kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def _min(self): """Getter for the minimum series value""" return ( self.range[0] if (self.range and self.range[0] is not None) else (min(self.yvals) if self.yvals else None) )	[ "def", "_min", "(", "self", ")", ":", "return", "(", "self", ".", "range", "[", "0", "]", "if", "(", "self", ".", "range", "and", "self", ".", "range", "[", "0", "]", "is", "not", "None", ")", "else", "(", "min", "(", "self", ".", "yvals", ")...	36.333333	21.5
def multiplot(self, f, lfilter=None, plot_xy=False, **kargs): """Uses a function that returns a label and a value for this label, then plots all the values label by label. A list of matplotlib.lines.Line2D is returned. """ # Python 2 backward compatibility f = lambda_tu...	[ "def", "multiplot", "(", "self", ",", "f", ",", "lfilter", "=", "None", ",", "plot_xy", "=", "False", ",", "", "", "kargs", ")", ":", "# Python 2 backward compatibility", "f", "=", "lambda_tuple_converter", "(", "f", ")", "lfilter", "=", "lambda_tuple_conv...	32	18.282051
def create_gtk_grid(self, row_spacing=6, col_spacing=6, row_homogenous=False, col_homogenous=True): """ Function creates a Gtk Grid with spacing and homogeous tags """ grid_lang = Gtk.Grid() grid_lang.set_column_spacing(row_spacing) grid_lang.set_row_spacing(col_s...	[ "def", "create_gtk_grid", "(", "self", ",", "row_spacing", "=", "6", ",", "col_spacing", "=", "6", ",", "row_homogenous", "=", "False", ",", "col_homogenous", "=", "True", ")", ":", "grid_lang", "=", "Gtk", ".", "Grid", "(", ")", "grid_lang", ".", "set_c...	40.916667	12.75
def _patch_tcpserver(): """ Patch shutdown_request to open blocking interaction after the end of the request """ shutdown_request = TCPServer.shutdown_request def shutdown_request_patched(args, kwargs): thread = current_thread() shutdown_request(args, **kwargs) if th...	[ "def", "_patch_tcpserver", "(", ")", ":", "shutdown_request", "=", "TCPServer", ".", "shutdown_request", "def", "shutdown_request_patched", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "thread", "=", "current_thread", "(", ")", "shutdown_request", "(", ...	31.857143	16.714286
def evaluation(evaluation_id): """Show or delete an ACMG evaluation.""" evaluation_obj = store.get_evaluation(evaluation_id) controllers.evaluation(store, evaluation_obj) if request.method == 'POST': link = url_for('.variant', institute_id=evaluation_obj['institute']['_id'], ...	[ "def", "evaluation", "(", "evaluation_id", ")", ":", "evaluation_obj", "=", "store", ".", "get_evaluation", "(", "evaluation_id", ")", "controllers", ".", "evaluation", "(", "store", ",", "evaluation_obj", ")", "if", "request", ".", "method", "==", "'POST'", "...	54.615385	18.923077
def _check_and_update_params(self, required, params): """ Ensure all required parameters were passed to the API call and format them correctly. """ for r in required: if r not in params: raise PayPalError("Missing required param: %s" % r) # Up...	[ "def", "_check_and_update_params", "(", "self", ",", "required", ",", "params", ")", ":", "for", "r", "in", "required", ":", "if", "r", "not", "in", "params", ":", "raise", "PayPalError", "(", "\"Missing required param: %s\"", "%", "r", ")", "# Upper case all ...	37.636364	17.454545
def get_route(self, route_id): """ Gets specified route. Will be detail-level if owned by authenticated user; otherwise summary-level. https://strava.github.io/api/v3/routes/#retreive :param route_id: The ID of route to fetch. :type route_id: int :rtype: :clas...	[ "def", "get_route", "(", "self", ",", "route_id", ")", ":", "raw", "=", "self", ".", "protocol", ".", "get", "(", "'/routes/{id}'", ",", "id", "=", "route_id", ")", "return", "model", ".", "Route", ".", "deserialize", "(", "raw", ",", "bind_client", "=...	31.066667	20.8
def Drop(self: Iterable, n): """ [ { 'self': [1, 2, 3, 4, 5], 'n': 3, 'assert': lambda ret: list(ret) == [1, 2] } ] """ con = tuple(self) n = len(con) - n if n <= 0: yield from con else: for i, e in enumerate(con): ...	[ "def", "Drop", "(", "self", ":", "Iterable", ",", "n", ")", ":", "con", "=", "tuple", "(", "self", ")", "n", "=", "len", "(", "con", ")", "-", "n", "if", "n", "<=", "0", ":", "yield", "from", "con", "else", ":", "for", "i", ",", "e", "in", ...	19.052632	18.842105
def is_businessdate(in_date): """ checks whether the provided date is a date :param BusinessDate, int or float in_date: :return bool: """ # Note: if the data range has been created from pace_xl, then all the dates are bank dates # and here it remains to check the ...	[ "def", "is_businessdate", "(", "in_date", ")", ":", "# Note: if the data range has been created from pace_xl, then all the dates are bank dates", "# and here it remains to check the validity.", "# !!! However, if the data has been read from json string via json.load() function", "# it does not rec...	48.65	20.05
def empty_like(self, shape): """ Make an empty LabelArray with the same categories as ``self``, filled with ``self.missing_value``. """ return type(self).from_codes_and_metadata( codes=np.full( shape, self.reverse_categories[self.missin...	[ "def", "empty_like", "(", "self", ",", "shape", ")", ":", "return", "type", "(", "self", ")", ".", "from_codes_and_metadata", "(", "codes", "=", "np", ".", "full", "(", "shape", ",", "self", ".", "reverse_categories", "[", "self", ".", "missing_value", "...	37.2	15.2
def search(self, q, labels, state='open,closed', **kwargs): """Search for issues in Github. :param q: query string to search :param state: state of the issue :returns: list of issue objects :rtype: list """ search_result = self.github_request.search(q=q, state=s...	[ "def", "search", "(", "self", ",", "q", ",", "labels", ",", "state", "=", "'open,closed'", ",", "", "", "kwargs", ")", ":", "search_result", "=", "self", ".", "github_request", ".", "search", "(", "q", "=", "q", ",", "state", "=", "state", ",", "...	35.6875	15.5625
def body(self): """Yields the encoded body.""" for chunk in self.gen_chunks(self.envelope.file_open(self.name)): yield chunk for chunk in self.gen_chunks(self.data): yield chunk for chunk in self.gen_chunks(self.envelope.file_close()): yield chunk ...	[ "def", "body", "(", "self", ")", ":", "for", "chunk", "in", "self", ".", "gen_chunks", "(", "self", ".", "envelope", ".", "file_open", "(", "self", ".", "name", ")", ")", ":", "yield", "chunk", "for", "chunk", "in", "self", ".", "gen_chunks", "(", ...	36.5	16.5
def getusers(self, context, request): """/@@API/getusers: Return users belonging to specified roles Required parameters: - roles: The role of which users to return { runtime: Function running time. error: true or string(message) if error. false if no error....	[ "def", "getusers", "(", "self", ",", "context", ",", "request", ")", ":", "roles", "=", "request", ".", "get", "(", "'roles'", ",", "''", ")", "if", "len", "(", "roles", ")", "==", "0", ":", "raise", "BadRequest", "(", "\"No roles specified\"", ")", ...	35.372549	20.941176
def join_content_version(self, to_cache): """ Add the version(s) to the content to cache : internal version at first and then the template version if versioning is activated. Each version, and the content, are separated with `VERSION_SEPARATOR`. This method is called after the en...	[ "def", "join_content_version", "(", "self", ",", "to_cache", ")", ":", "parts", "=", "[", "self", ".", "INTERNAL_VERSION", "]", "if", "self", ".", "options", ".", "versioning", ":", "parts", ".", "append", "(", "force_bytes", "(", "self", ".", "version", ...	43.428571	14.142857
def _cursor(self): """Asserts that the connection is open and returns a cursor""" if self._conn is None: self._conn = sqlite3.connect(self.filename, check_same_thread=False) return self._conn.cursor()	[ "def", "_cursor", "(", "self", ")", ":", "if", "self", ".", "_conn", "is", "None", ":", "self", ".", "_conn", "=", "sqlite3", ".", "connect", "(", "self", ".", "filename", ",", "check_same_thread", "=", "False", ")", "return", "self", ".", "_conn", "...	45.333333	13
def extend(self, step): """ Adds the data from another STObject to this object. Args: step: another STObject being added after the current one in time. """ self.timesteps.extend(step.timesteps) self.masks.extend(step.masks) self.x.extend(step....	[ "def", "extend", "(", "self", ",", "step", ")", ":", "self", ".", "timesteps", ".", "extend", "(", "step", ".", "timesteps", ")", "self", ".", "masks", ".", "extend", "(", "step", ".", "masks", ")", "self", ".", "x", ".", "extend", "(", "step", "...	38.8	14.3
def to_irc(self): """ Convert to mIRC color format :return: """ ignore_re = re.compile('[\x03\x02\x1D\x1F\x16\x0F]') text = ignore_re.sub('', self.text) if self.color and self.bg_color: return '\x03%02d,%02d%s' % (self.color.to_8bit().to_irc(), ...	[ "def", "to_irc", "(", "self", ")", ":", "ignore_re", "=", "re", ".", "compile", "(", "'[\\x03\\x02\\x1D\\x1F\\x16\\x0F]'", ")", "text", "=", "ignore_re", ".", "sub", "(", "''", ",", "self", ".", "text", ")", "if", "self", ".", "color", "and", "self", "...	36.952381	14
def init_repo(path): """clone the gh-pages repo if we haven't already.""" sh("git clone %s %s"%(pages_repo, path)) here = os.getcwd() cd(path) sh('git checkout gh-pages') cd(here)	[ "def", "init_repo", "(", "path", ")", ":", "sh", "(", "\"git clone %s %s\"", "%", "(", "pages_repo", ",", "path", ")", ")", "here", "=", "os", ".", "getcwd", "(", ")", "cd", "(", "path", ")", "sh", "(", "'git checkout gh-pages'", ")", "cd", "(", "her...	28.142857	15.285714
def save_unmet(self, job): """Save a message for later submission when its dependencies are met.""" msg_id = job.msg_id self.depending[msg_id] = job # track the ids in follow or after, but not those already finished for dep_id in job.after.union(job.follow).difference(self.all_do...	[ "def", "save_unmet", "(", "self", ",", "job", ")", ":", "msg_id", "=", "job", ".", "msg_id", "self", ".", "depending", "[", "msg_id", "]", "=", "job", "# track the ids in follow or after, but not those already finished", "for", "dep_id", "in", "job", ".", "after...	49.222222	11.666667
def get(): """Returns the current version without importing pymds.""" pkgnames = find_packages() if len(pkgnames) == 0: raise ValueError("Can't find any packages") pkgname = pkgnames[0] content = open(join(pkgname, '__init__.py')).read() c = re.compile(r"__version__ = ('[^']+'\|\"[^\...	[ "def", "get", "(", ")", ":", "pkgnames", "=", "find_packages", "(", ")", "if", "len", "(", "pkgnames", ")", "==", "0", ":", "raise", "ValueError", "(", "\"Can't find any packages\"", ")", "pkgname", "=", "pkgnames", "[", "0", "]", "content", "=", "open",...	27.176471	23.058824
def p_constant_declaration(p): 'constant_declaration : STRING EQUALS static_scalar' p[0] = ast.ConstantDeclaration(p[1], p[3], lineno=p.lineno(1))	[ "def", "p_constant_declaration", "(", "p", ")", ":", "p", "[", "0", "]", "=", "ast", ".", "ConstantDeclaration", "(", "p", "[", "1", "]", ",", "p", "[", "3", "]", ",", "lineno", "=", "p", ".", "lineno", "(", "1", ")", ")" ]	50.666667	17.333333
def transformProperMotionErrors(self, phi, theta, sigMuPhiStar, sigMuTheta, rhoMuPhiMuTheta=0): """ Converts the proper motion errors from one reference system to another, including the covariance term. Equations (1.5.4) and (1.5.20) from section 1.5 in the Hipparcos Explanatory Volume 1 are use...	[ "def", "transformProperMotionErrors", "(", "self", ",", "phi", ",", "theta", ",", "sigMuPhiStar", ",", "sigMuTheta", ",", "rhoMuPhiMuTheta", "=", "0", ")", ":", "return", "self", ".", "transformSkyCoordinateErrors", "(", "phi", ",", "theta", ",", "sigMuPhiStar",...	48.933333	35.133333
def read_int(self, lpBaseAddress): """ Reads a signed integer from the memory of the process. @see: L{peek_int} @type lpBaseAddress: int @param lpBaseAddress: Memory address to begin reading. @rtype: int @return: Integer value read from the process memory. ...	[ "def", "read_int", "(", "self", ",", "lpBaseAddress", ")", ":", "return", "self", ".", "__read_c_type", "(", "lpBaseAddress", ",", "compat", ".", "b", "(", "'@l'", ")", ",", "ctypes", ".", "c_int", ")" ]	30.466667	22.066667
def _setup_stats_total(self, redis_conn): ''' Sets up the total stats collectors @param redis_conn: the redis connection ''' self.stats_dict['total'] = {} self.stats_dict['fail'] = {} temp_key1 = 'stats:kafka-monitor:total' temp_key2 = 'stats:kafka-monito...	[ "def", "_setup_stats_total", "(", "self", ",", "redis_conn", ")", ":", "self", ".", "stats_dict", "[", "'total'", "]", "=", "{", "}", "self", ".", "stats_dict", "[", "'fail'", "]", "=", "{", "}", "temp_key1", "=", "'stats:kafka-monitor:total'", "temp_key2", ...	53.682927	20.02439
def next_sibling(self): """ Returns the next sibling of the current node. The next sibling is searched in the parent node if we are not considering a top-level node. Otherwise it is searched inside the list of nodes (which should be sorted by tree ID) that is associated with the conside...	[ "def", "next_sibling", "(", "self", ")", ":", "if", "self", ".", "parent", ":", "nodes", "=", "self", ".", "parent", ".", "children", "index", "=", "nodes", ".", "index", "(", "self", ")", "sibling", "=", "nodes", "[", "index", "+", "1", "]", "if",...	41.842105	20.789474
def template(page=None, layout=None, **kwargs): """ Decorator to change the view template and layout. It works on both View class and view methods on class only $layout is applied, everything else will be passed to the kwargs Using as first argument, it will be the layout. :fi...	[ "def", "template", "(", "page", "=", "None", ",", "layout", "=", "None", ",", "", "", "kwargs", ")", ":", "pkey", "=", "\"_template_extends__\"", "def", "decorator", "(", "f", ")", ":", "if", "inspect", ".", "isclass", "(", "f", ")", ":", "layout_"...	33.09375	16.09375
def _checkBuildDependencies(): compiler = distutils.ccompiler.new_compiler() """check if function without parameters from stdlib can be called There should be better way to check, if C compiler is installed """ if not compiler.has_function('rand', includes=['stdlib.h']): print("It seems like...	[ "def", "_checkBuildDependencies", "(", ")", ":", "compiler", "=", "distutils", ".", "ccompiler", ".", "new_compiler", "(", ")", "if", "not", "compiler", ".", "has_function", "(", "'rand'", ",", "includes", "=", "[", "'stdlib.h'", "]", ")", ":", "print", "(...	56.285714	28.685714
def create_template(self): """Create template (main function called by Stacker).""" template = self.template variables = self.get_variables() template.add_version('2010-09-09') template.add_description('Static Website - Bucket and Distribution') # Conditions temp...	[ "def", "create_template", "(", "self", ")", ":", "template", "=", "self", ".", "template", "variables", "=", "self", ".", "get_variables", "(", ")", "template", ".", "add_version", "(", "'2010-09-09'", ")", "template", ".", "add_description", "(", "'Static Web...	41.843511	19.041985
def show(source): """Merely returns the metadata for the provided archive. """ if is_verbose(): logger.info('Retrieving Metadata for: %s', source) processed_source = get_source(source) metadata = _get_metadata(processed_source) shutil.rmtree(processed_source) return metadata	[ "def", "show", "(", "source", ")", ":", "if", "is_verbose", "(", ")", ":", "logger", ".", "info", "(", "'Retrieving Metadata for: %s'", ",", "source", ")", "processed_source", "=", "get_source", "(", "source", ")", "metadata", "=", "_get_metadata", "(", "pro...	33.666667	10.444444
def p_instance_bodylist(self, p): 'instance_bodylist : instance_bodylist COMMA instance_body' p[0] = p[1] + (p[3],) p.set_lineno(0, p.lineno(1))	[ "def", "p_instance_bodylist", "(", "self", ",", "p", ")", ":", "p", "[", "0", "]", "=", "p", "[", "1", "]", "+", "(", "p", "[", "3", "]", ",", ")", "p", ".", "set_lineno", "(", "0", ",", "p", ".", "lineno", "(", "1", ")", ")" ]	41.25	12.25
def _process_collection(self, collection_id, label, page): """ This function will process the data supplied internally about the repository from Coriell. Triples: Repository a ERO:collection rdf:label Literal(label) foaf:page Literal(page) :p...	[ "def", "_process_collection", "(", "self", ",", "collection_id", ",", "label", ",", "page", ")", ":", "# ############# BUILD THE CELL LINE REPOSITORY #############", "for", "graph", "in", "[", "self", ".", "graph", ",", "self", ".", "testgraph", "]", ":", "#...	32.344828	16.758621
def _set_params_callback(self, **params): """Special handling for setting params on callbacks.""" # model after sklearn.utils._BaseCompostion._set_params # 1. All steps if 'callbacks' in params: setattr(self, 'callbacks', params.pop('callbacks')) # 2. Step replacemen...	[ "def", "_set_params_callback", "(", "self", ",", "", "", "params", ")", ":", "# model after sklearn.utils._BaseCompostion._set_params", "# 1. All steps", "if", "'callbacks'", "in", "params", ":", "setattr", "(", "self", ",", "'callbacks'", ",", "params", ".", "pop...	39.071429	15.25
def _convertNonNumericData(self, spatialOutput, temporalOutput, output): """ Converts all of the non-numeric fields from spatialOutput and temporalOutput into their scalar equivalents and records them in the output dictionary. :param spatialOutput: The results of topDownCompute() for the spatial input....	[ "def", "_convertNonNumericData", "(", "self", ",", "spatialOutput", ",", "temporalOutput", ",", "output", ")", ":", "encoders", "=", "self", ".", "encoder", ".", "getEncoderList", "(", ")", "types", "=", "self", ".", "encoder", ".", "getDecoderOutputFieldTypes",...	47.259259	21.62963
def p_expression_eq(self, p): 'expression : expression EQ expression' p[0] = Eq(p[1], p[3], lineno=p.lineno(1)) p.set_lineno(0, p.lineno(1))	[ "def", "p_expression_eq", "(", "self", ",", "p", ")", ":", "p", "[", "0", "]", "=", "Eq", "(", "p", "[", "1", "]", ",", "p", "[", "3", "]", ",", "lineno", "=", "p", ".", "lineno", "(", "1", ")", ")", "p", ".", "set_lineno", "(", "0", ",",...	40.25	7.75
def get_float(strings: Sequence[str], prefix: str, ignoreleadingcolon: bool = False, precedingline: str = "") -> Optional[float]: """ Fetches a float parameter via :func:`get_string`. """ return get_float_raw(get_string(strings, prefix, ...	[ "def", "get_float", "(", "strings", ":", "Sequence", "[", "str", "]", ",", "prefix", ":", "str", ",", "ignoreleadingcolon", ":", "bool", "=", "False", ",", "precedingline", ":", "str", "=", "\"\"", ")", "->", "Optional", "[", "float", "]", ":", "return...	42.6	12.6
def max_insertion(seqs, gene, domain): """ length of largest insertion """ seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain] lengths = [] for seq in seqs: for ins in seq: lengths.append(int(ins[2])) if lengths == []: retu...	[ "def", "max_insertion", "(", "seqs", ",", "gene", ",", "domain", ")", ":", "seqs", "=", "[", "i", "[", "2", "]", "for", "i", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", "if", "i", "[", "2", "]", "!=", "[", "]", "and", "i", "[",...	28.333333	15.5
def get_profile_info(self, obj): """Returns the info for a Profile """ info = self.get_base_info(obj) info.update({}) return info	[ "def", "get_profile_info", "(", "self", ",", "obj", ")", ":", "info", "=", "self", ".", "get_base_info", "(", "obj", ")", "info", ".", "update", "(", "{", "}", ")", "return", "info" ]	27.333333	8
def bulleted_list(items, indent=0, bullet_type='-'): """Format a bulleted list of values. Parameters ---------- items : sequence The items to make a list. indent : int, optional The number of spaces to add before each bullet. bullet_type : str, optional The bullet type t...	[ "def", "bulleted_list", "(", "items", ",", "indent", "=", "0", ",", "bullet_type", "=", "'-'", ")", ":", "format_string", "=", "' '", "*", "indent", "+", "bullet_type", "+", "' {}'", "return", "\"\\n\"", ".", "join", "(", "map", "(", "format_string", "."...	27.526316	17.157895
def SetScrollPercent(self, horizontalPercent: float, verticalPercent: float, waitTime: float = OPERATION_WAIT_TIME) -> bool: """ Call IUIAutomationScrollPattern::SetScrollPercent. Set the horizontal and vertical scroll positions as a percentage of the total content area within the UI Automation ...	[ "def", "SetScrollPercent", "(", "self", ",", "horizontalPercent", ":", "float", ",", "verticalPercent", ":", "float", ",", "waitTime", ":", "float", "=", "OPERATION_WAIT_TIME", ")", "->", "bool", ":", "ret", "=", "self", ".", "pattern", ".", "SetScrollPercent"...	70.307692	42.461538
def checkPrediction2(possibleOutcome, predictedOutcome): """ :param possibleOutcome: list of all possible outcomes :param predictedOutcome: list of all predicted outomes :return missN: number of misses (a possible outcome not predicted) fpN: number of false positives (a predicted outcome is not poss...	[ "def", "checkPrediction2", "(", "possibleOutcome", ",", "predictedOutcome", ")", ":", "missN", "=", "0", "for", "i", "in", "xrange", "(", "len", "(", "possibleOutcome", ")", ")", ":", "miss", "=", "1", "for", "j", "in", "xrange", "(", "len", "(", "pred...	30.25	19.583333
def timing_decorator(func): """Prints the time func takes to execute.""" @functools.wraps(func) def wrapper(args, *kwargs): """ Wrapper for printing execution time. Parameters ---------- print_time: bool, optional whether or not to print time function t...	[ "def", "timing_decorator", "(", "func", ")", ":", "@", "functools", ".", "wraps", "(", "func", ")", "def", "wrapper", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "\"\"\"\n Wrapper for printing execution time.\n\n Parameters\n ----------\n...	30.869565	11.478261
def comments_between_tokens(token1, token2): """Find all comments between two tokens""" if token2 is None: buf = token1.end_mark.buffer[token1.end_mark.pointer:] elif (token1.end_mark.line == token2.start_mark.line and not isinstance(token1, yaml.StreamStartToken) and not isinsta...	[ "def", "comments_between_tokens", "(", "token1", ",", "token2", ")", ":", "if", "token2", "is", "None", ":", "buf", "=", "token1", ".", "end_mark", ".", "buffer", "[", "token1", ".", "end_mark", ".", "pointer", ":", "]", "elif", "(", "token1", ".", "en...	34.533333	18.333333
def simple_transaction(self, from_address, to, op_return=None, min_confirmations=6): """ Args: from_address (str): bitcoin address originating the transaction to: tuple of ``(to_address, amount)`` or list of tuples ``[(to_addr1, amount1), (to_addr2, amount2)]``. Amounts are in *s...	[ "def", "simple_transaction", "(", "self", ",", "from_address", ",", "to", ",", "op_return", "=", "None", ",", "min_confirmations", "=", "6", ")", ":", "to", "=", "[", "to", "]", "if", "not", "isinstance", "(", "to", ",", "list", ")", "else", "to", "a...	42.535714	28.75
def pull_byte(self, stack_pointer): """ pulled a byte from stack """ addr = stack_pointer.value byte = self.memory.read_byte(addr) # log.info( # log.error( # "%x\|\tpull $%x from %s stack at $%x\t\|%s", # self.last_op_address, byte, stack_pointer.name, addr, # ...	[ "def", "pull_byte", "(", "self", ",", "stack_pointer", ")", ":", "addr", "=", "stack_pointer", ".", "value", "byte", "=", "self", ".", "memory", ".", "read_byte", "(", "addr", ")", "# log.info(", "# log.error(", "# \"%x\|\\tpull $%x from %s ...	32.333333	17.666667
def anomaly(self, test_data, per_feature=False): """ Obtain the reconstruction error for the input test_data. :param H2OFrame test_data: The dataset upon which the reconstruction error is computed. :param bool per_feature: Whether to return the square reconstruction error per feature. ...	[ "def", "anomaly", "(", "self", ",", "test_data", ",", "per_feature", "=", "False", ")", ":", "if", "test_data", "is", "None", "or", "test_data", ".", "nrow", "==", "0", ":", "raise", "ValueError", "(", "\"Must specify test data\"", ")", "j", "=", "h2o", ...	57.5	33.071429
def input_validation(group_idx, a, size=None, order='C', axis=None, ravel_group_idx=True, check_bounds=True): """ Do some fairly extensive checking of group_idx and a, trying to give the user as much help as possible with what is wrong. Also, convert ndim-indexing to 1d indexing. ""...	[ "def", "input_validation", "(", "group_idx", ",", "a", ",", "size", "=", "None", ",", "order", "=", "'C'", ",", "axis", "=", "None", ",", "ravel_group_idx", "=", "True", ",", "check_bounds", "=", "True", ")", ":", "if", "not", "isinstance", "(", "a", ...	45.391304	19.478261
def checksum(thing): """ Get the checksum of a calculation from the calculation ID (if already done) or from the job.ini/job.zip file (if not done yet). If `thing` is a source model logic tree file, get the checksum of the model by ignoring the job.ini, the gmpe logic tree file and possibly other fi...	[ "def", "checksum", "(", "thing", ")", ":", "try", ":", "job_id", "=", "int", "(", "thing", ")", "job_file", "=", "None", "except", "ValueError", ":", "job_id", "=", "None", "job_file", "=", "thing", "if", "not", "os", ".", "path", ".", "exists", "(",...	38.84	19
def _extract_multiple_hits(self, hits, reads_path, output_path): ''' splits out regions of a read that hit the HMM. For example when two of same gene are identified within the same contig, The regions mapping to the HMM will be split out and written out to a new file as a new record. ...	[ "def", "_extract_multiple_hits", "(", "self", ",", "hits", ",", "reads_path", ",", "output_path", ")", ":", "complement_information", "=", "{", "}", "try", ":", "reads", "=", "SeqIO", ".", "to_dict", "(", "SeqIO", ".", "parse", "(", "reads_path", ",", "\"f...	48.561404	31.508772
def run(self, inputcode, iterations=None, run_forever=False, frame_limiter=False, verbose=False, break_on_error=False): ''' Executes the contents of a Nodebox/Shoebot script in current surface's context. :param inputcode: Path to shoebot source or string containing source ...	[ "def", "run", "(", "self", ",", "inputcode", ",", "iterations", "=", "None", ",", "run_forever", "=", "False", ",", "frame_limiter", "=", "False", ",", "verbose", "=", "False", ",", "break_on_error", "=", "False", ")", ":", "source", "=", "None", "filena...	41.230769	22.791209
def update_issue_remote_link_by_id(self, issue_key, link_id, url, title, global_id=None, relationship=None): """ Update existing Remote Link on Issue :param issue_key: str :param link_id: str :param url: str :param title: str :param global_id: str, OPTIONAL: ...	[ "def", "update_issue_remote_link_by_id", "(", "self", ",", "issue_key", ",", "link_id", ",", "url", ",", "title", ",", "global_id", "=", "None", ",", "relationship", "=", "None", ")", ":", "data", "=", "{", "'object'", ":", "{", "'url'", ":", "url", ",",...	41.333333	18.333333
def toList(self): """ Return a list with the DataFrame data. """ if self.getNumCols() > 1: return [ tuple(self.getRowByIndex(i)) for i in range(self.getNumRows()) ] else: return [ self.getRowByInd...	[ "def", "toList", "(", "self", ")", ":", "if", "self", ".", "getNumCols", "(", ")", ">", "1", ":", "return", "[", "tuple", "(", "self", ".", "getRowByIndex", "(", "i", ")", ")", "for", "i", "in", "range", "(", "self", ".", "getNumRows", "(", ")", ...	27.071429	12.785714
def set_clock_divisor(self, clock_divisor): """ Sets the clock divisor value. The higher is the value, the faster is the clock in the virtual machine. The default is 4, but it is often required to adjust it. :param clock_divisor: clock divisor value (integer) """ yield ...	[ "def", "set_clock_divisor", "(", "self", ",", "clock_divisor", ")", ":", "yield", "from", "self", ".", "_hypervisor", ".", "send", "(", "'vm set_clock_divisor \"{name}\" {clock}'", ".", "format", "(", "name", "=", "self", ".", "_name", ",", "clock", "=", "cloc...	69	44.571429
def get_extname(self): """ Get the name for this extension, can be an empty string """ name = self._info['extname'] if name.strip() == '': name = self._info['hduname'] return name.strip()	[ "def", "get_extname", "(", "self", ")", ":", "name", "=", "self", ".", "_info", "[", "'extname'", "]", "if", "name", ".", "strip", "(", ")", "==", "''", ":", "name", "=", "self", ".", "_info", "[", "'hduname'", "]", "return", "name", ".", "strip", ...	30	8.5
def _initialize(self, runtime): """Common initializer for OsidManager and OsidProxyManager""" if runtime is None: raise NullArgument() if self._my_runtime is not None: raise IllegalState('this manager has already been initialized.') self._my_runtime = runtime ...	[ "def", "_initialize", "(", "self", ",", "runtime", ")", ":", "if", "runtime", "is", "None", ":", "raise", "NullArgument", "(", ")", "if", "self", ".", "_my_runtime", "is", "not", "None", ":", "raise", "IllegalState", "(", "'this manager has already been initia...	46.119048	26.047619
def cosi_pdf(z,k=1): """Equation (11) of Morton & Winn (2014) """ return 2k/(np.pinp.sinh(k)) * quad(cosi_integrand,z,1,args=(k,z))[0]	[ "def", "cosi_pdf", "(", "z", ",", "k", "=", "1", ")", ":", "return", "2", "", "k", "/", "(", "np", ".", "pi", "", "np", ".", "sinh", "(", "k", ")", ")", "*", "quad", "(", "cosi_integrand", ",", "z", ",", "1", ",", "args", "=", "(", "k",...	36.25	13.5
def load_factors(): """Load risk factor returns. Factors ------- Symbol Description Source ------ ---------- ------ MKT French ...	[ "def", "load_factors", "(", ")", ":", "# TODO: factors elegible for addition\r", "# VIIX, VIIZ, XIV, ZIV, CRP (AQR)\r", "# http://www.cboe.com/micro/buywrite/monthendpricehistory.xls ends 2016\r", "# could use:\r", "# http://www.cboe.com/publish/scheduledtask/mktdata/datahouse/putdailypric...	37.684211	23.20614
def register_plugin(self, plugin): """Registers a plugin and commands with the dispatcher for push()""" self.log.info("Registering plugin %s", type(plugin).__name__) self._register_commands(plugin) plugin.on_load()	[ "def", "register_plugin", "(", "self", ",", "plugin", ")", ":", "self", ".", "log", ".", "info", "(", "\"Registering plugin %s\"", ",", "type", "(", "plugin", ")", ".", "__name__", ")", "self", ".", "_register_commands", "(", "plugin", ")", "plugin", ".", ...	48.4	10.4
def ldcoeffs(teff,logg=4.5,feh=0): """ Returns limb-darkening coefficients in Kepler band. """ teffs = np.atleast_1d(teff) loggs = np.atleast_1d(logg) Tmin,Tmax = (LDPOINTS[:,0].min(),LDPOINTS[:,0].max()) gmin,gmax = (LDPOINTS[:,1].min(),LDPOINTS[:,1].max()) teffs[(teffs < Tmin)] = Tmi...	[ "def", "ldcoeffs", "(", "teff", ",", "logg", "=", "4.5", ",", "feh", "=", "0", ")", ":", "teffs", "=", "np", ".", "atleast_1d", "(", "teff", ")", "loggs", "=", "np", ".", "atleast_1d", "(", "logg", ")", "Tmin", ",", "Tmax", "=", "(", "LDPOINTS", ...	29.058824	13.882353
def model(x_train, y_train, x_test, y_test): """ Model providing function: Create Keras model with double curly brackets dropped-in as needed. Return value has to be a valid python dictionary with two customary keys: - loss: Specify a numeric evaluation metric to be minimized - status: ...	[ "def", "model", "(", "x_train", ",", "y_train", ",", "x_test", ",", "y_test", ")", ":", "model", "=", "Sequential", "(", ")", "model", ".", "add", "(", "Dense", "(", "512", ",", "input_shape", "=", "(", "784", ",", ")", ")", ")", "model", ".", "a...	38.952381	19.47619
def _error(self, request, status, headers={}, prefix_template_path=False, **kwargs): """ Convenience method to render an error response. The template is inferred from the status code. :param request: A django.http.HttpRequest instance. :param status: An integer describing the HTTP statu...	[ "def", "_error", "(", "self", ",", "request", ",", "status", ",", "headers", "=", "{", "}", ",", "prefix_template_path", "=", "False", ",", "", "", "kwargs", ")", ":", "return", "self", ".", "_render", "(", "request", "=", "request", ",", "template",...	42.565217	27
def human(self): """Human-readable timestamp.""" # get timezone offset delta_sec = time.timezone m, s = divmod(delta_sec, 60) h, m = divmod(m, 60) # create output format_string = "%Y-%m-%d %H:%M:%S" out = self.datetime.strftime(format_string) retur...	[ "def", "human", "(", "self", ")", ":", "# get timezone offset", "delta_sec", "=", "time", ".", "timezone", "m", ",", "s", "=", "divmod", "(", "delta_sec", ",", "60", ")", "h", ",", "m", "=", "divmod", "(", "m", ",", "60", ")", "# create output", "for...	31.6	11.1
def send(self, change): """send the given policy change""" self.buf.append(change) if len(self.buf) % self.BUF_SIZE == 0: self.flush()	[ "def", "send", "(", "self", ",", "change", ")", ":", "self", ".", "buf", ".", "append", "(", "change", ")", "if", "len", "(", "self", ".", "buf", ")", "%", "self", ".", "BUF_SIZE", "==", "0", ":", "self", ".", "flush", "(", ")" ]	33.2	9.6
def node_hist_fig( node_color_distribution, title="Graph Node Distribution", width=400, height=300, top=60, left=25, bottom=60, right=25, bgcolor="rgb(240,240,240)", y_gridcolor="white", ): """Define the plotly plot representing the node histogram Param...	[ "def", "node_hist_fig", "(", "node_color_distribution", ",", "title", "=", "\"Graph Node Distribution\"", ",", "width", "=", "400", ",", "height", "=", "300", ",", "top", "=", "60", ",", "left", "=", "25", ",", "bottom", "=", "60", ",", "right", "=", "25...	30.358491	24.433962
def create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None): """ Adds a new table to the network. :param keyColumn (string, optional): Specifies the name of a column in the table :param keyColumnType (string, optional): The syntactical type of the value ...	[ "def", "create_table", "(", "self", ",", "keyColumn", "=", "None", ",", "keyColumnType", "=", "None", ",", "title", "=", "None", ",", "verbose", "=", "None", ")", ":", "PARAMS", "=", "set_param", "(", "[", "'keyColumn'", ",", "'keyColumnType'", ",", "'ti...	41.529412	25.764706
def _get_contexts_for_squash(self, batch_signature): """Starting with the batch referenced by batch_signature, iterate back through the batches and for each valid batch collect the context_id. At the end remove contexts for txns that are other txn's predecessors. Args: batch...	[ "def", "_get_contexts_for_squash", "(", "self", ",", "batch_signature", ")", ":", "batch", "=", "self", ".", "_batches_by_id", "[", "batch_signature", "]", ".", "batch", "index", "=", "self", ".", "_batches", ".", "index", "(", "batch", ")", "contexts", "=",...	40.6	17.885714
def path_and_line(req): """Return the path and line number of the file from which an InstallRequirement came. """ path, line = (re.match(r'-r (.*) \(line (\d+)\)$', req.comes_from).groups()) return path, int(line)	[ "def", "path_and_line", "(", "req", ")", ":", "path", ",", "line", "=", "(", "re", ".", "match", "(", "r'-r (.*) \\(line (\\d+)\\)$'", ",", "req", ".", "comes_from", ")", ".", "groups", "(", ")", ")", "return", "path", ",", "int", "(", "line", ")" ]	31.75	13.625
def build(self, tool): """build the project""" tools = self._validate_tools(tool) if tools == -1: return -1 result = 0 for build_tool in tools: builder = ToolsSupported().get_tool(build_tool) # None is an error if builder is None...	[ "def", "build", "(", "self", ",", "tool", ")", ":", "tools", "=", "self", ".", "_validate_tools", "(", "tool", ")", "if", "tools", "==", "-", "1", ":", "return", "-", "1", "result", "=", "0", "for", "build_tool", "in", "tools", ":", "builder", "=",...	31.478261	20.043478
def from_dict(data, ctx): """ Instantiate a new TradeClientExtensionsModifyTransaction from a dict (generally from loading a JSON response). The data used to instantiate the TradeClientExtensionsModifyTransaction is a shallow copy of the dict passed in, with any complex child typ...	[ "def", "from_dict", "(", "data", ",", "ctx", ")", ":", "data", "=", "data", ".", "copy", "(", ")", "if", "data", ".", "get", "(", "'tradeClientExtensionsModify'", ")", "is", "not", "None", ":", "data", "[", "'tradeClientExtensionsModify'", "]", "=", "ctx...	38.888889	23.222222
def audit_1_4(self): """1.4 Ensure access keys are rotated every 90 days or less (Scored)""" for row in self.credential_report: for access_key in "1", "2": if json.loads(row["access_key_{}_active".format(access_key)]): last_rotated = row["access_key_{}_las...	[ "def", "audit_1_4", "(", "self", ")", ":", "for", "row", "in", "self", ".", "credential_report", ":", "for", "access_key", "in", "\"1\"", ",", "\"2\"", ":", "if", "json", ".", "loads", "(", "row", "[", "\"access_key_{}_active\"", ".", "format", "(", "acc...	68.333333	28.666667
def find_modules_with_decorators(path,decorator_module,decorator_name): ''' Finds all the modules decorated with the specified decorator in the path, file or module specified. Args : path : All modules in the directory and its sub-directories will be scanned. decorato...	[ "def", "find_modules_with_decorators", "(", "path", ",", "decorator_module", ",", "decorator_name", ")", ":", "modules_paths", "=", "[", "]", "#If a path to a module file", "if", "path", "[", "-", "3", ":", "]", "==", "'.py'", ":", "modules_paths", ".", "append"...	41.5	30.1
def format_to_http_prompt(context, excluded_options=None): """Format a Context object to HTTP Prompt commands.""" cmds = _extract_httpie_options(context, quote=True, join_key_value=True, excluded_keys=excluded_options) cmds.append('cd ' + smart_quote(context.url)) cmds...	[ "def", "format_to_http_prompt", "(", "context", ",", "excluded_options", "=", "None", ")", ":", "cmds", "=", "_extract_httpie_options", "(", "context", ",", "quote", "=", "True", ",", "join_key_value", "=", "True", ",", "excluded_keys", "=", "excluded_options", ...	57.428571	16.857143
def env_updated(cls, app, env): """Abort Sphinx after initializing config and discovering all pages to build. :param sphinx.application.Sphinx app: Sphinx application object. :param sphinx.environment.BuildEnvironment env: Sphinx build environment. """ if cls.ABORT_AFTER_READ: ...	[ "def", "env_updated", "(", "cls", ",", "app", ",", "env", ")", ":", "if", "cls", ".", "ABORT_AFTER_READ", ":", "config", "=", "{", "n", ":", "getattr", "(", "app", ".", "config", ",", "n", ")", "for", "n", "in", "(", "a", "for", "a", "in", "dir...	51.833333	22.833333
def send_packed_command(self, command): "Send an already packed command to the Redis server" if not self._sock: self.connect() try: if isinstance(command, str): command = [command] for item in command: self._sock.sendall(item) ...	[ "def", "send_packed_command", "(", "self", ",", "command", ")", ":", "if", "not", "self", ".", "_sock", ":", "self", ".", "connect", "(", ")", "try", ":", "if", "isinstance", "(", "command", ",", "str", ")", ":", "command", "=", "[", "command", "]", ...	35.44	12.24
def pipe_urlinput(context=None, _INPUT=None, conf=None, **kwargs): """An input that prompts the user for a url and yields it forever. Not loopable. Parameters ---------- context : pipe2py.Context object _INPUT : unused conf : { 'name': {'value': 'parameter name'}, 'prompt': ...	[ "def", "pipe_urlinput", "(", "context", "=", "None", ",", "_INPUT", "=", "None", ",", "conf", "=", "None", ",", "", "", "kwargs", ")", ":", "value", "=", "utils", ".", "get_input", "(", "context", ",", "conf", ")", "value", "=", "utils", ".", "ur...	24.208333	19.166667
def excel_to_html(path, sheetname='Sheet1', css_classes='', \ caption='', details=[], row_headers=False, merge=False): """ Convert an excel spreadsheet to an html table. This function supports the conversion of merged cells. It can be used in code or run from the command-line. If passed the co...	[ "def", "excel_to_html", "(", "path", ",", "sheetname", "=", "'Sheet1'", ",", "css_classes", "=", "''", ",", "caption", "=", "''", ",", "details", "=", "[", "]", ",", "row_headers", "=", "False", ",", "merge", "=", "False", ")", ":", "def", "get_data_on...	33.608142	17.709924
def get_aggregation_propensity(self, seq, outdir, cutoff_v=5, cutoff_n=5, run_amylmuts=False): """Run the AMYLPRED2 web server for a protein sequence and get the consensus result for aggregation propensity. Args: seq (str, Seq, SeqRecord): Amino acid sequence outdir (str): Direc...	[ "def", "get_aggregation_propensity", "(", "self", ",", "seq", ",", "outdir", ",", "cutoff_v", "=", "5", ",", "cutoff_n", "=", "5", ",", "run_amylmuts", "=", "False", ")", ":", "seq", "=", "ssbio", ".", "protein", ".", "sequence", ".", "utils", ".", "ca...	55.304348	39.826087
def create(self, email, phone, country_code=1, send_install_link_via_sms=False): """ sends request to create new user. :param string email: :param string phone: :param string country_code: :param bool send_install_link_via_sms: :return: """ data = ...	[ "def", "create", "(", "self", ",", "email", ",", "phone", ",", "country_code", "=", "1", ",", "send_install_link_via_sms", "=", "False", ")", ":", "data", "=", "{", "\"user\"", ":", "{", "\"email\"", ":", "email", ",", "\"cellphone\"", ":", "phone", ",",...	28.272727	17.818182
def build_module(self, module, loglevel=logging.DEBUG): """Build passed-in module. """ shutit_global.shutit_global_object.yield_to_draw() cfg = self.cfg self.log('Building ShutIt module: ' + module.module_id + ' with run order: ' + str(module.run_order), level=logging.INFO) self.build['report'] = (self.buil...	[ "def", "build_module", "(", "self", ",", "module", ",", "loglevel", "=", "logging", ".", "DEBUG", ")", ":", "shutit_global", ".", "shutit_global_object", ".", "yield_to_draw", "(", ")", "cfg", "=", "self", ".", "cfg", "self", ".", "log", "(", "'Building Sh...	87	53.194444
def temporal_from_rdf(period_of_time): '''Failsafe parsing of a temporal coverage''' try: if isinstance(period_of_time, Literal): return temporal_from_literal(str(period_of_time)) elif isinstance(period_of_time, RdfResource): return temporal_from_resource(period_of_time) ...	[ "def", "temporal_from_rdf", "(", "period_of_time", ")", ":", "try", ":", "if", "isinstance", "(", "period_of_time", ",", "Literal", ")", ":", "return", "temporal_from_literal", "(", "str", "(", "period_of_time", ")", ")", "elif", "isinstance", "(", "period_of_ti...	50.25	19.083333
def dragDip(self, (x0, y0), (x1, y1), duration, steps=1, orientation=-1): """ Sends drag event in DIP (actually it's using C{input swipe} command. @param (x0, y0): starting point in DIP @param (x1, y1): ending point in DIP @param duration: duration of the event in ms @pa...	[ "def", "dragDip", "(", "self", ",", "(", "x0", ",", "y0", ")", ",", "(", "x1", ",", "y1", ")", ",", "duration", ",", "steps", "=", "1", ",", "orientation", "=", "-", "1", ")", ":", "self", ".", "__checkTransport", "(", ")", "if", "orientation", ...	39.315789	19.210526
def valid_lock(self): """ See if the lock exists and is left over from an old process. """ lock_pid = self.get_lock_pid() # If we're unable to get lock_pid if lock_pid is None: return False # this is our process if self._pid == lock_pid: ...	[ "def", "valid_lock", "(", "self", ")", ":", "lock_pid", "=", "self", ".", "get_lock_pid", "(", ")", "# If we're unable to get lock_pid", "if", "lock_pid", "is", "None", ":", "return", "False", "# this is our process", "if", "self", ".", "_pid", "==", "lock_pid",...	22.04	17.96
def get_indic_syllabic_category_property(value, is_bytes=False): """Get `INDIC SYLLABIC CATEGORY` property.""" obj = unidata.ascii_indic_syllabic_category if is_bytes else unidata.unicode_indic_syllabic_category if value.startswith('^'): negated = value[1:] value = '^' + unidata.unicode_al...	[ "def", "get_indic_syllabic_category_property", "(", "value", ",", "is_bytes", "=", "False", ")", ":", "obj", "=", "unidata", ".", "ascii_indic_syllabic_category", "if", "is_bytes", "else", "unidata", ".", "unicode_indic_syllabic_category", "if", "value", ".", "startsw...	39.416667	31
def save(self, filething=None): """Save changes to a file. If no filename is given, the one most recently loaded is used. Tags are always written at the end of the file, and include a header and a footer. """ fileobj = filething.fileobj data = _APEv2Data(fileo...	[ "def", "save", "(", "self", ",", "filething", "=", "None", ")", ":", "fileobj", "=", "filething", ".", "fileobj", "data", "=", "_APEv2Data", "(", "fileobj", ")", "if", "data", ".", "is_at_start", ":", "delete_bytes", "(", "fileobj", ",", "data", ".", "...	32.830508	17.355932
def get_db_prep_save(self, value, connection=None): """ Returns field's value prepared for saving into a database. """ ## convert to settings.TIME_ZONE if value is not None: if value.tzinfo is None: value = default_tz.localize(value) else: ...	[ "def", "get_db_prep_save", "(", "self", ",", "value", ",", "connection", "=", "None", ")", ":", "## convert to settings.TIME_ZONE", "if", "value", "is", "not", "None", ":", "if", "value", ".", "tzinfo", "is", "None", ":", "value", "=", "default_tz", ".", "...	41.818182	14
def gen_radio_list(sig_dic): ''' For generating List view HTML file for RADIO. for each item. ''' view_zuoxiang = '''<span class="iga_pd_val">''' dic_tmp = sig_dic['dic'] for key in dic_tmp.keys(): tmp_str = '''{{% if postinfo.extinfo['{0}'][0] == "{1}" %}} {2} {{% end %}} '...	[ "def", "gen_radio_list", "(", "sig_dic", ")", ":", "view_zuoxiang", "=", "'''<span class=\"iga_pd_val\">'''", "dic_tmp", "=", "sig_dic", "[", "'dic'", "]", "for", "key", "in", "dic_tmp", ".", "keys", "(", ")", ":", "tmp_str", "=", "'''{{% if postinfo.extinfo['{0}'...	29.533333	20.466667
def check_eigen_solver(eigen_solver, solver_kwds, size=None, nvec=None): """Check that the selected eigensolver is valid Parameters ---------- eigen_solver : string string value to validate size, nvec : int (optional) if both provided, use the specified problem size and number of ve...	[ "def", "check_eigen_solver", "(", "eigen_solver", ",", "solver_kwds", ",", "size", "=", "None", ",", "nvec", "=", "None", ")", ":", "if", "eigen_solver", "in", "BAD_EIGEN_SOLVERS", ":", "raise", "ValueError", "(", "BAD_EIGEN_SOLVERS", "[", "eigen_solver", "]", ...	37.422222	17.6
def _check_stringify_year_column(self, column_index): ''' Same as _check_stringify_year_row but for columns. ''' table_column = TableTranspose(self.table)[column_index] # State trackers prior_year = None for row_index in range(self.start[0]+1, self.end[0]): ...	[ "def", "_check_stringify_year_column", "(", "self", ",", "column_index", ")", ":", "table_column", "=", "TableTranspose", "(", "self", ".", "table", ")", "[", "column_index", "]", "# State trackers", "prior_year", "=", "None", "for", "row_index", "in", "range", ...	39.352941	18.058824
def negotiate_forced_aspect(self, options, accepts): """Order specified options in function of the specified accept priorities.""" if not options: return None priorities = {} for i, o in enumerate(options): p = accepts.get(o, None) if p is No...	[ "def", "negotiate_forced_aspect", "(", "self", ",", "options", ",", "accepts", ")", ":", "if", "not", "options", ":", "return", "None", "priorities", "=", "{", "}", "for", "i", ",", "o", "in", "enumerate", "(", "options", ")", ":", "p", "=", "accepts",...	31.181818	17.545455
def images(self, type): """ Return the list of images available for this type on controller and on the compute node. """ images = [] res = yield from self.http_query("GET", "/{}/images".format(type), timeout=None) images = res.json try: if ty...	[ "def", "images", "(", "self", ",", "type", ")", ":", "images", "=", "[", "]", "res", "=", "yield", "from", "self", ".", "http_query", "(", "\"GET\"", ",", "\"/{}/images\"", ".", "format", "(", "type", ")", ",", "timeout", "=", "None", ")", "images", ...	38.047619	22.047619
def _get_stack_frame(stacklevel): """ utility functions to get a stackframe, skipping internal frames. """ stacklevel = stacklevel + 1 if stacklevel <= 1 or _is_internal_frame(sys._getframe(1)): # If frame is too small to care or if the warning originated in # internal code, then do ...	[ "def", "_get_stack_frame", "(", "stacklevel", ")", ":", "stacklevel", "=", "stacklevel", "+", "1", "if", "stacklevel", "<=", "1", "or", "_is_internal_frame", "(", "sys", ".", "_getframe", "(", "1", ")", ")", ":", "# If frame is too small to care or if the warning ...	38.352941	14.117647
def ped_parser(self, family_info): """ Parse .ped formatted family info. Add all family info to the parser object Arguments: family_info (iterator): An iterator with family info """ for line in family_info: # Che...	[ "def", "ped_parser", "(", "self", ",", "family_info", ")", ":", "for", "line", "in", "family_info", ":", "# Check if commented line or empty line:", "if", "not", "line", ".", "startswith", "(", "'#'", ")", "and", "not", "all", "(", "c", "in", "whitespace", "...	41.941176	19.470588
def _get_style_of_faulting_term(self, C, rup): """ Get fault type dummy variables Fault type (Strike-slip, Normal, Thrust/reverse) is derived from rake angle. Rakes angles within 30 of horizontal are strike-slip, angles from 30 to 150 are reverse, and angles from ...	[ "def", "_get_style_of_faulting_term", "(", "self", ",", "C", ",", "rup", ")", ":", "if", "np", ".", "abs", "(", "rup", ".", "rake", ")", "<=", "30.0", "or", "(", "180.0", "-", "np", ".", "abs", "(", "rup", ".", "rake", ")", ")", "<=", "30.0", "...	36.15	14.35
def pattern_to_str(pattern): """Convert regex pattern to string. If pattern is string it returns itself, if pattern is SRE_Pattern then return pattern attribute :param pattern: pattern object or string :return: str: pattern sttring """ if isinstance(pattern, str): return repr(patter...	[ "def", "pattern_to_str", "(", "pattern", ")", ":", "if", "isinstance", "(", "pattern", ",", "str", ")", ":", "return", "repr", "(", "pattern", ")", "else", ":", "return", "repr", "(", "pattern", ".", "pattern", ")", "if", "pattern", "else", "None" ]	31.583333	12.75
def dispatch_hook(key, hooks, hook_data, kwargs): """Dispatches a hook dictionary on a given piece of data.""" hooks = hooks or {} hooks = hooks.get(key) if hooks: if hasattr(hooks, '__call__'): hooks = [hooks] for hook in hooks: _hook_data = hook(hook_data, k...	[ "def", "dispatch_hook", "(", "key", ",", "hooks", ",", "hook_data", ",", "", "", "kwargs", ")", ":", "hooks", "=", "hooks", "or", "{", "}", "hooks", "=", "hooks", ".", "get", "(", "key", ")", "if", "hooks", ":", "if", "hasattr", "(", "hooks", "...	34.5	11
async def update_queue(self): """ Send waiting jobs to available agents """ # For now, round-robin not_found_for_agent = [] while len(self._available_agents) > 0 and len(self._waiting_jobs) > 0: agent_addr = self._available_agents.pop(0) # Find ...	[ "async", "def", "update_queue", "(", "self", ")", ":", "# For now, round-robin", "not_found_for_agent", "=", "[", "]", "while", "len", "(", "self", ".", "_available_agents", ")", ">", "0", "and", "len", "(", "self", ".", "_waiting_jobs", ")", ">", "0", ":"...	50.026316	31.447368
def sample(self, input_sample, num_samples, num_params, k_choices, num_groups): """Computes the optimum k_choices of trajectories from the input_sample. Arguments --------- input_sample : numpy.ndarray num_samples : int The number of samples to...	[ "def", "sample", "(", "self", ",", "input_sample", ",", "num_samples", ",", "num_params", ",", "k_choices", ",", "num_groups", ")", ":", "return", "self", ".", "_strategy", ".", "sample", "(", "input_sample", ",", "num_samples", ",", "num_params", ",", "k_ch...	31.041667	16.375
def find(cls, _id): """ Returns the individual instance with the given ID, if it exists. Raises :py:class:`PanoptesAPIException` if the object with that ID is not found. """ if not _id: return None try: return next(cls.where(id=_id)) ...	[ "def", "find", "(", "cls", ",", "_id", ")", ":", "if", "not", "_id", ":", "return", "None", "try", ":", "return", "next", "(", "cls", ".", "where", "(", "id", "=", "_id", ")", ")", "except", "StopIteration", ":", "raise", "PanoptesAPIException", "(",...	30.6	20.066667
def getEdgeDirected(self, networkId, edgeId, verbose=None): """ Returns true if the edge specified by the `edgeId` and `networkId` parameters is directed. :param networkId: SUID of the network containing the edge :param edgeId: SUID of the edge :param verbose: print more ...	[ "def", "getEdgeDirected", "(", "self", ",", "networkId", ",", "edgeId", ",", "verbose", "=", "None", ")", ":", "response", "=", "api", "(", "url", "=", "self", ".", "___url", "+", "'networks/'", "+", "str", "(", "networkId", ")", "+", "'/edges/'", "+",...	41.076923	27.692308
def get_report_data_rows(self, request, queryset): """ Using the builders for the queryset model, iterates over the queryset to generate a result with headers and rows. This queryset must be the exact same received in the .process method, which tells us that this function should be c...	[ "def", "get_report_data_rows", "(", "self", ",", "request", ",", "queryset", ")", ":", "model", "=", "queryset", ".", "model", "meta", "=", "model", ".", "_meta", "field_names", "=", "set", "(", "field", ".", "name", "for", "field", "in", "meta", ".", ...	47.909091	25.727273
def configuration_file(cfgfile): '''Find the best match for the configuration file. ''' if cfgfile is not None: return cfgfile # If no file is explicitely specified, probe for the configuration file # location. cfg = './etc/pyca.conf' if not os.path.isfile(cfg): return '/etc/...	[ "def", "configuration_file", "(", "cfgfile", ")", ":", "if", "cfgfile", "is", "not", "None", ":", "return", "cfgfile", "# If no file is explicitely specified, probe for the configuration file", "# location.", "cfg", "=", "'./etc/pyca.conf'", "if", "not", "os", ".", "pat...	30.454545	18.454545

def _min(self): """Getter for the minimum series value""" return ( self.range[0] if (self.range and self.range[0] is not None) else (min(self.yvals) if self.yvals else None) )

[ "def", "_min", "(", "self", ")", ":", "return", "(", "self", ".", "range", "[", "0", "]", "if", "(", "self", ".", "range", "and", "self", ".", "range", "[", "0", "]", "is", "not", "None", ")", "else", "(", "min", "(", "self", ".", "yvals", ")...

36.333333

21.5

def multiplot(self, f, lfilter=None, plot_xy=False, **kargs): """Uses a function that returns a label and a value for this label, then plots all the values label by label. A list of matplotlib.lines.Line2D is returned. """ # Python 2 backward compatibility f = lambda_tu...

[ "def", "multiplot", "(", "self", ",", "f", ",", "lfilter", "=", "None", ",", "plot_xy", "=", "False", ",", "*", "*", "kargs", ")", ":", "# Python 2 backward compatibility", "f", "=", "lambda_tuple_converter", "(", "f", ")", "lfilter", "=", "lambda_tuple_conv...

32

18.282051

def create_gtk_grid(self, row_spacing=6, col_spacing=6, row_homogenous=False, col_homogenous=True): """ Function creates a Gtk Grid with spacing and homogeous tags """ grid_lang = Gtk.Grid() grid_lang.set_column_spacing(row_spacing) grid_lang.set_row_spacing(col_s...

[ "def", "create_gtk_grid", "(", "self", ",", "row_spacing", "=", "6", ",", "col_spacing", "=", "6", ",", "row_homogenous", "=", "False", ",", "col_homogenous", "=", "True", ")", ":", "grid_lang", "=", "Gtk", ".", "Grid", "(", ")", "grid_lang", ".", "set_c...

40.916667

12.75

def _patch_tcpserver(): """ Patch shutdown_request to open blocking interaction after the end of the request """ shutdown_request = TCPServer.shutdown_request def shutdown_request_patched(*args, **kwargs): thread = current_thread() shutdown_request(*args, **kwargs) if th...

[ "def", "_patch_tcpserver", "(", ")", ":", "shutdown_request", "=", "TCPServer", ".", "shutdown_request", "def", "shutdown_request_patched", "(", "*", "args", ",", "*", "*", "kwargs", ")", ":", "thread", "=", "current_thread", "(", ")", "shutdown_request", "(", ...

31.857143

16.714286

def evaluation(evaluation_id): """Show or delete an ACMG evaluation.""" evaluation_obj = store.get_evaluation(evaluation_id) controllers.evaluation(store, evaluation_obj) if request.method == 'POST': link = url_for('.variant', institute_id=evaluation_obj['institute']['_id'], ...

[ "def", "evaluation", "(", "evaluation_id", ")", ":", "evaluation_obj", "=", "store", ".", "get_evaluation", "(", "evaluation_id", ")", "controllers", ".", "evaluation", "(", "store", ",", "evaluation_obj", ")", "if", "request", ".", "method", "==", "'POST'", "...

54.615385

18.923077

def _check_and_update_params(self, required, params): """ Ensure all required parameters were passed to the API call and format them correctly. """ for r in required: if r not in params: raise PayPalError("Missing required param: %s" % r) # Up...

[ "def", "_check_and_update_params", "(", "self", ",", "required", ",", "params", ")", ":", "for", "r", "in", "required", ":", "if", "r", "not", "in", "params", ":", "raise", "PayPalError", "(", "\"Missing required param: %s\"", "%", "r", ")", "# Upper case all ...

37.636364

17.454545

def get_route(self, route_id): """ Gets specified route. Will be detail-level if owned by authenticated user; otherwise summary-level. https://strava.github.io/api/v3/routes/#retreive :param route_id: The ID of route to fetch. :type route_id: int :rtype: :clas...

[ "def", "get_route", "(", "self", ",", "route_id", ")", ":", "raw", "=", "self", ".", "protocol", ".", "get", "(", "'/routes/{id}'", ",", "id", "=", "route_id", ")", "return", "model", ".", "Route", ".", "deserialize", "(", "raw", ",", "bind_client", "=...

31.066667

20.8

def Drop(self: Iterable, n): """ [ { 'self': [1, 2, 3, 4, 5], 'n': 3, 'assert': lambda ret: list(ret) == [1, 2] } ] """ con = tuple(self) n = len(con) - n if n <= 0: yield from con else: for i, e in enumerate(con): ...

[ "def", "Drop", "(", "self", ":", "Iterable", ",", "n", ")", ":", "con", "=", "tuple", "(", "self", ")", "n", "=", "len", "(", "con", ")", "-", "n", "if", "n", "<=", "0", ":", "yield", "from", "con", "else", ":", "for", "i", ",", "e", "in", ...

19.052632

18.842105

def is_businessdate(in_date): """ checks whether the provided date is a date :param BusinessDate, int or float in_date: :return bool: """ # Note: if the data range has been created from pace_xl, then all the dates are bank dates # and here it remains to check the ...

[ "def", "is_businessdate", "(", "in_date", ")", ":", "# Note: if the data range has been created from pace_xl, then all the dates are bank dates", "# and here it remains to check the validity.", "# !!! However, if the data has been read from json string via json.load() function", "# it does not rec...

48.65

20.05

def empty_like(self, shape): """ Make an empty LabelArray with the same categories as ``self``, filled with ``self.missing_value``. """ return type(self).from_codes_and_metadata( codes=np.full( shape, self.reverse_categories[self.missin...

[ "def", "empty_like", "(", "self", ",", "shape", ")", ":", "return", "type", "(", "self", ")", ".", "from_codes_and_metadata", "(", "codes", "=", "np", ".", "full", "(", "shape", ",", "self", ".", "reverse_categories", "[", "self", ".", "missing_value", "...

37.2

15.2

def search(self, q, labels, state='open,closed', **kwargs): """Search for issues in Github. :param q: query string to search :param state: state of the issue :returns: list of issue objects :rtype: list """ search_result = self.github_request.search(q=q, state=s...

[ "def", "search", "(", "self", ",", "q", ",", "labels", ",", "state", "=", "'open,closed'", ",", "*", "*", "kwargs", ")", ":", "search_result", "=", "self", ".", "github_request", ".", "search", "(", "q", "=", "q", ",", "state", "=", "state", ",", "...

35.6875

15.5625

def body(self): """Yields the encoded body.""" for chunk in self.gen_chunks(self.envelope.file_open(self.name)): yield chunk for chunk in self.gen_chunks(self.data): yield chunk for chunk in self.gen_chunks(self.envelope.file_close()): yield chunk ...

[ "def", "body", "(", "self", ")", ":", "for", "chunk", "in", "self", ".", "gen_chunks", "(", "self", ".", "envelope", ".", "file_open", "(", "self", ".", "name", ")", ")", ":", "yield", "chunk", "for", "chunk", "in", "self", ".", "gen_chunks", "(", ...

36.5

16.5

def getusers(self, context, request): """/@@API/getusers: Return users belonging to specified roles Required parameters: - roles: The role of which users to return { runtime: Function running time. error: true or string(message) if error. false if no error....

[ "def", "getusers", "(", "self", ",", "context", ",", "request", ")", ":", "roles", "=", "request", ".", "get", "(", "'roles'", ",", "''", ")", "if", "len", "(", "roles", ")", "==", "0", ":", "raise", "BadRequest", "(", "\"No roles specified\"", ")", ...

35.372549

20.941176

def join_content_version(self, to_cache): """ Add the version(s) to the content to cache : internal version at first and then the template version if versioning is activated. Each version, and the content, are separated with `VERSION_SEPARATOR`. This method is called after the en...

[ "def", "join_content_version", "(", "self", ",", "to_cache", ")", ":", "parts", "=", "[", "self", ".", "INTERNAL_VERSION", "]", "if", "self", ".", "options", ".", "versioning", ":", "parts", ".", "append", "(", "force_bytes", "(", "self", ".", "version", ...

43.428571

14.142857

def _cursor(self): """Asserts that the connection is open and returns a cursor""" if self._conn is None: self._conn = sqlite3.connect(self.filename, check_same_thread=False) return self._conn.cursor()

[ "def", "_cursor", "(", "self", ")", ":", "if", "self", ".", "_conn", "is", "None", ":", "self", ".", "_conn", "=", "sqlite3", ".", "connect", "(", "self", ".", "filename", ",", "check_same_thread", "=", "False", ")", "return", "self", ".", "_conn", "...

45.333333

13

def extend(self, step): """ Adds the data from another STObject to this object. Args: step: another STObject being added after the current one in time. """ self.timesteps.extend(step.timesteps) self.masks.extend(step.masks) self.x.extend(step....

[ "def", "extend", "(", "self", ",", "step", ")", ":", "self", ".", "timesteps", ".", "extend", "(", "step", ".", "timesteps", ")", "self", ".", "masks", ".", "extend", "(", "step", ".", "masks", ")", "self", ".", "x", ".", "extend", "(", "step", "...

38.8

14.3

def to_irc(self): """ Convert to mIRC color format :return: """ ignore_re = re.compile('[\x03\x02\x1D\x1F\x16\x0F]') text = ignore_re.sub('', self.text) if self.color and self.bg_color: return '\x03%02d,%02d%s' % (self.color.to_8bit().to_irc(), ...

[ "def", "to_irc", "(", "self", ")", ":", "ignore_re", "=", "re", ".", "compile", "(", "'[\\x03\\x02\\x1D\\x1F\\x16\\x0F]'", ")", "text", "=", "ignore_re", ".", "sub", "(", "''", ",", "self", ".", "text", ")", "if", "self", ".", "color", "and", "self", "...

36.952381

14

def init_repo(path): """clone the gh-pages repo if we haven't already.""" sh("git clone %s %s"%(pages_repo, path)) here = os.getcwd() cd(path) sh('git checkout gh-pages') cd(here)

[ "def", "init_repo", "(", "path", ")", ":", "sh", "(", "\"git clone %s %s\"", "%", "(", "pages_repo", ",", "path", ")", ")", "here", "=", "os", ".", "getcwd", "(", ")", "cd", "(", "path", ")", "sh", "(", "'git checkout gh-pages'", ")", "cd", "(", "her...

28.142857

15.285714

def save_unmet(self, job): """Save a message for later submission when its dependencies are met.""" msg_id = job.msg_id self.depending[msg_id] = job # track the ids in follow or after, but not those already finished for dep_id in job.after.union(job.follow).difference(self.all_do...

[ "def", "save_unmet", "(", "self", ",", "job", ")", ":", "msg_id", "=", "job", ".", "msg_id", "self", ".", "depending", "[", "msg_id", "]", "=", "job", "# track the ids in follow or after, but not those already finished", "for", "dep_id", "in", "job", ".", "after...

49.222222

11.666667

def get(): """Returns the current version without importing pymds.""" pkgnames = find_packages() if len(pkgnames) == 0: raise ValueError("Can't find any packages") pkgname = pkgnames[0] content = open(join(pkgname, '__init__.py')).read() c = re.compile(r"__version__ *= *('[^']+'|\"[^\...

[ "def", "get", "(", ")", ":", "pkgnames", "=", "find_packages", "(", ")", "if", "len", "(", "pkgnames", ")", "==", "0", ":", "raise", "ValueError", "(", "\"Can't find any packages\"", ")", "pkgname", "=", "pkgnames", "[", "0", "]", "content", "=", "open",...

27.176471

23.058824

def p_constant_declaration(p): 'constant_declaration : STRING EQUALS static_scalar' p[0] = ast.ConstantDeclaration(p[1], p[3], lineno=p.lineno(1))

[ "def", "p_constant_declaration", "(", "p", ")", ":", "p", "[", "0", "]", "=", "ast", ".", "ConstantDeclaration", "(", "p", "[", "1", "]", ",", "p", "[", "3", "]", ",", "lineno", "=", "p", ".", "lineno", "(", "1", ")", ")" ]

50.666667

17.333333

def transformProperMotionErrors(self, phi, theta, sigMuPhiStar, sigMuTheta, rhoMuPhiMuTheta=0): """ Converts the proper motion errors from one reference system to another, including the covariance term. Equations (1.5.4) and (1.5.20) from section 1.5 in the Hipparcos Explanatory Volume 1 are use...

[ "def", "transformProperMotionErrors", "(", "self", ",", "phi", ",", "theta", ",", "sigMuPhiStar", ",", "sigMuTheta", ",", "rhoMuPhiMuTheta", "=", "0", ")", ":", "return", "self", ".", "transformSkyCoordinateErrors", "(", "phi", ",", "theta", ",", "sigMuPhiStar",...

48.933333

35.133333

def read_int(self, lpBaseAddress): """ Reads a signed integer from the memory of the process. @see: L{peek_int} @type lpBaseAddress: int @param lpBaseAddress: Memory address to begin reading. @rtype: int @return: Integer value read from the process memory. ...

[ "def", "read_int", "(", "self", ",", "lpBaseAddress", ")", ":", "return", "self", ".", "__read_c_type", "(", "lpBaseAddress", ",", "compat", ".", "b", "(", "'@l'", ")", ",", "ctypes", ".", "c_int", ")" ]

30.466667

22.066667

def _setup_stats_total(self, redis_conn): ''' Sets up the total stats collectors @param redis_conn: the redis connection ''' self.stats_dict['total'] = {} self.stats_dict['fail'] = {} temp_key1 = 'stats:kafka-monitor:total' temp_key2 = 'stats:kafka-monito...

[ "def", "_setup_stats_total", "(", "self", ",", "redis_conn", ")", ":", "self", ".", "stats_dict", "[", "'total'", "]", "=", "{", "}", "self", ".", "stats_dict", "[", "'fail'", "]", "=", "{", "}", "temp_key1", "=", "'stats:kafka-monitor:total'", "temp_key2", ...

53.682927

20.02439

def next_sibling(self): """ Returns the next sibling of the current node. The next sibling is searched in the parent node if we are not considering a top-level node. Otherwise it is searched inside the list of nodes (which should be sorted by tree ID) that is associated with the conside...

[ "def", "next_sibling", "(", "self", ")", ":", "if", "self", ".", "parent", ":", "nodes", "=", "self", ".", "parent", ".", "children", "index", "=", "nodes", ".", "index", "(", "self", ")", "sibling", "=", "nodes", "[", "index", "+", "1", "]", "if",...

41.842105

20.789474

def template(page=None, layout=None, **kwargs): """ Decorator to change the view template and layout. It works on both View class and view methods on class only $layout is applied, everything else will be passed to the kwargs Using as first argument, it will be the layout. :fi...

[ "def", "template", "(", "page", "=", "None", ",", "layout", "=", "None", ",", "*", "*", "kwargs", ")", ":", "pkey", "=", "\"_template_extends__\"", "def", "decorator", "(", "f", ")", ":", "if", "inspect", ".", "isclass", "(", "f", ")", ":", "layout_"...

33.09375

16.09375

def _checkBuildDependencies(): compiler = distutils.ccompiler.new_compiler() """check if function without parameters from stdlib can be called There should be better way to check, if C compiler is installed """ if not compiler.has_function('rand', includes=['stdlib.h']): print("It seems like...

[ "def", "_checkBuildDependencies", "(", ")", ":", "compiler", "=", "distutils", ".", "ccompiler", ".", "new_compiler", "(", ")", "if", "not", "compiler", ".", "has_function", "(", "'rand'", ",", "includes", "=", "[", "'stdlib.h'", "]", ")", ":", "print", "(...

56.285714

28.685714

def create_template(self): """Create template (main function called by Stacker).""" template = self.template variables = self.get_variables() template.add_version('2010-09-09') template.add_description('Static Website - Bucket and Distribution') # Conditions temp...

[ "def", "create_template", "(", "self", ")", ":", "template", "=", "self", ".", "template", "variables", "=", "self", ".", "get_variables", "(", ")", "template", ".", "add_version", "(", "'2010-09-09'", ")", "template", ".", "add_description", "(", "'Static Web...

41.843511

19.041985

def show(source): """Merely returns the metadata for the provided archive. """ if is_verbose(): logger.info('Retrieving Metadata for: %s', source) processed_source = get_source(source) metadata = _get_metadata(processed_source) shutil.rmtree(processed_source) return metadata

[ "def", "show", "(", "source", ")", ":", "if", "is_verbose", "(", ")", ":", "logger", ".", "info", "(", "'Retrieving Metadata for: %s'", ",", "source", ")", "processed_source", "=", "get_source", "(", "source", ")", "metadata", "=", "_get_metadata", "(", "pro...

33.666667

10.444444

def p_instance_bodylist(self, p): 'instance_bodylist : instance_bodylist COMMA instance_body' p[0] = p[1] + (p[3],) p.set_lineno(0, p.lineno(1))

[ "def", "p_instance_bodylist", "(", "self", ",", "p", ")", ":", "p", "[", "0", "]", "=", "p", "[", "1", "]", "+", "(", "p", "[", "3", "]", ",", ")", "p", ".", "set_lineno", "(", "0", ",", "p", ".", "lineno", "(", "1", ")", ")" ]

41.25

12.25

def _process_collection(self, collection_id, label, page): """ This function will process the data supplied internally about the repository from Coriell. Triples: Repository a ERO:collection rdf:label Literal(label) foaf:page Literal(page) :p...

[ "def", "_process_collection", "(", "self", ",", "collection_id", ",", "label", ",", "page", ")", ":", "# ############# BUILD THE CELL LINE REPOSITORY #############", "for", "graph", "in", "[", "self", ".", "graph", ",", "self", ".", "testgraph", "]", ":", "#...

32.344828

16.758621

def _set_params_callback(self, **params): """Special handling for setting params on callbacks.""" # model after sklearn.utils._BaseCompostion._set_params # 1. All steps if 'callbacks' in params: setattr(self, 'callbacks', params.pop('callbacks')) # 2. Step replacemen...

[ "def", "_set_params_callback", "(", "self", ",", "*", "*", "params", ")", ":", "# model after sklearn.utils._BaseCompostion._set_params", "# 1. All steps", "if", "'callbacks'", "in", "params", ":", "setattr", "(", "self", ",", "'callbacks'", ",", "params", ".", "pop...

39.071429

15.25

def _convertNonNumericData(self, spatialOutput, temporalOutput, output): """ Converts all of the non-numeric fields from spatialOutput and temporalOutput into their scalar equivalents and records them in the output dictionary. :param spatialOutput: The results of topDownCompute() for the spatial input....

[ "def", "_convertNonNumericData", "(", "self", ",", "spatialOutput", ",", "temporalOutput", ",", "output", ")", ":", "encoders", "=", "self", ".", "encoder", ".", "getEncoderList", "(", ")", "types", "=", "self", ".", "encoder", ".", "getDecoderOutputFieldTypes",...

47.259259

21.62963

def p_expression_eq(self, p): 'expression : expression EQ expression' p[0] = Eq(p[1], p[3], lineno=p.lineno(1)) p.set_lineno(0, p.lineno(1))

[ "def", "p_expression_eq", "(", "self", ",", "p", ")", ":", "p", "[", "0", "]", "=", "Eq", "(", "p", "[", "1", "]", ",", "p", "[", "3", "]", ",", "lineno", "=", "p", ".", "lineno", "(", "1", ")", ")", "p", ".", "set_lineno", "(", "0", ",",...

40.25

7.75

def get_float(strings: Sequence[str], prefix: str, ignoreleadingcolon: bool = False, precedingline: str = "") -> Optional[float]: """ Fetches a float parameter via :func:`get_string`. """ return get_float_raw(get_string(strings, prefix, ...

[ "def", "get_float", "(", "strings", ":", "Sequence", "[", "str", "]", ",", "prefix", ":", "str", ",", "ignoreleadingcolon", ":", "bool", "=", "False", ",", "precedingline", ":", "str", "=", "\"\"", ")", "->", "Optional", "[", "float", "]", ":", "return...

42.6

12.6

def max_insertion(seqs, gene, domain): """ length of largest insertion """ seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain] lengths = [] for seq in seqs: for ins in seq: lengths.append(int(ins[2])) if lengths == []: retu...

[ "def", "max_insertion", "(", "seqs", ",", "gene", ",", "domain", ")", ":", "seqs", "=", "[", "i", "[", "2", "]", "for", "i", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", "if", "i", "[", "2", "]", "!=", "[", "]", "and", "i", "[",...

28.333333

15.5

def get_profile_info(self, obj): """Returns the info for a Profile """ info = self.get_base_info(obj) info.update({}) return info

[ "def", "get_profile_info", "(", "self", ",", "obj", ")", ":", "info", "=", "self", ".", "get_base_info", "(", "obj", ")", "info", ".", "update", "(", "{", "}", ")", "return", "info" ]

27.333333

8

def bulleted_list(items, indent=0, bullet_type='-'): """Format a bulleted list of values. Parameters ---------- items : sequence The items to make a list. indent : int, optional The number of spaces to add before each bullet. bullet_type : str, optional The bullet type t...

[ "def", "bulleted_list", "(", "items", ",", "indent", "=", "0", ",", "bullet_type", "=", "'-'", ")", ":", "format_string", "=", "' '", "*", "indent", "+", "bullet_type", "+", "' {}'", "return", "\"\\n\"", ".", "join", "(", "map", "(", "format_string", "."...

27.526316

17.157895

def SetScrollPercent(self, horizontalPercent: float, verticalPercent: float, waitTime: float = OPERATION_WAIT_TIME) -> bool: """ Call IUIAutomationScrollPattern::SetScrollPercent. Set the horizontal and vertical scroll positions as a percentage of the total content area within the UI Automation ...

[ "def", "SetScrollPercent", "(", "self", ",", "horizontalPercent", ":", "float", ",", "verticalPercent", ":", "float", ",", "waitTime", ":", "float", "=", "OPERATION_WAIT_TIME", ")", "->", "bool", ":", "ret", "=", "self", ".", "pattern", ".", "SetScrollPercent"...

70.307692

42.461538

def checkPrediction2(possibleOutcome, predictedOutcome): """ :param possibleOutcome: list of all possible outcomes :param predictedOutcome: list of all predicted outomes :return missN: number of misses (a possible outcome not predicted) fpN: number of false positives (a predicted outcome is not poss...

[ "def", "checkPrediction2", "(", "possibleOutcome", ",", "predictedOutcome", ")", ":", "missN", "=", "0", "for", "i", "in", "xrange", "(", "len", "(", "possibleOutcome", ")", ")", ":", "miss", "=", "1", "for", "j", "in", "xrange", "(", "len", "(", "pred...

30.25

19.583333

def timing_decorator(func): """Prints the time func takes to execute.""" @functools.wraps(func) def wrapper(*args, **kwargs): """ Wrapper for printing execution time. Parameters ---------- print_time: bool, optional whether or not to print time function t...

[ "def", "timing_decorator", "(", "func", ")", ":", "@", "functools", ".", "wraps", "(", "func", ")", "def", "wrapper", "(", "*", "args", ",", "*", "*", "kwargs", ")", ":", "\"\"\"\n Wrapper for printing execution time.\n\n Parameters\n ----------\n...

30.869565

11.478261

def comments_between_tokens(token1, token2): """Find all comments between two tokens""" if token2 is None: buf = token1.end_mark.buffer[token1.end_mark.pointer:] elif (token1.end_mark.line == token2.start_mark.line and not isinstance(token1, yaml.StreamStartToken) and not isinsta...

[ "def", "comments_between_tokens", "(", "token1", ",", "token2", ")", ":", "if", "token2", "is", "None", ":", "buf", "=", "token1", ".", "end_mark", ".", "buffer", "[", "token1", ".", "end_mark", ".", "pointer", ":", "]", "elif", "(", "token1", ".", "en...

34.533333

18.333333

def simple_transaction(self, from_address, to, op_return=None, min_confirmations=6): """ Args: from_address (str): bitcoin address originating the transaction to: tuple of ``(to_address, amount)`` or list of tuples ``[(to_addr1, amount1), (to_addr2, amount2)]``. Amounts are in *s...

[ "def", "simple_transaction", "(", "self", ",", "from_address", ",", "to", ",", "op_return", "=", "None", ",", "min_confirmations", "=", "6", ")", ":", "to", "=", "[", "to", "]", "if", "not", "isinstance", "(", "to", ",", "list", ")", "else", "to", "a...

42.535714

28.75

def pull_byte(self, stack_pointer): """ pulled a byte from stack """ addr = stack_pointer.value byte = self.memory.read_byte(addr) # log.info( # log.error( # "%x|\tpull $%x from %s stack at $%x\t|%s", # self.last_op_address, byte, stack_pointer.name, addr, # ...

[ "def", "pull_byte", "(", "self", ",", "stack_pointer", ")", ":", "addr", "=", "stack_pointer", ".", "value", "byte", "=", "self", ".", "memory", ".", "read_byte", "(", "addr", ")", "# log.info(", "# log.error(", "# \"%x|\\tpull $%x from %s ...

32.333333

17.666667

def anomaly(self, test_data, per_feature=False): """ Obtain the reconstruction error for the input test_data. :param H2OFrame test_data: The dataset upon which the reconstruction error is computed. :param bool per_feature: Whether to return the square reconstruction error per feature. ...

[ "def", "anomaly", "(", "self", ",", "test_data", ",", "per_feature", "=", "False", ")", ":", "if", "test_data", "is", "None", "or", "test_data", ".", "nrow", "==", "0", ":", "raise", "ValueError", "(", "\"Must specify test data\"", ")", "j", "=", "h2o", ...

57.5

33.071429

def input_validation(group_idx, a, size=None, order='C', axis=None, ravel_group_idx=True, check_bounds=True): """ Do some fairly extensive checking of group_idx and a, trying to give the user as much help as possible with what is wrong. Also, convert ndim-indexing to 1d indexing. ""...

[ "def", "input_validation", "(", "group_idx", ",", "a", ",", "size", "=", "None", ",", "order", "=", "'C'", ",", "axis", "=", "None", ",", "ravel_group_idx", "=", "True", ",", "check_bounds", "=", "True", ")", ":", "if", "not", "isinstance", "(", "a", ...

45.391304

19.478261

def checksum(thing): """ Get the checksum of a calculation from the calculation ID (if already done) or from the job.ini/job.zip file (if not done yet). If `thing` is a source model logic tree file, get the checksum of the model by ignoring the job.ini, the gmpe logic tree file and possibly other fi...

[ "def", "checksum", "(", "thing", ")", ":", "try", ":", "job_id", "=", "int", "(", "thing", ")", "job_file", "=", "None", "except", "ValueError", ":", "job_id", "=", "None", "job_file", "=", "thing", "if", "not", "os", ".", "path", ".", "exists", "(",...

38.84

19

def _extract_multiple_hits(self, hits, reads_path, output_path): ''' splits out regions of a read that hit the HMM. For example when two of same gene are identified within the same contig, The regions mapping to the HMM will be split out and written out to a new file as a new record. ...

[ "def", "_extract_multiple_hits", "(", "self", ",", "hits", ",", "reads_path", ",", "output_path", ")", ":", "complement_information", "=", "{", "}", "try", ":", "reads", "=", "SeqIO", ".", "to_dict", "(", "SeqIO", ".", "parse", "(", "reads_path", ",", "\"f...

48.561404

31.508772

def run(self, inputcode, iterations=None, run_forever=False, frame_limiter=False, verbose=False, break_on_error=False): ''' Executes the contents of a Nodebox/Shoebot script in current surface's context. :param inputcode: Path to shoebot source or string containing source ...

[ "def", "run", "(", "self", ",", "inputcode", ",", "iterations", "=", "None", ",", "run_forever", "=", "False", ",", "frame_limiter", "=", "False", ",", "verbose", "=", "False", ",", "break_on_error", "=", "False", ")", ":", "source", "=", "None", "filena...

41.230769

22.791209

def update_issue_remote_link_by_id(self, issue_key, link_id, url, title, global_id=None, relationship=None): """ Update existing Remote Link on Issue :param issue_key: str :param link_id: str :param url: str :param title: str :param global_id: str, OPTIONAL: ...

[ "def", "update_issue_remote_link_by_id", "(", "self", ",", "issue_key", ",", "link_id", ",", "url", ",", "title", ",", "global_id", "=", "None", ",", "relationship", "=", "None", ")", ":", "data", "=", "{", "'object'", ":", "{", "'url'", ":", "url", ",",...

41.333333

18.333333

def toList(self): """ Return a list with the DataFrame data. """ if self.getNumCols() > 1: return [ tuple(self.getRowByIndex(i)) for i in range(self.getNumRows()) ] else: return [ self.getRowByInd...

[ "def", "toList", "(", "self", ")", ":", "if", "self", ".", "getNumCols", "(", ")", ">", "1", ":", "return", "[", "tuple", "(", "self", ".", "getRowByIndex", "(", "i", ")", ")", "for", "i", "in", "range", "(", "self", ".", "getNumRows", "(", ")", ...

27.071429

12.785714

def set_clock_divisor(self, clock_divisor): """ Sets the clock divisor value. The higher is the value, the faster is the clock in the virtual machine. The default is 4, but it is often required to adjust it. :param clock_divisor: clock divisor value (integer) """ yield ...

[ "def", "set_clock_divisor", "(", "self", ",", "clock_divisor", ")", ":", "yield", "from", "self", ".", "_hypervisor", ".", "send", "(", "'vm set_clock_divisor \"{name}\" {clock}'", ".", "format", "(", "name", "=", "self", ".", "_name", ",", "clock", "=", "cloc...

69

44.571429

def get_extname(self): """ Get the name for this extension, can be an empty string """ name = self._info['extname'] if name.strip() == '': name = self._info['hduname'] return name.strip()

[ "def", "get_extname", "(", "self", ")", ":", "name", "=", "self", ".", "_info", "[", "'extname'", "]", "if", "name", ".", "strip", "(", ")", "==", "''", ":", "name", "=", "self", ".", "_info", "[", "'hduname'", "]", "return", "name", ".", "strip", ...

30

8.5

def _initialize(self, runtime): """Common initializer for OsidManager and OsidProxyManager""" if runtime is None: raise NullArgument() if self._my_runtime is not None: raise IllegalState('this manager has already been initialized.') self._my_runtime = runtime ...

[ "def", "_initialize", "(", "self", ",", "runtime", ")", ":", "if", "runtime", "is", "None", ":", "raise", "NullArgument", "(", ")", "if", "self", ".", "_my_runtime", "is", "not", "None", ":", "raise", "IllegalState", "(", "'this manager has already been initia...

46.119048

26.047619

def cosi_pdf(z,k=1): """Equation (11) of Morton & Winn (2014) """ return 2*k/(np.pi*np.sinh(k)) * quad(cosi_integrand,z,1,args=(k,z))[0]

[ "def", "cosi_pdf", "(", "z", ",", "k", "=", "1", ")", ":", "return", "2", "*", "k", "/", "(", "np", ".", "pi", "*", "np", ".", "sinh", "(", "k", ")", ")", "*", "quad", "(", "cosi_integrand", ",", "z", ",", "1", ",", "args", "=", "(", "k",...

36.25

13.5

def load_factors(): """Load risk factor returns. Factors ------- Symbol Description Source ------ ---------- ------ MKT French ...

[ "def", "load_factors", "(", ")", ":", "# TODO: factors elegible for addition\r", "# VIIX, VIIZ, XIV, ZIV, CRP (AQR)\r", "# http://www.cboe.com/micro/buywrite/monthendpricehistory.xls ends 2016\r", "# could use:\r", "# http://www.cboe.com/publish/scheduledtask/mktdata/datahouse/putdailypric...

37.684211

23.20614

def register_plugin(self, plugin): """Registers a plugin and commands with the dispatcher for push()""" self.log.info("Registering plugin %s", type(plugin).__name__) self._register_commands(plugin) plugin.on_load()

[ "def", "register_plugin", "(", "self", ",", "plugin", ")", ":", "self", ".", "log", ".", "info", "(", "\"Registering plugin %s\"", ",", "type", "(", "plugin", ")", ".", "__name__", ")", "self", ".", "_register_commands", "(", "plugin", ")", "plugin", ".", ...

48.4

10.4

def ldcoeffs(teff,logg=4.5,feh=0): """ Returns limb-darkening coefficients in Kepler band. """ teffs = np.atleast_1d(teff) loggs = np.atleast_1d(logg) Tmin,Tmax = (LDPOINTS[:,0].min(),LDPOINTS[:,0].max()) gmin,gmax = (LDPOINTS[:,1].min(),LDPOINTS[:,1].max()) teffs[(teffs < Tmin)] = Tmi...

[ "def", "ldcoeffs", "(", "teff", ",", "logg", "=", "4.5", ",", "feh", "=", "0", ")", ":", "teffs", "=", "np", ".", "atleast_1d", "(", "teff", ")", "loggs", "=", "np", ".", "atleast_1d", "(", "logg", ")", "Tmin", ",", "Tmax", "=", "(", "LDPOINTS", ...

29.058824

13.882353

def model(x_train, y_train, x_test, y_test): """ Model providing function: Create Keras model with double curly brackets dropped-in as needed. Return value has to be a valid python dictionary with two customary keys: - loss: Specify a numeric evaluation metric to be minimized - status: ...

[ "def", "model", "(", "x_train", ",", "y_train", ",", "x_test", ",", "y_test", ")", ":", "model", "=", "Sequential", "(", ")", "model", ".", "add", "(", "Dense", "(", "512", ",", "input_shape", "=", "(", "784", ",", ")", ")", ")", "model", ".", "a...

38.952381

19.47619

def _error(self, request, status, headers={}, prefix_template_path=False, **kwargs): """ Convenience method to render an error response. The template is inferred from the status code. :param request: A django.http.HttpRequest instance. :param status: An integer describing the HTTP statu...

[ "def", "_error", "(", "self", ",", "request", ",", "status", ",", "headers", "=", "{", "}", ",", "prefix_template_path", "=", "False", ",", "*", "*", "kwargs", ")", ":", "return", "self", ".", "_render", "(", "request", "=", "request", ",", "template",...

42.565217

27

def human(self): """Human-readable timestamp.""" # get timezone offset delta_sec = time.timezone m, s = divmod(delta_sec, 60) h, m = divmod(m, 60) # create output format_string = "%Y-%m-%d %H:%M:%S" out = self.datetime.strftime(format_string) retur...

[ "def", "human", "(", "self", ")", ":", "# get timezone offset", "delta_sec", "=", "time", ".", "timezone", "m", ",", "s", "=", "divmod", "(", "delta_sec", ",", "60", ")", "h", ",", "m", "=", "divmod", "(", "m", ",", "60", ")", "# create output", "for...

31.6

11.1

def send(self, change): """send the given policy change""" self.buf.append(change) if len(self.buf) % self.BUF_SIZE == 0: self.flush()

[ "def", "send", "(", "self", ",", "change", ")", ":", "self", ".", "buf", ".", "append", "(", "change", ")", "if", "len", "(", "self", ".", "buf", ")", "%", "self", ".", "BUF_SIZE", "==", "0", ":", "self", ".", "flush", "(", ")" ]

33.2

9.6

def node_hist_fig( node_color_distribution, title="Graph Node Distribution", width=400, height=300, top=60, left=25, bottom=60, right=25, bgcolor="rgb(240,240,240)", y_gridcolor="white", ): """Define the plotly plot representing the node histogram Param...

[ "def", "node_hist_fig", "(", "node_color_distribution", ",", "title", "=", "\"Graph Node Distribution\"", ",", "width", "=", "400", ",", "height", "=", "300", ",", "top", "=", "60", ",", "left", "=", "25", ",", "bottom", "=", "60", ",", "right", "=", "25...

30.358491

24.433962

def create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None): """ Adds a new table to the network. :param keyColumn (string, optional): Specifies the name of a column in the table :param keyColumnType (string, optional): The syntactical type of the value ...

[ "def", "create_table", "(", "self", ",", "keyColumn", "=", "None", ",", "keyColumnType", "=", "None", ",", "title", "=", "None", ",", "verbose", "=", "None", ")", ":", "PARAMS", "=", "set_param", "(", "[", "'keyColumn'", ",", "'keyColumnType'", ",", "'ti...

41.529412

25.764706

def _get_contexts_for_squash(self, batch_signature): """Starting with the batch referenced by batch_signature, iterate back through the batches and for each valid batch collect the context_id. At the end remove contexts for txns that are other txn's predecessors. Args: batch...

[ "def", "_get_contexts_for_squash", "(", "self", ",", "batch_signature", ")", ":", "batch", "=", "self", ".", "_batches_by_id", "[", "batch_signature", "]", ".", "batch", "index", "=", "self", ".", "_batches", ".", "index", "(", "batch", ")", "contexts", "=",...

40.6

17.885714

def path_and_line(req): """Return the path and line number of the file from which an InstallRequirement came. """ path, line = (re.match(r'-r (.*) $line (\d+)$$', req.comes_from).groups()) return path, int(line)

[ "def", "path_and_line", "(", "req", ")", ":", "path", ",", "line", "=", "(", "re", ".", "match", "(", "r'-r (.*) \$line (\\d+)\$$'", ",", "req", ".", "comes_from", ")", ".", "groups", "(", ")", ")", "return", "path", ",", "int", "(", "line", ")" ]

31.75

13.625

def build(self, tool): """build the project""" tools = self._validate_tools(tool) if tools == -1: return -1 result = 0 for build_tool in tools: builder = ToolsSupported().get_tool(build_tool) # None is an error if builder is None...

[ "def", "build", "(", "self", ",", "tool", ")", ":", "tools", "=", "self", ".", "_validate_tools", "(", "tool", ")", "if", "tools", "==", "-", "1", ":", "return", "-", "1", "result", "=", "0", "for", "build_tool", "in", "tools", ":", "builder", "=",...

31.478261

20.043478

def from_dict(data, ctx): """ Instantiate a new TradeClientExtensionsModifyTransaction from a dict (generally from loading a JSON response). The data used to instantiate the TradeClientExtensionsModifyTransaction is a shallow copy of the dict passed in, with any complex child typ...

[ "def", "from_dict", "(", "data", ",", "ctx", ")", ":", "data", "=", "data", ".", "copy", "(", ")", "if", "data", ".", "get", "(", "'tradeClientExtensionsModify'", ")", "is", "not", "None", ":", "data", "[", "'tradeClientExtensionsModify'", "]", "=", "ctx...

38.888889

23.222222

def audit_1_4(self): """1.4 Ensure access keys are rotated every 90 days or less (Scored)""" for row in self.credential_report: for access_key in "1", "2": if json.loads(row["access_key_{}_active".format(access_key)]): last_rotated = row["access_key_{}_las...

[ "def", "audit_1_4", "(", "self", ")", ":", "for", "row", "in", "self", ".", "credential_report", ":", "for", "access_key", "in", "\"1\"", ",", "\"2\"", ":", "if", "json", ".", "loads", "(", "row", "[", "\"access_key_{}_active\"", ".", "format", "(", "acc...

68.333333

28.666667

def find_modules_with_decorators(path,decorator_module,decorator_name): ''' Finds all the modules decorated with the specified decorator in the path, file or module specified. Args : path : All modules in the directory and its sub-directories will be scanned. decorato...

[ "def", "find_modules_with_decorators", "(", "path", ",", "decorator_module", ",", "decorator_name", ")", ":", "modules_paths", "=", "[", "]", "#If a path to a module file", "if", "path", "[", "-", "3", ":", "]", "==", "'.py'", ":", "modules_paths", ".", "append"...

41.5

30.1

def format_to_http_prompt(context, excluded_options=None): """Format a Context object to HTTP Prompt commands.""" cmds = _extract_httpie_options(context, quote=True, join_key_value=True, excluded_keys=excluded_options) cmds.append('cd ' + smart_quote(context.url)) cmds...

[ "def", "format_to_http_prompt", "(", "context", ",", "excluded_options", "=", "None", ")", ":", "cmds", "=", "_extract_httpie_options", "(", "context", ",", "quote", "=", "True", ",", "join_key_value", "=", "True", ",", "excluded_keys", "=", "excluded_options", ...

57.428571

16.857143

def env_updated(cls, app, env): """Abort Sphinx after initializing config and discovering all pages to build. :param sphinx.application.Sphinx app: Sphinx application object. :param sphinx.environment.BuildEnvironment env: Sphinx build environment. """ if cls.ABORT_AFTER_READ: ...

[ "def", "env_updated", "(", "cls", ",", "app", ",", "env", ")", ":", "if", "cls", ".", "ABORT_AFTER_READ", ":", "config", "=", "{", "n", ":", "getattr", "(", "app", ".", "config", ",", "n", ")", "for", "n", "in", "(", "a", "for", "a", "in", "dir...

51.833333

22.833333

def send_packed_command(self, command): "Send an already packed command to the Redis server" if not self._sock: self.connect() try: if isinstance(command, str): command = [command] for item in command: self._sock.sendall(item) ...

[ "def", "send_packed_command", "(", "self", ",", "command", ")", ":", "if", "not", "self", ".", "_sock", ":", "self", ".", "connect", "(", ")", "try", ":", "if", "isinstance", "(", "command", ",", "str", ")", ":", "command", "=", "[", "command", "]", ...

35.44

12.24

def pipe_urlinput(context=None, _INPUT=None, conf=None, **kwargs): """An input that prompts the user for a url and yields it forever. Not loopable. Parameters ---------- context : pipe2py.Context object _INPUT : unused conf : { 'name': {'value': 'parameter name'}, 'prompt': ...

[ "def", "pipe_urlinput", "(", "context", "=", "None", ",", "_INPUT", "=", "None", ",", "conf", "=", "None", ",", "*", "*", "kwargs", ")", ":", "value", "=", "utils", ".", "get_input", "(", "context", ",", "conf", ")", "value", "=", "utils", ".", "ur...

24.208333

19.166667

def excel_to_html(path, sheetname='Sheet1', css_classes='', \ caption='', details=[], row_headers=False, merge=False): """ Convert an excel spreadsheet to an html table. This function supports the conversion of merged cells. It can be used in code or run from the command-line. If passed the co...

[ "def", "excel_to_html", "(", "path", ",", "sheetname", "=", "'Sheet1'", ",", "css_classes", "=", "''", ",", "caption", "=", "''", ",", "details", "=", "[", "]", ",", "row_headers", "=", "False", ",", "merge", "=", "False", ")", ":", "def", "get_data_on...

33.608142

17.709924

def get_aggregation_propensity(self, seq, outdir, cutoff_v=5, cutoff_n=5, run_amylmuts=False): """Run the AMYLPRED2 web server for a protein sequence and get the consensus result for aggregation propensity. Args: seq (str, Seq, SeqRecord): Amino acid sequence outdir (str): Direc...

[ "def", "get_aggregation_propensity", "(", "self", ",", "seq", ",", "outdir", ",", "cutoff_v", "=", "5", ",", "cutoff_n", "=", "5", ",", "run_amylmuts", "=", "False", ")", ":", "seq", "=", "ssbio", ".", "protein", ".", "sequence", ".", "utils", ".", "ca...

55.304348

39.826087

def create(self, email, phone, country_code=1, send_install_link_via_sms=False): """ sends request to create new user. :param string email: :param string phone: :param string country_code: :param bool send_install_link_via_sms: :return: """ data = ...

[ "def", "create", "(", "self", ",", "email", ",", "phone", ",", "country_code", "=", "1", ",", "send_install_link_via_sms", "=", "False", ")", ":", "data", "=", "{", "\"user\"", ":", "{", "\"email\"", ":", "email", ",", "\"cellphone\"", ":", "phone", ",",...

28.272727

17.818182

def build_module(self, module, loglevel=logging.DEBUG): """Build passed-in module. """ shutit_global.shutit_global_object.yield_to_draw() cfg = self.cfg self.log('Building ShutIt module: ' + module.module_id + ' with run order: ' + str(module.run_order), level=logging.INFO) self.build['report'] = (self.buil...

[ "def", "build_module", "(", "self", ",", "module", ",", "loglevel", "=", "logging", ".", "DEBUG", ")", ":", "shutit_global", ".", "shutit_global_object", ".", "yield_to_draw", "(", ")", "cfg", "=", "self", ".", "cfg", "self", ".", "log", "(", "'Building Sh...

87

53.194444

def temporal_from_rdf(period_of_time): '''Failsafe parsing of a temporal coverage''' try: if isinstance(period_of_time, Literal): return temporal_from_literal(str(period_of_time)) elif isinstance(period_of_time, RdfResource): return temporal_from_resource(period_of_time) ...

[ "def", "temporal_from_rdf", "(", "period_of_time", ")", ":", "try", ":", "if", "isinstance", "(", "period_of_time", ",", "Literal", ")", ":", "return", "temporal_from_literal", "(", "str", "(", "period_of_time", ")", ")", "elif", "isinstance", "(", "period_of_ti...

50.25

19.083333

def dragDip(self, (x0, y0), (x1, y1), duration, steps=1, orientation=-1): """ Sends drag event in DIP (actually it's using C{input swipe} command. @param (x0, y0): starting point in DIP @param (x1, y1): ending point in DIP @param duration: duration of the event in ms @pa...

[ "def", "dragDip", "(", "self", ",", "(", "x0", ",", "y0", ")", ",", "(", "x1", ",", "y1", ")", ",", "duration", ",", "steps", "=", "1", ",", "orientation", "=", "-", "1", ")", ":", "self", ".", "__checkTransport", "(", ")", "if", "orientation", ...

39.315789

19.210526

def valid_lock(self): """ See if the lock exists and is left over from an old process. """ lock_pid = self.get_lock_pid() # If we're unable to get lock_pid if lock_pid is None: return False # this is our process if self._pid == lock_pid: ...

[ "def", "valid_lock", "(", "self", ")", ":", "lock_pid", "=", "self", ".", "get_lock_pid", "(", ")", "# If we're unable to get lock_pid", "if", "lock_pid", "is", "None", ":", "return", "False", "# this is our process", "if", "self", ".", "_pid", "==", "lock_pid",...

22.04

17.96

def get_indic_syllabic_category_property(value, is_bytes=False): """Get `INDIC SYLLABIC CATEGORY` property.""" obj = unidata.ascii_indic_syllabic_category if is_bytes else unidata.unicode_indic_syllabic_category if value.startswith('^'): negated = value[1:] value = '^' + unidata.unicode_al...

[ "def", "get_indic_syllabic_category_property", "(", "value", ",", "is_bytes", "=", "False", ")", ":", "obj", "=", "unidata", ".", "ascii_indic_syllabic_category", "if", "is_bytes", "else", "unidata", ".", "unicode_indic_syllabic_category", "if", "value", ".", "startsw...

39.416667

31

def save(self, filething=None): """Save changes to a file. If no filename is given, the one most recently loaded is used. Tags are always written at the end of the file, and include a header and a footer. """ fileobj = filething.fileobj data = _APEv2Data(fileo...

[ "def", "save", "(", "self", ",", "filething", "=", "None", ")", ":", "fileobj", "=", "filething", ".", "fileobj", "data", "=", "_APEv2Data", "(", "fileobj", ")", "if", "data", ".", "is_at_start", ":", "delete_bytes", "(", "fileobj", ",", "data", ".", "...

32.830508

17.355932

def get_db_prep_save(self, value, connection=None): """ Returns field's value prepared for saving into a database. """ ## convert to settings.TIME_ZONE if value is not None: if value.tzinfo is None: value = default_tz.localize(value) else: ...

[ "def", "get_db_prep_save", "(", "self", ",", "value", ",", "connection", "=", "None", ")", ":", "## convert to settings.TIME_ZONE", "if", "value", "is", "not", "None", ":", "if", "value", ".", "tzinfo", "is", "None", ":", "value", "=", "default_tz", ".", "...

41.818182

14

def gen_radio_list(sig_dic): ''' For generating List view HTML file for RADIO. for each item. ''' view_zuoxiang = '''<span class="iga_pd_val">''' dic_tmp = sig_dic['dic'] for key in dic_tmp.keys(): tmp_str = '''{{% if postinfo.extinfo['{0}'][0] == "{1}" %}} {2} {{% end %}} '...

[ "def", "gen_radio_list", "(", "sig_dic", ")", ":", "view_zuoxiang", "=", "'''<span class=\"iga_pd_val\">'''", "dic_tmp", "=", "sig_dic", "[", "'dic'", "]", "for", "key", "in", "dic_tmp", ".", "keys", "(", ")", ":", "tmp_str", "=", "'''{{% if postinfo.extinfo['{0}'...

29.533333

20.466667

def check_eigen_solver(eigen_solver, solver_kwds, size=None, nvec=None): """Check that the selected eigensolver is valid Parameters ---------- eigen_solver : string string value to validate size, nvec : int (optional) if both provided, use the specified problem size and number of ve...

[ "def", "check_eigen_solver", "(", "eigen_solver", ",", "solver_kwds", ",", "size", "=", "None", ",", "nvec", "=", "None", ")", ":", "if", "eigen_solver", "in", "BAD_EIGEN_SOLVERS", ":", "raise", "ValueError", "(", "BAD_EIGEN_SOLVERS", "[", "eigen_solver", "]", ...

37.422222

17.6

def _check_stringify_year_column(self, column_index): ''' Same as _check_stringify_year_row but for columns. ''' table_column = TableTranspose(self.table)[column_index] # State trackers prior_year = None for row_index in range(self.start[0]+1, self.end[0]): ...

[ "def", "_check_stringify_year_column", "(", "self", ",", "column_index", ")", ":", "table_column", "=", "TableTranspose", "(", "self", ".", "table", ")", "[", "column_index", "]", "# State trackers", "prior_year", "=", "None", "for", "row_index", "in", "range", ...

39.352941

18.058824

def negotiate_forced_aspect(self, options, accepts): """Order specified options in function of the specified accept priorities.""" if not options: return None priorities = {} for i, o in enumerate(options): p = accepts.get(o, None) if p is No...

[ "def", "negotiate_forced_aspect", "(", "self", ",", "options", ",", "accepts", ")", ":", "if", "not", "options", ":", "return", "None", "priorities", "=", "{", "}", "for", "i", ",", "o", "in", "enumerate", "(", "options", ")", ":", "p", "=", "accepts",...

31.181818

17.545455

def images(self, type): """ Return the list of images available for this type on controller and on the compute node. """ images = [] res = yield from self.http_query("GET", "/{}/images".format(type), timeout=None) images = res.json try: if ty...

[ "def", "images", "(", "self", ",", "type", ")", ":", "images", "=", "[", "]", "res", "=", "yield", "from", "self", ".", "http_query", "(", "\"GET\"", ",", "\"/{}/images\"", ".", "format", "(", "type", ")", ",", "timeout", "=", "None", ")", "images", ...

38.047619

22.047619

def _get_stack_frame(stacklevel): """ utility functions to get a stackframe, skipping internal frames. """ stacklevel = stacklevel + 1 if stacklevel <= 1 or _is_internal_frame(sys._getframe(1)): # If frame is too small to care or if the warning originated in # internal code, then do ...

[ "def", "_get_stack_frame", "(", "stacklevel", ")", ":", "stacklevel", "=", "stacklevel", "+", "1", "if", "stacklevel", "<=", "1", "or", "_is_internal_frame", "(", "sys", ".", "_getframe", "(", "1", ")", ")", ":", "# If frame is too small to care or if the warning ...

38.352941

14.117647

def ped_parser(self, family_info): """ Parse .ped formatted family info. Add all family info to the parser object Arguments: family_info (iterator): An iterator with family info """ for line in family_info: # Che...

[ "def", "ped_parser", "(", "self", ",", "family_info", ")", ":", "for", "line", "in", "family_info", ":", "# Check if commented line or empty line:", "if", "not", "line", ".", "startswith", "(", "'#'", ")", "and", "not", "all", "(", "c", "in", "whitespace", "...

41.941176

19.470588

def _get_style_of_faulting_term(self, C, rup): """ Get fault type dummy variables Fault type (Strike-slip, Normal, Thrust/reverse) is derived from rake angle. Rakes angles within 30 of horizontal are strike-slip, angles from 30 to 150 are reverse, and angles from ...

[ "def", "_get_style_of_faulting_term", "(", "self", ",", "C", ",", "rup", ")", ":", "if", "np", ".", "abs", "(", "rup", ".", "rake", ")", "<=", "30.0", "or", "(", "180.0", "-", "np", ".", "abs", "(", "rup", ".", "rake", ")", ")", "<=", "30.0", "...

36.15

14.35

def pattern_to_str(pattern): """Convert regex pattern to string. If pattern is string it returns itself, if pattern is SRE_Pattern then return pattern attribute :param pattern: pattern object or string :return: str: pattern sttring """ if isinstance(pattern, str): return repr(patter...

[ "def", "pattern_to_str", "(", "pattern", ")", ":", "if", "isinstance", "(", "pattern", ",", "str", ")", ":", "return", "repr", "(", "pattern", ")", "else", ":", "return", "repr", "(", "pattern", ".", "pattern", ")", "if", "pattern", "else", "None" ]

31.583333

12.75

def dispatch_hook(key, hooks, hook_data, **kwargs): """Dispatches a hook dictionary on a given piece of data.""" hooks = hooks or {} hooks = hooks.get(key) if hooks: if hasattr(hooks, '__call__'): hooks = [hooks] for hook in hooks: _hook_data = hook(hook_data, **k...

[ "def", "dispatch_hook", "(", "key", ",", "hooks", ",", "hook_data", ",", "*", "*", "kwargs", ")", ":", "hooks", "=", "hooks", "or", "{", "}", "hooks", "=", "hooks", ".", "get", "(", "key", ")", "if", "hooks", ":", "if", "hasattr", "(", "hooks", "...

34.5

11

async def update_queue(self): """ Send waiting jobs to available agents """ # For now, round-robin not_found_for_agent = [] while len(self._available_agents) > 0 and len(self._waiting_jobs) > 0: agent_addr = self._available_agents.pop(0) # Find ...

[ "async", "def", "update_queue", "(", "self", ")", ":", "# For now, round-robin", "not_found_for_agent", "=", "[", "]", "while", "len", "(", "self", ".", "_available_agents", ")", ">", "0", "and", "len", "(", "self", ".", "_waiting_jobs", ")", ">", "0", ":"...

50.026316

31.447368

def sample(self, input_sample, num_samples, num_params, k_choices, num_groups): """Computes the optimum k_choices of trajectories from the input_sample. Arguments --------- input_sample : numpy.ndarray num_samples : int The number of samples to...

[ "def", "sample", "(", "self", ",", "input_sample", ",", "num_samples", ",", "num_params", ",", "k_choices", ",", "num_groups", ")", ":", "return", "self", ".", "_strategy", ".", "sample", "(", "input_sample", ",", "num_samples", ",", "num_params", ",", "k_ch...

31.041667

16.375

def find(cls, _id): """ Returns the individual instance with the given ID, if it exists. Raises :py:class:`PanoptesAPIException` if the object with that ID is not found. """ if not _id: return None try: return next(cls.where(id=_id)) ...

[ "def", "find", "(", "cls", ",", "_id", ")", ":", "if", "not", "_id", ":", "return", "None", "try", ":", "return", "next", "(", "cls", ".", "where", "(", "id", "=", "_id", ")", ")", "except", "StopIteration", ":", "raise", "PanoptesAPIException", "(",...

30.6

20.066667

def getEdgeDirected(self, networkId, edgeId, verbose=None): """ Returns true if the edge specified by the `edgeId` and `networkId` parameters is directed. :param networkId: SUID of the network containing the edge :param edgeId: SUID of the edge :param verbose: print more ...

[ "def", "getEdgeDirected", "(", "self", ",", "networkId", ",", "edgeId", ",", "verbose", "=", "None", ")", ":", "response", "=", "api", "(", "url", "=", "self", ".", "___url", "+", "'networks/'", "+", "str", "(", "networkId", ")", "+", "'/edges/'", "+",...

41.076923

27.692308

def get_report_data_rows(self, request, queryset): """ Using the builders for the queryset model, iterates over the queryset to generate a result with headers and rows. This queryset must be the exact same received in the .process method, which tells us that this function should be c...

[ "def", "get_report_data_rows", "(", "self", ",", "request", ",", "queryset", ")", ":", "model", "=", "queryset", ".", "model", "meta", "=", "model", ".", "_meta", "field_names", "=", "set", "(", "field", ".", "name", "for", "field", "in", "meta", ".", ...

47.909091

25.727273

def configuration_file(cfgfile): '''Find the best match for the configuration file. ''' if cfgfile is not None: return cfgfile # If no file is explicitely specified, probe for the configuration file # location. cfg = './etc/pyca.conf' if not os.path.isfile(cfg): return '/etc/...

[ "def", "configuration_file", "(", "cfgfile", ")", ":", "if", "cfgfile", "is", "not", "None", ":", "return", "cfgfile", "# If no file is explicitely specified, probe for the configuration file", "# location.", "cfg", "=", "'./etc/pyca.conf'", "if", "not", "os", ".", "pat...

30.454545

18.454545