sequence stringlengths 1.19k 35k | code stringlengths 75 8.58k |
|---|---|
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'commit_check'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'va... | def commit_check(self, commands="", req_format="text"):
if not commands:
raise InvalidCommandError('No commands specified')
clean_cmds = []
for cmd in clean_lines(commands):
clean_cmds.append(cmd)
self.lock()
self._session.load_configuration(action='set', ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'connect'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {... | def connect(self):
if self.conn_type == 'paramiko':
self._session = paramiko.SSHClient()
logger = logging.Logger.manager.getLogger('paramiko.transport')
logger.setLevel(logging.CRITICAL)
self._session.set_missing_host_key_policy(
paramiko.AutoAddPo... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'script'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'inbox... | def script(inbox, cfg):
script_name = cfg["id"]
script_id = str(abs(hash((cfg["id"],) + tuple(inbox[0].values()))))[0:8]
args = {}
args["params"] = dict(cfg["params"])
args["in"] = {}
for in_port in cfg["in"]:
for inin_ports in inbox:
in_path = inin_ports.get(in_port, None)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_create_update_tracking_related_event'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'chil... | def _create_update_tracking_related_event(instance):
events = {}
for field, related_fields in instance._tracked_related_fields.items():
if not isinstance(instance._meta.get_field(field), ManyToManyField):
if isinstance(instance._meta.get_field(field), ForeignKey):
value = get... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children... | def list(self, filter=None, type=None, sort=None, limit=None, page=None):
schema = PackageSchema(exclude=('testlist', 'extra_cli_args', 'agent_id', 'options', 'note'))
resp = self.service.list(self.base, filter, type, sort, limit, page)
ps, l = self.service.decode(schema, resp, many=True, links=... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'clean_lines'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'comma... | def clean_lines(commands):
if isinstance(commands, basestring):
if path.isfile(commands):
commands = open(commands, 'rb')
elif len(commands.split(',')) > 1:
commands = commands.split(',')
else:
try:
if commands.strip()[0] != "
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'xpath'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 's... | def xpath(source_xml, xpath_expr, req_format='string'):
tree = source_xml
if not isinstance(source_xml, ET.Element):
tree = objectify.fromstring(source_xml)
for elem in tree.getiterator():
if isinstance(elem.tag, basestring):
i = elem.tag.find('}')
if i >= 0:
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'model_to_dict'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value':... | def model_to_dict(instance, **options):
"Takes a model instance and converts it into a dict."
options = _defaults(options)
attrs = {}
if options['prehook']:
if isinstance(options['prehook'], collections.Callable):
instance = options['prehook'](instance)
if instance is Non... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']}; {'id': '4', 'type': 'identifier', 'chi... | def list(self, id, filter=None, type=None, sort=None, limit=None, page=None):
schema = AttachmentSchema(exclude=('path'))
resp = self.service.list(self._base(id), filter, type, sort, limit, page)
at, l = self.service.decode(schema, resp, many=True, links=True)
return Page(at, l) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'load_item'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def load_item(inbox, type="string", remove=True, buffer=None):
is_file, is_fifo, is_socket = False, False, False
file = inbox[0]
try:
file_type = file[0]
except:
raise ValueError("invalid inbox item")
if file_type == "file":
is_file = os.path.exists(file[1])
elif file_typ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'write_validate'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def write_validate(ctx, param, value):
if value != ("default", "default"):
try:
mode, dest_file = (value[0], value[1])
except IndexError:
raise click.BadParameter('Expecting two arguments, one for how to '
'output (s, single, m, multiple),... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'write_out'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'input'}... | def write_out(input):
to_file, output = input
if to_file != "quiet":
try:
mode, dest_file = to_file
except TypeError:
click.echo(output)
else:
ip = output.split('device: ')[1].split('\n')[0].strip()
if mode in ['m', 'multiple']:
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'endpoint'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'request'... | def endpoint(request):
if request.method != 'POST':
raise Http404
if hasattr(settings, 'BOUNCY_TOPIC_ARN'):
if 'HTTP_X_AMZ_SNS_TOPIC_ARN' not in request.META:
return HttpResponseBadRequest('No TopicArn Header')
if (not request.META['HTTP_X_AMZ_SNS_TOPIC_ARN']
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_process_value'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'v... | def _process_value(self, value, type):
if not isinstance(value, six.string_types + (list,)):
value = json.dumps(value)
return value |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'representatives'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def representatives(self, count=None, sorting=False):
payload = {}
if count is not None:
payload['count'] = self._process_value(count, 'int')
if sorting:
payload['sorting'] = self._process_value(sorting, 'strbool')
resp = self.call('representatives', payload)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iterative_overlap_assembly'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children':... | def iterative_overlap_assembly(
variant_sequences,
min_overlap_size=MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE):
if len(variant_sequences) <= 1:
return variant_sequences
n_before_collapse = len(variant_sequences)
variant_sequences = collapse_substrings(variant_sequences)
n_after_... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ortho_basis'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def ortho_basis(normal, ref_vec=None):
import numpy as np
from scipy import linalg as spla
from scipy import random as sprnd
from ..const import PRM
from ..error import VectorError
RAND_MAG = 0.25
if not len(normal.shape) == 1:
raise ValueError("'normal' is not a vector")
if not ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'orthonorm_check'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '10']}; {'id': '4', 'type': 'identifier', 'children': [],... | def orthonorm_check(a, tol=_DEF.ORTHONORM_TOL, report=False):
import numpy as np
from .base import delta_fxn
orth = True
n_fail = []
o_fail = []
if len(a.shape) == 1:
a_mx = np.matrix(a, dtype=np.float_).T
else:
a_mx = np.matrix(a, dtype=np.float_)
a_split = np.hsplit(a_m... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parallel_check'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def parallel_check(vec1, vec2):
from ..const import PRM
import numpy as np
par = False
for n,v in enumerate([vec1, vec2]):
if not len(v.shape) == 1:
raise ValueError("Bad shape for vector
if not vec1.shape[0] == vec2.shape[0]:
raise ValueError("Vector length mismatch")
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'vec_angle'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 've... | def vec_angle(vec1, vec2):
import numpy as np
from scipy import linalg as spla
from ..const import PRM
if len(vec1.shape) != 1:
raise ValueError("'vec1' is not a vector")
if len(vec2.shape) != 1:
raise ValueError("'vec2' is not a vector")
if vec1.shape[0] != vec2.shape[0]:
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ctr_mass'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'geo... | def ctr_mass(geom, masses):
import numpy as np
from .base import safe_cast as scast
if len(geom.shape) != 1:
raise ValueError("Geometry is not a vector")
if len(masses.shape) != 1:
raise ValueError("Masses cannot be parsed as a vector")
if not geom.shape[0] % 3 == 0:
raise Va... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'inertia_tensor'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def inertia_tensor(geom, masses):
import numpy as np
geom = ctr_geom(geom, masses)
if geom.shape[0] == 3*masses.shape[0]:
masses = masses.repeat(3)
tensor = np.zeros((3,3))
for i in range(3):
for j in range(i,3):
if i == j:
ind = np.concatenate([np.array(l... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '16']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'rot_consts'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '11']}; {'id': '4', 'type': 'identifier', 'children': [],... | def rot_consts(geom, masses, units=_EURC.INV_INERTIA, on_tol=_DEF.ORTHONORM_TOL):
import numpy as np
from ..const import EnumTopType as ETT, EnumUnitsRotConst as EURC, PRM, PHYS
if not units in EURC:
raise ValueError("'{0}' is not a valid units value".format(units))
mom, ax, top = principals(geo... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_fadn_orth'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'v... | def _fadn_orth(vec, geom):
import numpy as np
from scipy import linalg as spla
from ..const import PRM
from ..error import InertiaError
from .vector import orthonorm_check as onchk
if not (len(geom.shape) == 1 and geom.shape[0] % 3 == 0):
raise ValueError("Geometry is not length 3N")
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_fadn_par'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 've... | def _fadn_par(vec, geom):
import numpy as np
from scipy import linalg as spla
from ..const import PRM
from ..error import InertiaError
from .vector import parallel_check as parchk
if not (len(geom.shape) == 1 and geom.shape[0] % 3 == 0):
raise ValueError("Geometry is not length 3N")
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'reference_contexts_for_variants'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', '... | def reference_contexts_for_variants(
variants,
context_size,
transcript_id_whitelist=None):
result = OrderedDict()
for variant in variants:
result[variant] = reference_contexts_for_variant(
variant=variant,
context_size=context_size,
transcript... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'pack_tups'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'list_splat_pattern', 'children': ['5']}, {'id'... | def pack_tups(*args):
import numpy as np
_DEBUG = False
NOT_ITER = -1
UNINIT_VAL = -1
if _DEBUG:
print("args = {0}".format(args))
class StrNoIter(str):
def __iter__(self):
raise NotImplementedError("Non-iterable string")
mod_args = [(StrNoIter(a) if isinstance(a, ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'check_geom'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children':... | def check_geom(c1, a1, c2, a2, tol=_DEF.XYZ_COORD_MATCH_TOL):
from ..const import atom_num
import numpy as np
from ..const import EnumCheckGeomMismatch as ECGM
match = True
if not len(c1.shape) == 1:
raise ValueError(("'c1' is not a vector."))
if not len(c2.shape) == 1:
raise Val... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'assert_npfloatarray'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier... | def assert_npfloatarray(obj, varname, desc, exc, tc, errsrc):
import numpy as np
if varname is None:
var = obj
else:
try:
var = getattr(obj, varname)
except AttributeError:
raise exc(tc, "Attribute '{0}' not defined in '{1}'"
.format(varnam... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_advance_pattern_generators'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children'... | def _advance_pattern_generators(self,p):
valid_generators = []
for g in p.generators:
for trial in range(self.max_trials):
if np.alltrue([self.__distance_valid(g,v,p) for v in valid_generators]):
valid_generators.append(g)
break
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'register'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '10']}; {'id': '4', 'type': 'identifier', 'children': [], '... | def register(self, settings_class=NoSwitcher, *simple_checks,
**conditions):
if settings_class is NoSwitcher:
def decorator(cls):
self.register(cls, *simple_checks, **conditions)
return cls
return decorator
available_checks = self.... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_load_data'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def _load_data(self, atom_syms, coords, bohrs=True):
import numpy as np
from .const import atom_num, PHYS
from .error import XYZError
if 'geoms' in dir(self):
raise XYZError(XYZError.OVERWRITE,
"Cannot overwrite contents of existing OpanXYZ", "")
i... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dist_single'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def dist_single(self, g_num, at_1, at_2):
import numpy as np
from scipy import linalg as spla
from .utils import safe_cast as scast
if not (-self.num_atoms <= at_1 < self.num_atoms):
raise IndexError("Invalid index for 'at_1' ({0})".format(at_1))
if not (-self.num_ato... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dist_iter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': ... | def dist_iter(self, g_nums, ats_1, ats_2, invalid_error=False):
import numpy as np
from .utils import pack_tups
if _DEBUG:
print("g_nums = {0}".format(g_nums))
print("ats_1 = {0}".format(ats_1))
print("ats_2 = {0}".format(ats_2))
arglist = self._none_s... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'angle_single'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children'... | def angle_single(self, g_num, at_1, at_2, at_3):
import numpy as np
from .utils import safe_cast as scast
from .utils.vector import vec_angle
if not(-self.num_atoms <= at_1 < self.num_atoms):
raise IndexError("Invalid index for 'at_1' ({0})".format(at_1))
if not(-self... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'angle_iter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier', 'child... | def angle_iter(self, g_nums, ats_1, ats_2, ats_3, invalid_error=False):
from .utils import pack_tups
if _DEBUG:
print("g_nums = {0}".format(g_nums))
print("ats_1 = {0}".format(ats_1))
print("ats_2 = {0}".format(ats_2))
print("ats_3 = {0}".format(ats_3))
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dihed_iter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11']}; {'id': '4', 'type': 'identif... | def dihed_iter(self, g_nums, ats_1, ats_2, ats_3, ats_4, \
invalid_error=False):
from .utils import pack_tups
if _DEBUG:
print("g_nums = {0}".format(g_nums))
print("ats_1 = {0}".format(ats_1))
print("ats_2 = {0}".for... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'displ_single'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [],... | def displ_single(self, g_num, at_1, at_2):
import numpy as np
from .utils import safe_cast as scast
if not (-self.num_atoms <= at_1 < self.num_atoms):
raise IndexError("Invalid index for 'at_1' ({0})".format(at_1))
if not (-self.num_atoms <= at_2 < self.num_atoms):
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'displ_iter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children':... | def displ_iter(self, g_nums, ats_1, ats_2, invalid_error=False):
from .utils import pack_tups
if _DEBUG:
print("g_nums = {0}".format(g_nums))
print("ats_1 = {0}".format(ats_1))
print("ats_2 = {0}".format(ats_2))
arglist = self._none_subst(g_nums, ats_1, ats_2)... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_none_subst'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': '... | def _none_subst(self, *args):
import numpy as np
arglist = [a for a in args]
none_found = False
none_vals = list(map(lambda e: isinstance(e, type(None)), arglist))
if np.count_nonzero(none_vals) > 1:
raise ValueError(
"Multiple 'None' values [indic... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'new_from_files'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '12', '13', '18', '19', '22']}; {'id':... | def new_from_files(self, basepath, basename, repo, \
bohrs=False, \
software=_E_SW.ORCA, \
repo_clobber=False, **kwargs):
import os
from os import path as osp
from ..xyz import OpanXYZ as OX
from ..grad import OrcaEngrad as OE
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_locus_read'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], '... | def from_locus_read(cls, locus_read, n_ref):
sequence = locus_read.sequence
reference_positions = locus_read.reference_positions
read_pos_before = locus_read.base0_read_position_before_variant
read_pos_after = locus_read.base0_read_position_after_variant
ref_pos_before = referenc... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'mtx_refl'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'nv'... | def mtx_refl(nv, reps=1):
import numpy as np
from scipy import linalg as spla
from ..const import PRM
if spla.norm(nv) < PRM.ZERO_VEC_TOL:
raise ValueError("Norm of 'nv' is too small.")
nv = make_nd_vec(nv, nd=3, t=np.float64, norm=True)
if not np.isscalar(reps):
raise ValueError... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'mtx_rot'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def mtx_rot(ax, theta, reps=1):
import numpy as np
from scipy import linalg as spla
from ..const import PRM
if spla.norm(ax) < PRM.ZERO_VEC_TOL:
raise ValueError("Norm of 'ax' is too small.")
ax = make_nd_vec(ax, nd=3, t=np.float64, norm=True)
if not np.isscalar(reps):
raise Valu... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ffd'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ite... | def ffd(items, targets, **kwargs):
sizes = zip(items, weight(items, **kwargs))
sizes = sorted(sizes, key=operator.itemgetter(1), reverse=True)
items = map(operator.itemgetter(0), sizes)
return ff(items, targets) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'match_variant_sequence_to_reference_context'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '11']}; {'id':... | def match_variant_sequence_to_reference_context(
variant_sequence,
reference_context,
min_transcript_prefix_length,
max_transcript_mismatches,
include_mismatches_after_variant=False,
max_trimming_attempts=2):
variant_sequence_in_reading_frame = None
for i in range... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'predicted_effects_for_variant'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'c... | def predicted_effects_for_variant(
variant,
transcript_id_whitelist=None,
only_coding_changes=True):
effects = []
for transcript in variant.transcripts:
if only_coding_changes and not transcript.complete:
logger.info(
"Skipping transcript %s for varian... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_protein_sequences'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'val... | def sort_protein_sequences(protein_sequences):
return list(
sorted(
protein_sequences,
key=ProteinSequence.ascending_sort_key,
reverse=True)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '32']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'reads_generator_to_protein_sequences_generator'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20... | def reads_generator_to_protein_sequences_generator(
variant_and_overlapping_reads_generator,
transcript_id_whitelist=None,
protein_sequence_length=PROTEIN_SEQUENCE_LENGTH,
min_alt_rna_reads=MIN_ALT_RNA_READS,
min_variant_sequence_coverage=MIN_VARIANT_SEQUENCE_COVERAGE,
mi... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_variant_and_transcript'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', ... | def from_variant_and_transcript(
cls,
variant,
transcript,
context_size):
if not transcript.contains_start_codon:
logger.info(
"Expected transcript %s for variant %s to have start codon",
transcript.name,
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'info'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def info(package, long_description, classifiers, license):
client = requests.Session()
for name_or_url in package:
package = get_package(name_or_url, client)
if not package:
secho(u'Invalid name or URL: "{name}"'.format(name=name_or_url),
fg='red', file=sys.stderr)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'install_packages'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'valu... | def install_packages(packages,
what_for='for a complete setup to work properly'):
'''Try to install .deb packages given by list.
Return True, if packages could be installed or are installed already, or if
they cannot be installed but the user gives feedback to continue.
Else return ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'scan'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children... | def scan(host, port=80, url=None, https=False, timeout=1, max_size=65535):
starts = OrderedDict()
ends = OrderedDict()
port = int(port)
result = dict(
host=host, port=port, state='closed', durations=OrderedDict()
)
if url:
timeout = 1
result['code'] = None
starts['all... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '45']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'redirect'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27', '30', '33', '36', ... | def redirect(pattern, to, permanent=True, locale_prefix=True, anchor=None, name=None,
query=None, vary=None, cache_timeout=12, decorators=None, re_flags=None,
to_args=None, to_kwargs=None, prepend_locale=True, merge_query=False):
if permanent:
redirect_class = HttpResponsePermanent... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'FD'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id':... | def FD(self):
if self.Verbose:
print("Finite Difference Solution Technique")
try:
self.qs
except:
self.qs = self.q0.copy()
del self.q0
self.x = np.arange(self.dx/2., self.dx * self.qs.shape[0], self.dx)
if self.dimension == 2:
self.y = np.arange(self.dy/2., self.dy * se... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'SAS_NG'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'... | def SAS_NG(self):
if self.filename:
self.Te = self.configGet("float", "input", "ElasticThickness")
self.latlon = self.configGet("string", "numerical2D", "latlon", optional=True)
self.PlanetaryRadius = self.configGet("float", "numerical2D", "PlanetaryRadius", optional=True)
if self.dimension ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_c3_mro'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'... | def _c3_mro(cls, abcs=None):
for i, base in enumerate(reversed(cls.__bases__)):
if hasattr(base, '__abstractmethods__'):
boundary = len(cls.__bases__) - i
break
else:
boundary = 0
abcs = list(abcs) if abcs else []
explicit_bases = list(cls.__bases__[:boundary])
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'singledispatch'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fu... | def singledispatch(function):
registry = {}
dispatch_cache = WeakKeyDictionary()
def ns():
pass
ns.cache_token = None
def dispatch(cls):
if ns.cache_token is not None:
current_token = get_cache_token()
if ns.cache_token != current_token:
dispat... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '40']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'createResource'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19', '22', '25', '28', '31', ... | def createResource(self, resource_type, title, resource_file=None, resource_filename=None,
abstract=None, keywords=None,
edit_users=None, view_users=None, edit_groups=None, view_groups=None,
metadata=None, extra_metadata=None, progress_callback=None):... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'getResourceFile'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children':... | def getResourceFile(self, pid, filename, destination=None):
url = "{url_base}/resource/{pid}/files/{filename}".format(url_base=self.url_base,
pid=pid,
filename=filename)
if... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'upsert'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'... | def upsert(self):
required_parameters = []
self._stackParameters = []
try:
self._initialize_upsert()
except Exception:
return False
try:
available_parameters = self._parameters.keys()
for parameter_name in self._template.get('Parame... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '16']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dump'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [],... | def dump(obj, fp=None, indent=None, sort_keys=False, **kw):
if fp:
iterable = YAMLEncoder(indent=indent, sort_keys=sort_keys, **kw).iterencode(obj)
for chunk in iterable:
fp.write(chunk)
else:
return dumps(obj, indent=indent, sort_keys=sort_keys, **kw) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_reference'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'roo... | def get_reference(root):
reference = {}
elem = root.find('bibliographyLink')
if elem is None:
raise MissingElementError('bibliographyLink')
ref_doi = elem.get('doi', None)
ref_key = elem.get('preferredKey', None)
if ref_doi is not None:
try:
ref = crossref_api.works(i... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ReSpecTh_to_ChemKED'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '12']}; {'id': '4', 'type': 'identifier', ... | def ReSpecTh_to_ChemKED(filename_xml, file_author='', file_author_orcid='', *, validate=False):
tree = etree.parse(filename_xml)
root = tree.getroot()
properties = get_file_metadata(root)
properties['reference'] = get_reference(root)
properties['reference']['detail'] = (properties['reference'].get('... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_cantera_composition_string'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'childr... | def get_cantera_composition_string(self, species_conversion=None):
if self.composition_type in ['mole fraction', 'mass fraction']:
factor = 1.0
elif self.composition_type == 'mole percent':
factor = 100.0
else:
raise ValueError('Unknown composition type: {}'.f... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'compare_name'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'val... | def compare_name(given_name, family_name, question_name):
given_name = given_name.lower()
family_name = family_name.lower()
question_name = question_name.lower()
if ',' in question_name:
name_split = question_name.split(',')
name_split.reverse()
question_name = ' '.join(name_spli... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sorted_options'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'so... | def sorted_options(sort_options):
return [
{
'title': v['title'],
'value': ('-{0}'.format(k)
if v.get('default_order', 'asc') == 'desc' else k),
}
for k, v in
sorted(sort_options.items(), key=lambda x: x[1].get('order', 0))
] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'insert_files'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21']}; {'id': '4', 'type': 'ide... | def insert_files(self, rootpath, directoryInFilter=None, directoryExFilter=None, compileInFilter=None, compileExFilter=None, contentInFilter=None, contentExFilter=None):
directoryInFilter = self.DirectoryInFilter if directoryInFilter is None else directoryInFilter
directoryExFilter = self.DirectoryExFil... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_variant'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'childre... | def make_variant(cls, converters, re_opts=None, compiled=False, strict=True):
assert converters, "REQUIRE: Non-empty list."
if len(converters) == 1:
return converters[0]
if re_opts is None:
re_opts = cls.default_re_opts
pattern = r")|(".join([tc.pattern for tc in ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'info'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id... | def info(self):
''' Returns information on all the registered checkers.
Sorted by namespace and then name
:returns a list of CheckerInfo
'''
return sorted(self._checkers.values(), key=lambda x: (x.ns, x.name)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_from_text'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def extract_from_text(text):
return tools.remove_duplicates([i[0]
for i in REGEX.findall(text) if i != '']) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'add_caveat'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def add_caveat(self, cav, key=None, loc=None):
'''Add a caveat to the macaroon.
It encrypts it using the given key pair
and by looking up the location using the given locator.
As a special case, if the caveat's Location field has the prefix
"local " the caveat is added as a clien... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_new_caveat_id'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def _new_caveat_id(self, base):
'''Return a third party caveat id
This does not duplicate any third party caveat ids already inside
macaroon. If base is non-empty, it is used as the id prefix.
@param base bytes
@return bytes
'''
id = bytearray()
if len(bas... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_macaroons'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def extract_macaroons(headers_or_request):
''' Returns an array of any macaroons found in the given slice of cookies.
If the argument implements a get_header method, that will be used
instead of the get method to retrieve headers.
@param headers_or_request: dict of headers or a
urllib.request.Reques... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'http_error_handler'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value':... | def http_error_handler(f):
def hrefs_to_resources(hrefs):
for href in hrefs.replace(',', '').split():
type, uuid = href.split('/')[-2:]
yield Resource(type, uuid=uuid)
def hrefs_list_to_resources(hrefs_list):
for href in eval(hrefs_list):
type, uuid = href.spl... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_handle_windows'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value... | def _handle_windows(self, event):
vkey = self._keyname(event.GetKey())
if event.Message in self.KEYS_UP + self.KEYS_DOWN:
if vkey in self.MODIFIERNAMES:
self._realmodifiers[vkey] = event.Message in self.KEYS_DOWN
self._modifiers[self.MODIFIERNAMES[vkey]] ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_handle_linux'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': []... | def _handle_linux(self, keycode, character, press):
if character is None: return
key = self._keyname(character, keycode)
if key in self.MODIFIERNAMES:
self._modifiers[self.MODIFIERNAMES[key]] = press
self._realmodifiers[key] = press
if press:
se... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_store_documentation'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'c... | def _store_documentation(self, path, html, overwrite, quiet):
echo("Storing groundwork application documents\n")
echo("Application: %s" % self.app.name)
echo("Number of documents: %s\n" % len(self.app.documents.get()))
if not os.path.isabs(path):
path = os.path.abspath(path)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_show_documentation'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def _show_documentation(self):
documents = []
for key, document in self.app.documents.get().items():
if key != "main":
documents.append((key, document))
documents = sorted(documents, key=lambda x: x[0])
main = self.app.documents.get("main")
if main is ... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'infer_declared_from_conditions'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'childr... | def infer_declared_from_conditions(conds, namespace=None):
''' like infer_declared except that it is passed a set of first party
caveat conditions as a list of string rather than a set of macaroons.
'''
conflicts = []
if namespace is None:
namespace = Namespace()
prefix = namespace.resol... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_cited_dois'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fi... | def get_cited_dois(file):
if not isinstance(file, list):
plaintext_citations = get_plaintext_citations(file)
else:
plaintext_citations = file
dois = {}
crossref_queue = []
for citation in plaintext_citations[:]:
matched_dois = doi.extract_from_text(citation)
if len(ma... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'used_args'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},... | def used_args(self):
values = []
for idx, c in enumerate(self.words[1:]):
if c.startswith('-'):
continue
option_str = self.words[1:][idx - 1]
option = self.get_option(option_str)
if option is None or not option.need_value:
v... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_preprocess'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'inp'}... | def _preprocess(inp):
inp = re.sub(r'(\b)a(\b)', r'\g<1>one\g<2>', inp)
inp = re.sub(r'to the (.*) power', r'to \g<1>', inp)
inp = re.sub(r'to the (.*?)(\b)', r'to \g<1>\g<2>', inp)
inp = re.sub(r'log of', r'log', inp)
inp = re.sub(r'(square )?root( of)?', r'sqrt', inp)
i... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parseEquation'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value':... | def parseEquation(self, inp):
inp = MathService._preprocess(inp)
split = inp.split(' ')
for i, w in enumerate(split):
if w in self.__unaryOperators__:
op = self.__unaryOperators__[w]
eq1 = ' '.join(split[:i])
eq2 = ' '.join(split[i + 1:... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'activate'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sel... | def activate(self, plugins=[]):
self._log.debug("Plugins Activation started")
if not isinstance(plugins, list):
raise AttributeError("plugins must be a list, not %s" % type(plugins))
self._log.debug("Plugins to activate: %s" % ", ".join(plugins))
plugins_activated = []
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'dispersion_ranking_NN'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children':... | def dispersion_ranking_NN(self, nnm, num_norm_avg=50):
self.knn_avg(nnm)
D_avg = self.adata.layers['X_knn_avg']
mu, var = sf.mean_variance_axis(D_avg, axis=0)
dispersions = np.zeros(var.size)
dispersions[mu > 0] = var[mu > 0] / mu[mu > 0]
self.adata.var['spatial_dispersio... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '31']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'scatter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23', '26', '29']}; {'id': '4', 'typ... | def scatter(self, projection=None, c=None, cmap='rainbow', linewidth=0.0,
edgecolor='k', axes=None, colorbar=True, s=10, **kwargs):
if (not PLOTTING):
print("matplotlib not installed!")
else:
if(isinstance(projection, str)):
try:
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parseFloat'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 's... | def parseFloat(self, words):
def pointFloat(words):
m = re.search(r'(.*) point (.*)', words)
if m:
whole = m.group(1)
frac = m.group(2)
total = 0.0
coeff = 0.10
for digit in frac.split(' '):
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], '... | def run(self, cmd, stdin=None, marshal_output=True, **kwargs):
records = []
args = [self._executable, "-u", self._user, "-p", self._port]
if self._client:
args += ["-c", str(self._client)]
if marshal_output:
args.append('-G')
if isinstance(cmd, six.string_... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'canonical_ops'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ops... | def canonical_ops(ops):
''' Returns the given operations array sorted with duplicates removed.
@param ops checker.Ops
@return: checker.Ops
'''
new_ops = sorted(set(ops), key=lambda x: (x.entity, x.action))
return new_ops |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_from_text'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def extract_from_text(text):
return tools.remove_duplicates([re.sub("arxiv:", "", i[0],
flags=re.IGNORECASE)
for i in REGEX.findall(text) if i[0] != '']) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extractTimes'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ... | def extractTimes(self, inp):
def handleMatch(time):
relative = False
if not time:
return None
elif time.group(1) == 'morning':
h = 8
m = 0
elif time.group(1) == 'afternoon':
h = 12
m =... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'serialize_text'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'se... | def serialize_text(self):
'''Returns a serialized form of the Namepace.
All the elements in the namespace are sorted by
URI, joined to the associated prefix with a colon and
separated with spaces.
:return: bytes
'''
if self._uri_to_prefix is None or len(self._uri_... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'with_zero_or_one'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], ... | def with_zero_or_one(cls, converter, pattern=None):
cardinality = Cardinality.zero_or_one
if not pattern:
pattern = getattr(converter, "pattern", cls.default_pattern)
optional_pattern = cardinality.make_pattern(pattern)
group_count = cardinality.compute_group_count(pattern)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'stats_keyboard'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value'... | def stats_keyboard(events, table):
if len(events) < 2: return [], []
deltas, prev_dt = [], None
sessions, session = [], None
UNBROKEN_DELTA = datetime.timedelta(seconds=conf.KeyboardSessionMaxDelta)
blank = collections.defaultdict(lambda: collections.defaultdict(int))
collated = [blank.cop... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_perseus'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'chi... | def to_perseus(df, path_or_file, main_columns=None,
separator=separator,
convert_bool_to_category=True,
numerical_annotation_rows = set([])):
_df = df.copy()
if not _df.columns.name:
_df.columns.name = 'Column Name'
column_names = _df.columns.get_level_values('Column Name')
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'do_your_job'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'... | def do_your_job(self):
y,x = self.get_intended_direction()
if self.target_x == self.current_x and self.target_y == self.current_y:
if len(self.results) == 0:
self.results.append("TARGET ACQUIRED")
self.lg_mv(2, self.name + ": TARGET ACQUIRED" )
ret... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'save_filelist'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10']}; {'id': '4', 'type': 'identifier', 'childr... | def save_filelist(self, opFile, opFormat, delim=',', qu='"'):
op_folder = os.path.dirname(opFile)
if op_folder is not None:
if not os.path.exists(op_folder):
os.makedirs(op_folder)
with open(opFile,'w') as fout:
fout.write("fullFilename" + delim)
... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'type'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'se... | def type(self, variant_probe_coverages, variant=None):
if not isinstance(variant_probe_coverages, list):
variant_probe_coverages = [variant_probe_coverages]
calls = []
for variant_probe_coverage in variant_probe_coverages:
calls.append(
self._type_variant_... |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'process'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self... | def process(self, versions):
for tool_name in sorted(versions.keys()):
version = versions[tool_name]
self._log("Using tool '%s', %s" % (tool_name, version)) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.