text stringlengths 75 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 0.18 |
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def get_client(self, email=None, password=None, **__):
"""Get the google data client."""
if self.client is not None:
return self.client
return Auth(email, password) | [
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def addclassifications(agdir, prop, version=None, statfeats = [0,4,5,6,7,8]):
""" Calculates real score probability of prop from an activegit repo.
version is string name of activegit tag.
Default agdir initialization will have latest tag, so version is optional.
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def choropleth():
"""
Returns
"""
path=os.path.join(os.path.dirname(__file__), '../data/choropleth.csv')
df=pd.read_csv(path)
del df['Unnamed: 0']
df['z']=[np.random.randint(0,100) for _ in range(len(df))]
return df | [
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def map_statistic(self, plot):
"""
Mapping aesthetics to computed statistics
"""
data = self.data
if not len(data):
return type(data)()
# Assemble aesthetics from layer, plot and stat mappings
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def _reciprocal_condition_number(lu_mat, one_norm):
r"""Compute reciprocal condition number of a matrix.
Args:
lu_mat (numpy.ndarray): A 2D array of a matrix :math:`A` that has been
LU-factored, with the non-diagonal part of :math:`L` stored in the
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def _get_focused_item(self):
""" Returns the currently focused item """
focused_model = self._selection.focus
if not focused_model:
return None
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def filter_on_wire_representation(ava, acs, required=None, optional=None):
"""
:param ava: A dictionary with attributes and values
:param acs: List of tuples (Attribute Converter name,
Attribute Converter instance)
:param required: A list of saml.Attributes
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def ascii2h5(bh_dir=None):
"""
Convert the Burstein & Heiles (1982) dust map from ASCII to HDF5.
"""
if bh_dir is None:
bh_dir = os.path.join(data_dir_default, 'bh')
fname = os.path.join(bh_dir, '{}.ascii')
f = h5py.File('bh.h5', 'w')
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def call_arg_index(self):
"""Determines the index of the parameter in a call list using
string manipulation and context information."""
#The function name we are calling should be in el_name by now
if self._call_index is None:
if (self.el_section == "body" and
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def _push_next(self):
"""Assign next batch workload to workers."""
r = next(self._iter, None)
if r is None:
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def _extension_module_tags():
"""
Returns valid tags an extension module might have
"""
import sysconfig
tags = []
if six.PY2:
# see also 'SHLIB_EXT'
multiarch = sysconfig.get_config_var('MULTIARCH')
if multiarch is not None:
tags.append(multiarch)
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def deserialize(cls, assoc_s):
"""
Parse an association as stored by serialize().
inverse of serialize
@param assoc_s: Association as serialized by serialize()
@type assoc_s: str
@return: instance of this class
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def _read_file(filename):
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Read a res2dinv-file and return the header
Parameters
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filename : string
Data filename
Returns
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type : int
type of array extracted from header
file_data : :py:class:`StringIO.StringIO`
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def downgrade():
"""Downgrade database."""
ctx = op.get_context()
insp = Inspector.from_engine(ctx.connection.engine)
for fk in insp.get_foreign_keys('transaction'):
if fk['referred_table'] == 'accounts_user':
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def unbounded(self):
"""Whether the solution is unbounded"""
self._check_valid()
return (self._problem._p.get_status() ==
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def center_crop(im, min_sz=None):
""" Return a center crop of an image """
r,c,*_ = im.shape
if min_sz is None: min_sz = min(r,c)
start_r = math.ceil((r-min_sz)/2)
start_c = math.ceil((c-min_sz)/2)
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def parse_if_header_dict(environ):
"""Parse HTTP_IF header into a dictionary and lists, and cache the result.
@see http://www.webdav.org/specs/rfc4918.html#HEADER_If
"""
if "wsgidav.conditions.if" in environ:
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def do_max(environment, value, case_sensitive=False, attribute=None):
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def get_tasks(self):
"""Returns an ordered dictionary {task_name: task} of all tasks within this workflow.
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:rtype: OrderedDict
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def to_ufo_background_image(self, ufo_glyph, layer):
"""Copy the backgound image from the GSLayer to the UFO Glyph."""
image = layer.backgroundImage
if image is None:
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ufo_image = ufo_glyph.image
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def import_modules_from_package(package):
"""Import modules from package and append into sys.modules
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def escape_string(string):
"""Escape a string for use in Gerrit commands.
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def read_csv(user_id, records_path, antennas_path=None, attributes_path=None,
recharges_path=None, network=False, duration_format='seconds',
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Load user records from a CSV file.
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def retrieve_element_or_default(self, location, default=None):
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def get_peak_pos(im, wrap=False):
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The image containing a peak
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def visit_Assign(self, node):
"""
Implement assignment walker.
Parse class properties defined via the property() function
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def tplot_rename(old_name, new_name):
"""
This function will rename tplot variables that are already stored in memory.
Parameters:
old_name : str
Old name of the Tplot Variable
new_name : str
New name of the Tplot Variable
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def popup(self):
""" Show the notification from code. This will initialize and activate
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Notes
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This does NOT block. Callbacks should be used to handle click events
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def step3(self):
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def prune_by_ngram_count_per_work(self, minimum=None, maximum=None,
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def flush(self, using=None, **kwargs):
"""
Preforms a flush operation on the index.
Any additional keyword arguments will be passed to
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... | 37.5 | 0.009772 |
def _check_depth_limits(input_dict):
'''Returns the default upper and lower depth values if not in dictionary
:param input_dict:
Dictionary corresponding to the kwargs dictionary of calling function
:returns:
'upper_depth': Upper seismogenic depth (float)
'lower_depth': Lower seism... | [
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def main():
"""
NAME
squish.py
DESCRIPTION
takes dec/inc data and "squishes" with specified flattening factor, flt
using formula tan(Io)=flt*tan(If)
INPUT
declination inclination
OUTPUT
"squished" declincation inclination
SYNTAX
... | [
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def handle_translocation_illegal(self, line: str, position: int, tokens: ParseResults) -> None:
"""Handle a malformed translocation."""
raise MalformedTranslocationWarning(self.get_line_number(), line, position, tokens) | [
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def getPeerStats(self):
"""Get NTP Peer Stats for localhost by querying local NTP Server.
@return: Dictionary of NTP stats converted to seconds.
"""
info_dict = {}
output = util.exec_command([ntpqCmd, '-n', '-c', 'peers'])
for line in output.splitlines():
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def write(self, data):
"""
Write the given data to the file.
"""
# Do the write
self.backingStream.write(data)
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# Send out notifications
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def discover(url, options={}):
"""
Retrieve the API definition from the given URL and construct
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"""
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def get_gpubsub_publisher(config, metrics, changes_channel, **kw):
"""Get a GPubsubPublisher client.
A factory function that validates configuration, creates an auth
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def p_function_statement(self, p):
'function_statement : funcvardecls function_calc'
p[0] = p[1] + (p[2],)
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def gpg_app_put_key( blockchain_id, appname, keyname, key_data, txid=None, immutable=False, proxy=None, wallet_keys=None, config_dir=None ):
"""
Put an application GPG key.
Stash the private key locally to an app-specific keyring.
Return {'status': True, 'key_url': ..., 'key_data': ...} on success
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def thaw(vault_client, src_file, opt):
"""Given the combination of a Secretfile and the output of
a freeze operation, will restore secrets to usable locations"""
if not os.path.exists(src_file):
raise aomi.exceptions.AomiFile("%s does not exist" % src_file)
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def has_true(self, e, extra_constraints=(), solver=None, model_callback=None): #pylint:disable=unused-argument
"""
Should return True if `e` can possible be True.
:param e: The AST.
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def save(self):
"""The save method for Animal class is over-ridden to set Alive=False when a Death date is entered. This is not the case for a cause of death."""
if self.Death:
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def getID(code_file):
"""Get the language ID of the input file language"""
json_path = ghostfolder+'/'+json_file
if os.path.exists(json_path):
pass
else:
download_file('https://ghostbin.com/languages.json')
lang = detect_lang(code_file)
json_data = json.load(file(json_path))#don't think i need this though
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def do_reload(module: types.ModuleType, newer_than: int) -> bool:
"""
Executes the reload of the specified module if the source file that it was
loaded from was updated more recently than the specified time
:param module:
A module object to be reloaded
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def pdftotext_conversion_is_bad(txtlines):
"""Check if conversion after pdftotext is bad.
Sometimes pdftotext performs a bad conversion which consists of many
spaces and garbage characters.
This method takes a list of strings obtained from a pdftotext conversion
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def is_multi_timeseries_orthogonal(nc, variable):
'''
Returns true if the variable is a orthogonal multidimensional array
representation of time series. For more information on what this means see
CF 1.6 §H.2.1
http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#_orthogonal_multidime... | [
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def k_means(points, k, **kwargs):
"""
Find k centroids that attempt to minimize the k- means problem:
https://en.wikipedia.org/wiki/Metric_k-center
Parameters
----------
points: (n, d) float
Points in a space
k : int
Number of centroids to compute
**kwargs : dict
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def find_declaration(
declarations,
decl_type=None,
name=None,
parent=None,
recursive=True,
fullname=None):
"""
Returns single declaration that match criteria, defined by developer.
If more the one declaration was found None will be returned.
For more inf... | [
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def _request(self, url, params=None, data=None, files=None, auth=None,
timeout=None, raw_response=False, retry_on_error=True,
method=None):
"""Given a page url and a dict of params, open and return the page.
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def is_ready(self):
"""
Check if pod is in READY condition
:return: bool
"""
if PodCondition.READY in self.get_conditions():
logger.info("Pod: %s in namespace: %s is ready!", self.name, self.namespace)
return True
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def clear(self):
"Remove all items and reset internal structures"
dict.clear(self)
self._key = 0
if hasattr(self._tree_view, "wx_obj"):
self._tree_view.wx_obj.DeleteAllItems() | [
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def get_paths(self, connection, path):
"""
Return *real* and *virtual* paths, resolves ".." with "up" action.
*Real* path is path for path_io, when *virtual* deals with
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def unlink(self, node, hyperedge):
"""
Unlink given node and hyperedge.
@type node: node
@param node: Node.
@type hyperedge: hyperedge
@param hyperedge: Hyperedge.
"""
self.node_links[node].remove(hyperedge)
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def clean(amount):
"""
Converts a number to a number with decimal point.
:param str amount: The input number.
:rtype: str
"""
# Return empty input immediately.
if not amount:
return amount
if re.search(r'[\. ][0-9]{3},[0-9]{1,2}$', amount):
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def summarizeReads(file_handle, file_type):
"""
open a fasta or fastq file, prints number of of reads,
average length of read, total number of bases, longest,
shortest and median read, total number and average of
individual base (A, T, G, C, N).
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def attachedimages_inline_factory(lang='en', max_width='', debug=False):
''' Returns InlineModelAdmin for attached images.
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moment). 'max_width' is default resize width parameter to be set in
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def cli(env, billing_id, datacenter):
"""Adds a load balancer given the id returned from create-options."""
mgr = SoftLayer.LoadBalancerManager(env.client)
if not formatting.confirm("This action will incur charges on your "
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def name(self):
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The name of the functional. If the functional is not found in the aliases,
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if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].name
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def peel_around(method):
"""
This function will be deprecated.
Removes one wrap around the method (given as a parameter) and
returns the wrap. If the method is not wrapped, returns None.
"""
_permission_to_touch_wraps.acquire() # released in finally part
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def _lstat(self, path):
'''IMPORTANT: expects `path`'s parent to already be deref()'erenced.'''
if path not in self.entries:
return OverlayStat(*self.originals['os:lstat'](path)[:10], st_overlay=0)
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def float_encode(self, value):
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def train(target, dataset, cluster_spec, ctx):
"""Train Inception on a dataset for a number of steps."""
# Number of workers and parameter servers are infered from the workers and ps
# hosts string.
num_workers = len(cluster_spec.as_dict()['worker'])
num_parameter_servers = len(cluster_spec.as_dict()['ps'])
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def temporary_file(mode):
"""Cross platform temporary file creation.
This is an alternative to ``tempfile.NamedTemporaryFile`` that
also works on windows and avoids the "file being used by
another process" error.
"""
tempdir = tempfile.gettempdir()
basename = 'tmpfile-%s' % (uuid.uuid4())
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def grant(self, lock, unit):
'''Maybe grant the lock to a unit.
The decision to grant the lock or not is made for $lock
by a corresponding method grant_$lock, which you may define
in a subclass. If no such method is defined, the default_grant
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def load(self, cnf, metadata_construction=False):
""" The base load method, loads the configuration
:param cnf: The configuration as a dictionary
:param metadata_construction: Is this only to be able to construct
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def erf(f=Ellipsis):
'''
erf(x) yields a potential function that calculates the error function over the input x. If x is
a constant, yields a constant potential function.
erf() is equivalent to erf(...), which is just the error function, calculated over its inputs.
'''
f = to_potential(f)
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def _windows_remotes_on(port, which_end):
r'''
Windows specific helper function.
Returns set of ipv4 host addresses of remote established connections
on local or remote tcp port.
Parses output of shell 'netstat' to get connections
C:\>netstat -n
Active Connections
Proto Local Add... | [
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def create(cls, mr_spec, shard_number, shard_attempt, _writer_state=None):
"""Inherit docs."""
writer_spec = cls.get_params(mr_spec.mapper, allow_old=False)
# Determine parameters
key = cls._generate_filename(writer_spec, mr_spec.name,
mr_spec.mapreduce_id,
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def rm(path, isdir=False):
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returns True if deleted, if file/dir not exists, return False
:param path: path to delete
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"""
if isdir:
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def _build_collapse_to_gene_dict(graph) -> Dict[BaseEntity, Set[BaseEntity]]:
"""Build a collapse dictionary.
:param pybel.BELGraph graph: A BEL graph
:return: A dictionary of {node: set of PyBEL node tuples}
"""
collapse_dict = defaultdict(set)
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def COM(z, M, **cosmo):
""" Calculate concentration for halo of mass 'M' at redshift 'z'
Parameters
----------
z : float / numpy array
Redshift to find concentration of halo
M : float / numpy array
Halo mass at redshift 'z'. Must be same size as 'z'
cosmo : dict
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def rename(args):
"""
%prog rename genes.bed [gaps.bed]
Rename genes for annotation release.
For genes on chromosomes (e.g. the 12th gene on C1):
Bo1g00120
For genes on scaffolds (e.g. the 12th gene on unplaced Scaffold00285):
Bo00285s120
The genes identifiers will increment by 10. S... | [
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def normalizeLibValue(value):
"""
Normalizes lib value.
* **value** must not be ``None``.
* Returned value is the same type as the input value.
"""
if value is None:
raise ValueError("Lib value must not be None.")
if isinstance(value, (list, tuple)):
for v in value:
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def set_ec2_settings(self,
aws_region=None,
aws_availability_zone=None,
vpc_id=None,
subnet_id=None,
master_elastic_ip=None,
role_instance_profile=None,
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def apply_complement(self, a, return_Ya=False):
"""Apply the complementary projection to an array.
:param z: array with ``shape==(N,m)``.
:return: :math:`P_{\\mathcal{Y}^\\perp,\\mathcal{X}}z =
z - P_{\\mathcal{X},\\mathcal{Y}^\\perp} z`.
"""
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def ConstructObject(self, py_obj):
''' note py_obj items are NOT converted to PyJs types! '''
obj = self.NewObject()
for k, v in py_obj.items():
obj.put(unicode(k), v)
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def get_equation_components(equation_str):
"""
Breaks down a string representing only the equation part of a model element.
Recognizes the various types of model elements that may exist, and identifies them.
Parameters
----------
equation_str : basestring
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def get_diversity(self,X):
"""compute mean diversity of individual outputs"""
# diversity in terms of cosine distances between features
feature_correlations = np.zeros(X.shape[0]-1)
for i in np.arange(1,X.shape[0]-1):
feature_correlations[i] = max(0.0,r2_score(X[0],X[i]))
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def pickle_to_param(obj, name):
"""
Return the top-level element of a document sub-tree containing the
pickled serialization of a Python object.
"""
return from_pyvalue(u"pickle:%s" % name, unicode(pickle.dumps(obj))) | [
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def get_ppis(self, ppi_df):
"""Generate Complex Statements from the HPRD PPI data.
Parameters
----------
ppi_df : pandas.DataFrame
DataFrame loaded from the BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt
file.
"""
logger.info('Processing PPIs...')
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def add_slot_ports(self, slot):
"""
Add the ports to be added for a adapter card
:param str slot: Slot name
"""
slot_nb = int(slot[4])
# slot_adapter = None
# if slot in self.node['properties']:
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def prepare_for_reraise(error, exc_info=None):
"""Prepares the exception for re-raising with reraise method.
This method attaches type and traceback info to the error object
so that reraise can properly reraise it using this info.
"""
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def browse(self):
''' Browse the history of a single file
adds one commit that doesn't contain changes in test_file_1.
there are four commits in summary, so the check for buffer line
count compares with 3.
at the end, a fifth commit must be present due to resetting the
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def filter_by_key(self, keys, ID=None):
"""
Keep only Measurements with given keys.
"""
keys = to_list(keys)
fil = lambda x: x in keys
if ID is None:
ID = self.ID
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def set_config(**kwargs):
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filename : string,
output file for profile data
profile_all : boolean,
all profile types enabled
profile_symbolic : boolean,
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def create_class_from_xml_string(target_class, xml_string):
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:param target_class: The class which will be instantiated and populated
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def compute_offset_nuth(dh, slope, aspect, min_count=100, remove_outliers=True, plot=True):
"""Compute horizontal offset between input rasters using Nuth and Kaab [2011] (nuth) method
"""
import scipy.optimize as optimization
if dh.count() < min_count:
sys.exit("Not enough dh samples")
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def egress(self, envelope, http_headers, operation, binding_options):
"""Overriding the egress function to set our headers.
Args:
envelope: An Element with the SOAP request data.
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def return_hdr(self):
"""Return the header for further use.
Returns
-------
subj_id : str
subject identification code
start_time : datetime
start time of the dataset
s_freq : float
sampling frequency
chan_name : list of str
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def validAspects(self, ID, aspList):
""" Returns a list with the aspects an object
makes with the other six planets, considering a
list of possible aspects.
"""
obj = self.chart.getObject(ID)
res = []
for otherID in const.LIST_SEVEN_PLANETS:
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def rates_for_location(self, postal_code, location_deets=None):
"""Shows the sales tax rates for a given location."""
request = self._get("rates/" + postal_code, location_deets)
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def parse_xml(self, node):
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self._set_properties(node)
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def combine_intersections(
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r"""Combine curve-curve intersections into curved polygon(s).
.. note::
This is a helper used only by :meth:`.Surface.intersect`.
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"... | 39.104167 | 0.00052 |
def _process_scopes(scopes):
"""Parse a scopes list into a set of all scopes and a set of sufficient scope sets.
scopes: A list of strings, each of which is a space-separated list of scopes.
Examples: ['scope1']
['scope1', 'scope2']
['scope1', 'scope2 scope3']
Retu... | [
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... | 39 | 0.009535 |
def uncompress_files(original, destination):
"""
Move file from original path to destination path.
:type original: str
:param original: The location of zip file
:type destination: str
:param destination: The extract path
"""
with zipfile.ZipFile(original) as zips:
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... | 30.230769 | 0.002469 |
def setup(self, phase=None, quantity='', conductance='', **kwargs):
r"""
This method takes several arguments that are essential to running the
algorithm and adds them to the settings.
Parameters
----------
phase : OpenPNM Phase object
The phase on which the a... | [
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def cumulative_time_on_drug(
drug_events_df: DataFrame,
query_times_df: DataFrame,
event_lasts_for_timedelta: datetime.timedelta = None,
event_lasts_for_quantity: float = None,
event_lasts_for_units: str = None,
patient_colname: str = DEFAULT_PATIENT_COLNAME,
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def is_known_type(self, type_name):
"""Check if type is known to the type system.
Returns:
bool: True if the type is a known instantiated simple type, False otherwise
"""
type_name = str(type_name)
if type_name in self.known_types:
return True
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] | 26.666667 | 0.009063 |
def makeMany2ManyRelatedManager(formodel, name_relmodel, name_formodel):
'''formodel is the model which the manager .'''
class _Many2ManyRelatedManager(Many2ManyRelatedManager):
pass
_Many2ManyRelatedManager.formodel = formodel
_Many2ManyRelatedManager.name_relmodel = name_relmodel
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"_Many2ManyRel... | 40.3 | 0.002427 |
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