sequence stringlengths 492 15.9k | code stringlengths 75 8.58k |
|---|---|
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:write_file; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 4, identifier:self; 5, identifier:content; 6, default_parameter; 6, 7; 6, 8; 7, identifier:filepath; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:filename; 11, Non... | def write_file(self, content, filepath=None, filename=None, indent=None, keys_to_write=None):
'''
Write a Python dictionary as JSON to a file.
:param content: Dictionary of key-value pairs to save to a file
:param filepath: Path where the file is to be created
:param filename: Na... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:write_values; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 4, identifier:self; 5, identifier:data; 6, default_parameter; 6, 7; 6, 8; 7, identifier:filepath; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:filename; 11, None... | def write_values(self, data, filepath=None, filename=None, indent=None, keys_to_write=None):
name = filename if filename else self.filename
path = filepath if filepath else self.filepath
name = self._ends_with(name, ".json")
path = self._ends_with(path, os.path.sep)
if not os.pat... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_resolve_requirements; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:requirements; 6, block; 6, 7; 6, 24; 6, 37; 6, 48; 6, 52; 6, 63; 6, 73; 6, 84; 6, 186; 6, 246; 6, 252; 7, try_statement; 7, 8; 7, 19; 8, block; 8, 9; 9, express... | def _resolve_requirements(self, requirements):
try:
dut_count = requirements["duts"]["*"]["count"]
except KeyError:
return []
default_values = {
"type": "hardware",
"allowed_platforms": [],
"nick": None,
}
default_values... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:flash; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:binary_location; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:forceflash; 10, None; 11, block; 11, 12; 11, 30; 11, 74; 11,... | def flash(self, binary_location=None, forceflash=None):
if not Flash:
self.logger.error("Mbed-flasher not installed!")
raise ImportError("Mbed-flasher not installed!")
try:
self.build = Build.init(binary_location)
except NotImplementedError as error:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:open_connection; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 18; 5, 46; 5, 64; 5, 82; 5, 197; 5, 251; 5, 264; 5, 282; 6, if_statement; 6, 7; 6, 12; 7, comparison_operator:is; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier... | def open_connection(self):
if self.readthread is not None:
raise DutConnectionError("Trying to open serial port which was already open")
self.logger.info("Open Connection "
"for '%s' using '%s' baudrate: %d" % (self.dut_name,
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:print_info; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 12; 5, 23; 5, 27; 5, 31; 5, 49; 5, 71; 5, 188; 5, 222; 5, 231; 5, 240; 5, 247; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:table; 9, call; 9, 10... | def print_info(self):
table = PrettyTable()
start_string = "DutSerial {} \n".format(self.name)
row = []
info_string = ""
if self.config:
info_string = info_string + "Configuration for this DUT:\n\n {} \n".format(self.config)
if self.comport:
table.... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:check; 3, parameters; 3, 4; 4, identifier:labels; 5, block; 5, 6; 5, 19; 5, 31; 5, 53; 5, 61; 5, 73; 5, 93; 5, 130; 6, if_statement; 6, 7; 6, 13; 7, not_operator; 7, 8; 8, call; 8, 9; 8, 10; 9, identifier:isinstance; 10, argument_list; 10, 11; ... | def check(labels):
if not isinstance(labels, list):
raise IOError('labels are not in a list')
if not len(labels):
raise IOError('the labels list is empty')
if not all([isinstance(l, np.ndarray) for l in labels]):
raise IOError('all labels must be numpy arrays'... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 24; 2, function_name:write; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 12; 3, 15; 3, 18; 3, 21; 4, identifier:filename; 5, identifier:groupname; 6, identifier:items; 7, identifier:times; 8, identifier:features; 9, default_parameter; 9, 10; 9, 11; 10, id... | def write(filename, groupname, items, times, features, properties=None,
dformat='dense', chunk_size='auto', sparsity=0.1, mode='a'):
sparsity = sparsity if dformat == 'sparse' else None
data = Data(items, times, features, properties=properties,
sparsity=sparsity, check=True)
Writer... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 2, function_name:read; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:from_item; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:to_item; 10, None; 11, default_parameter; 11, 12; 11,... | def read(self, from_item=None, to_item=None,
from_time=None, to_time=None):
if to_item is None:
to_item = self.items.data[-1] if from_item is None else from_item
if from_item is None:
from_item = self.items.data[0]
if not self.items.is_valid_interval(from_ite... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:parse; 3, parameters; 3, 4; 4, identifier:s; 5, block; 5, 6; 5, 32; 5, 48; 5, 373; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:d; 9, call; 9, 10; 9, 11; 10, identifier:dict; 11, argument_list; 11, 12; 11, 15; 11, 18;... | def parse(s):
d = dict(ninputs=None, noutputs=None,
input_labels=None, output_labels=None,
intype=None, cover=set())
lines = [line.strip() for line in s.splitlines()]
for i, line in enumerate(lines, start=1):
if not line or _COMMENT.match(line):
continue
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:var; 3, parameters; 3, 4; 3, 5; 4, identifier:name; 5, default_parameter; 5, 6; 5, 7; 6, identifier:index; 7, None; 8, block; 8, 9; 8, 16; 8, 51; 8, 60; 8, 90; 8, 145; 8, 194; 8, 223; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, ... | def var(name, index=None):
tname = type(name)
if tname is str:
names = (name, )
elif tname is tuple:
names = name
else:
fstr = "expected name to be a str or tuple, got {0.__name__}"
raise TypeError(fstr.format(tname))
if not names:
raise ValueError("expected a... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_itemize; 3, parameters; 3, 4; 4, identifier:objs; 5, block; 5, 6; 5, 21; 5, 35; 6, if_statement; 6, 7; 6, 15; 7, not_operator; 7, 8; 8, call; 8, 9; 8, 10; 9, identifier:isinstance; 10, argument_list; 10, 11; 10, 12; 11, identifier:objs; 12, at... | def _itemize(objs):
if not isinstance(objs, collections.Sequence):
raise TypeError("expected a sequence of Function")
isseq = [isinstance(obj, collections.Sequence) for obj in objs]
if not any(isseq):
ftype = None
for obj in objs:
if ftype is None:
if isin... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_filtdim; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:items; 5, identifier:shape; 6, identifier:dim; 7, identifier:nsl; 8, block; 8, 9; 8, 23; 8, 30; 8, 36; 8, 52; 8, 61; 8, 67; 8, 341; 9, expression_statement; 9, 10; 10, assignment; 1... | def _filtdim(items, shape, dim, nsl):
normshape = tuple(stop - start for start, stop in shape)
nsl_type = type(nsl)
newitems = list()
num = reduce(operator.mul, normshape[:dim+1])
size = len(items) // num
n = normshape[dim]
if nsl_type is int:
for i in range(num):
if i % ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 1, 10; 2, function_name:parse; 3, parameters; 3, 4; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:text; 6, type; 6, 7; 7, identifier:str; 8, type; 8, 9; 9, identifier:Docstring; 10, block; 10, 11; 10, 17; 10, 23; 10, 32; 10, 41; 10, 78; 10, 88; 10, 98; 10, 148;... | def parse(text: str) -> Docstring:
ret = Docstring()
if not text:
return ret
text = inspect.cleandoc(text)
match = _titles_re.search(text)
if match:
desc_chunk = text[: match.start()]
meta_chunk = text[match.start() :]
else:
desc_chunk = text
meta_chunk = ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:generate; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:self; 5, identifier:tool; 6, default_parameter; 6, 7; 6, 8; 7, identifier:copied; 8, False; 9, default_parameter; 9, 10; 9, 11; 10, identifier:copy; 11, False; 12, block; 12, 13; 1... | def generate(self, tool, copied=False, copy=False):
tools = []
if not tool:
logger.info("Workspace supports one tool for all projects within.")
return -1
else:
tools = [tool]
result = 0
for export_tool in tools:
tool_export = ToolsS... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_send_request; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:request; 6, block; 6, 7; 6, 16; 6, 31; 6, 40; 6, 46; 6, 70; 6, 79; 6, 109; 6, 116; 6, 153; 6, 159; 6, 190; 6, 244; 6, 252; 6, 260; 6, 266; 6, 302; 7, expression_stateme... | def _send_request(self, request):
headers = {"X-Experience-API-Version": self.version}
if self.auth is not None:
headers["Authorization"] = self.auth
headers.update(request.headers)
params = request.query_params
params = {k: unicode(params[k]).encode('utf-8') for k in... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:query_statements; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:query; 6, block; 6, 7; 6, 11; 6, 24; 6, 85; 6, 97; 6, 103; 6, 112; 6, 130; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:params; 10, dicti... | def query_statements(self, query):
params = {}
param_keys = [
"registration",
"since",
"until",
"limit",
"ascending",
"related_activities",
"related_agents",
"format",
"attachments",
]
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:retrieve_state; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:self; 5, identifier:activity; 6, identifier:agent; 7, identifier:state_id; 8, default_parameter; 8, 9; 8, 10; 9, identifier:registration; 10, None; 11, block; 11, 12; 1... | def retrieve_state(self, activity, agent, state_id, registration=None):
if not isinstance(activity, Activity):
activity = Activity(activity)
if not isinstance(agent, Agent):
agent = Agent(agent)
request = HTTPRequest(
method="GET",
resource="activi... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:as_version; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:version; 7, attribute; 7, 8; 7, 9; 8, identifier:Version; 9, identifier:latest; 10, block; 10, 11; 10, 235; 11, if_statement; 11, 12; 11... | def as_version(self, version=Version.latest):
if not isinstance(self, list):
result = {}
for k, v in self.iteritems() if isinstance(self, dict) else vars(self).iteritems():
k = self._props_corrected.get(k, k)
if isinstance(v, SerializableBase):
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 22; 2, function_name:xrun; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 19; 4, identifier:command; 5, identifier:options; 6, default_parameter; 6, 7; 6, 8; 7, identifier:log; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:_log_container_as_... | def xrun(command, options, log=None, _log_container_as_started=False, logfile=None, timeout=-1, kill_callback=None):
cmd = " ".join([command] + list(map(str, options)) )
def _print_info(msg):
if msg is None: return
if log:
log.info(msg)
else:
print(msg)
def _p... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:to_items; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:func; 7, identifier:str; 8, block; 8, 9; 9, return_statement; 9, 10; 10, list_comprehension; 10, 11; 10, 21; 11, tuple; 11, 12; 11, 13; 12,... | def to_items(self, func=str):
return [
(key, func(self.kwargs[key]))
for key in sorted(self.kwargs.keys())
] |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_apply_sub_frames; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:cls; 5, identifier:documents; 6, identifier:subs; 7, block; 7, 8; 8, for_statement; 8, 9; 8, 12; 8, 17; 9, pattern_list; 9, 10; 9, 11; 10, identifier:path; 11, identifier:project... | def _apply_sub_frames(cls, documents, subs):
for path, projection in subs.items():
sub = None
expect_map = False
if '$sub' in projection:
sub = projection.pop('$sub')
elif '$sub.' in projection:
sub = projection.pop('$sub.')
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_dereference; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:cls; 5, identifier:documents; 6, identifier:references; 7, block; 7, 8; 8, for_statement; 8, 9; 8, 12; 8, 17; 9, pattern_list; 9, 10; 9, 11; 10, identifier:path; 11, identifier:projec... | def _dereference(cls, documents, references):
for path, projection in references.items():
if '$ref' not in projection:
continue
ids = set()
for document in documents:
value = cls._path_to_value(path, document)
if not value:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:p; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:i; 5, identifier:sample_size; 6, identifier:weights; 7, block; 7, 8; 7, 14; 7, 21; 7, 28; 7, 32; 7, 36; 7, 125; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10, identifier:weight_... | def p(i, sample_size, weights):
weight_i = weights[i]
weights_sum = sum(weights)
other_weights = list(weights)
del other_weights[i]
probability_of_i = 0
for picks in range(0, sample_size):
permutations = list(itertools.permutations(other_weights, picks))
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:diff_to_html; 3, parameters; 3, 4; 3, 5; 4, identifier:cls; 5, identifier:details; 6, block; 6, 7; 6, 11; 6, 17; 6, 63; 6, 76; 6, 139; 6, 152; 6, 256; 6, 269; 6, 332; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:chan... | def diff_to_html(cls, details):
changes = []
if not details:
return ''
def _frame(value):
if isinstance(value, dict) and '_str' in value:
return value['_str']
elif isinstance(value, list):
return ', '.join([_frame(v) for v in va... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:SortBy; 3, parameters; 3, 4; 4, list_splat_pattern; 4, 5; 5, identifier:qs; 6, block; 6, 7; 6, 11; 6, 54; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:sort; 10, list:[]; 11, for_statement; 11, 12; 11, 13; 11, 14; 12,... | def SortBy(*qs):
sort = []
for q in qs:
if q._path.endswith('.desc'):
sort.append((q._path[:-5], DESCENDING))
else:
sort.append((q._path, ASCENDING))
return sort |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 2, function_name:refresh; 3, parameters; 4, block; 4, 5; 4, 9; 4, 51; 4, 65; 4, 72; 4, 141; 5, expression_statement; 5, 6; 6, assignment; 6, 7; 6, 8; 7, identifier:override_files; 8, list:[]; 9, for_statement; 9, 10; 9, 11; 9, 16; 10, identifier:stack; 11, call... | def refresh():
override_files = []
for stack in traceback.extract_stack():
f = os.path.join(os.path.dirname(stack[0]), OVERRIDE_FILE)
if f not in override_files:
override_files.insert(0, f)
if OVERRIDE_FILE in override_files:
del override_files[override_files.index(OVERRI... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 23; 2, function_name:setup; 3, parameters; 3, 4; 3, 14; 3, 18; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:level; 6, type; 6, 7; 7, generic_type; 7, 8; 7, 9; 8, identifier:Union; 9, type_parameter; 9, 10; 9, 12; 10, type; 10, 11; 11, identifier:str; 12, type; 12... | def setup(level: Union[str, int], structured: bool, config_path: str = None):
global logs_are_structured
logs_are_structured = structured
if not isinstance(level, int):
level = logging._nameToLevel[level]
def ensure_utf8_stream(stream):
if not isinstance(stream, io.StringIO) and hasattr(... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:getMessage; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 39; 5, 148; 6, if_statement; 6, 7; 6, 16; 6, 28; 7, call; 7, 8; 7, 9; 8, identifier:isinstance; 9, argument_list; 9, 10; 9, 13; 10, attribute; 10, 11; 10, 12; 11, identifie... | def getMessage(self):
if isinstance(self.msg, numpy.ndarray):
msg = self.array2string(self.msg)
else:
msg = str(self.msg)
if self.args:
a2s = self.array2string
if isinstance(self.args, Dict):
args = {k: (a2s(v) if isinstance(v, nump... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:toposorted; 3, parameters; 3, 4; 3, 5; 4, identifier:nodes; 5, identifier:edges; 6, block; 6, 7; 6, 14; 6, 21; 6, 51; 6, 62; 6, 66; 6, 138; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:incoming; 10, call; 10, 11; 10,... | def toposorted(nodes, edges):
incoming = defaultdict(set)
outgoing = defaultdict(set)
for edge in edges:
incoming[edge.to_id].add(edge.from_id)
outgoing[edge.from_id].add(edge.to_id)
working_set = list(nodes.values())
results = []
while working_set:
remaining = []
... |
0, ERROR; 0, 1; 0, 2; 0, 5; 0, 7; 0, 41; 0, 51; 0, 63; 0, 74; 0, 77; 0, 303; 0, 306; 0, 324; 0, 334; 0, 335; 1, identifier:proc; 2, parameters; 2, 3; 2, 4; 3, identifier:ctx; 4, identifier:files; 5, expression_statement; 5, 6; 6, string:'''Process calculated structures'''; 7, function_definition; 7, 8; 7, 9; 7, 12; 8, ... | def proc(ctx, files):
'''Process calculated structures'''
def calc_reader(fn, verb):
if verb:
echo('Reading: {:<60s}\r'.format(fn), nl=False, err=True)
return ase.io.read(fn)
action = ctx.parent.params['action']
systems = [calc_reader(calc, verbose) for calc in files]
if ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:sample; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 4, identifier:self; 5, identifier:bqm; 6, default_parameter; 6, 7; 6, 8; 7, identifier:init_solution; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:tenure; 11, N... | def sample(self, bqm, init_solution=None, tenure=None, scale_factor=1, timeout=20, num_reads=1):
if init_solution is not None:
if not isinstance(init_solution, dimod.SampleSet):
raise TypeError("'init_solution' should be a 'dimod.SampleSet' instance")
if len(init_solution... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:mmi_to_raster; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:force_flag; 7, False; 8, default_parameter; 8, 9; 8, 10; 9, identifier:algorithm; 10, identifier:USE_ASCII; 11, block; 11, 12; ... | def mmi_to_raster(self, force_flag=False, algorithm=USE_ASCII):
LOGGER.debug('mmi_to_raster requested.')
if algorithm is None:
algorithm = USE_ASCII
if self.algorithm_name:
tif_path = os.path.join(
self.output_dir, '%s-%s.tif' % (
self.... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:create_keyword_file; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:algorithm; 6, block; 6, 7; 6, 13; 6, 20; 6, 35; 6, 42; 6, 57; 6, 61; 6, 90; 6, 190; 6, 211; 6, 215; 6, 240; 6, 251; 6, 302; 6, 347; 6, 375; 6, 381; 6, 389; 6, 401... | def create_keyword_file(self, algorithm):
keyword_io = KeywordIO()
mmi_default_classes = default_classification_thresholds(
earthquake_mmi_scale
)
mmi_default_threshold = {
earthquake_mmi_scale['key']: {
'active': True,
'classes': m... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_check_value_mapping; 3, parameters; 3, 4; 3, 5; 4, identifier:layer; 5, default_parameter; 5, 6; 5, 7; 6, identifier:exposure_key; 7, None; 8, block; 8, 9; 8, 24; 8, 33; 8, 83; 8, 89; 8, 136; 8, 143; 8, 147; 8, 167; 8, 171; 8, 189; 8, 201; 8, ... | def _check_value_mapping(layer, exposure_key=None):
index = layer.fields().lookupField(exposure_type_field['field_name'])
unique_exposure = layer.uniqueValues(index)
if layer.keywords['layer_purpose'] == layer_purpose_hazard['key']:
if not exposure_key:
message = tr('Hazard value mapping... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:clean_inasafe_fields; 3, parameters; 3, 4; 4, identifier:layer; 5, block; 5, 6; 5, 10; 5, 86; 5, 110; 5, 124; 5, 128; 5, 180; 5, 191; 5, 195; 5, 238; 5, 244; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:fields; 9, lis... | def clean_inasafe_fields(layer):
fields = []
if layer.keywords['layer_purpose'] == layer_purpose_exposure['key']:
fields = get_fields(
layer.keywords['layer_purpose'], layer.keywords['exposure'])
elif layer.keywords['layer_purpose'] == layer_purpose_hazard['key']:
fields = get_fi... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_size_is_needed; 3, parameters; 3, 4; 4, identifier:layer; 5, block; 5, 6; 5, 17; 5, 23; 5, 33; 5, 40; 5, 53; 5, 61; 5, 71; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:exposure; 9, call; 9, 10; 9, 15; 10, attribute; ... | def _size_is_needed(layer):
exposure = layer.keywords.get('exposure')
if not exposure:
return False
indivisible_exposure_keys = [f['key'] for f in indivisible_exposure]
if exposure in indivisible_exposure_keys:
return False
if layer.geometryType() == QgsWkbTypes.PointGeometry:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_remove_features; 3, parameters; 3, 4; 4, identifier:layer; 5, block; 5, 6; 5, 14; 5, 25; 5, 33; 5, 41; 5, 52; 5, 65; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:layer_purpose; 9, subscript; 9, 10; 9, 13; 10, attribu... | def _remove_features(layer):
layer_purpose = layer.keywords['layer_purpose']
layer_subcategory = layer.keywords.get(layer_purpose)
compulsory_field = get_compulsory_fields(layer_purpose, layer_subcategory)
inasafe_fields = layer.keywords['inasafe_fields']
field_names = inasafe_fields.get(compulsory_... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_profiles; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:overwrite; 7, False; 8, block; 8, 9; 8, 69; 9, function_definition; 9, 10; 9, 11; 9, 14; 10, function_name:sort_by_locale; 11, paramete... | def get_profiles(self, overwrite=False):
def sort_by_locale(unsorted_profiles, locale):
if locale is None:
return unsorted_profiles
locale = '_%s' % locale[:2]
profiles_our_locale = []
profiles_remaining = []
for profile_name in unsorte... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sorted_keywords_by_order; 3, parameters; 3, 4; 3, 5; 4, identifier:keywords; 5, identifier:order; 6, block; 6, 7; 6, 29; 6, 35; 6, 62; 6, 82; 7, for_statement; 7, 8; 7, 11; 7, 19; 8, pattern_list; 8, 9; 8, 10; 9, identifier:key; 10, identifier:... | def sorted_keywords_by_order(keywords, order):
for key, value in list(keywords.items()):
if value is None:
del keywords[key]
ordered_keywords = OrderedDict()
for key in order:
if key in list(keywords.keys()):
ordered_keywords[key] = keywords.get(key)
for keyword i... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_layer_modes; 3, parameters; 3, 4; 4, identifier:subcategory; 5, block; 5, 6; 5, 15; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:layer_modes; 9, subscript; 9, 10; 9, 14; 10, call; 10, 11; 10, 12; 11, identifier:de... | def get_layer_modes(subcategory):
layer_modes = definition(subcategory)['layer_modes']
return sorted(layer_modes, key=lambda k: k['key']) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 15; 2, function_name:add_ordered_combo_item; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 4, identifier:combo; 5, identifier:text; 6, default_parameter; 6, 7; 6, 8; 7, identifier:data; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:count_selected_fea... | def add_ordered_combo_item(
combo, text, data=None, count_selected_features=None, icon=None):
if count_selected_features is not None:
text += ' (' + tr('{count} selected features').format(
count=count_selected_features) + ')'
size = combo.count()
for combo_index in range(0, size)... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:sort; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 15; 8, attribute; 8, 9; 8, 14; 9, call; 9, 10; 9, 11; 10, identifier:super; 11, argument_list; 11, 12; 11, 13; 12, identifier:JSSObj... | def sort(self):
super(JSSObjectList, self).sort(key=lambda k: k.id) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:sort_by_name; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, expression_statement; 6, 7; 7, call; 7, 8; 7, 15; 8, attribute; 8, 9; 8, 14; 9, call; 9, 10; 9, 11; 10, identifier:super; 11, argument_list; 11, 12; 11, 13; 12, identifie... | def sort_by_name(self):
super(JSSObjectList, self).sort(key=lambda k: k.name) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:find_sorted_task_dependencies; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:task; 5, identifier:task_name; 6, identifier:task_id; 7, block; 7, 8; 7, 21; 7, 54; 7, 83; 7, 91; 7, 98; 7, 110; 7, 114; 7, 123; 7, 131; 7, 143; 8, expression_stateme... | def find_sorted_task_dependencies(task, task_name, task_id):
log.info("find_sorted_task_dependencies {} {}".format(task_name, task_id))
cot_input_dependencies = [
_craft_dependency_tuple(task_name, task_type, task_id)
for task_type, task_id in task['extra'].get('chainOfTrust', {}).get('inputs', ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:get_all_artifacts_per_task_id; 3, parameters; 3, 4; 3, 5; 4, identifier:chain; 5, identifier:upstream_artifacts; 6, block; 6, 7; 6, 11; 6, 76; 6, 100; 6, 122; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:all_artifact... | def get_all_artifacts_per_task_id(chain, upstream_artifacts):
all_artifacts_per_task_id = {}
for link in chain.links:
if link.task_type in PARENT_TASK_TYPES:
add_enumerable_item_to_dict(
dict_=all_artifacts_per_task_id, key=link.task_id, item='public/task-graph.json'
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_upstream_artifacts_full_paths_per_task_id; 3, parameters; 3, 4; 4, identifier:context; 5, block; 5, 6; 5, 16; 5, 30; 5, 37; 5, 41; 5, 45; 5, 122; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:upstream_artifacts; 9,... | def get_upstream_artifacts_full_paths_per_task_id(context):
upstream_artifacts = context.task['payload']['upstreamArtifacts']
task_ids_and_relative_paths = [
(artifact_definition['taskId'], artifact_definition['paths'])
for artifact_definition in upstream_artifacts
]
optional_artifacts_p... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_PreparedData; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:order_by; 7, tuple; 8, block; 8, 9; 8, 17; 8, 26; 8, 66; 8, 175; 9, if_statement; 9, 10; 9, 12; 10, not_operator; 10, 11; 11, identifi... | def _PreparedData(self, order_by=()):
if not order_by:
return self.__data
sorted_data = self.__data[:]
if isinstance(order_by, six.string_types) or (
isinstance(order_by, tuple) and len(order_by) == 2 and
order_by[1].lower() in ["asc", "desc"]):
order_by = (order_by,)
for key... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:ToJSCode; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:self; 5, identifier:name; 6, default_parameter; 6, 7; 6, 8; 7, identifier:columns_order; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:order_by; 11, tuple; 12, block;... | def ToJSCode(self, name, columns_order=None, order_by=()):
encoder = DataTableJSONEncoder()
if columns_order is None:
columns_order = [col["id"] for col in self.__columns]
col_dict = dict([(col["id"], col) for col in self.__columns])
jscode = "var %s = new google.visualization.DataTable();\n" % na... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:ToHtml; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:columns_order; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:order_by; 10, tuple; 11, block; 11, 12; 11, 16; 11, 20; 11, 2... | def ToHtml(self, columns_order=None, order_by=()):
table_template = "<html><body><table border=\"1\">%s</table></body></html>"
columns_template = "<thead><tr>%s</tr></thead>"
rows_template = "<tbody>%s</tbody>"
row_template = "<tr>%s</tr>"
header_cell_template = "<th>%s</th>"
cell_template = "<t... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 14; 2, function_name:ToCsv; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:columns_order; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:order_by; 10, tuple; 11, default_parameter; 11, 12; 11,... | def ToCsv(self, columns_order=None, order_by=(), separator=","):
csv_buffer = six.StringIO()
writer = csv.writer(csv_buffer, delimiter=separator)
if columns_order is None:
columns_order = [col["id"] for col in self.__columns]
col_dict = dict([(col["id"], col) for col in self.__columns])
def en... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:_ToJSonObj; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:columns_order; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:order_by; 10, tuple; 11, block; 11, 12; 11, 29; 11, 46; 1... | def _ToJSonObj(self, columns_order=None, order_by=()):
if columns_order is None:
columns_order = [col["id"] for col in self.__columns]
col_dict = dict([(col["id"], col) for col in self.__columns])
col_objs = []
for col_id in columns_order:
col_obj = {"id": col_dict[col_id]["id"],
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:ToJSon; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:columns_order; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:order_by; 10, tuple; 11, block; 11, 12; 11, 29; 11, 44; 12, e... | def ToJSon(self, columns_order=None, order_by=()):
encoded_response_str = DataTableJSONEncoder().encode(self._ToJSonObj(columns_order, order_by))
if not isinstance(encoded_response_str, str):
return encoded_response_str.encode("utf-8")
return encoded_response_str |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_radix_sort; 3, parameters; 3, 4; 3, 5; 4, identifier:L; 5, default_parameter; 5, 6; 5, 7; 6, identifier:i; 7, integer:0; 8, block; 8, 9; 8, 19; 8, 23; 8, 34; 8, 69; 8, 83; 9, if_statement; 9, 10; 9, 16; 10, comparison_operator:<=; 10, 11; 10, ... | def _radix_sort(L, i=0):
if len(L) <= 1:
return L
done_bucket = []
buckets = [ [] for x in range(255) ]
for s in L:
if i >= len(s):
done_bucket.append(s)
else:
buckets[ ord(s[i]) ].append(s)
buckets = [ _radix_sort(b, i + 1) for b in buckets ]
return done_bucket + [ b for blist in b... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:fixed_legend_filter_sort; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:fixed_legend_filter_sort; 6, block; 6, 7; 6, 13; 6, 29; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:allowed_values; 10, list:["T... | def fixed_legend_filter_sort(self, fixed_legend_filter_sort):
allowed_values = ["TOP", "BOTTOM"]
if fixed_legend_filter_sort not in allowed_values:
raise ValueError(
"Invalid value for `fixed_legend_filter_sort` ({0}), must be one of {1}"
.format(fixed_legend_... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:print_table; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:title; 5, identifier:headers; 6, identifier:rows; 7, default_parameter; 7, 8; 7, 9; 8, identifier:sort_columns; 9, None; 10, block; 10, 11; 10, 64; 10, 81; 10, 95; 11, if_statem... | def print_table(title, headers, rows, sort_columns=None):
if sort_columns is not None:
if isinstance(sort_columns, int):
rows = sorted(rows, key=itemgetter(sort_columns))
elif isinstance(sort_columns, (list, tuple)):
rows = sorted(rows, key=itemgetter(*sort_columns))
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:formatted; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 10; 5, 96; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:ret; 9, string:"Statistics (times in seconds, lengths in Bytes):\n"; 10, if_statement; 10,... | def formatted(self):
ret = "Statistics (times in seconds, lengths in Bytes):\n"
if self.enabled:
snapshot = sorted(self.snapshot(),
key=lambda item: item[1].avg_time,
reverse=True)
include_svr = False
for nam... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_clusters; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:platform; 6, identifier:retry_contexts; 7, identifier:all_clusters; 8, block; 8, 9; 8, 11; 8, 15; 8, 27; 8, 120; 8, 141; 8, 156; 9, expression_statement; 9, ... | def get_clusters(self, platform, retry_contexts, all_clusters):
''' return clusters sorted by load. '''
possible_cluster_info = {}
candidates = set(copy.copy(all_clusters))
while candidates and not possible_cluster_info:
wait_for_any_cluster(retry_contexts)
for cl... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 1, 20; 2, function_name:get_profile_names_and_default; 3, parameters; 4, type; 4, 5; 5, parenthesized_expression; 5, 6; 6, subscript; 6, 7; 6, 10; 6, 15; 7, attribute; 7, 8; 7, 9; 8, identifier:typing; 9, identifier:Tuple; 10, subscript; 10, 11; 10, 14; 11, att... | def get_profile_names_and_default() -> (
typing.Tuple[typing.Sequence[str], typing.Optional[Profile]]):
with ProfileStore.open() as config:
return sorted(config), config.default |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:print_all_commands; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, keyword_separator; 6, default_parameter; 6, 7; 6, 8; 7, identifier:no_pager; 8, False; 9, block; 9, 10; 9, 20; 9, 37; 9, 53; 9, 57; 9, 174; 10, expression_statement; 10... | def print_all_commands(self, *, no_pager=False):
formatter = self.parent_parser._get_formatter()
command_names = sorted(self.parent_parser.subparsers.choices.keys())
max_name_len = max([len(name) for name in command_names]) + 1
commands = ""
for name in command_names:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:rank_dated_files; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:pattern; 5, identifier:dir; 6, default_parameter; 6, 7; 6, 8; 7, identifier:descending; 8, True; 9, block; 9, 10; 9, 25; 10, expression_statement; 10, 11; 11, assignment; 11, 12; ... | def rank_dated_files(pattern, dir, descending=True):
files = glob.glob(op.join(dir, pattern))
return sorted(files, reverse=descending) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 17; 2, function_name:best_structures; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 4, identifier:uniprot_id; 5, default_parameter; 5, 6; 5, 7; 6, identifier:outname; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:outdir; 10, None; 11, default_paramete... | def best_structures(uniprot_id, outname=None, outdir=None, seq_ident_cutoff=0.0, force_rerun=False):
outfile = ''
if not outdir:
outdir = ''
if not outname and outdir:
outname = uniprot_id
if outname:
outname = op.join(outdir, outname)
outfile = '{}.json'.format(outname)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 14; 2, function_name:map_uniprot_to_pdb; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:seq_ident_cutoff; 7, float:0.0; 8, default_parameter; 8, 9; 8, 10; 9, identifier:outdir; 10, None; 11, default_para... | def map_uniprot_to_pdb(self, seq_ident_cutoff=0.0, outdir=None, force_rerun=False):
if not self.representative_sequence:
log.error('{}: no representative sequence set, cannot use best structures API'.format(self.id))
return None
uniprot_id = self.representative_sequence.uniprot
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 14; 2, function_name:map_uniprot_to_pdb; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:seq_ident_cutoff; 7, float:0.0; 8, default_parameter; 8, 9; 8, 10; 9, identifier:outdir; 10, None; 11, default_para... | def map_uniprot_to_pdb(self, seq_ident_cutoff=0.0, outdir=None, force_rerun=False):
all_representative_uniprots = []
for g in self.genes_with_a_representative_sequence:
uniprot_id = g.protein.representative_sequence.uniprot
if uniprot_id:
if '-' in uniprot_id:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:get_properties_by_type; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:self; 5, identifier:type; 6, default_parameter; 6, 7; 6, 8; 7, identifier:recursive; 8, True; 9, default_parameter; 9, 10; 9, 11; 10, identifier:parent_path; 11, stri... | def get_properties_by_type(self, type, recursive=True, parent_path=""):
if parent_path:
parent_path += "."
if isinstance(type, str):
if type == "*":
type = set(MAPPING_NAME_TYPE.keys()) - set(["nested", "multi_field", "multifield"])
else:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:insert; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:index; 6, identifier:key; 7, identifier:value; 8, block; 8, 9; 8, 42; 8, 52; 9, if_statement; 9, 10; 9, 15; 10, comparison_operator:in; 10, 11; 10, 12; 11, identif... | def insert(self, index, key, value):
if key in self.keyOrder:
n = self.keyOrder.index(key)
del self.keyOrder[n]
if n < index:
index -= 1
self.keyOrder.insert(index, key)
super(SortedDict, self).__setitem__(key, value) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 11; 2, function_name:sort_qualified_edges; 3, parameters; 3, 4; 4, identifier:graph; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Iterable; 8, type_parameter; 8, 9; 9, type; 9, 10; 10, identifier:EdgeTuple; 11, block; 11, 12; 11, 56; 12, express... | def sort_qualified_edges(graph) -> Iterable[EdgeTuple]:
qualified_edges = (
(u, v, k, d)
for u, v, k, d in graph.edges(keys=True, data=True)
if graph.has_edge_citation(u, v, k) and graph.has_edge_evidence(u, v, k)
)
return sorted(qualified_edges, key=_sort_qualified_edges_helper) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 1, 10; 2, function_name:_citation_sort_key; 3, parameters; 3, 4; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:t; 6, type; 6, 7; 7, identifier:EdgeTuple; 8, type; 8, 9; 9, identifier:str; 10, block; 10, 11; 11, return_statement; 11, 12; 12, call; 12, 13; 12, 16... | def _citation_sort_key(t: EdgeTuple) -> str:
return '"{}", "{}"'.format(t[3][CITATION][CITATION_TYPE], t[3][CITATION][CITATION_REFERENCE]) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 1, 18; 2, function_name:clean_pubmed_identifiers; 3, parameters; 3, 4; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:pmids; 6, type; 6, 7; 7, generic_type; 7, 8; 7, 9; 8, identifier:Iterable; 9, type_parameter; 9, 10; 10, type; 10, 11; 11, identifier:str; 12, ... | def clean_pubmed_identifiers(pmids: Iterable[str]) -> List[str]:
return sorted({str(pmid).strip() for pmid in pmids}) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 7; 2, function_name:hash_dump; 3, parameters; 3, 4; 4, identifier:data; 5, type; 5, 6; 6, identifier:str; 7, block; 7, 8; 8, return_statement; 8, 9; 9, call; 9, 10; 9, 31; 10, attribute; 10, 11; 10, 30; 11, call; 11, 12; 11, 15; 12, attribute; 12, 13; 12, 14... | def hash_dump(data) -> str:
return hashlib.sha512(json.dumps(data, sort_keys=True).encode('utf-8')).hexdigest() |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:yield_sorted_by_type; 3, parameters; 3, 4; 4, list_splat_pattern; 4, 5; 5, identifier:typelist; 6, block; 6, 7; 6, 40; 7, function_definition; 7, 8; 7, 9; 7, 11; 8, function_name:decorate; 9, parameters; 9, 10; 10, identifier:fun; 11, block; 11... | def yield_sorted_by_type(*typelist):
def decorate(fun):
@wraps(fun)
def decorated(*args, **kwds):
return iterate_by_type(fun(*args, **kwds), typelist)
return decorated
return decorate |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 20; 1, 22; 2, function_name:build_route_timetable; 3, parameters; 3, 4; 3, 8; 3, 12; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:feed; 6, type; 6, 7; 7, string:"Feed"; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:route_id; 10, type; 10, 11; 11, identifier:str;... | def build_route_timetable(
feed: "Feed", route_id: str, dates: List[str]
) -> DataFrame:
dates = feed.restrict_dates(dates)
if not dates:
return pd.DataFrame()
t = pd.merge(feed.trips, feed.stop_times)
t = t[t["route_id"] == route_id].copy()
a = feed.compute_trip_activity(dates)
fram... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 1, 14; 2, function_name:almost_equal; 3, parameters; 3, 4; 3, 8; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:f; 6, type; 6, 7; 7, identifier:DataFrame; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:g; 10, type; 10, 11; 11, identifier:DataFrame; 12, type; 12... | def almost_equal(f: DataFrame, g: DataFrame) -> bool:
if f.empty or g.empty:
return f.equals(g)
else:
F = (
f.sort_index(axis=1)
.sort_values(list(f.columns))
.reset_index(drop=True)
)
G = (
g.sort_index(axis=1)
.sort_va... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 20; 1, 22; 2, function_name:build_stop_timetable; 3, parameters; 3, 4; 3, 8; 3, 12; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:feed; 6, type; 6, 7; 7, string:"Feed"; 8, typed_parameter; 8, 9; 8, 10; 9, identifier:stop_id; 10, type; 10, 11; 11, identifier:str; 1... | def build_stop_timetable(
feed: "Feed", stop_id: str, dates: List[str]
) -> DataFrame:
dates = feed.restrict_dates(dates)
if not dates:
return pd.DataFrame()
t = pd.merge(feed.trips, feed.stop_times)
t = t[t["stop_id"] == stop_id].copy()
a = feed.compute_trip_activity(dates)
frames =... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_unit_property_names; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:unit_id; 7, None; 8, block; 8, 9; 8, 11; 8, 63; 9, expression_statement; 9, 10; 10, string:'''Get a list of property names f... | def get_unit_property_names(self, unit_id=None):
'''Get a list of property names for a given unit, or for all units if unit_id is None
Parameters
----------
unit_id: int
The unit id for which the property names will be returned
If None (default), will return prope... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:copy_unit_properties; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:sorting; 6, default_parameter; 6, 7; 6, 8; 7, identifier:unit_ids; 8, None; 9, block; 9, 10; 9, 12; 9, 25; 10, expression_statement; 10, 11; 11, string:'''... | def copy_unit_properties(self, sorting, unit_ids=None):
'''Copy unit properties from another sorting extractor to the current
sorting extractor.
Parameters
----------
sorting: SortingExtractor
The sorting extractor from which the properties will be copied
unit... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:copy_unit_spike_features; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:sorting; 6, default_parameter; 6, 7; 6, 8; 7, identifier:unit_ids; 8, None; 9, block; 9, 10; 9, 12; 9, 25; 10, expression_statement; 10, 11; 11, string... | def copy_unit_spike_features(self, sorting, unit_ids=None):
'''Copy unit spike features from another sorting extractor to the current
sorting extractor.
Parameters
----------
sorting: SortingExtractor
The sorting extractor from which the spike features will be copied
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:merge_units; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:unit_ids; 6, block; 6, 7; 6, 9; 6, 13; 6, 42; 6, 46; 7, expression_statement; 7, 8; 8, string:'''This function merges two roots from the curation tree according to the gi... | def merge_units(self, unit_ids):
'''This function merges two roots from the curation tree according to the given unit_ids. It creates a new unit_id and root
that has the merged roots as children.
Parameters
----------
unit_ids: list
The unit ids to be merged
'... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:split_unit; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:unit_id; 6, identifier:indices; 7, block; 7, 8; 7, 10; 7, 14; 7, 43; 8, expression_statement; 8, 9; 9, string:'''This function splits a root from the curation tree a... | def split_unit(self, unit_id, indices):
'''This function splits a root from the curation tree according to the given unit_id and indices. It creates two new unit_ids
and roots that have the split root as a child. This function splits the spike train of the root by the given indices.
Parameters
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_find_best_fit; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:pbin; 6, block; 6, 7; 6, 35; 6, 49; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:fit; 10, generator_expression; 10, 11; 10, 24; 11, tuple; ... | def _find_best_fit(self, pbin):
fit = ((pbin.fitness(r[0], r[1]), k) for k, r in self._sorted_rect.items())
fit = (f for f in fit if f[0] is not None)
try:
_, rect = min(fit, key=self.first_item)
return rect
except ValueError:
return None |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_item_attributes_match; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:crypto_config; 5, identifier:plaintext_item; 6, identifier:encrypted_item; 7, block; 7, 8; 7, 45; 8, for_statement; 8, 9; 8, 12; 8, 17; 9, pattern_list; 9, 10; 9, 11; 10, id... | def _item_attributes_match(crypto_config, plaintext_item, encrypted_item):
for name, value in plaintext_item.items():
if crypto_config.attribute_actions.action(name) == CryptoAction.ENCRYPT_AND_SIGN:
continue
if encrypted_item.get(name) != value:
return False
return True |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:load_css; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 12; 5, 16; 5, 25; 5, 36; 5, 45; 5, 181; 5, 187; 5, 231; 5, 253; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:icons; 9, call; 9, 10; 9, 11; 10, iden... | def load_css(self):
icons = dict()
common_prefix = None
parser = tinycss.make_parser('page3')
stylesheet = parser.parse_stylesheet_file(self.css_file)
is_icon = re.compile("\.(.*):before,?")
for rule in stylesheet.rules:
selector = rule.selector.as_css()
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:rules; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 10; 5, 252; 5, 325; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:list_of_rules; 9, list:[]; 10, for_statement; 10, 11; 10, 12; 10, 15; 11, identifier:... | def rules(self):
list_of_rules = []
for main_row in self.dict_rules:
if 'rules' in main_row:
for rule_row in main_row['rules']:
if 'grants' in rule_row:
for grant_row in rule_row['grants']:
if 'group_id' ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_select_mgmt_networks; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:conf; 6, block; 6, 7; 6, 13; 6, 39; 6, 84; 6, 109; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:nets; 10, subscript; 10, 11; 10, 12;... | def _select_mgmt_networks(self, conf):
nets = conf['nets']
mgmts = sorted(
[
name for name, net in nets.iteritems()
if net.get('management') is True
]
)
if len(mgmts) == 0:
mgmt_name = sorted((nets.keys()))[0]
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:validate_wavetable; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 12; 5, 45; 5, 54; 5, 107; 5, 122; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:wave; 9, attribute; 9, 10; 9, 11; 10, identifier:self; 11,... | def validate_wavetable(self):
wave = self._wavetable
if N.any(wave <= 0):
wrong = N.where(wave <= 0)[0]
raise exceptions.ZeroWavelength(
'Negative or Zero wavelength occurs in wavelength array',
rows=wrong)
sorted = N.sort(wave)
if ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:getStateIndex; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:state; 6, block; 6, 7; 6, 16; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:statecodes; 10, call; 10, 11; 10, 14; 11, attribute; 11, 12; 11, ... | def getStateIndex(self,state):
statecodes = self.getStateCode(state)
return np.searchsorted(self.codes,statecodes).astype(int) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:guess_chimera_path; 3, parameters; 3, 4; 4, default_parameter; 4, 5; 4, 6; 5, identifier:search_all; 6, False; 7, block; 7, 8; 7, 20; 7, 55; 7, 71; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10, identifier:paths; 11, call; 11, ... | def guess_chimera_path(search_all=False):
paths = _search_chimera(CHIMERA_BINARY, CHIMERA_LOCATIONS, CHIMERA_PREFIX,
search_all=search_all)
if not paths and search_all:
headless = '{0[0]}{1}{0[1]}'.format(os.path.split(CHIMERA_BINARY), '-headless')
paths = _search_chi... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_topo_sort; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:forward; 7, True; 8, block; 8, 9; 8, 13; 8, 19; 8, 23; 8, 64; 8, 97; 8, 154; 8, 179; 9, expression_statement; 9, 10; 10, assignment; 10, ... | def _topo_sort(self, forward=True):
topo_list = []
queue = deque()
indeg = {}
if forward:
get_edges = self.out_edges
get_degree = self.inc_degree
get_next = self.tail
else:
get_edges = self.inc_edges
get_degree = self.ou... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 34; 2, function_name:execute_sql; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 10; 3, 13; 3, 16; 3, 19; 3, 22; 3, 25; 3, 28; 3, 31; 4, identifier:server_context; 5, identifier:schema_name; 6, identifier:sql; 7, default_parameter; 7, 8; 7, 9; 8, identifier:container_p... | def execute_sql(server_context, schema_name, sql, container_path=None,
max_rows=None,
sort=None,
offset=None,
container_filter=None,
save_in_session=None,
parameters=None,
required_version=None,
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:find_missing_projections; 3, parameters; 3, 4; 3, 5; 4, identifier:label_list; 5, identifier:projections; 6, block; 6, 7; 6, 13; 6, 20; 6, 58; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:unmapped_combinations; 10, c... | def find_missing_projections(label_list, projections):
unmapped_combinations = set()
if WILDCARD_COMBINATION in projections:
return []
for labeled_segment in label_list.ranges():
combination = tuple(sorted([label.value for label in labeled_segment[2]]))
if combination not in projecti... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:load_projections; 3, parameters; 3, 4; 4, identifier:projections_file; 5, block; 5, 6; 5, 10; 5, 61; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:projections; 9, dictionary; 10, for_statement; 10, 11; 10, 12; 10, 19; ... | def load_projections(projections_file):
projections = {}
for parts in textfile.read_separated_lines_generator(projections_file, '|'):
combination = tuple(sorted([label.strip() for label in parts[0].split(' ')]))
new_label = parts[1].strip()
projections[combination] = new_label
return... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:label_values; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 19; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:all_labels; 9, call; 9, 10; 9, 11; 10, identifier:set; 11, argument_list; 11, 12; 12, list_com... | def label_values(self):
all_labels = set([l.value for l in self])
return sorted(all_labels) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_utt_regions; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 10; 5, 14; 5, 129; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:regions; 9, list:[]; 10, expression_statement; 10, 11; 11, assignment; 11, 1... | def get_utt_regions(self):
regions = []
current_offset = 0
for utt_idx in sorted(self.utt_ids):
offset = current_offset
num_frames = []
refs = []
for cnt in self.containers:
num_frames.append(cnt.get(utt_idx).shape[0])
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:write_separated_lines; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:path; 5, identifier:values; 6, default_parameter; 6, 7; 6, 8; 7, identifier:separator; 8, string:' '; 9, default_parameter; 9, 10; 9, 11; 10, identifier:sort_by_column... | def write_separated_lines(path, values, separator=' ', sort_by_column=0):
f = open(path, 'w', encoding='utf-8')
if type(values) is dict:
if sort_by_column in [0, 1]:
items = sorted(values.items(), key=lambda t: t[sort_by_column])
else:
items = values.items()
for k... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:sort_set; 3, parameters; 3, 4; 4, identifier:s; 5, block; 5, 6; 5, 19; 5, 26; 5, 43; 6, if_statement; 6, 7; 6, 13; 7, not_operator; 7, 8; 8, call; 8, 9; 8, 10; 9, identifier:isinstance; 10, argument_list; 10, 11; 10, 12; 11, identifier:s; 12, i... | def sort_set(s):
if not isinstance(s, Set):
raise TypeError("sets only")
s = frozenset(s)
if s not in _sort_set_memo:
_sort_set_memo[s] = sorted(s, key=_sort_set_key)
return _sort_set_memo[s] |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:parse_tags; 3, parameters; 3, 4; 4, identifier:tagstring; 5, block; 5, 6; 5, 12; 5, 19; 5, 23; 5, 27; 5, 31; 5, 38; 5, 163; 5, 185; 5, 195; 5, 201; 6, if_statement; 6, 7; 6, 9; 7, not_operator; 7, 8; 8, identifier:tagstring; 9, block; 9, 10; 10... | def parse_tags(tagstring):
if not tagstring:
return []
tagstring = force_text(tagstring)
words = []
buffer = []
to_be_split = []
i = iter(tagstring)
try:
while True:
c = six.next(i)
if c == '"':
if buffer:
to_be_spli... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:_sort_by_unique_fields; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:model; 5, identifier:model_objs; 6, identifier:unique_fields; 7, block; 7, 8; 7, 26; 7, 51; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10, identifier:unique... | def _sort_by_unique_fields(model, model_objs, unique_fields):
unique_fields = [
field for field in model._meta.fields
if field.attname in unique_fields
]
def sort_key(model_obj):
return tuple(
field.get_db_prep_save(getattr(model_obj, field.attname),
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:find; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:datum; 6, block; 6, 7; 6, 22; 6, 78; 7, if_statement; 7, 8; 7, 19; 8, boolean_operator:and; 8, 9; 8, 16; 9, call; 9, 10; 9, 11; 10, identifier:isinstance; 11, argument_list; 11,... | def find(self, datum):
if isinstance(datum.value, dict) and self.expressions:
return datum
if isinstance(datum.value, dict) or isinstance(datum.value, list):
key = (functools.cmp_to_key(self._compare)
if self.expressions else None)
return [jsonpath_... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:get_subset_riverid_index_list; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:river_id_list; 6, block; 6, 7; 6, 11; 6, 15; 6, 19; 6, 68; 6, 77; 6, 86; 6, 95; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier... | def get_subset_riverid_index_list(self, river_id_list):
netcdf_river_indices_list = []
valid_river_ids = []
missing_river_ids = []
for river_id in river_id_list:
try:
netcdf_river_indices_list \
.append(self.get_river_index(river_id))
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:get_child_type_choices; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:request; 6, identifier:action; 7, block; 7, 8; 7, 23; 7, 33; 7, 37; 7, 41; 7, 118; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10, identi... | def get_child_type_choices(self, request, action):
choices = super(ChildModelPluginPolymorphicParentModelAdmin, self) \
.get_child_type_choices(request, action)
plugins = self.child_model_plugin_class.get_plugins()
labels = {}
sort_priorities = {}
if plugins:
... |
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