and run a tcp modbus server .
train
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def number_for_course_location(location): return location.course
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given a courses block usage locator .
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def attr_le(accessing_obj, accessed_obj, *args, **kwargs): return attr(accessing_obj, accessed_obj, *args, **{'compare': 'le'})
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usage: attr_gt only true if access_objs attribute <= the value given .
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def grad_undefined(op, x_pos, x, comment=''): return NullType(('This variable is Null because the grad method for input %s (%s) of the %s op is mathematically undefined. %s' % (x_pos, x, op, comment)))()
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return an un-computable symbolic variable of type x .
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def show_main(path=MAIN_CF): (pairs, conf_list) = _parse_main(path) return pairs
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return a dict of active config values .
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@task(queue='web') def update_static_metadata(project_pk, path=None): project = Project.objects.get(pk=project_pk) if (not path): path = project.static_metadata_path() log.info(LOG_TEMPLATE.format(project=project.slug, version='', msg='Updating static metadata')) translations = [trans.language for trans in project.translations.all()] languages = set(translations) metadata = {'version': project.default_version, 'language': project.language, 'languages': list(languages), 'single_version': project.single_version} try: fh = open(path, 'w+') json.dump(metadata, fh) fh.close() Syncer.copy(path, path, host=socket.gethostname(), file=True) except (AttributeError, IOError) as e: log.debug(LOG_TEMPLATE.format(project=project.slug, version='', msg='Cannot write to metadata.json: {0}'.format(e)))
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this is here to avoid circular imports in models .
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def _launchd_paths(): return ['/Library/LaunchAgents', '/Library/LaunchDaemons', '/System/Library/LaunchAgents', '/System/Library/LaunchDaemons']
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paths where launchd services can be found .
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def _check_h5py(): try: import h5py except ImportError: raise ImportError('the h5py module is required to use HDF5 I/O') return h5py
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helper to check if h5py is installed .
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def _convert_between_ucsc_and_ensemble_naming(chrom): if chrom.startswith('chr'): return chrom[3:] else: return ('chr' + chrom)
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convert between ucsc chromosome naming conventions and ensembl naming conventions (1) .
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def _unmount(path, idempotent=False): try: run_process(['umount', '-l', path.path]) except CalledProcessError as e: if (idempotent and (e.returncode in (1, 32))): pass else: raise UnmountError(blockdevice=path.path, source_message=e.output)
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unmount the path .
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def iter_bad_values(): for (ctype, values) in sorted(BAD_VALUES.items()): for (value, repl) in values: (yield (ctype, value, repl))
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yield pairs of "bad" tuples .
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def write_error_summary(error): fullpath = request.environ.get('FULLPATH', request.path) uid = (c.user._id if c.user_is_loggedin else '-') g.log.error('E: %s U: %s FP: %s', error, uid, fullpath)
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log a single-line summary of the error for easy log grepping .
train
false
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@register.inclusion_tag(u'generic/includes/comments.html', takes_context=True) def comments_for(context, obj): form_class = import_dotted_path(settings.COMMENT_FORM_CLASS) form = form_class(context[u'request'], obj) context_form = context.get(u'posted_comment_form', form) context.update({u'posted_comment_form': (context_form if (context_form.target_object == obj) else form), u'unposted_comment_form': form, u'comment_url': reverse(u'comment'), u'object_for_comments': obj}) return context
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provides a generic context variable name for the object that comments are being rendered for .
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def get_diff_chunk_generator(*args, **kwargs): return _generator(*args, **kwargs)
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returns a diffchunkgenerator instance used for generating chunks .
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def task_pull_docker_images(images=ACCEPTANCE_IMAGES): return sequence([run_from_args(['docker', 'pull', image]) for image in images])
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pull docker images .
train
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def transform_old_to_new(line, old_module, new_module, ignore_import_from=False): if (not ignore_import_from): import_from_statement = (IMPORT_FROM_TEMPLATE % (old_module,)) if line.startswith(import_from_statement): new_import_from_statement = (IMPORT_FROM_TEMPLATE % (new_module,)) return line.replace(import_from_statement, new_import_from_statement, 1) import_statement = (IMPORT_TEMPLATE % (old_module,)) if (import_statement in line): new_import_statement = (IMPORT_TEMPLATE % (new_module,)) return line.replace(import_statement, new_import_statement, 1) if line.lstrip().startswith(old_module): return line.replace(old_module, new_module, 1) if ((': ' + old_module) in line): return line.replace((': ' + old_module), (': ' + new_module), 1)
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transforms from an old module to a new one .
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def _theano_leapfrog_integrator(H, q, p, **theano_kwargs): epsilon = tt.dscalar('epsilon') epsilon.tag.test_value = 1 n_steps = tt.iscalar('n_steps') n_steps.tag.test_value = 2 (q_new, p_new) = leapfrog(H, q, p, epsilon, n_steps) energy_new = energy(H, q_new, p_new) f = theano.function([q, p, epsilon, n_steps], [q_new, p_new, energy_new], **theano_kwargs) f.trust_input = True return f
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computes a theano function that computes one leapfrog step and the energy at the end of the trajectory .
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def port_standard(standard_annotations, sel, sample, extractors): new_annotations = [] for annotation in standard_annotations: if (not annotation.get('tagid')): continue element = find_element(annotation, sel) if (element is None): continue selector = find_generalized_css_selector(element, sel) if (not selector): continue annotation['accept_selectors'] = [selector] annotation['selector'] = selector annotation['reject_selectors'] = [] annotation = _add_annotation_data(annotation, sample, extractors) for (_id, data) in annotation.get('data', {}).items(): a = copy.deepcopy(annotation) a['id'] = gen_predictable_id(_id, a['id']) a['data'] = {gen_predictable_id(a['id'], 1): data} new_annotations.append(a) return new_annotations
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add accept selectors for existing annotations .
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def set_vif_bandwidth_config(conf, inst_type): bandwidth_items = ['vif_inbound_average', 'vif_inbound_peak', 'vif_inbound_burst', 'vif_outbound_average', 'vif_outbound_peak', 'vif_outbound_burst'] for (key, value) in inst_type.get('extra_specs', {}).items(): scope = key.split(':') if ((len(scope) > 1) and (scope[0] == 'quota')): if (scope[1] in bandwidth_items): setattr(conf, scope[1], value)
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config vif inbound/outbound bandwidth limit .
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def generate_oauth_authorization_url(token, next=None, hd=DEFAULT_DOMAIN, hl=None, btmpl=None, auth_server=OAUTH_AUTHORIZE_URL): uri = atom.http_core.Uri.parse_uri(auth_server) uri.query['oauth_token'] = token uri.query['hd'] = hd if (next is not None): uri.query['oauth_callback'] = str(next) if (hl is not None): uri.query['hl'] = hl if (btmpl is not None): uri.query['btmpl'] = btmpl return uri
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creates a url for the page where the request token can be authorized .
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def disk_partition_usage(all=False): result = disk_partitions(all) for partition in result: partition.update(disk_usage(partition['mountpoint'])) return result
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return a list of disk partitions plus the mount point .
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@local_optimizer([GpuSparseBlockOuter], inplace=True) def local_inplace_gpu_sparse_block_outer(node): if (isinstance(node.op, GpuSparseBlockOuter) and (not node.op.inplace)): new_node = gpu_sparse_block_outer_inplace(*node.inputs) return [new_node] return False
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gpusparseblockouter -> gpusparseblockouter .
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def setCacheCapacity(capacity=DEFAULT_CACHE_CAPACITY): enableCache() _entityCache.setCapacity(capacity)
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set the capacity of the entity cache .
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def parse_grid_id_args(grid, grid_url): if (grid is not None): id_from_grid = grid.id else: id_from_grid = None args = [id_from_grid, grid_url] arg_names = ('grid', 'grid_url') supplied_arg_names = [arg_name for (arg_name, arg) in zip(arg_names, args) if (arg is not None)] if (not supplied_arg_names): raise exceptions.InputError("One of the two keyword arguments is required:\n `grid` or `grid_url`\n\ngrid: a plotly.graph_objs.Grid object that has already\n been uploaded to Plotly.\n\ngrid_url: the url where the grid can be accessed on\n Plotly, e.g. 'https://plot.ly/~chris/3043'\n\n") elif (len(supplied_arg_names) > 1): raise exceptions.InputError('Only one of `grid` or `grid_url` is required. \nYou supplied both. \n') else: supplied_arg_name = supplied_arg_names.pop() if (supplied_arg_name == 'grid_url'): path = six.moves.urllib.parse.urlparse(grid_url).path (file_owner, file_id) = path.replace('/~', '').split('/')[0:2] return '{0}:{1}'.format(file_owner, file_id) else: return grid.id
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return the grid_id from the non-none input argument .
train
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@pytest.mark.parametrize('console_scripts', ['test_ = distutils_install', 'test_:test_ = distutils_install']) def test_uninstall_entry_point(script, console_scripts): pkg_name = 'ep_install' pkg_path = create_test_package_with_setup(script, name=pkg_name, version='0.1', entry_points={'console_scripts': [console_scripts], 'pip_test.ep': ['ep:name1 = distutils_install', 'ep:name2 = distutils_install']}) script_name = script.bin_path.join(console_scripts.split('=')[0].strip()) result = script.pip('install', pkg_path) assert script_name.exists result = script.pip('list', '--format=legacy') assert ('ep-install (0.1)' in result.stdout) script.pip('uninstall', 'ep_install', '-y') assert (not script_name.exists) result2 = script.pip('list', '--format=legacy') assert ('ep-install (0.1)' not in result2.stdout)
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test uninstall package with two or more entry points in the same section .
train
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def repeat_last_axis(array, count): return as_strided(array, (array.shape + (count,)), (array.strides + (0,)))
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restride array to repeat count times along the last axis .
train
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def get_language_name(lang_code, native=None, error_on_missing=False): lang_code = lcode_to_ietf(lang_code) language_entry = get_code2lang_map(lang_code) if (not language_entry): if error_on_missing: raise LanguageNotFoundError(("We don't have language code '%s' saved in our lookup dictionary (location: %s). Please manually add it before re-running this command." % (lang_code, settings.LANG_LOOKUP_FILEPATH))) else: language_entry = {'name': lang_code, 'native_name': lang_code} if (not isinstance(language_entry, dict)): return language_entry elif (native is None): return (language_entry.get('native_name') or language_entry.get('ka_name') or language_entry.get('name')) elif (not native): return language_entry.get('name') else: return language_entry.get('native_name')
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get a languages name in the currently active locale .
train
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def get_suggestions(request, user, project_ids): base = Translation.objects.prefetch().filter(subproject__project_id__in=project_ids).exclude(total=F('translated')).order_by('-translated') all_matching = base.none() if (user.is_authenticated() and user.profile.languages.exists()): all_matching = base.filter(language__in=user.profile.languages.all()).exclude(subproject__project__in=user.profile.subscriptions.all()) else: session_lang = translation.get_language() if (session_lang and (session_lang != 'en')): all_matching = base.filter(language__code=session_lang) if (not all_matching): all_matching = base.exclude(language__code='en') return all_matching[:10]
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filter a list of folders with a given search path .
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def get_dir_time_suffix(): dirfmt = '%4d-%02d-%02d_%02d%02d%02d' now = time.localtime()[0:6] dirname = (dirfmt % now) return dirname
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returns the name of a folder with the now time as suffix .
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@event(u'manager.before_config_validate') def process_variables(config, manager): env_params = {u'block_start_string': u'^^disabled^^', u'block_end_string': u'^^disabled^^', u'variable_start_string': u'{?', u'variable_end_string': u'?}'} if ((u'variables' not in config) or (config.get(u'variables') is False)): return env = Environment(**env_params) if isinstance(config[u'variables'], bool): log.debug(u'trying to load variables from DB') variables = variables_from_db() else: log.debug(u'trying to load variables from file') variables = variables_from_file(manager.config_base, config[u'variables']) log.debug(u'updating DB with variable file contents') variables_to_db(variables) env.globals = variables _process(config, env) return config
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render all string elements of the config against defined variables .
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def drop_missing(Y, X=None, axis=1): Y = np.asarray(Y) if (Y.ndim == 1): Y = Y[:, None] if (X is not None): X = np.array(X) if (X.ndim == 1): X = X[:, None] keepidx = np.logical_and((~ np.isnan(Y).any(axis)), (~ np.isnan(X).any(axis))) return (Y[keepidx], X[keepidx]) else: keepidx = (~ np.isnan(Y).any(axis)) return Y[keepidx]
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returns views on the arrays y and x where missing observations are dropped .
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def _diff_replication_group(current, desired): if (current.get('AutomaticFailover') is not None): current['AutomaticFailoverEnabled'] = (True if (current['AutomaticFailover'] in ('enabled', 'enabling')) else False) modifiable = {'AutomaticFailoverEnabled': 'AutomaticFailoverEnabled', 'AutoMinorVersionUpgrade': None, 'CacheNodeType': None, 'CacheParameterGroupName': None, 'CacheSecurityGroupNames': None, 'EngineVersion': None, 'NotificationTopicArn': None, 'NotificationTopicStatus': None, 'PreferredMaintenanceWindow': None, 'PrimaryClusterId': None, 'ReplicationGroupDescription': 'Description', 'SecurityGroupIds': None, 'SnapshotRetentionLimit': 'SnapshotRetentionLimit', 'SnapshottingClusterId': 'SnapshottingClusterId', 'SnapshotWindow': 'SnapshotWindow'} need_update = {} for (m, o) in modifiable.items(): if (m in desired): if (not o): need_update[m] = desired[m] elif (m in current): if (current[m] != desired[m]): need_update[m] = desired[m] return need_update
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if you need to enhance what modify_replication_group() considers when deciding what is to be updated .
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def service_present(name, service_type, description=None, profile=None, **connection_args): ret = {'name': name, 'changes': {}, 'result': True, 'comment': 'Service "{0}" already exists'.format(name)} role = __salt__['keystone.service_get'](name=name, profile=profile, **connection_args) if ('Error' not in role): return ret else: if __opts__.get('test'): ret['result'] = None ret['comment'] = 'Service "{0}" will be added'.format(name) return ret __salt__['keystone.service_create'](name, service_type, description, profile=profile, **connection_args) ret['comment'] = 'Service "{0}" has been added'.format(name) ret['changes']['Service'] = 'Created' return ret
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ensure service present in keystone catalog name the name of the service service_type the type of openstack service description description of the service .
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def strip_quotes(table_name): has_quotes = (table_name.startswith('"') and table_name.endswith('"')) return (table_name[1:(-1)] if has_quotes else table_name)
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strip quotes of doctests output values: .
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def notify_errors(request_id, error): try: _REQUESTS[request_id].notify_errors(request_id, error) except KeyError: pass
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add errors to a config request .
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@skip_if_on_windows @pytest.mark.parametrize('cmd, fmt, exp', [('pwd', None, (lambda : (os.getcwd() + '\n'))), ('echo WORKING', None, 'WORKING\n'), ('ls -f', (lambda out: out.splitlines().sort()), os.listdir().sort())]) def test_single_command(cmd, fmt, exp): (out, err, rtn) = run_xonsh(cmd, stderr=sp.DEVNULL) if callable(fmt): out = fmt(out) if callable(exp): exp = exp() assert (out == exp) assert (rtn == 0)
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the fmt parameter is a function that formats the output of cmd .
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def _load_provider_feature(feature, providers): features = [] for provider in providers: mod = __import__(provider, fromlist=[feature]) features = getattr(mod, feature)(features) return features
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load the named feature from an ordered list of dotted-notation modules which each implements the feature .
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@utils.arg('backup', metavar='<backup>', help='ID of the backup.') @utils.service_type('monitor') def do_backup_show(cs, args): backup = _find_backup(cs, args.backup) info = dict() info.update(backup._info) if ('links' in info): info.pop('links') utils.print_dict(info)
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show details about a backup .
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def _load_encryption(proxy_conf_file, **kwargs): _debug('Setting configuration for encryption') conf = ConfigParser() conf.read(proxy_conf_file) try: section = 'pipeline:main' pipeline = conf.get(section, 'pipeline') pipeline = pipeline.replace('proxy-logging proxy-server', 'keymaster encryption proxy-logging proxy-server') conf.set(section, 'pipeline', pipeline) root_secret = os.urandom(32).encode('base64') conf.set('filter:keymaster', 'encryption_root_secret', root_secret) except NoSectionError as err: msg = ('Error problem with proxy conf file %s: %s' % (proxy_conf_file, err)) raise InProcessException(msg) test_conf_file = os.path.join(_testdir, 'proxy-server.conf') with open(test_conf_file, 'w') as fp: conf.write(fp) return test_conf_file
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load encryption configuration and override proxy-server .
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@task() @timeit def measure_queue_lag(queued_time): lag = (datetime.now() - queued_time) lag = (((lag.days * 3600) * 24) + lag.seconds) statsd.gauge('rabbitmq.lag', max(lag, 0))
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a task that measures the time it was sitting in the queue .
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@task @needs('pavelib.i18n.i18n_validate_transifex_config', 'pavelib.i18n.i18n_generate') @timed def i18n_release_push(): resources = find_release_resources() sh(('i18n_tool transifex push ' + ' '.join(resources)))
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push release-specific resources to transifex .
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def yearly_activity(request, project=None, subproject=None, lang=None, user=None): activity = get_json_stats(request, 364, 7, project, subproject, lang, user) serie = [] labels = [] month = (-1) for item in activity: serie.append(item[1]) if (month != item[0].month): labels.append(pgettext('Format string for yearly activity chart', '{month}/{year}').format(month=item[0].month, year=item[0].year)) month = item[0].month else: labels.append('') return JsonResponse(data={'series': [serie], 'labels': labels})
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returns yearly activity for matching changes as json .
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def projective_transform_by_points(x, src, dst, map_args={}, output_shape=None, order=1, mode='constant', cval=0.0, clip=True, preserve_range=False): if (type(src) is list): src = np.array(src) if (type(dst) is list): dst = np.array(dst) if (np.max(x) > 1): x = (x / 255) m = transform.ProjectiveTransform() m.estimate(dst, src) warped = transform.warp(x, m, map_args=map_args, output_shape=output_shape, order=order, mode=mode, cval=cval, clip=clip, preserve_range=preserve_range) return warped
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projective transform by given coordinates .
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def _allmsgs(obj): if isinstance(obj, MultiMessage): return obj.messages elif (obj == BUBBLE): return [] else: return [obj]
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returns a list of all the messages encapsulated in obj .
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def safechardecode(value, binary=False): retVal = value if isinstance(value, basestring): retVal = retVal.replace('\\\\', SLASH_MARKER) while True: match = re.search(HEX_ENCODED_CHAR_REGEX, retVal) if match: retVal = retVal.replace(match.group('result'), (unichr if isinstance(value, unicode) else chr)(ord(binascii.unhexlify(match.group('result').lstrip('\\x'))))) else: break for char in SAFE_ENCODE_SLASH_REPLACEMENTS[::(-1)]: retVal = retVal.replace(repr(char).strip("'"), char) retVal = retVal.replace(SLASH_MARKER, '\\') if binary: if isinstance(retVal, unicode): retVal = retVal.encode('utf8') while True: match = re.search(INVALID_UNICODE_CHAR_REGEX, retVal) if match: retVal = retVal.replace(match.group('result'), chr(ord(binascii.unhexlify(match.group('result').lstrip('\\?'))))) else: break elif isinstance(value, (list, tuple)): for i in xrange(len(value)): retVal[i] = safechardecode(value[i]) return retVal
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reverse function to safecharencode .
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def xtext_decode(s, errors=None): r = [] i = 0 while (i < len(s)): if (s[i] == '+'): try: r.append(chr(int(s[(i + 1):(i + 3)], 16))) except ValueError: r.append(s[i:(i + 3)]) i += 3 else: r.append(s[i]) i += 1 return (''.join(r), len(s))
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decode the xtext-encoded string c{s} .
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def view_config_changes(config, num=None): rev = reverter.Reverter(config) rev.recovery_routine() rev.view_config_changes(num)
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view checkpoints and associated configuration changes .
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def translate_jobconf(variable, version): if (version is None): raise TypeError if (variable in _JOBCONF_MAP): return map_version(version, _JOBCONF_MAP[variable]) else: return variable
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translate *variable* to hadoop version *version* .
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def get_qos(tenant_id, qos_id): LOG.debug(_('get_qos() called')) session = db.get_session() try: qos = session.query(l2network_models.QoS).filter_by(tenant_id=tenant_id).filter_by(qos_id=qos_id).one() return qos except exc.NoResultFound: raise c_exc.QosNotFound(qos_id=qos_id, tenant_id=tenant_id)
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lists the qos given a tenant_id and qos_id .
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def l(path): if (path and path.startswith('/')): base_url = getattr(settings, 'SCRIPT_NAME', '') return (base_url + path) return path
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filter urls adding base_path prefix if required .
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def strip_formatted_string(str): return re.sub('\\s\\s+', ' ', str).strip()
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remove multiple whitespaces and whitespaces at the beginning and end of the given string .
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@conf.commands.register def fragment(pkt, fragsize=1480): fragsize = (((fragsize + 7) / 8) * 8) lst = [] for p in pkt: s = str(p[IP].payload) nb = (((len(s) + fragsize) - 1) / fragsize) for i in range(nb): q = p.copy() del q[IP].payload del q[IP].chksum del q[IP].len if (i == (nb - 1)): q[IP].flags &= (~ 1) else: q[IP].flags |= 1 q[IP].frag = ((i * fragsize) / 8) r = Raw(load=s[(i * fragsize):((i + 1) * fragsize)]) r.overload_fields = p[IP].payload.overload_fields.copy() q.add_payload(r) lst.append(q) return lst
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appends the given content to the fragment .
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def _common_bytes(blocks1, blocks2): if (len(blocks1) > len(blocks2)): (blocks1, blocks2) = (blocks2, blocks1) score = 0 for (block, count1) in blocks1.items(): count2 = blocks2.get(block) if count2: score += min(count1, count2) return score
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count the number of common bytes in two block count dicts .
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def _get_image_properties(image): (immin, immax) = (np.min(image), np.max(image)) imtype = image.dtype.type try: (lo, hi) = dtypes.dtype_range[imtype] except KeyError: (lo, hi) = (immin, immax) signed = (immin < 0) out_of_range_float = (np.issubdtype(image.dtype, np.float) and ((immin < lo) or (immax > hi))) low_data_range = ((immin != immax) and is_low_contrast(image)) unsupported_dtype = (image.dtype not in dtypes._supported_types) return ImageProperties(signed, out_of_range_float, low_data_range, unsupported_dtype)
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determine nonstandard properties of an input image .
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def contracted_nodes(G, u, v, self_loops=True): H = G.copy() if H.is_directed(): in_edges = ((w, u, d) for (w, x, d) in G.in_edges(v, data=True) if (self_loops or (w != u))) out_edges = ((u, w, d) for (x, w, d) in G.out_edges(v, data=True) if (self_loops or (w != u))) new_edges = chain(in_edges, out_edges) else: new_edges = ((u, w, d) for (x, w, d) in G.edges(v, data=True) if (self_loops or (w != u))) v_data = H.node[v] H.remove_node(v) H.add_edges_from(new_edges) if ('contraction' in H.node[u]): H.node[u]['contraction'][v] = v_data else: H.node[u]['contraction'] = {v: v_data} return H
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returns the graph that results from contracting u and v .
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def _dep_eeg_ref(add_eeg_ref): add_eeg_ref = bool(add_eeg_ref) if add_eeg_ref: warn('add_eeg_ref will be removed in 0.15, use set_eeg_reference() instead', DeprecationWarning) return add_eeg_ref
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helper for deprecation add_eeg_ref -> false .
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@with_setup(prepare_stdout) def test_commented_scenario(): runner = Runner(feature_name('commented_feature'), verbosity=1) runner.run() assert_stdout_lines('.\n1 feature (1 passed)\n1 scenario (1 passed)\n1 step (1 passed)\n')
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test one commented scenario .
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def parse_host_port(address, default_port=None): if (address[0] == '['): (_host, _port) = address[1:].split(']') host = _host if (':' in _port): port = _port.split(':')[1] else: port = default_port elif (address.count(':') == 1): (host, port) = address.split(':') else: host = address port = default_port return (host, (None if (port is None) else int(port)))
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interpret a string as a host:port pair .
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@register.inclusion_tag('utilities/render_custom_fields.html') def render_custom_fields(form): return {'form': form}
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render all custom fields in a form .
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def axapi_enabled_disabled(flag): if (flag == 'enabled'): return 1 else: return 0
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def processtime(): (user, system) = systimes() return (user + system)
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return the total time spent on the process .
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def RetryWithBackoff(callable_func, retry_notify_func, initial_delay=1, backoff_factor=2, max_delay=60, max_tries=20): delay = initial_delay num_tries = 0 while True: (done, opaque_value) = callable_func() num_tries += 1 if done: return (True, opaque_value) if (num_tries >= max_tries): return (False, opaque_value) retry_notify_func(opaque_value, delay) time.sleep(delay) delay = min((delay * backoff_factor), max_delay)
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calls a function multiple times .
train
false
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def _get_source_sum(source_hash, file_path, saltenv): ret = dict() schemes = (u'salt', u'http', u'https', u'ftp', u'swift', u's3', u'file') invalid_hash_msg = u"Source hash '{0}' format is invalid. It must be in the format <hash type>=<hash>".format(source_hash) source_hash = str(source_hash) source_hash_scheme = _urlparse(source_hash).scheme if (source_hash_scheme in schemes): cached_hash_file = __salt__[u'cp.cache_file'](source_hash, saltenv) if (not cached_hash_file): raise CommandExecutionError(u'Source hash file {0} not found'.format(source_hash)) ret = __salt__[u'file.extract_hash'](cached_hash_file, u'', file_path) if (ret is None): raise SaltInvocationError(invalid_hash_msg) else: items = source_hash.split(u'=', 1) if (len(items) != 2): invalid_hash_msg = u'{0}, or it must be a supported protocol: {1}'.format(invalid_hash_msg, u', '.join(schemes)) raise SaltInvocationError(invalid_hash_msg) (ret[u'hash_type'], ret[u'hsum']) = [item.strip().lower() for item in items] return ret
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extract the hash sum .
train
false
7,685
def rgb2rgbcie(rgb): return _convert(rgbcie_from_rgb, rgb)
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rgb to rgb cie color space conversion .
train
false
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def _valid_method_call_check_resources(resource, method): for name in resource.keys(): _valid_method_call_check_resource(name, method)
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a method to check whether the resource can use the quota method .
train
false
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def action_peek_xml(body): dom = utils.safe_minidom_parse_string(body) action_node = dom.childNodes[0] return action_node.tagName
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determine action to invoke .
train
false
7,690
def list_firewalls(profile=None): conn = _auth(profile) return conn.list_firewalls()
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fetches a list of all firewalls for a tenant cli example: .
train
false