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def _get_features_string(self, features=None): """ Generates the extended newick string NHX with extra data about a node.""" string = "" if features is None: features = [] elif features == []: features = self.features for pr in features: if hasattr(self, pr): raw...
def get_column_width(column, table): """ Get the character width of a column in a table Parameters ---------- column : int The column index analyze table : list of lists of str The table of rows of strings. For this to be accurate, each string must only be 1 line long. ...
def get_text_mark(ttree): """ makes a simple Text Mark object""" if ttree._orient in ["right"]: angle = 0. ypos = ttree.verts[-1*len(ttree.tree):, 1] if ttree._kwargs["tip_labels_align"]: xpos = [ttree.verts[:, 0].max()] * len(ttree.tree) start = xpos ...
def get_edge_mark(ttree): """ makes a simple Graph Mark object""" ## tree style if ttree._kwargs["tree_style"] in ["c", "cladogram"]: a=ttree.edges vcoordinates=ttree.verts else: a=ttree._lines vcoordinates=ttree._coords ## fixed args a...
def split_styles(mark): """ get shared styles """ markers = [mark._table[key] for key in mark._marker][0] nstyles = [] for m in markers: ## fill and stroke are already rgb() since already in markers msty = toyplot.style.combine({ "fill": m.mstyle['fill'], "st...
def center_cell_text(cell): """ Horizontally center the text within a cell's grid Like this:: +---------+ +---------+ | foo | --> | foo | +---------+ +---------+ Parameters ---------- cell : dashtable.data2rst.Cell Returns ------- cell : da...
def hamming_distance(word1, word2): """ Computes the Hamming distance. [Reference]: https://en.wikipedia.org/wiki/Hamming_distance [Article]: Hamming, Richard W. (1950), "Error detecting and error correcting codes", Bell System Technical Journal 29 (2): 147–160 """ from operator import ...
def polygen(*coefficients): '''Polynomial generating function''' if not coefficients: return lambda i: 0 else: c0 = coefficients[0] coefficients = coefficients[1:] def _(i): v = c0 for c in coefficients: v += c*i ...
def timeseries(name='', backend=None, date=None, data=None, **kwargs): '''Create a new :class:`dynts.TimeSeries` instance using a ``backend`` and populating it with provided the data. :parameter name: optional timeseries name. For multivarate timeseries the :func:`dynts.tsname` ut...
def ensure_table_strings(table): """ Force each cell in the table to be a string Parameters ---------- table : list of lists Returns ------- table : list of lists of str """ for row in range(len(table)): for column in range(len(table[row])): table[row][colum...
def left_sections(self): """ The number of sections that touch the left side. During merging, the cell's text will grow to include other cells. This property keeps track of the number of sections that are touching the left side. For example:: +-----+----...
def right_sections(self): """ The number of sections that touch the right side. Returns ------- sections : int The number of sections on the right """ lines = self.text.split('\n') sections = 0 for i in range(len(lines)): i...
def top_sections(self): """ The number of sections that touch the top side. Returns ------- sections : int The number of sections on the top """ top_line = self.text.split('\n')[0] sections = len(top_line.split('+')) - 2 return secti...
def bottom_sections(self): """ The number of cells that touch the bottom side. Returns ------- sections : int The number of sections on the top """ bottom_line = self.text.split('\n')[-1] sections = len(bottom_line.split('+')) - 2 ret...
def is_header(self): """ Whether or not the cell is a header Any header cell will have "=" instead of "-" on its border. For example, this is a header cell:: +-----+ | foo | +=====+ while this cell is not:: +-----+ ...
def get_git_changeset(filename=None): """Returns a numeric identifier of the latest git changeset. The result is the UTC timestamp of the changeset in YYYYMMDDHHMMSS format. This value isn't guaranteed to be unique, but collisions are very unlikely, so it's sufficient for generating the developmen...
def headers_present(html_string): """ Checks if the html table contains headers and returns True/False Parameters ---------- html_string : str Returns ------- bool """ try: from bs4 import BeautifulSoup except ImportError: print("ERROR: You must have Beautif...
def extract_spans(html_string): """ Creates a list of the spanned cell groups of [row, column] pairs. Parameters ---------- html_string : str Returns ------- list of lists of lists of int """ try: from bs4 import BeautifulSoup except ImportError: print("ERRO...
def translation(first, second): """Create an index of mapped letters (zip to dict).""" if len(first) != len(second): raise WrongLengthException('The lists are not of the same length!') return dict(zip(first, second))
def process_tag(node): """ Recursively go through a tag's children, converting them, then convert the tag itself. """ text = '' exceptions = ['table'] for element in node.children: if isinstance(element, NavigableString): text += element elif not node.name in e...
def laggeddates(ts, step=1): '''Lagged iterator over dates''' if step == 1: dates = ts.dates() if not hasattr(dates, 'next'): dates = dates.__iter__() dt0 = next(dates) for dt1 in dates: yield dt1, dt0 dt0 = dt1 else: whi...
def make_skiplist(*args, use_fallback=False): '''Create a new skiplist''' sl = fallback.Skiplist if use_fallback else Skiplist return sl(*args)
def data2md(table): """ Creates a markdown table. The first row will be headers. Parameters ---------- table : list of lists of str A list of rows containing strings. If any of these strings consist of multiple lines, they will be converted to single line because markdown ta...
def v_center_cell_text(cell): """ Vertically center the text within the cell's grid. Like this:: +--------+ +--------+ | foobar | | | | | | | | | --> | foobar | | | | | | | | | ...
def data2rst(table, spans=[[[0, 0]]], use_headers=True, center_cells=False, center_headers=False): """ Convert a list of lists of str into a reStructuredText Grid Table Parameters ---------- table : list of lists of str spans : list of lists of lists of int, optional These ...
def set_dims_from_tree_size(self): "Calculate reasonable height and width for tree given N tips" tlen = len(self.treelist[0]) if self.style.orient in ("right", "left"): # long tip-wise dimension if not self.style.height: self.style.height = max(275, min(10...
def add_tip_labels_to_axes(self): """ Add text offset from tips of tree with correction for orientation, and fixed_order which is usually used in multitree plotting. """ # get tip-coords and replace if using fixed_order if self.style.orient in ("up", "down"): ...
def fit_tip_labels(self): """ Modifies display range to ensure tip labels fit. This is a bit hackish still. The problem is that the 'extents' range of the rendered text is totally correct. So we add a little buffer here. Should add for user to be able to modify this if needed. I...
def convert_p(element, text): """ Adds 2 newlines to the end of text """ depth = -1 while element: if (not element.name == '[document]' and not element.parent.get('id') == '__RESTRUCTIFY_WRAPPER__'): depth += 1 element = element.parent if text: ...
def simple2data(text): """ Convert a simple table to data (the kind used by DashTable) Parameters ---------- text : str A valid simple rst table Returns ------- table : list of lists of str spans : list of lists of lists of int A span is a [row, column] pair that de...
def get_output_column_widths(table, spans): """ Gets the widths of the columns of the output table Parameters ---------- table : list of lists of str The table of rows of text spans : list of lists of int The [row, column] pairs of combined cells Returns ------- wid...
def make_empty_table(row_count, column_count): """ Make an empty table Parameters ---------- row_count : int The number of rows in the new table column_count : int The number of columns in the new table Returns ------- table : list of lists of str Each cell ...
def beta(self): '''\ The linear estimation of the parameter vector :math:`\beta` given by .. math:: \beta = (X^T X)^-1 X^T y ''' t = self.X.transpose() XX = dot(t,self.X) XY = dot(t,self.y) return linalg.solve(XX,XY)
def oftype(self, typ): '''Return a generator of formatters codes of type typ''' for key, val in self.items(): if val.type == typ: yield key
def names(self, with_namespace=False): '''List of names for series in dataset. It will always return a list or names with length given by :class:`~.DynData.count`. ''' N = self.count() names = self.name.split(settings.splittingnames)[:N] n = 0 while len(n...
def dump(self, format=None, **kwargs): """Dump the timeseries using a specific ``format``. """ formatter = Formatters.get(format, None) if not format: return self.display() elif not formatter: raise FormattingException('Formatter %s not available' % format...
def p_expression_binop(p): '''expression : expression PLUS expression | expression MINUS expression | expression TIMES expression | expression DIVIDE expression | expression EQUAL expression | expression CONCAT expressio...
def p_expression_group(p): '''expression : LPAREN expression RPAREN | LSQUARE expression RSQUARE''' v = p[1] if v == '(': p[0] = functionarguments(p[2]) elif v == '[': p[0] = tsentry(p[2])
def merge_cells(cell1, cell2, direction): """ Combine the side of cell1's grid text with cell2's text. For example:: cell1 cell2 merge "RIGHT" +-----+ +------+ +-----+------+ | foo | | dog | | foo | dog | | | +------+ | +------+ | | ...
def iterclass(cls): """Iterates over (valid) attributes of a class. Args: cls (object): the class to iterate over Yields: (str, obj) tuples: the class-level attributes. """ for field in dir(cls): if hasattr(cls, field): value = getattr(cls, field) yi...
def _mksocket(host, port, q, done, stop): """Returns a tcp socket to (host/port). Retries forever if connection fails""" s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) s.settimeout(2) attempt = 0 while not stop.is_set(): try: s.connect((host, port)) return s ...
def _push(host, port, q, done, mps, stop, test_mode): """Worker thread. Connect to host/port, pull data from q until done is set""" sock = None retry_line = None while not ( stop.is_set() or ( done.is_set() and retry_line == None and q.empty()) ): stime = time.time() if sock == None and...
def log(self, name, val, **tags): """Log metric name with value val. You must include at least one tag as a kwarg""" global _last_timestamp, _last_metrics # do not allow .log after closing assert not self.done.is_set(), "worker thread has been closed" # check if valid metric nam...
def available_ports(): """ Scans COM1 through COM255 for available serial ports returns a list of available ports """ ports = [] for i in range(256): try: p = Serial('COM%d' % i) p.close() ports.append(p) ...
def get_current_response(self): """ reads the current response data from the object and returns it in a dict. Currently 'time' is reported as 0 until clock drift issues are resolved. """ response = {'port': 0, 'pressed': False, ...
def detect_xid_devices(self): """ For all of the com ports connected to the computer, send an XID command '_c1'. If the device response with '_xid', it is an xid device. """ self.__xid_cons = [] for c in self.__com_ports: device_found = False ...
def device_at_index(self, index): """ Returns the device at the specified index """ if index >= len(self.__xid_cons): raise ValueError("Invalid device index") return self.__xid_cons[index]
def query_base_timer(self): """ gets the value from the device's base timer """ (_, _, time) = unpack('<ccI', self.con.send_xid_command("e3", 6)) return time
def poll_for_response(self): """ Polls the device for user input If there is a keymapping for the device, the key map is applied to the key reported from the device. If a response is waiting to be processed, the response is appended to the internal response_queue ...
def set_pulse_duration(self, duration): """ Sets the pulse duration for events in miliseconds when activate_line is called """ if duration > 4294967295: raise ValueError('Duration is too long. Please choose a value ' 'less than 4294967296....
def activate_line(self, lines=None, bitmask=None, leave_remaining_lines=False): """ Triggers an output line on StimTracker. There are 8 output lines on StimTracker that can be raised in any combination. To raise lines 1 and 7, for example, you pass in the ...
def clear_line(self, lines=None, bitmask=None, leave_remaining_lines=False): """ The inverse of activate_line. If a line is active, it deactivates it. This has the same parameters as activate_line() """ if lines is None and bitmask is None: raise ...
def init_device(self): """ Initializes the device with the proper keymaps and name """ try: product_id = int(self._send_command('_d2', 1)) except ValueError: product_id = self._send_command('_d2', 1) if product_id == 0: self._impl = Re...
def _send_command(self, command, expected_bytes): """ Send an XID command to the device """ response = self.con.send_xid_command(command, expected_bytes) return response
def get_xid_devices(): """ Returns a list of all Xid devices connected to your computer. """ devices = [] scanner = XidScanner() for i in range(scanner.device_count()): com = scanner.device_at_index(i) com.open() device = XidDevice(com) devices.append(device) ...
def get_xid_device(device_number): """ returns device at a given index. Raises ValueError if the device at the passed in index doesn't exist. """ scanner = XidScanner() com = scanner.device_at_index(device_number) com.open() return XidDevice(com)
def connect(self, receiver): """Append receiver.""" if not callable(receiver): raise ValueError('Invalid receiver: %s' % receiver) self.receivers.append(receiver)
def disconnect(self, receiver): """Remove receiver.""" try: self.receivers.remove(receiver) except ValueError: raise ValueError('Unknown receiver: %s' % receiver)
def send(self, instance, *args, **kwargs): """Send signal.""" for receiver in self.receivers: receiver(instance, *args, **kwargs)
def select(cls, *args, **kwargs): """Support read slaves.""" query = super(Model, cls).select(*args, **kwargs) query.database = cls._get_read_database() return query
def save(self, force_insert=False, **kwargs): """Send signals.""" created = force_insert or not bool(self.pk) self.pre_save.send(self, created=created) super(Model, self).save(force_insert=force_insert, **kwargs) self.post_save.send(self, created=created)
def delete_instance(self, *args, **kwargs): """Send signals.""" self.pre_delete.send(self) super(Model, self).delete_instance(*args, **kwargs) self.post_delete.send(self)
def get_database(obj, **params): """Get database from given URI/Object.""" if isinstance(obj, string_types): return connect(obj, **params) return obj
def init_app(self, app, database=None): """Initialize application.""" # Register application if not app: raise RuntimeError('Invalid application.') self.app = app if not hasattr(app, 'extensions'): app.extensions = {} app.extensions['peewee'] = se...
def close(self, response): """Close connection to database.""" LOGGER.info('Closing [%s]', os.getpid()) if not self.database.is_closed(): self.database.close() return response
def Model(self): """Bind model to self database.""" Model_ = self.app.config['PEEWEE_MODELS_CLASS'] meta_params = {'database': self.database} if self.slaves and self.app.config['PEEWEE_USE_READ_SLAVES']: meta_params['read_slaves'] = self.slaves Meta = type('Meta', ()...
def models(self): """Return self.application models.""" Model_ = self.app.config['PEEWEE_MODELS_CLASS'] ignore = self.app.config['PEEWEE_MODELS_IGNORE'] models = [] if Model_ is not Model: try: mod = import_module(self.app.config['PEEWEE_MODELS_MODULE...
def cmd_create(self, name, auto=False): """Create a new migration.""" LOGGER.setLevel('INFO') LOGGER.propagate = 0 router = Router(self.database, migrate_dir=self.app.config['PEEWEE_MIGRATE_DIR'], migrate_table=self.app.config['PEEWEE_MIG...
def cmd_migrate(self, name=None, fake=False): """Run migrations.""" from peewee_migrate.router import Router, LOGGER LOGGER.setLevel('INFO') LOGGER.propagate = 0 router = Router(self.database, migrate_dir=self.app.config['PEEWEE_MIGRATE_DIR'], ...
def cmd_rollback(self, name): """Rollback migrations.""" from peewee_migrate.router import Router, LOGGER LOGGER.setLevel('INFO') LOGGER.propagate = 0 router = Router(self.database, migrate_dir=self.app.config['PEEWEE_MIGRATE_DIR'], ...
def cmd_list(self): """List migrations.""" from peewee_migrate.router import Router, LOGGER LOGGER.setLevel('DEBUG') LOGGER.propagate = 0 router = Router(self.database, migrate_dir=self.app.config['PEEWEE_MIGRATE_DIR'], migrate_ta...
def cmd_merge(self): """Merge migrations.""" from peewee_migrate.router import Router, LOGGER LOGGER.setLevel('DEBUG') LOGGER.propagate = 0 router = Router(self.database, migrate_dir=self.app.config['PEEWEE_MIGRATE_DIR'], migrate_...
def manager(self): """Integrate a Flask-Script.""" from flask_script import Manager, Command manager = Manager(usage="Migrate database.") manager.add_command('create', Command(self.cmd_create)) manager.add_command('migrate', Command(self.cmd_migrate)) manager.add_command...
def restart_program(): """ DOES NOT WORK WELL WITH MOPIDY Hack from https://www.daniweb.com/software-development/python/code/260268/restart-your-python-program to support updating the settings, since mopidy is not able to do that yet Restarts the current program Note: this function does not ...
def __load(arff): """ load liac-arff to pandas DataFrame :param dict arff:arff dict created liac-arff :rtype: DataFrame :return: pandas DataFrame """ attrs = arff['attributes'] attrs_t = [] for attr in attrs: if isinstance(attr[1], list): attrs_t.append("%s@{%s}" ...
def __dump(df,relation='data',description=''): """ dump DataFrame to liac-arff :param DataFrame df: :param str relation: :param str description: :rtype: dict :return: liac-arff dict """ attrs = [] for col in df.columns: attr = col.split('@') if attr[1].count('...
def dump(df,fp): """ dump DataFrame to file :param DataFrame df: :param file fp: """ arff = __dump(df) liacarff.dump(arff,fp)
def markup_line(text, offset, marker='>>!<<'): """Insert `marker` at `offset` into `text`, and return the marked line. .. code-block:: python >>> markup_line('0\\n1234\\n56', 3) 1>>!<<234 """ begin = text.rfind('\n', 0, offset) begin += 1 end = text.find('\n', offset) ...
def tokenize_init(spec): """Initialize a tokenizer. Should only be called by the :func:`~textparser.Parser.tokenize` method in the parser. """ tokens = [Token('__SOF__', '__SOF__', 0)] re_token = '|'.join([ '(?P<{}>{})'.format(name, regex) for name, regex in spec ]) return tokens,...
def tokenize(self, text): """Tokenize given string `text`, and return a list of tokens. Raises :class:`~textparser.TokenizeError` on failure. This method should only be called by :func:`~textparser.Parser.parse()`, but may very well be overridden if the default implementation do...
def parse(self, text, token_tree=False, match_sof=False): """Parse given string `text` and return the parse tree. Raises :class:`~textparser.ParseError` on failure. Returns a parse tree of tokens if `token_tree` is ``True``. .. code-block:: python >>> MyParser().parse('Hell...
def x_at_y(self, y, reverse=False): """ Calculates inverse profile - for given y returns x such that f(x) = y If given y is not found in the self.y, then interpolation is used. By default returns first result looking from left, if reverse argument set to True, looks from ...
def width(self, level): """ Width at given level :param level: :return: """ return self.x_at_y(level, reverse=True) - self.x_at_y(level)
def normalize(self, dt, allow_cast=True): """ Normalize to 1 over [-dt, +dt] area, if allow_cast is set to True, division not in place and casting may occur. If division in place is not possible and allow_cast is False an exception is raised. >>> a = Profile([[0, 0], [1,...
def rescale(self, factor=1.0, allow_cast=True): """ Rescales self.y by given factor, if allow_cast is set to True and division in place is impossible - casting and not in place division may occur occur. If in place is impossible and allow_cast is set to False - an exception is ra...
def change_domain(self, domain): """ Creating new Curve object in memory with domain passed as a parameter. New domain must include in the original domain. Copies values from original curve and uses interpolation to calculate values for new points in domain. Calculate y ...
def rebinned(self, step=0.1, fixp=0): """ Provides effective way to compute new domain basing on step and fixp parameters. Then using change_domain() method to create new object with calculated domain and returns it. fixp doesn't have to be inside original domain. Retur...
def evaluate_at_x(self, arg, def_val=0): """ Returns Y value at arg of self. Arg can be a scalar, but also might be np.array or other iterable (like list). If domain of self is not wide enough to interpolate the value of Y, method will return def_val for those arguments i...
def subtract(self, curve2, new_obj=False): """ Method that calculates difference between 2 curves (or subclasses of curves). Domain of self must be in domain of curve2 what means min(self.x) >= min(curve2.x) and max(self.x) <= max(curve2.x). Might modify self, and can ret...
def alert(text='', title='', button='OK'): """Displays a simple message box with text and a single OK button. Returns the text of the button clicked on.""" messageBoxFunc(0, text, title, MB_OK | MB_SETFOREGROUND | MB_TOPMOST) return button
def confirm(text='', title='', buttons=['OK', 'Cancel']): """Displays a message box with OK and Cancel buttons. Number and text of buttons can be customized. Returns the text of the button clicked on.""" retVal = messageBoxFunc(0, text, title, MB_OKCANCEL | MB_ICONQUESTION | MB_SETFOREGROUND | MB_TOPMOST) i...
def subtract(curve1, curve2, def_val=0): """ Function calculates difference between curve1 and curve2 and returns new object which domain is an union of curve1 and curve2 domains Returned object is of type type(curve1) and has same metadata as curve1 object :param curve1: first curve to cal...
def medfilt(vector, window): """ Apply a window-length median filter to a 1D array vector. Should get rid of 'spike' value 15. >>> print(medfilt(np.array([1., 15., 1., 1., 1.]), 3)) [1. 1. 1. 1. 1.] The 'edge' case is a bit tricky... >>> print(medfilt(np.array([15., 1., 1., 1., 1.]), 3)) ...
def interpn(*args, **kw): """Interpolation on N-D. ai = interpn(x, y, z, ..., a, xi, yi, zi, ...) where the arrays x, y, z, ... define a rectangular grid and a.shape == (len(x), len(y), len(z), ...) are the values interpolate at xi, yi, zi, ... """ method = kw.pop('method', 'cubic') if kw: raise ValueError(...
def npinterpn(*args, **kw): """Interpolation on N-D. ai = interpn(x, y, z, ..., a, xi, yi, zi, ...) where the arrays x, y, z, ... define a rectangular grid and a.shape == (len(x), len(y), len(z), ...) are the values interpolate at xi, yi, zi, ... """ method = kw.pop('method', 'cubic') if kw: raise ValueErro...
def model_fields(model, allow_pk=False, only=None, exclude=None, field_args=None, converter=None): """ Generate a dictionary of fields for a given Peewee model. See `model_form` docstring for description of parameters. """ converter = converter or ModelConverter() field_args = ...
def model_form(model, base_class=Form, allow_pk=False, only=None, exclude=None, field_args=None, converter=None): """ Create a wtforms Form for a given Peewee model class:: from wtfpeewee.orm import model_form from myproject.myapp.models import User UserForm = model_form(...
def alert(text='', title='', button=OK_TEXT, root=None, timeout=None): """Displays a simple message box with text and a single OK button. Returns the text of the button clicked on.""" assert TKINTER_IMPORT_SUCCEEDED, 'Tkinter is required for pymsgbox' return _buttonbox(msg=text, title=title, choices=[str(bu...
def confirm(text='', title='', buttons=[OK_TEXT, CANCEL_TEXT], root=None, timeout=None): """Displays a message box with OK and Cancel buttons. Number and text of buttons can be customized. Returns the text of the button clicked on.""" assert TKINTER_IMPORT_SUCCEEDED, 'Tkinter is required for pymsgbox' retur...
def prompt(text='', title='' , default='', root=None, timeout=None): """Displays a message box with text input, and OK & Cancel buttons. Returns the text entered, or None if Cancel was clicked.""" assert TKINTER_IMPORT_SUCCEEDED, 'Tkinter is required for pymsgbox' return __fillablebox(text, title, default=d...