Unnamed: 0 int64 0 389k | code stringlengths 26 79.6k | docstring stringlengths 1 46.9k |
|---|---|---|
14,100 | def find_one(cls, pattern, string, flags=0):
item = re.search(pattern, string, flags=flags)
return cls(item) | JS-like match object. Use index number to get groups, if not match or no group, will return ''.
Basic Usage::
>>> from torequests.utils import find_one
>>> string = "abcd"
>>> find_one("a.*", string)
<torequests.utils.RegMatch object at 0x0705F1D0>
>... |
14,101 | def loadf(path, encoding=None, model=None, parser=None):
path = str(path)
if path.endswith():
with gzip.open(path, mode=, encoding=encoding) as f:
return load(f, model=model, parser=parser)
else:
with open(path, mode=, encoding=encoding) as f:
return load(f, mode... | Deserialize path (.arpa, .gz) to a Python object. |
14,102 | def populate_obj(obj, attrs):
for k, v in attrs.iteritems():
setattr(obj, k, v) | Populates an object's attributes using the provided dict |
14,103 | def merge_dict_of_lists(adict, indices, pop_later=True, copy=True):
def check_indices(idxs, x):
for i in chain(*idxs):
if i < 0 or i >= x:
raise IndexError("Given indices are out of dict range.")
check_indices(indices, len(adict))
rdict = adict.copy() if copy else ... | Extend the within a dict of lists. The indices will indicate which
list have to be extended by which other list.
Parameters
----------
adict: OrderedDict
An ordered dictionary of lists
indices: list or tuple of 2 iterables of int, bot having the same length
The indices of the lists... |
14,104 | def conditions(self) -> Dict[str, Dict[str, Union[float, numpy.ndarray]]]:
conditions = {}
for subname in NAMES_CONDITIONSEQUENCES:
subseqs = getattr(self, subname, ())
subconditions = {seq.name: copy.deepcopy(seq.values)
for seq in subseqs}
... | Nested dictionary containing the values of all condition
sequences.
See the documentation on property |HydPy.conditions| for further
information. |
14,105 | def update(self):
self.frontends = []
self.backends = []
self.listeners = []
csv = [ l for l in self._fetch().strip().split() if l ]
if self.failed:
return
self.fields = [ f for f in csv.pop(0).split() if f ]
for line ... | Fetch and parse stats |
14,106 | def check_elasticsearch(record, *args, **kwargs):
def can(self):
search = request._methodview.search_class()
search = search.get_record(str(record.id))
return search.count() == 1
return type(, (), {: can})() | Return permission that check if the record exists in ES index.
:params record: A record object.
:returns: A object instance with a ``can()`` method. |
14,107 | def cat(tensors, dim=0):
assert isinstance(tensors, (list, tuple))
if len(tensors) == 1:
return tensors[0]
return torch.cat(tensors, dim) | Efficient version of torch.cat that avoids a copy if there is only a single element in a list |
14,108 | async def callproc(self, procname, args=()):
conn = self._get_db()
if self._echo:
logger.info("CALL %s", procname)
logger.info("%r", args)
for index, arg in enumerate(args):
q = "SET @_%s_%d=%s" % (procname, index, conn.escape(arg))
await... | Execute stored procedure procname with args
Compatibility warning: PEP-249 specifies that any modified
parameters must be returned. This is currently impossible
as they are only available by storing them in a server
variable and then retrieved by a query. Since stored
procedures... |
14,109 | def ordinal(self, num):
if re.match(r"\d", str(num)):
try:
num % 2
n = num
except TypeError:
if "." in str(num):
try:
n = int(num[-1])
... | Return the ordinal of num.
num can be an integer or text
e.g. ordinal(1) returns '1st'
ordinal('one') returns 'first' |
14,110 | def boolean_difference(self, mesh, inplace=False):
bfilter = vtk.vtkBooleanOperationPolyDataFilter()
bfilter.SetOperationToDifference()
bfilter.SetInputData(1, mesh)
bfilter.SetInputData(0, self)
bfilter.ReorientDifferenceCellsOff()
bfilter.Update()
mesh... | Combines two meshes and retains only the volume in common
between the meshes.
Parameters
----------
mesh : vtki.PolyData
The mesh to perform a union against.
inplace : bool, optional
Updates mesh in-place while returning nothing.
Returns
... |
14,111 | def __load_project(path):
file_path = __get_docker_file_path(path)
if file_path is None:
msg = .format(path)
return __standardize_result(False,
msg,
None, None)
return __load_project_from_file_path(file_path) | Load a docker-compose project from path
:param path:
:return: |
14,112 | def get_fields_from_job_name(self, job_name):
extra_fields = {
: None,
: None,
: None,
: None,
: None,
: None,
: None
}
try:
components = job_name.split()
if len(components) < ... | Analyze a Jenkins job name, producing a dictionary
The produced dictionary will include information about the category
and subcategory of the job name, and any extra information which
could be useful.
For each deployment of a Jenkins dashboard, an implementation of
this functio... |
14,113 | def to_array(self):
array = super(PreCheckoutQuery, self).to_array()
array[] = u(self.id)
array[] = self.from_peer.to_array()
array[] = u(self.currency)
array[] = int(self.total_amount)
array[] = u(self.invoice_payload)
if self.shipping_option_i... | Serializes this PreCheckoutQuery to a dictionary.
:return: dictionary representation of this object.
:rtype: dict |
14,114 | def expose(self, binder, interface, annotation=None):
private_module = self
class Provider(object):
def get(self):
return private_module.private_injector.get_instance(
interface, annotation)
self.original_binder.bind(interface, annota... | Expose the child injector to the parent inject for a binding. |
14,115 | def names_labels(self, do_print=False):
if do_print:
for name, label in zip(self.field_names, self.field_labels):
print( % (str(name), str(label)))
return self.field_names, self.field_labels | Simple helper function to get all field names and labels |
14,116 | def inserir(self, id_equipment, id_script):
equipment_script_map = dict()
equipment_script_map[] = id_equipment
equipment_script_map[] = id_script
code, xml = self.submit(
{: equipment_script_map}, , )
return self.response(code, xml) | Inserts a new Related Equipment with Script and returns its identifier
:param id_equipment: Identifier of the Equipment. Integer value and greater than zero.
:param id_script: Identifier of the Script. Integer value and greater than zero.
:return: Dictionary with the following structure:
... |
14,117 | def write(self, fileobj = sys.stdout, indent = u""):
fileobj.write(self.start_tag(indent))
fileobj.write(u"\n") | Recursively write an element and it's children to a file. |
14,118 | def load_plugins(self, plugin_class_name):
continue
for name in dir(f_module):
binding = getattr(f_module, name, None)
try:
is_sub = issubclass(binding, plugin_class)
except TypeErr... | load all available plugins
:param plugin_class_name: str, name of plugin class (e.g. 'PreBuildPlugin')
:return: dict, bindings for plugins of the plugin_class_name class |
14,119 | def OxmlElement(nsptag_str, attrs=None, nsdecls=None):
nsptag = NamespacePrefixedTag(nsptag_str)
if nsdecls is None:
nsdecls = nsptag.nsmap
return oxml_parser.makeelement(
nsptag.clark_name, attrib=attrs, nsmap=nsdecls
) | Return a 'loose' lxml element having the tag specified by *nsptag_str*.
*nsptag_str* must contain the standard namespace prefix, e.g. 'a:tbl'.
The resulting element is an instance of the custom element class for this
tag name if one is defined. A dictionary of attribute values may be
provided as *attrs*... |
14,120 | def get_prefixed_config(self, section, option, **kwargs):
cfg = Config.instance()
default = cfg.get_expanded(section, option, **kwargs)
return cfg.get_expanded(section, "{}_{}".format(self.workflow_type, option),
default=default, **kwargs) | TODO. |
14,121 | def relpath(path, start=None):
relative = get_instance(path).relpath(path)
if start:
return os_path_relpath(relative, start=start).replace(, )
return relative | Return a relative file path to path either from the
current directory or from an optional start directory.
For storage objects, "path" and "start" are relative to
storage root.
"/" are not stripped on storage objects path. The ending slash is required
on some storage to signify that target is a di... |
14,122 | def exec_after_request_actions(actions, response, **kwargs):
current_context["response"] = response
groups = ("after_" + flask.request.method.lower(), "after")
try:
rv = execute_actions(actions, limit_groups=groups, **kwargs)
except ReturnValueException as e:
rv = e.value
if rv:... | Executes actions of the "after" and "after_METHOD" groups.
A "response" var will be injected in the current context. |
14,123 | def updateShape(self):
x = self.tags[]
y = -self.tags[]
z = self.tags[]
for sec in list(self.secs.values()):
if in sec and not in sec[]:
h.pop_section() | Call after h.define_shape() to update cell coords |
14,124 | def check_sim_in(self):
try:
pkt = self.sim_in.recv(17*8 + 4)
except socket.error as e:
if not e.errno in [ errno.EAGAIN, errno.EWOULDBLOCK ]:
raise
return
if len(pkt) != 17*8 + 4:
print("wrong size %u" % len(p... | check for FDM packets from runsim |
14,125 | def format_crypto_units(input_quantity, input_type, output_type, coin_symbol=None, print_cs=False, safe_trimming=False, round_digits=0):
assert input_type in UNIT_CHOICES, input_type
assert output_type in UNIT_CHOICES, output_type
if print_cs:
assert is_valid_coin_symbol(coin_symbol=coin_symbol... | Take an input like 11002343 satoshis and convert it to another unit (e.g. BTC) and format it with appropriate units
if coin_symbol is supplied and print_cs == True then the units will be added (e.g. BTC or satoshis)
Smart trimming gets rid of trailing 0s in the decimal place, except for satoshis (irrelevant) ... |
14,126 | def get_arsc_info(arscobj):
buff = ""
for package in arscobj.get_packages_names():
buff += package + ":\n"
for locale in arscobj.get_locales(package):
buff += "\t" + repr(locale) + ":\n"
for ttype in arscobj.get_types(package, locale):
buff += "\t\t" ... | Return a string containing all resources packages ordered by packagename, locale and type.
:param arscobj: :class:`~ARSCParser`
:return: a string |
14,127 | def parse_iparamvalue(self, tup_tree):
self.check_node(tup_tree, , (,))
child = self.optional_child(tup_tree,
(, , ,
, ,
, ,
, ))
_name =... | Parse expected IPARAMVALUE element. I.e.
::
<!ELEMENT IPARAMVALUE (VALUE | VALUE.ARRAY | VALUE.REFERENCE |
INSTANCENAME | CLASSNAME |
QUALIFIER.DECLARATION |
CLASS | INSTANCE | VALUE.NAMEDINSTAN... |
14,128 | def summary(self):
if self._summary is None:
self._summary = CallSummaryList(self)
return self._summary | :rtype: twilio.rest.insights.v1.summary.CallSummaryList |
14,129 | def set_feature_generator(self):
self.features = preparation.build_proteintable(self.lookup,
self.headerfields,
self.mergecutoff,
self.iso... | Generates proteins with quant from the lookup table |
14,130 | def _estimate_transforms(self, nsamples):
M = len(self.coef)
mean_transform = np.zeros((M,M))
x_transform = np.zeros((M,M))
inds = np.arange(M, dtype=np.int)
for _ in tqdm(range(nsamples), "Estimating transforms"):
np.random.shuffle(inds)
cov_inv... | Uses block matrix inversion identities to quickly estimate transforms.
After a bit of matrix math we can isolate a transform matrix (# features x # features)
that is independent of any sample we are explaining. It is the result of averaging over
all feature permutations, but we just use a fixed... |
14,131 | def join(self, other):
return Heading(
[self.attributes[name].todict() for name in self.primary_key] +
[other.attributes[name].todict() for name in other.primary_key if name not in self.primary_key] +
[self.attributes[name].todict() for name in self.dependent_attribu... | Join two headings into a new one.
It assumes that self and other are headings that share no common dependent attributes. |
14,132 | def pixy_set_brightness(self, brightness):
task = asyncio.ensure_future(self.core.pixy_set_brightness(brightness))
self.loop.run_until_complete(task) | Sends the setBrightness Pixy command.
This method sets the brightness (exposure) of Pixy's camera.
:param brightness: range between 0 and 255 with 255 being the
brightest setting
:returns: No return value. |
14,133 | def _regex_from_encoded_pattern(s):
if s.startswith() and s.rfind() != 0:
idx = s.rfind()
pattern, flags_str = s[1:idx], s[idx+1:]
flag_from_char = {
"i": re.IGNORECASE,
"l": re.LOCALE,
"s": re.DOTALL,
"m": re.MULTILINE,
... | foo' -> re.compile(re.escape('foo'))
'/foo/' -> re.compile('foo')
'/foo/i' -> re.compile('foo', re.I) |
14,134 | def CountFlowResultsByType(self, client_id, flow_id):
result = collections.Counter()
for hr in self.ReadFlowResults(client_id, flow_id, 0, sys.maxsize):
key = compatibility.GetName(hr.payload.__class__)
result[key] += 1
return result | Returns counts of flow results grouped by result type. |
14,135 | def BVirial_Abbott(T, Tc, Pc, omega, order=0):
r
Tr = T/Tc
if order == 0:
B0 = 0.083 - 0.422/Tr**1.6
B1 = 0.139 - 0.172/Tr**4.2
elif order == 1:
B0 = 0.6752*Tr**(-1.6)/T
B1 = 0.7224*Tr**(-4.2)/T
elif order == 2:
B0 = -1.75552*Tr**(-1.6)/T**2
B1 = -3.75... | r'''Calculates the second virial coefficient using the model in [1]_.
Simple fit to the Lee-Kesler equation.
.. math::
B_r=B^{(0)}+\omega B^{(1)}
B^{(0)}=0.083+\frac{0.422}{T_r^{1.6}}
B^{(1)}=0.139-\frac{0.172}{T_r^{4.2}}
Parameters
----------
T : float
Temperatur... |
14,136 | def convert_ram_sp_rf(ADDR_WIDTH=8, DATA_WIDTH=8):
clk = Signal(bool(0))
we = Signal(bool(0))
addr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
do = Signal(intbv(0)[DATA_WIDTH:])
toVerilog(ram_sp_rf, clk, we, addr, di, do) | Convert RAM: Single-Port, Read-First |
14,137 | def get_icon_url(self, icon):
if not icon.startswith() \
and not icon.startswith() \
and not icon.startswith():
if in icon:
return self.icon_static_root + icon
else:
return self.icon_theme_root + icon
else:... | Replaces the "icon name" with a full usable URL.
* When the icon is an absolute URL, it is used as-is.
* When the icon contains a slash, it is relative from the ``STATIC_URL``.
* Otherwise, it's relative to the theme url folder. |
14,138 | def average_s_rad(site, hypocenter, reference, pp,
normal, dist_to_plane, e, p0, p1, delta_slip):
site_xyz = get_xyz_from_ll(site, reference)
zs = dst.pdist([pp, site_xyz])
if site_xyz[0] * normal[0] + site_xyz[1] * normal[1] + site_xyz[2] * \
normal[2] - dist_to_pla... | Gets the average S-wave radiation pattern given an e-path as described in:
Spudich et al. (2013) "Final report of the NGA-West2 directivity working
group", PEER report, page 90- 92 and computes: the site to the direct point
distance, rd, and the hypocentral distance, r_hyp.
:param site:
:class:... |
14,139 | def create_time_series(self, label_values, func):
if label_values is None:
raise ValueError
if any(lv is None for lv in label_values):
raise ValueError
if len(label_values) != self._len_label_keys:
raise ValueError
if func is None:
... | Create a derived measurement to trac `func`.
:type label_values: list(:class:`LabelValue`)
:param label_values: The measurement's label values.
:type func: function
:param func: The function to track.
:rtype: :class:`DerivedGaugePoint`
:return: A read-only measurement ... |
14,140 | def visit_If(self, node):
self.visit(node.test)
old_range = self.result
self.result = old_range.copy()
for stmt in node.body:
self.visit(stmt)
body_range = self.result
self.result = old_range.copy()
for stmt in node.orelse:
self.... | Handle iterate variable across branches
>>> import gast as ast
>>> from pythran import passmanager, backend
>>> node = ast.parse('''
... def foo(a):
... if a > 1: b = 1
... else: b = 3''')
>>> pm = passmanager.PassManager("test")
>>> res = pm.gat... |
14,141 | def infer_struct(value: Mapping[str, GenericAny]) -> Struct:
if not value:
raise TypeError()
return Struct(list(value.keys()), list(map(infer, value.values()))) | Infer the :class:`~ibis.expr.datatypes.Struct` type of `value`. |
14,142 | def get_broadcast_date(pid):
print("Extracting first broadcast date...")
broadcast_etree = open_listing_page(pid + )
original_broadcast_date, = broadcast_etree.xpath(
)
return original_broadcast_date | Take BBC pid (string); extract and return broadcast date as string. |
14,143 | def hacking_no_locals(logical_line, tokens, noqa):
if noqa:
return
for_formatting = False
for token_type, text, start, _, _ in tokens:
if text == "%" and token_type == tokenize.OP:
for_formatting = True
if for_formatting and token_type == tokenize.NAME:
f... | Do not use locals() or self.__dict__ for string formatting.
Okay: 'locals()'
Okay: 'locals'
Okay: locals()
Okay: print(locals())
H501: print("%(something)" % locals())
H501: LOG.info(_("%(something)") % self.__dict__)
Okay: print("%(something)" % locals()) # noqa |
14,144 | def strip_html(text):
def reply_to(text):
replying_to = []
split_text = text.split()
for index, token in enumerate(split_text):
if token.startswith(): replying_to.append(token[1:])
else:
message = split_text[index:]
break
r... | Get rid of ugly twitter html |
14,145 | def set_layout(self, value):
visibility_changed = True
if visibility_changed:
self.update_modified()
self.update_exportable()
self.update_block_endpoints() | Set the layout table value. Called on attribute put |
14,146 | async def do_after_sleep(delay: float, coro, *args, **kwargs):
await asyncio.sleep(delay)
return await coro(*args, **kwargs) | Performs an action after a set amount of time.
This function only calls the coroutine after the delay,
preventing asyncio complaints about destroyed coros.
:param delay: Time in seconds
:param coro: Coroutine to run
:param args: Arguments to pass to coroutine
:param kwargs: Keyword arguments t... |
14,147 | def check_request(name=None):
*
notify_path = os.path.join(__opts__[], )
serial = salt.payload.Serial(__opts__)
if os.path.isfile(notify_path):
with salt.utils.files.fopen(notify_path, ) as fp_:
req = serial.load(fp_)
if name:
return req[name]
return req
... | .. versionadded:: 2015.5.0
Return the state request information, if any
CLI Example:
.. code-block:: bash
salt '*' state.check_request |
14,148 | def do_upload(post_data, callback=None):
encoder = MultipartEncoder(post_data)
monitor = MultipartEncoderMonitor(encoder, callback)
headers = {: USER_AGENT, : monitor.content_type}
response = post(API_URL, data=monitor, headers=headers)
check_response(response)
return response.json()[0] | does the actual upload also sets and generates the user agent string |
14,149 | def trim(stream, **kwargs):
return FilterNode(stream, trim.__name__, kwargs=kwargs).stream() | Trim the input so that the output contains one continuous subpart of the input.
Args:
start: Specify the time of the start of the kept section, i.e. the frame with the timestamp start will be the
first frame in the output.
end: Specify the time of the first frame that will be dropped, i... |
14,150 | def load(self, game_json=None, mode=None):
if game_json is None:
if mode is not None:
if isinstance(mode, str):
_game_object = GameObject(mode=self._match_mode(mode=mode))
elif isinstance(mode, GameMode):
_game_obj... | Load a game from a serialized JSON representation. The game expects a well defined
structure as follows (Note JSON string format):
'{
"guesses_made": int,
"key": "str:a 4 word",
"status": "str: one of playing, won, lost",
"mode": {
"digits... |
14,151 | def filter(self, value, model=None, context=None):
http = [, ]
if all(not str(value).startswith(s) for s in http):
value = .format(value)
return value | Filter
Performs value filtering and returns filtered result.
:param value: input value
:param model: parent model being validated
:param context: object, filtering context
:return: filtered value |
14,152 | def alias_create(indices, alias, hosts=None, body=None, profile=None, source=None):
es = _get_instance(hosts, profile)
if source and body:
message =
raise SaltInvocationError(message)
if source:
body = __salt__[](
source,
saltenv=__opts__.get... | Create an alias for a specific index/indices
indices
Single or multiple indices separated by comma, use _all to perform the operation on all indices.
alias
Alias name
body
Optional definition such as routing or filter as defined in https://www.elastic.co/guide/en/elasticsearch/refer... |
14,153 | def _getEngineRoot(self):
override = ConfigurationManager.getConfigKey()
if override != None:
Utility.printStderr( + override)
return override
else:
return self._detectEngineRoot() | Retrieves the user-specified engine root directory override (if set), or else performs auto-detection |
14,154 | def validate_string_dict(dct):
for k,v in dct.iteritems():
if not isinstance(k, basestring):
raise ValueError( % k)
if not isinstance(v, basestring):
raise ValueError( % v) | Validate that the input is a dict with string keys and values.
Raises ValueError if not. |
14,155 | def counter(metatdata, value):
if not str(value).isdigit():
return None
arg = str(metatdata[][0]).replace(, )
repeated_args = arg * int(value)
return + repeated_args | Returns
str(option_string * DropDown Value)
e.g.
-vvvvv |
14,156 | def imread(path, grayscale=False, size=None, interpolate="bilinear",
channel_first=False, as_uint16=False, num_channels=-1):
_imread_before(grayscale, num_channels)
f = path if hasattr(path, "read") else open(path, "rb")
r = png.Reader(file=f)
width, height, pixels, metadata = r.asDir... | Read image by pypng module.
Args:
path (str or 'file object'): File path or object to read.
grayscale (bool):
size (tupple of int):
(width, height).
If None, output img shape depends on the files to read.
channel_first (bool):
This argument specif... |
14,157 | def to_task(self):
from google.appengine.api.taskqueue import Task
task_args = self.get_task_args().copy()
payload = None
if in task_args:
payload = task_args.pop()
kwargs = {
: METHOD_TYPE,
: json.dumps(payload)
}
... | Return a task object representing this message. |
14,158 | def isIn(val, schema, name = None):
if name is None:
name = schema
if not _lists.has_key(name):
return False
try:
return val in _lists[name]
except TypeError:
return False | !~~isIn(data) |
14,159 | def from_flag(cls, flag):
if not is_flag_set(flag) or not in flag:
return None
parts = flag.split()
if parts[0] == :
return cls.from_name(parts[1])
else:
return cls.from_name(parts[0]) | Return an Endpoint subclass instance based on the given flag.
The instance that is returned depends on the endpoint name embedded
in the flag. Flags should be of the form ``endpoint.{name}.extra...``,
though for legacy purposes, the ``endpoint.`` prefix can be omitted.
The ``{name}}`` ... |
14,160 | def _jgezerou16(ins):
output = []
value = ins.quad[1]
if not is_int(value):
output = _16bit_oper(value)
output.append( % str(ins.quad[2]))
return output | Jumps if top of the stack (16bit) is >= 0 to arg(1)
Always TRUE for unsigned |
14,161 | def fromutc(self, dt):
if not isinstance(dt, datetime.datetime):
raise TypeError("fromutc() requires a datetime argument")
if dt.tzinfo is not self:
raise ValueError("dt.tzinfo is not self")
idx = self._find_last_transition(dt, in_utc=True)
... | The ``tzfile`` implementation of :py:func:`datetime.tzinfo.fromutc`.
:param dt:
A :py:class:`datetime.datetime` object.
:raises TypeError:
Raised if ``dt`` is not a :py:class:`datetime.datetime` object.
:raises ValueError:
Raised if this is called with a ``... |
14,162 | def get_all(self) -> List[Commodity]:
query = (
self.query
.order_by(Commodity.namespace, Commodity.mnemonic)
)
return query.all() | Loads all non-currency commodities, assuming they are stocks. |
14,163 | def warn(self, message, container=None):
if self.source is not None:
message = .format(self.source.location) + message
if container is not None:
try:
message += .format(container.page.formatted_number)
except AttributeError:
pa... | Present the warning `message` to the user, adding information on the
location of the related element in the input file. |
14,164 | def addReferences(self, reference, service_uids):
addedanalyses = []
wf = getToolByName(self, )
bsc = getToolByName(self, )
bac = getToolByName(self, )
ref_type = reference.getBlank() and or
ref_uid = reference.UID()
postfix = 1
for ref... | Add reference analyses to reference |
14,165 | def block1(self):
value = None
for option in self.options:
if option.number == defines.OptionRegistry.BLOCK1.number:
value = parse_blockwise(option.value)
return value | Get the Block1 option.
:return: the Block1 value |
14,166 | def fai_from_bam(ref_file, bam_file, out_file, data):
contigs = set([x.contig for x in idxstats(bam_file, data)])
if not utils.file_uptodate(out_file, bam_file):
with open(ref.fasta_idx(ref_file, data["config"])) as in_handle:
with file_transaction(data, out_file) as tx_out_file:
... | Create a fai index with only contigs in the input BAM file. |
14,167 | def _find_day_section_from_indices(indices, split_interval):
cells_day = 24 * 60 // split_interval
rv = [[int(math.floor(i / cells_day)), i % cells_day] for i in indices]
return rv | Returns a list with [weekday, section] identifiers found
using a list of indices. |
14,168 | def at_depth(self, level):
return Zconfig(lib.zconfig_at_depth(self._as_parameter_, level), False) | Locate the last config item at a specified depth |
14,169 | def create(self, req, parent, name, mode, fi):
self.reply_err(req, errno.ENOSYS) | Create and open a file
Valid replies:
reply_create
reply_err |
14,170 | def index_queryset(self, using=None):
translation.activate(settings.LANGUAGE_CODE)
return self.get_model().objects.filter(status=UrlNode.PUBLISHED).select_related() | Index current language translation of published objects.
TODO: Find a way to index all translations of the given model, not just
the current site language's translation. |
14,171 | def main():
parser = ArgumentParser(description="search files using n-grams")
parser.add_argument(, dest=, help="where to search", nargs=1, action="store", default=getcwd())
parser.add_argument(, dest=, help="update the index", action=, default=True)
parser.add_argument(, dest=, help="any, images,... | Function for command line execution |
14,172 | def post(self, request):
serializer = self.get_serializer(data=request.data)
if serializer.is_valid():
serializer.save()
return Response(serializer.data)
return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST) | Save the provided data using the class' serializer.
Args:
request:
The request being made.
Returns:
An ``APIResponse`` instance. If the request was successful
the response will have a 200 status code and contain the
serializer's data. Oth... |
14,173 | def editprojecthook(self, project_id, hook_id, url, push=False, issues=False, merge_requests=False, tag_push=False):
data = {
"id": project_id,
"hook_id": hook_id,
"url": url,
: int(bool(push)),
: int(bool(issues)),
: int(bool(merg... | edit an existing hook from a project
:param id_: project id
:param hook_id: hook id
:param url: the new url
:return: True if success |
14,174 | def _uptrace(nodelist, node):
if node.parent_index is None:
return
parent = nodelist[node.parent_index]
for x in _uptrace(nodelist, parent):
yield x
yield node | ๋
ธ๋๋ฅผ ์ํฅ ์ถ์ ํ๋ค.
ํ ๋
ธ๋๋ก๋ถํฐ ์กฐ์ ๋
ธ๋๋ค์ ์ฐจ๋ก๋ก ์ํํ๋ฉฐ ๋ฐํํ๋ค.
๋ฃจํธ ๋
ธ๋๋ ์ ์ธํ๋ค. |
14,175 | def slice(x, start, length):
sc = SparkContext._active_spark_context
return Column(sc._jvm.functions.slice(_to_java_column(x), start, length)) | Collection function: returns an array containing all the elements in `x` from index `start`
(or starting from the end if `start` is negative) with the specified `length`.
>>> df = spark.createDataFrame([([1, 2, 3],), ([4, 5],)], ['x'])
>>> df.select(slice(df.x, 2, 2).alias("sliced")).collect()
[Row(sli... |
14,176 | def extract_date(self, date):
if isinstance(date, six.string_types):
try:
date = dateutil.parser.parse(date)
except ValueError:
raise ValueError(
).format(self.query_name)
if not isinstance(date, dateti... | Extract date from string if necessary.
:returns: the extracted date. |
14,177 | def _install(self, name, autoinstall):
import importlib
import pkg_resources
spam_spec = importlib.util.find_spec(name)
reinstall = False
if spam_spec is not None:
if self._version:
mod = importlib.__import__(name)
if hasattr(m... | Check existence of Python module and install it using command
pip install if necessary. |
14,178 | def update_user(self, user_is_artist="", artist_level="", artist_specialty="", real_name="", tagline="", countryid="", website="", bio=""):
if self.standard_grant_type is not "authorization_code":
raise DeviantartError("Authentication through Authorization Code (Grant Type) is required ... | Update the users profile information
:param user_is_artist: Is the user an artist?
:param artist_level: If the user is an artist, what level are they
:param artist_specialty: If the user is an artist, what is their specialty
:param real_name: The users real name
:param tagline: ... |
14,179 | def comment (self, s, **args):
self.write(u"<!-- ")
self.write(s, **args)
self.writeln(u" -->") | Write XML comment. |
14,180 | def feed_eof(self):
self._incoming.write_eof()
ssldata, appdata = self.feed_ssldata(b)
assert appdata == [] or appdata == [b] | Send a potentially "ragged" EOF.
This method will raise an SSL_ERROR_EOF exception if the EOF is
unexpected. |
14,181 | def _add_session(self, session, start_info, groups_by_name):
for (key, value) in six.iteritems(start_info.hparams):
group.hparams[key].CopyFrom(value)
groups_by_name[group_name] = group | Adds a new Session protobuffer to the 'groups_by_name' dictionary.
Called by _build_session_groups when we encounter a new session. Creates
the Session protobuffer and adds it to the relevant group in the
'groups_by_name' dict. Creates the session group if this is the first time
we encounter it.
A... |
14,182 | def libvlc_media_event_manager(p_md):
t increment reference counting.
@param p_md: a media descriptor object.
@return: event manager object.
libvlc_media_event_managerlibvlc_media_event_manager', ((1,),), class_result(EventManager),
ctypes.c_void_p, Media)
return f(p_md) | Get event manager from media descriptor object.
NOTE: this function doesn't increment reference counting.
@param p_md: a media descriptor object.
@return: event manager object. |
14,183 | def pipeline_counter(self):
if in self.data and self.data.pipeline_counter:
return self.data.get()
elif self.stage.pipeline is not None:
return self.stage.pipeline.data.counter
else:
return self.stage.data.pipeline_counter | Get pipeline counter of current job instance.
Because instantiating job instance could be performed in different ways and those return different results,
we have to check where from to get counter of the pipeline.
:return: pipeline counter. |
14,184 | def patched_model():
patched = (, , )
originals = {}
for patch in patched:
try:
originals[patch] = getattr(models.Model, patch)
except:
pass
try:
models.Model.__reduce__ = _reduce
try:
del models.Model.__getstate__
... | Context Manager that safely patches django.db.Model.__reduce__(). |
14,185 | def calculate_betweenness_centality(graph: BELGraph, number_samples: int = CENTRALITY_SAMPLES) -> Counter:
try:
res = nx.betweenness_centrality(graph, k=number_samples)
except Exception:
res = nx.betweenness_centrality(graph)
return Counter(res) | Calculate the betweenness centrality over nodes in the graph.
Tries to do it with a certain number of samples, but then tries a complete approach if it fails. |
14,186 | def write_preferences_file(self):
user_data_dir = find_pmag_dir.find_user_data_dir("thellier_gui")
if not os.path.exists(user_data_dir):
find_pmag_dir.make_user_data_dir(user_data_dir)
pref_file = os.path.join(user_data_dir, "thellier_gui_preferences.json")
with open... | Write json preferences file to (platform specific) user data directory,
or PmagPy directory if appdirs module is missing. |
14,187 | def list_experiment(args):
nni_config = Config(get_config_filename(args))
rest_port = nni_config.get_config()
rest_pid = nni_config.get_config()
if not detect_process(rest_pid):
print_error()
return
running, _ = check_rest_server_quick(rest_port)
if running:
response... | Get experiment information |
14,188 | def way(self, w):
if w.id not in self.way_ids:
return
way_points = []
for n in w.nodes:
try:
way_points.append(Point(n.location.lon, n.location.lat))
except o.InvalidLocationError:
logging.debug(, w.id, n.ref)
... | Process each way. |
14,189 | def is_quoted(arg: str) -> bool:
return len(arg) > 1 and arg[0] == arg[-1] and arg[0] in constants.QUOTES | Checks if a string is quoted
:param arg: the string being checked for quotes
:return: True if a string is quoted |
14,190 | def descendants(self):
for i in self.current_item.items:
self.move_to(i)
if i.type == TYPE_COLLECTION:
for c in self.children:
yield c
else:
yield i
self.move_up() | Recursively return every dataset below current item. |
14,191 | def chi_eff(mass1, mass2, spin1z, spin2z):
return (spin1z * mass1 + spin2z * mass2) / (mass1 + mass2) | Returns the effective spin from mass1, mass2, spin1z, and spin2z. |
14,192 | def _getScalesDiag(self,termx=0):
assert self.P>1,
assert self.noisPos!=None,
assert termx<self.n_terms-1,
assert self.covar_type[self.noisPos] not in [,,],
assert self.covar_type[termx] not in [,,],
scales = []
res = self.estimateHeritabilities(sel... | Uses 2 term single trait model to get covar params for initialization
Args:
termx: non-noise term terms that is used for initialization |
14,193 | def energy_minimize(self, forcefield=, steps=1000, **kwargs):
tmp_dir = tempfile.mkdtemp()
original = clone(self)
self._kick()
self.save(os.path.join(tmp_dir, ))
extension = os.path.splitext(forcefield)[-1]
openbabel_ffs = [, , , , ]
if forcefield in open... | Perform an energy minimization on a Compound
Default beahvior utilizes Open Babel (http://openbabel.org/docs/dev/)
to perform an energy minimization/geometry optimization on a
Compound by applying a generic force field
Can also utilize OpenMM (http://openmm.org/) to energy minimize
... |
14,194 | def is_connected(C, directed=True):
if isdense(C):
return sparse.connectivity.is_connected(csr_matrix(C), directed=directed)
else:
return sparse.connectivity.is_connected(C, directed=directed) | Check connectivity of the given matrix.
Parameters
----------
C : scipy.sparse matrix
Count matrix specifying edge weights.
directed : bool, optional
Whether to compute connected components for a directed or
undirected graph. Default is True.
Returns
-------
is_connec... |
14,195 | def create(name, template_body=None, template_url=None, parameters=None, notification_arns=None, disable_rollback=None,
timeout_in_minutes=None, capabilities=None, tags=None, on_failure=None, stack_policy_body=None,
stack_policy_url=None, region=None, key=None, keyid=None, profile=None):
https... | Create a CFN stack.
CLI Example:
.. code-block:: bash
salt myminion boto_cfn.create mystack template_url='https://s3.amazonaws.com/bucket/template.cft' \
region=us-east-1 |
14,196 | def get_wu_settings():
*
ret = {}
day = [,
,
,
,
,
,
,
]
with salt.utils.winapi.Com():
obj_au = win32com.client.Dispatch()
obj_au_settings = obj_au.Settings
ret[] = obj_au_settings.Fe... | Get current Windows Update settings.
Returns:
dict: A dictionary of Windows Update settings:
Featured Updates:
Boolean value that indicates whether to display notifications for
featured updates.
Group Policy Required (Read-only):
Boolean value that indi... |
14,197 | def get_color(name, number=None):
foregroundfgbackgroundbgindexDEADBEEFCAFEbg000000000000index4e4d9a9a0605
colors = ()
if is_a_tty() and not env.SSH_CLIENT:
if not in _color_code_map:
_color_code_map[] = + str(number or )
if os_name == :
from .windows import get_co... | Query the default terminal, for colors, etc.
Direct queries supported on xterm, iTerm, perhaps others.
Arguments:
str: name, one of ('foreground', 'fg', 'background', 'bg',
or 'index') # index grabs a palette index
int: or a "dynamic color n... |
14,198 | def subparsers(self):
try:
return self.__subparsers
except AttributeError:
parent = super(ArgumentParser, self)
self.__subparsers = parent.add_subparsers(title="drill down")
self.__subparsers.metavar = "COMMAND"
return self.__subparser... | Obtain the subparser's object. |
14,199 | def p_expr(self, p):
if len(p) == 2:
p[0] = p[1]
else:
p[0] = ast.Comma(left=p[1], right=p[3]) | expr : assignment_expr
| expr COMMA assignment_expr |
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