Unnamed: 0 int64 0 389k | code stringlengths 26 79.6k | docstring stringlengths 1 46.9k |
|---|---|---|
2,800 | def acquire_connection(settings, tag=None, logger_name=None, auto_commit=False):
try:
connection_properties = settings.get(tag, settings[None])
except KeyError:
raise RdbmsConnection.DefaultConnectionPropertiesSettingException()
return RdbmsConnection(
... | Return a connection to a Relational DataBase Management System (RDBMS)
the most appropriate for the service requesting this connection.
@param settings: a dictionary of connection properties::
{
None: {
'rdbms_hostname': "...",
... |
2,801 | def plot_xtf(fignum, XTF, Fs, e, b):
plt.figure(num=fignum)
plt.xlabel()
plt.ylabel()
k = 0
Flab = []
for freq in XTF:
T, X = [], []
for xt in freq:
X.append(xt[0])
T.append(xt[1])
plt.plot(T, X)
plt.text(T[-1], X[-1], str(int(Fs[k])) ... | function to plot series of chi measurements as a function of temperature, holding field constant and varying frequency |
2,802 | def distance_to_edge(labels):
colors = color_labels(labels)
max_color = np.max(colors)
result = np.zeros(labels.shape)
if max_color == 0:
return result
for i in range(1, max_color+1):
mask = (colors==i)
result[mask] = scind.distance_transform_edt(mask)[mask]
ret... | Compute the distance of a pixel to the edge of its object
labels - a labels matrix
returns a matrix of distances |
2,803 | def _parse_mirteFile(path, logger=None):
l = logging.getLogger() if logger is None else logger
cache_path = os.path.join(os.path.dirname(path),
CACHE_FILENAME_TEMPLATE % os.path.basename(path))
if (os.path.exists(cache_path) and
os.path.getmtime(cache_path) >= ... | Open and parses the mirteFile at <path>. |
2,804 | def transform_obs(self, obs):
empty = np.array([], dtype=np.int32).reshape((0, 7))
out = named_array.NamedDict({
"single_select": empty,
"multi_select": empty,
"build_queue": empty,
"cargo": empty,
"cargo_slots_available": np.array([0], dtype=np.int32),
})
... | Render some SC2 observations into something an agent can handle. |
2,805 | def _simplify_non_context_field_binary_composition(expression):
if any((isinstance(expression.left, ContextField),
isinstance(expression.right, ContextField))):
raise AssertionError(u
u.format(expression))
if expression.operator == u:
if expression.... | Return a simplified BinaryComposition if either operand is a TrueLiteral.
Args:
expression: BinaryComposition without any ContextField operand(s)
Returns:
simplified expression if the given expression is a disjunction/conjunction
and one of it's operands is a TrueLiteral,
and t... |
2,806 | def __is_valid_type(self, typ, typlist):
typ_is_str = typ == "string"
str_list_in_typlist = "stringlist" in typlist
return typ in typlist or (typ_is_str and str_list_in_typlist) | Check if type is valid based on input type list
"string" is special because it can be used for stringlist
:param typ: the type to check
:param typlist: the list of type to check
:return: True on success, False otherwise |
2,807 | def dump(deposition, from_date, with_json=True, latest_only=False, **kwargs):
dep_json = json.dumps(deposition.__getstate__(),
default=default_serializer)
dep_dict = json.loads(dep_json)
dep_dict[] = {}
dep_dict[][] = deposition.id
dep_dict[][] = dt2utc_timestamp(... | Dump the deposition object as dictionary. |
2,808 | def is_valid_short_number_for_region(short_numobj, region_dialing_from):
if not _region_dialing_from_matches_number(short_numobj, region_dialing_from):
return False
metadata = PhoneMetadata.short_metadata_for_region(region_dialing_from)
if metadata is None:
return False
short_numb... | Tests whether a short number matches a valid pattern in a region.
Note that this doesn't verify the number is actually in use, which is
impossible to tell by just looking at the number itself.
Arguments:
short_numobj -- the short number to check as a PhoneNumber object.
region_dialing_from -- the ... |
2,809 | def create_project(self, name=None, project_id=None, path=None):
if project_id is not None and project_id in self._projects:
return self._projects[project_id]
project = Project(name=name, project_id=project_id, path=path)
self._check_available_disk_space(project)
se... | Create a project and keep a references to it in project manager.
See documentation of Project for arguments |
2,810 | def get_vcs_details_output_vcs_details_principal_switch_wwn(self, **kwargs):
config = ET.Element("config")
get_vcs_details = ET.Element("get_vcs_details")
config = get_vcs_details
output = ET.SubElement(get_vcs_details, "output")
vcs_details = ET.SubElement(output, "vcs-... | Auto Generated Code |
2,811 | def getPort(self):
disp = self.pbmanager.dispatchers[self.portstr]
return disp.port.getHost().port | Helper method for testing; returns the TCP port used for this
registration, even if it was specified as 0 and thus allocated by the
OS. |
2,812 | def _stdin_raw_block(self):
try:
data = sys.stdin.read(1)
data = data.replace(, )
return data
except WindowsError as we:
if we.winerror == ERROR_NO_DATA:
return None
else:
... | Use a blocking stdin read |
2,813 | def bovy_text(*args,**kwargs):
if kwargs.pop(,False):
pyplot.annotate(args[0],(0.5,1.05),xycoords=,
horizontalalignment=,
verticalalignment=,**kwargs)
elif kwargs.pop(,False):
pyplot.annotate(args[0],(0.05,0.05),xycoords=,**kwargs)
elif kw... | NAME:
bovy_text
PURPOSE:
thin wrapper around matplotlib's text and annotate
use keywords:
'bottom_left=True'
'bottom_right=True'
'top_left=True'
'top_right=True'
'title=True'
to place the text in one of the corners or use it as ... |
2,814 | def generate_messages(outf, msgs):
print("Generating Messages")
t.write(outf, )
for msg in msgs:
t.write(outf, , msg) | Generate Swift structs to represent all MAVLink messages |
2,815 | def _fix_component_id(self, component):
theID = getattr(component, "id", None)
if theID is not None:
setattr(component, "id", self._fix_id(theID))
try:
for c in component.children:
self._fix_component_id(c)
except:
pass | Fix name of component ad all of its children |
2,816 | def get_interval_timedelta(self):
now_datetime = timezone.now()
current_month_days = monthrange(now_datetime.year, now_datetime.month)[1]
if self.interval == reminders_choices.INTERVAL_2_WEEKS:
interval_timedelta = datetime.timedelta(days=14)
eli... | Spits out the timedelta in days. |
2,817 | def basic_qos(self, prefetch_size, prefetch_count, a_global):
args = AMQPWriter()
args.write_long(prefetch_size)
args.write_short(prefetch_count)
args.write_bit(a_global)
self._send_method((60, 10), args)
return self.wait(allowed_methods=[
(60, 11), ... | Specify quality of service
This method requests a specific quality of service. The QoS
can be specified for the current channel or for all channels
on the connection. The particular properties and semantics of
a qos method always depend on the content class semantics.
Though t... |
2,818 | def from_json(cls, data):
required_keys = (, , , )
for key in required_keys:
assert key in data, .format(key)
if not in data:
data[] =
return cls(data[], data[], data[],
data[]) | Create a Sky Condition from a dictionary.
Args:
data = {
"solar_model": string,
"month": int,
"day_of_month": int,
"clearness": float,
"daylight_savings_indicator": string // "Yes" or "No"} |
2,819 | def romanize(text: str, engine: str = "royin") -> str:
if not text or not isinstance(text, str):
return ""
if engine == "thai2rom":
from .thai2rom import romanize
else:
from .royin import romanize
return romanize(text) | Rendering Thai words in the Latin alphabet or "romanization",
using the Royal Thai General System of Transcription (RTGS),
which is the official system published by the Royal Institute of Thailand.
ถอดเสียงภาษาไทยเป็นอักษรละติน
:param str text: Thai text to be romanized
:param str engine: 'royin' (d... |
2,820 | def deploy_api_gateway( self,
api_id,
stage_name,
stage_description="",
description="",
cache_cluster_enabled=False,
cache_cluster_size=,
... | Deploy the API Gateway!
Return the deployed API URL. |
2,821 | def guess_format( filename, ext, formats, io_table ):
ok = False
for format in formats:
output( % format )
try:
ok = io_table[format].guess( filename )
except AttributeError:
pass
if ok: break
else:
raise NotImplementedError( % ext)
... | Guess the format of filename, candidates are in formats. |
2,822 | def get_field_lookups(field_type, nullable):
return LOOKUP_TABLE.get(field_type) + [] if nullable else LOOKUP_TABLE.get(field_type) | Return lookup table value and append isnull if
this is a nullable field |
2,823 | def total(self):
total = 0
for item in self.items.all():
total += item.total
return total | Total cost of the order |
2,824 | def element(self, inp=None):
if inp is not None:
s = str(inp)[:self.length]
s += * (self.length - len(s))
return s
else:
return * self.length | Return an element from ``inp`` or from scratch. |
2,825 | def comment(self, text, comment_prefix=):
comment = Comment(self._container)
if not text.startswith(comment_prefix):
text = "{} {}".format(comment_prefix, text)
if not text.endswith():
text = "{}{}".format(text, )
comment.add_line(text)
self._cont... | Creates a comment block
Args:
text (str): content of comment without #
comment_prefix (str): character indicating start of comment
Returns:
self for chaining |
2,826 | def _add_default_exposure_class(layer):
layer.startEditing()
field = create_field_from_definition(exposure_class_field)
layer.keywords[][exposure_class_field[]] = (
exposure_class_field[])
layer.addAttribute(field)
index = layer.fields().lookupField(exposure_class_field[])
exposu... | The layer doesn't have an exposure class, we need to add it.
:param layer: The vector layer.
:type layer: QgsVectorLayer |
2,827 | def len_cdc_tube(FlowPlant, ConcDoseMax, ConcStock,
DiamTubeAvail, HeadlossCDC, LenCDCTubeMax, temp,
en_chem, KMinor):
index = i_cdc(FlowPlant, ConcDoseMax, ConcStock,
DiamTubeAvail, HeadlossCDC, LenCDCTubeMax, temp,
en_chem, KMinor)
len_cdc_tu... | The length of tubing may be longer than the max specified if the stock
concentration is too high to give a viable solution with the specified
length of tubing. |
2,828 | def current_version():
import setuptools
version = [None]
def monkey_setup(**settings):
version[0] = settings[]
old_setup = setuptools.setup
setuptools.setup = monkey_setup
import setup
reload(setup)
setuptools.setup = old_setup
return version[0] | Get the current version number from setup.py |
2,829 | def from_json(json_data):
return oauth | Returns a pyalveo.OAuth2 given a json string built from the oauth.to_json() method. |
2,830 | def headers(self):
self.__dict__[] = hdict = HeaderDict()
hdict.dict = self._headers
return hdict | An instance of :class:`HeaderDict`, a case-insensitive dict-like
view on the response headers. |
2,831 | def extract_first_jpeg_in_pdf(fstream):
parser = PDFParser(fstream)
if PY2:
document = PDFDocument(parser)
else:
document = PDFDocument()
parser.set_document(document)
document.set_parser(parser)
document.initialize()
rsrcmgr = PDFResourceManager()
device... | Reads a given PDF file and scans for the first valid embedded JPEG image.
Returns either None (if none found) or a string of data for the image.
There is no 100% guarantee for this code, yet it seems to work fine with most
scanner-produced images around.
More testing might be needed though.
Note th... |
2,832 | def load(self, filename=None):
if not filename:
filename = self.default_config_file
files = self._cfgs_to_read()
files.insert(-1, filename)
try:
config = self.__read_cfg(files)
except ReadConfigException as e:
print... | load runtime configuration from given filename.
If filename is None try to read from default file from
default location. |
2,833 | def _connect(self, config):
if not in self._config:
self._config[] = 480
try:
self._cnx = connect(**config)
self._cursor = self._cnx.cursor()
self._printer(, config[])
except Error as err:
if err.errno == errorcode.ER_ACCESS_D... | Establish a connection with a MySQL database. |
2,834 | def copy_file(
host,
file_path,
remote_path=,
username=None,
key_path=None,
action=
):
if not username:
username = shakedown.cli.ssh_user
if not key_path:
key_path = shakedown.cli.ssh_key_file
key = validate_key(key_path)
transport... | Copy a file via SCP, proxied through the mesos master
:param host: host or IP of the machine to execute the command on
:type host: str
:param file_path: the local path to the file to be copied
:type file_path: str
:param remote_path: the remote path to copy the file to
:... |
2,835 | def picard_index_ref(picard, ref_file):
dict_file = "%s.dict" % os.path.splitext(ref_file)[0]
if not file_exists(dict_file):
with file_transaction(picard._config, dict_file) as tx_dict_file:
opts = [("REFERENCE", ref_file),
("OUTPUT", tx_dict_file)]
picar... | Provide a Picard style dict index file for a reference genome. |
2,836 | def add_file_dep(self, doc, value):
if self.has_package(doc) and self.has_file(doc):
self.file(doc).add_depend(value)
else:
raise OrderError() | Raises OrderError if no package or file defined. |
2,837 | def _get_kvc(kv_arg):
if isinstance(kv_arg, Mapping):
return six.iterkeys(kv_arg), six.itervalues(kv_arg), len(kv_arg)
assert 2 <= len(kv_arg) <= 3, \
return (
kv_arg[0],
kv_arg[1],
kv_arg[2] if len(kv_arg) == 3 else len(kv_arg[0])) | Returns a tuple keys, values, count for kv_arg (which can be a dict or a
tuple containing keys, values and optinally count. |
2,838 | def check_entry_points(dist, attr, value):
try:
pkg_resources.EntryPoint.parse_map(value)
except ValueError, e:
raise DistutilsSetupError(e) | Verify that entry_points map is parseable |
2,839 | def get_repository_state(self, relaPath=None):
state = []
def _walk_dir(relaPath, dirList):
dirDict = {:,
:os.path.isdir(os.path.join(self.__path,relaPath)),
:os.path.isfile(os.path.join(self.__path,relaPath,self.__dirInfo)),
... | Get a list representation of repository state along with useful
information. List state is ordered relativeley to directories level
:Parameters:
#. relaPath (None, str): relative directory path from where to
start. If None all repository representation is returned.
:... |
2,840 | def toDict(self):
result = _Base.toDict(self)
result[] = self.score.score
return result | Get information about the HSP as a dictionary.
@return: A C{dict} representation of the HSP. |
2,841 | def get_template(self, project, template_id):
route_values = {}
if project is not None:
route_values[] = self._serialize.url(, project, )
if template_id is not None:
route_values[] = self._serialize.url(, template_id, )
response = self._send(http_method=,... | GetTemplate.
Gets a specific build definition template.
:param str project: Project ID or project name
:param str template_id: The ID of the requested template.
:rtype: :class:`<BuildDefinitionTemplate> <azure.devops.v5_0.build.models.BuildDefinitionTemplate>` |
2,842 | def add_source(zone, source, permanent=True):
*
if source in get_sources(zone, permanent):
log.info()
cmd = .format(zone, source)
if permanent:
cmd +=
return __firewall_cmd(cmd) | Bind a source to a zone
.. versionadded:: 2016.3.0
CLI Example:
.. code-block:: bash
salt '*' firewalld.add_source zone 192.168.1.0/24 |
2,843 | def delete(self, block_type, block_num):
logger.info("deleting block")
blocktype = snap7.snap7types.block_types[block_type]
result = self.library.Cli_Delete(self.pointer, blocktype, block_num)
return result | Deletes a block
:param block_type: Type of block
:param block_num: Bloc number |
2,844 | def listen_error_messages_raylet(worker, task_error_queue, threads_stopped):
worker.error_message_pubsub_client = worker.redis_client.pubsub(
ignore_subscribe_messages=True)
error_pubsub_channel = str(
ray.gcs_utils.TablePubsub.ERROR_INFO).encode("ascii")
worke... | Listen to error messages in the background on the driver.
This runs in a separate thread on the driver and pushes (error, time)
tuples to the output queue.
Args:
worker: The worker class that this thread belongs to.
task_error_queue (queue.Queue): A queue used to communicate with the
... |
2,845 | def instance(cls):
if not hasattr(cls, "_instance") or cls._instance is None:
cls._instance = cls()
return cls._instance | Singleton to return only one instance of BaseManager.
:returns: instance of BaseManager |
2,846 | def stats(self):
load_count = self.last_level_load.MISS_count
load_byte = self.last_level_load.MISS_byte
if self.last_level_load.victims_to is not None:
load_count -= self.last_level_load.victims_to.HIT_count
load_byte -= self.last_level_load.victim... | Return dictionay with all stats at this level. |
2,847 | def inspect(self):
last_attempt = self.get_last_failed_access_attempt(
ip_address=self.ip,
captcha_enabled=True,
captcha_passed=False,
is_expired=False
)
if last_attempt is None and not self.request.user.is_authenticated():
... | Inspect access attempt, used for catpcha flow
:return: |
2,848 | def structure(self, obj, cl):
return self._structure_func.dispatch(cl)(obj, cl) | Convert unstructured Python data structures to structured data. |
2,849 | def _ProcessGrepSource(self, source):
attributes = source.base_source.attributes
paths = artifact_utils.InterpolateListKbAttributes(
attributes["paths"], self.knowledge_base,
self.ignore_interpolation_errors)
regex = utils.RegexListDisjunction(attributes["content_regex_list"])
condi... | Find files fulfilling regex conditions. |
2,850 | def bll_version(self):
if not self.started():
return None
status, data = self._rest.get_request(, ,
[, ])
return data[] | Get the BLL version this session is connected to.
Return:
Version string if session started. None if session not started. |
2,851 | def get_serializer(name):
try:
log.debug(, name)
return SERIALIZER_LOOKUP[name]
except KeyError:
msg = .format(name)
log.error(msg, exc_info=True)
raise InvalidSerializerException(msg) | Return the serialize function. |
2,852 | def generate_changelog(from_version: str, to_version: str = None) -> dict:
debug(.format(from_version, to_version))
changes: dict = {: [], : [],
: [], : [], : []}
found_the_release = to_version is None
rev = None
if from_version:
rev = .format(from_version)
f... | Generates a changelog for the given version.
:param from_version: The last version not in the changelog. The changelog
will be generated from the commit after this one.
:param to_version: The last version in the changelog.
:return: a dict with different changelog sections |
2,853 | def reverse_taskname(name: str) -> str:
components = name.split()
assert len(components) <= 3
return .join(components[::-1]) | Reverses components in the name of task. Reversed convention is used for filenames since
it groups log/scratch files of related tasks together
0.somejob.somerun -> somerun.somejob.0
0.somejob -> somejob.0
somename -> somename
Args:
name: name of task |
2,854 | def _validate_columns(self):
geom_cols = {, , }
col_overlap = set(self.style_cols) & geom_cols
if col_overlap:
raise ValueError(
.format(
col=.join(col_overlap))) | Validate the options in the styles |
2,855 | def nested_assign(self, key_list, value):
if len(key_list) == 1:
self[key_list[0]] = value
elif len(key_list) > 1:
if key_list[0] not in self:
self[key_list[0]] = LIVVDict()
self[key_list[0]].nested_assign(key_list[1:], value) | Set the value of nested LIVVDicts given a list |
2,856 | def _prepare_text(self, text):
text = re.sub(r, , text)
pattern = r.format(self._tokenizer.pattern)
return re.sub(pattern, self._base_token_markup, text) | Returns `text` with each consituent token wrapped in HTML markup
for later match annotation.
:param text: text to be marked up
:type text: `str`
:rtype: `str` |
2,857 | def get_diff(self, rev1, rev2, path=, ignore_whitespace=False,
context=3):
if hasattr(rev1, ):
rev1 = getattr(rev1, )
if hasattr(rev2, ):
rev2 = getattr(rev2, )
if rev1 != self.EMPTY_CHANGESET:
self.get_changeset(... | Returns (git like) *diff*, as plain text. Shows changes introduced by
``rev2`` since ``rev1``.
:param rev1: Entry point from which diff is shown. Can be
``self.EMPTY_CHANGESET`` - in this case, patch showing all
the changes since empty state of the repository until ``rev2``
... |
2,858 | async def deserialize(data: dict):
return await Connection._deserialize("vcx_connection_deserialize",
json.dumps(data),
data.get()) | Create the object from a previously serialized object.
:param data: The output of the "serialize" call
Example:
data = await connection1.serialize()
connection2 = await Connection.deserialize(data)
:return: A re-instantiated object |
2,859 | def issuer_cert_urls(self):
if self._issuer_cert_urls is None:
self._issuer_cert_urls = []
if self.authority_information_access_value:
for entry in self.authority_information_access_value:
if entry[].native == :
locati... | :return:
A list of unicode strings that are URLs that should contain either
an individual DER-encoded X.509 certificate, or a DER-encoded CMS
message containing multiple certificates |
2,860 | def create(self, **kwargs):
obj = self.model(**kwargs)
meta = obj.get_meta()
meta.connection = get_es_connection(self.es_url, self.es_kwargs)
meta.index=self.index
meta.type=self.type
obj.save(force=True)
return obj | Creates a new object with the given kwargs, saving it to the database
and returning the created object. |
2,861 | def validate(self, value):
if value is None:
return True
else:
try:
with value.open() as hdulist:
self.validate_hdulist(hdulist)
except Exception:
_type, exc, tb = sys.exc_info()
six... | validate |
2,862 | def custom(command, user=None, conf_file=None, bin_env=None):
**gunicorn*
ret = __salt__[](
_ctl_cmd(command, None, conf_file, bin_env),
runas=user,
python_shell=False,
)
return _get_return(ret) | Run any custom supervisord command
user
user to run supervisorctl as
conf_file
path to supervisord config file
bin_env
path to supervisorctl bin or path to virtualenv with supervisor
installed
CLI Example:
.. code-block:: bash
salt '*' supervisord.custom "... |
2,863 | def send_message(message, params, site, logger):
client.capture(
,
message=message,
params=tuple(params),
data={
: site,
: logger,
},
) | Send a message to the Sentry server |
2,864 | async def _start(self):
self.agent._alive.wait()
try:
await self.on_start()
except Exception as e:
logger.error("Exception running on_start in behaviour {}: {}".format(self, e))
self.kill(exit_code=e)
await self._step()
self._is_done.c... | Start coroutine. runs on_start coroutine and then
runs the _step coroutine where the body of the behaviour
is called. |
2,865 | def p_out(p):
p[0] = make_sentence(,
make_typecast(TYPE.uinteger, p[2], p.lineno(3)),
make_typecast(TYPE.ubyte, p[4], p.lineno(4))) | statement : OUT expr COMMA expr |
2,866 | def update_rho(self, k, r, s):
if self.opt[, ]:
tau = self.rho_tau
mu = self.rho_mu
xi = self.rho_xi
if k != 0 and np.mod(k + 1, self.opt[, ]) == 0:
if self.opt[, ]:
if s == 0.0 or r == 0.0:
rho... | Automatic rho adjustment. |
2,867 | def database_renderer(self, name=None, site=None, role=None):
name = name or self.env.default_db_name
site = site or self.genv.SITE
role = role or self.genv.ROLE
key = (name, site, role)
self.vprint(, key)
if key not in self._database_renderers:
s... | Renders local settings for a specific database. |
2,868 | def create_event(component, tz=UTC):
event = Event()
event.start = normalize(component.get().dt, tz=tz)
if component.get():
event.end = normalize(component.get().dt, tz=tz)
elif component.get():
event.end = event.start + component.get().dt
else:
event.end = even... | Create an event from its iCal representation.
:param component: iCal component
:param tz: timezone for start and end times
:return: event |
2,869 | def N_to_Ntriangles(N):
theta = np.array([np.pi/2*(k-0.5)/N for k in range(1, N+1)])
phi = np.array([[np.pi*(l-0.5)/Mk for l in range(1, Mk+1)] for Mk in np.array(1 + 1.3*N*np.sin(theta), dtype=int)])
Ntri = 2*np.array([len(p) for p in phi]).sum()
return Ntri | @N: WD style gridsize
Converts WD style grid size @N to the number of triangles on the
surface.
Returns: number of triangles. |
2,870 | def list_storages(self):
| Returns a list of existing stores. The returned names can then be
used to call get_storage(). |
2,871 | def write_matrix_to_csv(self, headers, data):
with open(self.path, "w") as out_file:
data_writer = csv.writer(out_file, delimiter=",")
data_writer.writerow(headers)
data_writer.writerows(data) | Saves .csv file with data
:param headers: column names
:param data: Data |
2,872 | def pybel_to_json(molecule, name=None):
atoms = [{: table.GetSymbol(atom.atomicnum),
: list(atom.coords)}
for atom in molecule.atoms]
for json_atom, pybel_atom in zip(atoms, molecule.atoms):
if pybel_atom.partialcharge != 0:
json_atom[] = pybel_atom.... | Converts a pybel molecule to json.
Args:
molecule: An instance of `pybel.Molecule`
name: (Optional) If specified, will save a "name" property
Returns:
A Python dictionary containing atom and bond data |
2,873 | def start(self):
t work'
thread = threading.Thread(target=reactor.run)
thread.start() | doesn't work |
2,874 | def solve(self):
aLvl,trash = self.prepareToCalcEndOfPrdvP()
EndOfPrdvP = self.calcEndOfPrdvP()
if self.vFuncBool:
self.makeEndOfPrdvFunc(EndOfPrdvP)
if self.CubicBool:
interpolator = self.makeCubicxFunc
else:
interpolator = self.make... | Solves a one period consumption saving problem with risky income and
shocks to medical need.
Parameters
----------
None
Returns
-------
solution : ConsumerSolution
The solution to the one period problem, including a consumption
function, ... |
2,875 | def removeStages(self, personID):
while self.getRemainingStages(personID) > 1:
self.removeStage(personID, 1)
self.removeStage(personID, 0) | remove(string)
Removes all stages of the person. If no new phases are appended,
the person will be removed from the simulation in the next simulationStep(). |
2,876 | def ReportConfiguration(self, f):
if BoundaryCheck.chrom != -1:
print >> f, BuildReportLine("CHROM", BoundaryCheck.chrom)
if len(self.start_bounds) > 0:
bounds = ",".join(["%s-%s" % (a[0], a[1]) for a in zip(self.start_bounds, self.end_bounds)])
... | Report the boundary configuration details
:param f: File (or standard out/err)
:return: None |
2,877 | def getCSD (lfps,sampr,minf=0.05,maxf=300,norm=True,vaknin=False,spacing=1.0):
datband = getbandpass(lfps,sampr,minf,maxf)
if datband.shape[0] > datband.shape[1]:
ax = 1
else:
ax = 0
if vaknin: datband = Vaknin(datband)
if norm: removemean(datband,ax=ax)
CSD = -numpy.diff(datband,n=2... | get current source density approximation using set of local field potentials with equidistant spacing
first performs a lowpass filter
lfps is a list or numpy array of LFPs arranged spatially by column
spacing is in microns |
2,878 | def get_ngroups(self, field=None):
field = field if field else self._determine_group_field(field)
if in self.data[][field]:
return self.data[][field][]
raise ValueError("ngroups not found in response. specify group.ngroups in the query.") | Returns ngroups count if it was specified in the query, otherwise ValueError.
If grouping on more than one field, provide the field argument to specify which count you are looking for. |
2,879 | def _GetComplexConjugateArray(Array):
ConjArray = _np.array([num.conj() for num in Array])
return ConjArray | Calculates the complex conjugate of each element in an array and returns the resulting array.
Parameters
----------
Array : ndarray
Input array
Returns
-------
ConjArray : ndarray
The complex conjugate of the input array. |
2,880 | def generate_random_schema(valid):
schema_type = choice([, ])
if schema_type == :
type, gen = generate_random_type(valid)
value = next(gen)
return value, (value if valid else None for i in itertools.count())
elif schema_type == :
return generate_random_type(valid)
e... | Generate a random plain schema, and a sample generation function.
:param valid: Generate valid samples?
:type valid: bool
:returns: schema, sample-generator
:rtype: *, generator |
2,881 | def dt_day(x):
import pandas as pd
return pd.Series(x).dt.day.values | Extracts the day from a datetime sample.
:returns: an expression containing the day extracted from a datetime column.
Example:
>>> import vaex
>>> import numpy as np
>>> date = np.array(['2009-10-12T03:31:00', '2016-02-11T10:17:34', '2015-11-12T11:34:22'], dtype=np.datetime64)
>>> df = vaex.f... |
2,882 | def save_file(self, path=None, filters=, force_extension=None, force_overwrite=False, header_only=False, delimiter=, binary=None):
if not _os.path.splitext(path)[-1][1:] == force_extension:
path = path + + force_extension
self.path=path
... | This will save all the header info and columns to an ascii file with
the specified path.
Parameters
----------
path=None
Path for saving the data. If None, this will bring up
a save file dialog.
filters='*.dat'
File filter for the fil... |
2,883 | def parse_expr(e):
m = relation_re.match(e)
if m is None:
raise ValueError("error parsing expression ".format(e))
field, op, val = m.groups()
try:
val_int = int(val)
val = val_int
except ValueError:
try:
val_float = float(va... | Parse a single constraint expression.
Legal expressions are defined by the regular expression `relation_re`.
:param e: Expression
:type e: str
:return: Tuple of field, operator, and value
:rtype: tuple |
2,884 | def pool(args):
from jcvi.formats.base import longest_unique_prefix
p = OptionParser(pool.__doc__)
p.add_option("--sep", default=".", help="Separator between prefix and name")
p.add_option("--sequential", default=False, action="store_true",
help="Add sequential IDs")
opts, args = p... | %prog pool fastafiles > pool.fasta
Pool a bunch of FASTA files, and add prefix to each record based on
filenames. File names are simplified to longest unique prefix to avoid
collisions after getting shortened. |
2,885 | def _set_client_pw(self, v, load=False):
if hasattr(v, "_utype"):
v = v._utype(v)
try:
t = YANGDynClass(v,base=client_pw.client_pw, is_container=, presence=True, yang_name="client-pw", rest_name="client-pw", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths... | Setter method for client_pw, mapped from YANG variable /cluster/client_pw (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_client_pw is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_client_pw()... |
2,886 | def load_requires_from_file(filepath):
with open(filepath) as fp:
return [pkg_name.strip() for pkg_name in fp.readlines()] | Read a package list from a given file path.
Args:
filepath: file path of the package list.
Returns:
a list of package names. |
2,887 | def insert_completions(self, e):
u
completions = self._get_completions()
b = self.begidx
e = self.endidx
for comp in completions:
rep = [ c for c in comp ]
rep.append()
self.l_buffer[b:e] = rep
b += len(rep)
e ... | u"""Insert all completions of the text before point that would have
been generated by possible-completions. |
2,888 | def addStream(self, stream, interpolator="closest", t1=None, t2=None, dt=None, limit=None, i1=None, i2=None, transform=None,colname=None):
streamquery = query_maker(t1, t2, limit, i1, i2, transform)
param_stream(self.cdb, streamquery, stream)
streamquery["interpolator"] = interpolator... | Adds the given stream to the query construction. Additionally, you can choose the interpolator to use for this stream, as well as a special name
for the column in the returned dataset. If no column name is given, the full stream path will be used.
addStream also supports Merge queries. You can insert a... |
2,889 | def _check_file(parameters):
(filename, args) = parameters
if filename == :
contents = sys.stdin.read()
else:
with contextlib.closing(
docutils.io.FileInput(source_path=filename)
) as input_file:
contents = input_file.read()
args = load_configuratio... | Return list of errors. |
2,890 | def parse_complex_fault_node(node, mfd_spacing=0.1, mesh_spacing=4.0):
assert "complexFaultSource" in node.tag
sf_taglist = get_taglist(node)
sf_id, name, trt = (node.attrib["id"],
node.attrib["name"],
node.attrib["tectonicRegion"])
edges = ... | Parses a "complexFaultSource" node and returns an instance of the :class:
openquake.hmtk.sources.complex_fault.mtkComplexFaultSource |
2,891 | def from_dict(self, d):
if in d:
if d[]:
self._uid = d[]
if in d:
if d[]:
self._name = d[]
if in d:
if isinstance(d[], str) or isinstance(d[], unicode):
if d[] in states._stage_state_values.keys():... | Create a Stage from a dictionary. The change is in inplace.
:argument: python dictionary
:return: None |
2,892 | def gaussian_kernel(data_shape, sigma, norm=):
r
if not import_astropy:
raise ImportError()
if norm not in (, , ):
raise ValueError()
kernel = np.array(Gaussian2DKernel(sigma, x_size=data_shape[1],
y_size=data_shape[0]))
if norm == :
return kernel ... | r"""Gaussian kernel
This method produces a Gaussian kerenal of a specified size and dispersion
Parameters
----------
data_shape : tuple
Desiered shape of the kernel
sigma : float
Standard deviation of the kernel
norm : str {'max', 'sum', 'none'}, optional
Normalisation ... |
2,893 | def _get_switchports(profile):
switchports = []
if profile.get():
for link in profile[]:
if in link and in link:
switch = link[]
interface = link[]
switchports.append((switch, interface))
e... | Return list of (switch_ip, interface) tuples from local_link_info |
2,894 | def write_results(filename,config,srcfile,samples):
results = createResults(config,srcfile,samples=samples)
results.write(filename) | Package everything nicely |
2,895 | def ustep(self):
super(ConvCnstrMODMaskDcpl_Consensus, self).ustep()
self.U1 += self.AX1 - self.Y1 - self.S | The parent class ystep method is overridden to allow also
performing the ystep for the additional variables introduced in
the modification to the baseline algorithm. |
2,896 | def enqueue_task(self, source, *args):
yield from self.cell.coord.enqueue(self)
route = Route(source, self.cell, self.spec, self.emit)
self.cell.loop.create_task(self.coord_wrap(route, *args))
yield | Enqueue a task execution. It will run in the background as soon
as the coordinator clears it to do so. |
2,897 | def _call(self, x, out=None):
if out is None:
return self.range.element(copy(self.constant))
else:
out.assign(self.constant) | Return the constant vector or assign it to ``out``. |
2,898 | def trigger_audited(self, id, rev, **kwargs):
kwargs[] = True
if kwargs.get():
return self.trigger_audited_with_http_info(id, rev, **kwargs)
else:
(data) = self.trigger_audited_with_http_info(id, rev, **kwargs)
return data | Triggers a build of a specific Build Configuration in a specific revision
This method makes a synchronous HTTP request by default. To make an
asynchronous HTTP request, please define a `callback` function
to be invoked when receiving the response.
>>> def callback_function(respo... |
2,899 | def print_head(self, parent_plate_value, plate_values, interval, n=10, print_func=logging.info):
if isinstance(plate_values, Plate):
self.print_head(parent_plate_value, plate_values.values, interval, n, print_func)
return
if len(plate_values) == 1 and len(plate_values[0... | Print the first n values from the streams in the given time interval.
The parent plate value is the value of the parent plate,
and then the plate values are the values for the plate that are to be printed.
e.g. print_head(None, ("house", "1"))
:param parent_plate_value: The (fixed) pare... |
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