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def report_role(self, role): """ Return the fields gathered. """ self.yaml_files = [] fields = { "state": "skipped", "total_files": self.gather_files(), "total_lines": self.gather_lines(), "total_facts": self.gather_facts(), ...
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def min(self): """ Returns the minimum value of the domain. :rtype: `float` or `np.inf` """ return int(self._min) if not np.isinf(self._min) else self._min
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def execute_update(args): """Execute the update based on command line args and returns a dictionary with 'execution result, ''response code', 'response info' and 'process friendly message'. """ provider_class = getattr(dnsupdater, dnsupdater.AVAILABLE_PLUGINS.get(args.p...
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def copy(self): """ Safely get a copy of the current mesh. Copied objects will have emptied caches to avoid memory issues and so may be slow on initial operations until caches are regenerated. Current object will *not* have its cache cleared. Returns --...
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def extract_wininst_cfg(dist_filename): """Extract configuration data from a bdist_wininst .exe Returns a ConfigParser.RawConfigParser, or None """ f = open(dist_filename,'rb') try: endrec = zipfile._EndRecData(f) if endrec is None: return None prepended = (endr...
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def forum_topic_get_by_tag_for_user(self, tag=None, author=None): """Get all forum topics with a specific tag""" if not tag: return None if author: r = self._request('ebuio/forum/search/bytag/' + tag + '?u=' + author) else: r = self._request('ebuio/f...
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def validate_metadata_sign(xml, cert=None, fingerprint=None, fingerprintalg='sha1', validatecert=False, debug=False): """ Validates a signature of a EntityDescriptor. :param xml: The element we should validate :type: string | Document :param cert: The public cert :type:...
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def initialize(self): """ A reimplemented initializer. This method will add the include objects to the parent of the include and ensure that they are initialized. """ super(Block, self).initialize() block = self.block if block: #: This block is setting the con...
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def _get_http(url, temp_file_name, initial_size, file_size, verbose_bool, progressbar, ncols=80): """Safely (resume a) download to a file from http(s).""" # Actually do the reading req = urllib.request.Request(url) if initial_size > 0: req.headers['Range'] = 'bytes=%s-' % (initial_...
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def loader_cls(self): """Loader class used in `JsonRef.replace_refs`.""" cls = self.app.config['JSONSCHEMAS_LOADER_CLS'] if isinstance(cls, six.string_types): return import_string(cls) return cls
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def f_get_explored_parameters(self, fast_access=False, copy=True): """ Returns a dictionary containing the full parameter names as keys and the parameters or the parameter data items as values. IMPORTANT: This dictionary always contains all explored parameters as keys. Even when they...
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def end_parallel(self): """ Ends a parallel region by merging the channels into a single stream. Returns: Stream: Stream for which subsequent transformations are no longer parallelized. .. seealso:: :py:meth:`set_parallel`, :py:meth:`parallel` """ outport = ...
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def resize(self, dims): """Resize our drawing area to encompass a space defined by the given dimensions. """ width, height = dims[:2] self.gl_resize(width, height)
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def open_any(cls, file): """Open an image file. If the image is not PNG format, it would convert the image into PNG with Pillow module. If the module is not installed, :class:`ImportError` would be raised. :arg file: Input file. :type file: path-like or file-like :rtype: :class:`PNG` """ with open_fi...
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def enqueue_jobs(self): """ Move scheduled jobs into queues. """ self.log.debug('Checking for scheduled jobs') jobs = self.get_jobs_to_queue() for job in jobs: self.enqueue_job(job) # Refresh scheduler key's expiry self.connection.expire(self...
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def action(self): """ This class overrides this method """ commandline = "{0} {1}".format(self.command, " ".join(self.arguments)) try: completed_process = subprocess.run(commandline, shell=True) self.exit_status = completed_process.returncode excep...
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def simulation_manager(self, thing=None, **kwargs): """ Constructs a new simulation manager. :param thing: Optional - What to put in the new SimulationManager's active stash (either a SimState or a list of SimStates). :param kwargs: Any additional keyword arguments wi...
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def _if_to_py_ast(ctx: GeneratorContext, node: If) -> GeneratedPyAST: """Generate an intermediate if statement which assigns to a temporary variable, which is returned as the expression value at the end of evaluation. Every expression in Basilisp is true if it is not the literal values nil or false...
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def Glyph(actor, glyphObj, orientationArray="", scaleByVectorSize=False, c=None, alpha=1): """ At each vertex of a mesh, another mesh - a `'glyph'` - is shown with various orientation options and coloring. Color can be specfied as a colormap which maps the size of the orientation vec...
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def symbol_to_id(self, symbol): """Returns the list of Entrez IDs for a given Geneways symbol (there may be more than one)""" if symbol not in self.symbols_to_ids: m = 'Could not look up Entrez ID for Geneways symbol ' + symbol raise Exception(m) return self.symb...
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def element_at(index): """Create a transducer which obtains the item at the specified index.""" if index < 0: raise IndexError("element_at used with illegal index {}".format(index)) def element_at_transducer(reducer): return ElementAt(reducer, index) return element_at_transducer
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def eval_in_new(cls, expr, *args, **kwargs): """:meth:`eval` an expression in a new, temporary :class:`Context`. This should be safe to use directly on user input. Args: expr (LispVal): The expression to evaluate. *args: Args for the :class:`Context` constructor. ...
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def wantMethod(self, method): """Accept the method if its attributes match. """ try: cls = method.im_class except AttributeError: return False return self.validateAttrib(method, cls)
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def sync_perm_for_dag(self, dag_id, access_control=None): """ Sync permissions for given dag id. The dag id surely exists in our dag bag as only / refresh button or cli.sync_perm will call this function :param dag_id: the ID of the DAG whose permissions should be updated :type d...
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def _generateOverlapping(filename="overlap.csv", numSequences=2, elementsPerSeq=3, numRepeats=10, hub=[0,1], hubOffset=1, resets=False): """ Generate a temporal dataset containing sequences that overlap one or more elements with other sequences. Parameters: --------------------------...
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def decorate(text, style): """ Console decoration style definitions :param text: the text string to decorate :type text: str :param style: the style used to decorate the string :type style: str :return: a decorated string :rtype: str """ return { 's...
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def index_data(self, data, index_name, doc_type): """Index data in Stub Indexer.""" print 'ELS Stub Indexer getting called...' print '%s %s %s %s' % (self, data, index_name, doc_type)
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def get_route53_records(self): ''' Get and store the map of resource records to domain names that point to them. ''' r53_conn = route53.Route53Connection() all_zones = r53_conn.get_zones() route53_zones = [ zone for zone in all_zones if zone.name[:-1] ...
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def setTxPower(self, tx_power): """Set the transmission power for one or more antennas. @param tx_power: index into self.tx_power_table """ tx_pow_validated = self.get_tx_power(tx_power) logger.debug('tx_pow_validated: %s', tx_pow_validated) needs_update = False ...
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def _determine_supported_alleles(command, supported_allele_flag): """ Try asking the commandline predictor (e.g. netMHCpan) which alleles it supports. """ try: # convert to str since Python3 returns a `bytes` object supported_alleles_output = check_output(...
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def add_element(self, element): """ Element can be href or type :py:class:`smc.base.model.Element` :: >>> from smc.elements.other import Category >>> category = Category('foo') >>> category.add_element(Host('kali')) :param str,Element element: elemen...
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def freeze_of_gait(self, x): """ This method assess freeze of gait following :cite:`g-BachlinPRMHGT10`. :param x: The time series to assess freeze of gait on. This could be x, y, z or mag_sum_acc. :type x: pandas.Series :return freeze_time: What times do freeze ...
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def as_download(self, data, block_num=-1): """ Downloads a DB data into the AG asynchronously. A whole block (including header and footer) must be available into the user buffer. :param block_num: New Block number (or -1) :param data: the user buffer """ ...
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def flatten(iterable, check=is_iterable): """Produces a recursively flattened version of ``iterable`` ``check`` Recurses only if check(value) is true. """ for value in iterable: if check(value): for flat in flatten(value, check): yield flat else: ...
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def update_resource_value(self, device_id, _resource_path, resource_value, **kwargs): # noqa: E501 """Write to a resource or use write-attributes for a resource # noqa: E501 With this API, you can [write a new value to existing resources](/docs/current/connecting/handle-resource-webapp.html) or [use ...
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def dict2kvlist(o): ''' Serializes a dict-like object into a generator of the flatten list of repeating key-value pairs. It is useful when using HMSET method in Redis. Example: >>> list(dict2kvlist({'a': 1, 'b': 2})) ['a', 1, 'b', 2] ''' return chain.from_iterable((k, v) for k, v in o....
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def structure_to_abivars(structure, **kwargs): """ Receives a structure and returns a dictionary with the ABINIT variables. """ if not structure.is_ordered: raise ValueError("""\ Received disordered structure with partial occupancies that cannot be converted into an Abinit input Please use Order...
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def nlmsg_seq(self, value): """Sequence setter.""" self.bytearray[self._get_slicers(3)] = bytearray(c_uint32(value or 0))
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def make_path(base_uri, path, filename, path_dimensions, split_length): """Generate a path as base location for file instance. :param base_uri: The base URI. :param path: The relative path. :param path_dimensions: Number of chunks the path should be split into. :param split_length: The length of an...
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def actual_query_range(self): """This is the actual query range for the positive strand :returns: Range of query positive strand covered :rtype: GenomicRange """ a = self.alignment_ranges #return GenomicRange(a[0][1].chr,a[0][1].start,a[-1][1].end,self.get_strand()) if self.get_strand() ==...
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def rewrite_record(bdist_dir): """ Rewrite RECORD file with hashes for all files in `wheel_sdir` Copied from :method:`wheel.bdist_wheel.bdist_wheel.write_record` Will also unsign wheel Parameters ---------- bdist_dir : str Path of unpacked wheel file """ info_dirs = glob.glob(...
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def derive_key(self, derivation_method, derivation_length, derivation_data=None, key_material=None, hash_algorithm=None, salt=None, iteration_count=None, encryption_alg...
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def _vminFindStart(v,E,Lz,I3V,delta,u0,cosh2u0,sinh2u0, potu0pi2,pot): """ NAME: _vminFindStart PURPOSE: Find adequate start point to solve for vmin INPUT: same as JzStaeckelIntegrandSquared OUTPUT: rstart HISTORY: 2012-11-28 - W...
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def natural_name(self) -> str: """Valid python identifier representation of the expession.""" name = self.expression.strip() for op in operators: name = name.replace(op, operator_to_identifier[op]) return wt_kit.string2identifier(name)
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def find_nonzero_constrained_reactions(model): """Return list of reactions with non-zero, non-maximal bounds.""" lower_bound, upper_bound = helpers.find_bounds(model) return [rxn for rxn in model.reactions if 0 > rxn.lower_bound > lower_bound or 0 < rxn.upper_bound < upper_bound]
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def is_playing_shared_game(self, steamID, appid_playing, format=None): """Returns valid lender SteamID if game currently played is borrowed. steamID: The users ID appid_playing: The game player is currently playing format: Return format. None defaults to json. (json, xml, vdf) ...
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def dump(exif_dict_original): """ py:function:: piexif.load(data) Return exif as bytes. :param dict exif: Exif data({"0th":dict, "Exif":dict, "GPS":dict, "Interop":dict, "1st":dict, "thumbnail":bytes}) :return: Exif :rtype: bytes """ exif_dict = copy.deepcopy(exif_dict_original) he...
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def lower_backtrack_blocks(match_query, location_types): """Lower Backtrack blocks into (QueryRoot, MarkLocation) pairs of blocks.""" # The lowering works as follows: # 1. Upon seeing a Backtrack block, end the current traversal (if non-empty). # 2. Start new traversal from the type and location to ...
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def file_exists(db, user_id, path): """ Check if a file exists. """ try: get_file( db, user_id, path, include_content=False, decrypt_func=unused_decrypt_func, ) return True except NoSuchFile: return False
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def _fetch_type_main(cls, cls_in, match): """ :type cls_in: type :type match: _sre.SRE_Match :rtype: type """ return cls._str_to_type( cls_in, match.group(cls._SUBMATCH_INDEX_TYPE_MAIN) )
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def Lr(self,value): """ set row rotation """ assert value.shape==(self.N, self.N), 'dimension mismatch' self._Lr = value self.clear_cache()
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def get_img_name(self, band, resolution=None): """ :param band: band name :type band: str :param resolution: Specifies the resolution in case of Sentinel-2 L2A products :type resolution: str or None :return: name of band image file :rtype: str """ ...
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def create_blueprint(self, appbuilder, endpoint=None, static_folder=None): """ Create Flask blueprint. You will generally not use it :param appbuilder: the AppBuilder object :param endpoint: endpoint override for this blueprint, w...
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def get_mfa(self): """Return the currently-valid MFA token for this application.""" token = str(self.totp.now()) # PyOTP doesn't pre-pad tokens shorter than 6 characters # ROTP does, so we have to. while len(token) < 6: token = '0{}'.format(token) return token
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def moment_magnitude_scalar(moment): ''' Uses Hanks & Kanamori formula for calculating moment magnitude from a scalar moment (Nm) ''' if isinstance(moment, np.ndarray): return (2. / 3.) * (np.log10(moment) - 9.05) else: return (2. / 3.) * (log10(moment) - 9.05)
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def generate_base(path: str) -> str: """ Convert path, which can be a URL or a file path into a base URI :param path: file location or url :return: file location or url sans actual name """ if ':' in path: parts = urlparse(path) parts_dict = parts._asdict() parts_dict['path'...
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def H11(self): "Difference entropy." return -(self.p_xminusy * np.log(self.p_xminusy + self.eps)).sum(1)
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def update_record_ip(self, ip, domain, name, record_type): """Update the IP address(es) for (a) domain(s) specified by type and name. :param ip: the new IP for the DNS record (ex. '123.1.2.255') :param domain: the domain where the DNS belongs to (ex. 'example.com') :param name: the DNS ...
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def showsyntaxerror(self, filename=None): """Display the syntax error that just occurred.""" # Override for avoid using sys.excepthook PY-12600 type, value, tb = sys.exc_info() sys.last_type = type sys.last_value = value sys.last_traceback = tb if filename and typ...
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def _fake_openassociatorinstancepaths(self, namespace, **params): # pylint: disable=invalid-name """ Implements WBEM server responder for :meth:`~pywbem.WBEMConnection.OpenAssociatorInstancePaths` with data from the instance repository. """ self._validate_namespac...
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def always_iterable(obj, base_type=(str, bytes)): """If *obj* is iterable, return an iterator over its items:: >>> obj = (1, 2, 3) >>> list(always_iterable(obj)) [1, 2, 3] If *obj* is not iterable, return a one-item iterable containing *obj*:: >>> obj = 1 >>> list(alwa...
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def from_blob(cls, blob, stage=0): """:return: Fully equipped BaseIndexEntry at the given stage""" return cls((blob.mode, blob.binsha, stage << CE_STAGESHIFT, blob.path))
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def convert(self, obj): """Takes a dict corresponding to the honeybadgerfish JSON blob of the 1.0.* type and converts it to BY_ID_HONEY_BADGERFISH version. The object is modified in place and returned. """ if self.pristine_if_invalid: raise NotImplementedError('pristi...
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def pwa(self, val, wa='WARN'): """ Print val: WARN in yellow on STDOUT """ self.pstd(self.color.yellow('{}: {}'.format(val, wa)))
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def rotateCoords(coords, R): """ Rotate the list of points using rotation matrix R :param coords: List of points to be rotated :param R: Rotation matrix :return: List of rotated points """ newlist = list() for pp in coords: rpp = matrixTimesVector(R, pp) newlist.append(rp...
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def delete(self, symbol, chunk_range=None, audit=None): """ Delete all chunks for a symbol, or optionally, chunks within a range Parameters ---------- symbol : str symbol name for the item chunk_range: range object a date range to delete a...
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def infos(cls, fqdn): """ Display information about hosted certificates for a fqdn. """ if isinstance(fqdn, (list, tuple)): ids = [] for fqd_ in fqdn: ids.extend(cls.infos(fqd_)) return ids ids = cls.usable_id(fqdn) if not ids: ...
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def addSingleTraitTerm(self,K=None,is_noise=False,normalize=True,Ks=None): """ add random effects term for single trait models (no trait-trait covariance matrix) Args: K: NxN sample covariance matrix is_noise: bool labeling the noise term (noise term has...
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def set_logging_formatter(self): """ Sets the logging formatter. """ for handler in (RuntimeGlobals.logging_console_handler, RuntimeGlobals.logging_file_handler, RuntimeGlobals.logging_session_handler): handler and handler.setF...
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def format(self, attrs, args=None): """Format attributes including {} tags with arguments.""" if args is None: return attrs out = {} for key, val in attrs.items(): mba = {'indexer': 'annual'} # Add formatting {} around values to be able to replace the...
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def strip_accents(s, pass_symbols=(u'й', u'Й', u'\n')): """ Strip accents from a string """ result = [] for char in s: # Pass these symbols without processing if char in pass_symbols: result.append(char) continue for c in unicodedata.normalize('NFD', char): ...
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def max_pool(arr, block_size, cval=0, preserve_dtype=True): """ Resize an array using max-pooling. dtype support:: See :func:`imgaug.imgaug.pool`. Parameters ---------- arr : (H,W) ndarray or (H,W,C) ndarray Image-like array to pool. See :func:`imgaug.pool` for details. b...
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def Scharr_edge(im, blurRadius=10, imblur=None): """Extract the edges using Scharr kernel (Sobel optimized for rotation invariance) Parameters: ----------- im: 2d array The image blurRadius: number, default 10 The gaussian blur raduis (The kernel has size 2*blurRadius+1) imb...
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def get_gene(self, gene_name=None, gene_symbol=None, gene_id=None, synonym=None, uniprot_id=None, pharmgkb_id=None, biogrid_id=None, alt_gene_id=None, limit=None, as_df=False): """Get genes :param bool as_df: if set to True result returns as `pandas.DataFrame` :param alt_gene_i...
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def SensorsDataGet(self, sensorIds, parameters): """ Retrieve sensor data for the specified sensors from CommonSense. If SensorsDataGet is successful, the result can be obtained by a call to getResponse(), and should be a json string. @param sensorIds (list) a list of s...
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def dtype_repr(dtype): """Stringify ``dtype`` for ``repr`` with default for int and float.""" dtype = np.dtype(dtype) if dtype == np.dtype(int): return "'int'" elif dtype == np.dtype(float): return "'float'" elif dtype == np.dtype(complex): return "'complex'" elif dtype.s...
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def process_udp_frame(self, id=None, msg=None): """process_udp_frame Convert a complex nested json dictionary to a flattened dictionary and capture all unique keys for table construction :param id: key for this msg :pa...
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def create_parameter_group(self, name, engine='MySQL5.1', description=''): """ Create a new dbparameter group for your account. :type name: string :param name: The name of the new dbparameter group :type engine: str :param engine: Name of database engine. :type...
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def diff_in_days(start, end): """ calculate difference between given dates in days :param BaseDateTuple start: state date :param BaseDateTuple end: end date :return float: difference between end date and start date in days """ diff = from_ymd_to_excel(*end.date)...
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def codemirror_script(self, inputid): """ Build CodeMirror HTML script tag which contains CodeMirror init. Arguments: inputid (string): Input id. Returns: string: HTML for field CodeMirror instance. """ varname = "{}_codemirror".format(inputid) ...
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def swap_channels(self, channel_swap): """ Swaps the two channels specified in the tuple. Parameters ---------- channel_swap : :obj:`tuple` of int the two channels to swap Returns ------- :obj:`ColorImage` color image with cols swapped ...
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def get_common_session_key(self, premaster_secret): """K = H(S). Special implementation for Apple TV. """ k_1 = self.hash(premaster_secret, b'\x00\x00\x00\x00', as_bytes=True) k_2 = self.hash(premaster_secret, b'\x00\x00\x00\x01', as_bytes=True) return k_1 + k_2
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def _load(self, scale=1.0): """Load the MetImage RSR data for the band requested""" data = np.genfromtxt(self.requested_band_filename, unpack=True, names=['wavenumber', 'response'], ...
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def are_imaging_dicoms(dicom_input): """ This function will check the dicom headers to see which type of series it is Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used) :param dicom_input: directory with dicom files or a list of dicom objects """ # if it is ...
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def prepare_dataset(dataset, formula_id2index, feature_list, is_traindata, do_normalization=False): """Transform each instance of dataset to a (Features, Label) tuple.""" prepared = [] start_time = time.time() translation = ...
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def get_commits(self): ''' Get all commits involving this filename :returns: List of commits newest to oldest ''' if not self.is_managed_by_git(): return [] return self.git.get_commits(self.content.source_path, self.follow)
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def parse_all(self): """Parse the __all__ definition in a module.""" assert self.current.value == "__all__" self.consume(tk.NAME) if self.current.value != "=": raise AllError("Could not evaluate contents of __all__. ") self.consume(tk.OP) if self.current.value...
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def _calculate_states(self, solution, t, step, int_step): """! @brief Calculates new states for neurons using differential calculus. Returns new states for neurons. @param[in] solution (solve_type): Type solver of the differential equation. @param[in] t (double): Current ti...
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def lraise(self,message): """log an exception, close the log file, then raise the exception Parameters ---------- message : str the exception message Raises ------ exception with message """ s = str(datetime.now()) + " ERROR: " + ...
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def weather(api_key, latitude, longitude, date_time=None): # type:(str, float, float) -> Weather """ This is a shortcut method that can be used to perform a basic weather request with the default settings. :param str api_key: Darksky.net API key :param float latitude: The requested latitude. Maybe ...
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def default(self, vid): """ Defaults the VLAN configuration .. code-block:: none default vlan <vlanid> Args: vid (str): The VLAN ID to default Returns: True if the operation was successful otherwise False """ command = 'default vlan...
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def from_api_repr(cls, resource, client): """Factory: construct a job given its API representation .. note: This method assumes that the project found in the resource matches the client's project. :type resource: dict :param resource: dataset job representation ...
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def _create_new_thread_loop(self): """ Create a daemonized thread that will run Tornado IOLoop. :return: the IOLoop backed by the new thread. """ self._thread_loop = ThreadLoop() if not self._thread_loop.is_ready(): self._thread_loop.start() return sel...
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def create_filebase_name(self, group_info, extension='gz', file_name=None): """ Return tuple of resolved destination folder name and file name """ dirname = self.filebase.formatted_dirname(groups=group_info) if not file_name: file_name = self.filebase.prefix_template ...
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def manipulate(self, stored_instance, component_instance): """ Manipulates the component instance :param stored_instance: The iPOPO component StoredInstance :param component_instance: The component instance """ # Store the stored instance self._ipopo_instance = s...
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def get_parameter_vector(self, include_frozen=False): """ Get an array of the parameter values in the correct order Args: include_frozen (Optional[bool]): Should the frozen parameters be included in the returned value? (default: ``False``) """ if inc...
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def any2unicode(text, encoding='utf8', errors='strict'): """Convert a string (bytestring in `encoding` or unicode), to unicode.""" if isinstance(text, unicode): return text return unicode(text, encoding, errors=errors)
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def make_inaturalist_api_get_call(endpoint: str, params: Dict, **kwargs) -> requests.Response: """Make an API call to iNaturalist. endpoint is a string such as 'observations' !! do not put / in front method: 'GET', 'HEAD', 'POST', 'PUT', 'PATCH', 'DELETE' kwargs are passed to requests.request Retur...
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def example_protos_from_path(path, num_examples=10, start_index=0, parse_examples=True, sampling_odds=1, example_class=tf.train.Example): """Returns a number of examples fro...
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def XOR(a, b, exc=CertifierValueError('Expected at least one certified value')): """ Only one arg must not raise a Certifier exception when called overall. Raise the specified exception on failure. :params Certifier a: The first certifiers to call :params Certifier b: The second cer...
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