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def gapfill(model, universal=None, lower_bound=0.05, penalties=None, demand_reactions=True, exchange_reactions=False, iterations=1): """Perform gapfilling on a model. See documentation for the class GapFiller. Parameters ---------- model : cobra.Model The model to p...
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def do_build(self): """ Create the default version of the layer :return: a string of the packet with the payload """ if not self.explicit: self = next(iter(self)) pkt = self.self_build() for t in self.post_transforms: pkt = t(pkt) ...
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def lv_load_areas(self): """Returns a generator for iterating over load_areas Yields ------ int generator for iterating over load_areas """ for load_area in sorted(self._lv_load_areas, key=lambda _: repr(_)): yield load_area
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def array_to_base64_png(array): """Convert an array into base64-enoded PNG image. Args: array: A 2D np.ndarray or nested list of items. Returns: A base64-encoded string the image. The image is grayscale if the array is 2D. The image is RGB color if the image is 3D with lsat dimension equal to 3....
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def _add_post_data(self, request: Request): '''Add data to the payload.''' if self._item_session.url_record.post_data: data = wpull.string.to_bytes(self._item_session.url_record.post_data) else: data = wpull.string.to_bytes( self._processor.fetch_params.po...
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def _parse_message(self, data): """ Parses the raw message from the device. :param data: message data :type data: string :raises: :py:class:`~alarmdecoder.util.InvalidMessageError` """ try: _, values = data.split(':') self.serial_number, ...
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def set_string(self, string_options): """Set a series of properties using a string. For example:: 'fred=12, tile' '[fred=12]' """ vo = ffi.cast('VipsObject *', self.pointer) cstr = _to_bytes(string_options) result = vips_lib.vips_object_set_fro...
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def reload_manifest(self, manifest): """ Reloads a manifest from the disk :param manifest: The manifest to reload """ self._logger.debug("Reloading manifest for {}.".format(manifest.get("name", "Unnamed Plugin"))) self._manifests.remove(manifest) self.load_manifes...
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def z_angle_rotate(xy, theta): """ Rotated the input vector or set of vectors `xy` by the angle `theta`. Parameters ---------- xy : array_like The vector or array of vectors to transform. Must have shape """ xy = np.array(xy).T theta = np.array(theta).T out = np.zeros_lik...
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def _HandleLegacy(self, args, token=None): """Retrieves the stats for a hunt.""" hunt_obj = aff4.FACTORY.Open( args.hunt_id.ToURN(), aff4_type=implementation.GRRHunt, token=token) stats = hunt_obj.GetRunner().context.usage_stats return ApiGetHuntStatsResult(stats=stats)
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def figures(df,specs,asList=False): """ Generates multiple Plotly figures for a given DataFrame Parameters: ----------- df : DataFrame Pandas DataFrame specs : list(dict) List of dictionaries with the properties of each figure. All properties avaialbe can be seen with help(cufflinks.pd.DataFrame...
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def plot_fluxseries( self, names: Optional[Iterable[str]] = None, average: bool = False, **kwargs: Any) \ -> None: """Plot the `flux` series of the handled model. See the documentation on method |Element.plot_inputseries| for additional information. "...
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async def send_contact(self, phone_number: base.String, first_name: base.String, last_name: typing.Union[base.String, None] = None, disable_notification: typing.Union[base.Boolean, None] = None, reply_markup=None, ...
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def query(self, expr, **kwargs): """Query columns of the DataManager with a boolean expression. Args: expr: Boolean expression to query the columns with. Returns: DataManager containing the rows where the boolean expression is satisfied. """ columns = se...
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def warp_object(self, tileMapObj): """Warp the tile map object from one warp to another.""" print "Collision" if tileMapObj.can_warp: #Check to see if we need to load a different tile map if self.map_association != self.exitWarp.map_association: #Load the ...
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def _init_filters(self): """Initialize the default pywb provided Jninja filters available during template rendering""" self.filters = {} @self.template_filter() def format_ts(value, format_='%a, %b %d %Y %H:%M:%S'): """Formats the supplied timestamp using format_ ...
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def load_features(self, features, image_type=None, from_array=False, threshold=0.001): """ Load features from current Dataset instance or a list of files. Args: features: List containing paths to, or names of, features to extract. Each element in the lis...
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def _send_locked(self, cmd): """Sends the specified command to the lutron controller. Assumes self._lock is held. """ _LOGGER.debug("Sending: %s" % cmd) try: self._telnet.write(cmd.encode('ascii') + b'\r\n') except BrokenPipeError: self._disconnect_locked()
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def suites(self, request, pk=None): """ List of test suite names available in this project """ suites_names = self.get_object().suites.values_list('slug') suites_metadata = SuiteMetadata.objects.filter(kind='suite', suite__in=suites_names) page = self.paginate_queryset(su...
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def hilbert(self, num_taps=None): '''Apply an odd-tap Hilbert transform filter, phase-shifting the signal by 90 degrees. This is used in many matrix coding schemes and for analytic signal generation. The process is often written as a multiplication by i (or j), the imaginary unit. An odd...
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def regionsIntersection(s1, s2, collapse=True): """ given two lists of genomic regions with chromosome, start and end coordinates, return a new list of regions which is the intersection of those two sets. Lists must be sorted by chromosome and start index :return: new list that represents the intersection of...
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def _init_transforms(self, subjs, voxels, features, random_state): """Initialize the mappings (Wi) with random orthogonal matrices. Parameters ---------- subjs : int The number of subjects. voxels : list of int A list with the number of voxels per subjec...
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def _removeContentPanels(cls, remove): """ Remove the panels and so hide the fields named. """ if type(remove) is str: remove = [remove] cls.content_panels = [panel for panel in cls.content_panels if getattr(panel, "field_name", None) not...
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def loads(s: str, load_module: types.ModuleType, **kwargs): """ Convert a JSON string into a JSGObject :param s: string representation of JSON document :param load_module: module that contains declarations for types :param kwargs: arguments see: json.load for details :return: JSGObject representing...
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def file_counts(container=None, patterns=None, image_package=None, file_list=None): '''file counts will return a list of files that match one or more regular expressions. if no patterns is defined, a default of readme is used. All patterns and files are made ...
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def fail(self, key, **kwargs): """A helper method that simply raises a `ValidationError`. """ try: msg = self.error_messages[key] except KeyError: class_name = self.__class__.__name__ msg = MISSING_ERROR_MESSAGE.format(class_name=class_name, ...
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def flush(name, family='ipv4', **kwargs): ''' .. versionadded:: 2014.7.0 Flush current ipset set family Networking family, either ipv4 or ipv6 ''' ret = {'name': name, 'changes': {}, 'result': None, 'comment': ''} set_check = __salt__['ipset.check...
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def leave(self, screen_id): """Informs the target about a drag and drop leave event. in screen_id of type int The screen ID where the drag and drop event occurred. raises :class:`VBoxErrorVmError` VMM device is not available. """ if not isinstan...
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def count_fingerprint(word, n_bits=16, most_common=MOST_COMMON_LETTERS_CG): """Return the count fingerprint. This is a wrapper for :py:meth:`Count.fingerprint`. Parameters ---------- word : str The word to fingerprint n_bits : int Number of bits in the fingerprint returned ...
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def get_queryset(self, request): """ Make special filtering by user's permissions. """ if not request.user.has_perm('zinnia.can_view_all'): queryset = self.model.objects.filter(authors__pk=request.user.pk) else: queryset = super(EntryAdmin, self).get_query...
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def add_library(self, name): """Add a library to the database This method is for adding a library by name (eg: "BuiltIn") rather than by a file. """ libdoc = LibraryDocumentation(name) if len(libdoc.keywords) > 0: # FIXME: figure out the path to the library f...
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def _zlib_no_compress(data): """Compress data with zlib level 0.""" cobj = zlib.compressobj(0) return b"".join([cobj.compress(data), cobj.flush()])
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def infer_call_result(self, caller, context=None): """infer what a class instance is returning when called""" context = contextmod.bind_context_to_node(context, self) inferred = False for node in self._proxied.igetattr("__call__", context): if node is util.Uninferable or not ...
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def commit(self): """ Insert the specified text in all selected lines, always at the same column position. """ # Get the number of lines and columns in last line. last_line, last_col = self.qteWidget.getNumLinesAndColumns() # If this is the first ever call to th...
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def login_required(obj): """ Requires that the user be logged in order to gain access to the resource at the specified the URI. """ decorator = request_passes_test(lambda r, *args, **kwargs: r.user.is_authenticated()) return wrap_object(obj, decorator)
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def generate(self, callback=None): """ Computes and stores piece data. Returns ``True`` on success, ``False`` otherwise. :param callback: progress/cancellation callable with method signature ``(filename, pieces_completed, pieces_total)``. Useful for reporting pro...
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def hide_routemap_holder_route_map_content_match_extcommunity_extcommunity_num(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") hide_routemap_holder = ET.SubElement(config, "hide-routemap-holder", xmlns="urn:brocade.com:mgmt:brocade-ip-policy") route_map ...
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def get_instance_from_id(unique_id): """Get an instance of the `PolygonFilter` using a unique id""" for instance in PolygonFilter.instances: if instance.unique_id == unique_id: return instance # if this does not work: raise KeyError("PolygonFilter with unique_...
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def trace_dispatch(self, frame, event, arg): """allow to switch to Pdb instance""" if hasattr(self, 'pdb'): return self.pdb.trace_dispatch(frame, event, arg) else: return Pdb.trace_dispatch(self, frame, event, arg)
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def find_external_metabolites(model): """Return all metabolites in the external compartment.""" ex_comp = find_external_compartment(model) return [met for met in model.metabolites if met.compartment == ex_comp]
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def get_cif(code, mmol_number, outfile=None): """ Parameters ---------- code : str PDB code. mmol_number : int mmol number (biological assembly number) of file to download. Numbers from PDBe. If None, defaults to the preferred biological assembly listed for code on the PDBe. ...
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def post(self): '''This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file. ''' # if self.readonly is set, then don't accept any changes # return immediately with a 400 if self.readonly: ...
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def _unpickle_collection(self, collection): """Unpickles all members of the specified dictionary.""" for mkey in collection: if isinstance(collection[mkey], list): for item in collection[mkey]: item.unpickle(self) else: collecti...
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def percentOverlap(x1, x2): """ Computes the percentage of overlap between vectors x1 and x2. @param x1 (array) binary vector @param x2 (array) binary vector @param size (int) length of binary vectors @return percentOverlap (float) percentage overlap between x1 and x2 """ nonZeroX1 = np.count_no...
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def _read_response(self, response): """ JSON Documentation: https://www.jfrog.com/confluence/display/RTF/Repository+Configuration+JSON """ rclass = response['rclass'] if rclass != "virtual": raise ArtifactoryException("Repositiry '{}' have '{}', but expect 'virtual'"....
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def _add_io_handler(self, handler): """Add an I/O handler to the loop.""" logger.debug('adding io handler: %r', handler) self._unprepared_handlers[handler] = None self._configure_io_handler(handler)
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def run(self, force=False, ipyclient=None, name_fields=30, name_separator="_", dry_run=False): """ Download the accessions into a the designated workdir. Parameters ---------- force: (bool) If force=True then existing fil...
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def all_active(cls): """ List active queues, based on their lengths in Redis. Warning, uses the unscalable KEYS redis command """ prefix = context.get_current_config()["redis_prefix"] queues = [] for key in context.connections.redis.keys(): if key.startswith(prefix): ...
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def create_option_value(cls, option_value, **kwargs): """Create OptionValue Create a new OptionValue This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async=True >>> thread = api.create_option_value(option_value, async=Tru...
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def head(records, head): """ Limit results to the top N records. With the leading `-', print all but the last N records. """ logging.info('Applying _head generator: ' 'limiting results to top ' + head + ' records.') if head == '-0': for record in records: yi...
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def create_nsg_rule(access_token, subscription_id, resource_group, nsg_name, nsg_rule_name, description, protocol='Tcp', source_range='*', destination_range='*', source_prefix='*', destination_prefix='*', access='Allow', priority=100, direction='Inbound'): ...
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def set_tags(name, tags, region=None, key=None, keyid=None, profile=None): ''' Add the tags on an ELB .. versionadded:: 2016.3.0 name name of the ELB tags dict of name/value pair tags CLI Example: .. code-block:: bash salt myminion boto_elb.set_tags my-elb-name ...
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def add_scanner_param(self, name, scanner_param): """ Add a scanner parameter. """ assert name assert scanner_param self.scanner_params[name] = scanner_param command = self.commands.get('start_scan') command['elements'] = { 'scanner_params': {...
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def learn(self, bottomUpInput, enableInference=None): """ TODO: document :param bottomUpInput: :param enableInference: :return: """ return self.compute(bottomUpInput, enableLearn=True, enableInference=enableInference)
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def packet_read(self): """Read packet from network.""" bytes_received = 0 if self.sock == NC.INVALID_SOCKET: return NC.ERR_NO_CONN if self.in_packet.command == 0: ba_data, errnum, errmsg = nyamuk_net.read(self.sock, 1) if errnum == 0 ...
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def _game_image_from_screen(self, game_type): """Return the image of the given game type from the screen. Return None if no game is found. """ # screen screen_img = self._screen_shot() # game image game_rect = self._game_finders[game_type].locate_in(screen_img) ...
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def parse_release_id(release_id): """ Parse release_id to parts: {short, version, type} or {short, version, type, bp_short, bp_version, bp_type} :param release_id: Release ID string :type release_id: str :rtype: dict """ if "@" in release_id: release, base_product = rele...
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def packages( state, host, packages=None, present=True, latest=False, update=False, cache_time=None, upgrade=False, force=False, no_recommends=False, allow_downgrades=False, ): ''' Install/remove/update packages & update apt. + packages: list of packages to ensure + present: whether...
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def transformer_parsing_base(): """HParams for parsing on WSJ only.""" hparams = transformer_base() hparams.attention_dropout = 0.2 hparams.layer_prepostprocess_dropout = 0.2 hparams.max_length = 512 hparams.learning_rate_warmup_steps = 16000 hparams.hidden_size = 1024 hparams.learning_rate = 0.05 hpa...
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def populate_unique_identifiers(self, metamodel): ''' Populate a *metamodel* with class unique identifiers previously encountered from input. ''' for stmt in self.statements: if isinstance(stmt, CreateUniqueStmt): metamodel.define_unique_identifier(stm...
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def start_search(self): """ Start the Gateway Search Request and return the address information :rtype: (string,int) :return: a tuple(string(IP),int(Port) when found or None when timeout occurs """ self._asyncio_loop = asyncio.get_event_loop() # Cre...
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def create_authentication_string(username, password): ''' Creates an authentication string from the username and password. :username: Username. :password: Password. :return: The encoded string. ''' username_utf8 = username.encode('utf-8') userpw_utf8 = password.encode('utf-8') user...
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def clean_password(self, password, user=None): """ Validates a password. You can hook into this if you want to restric the allowed password choices. """ min_length = app_settings.PASSWORD_MIN_LENGTH if min_length and len(password) < min_length: raise forms.Val...
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def cql_encode_float(self, val): """ Encode floats using repr to preserve precision """ if math.isinf(val): return 'Infinity' if val > 0 else '-Infinity' elif math.isnan(val): return 'NaN' else: return repr(val)
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def unique_categories(categories): """Pass array-like categories, return sorted cleaned unique categories.""" categories = np.unique(categories) categories = np.setdiff1d(categories, np.array(settings.categories_to_ignore)) categories = np.array(natsorted(categories, key=lambda v: v.upper())) return...
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def handle(self, *args, **options): """ Transmit the courseware data for the EnterpriseCustomer(s) to the active integration channels. """ username = options['catalog_user'] # Before we do a whole bunch of database queries, make sure that the user we were passed exists. ...
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def hll_count(expr, error_rate=0.01, splitter=None): """ Calculate HyperLogLog count :param expr: :param error_rate: error rate :type error_rate: float :param splitter: the splitter to split the column value :return: sequence or scalar :Example: >>> df = DataFrame(pd.DataFrame({'a...
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def mid_lvl_cmds_encode(self, target, hCommand, uCommand, rCommand): ''' Mid Level commands sent from the GS to the autopilot. These are only sent when being operated in mid-level commands mode from the ground. target : ...
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def Mersmann_Kind_predictor(atoms, coeff=3.645, power=0.5, covalent_radii=rcovs_Mersmann_Kind): r'''Predicts the critical molar volume of a chemical based only on its atomic composition according to [1]_ and [2]_. This is a crude approach, but provides very reasonable estima...
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def register_cache_buster(self, app, config=None): """ Register `app` in cache buster so that `url_for` adds a unique prefix to URLs generated for the `'static'` endpoint. Also make the app able to serve cache-busted static files. This allows setting long cache expiration values...
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def clean_inputs(data): """Clean BED input files to avoid overlapping segments that cause downstream issues. Per-merges inputs to avoid needing to call multiple times during later parallel steps. """ if not utils.get_in(data, ("config", "algorithm", "variant_regions_orig")): data["config"]["alg...
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def bootstrap(**kwargs): """ Bootstrap an EC2 instance that has been booted into an AMI from http://www.daemonology.net/freebsd-on-ec2/ Note: deprecated, current AMI images are basically pre-bootstrapped, they just need to be configured. """ # the user for the image is `ec2-user`, there is no sudo, but ...
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def get_entries(self, start=0, end=0, data_request=None, steam_ids=None): """Get leaderboard entries. :param start: start entry, not index (e.g. rank 1 is ``start=1``) :type start: :class:`int` :param end: end entry, not index (e.g. only one entry then ``start=1,end=1``) :type e...
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def leaves(self, fragment_type=None): """ The current list of sync map fragments which are (the values of) the leaves of the sync map tree. :rtype: list of :class:`~aeneas.syncmap.fragment.SyncMapFragment` .. versionadded:: 1.7.0 """ leaves = self.fragme...
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def pull_all_rtl(configuration): """ Pulls all translations - reviewed or not - for RTL languages """ print("Pulling all translated RTL languages from transifex...") for lang in configuration.rtl_langs: print('rm -rf conf/locale/' + lang) execute('rm -rf conf/locale/' + lang) ...
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def get_bin(self): """Return the binary notation of the address/netmask.""" return _convert(self._ip_dec, notation=IP_BIN, inotation=IP_DEC, _check=False, _isnm=self._isnm)
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def find(self, other): """Return an interable of elements that overlap other in the tree.""" iset = self._iset l = binsearch_left_start(iset, other[0] - self._maxlen, 0, len(iset)) r = binsearch_right_end(iset, other[1], 0, len(iset)) iopts = iset[l:r] iiter = (s for s in...
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def stop_server(self, datacenter_id, server_id): """ Stops the server. :param datacenter_id: The unique ID of the data center. :type datacenter_id: ``str`` :param server_id: The unique ID of the server. :type server_id: ``str`` """ ...
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def for_branch(self, branch): """ Return a new CourseLocator for another branch of the same library (also version agnostic) """ if self.org is None and branch is not None: raise InvalidKeyError(self.__class__, "Branches must have full library ids not just versions") r...
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def td_taper(out, start, end, beta=8, side='left'): """Applies a taper to the given TimeSeries. A half-kaiser window is used for the roll-off. Parameters ---------- out : TimeSeries The ``TimeSeries`` to taper. start : float The time (in s) to start the taper window. end :...
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def get_array_shape(self, key): """Return array's shape""" data = self.model.get_data() return data[key].shape
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def _report_completion(self): """Update shared counters to signal that we are done with this cluster. Call just before exiting run() method (in a finally clause)""" rem_clust = self.remaining_clusters if rem_clust is not None: # -= is non-atomic, need to acquire a lock ...
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def get_catalog_hierarchy_session(self, proxy): """Gets the catalog hierarchy traversal session. arg: proxy (osid.proxy.Proxy): proxy return: (osid.cataloging.CatalogHierarchySession) - a ``CatalogHierarchySession`` raise: NullArgument - ``proxy`` is null rai...
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def var(inlist): """ Returns the variance of the values in the passed list using N-1 for the denominator (i.e., for estimating population variance). Usage: lvar(inlist) """ n = len(inlist) mn = mean(inlist) deviations = [0] * len(inlist) for i in range(len(inlist)): deviations[i] = inlist...
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def minkowski_distance(point1, point2, degree=2): """! @brief Calculate Minkowski distance between two vectors. \f[ dist(a, b) = \sqrt[p]{ \sum_{i=0}^{N}\left(a_{i} - b_{i}\right)^{p} }; \f] @param[in] point1 (array_like): The first vector. @param[in] point2 (array_like): The seco...
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def find_protein_complexes(model): """ Find reactions that are catalyzed by at least a heterodimer. Parameters ---------- model : cobra.Model The metabolic model under investigation. Returns ------- list Reactions whose gene-protein-reaction association contains at leas...
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def make_draft(self): """ Make this version the draft """ assert self.__class__ == self.get_version_class() # If this is draft do nothing if self.state == self.DRAFT: return with xact(): # Delete whatever is currently this draft ...
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def from_file(cls, filename="CTRL", **kwargs): """ Creates a CTRL file object from an existing file. Args: filename: The name of the CTRL file. Defaults to 'CTRL'. Returns: An LMTOCtrl object. """ with zopen(filename, "rt") as f: cont...
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def initialize(self): """ Initialize the self._tm if not already initialized. """ if self._tm is None: params = { "columnCount": self.columnCount, "basalInputSize": self.basalInputWidth, "apicalInputSize": self.apicalInputWidth, "cellsPerColumn": self.cellsPerColum...
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def scheme(name, bins, bin_method='quantiles'): """Return a custom scheme based on CARTOColors. Args: name (str): Name of a CARTOColor. bins (int or iterable): If an `int`, the number of bins for classifying data. CARTOColors have 7 bins max for quantitative data, and 11 max ...
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def classes_can_admin(self): """Return all the classes (sorted) that this user can admin.""" if self.is_admin: return sorted(Session.query(Class).all()) else: return sorted(self.admin_for)
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def _load_embedding(self, pretrained_file_path, elem_delim, encoding='utf8'): """Load embedding vectors from a pre-trained token embedding file. Both text files and TokenEmbedding serialization files are supported. elem_delim and encoding are ignored for non-text files. ...
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def html_factory(tag, **defaults): '''Returns an :class:`Html` factory function for ``tag`` and a given dictionary of ``defaults`` parameters. For example:: >>> input_factory = html_factory('input', type='text') >>> html = input_factory(value='bla') ''' def html_input(*children, **params): ...
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def get_sign_key(exported_session_key, magic_constant): """ 3.4.5.2 SIGNKEY @param exported_session_key: A 128-bit session key used to derive signing and sealing keys @param magic_constant: A constant value set in the MS-NLMP documentation (constants.SignSealConstants) @return sign_key: Key used to...
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def _add_kwarg_datasets(datasets, kwargs): """Add data sets of the given kwargs. :param datasets: The dict where to accumulate data sets. :type datasets: `dict` :param kwargs: Dict of pre-named data sets. :type kwargs: `dict` of `unicode` to varies """ for te...
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async def send_script(self, conn_id, data): """Send a a script to this IOTile device Args: conn_id (int): A unique identifier that will refer to this connection data (bytes): the script to send to the device """ self._ensure_connection(conn_id, True) con...
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def start(self, attempts=5, timeout=2): """ Start the network, will check if the network is active ``attempts`` times, waiting ``timeout`` between each attempt. Args: attempts (int): number of attempts to check the network is active timeout (int): timeout for ea...
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def __model_class(self, model_name): """ this method is used by the lru_cache, do not call directly """ build_schema = deepcopy(self.definitions[model_name]) return self.schema_class(build_schema, model_name)
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def create_data_element_from_resource(self, resource): """ Returns a new data element for the given resource object. :returns: object implementing :class:`IResourceDataElement`. """ mp = self.__mp_reg.find_or_create_mapping(type(resource)) return mp.data_element_class.cr...
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def reactions_to_files(model, dest, writer, split_subsystem): """Turn the reaction subsystems into their own files. If a subsystem has a number of reactions over the threshold, it gets its own YAML file. All other reactions, those that don't have a subsystem or are in a subsystem that falls below the t...
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