text stringlengths 89 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 630 |
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def publish(build):
""" publish the package itself """
build.packages.install("wheel")
build.packages.install("twine")
build.executables.run([
"python", "setup.py",
"sdist", "bdist_wheel", "--universal", "--release"
])
build.executables.run([
"twine", "upload", "dist/*"
... | [
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def CompileReport(self, mediator):
"""Compiles an analysis report.
Args:
mediator (AnalysisMediator): mediates interactions between
analysis plugins and other components, such as storage and dfvfs.
Returns:
AnalysisReport: the analysis report.
"""
lines_of_text = ['Listing do... | [
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def clean_locals(data):
"""
Clean up locals dict, remove empty and self/session/params params
and convert to camelCase.
:param {} data: locals dicts from a function.
:returns: dict
"""
if data.get('params') is not None:
return data.get('params')
else:
return {
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def main(sample_id, fastq_pair, max_len, kmer, clear):
"""Main executor of the spades template.
Parameters
----------
sample_id : str
Sample Identification string.
fastq_pair : list
Two element list containing the paired FastQ files.
max_len : int
Maximum read length. Th... | [
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def add_vq(self, parser):
''' Add verbose & quiet options '''
group = parser.add_mutually_exclusive_group()
group.add_argument("-v", "--verbose", action="store_true")
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def get_fd_from_final_mass_spin(template=None, distance=None, **kwargs):
"""Return frequency domain ringdown with all the modes specified.
Parameters
----------
template: object
An object that has attached properties. This can be used to substitute
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def get_cached_output(self, placeholder_name, instance):
"""
.. versionadded:: 0.9
Return the cached output for a rendered item, or ``None`` if no output is cached.
This method can be overwritten to implement custom caching mechanisms.
By default, this function generate... | [
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def _createConnection(self, connections):
"""
Create GSSHAPY Connection Objects Method
"""
for c in connections:
# Create GSSHAPY Connection object
connection = Connection(slinkNumber=c['slinkNumber'],
upSjuncNumber=c['upSjunc'... | [
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def send_request(self, request):
"""Send request and store response in self.url_connection."""
# throttle the number of requests to each host
self.aggregate.wait_for_host(self.urlparts[1])
kwargs = self.get_request_kwargs()
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def _fill_row_holes(self):
'''
Fill any remaining row title cells that are empty. This must be done after the other passes
to avoid preemptively filling in empty cells reserved for other operations.
'''
for row_index in range(self.start[0], self.max_title_row):
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def get_calls(self, job_name):
'''
Reads file by given name and returns CallEdge array
'''
config = self.file_index.get_by_name(job_name).yaml
calls = self.get_calls_from_dict(config, from_name=job_name)
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def _generate_appsecret_proof(self):
"""
Returns a SHA256 of the oauth_token signed by appsecret.
https://developers.facebook.com/docs/graph-api/securing-requests/
"""
if six.PY2:
key = self.appsecret
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def main():
'''monica helps you order food from the timeline'''
arguments = docopt(__doc__, version=__version__)
if arguments['configure'] and flag:
configure()
if arguments['cuisine']:
if arguments['list']:
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def ang2pix(nside, theta, phi, nest=False, lonlat=False):
"""Drop-in replacement for healpy `~healpy.pixelfunc.ang2pix`."""
lon, lat = _healpy_to_lonlat(theta, phi, lonlat=lonlat)
return lonlat_to_healpix(lon, lat, nside, order='nested' if nest else 'ring') | [
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def consumer(function):
"""Decorator that makes a generator function automatically advance to its
first yield point when initially called (PEP 342)."""
@wraps(function)
def wrapper(*args, **kwargs):
generator = function(*args, **kwargs)
next(generator)
return generator
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def structureOutput(fileUrl, fileName, searchFiles, format=True, space=40):
"""Formats the output of a list of packages"""
#First, remove the filename
if format:
splitUrls = fileUrl[1:].split('/')
fileUrl = ""
for splitUrl in splitUrls:
# This is a gimmicky fix to make formatting consistent
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def browse(self, path=None):
""" Returns a list of directories matching the path given.
Args:
path (str): glob pattern.
Returns:
List[str]
"""
params = None
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assert isinstance(path, string_types)
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def _indexes(arr):
""" Returns the list of all indexes of the given array.
Currently works for one and two-dimensional arrays
"""
myarr = np.array(arr)
if myarr.ndim == 1:
return list(range(len(myarr)))
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def array_to_img(x, scale=True):
"""
x should be shape (channels, width, height)
"""
from PIL import Image
if x.ndim != 3:
raise Exception('Unsupported shape : ', str(x.shape), '. Need (channels, width, height)')
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def is_active(self):
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Returns True when the start date is today or in the past and the
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def bulk_exports(self):
"""
:returns: Version bulk_exports of preview
:rtype: twilio.rest.preview.bulk_exports.BulkExports
"""
if self._bulk_exports is None:
self._bulk_exports = BulkExports(self)
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def set_attribute_label(span, resource_type, resource_labels, attribute_key,
canonical_key=None, label_value_prefix=''):
"""Set a label to span that can be used for tracing.
:param span: Span object
:param resource_type: resource type
:param resource_labels: collection of labels
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def get_language(self):
"""
Get the language parameter from the current request.
"""
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def complex_type(name=None):
'''Decorator for registering complex types'''
def wrapped(cls):
ParseType.type_mapping[name or cls.__name__] = cls
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def circular_layout(nodes):
"""
Lay out nodes on a circle and add node index.
"""
N = len(nodes)
if not N:
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circ = np.pi/N*np.arange(N)*2
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def to_json(self):
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def get_page_tpl_ctx(page, request):
"""
Возвращает контекст для рендеринга представления текстовой страницы
:param page: модель страницы
:param request: запрос
:return:
"""
text = Template(page.text).render(Context())
meta = MetaSeo(page)
comments = get_object_comments(PageComment, ... | [
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def get_os_file_names(files):
"""
returns file names
:param files: list of strings and\\or :class:`file_configuration_t`
instances.
:type files: list
"""
fnames = []
for f in files:
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def add_object(self, obj):
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def calculate_windows(self, **kwargs):
"""
Return the diameters of all windows in a molecule.
This function first finds and then measures the diameters of all the
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def getSensoryAssociatedLocationRepresentation(self):
"""
Get the location cells in the location layer that were driven by the input
layer (or, during learning, were associated with this input.)
"""
cells = np.array([], dtype="uint32")
totalPrevCells = 0
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def fill_x509_data(self, x509_data):
"""
Fills the X509Data Node
:param x509_data: X509Data Node
:type x509_data: lxml.etree.Element
:return: None
"""
x509_issuer_serial = x509_data.find(
'ds:X509IssuerSerial', namespaces=constants.NS_MAP
)
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def derivativeY(self,x,y):
'''
Evaluate the first derivative with respect to y of the function at given
state space points.
Parameters
----------
x : np.array
First input values.
y : np.array
Second input values; should be of same shape ... | [
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... | 33.333333 | 25.428571 |
def _move_begin_to_cxn(self, shape, cxn_pt_idx):
"""
Move the begin point of this connector to coordinates of the
connection point of *shape* specified by *cxn_pt_idx*.
"""
x, y, cx, cy = shape.left, shape.top, shape.width, shape.height
self.begin_x, self.begin_y = {
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"... | 39.666667 | 10.333333 |
def filter_inconsequential_acts(stmts_in, whitelist=None, **kwargs):
"""Filter out Activations that modify inconsequential activities
Inconsequential here means that the site is not mentioned / tested
in any other statement. In some cases specific activity types should be
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def clear_display_name(self):
"""Clears the display name.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
if (self.get_display_name_metadata().is_read_only() or... | [
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def _overwrite_special_dates(midnight_utcs,
opens_or_closes,
special_opens_or_closes):
"""
Overwrite dates in open_or_closes with corresponding dates in
special_opens_or_closes, using midnight_utcs for alignment.
"""
# Short circuit when noth... | [
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def __username(self, fname, lname): # pragma: no cover
"""Convert first name + last name into first.last style username."""
self.username = '.'.join([i.lower() for i in [fname, lname]]) | [
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def update(gandi, fqdn, name, type, value, ttl, file):
"""Update record entry for a domain.
--file option will ignore other parameters and overwrite current zone
content with provided file content.
"""
domains = gandi.dns.list()
domains = [domain['fqdn'] for domain in domains]
if fqdn not i... | [
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def apps_installation_delete(self, id, **kwargs):
"https://developer.zendesk.com/rest_api/docs/core/apps#remove-app-installation"
api_path = "/api/v2/apps/installations/{id}.json"
api_path = api_path.format(id=id)
return self.call(api_path, method="DELETE", **kwargs) | [
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def delete_pull_request_status(self, repository_id, pull_request_id, status_id, project=None):
"""DeletePullRequestStatus.
[Preview API] Delete pull request status.
:param str repository_id: The repository ID of the pull request’s target branch.
:param int pull_request_id: ID of the pull... | [
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def make_registryitem_text(text, condition='contains', negate=False, preserve_case=False):
"""
Create a node for RegistryItem/Text
:return: A IndicatorItem represented as an Element node
"""
document = 'RegistryItem'
search = 'RegistryItem/Text'
content_type = 'string'
content = tex... | [
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def trace():
"""
trace finds the line, the filename
and error message and returns it
to the user
"""
import traceback, inspect, sys
tb = sys.exc_info()[2]
tbinfo = traceback.format_tb(tb)[0]
filename = inspect.getfile(inspect.currentframe())
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def __build_index(self, until=None, flush=False, verbose=False):
"""
build/expand the index for this file.
:param until: expand the index until the record with this hash has been
incorporated and then stop. If None, go until the iterator
is exhausted. Note that if this h... | [
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def get_card(cards, term, limit=0, sort=False, ranks=None):
"""
Get the specified card from the stack.
:arg cards:
The cards to get from. Can be a ``Stack``, ``Deck`` or ``list``.
:arg str term:
The card's full name, value, suit, abbreviation, or stack indice.
:arg int limit:
... | [
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"=... | 30.588235 | 22.352941 |
def _worker_status(target,
worker,
activation,
profile='default',
tgt_type='glob'):
'''
Check if the worker is in `activation` state in the targeted load balancers
The function will return the following dictionary:
result -... | [
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def FromEvent(cls, service_event):
"""Creates a service object from an event.
Args:
service_event (EventObject): event to create a new service object from.
Returns:
WindowsService: service.
"""
_, _, name = service_event.key_path.rpartition(
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def Expandkey(key, clen):
""" Internal method supporting encryption and decryption functionality. """
import sha
from string import join
from array import array
blocks = (clen + 19) / 20
xkey = []
seed = key
for i in xrange(blocks):
seed = sha.new(key + seed).digest()
xkey.append(seed)
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def access_request(pid, record, template, **kwargs):
"""Create an access request."""
recid = int(pid.pid_value)
datastore = LocalProxy(
lambda: current_app.extensions['security'].datastore)
# Record must be in restricted access mode.
if record.get('access_right') != 'restricted' or \
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def match_app_version(self, app=None, label=None, version=None, default=False):
"""Match app version against a semantic version string.
Checks if a KE-chain app matches a version comparison. Uses the `semver` matcher to check.
`match("2.0.0", ">=1.0.0")` => `True`
`match("1.0.0", ">1.0... | [
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def append_block(self, node, reverse=False):
"""Append a statement to the current block.
Args:
node: The statement to prepend.
reverse: When called multiple times, this flag determines whether the
statement should be prepended or appended to the already inserted
statements.
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def _add_plots_to_output(out, data):
"""Add CNVkit plots summarizing called copy number values.
"""
out["plot"] = {}
diagram_plot = _add_diagram_plot(out, data)
if diagram_plot:
out["plot"]["diagram"] = diagram_plot
scatter = _add_scatter_plot(out, data)
if scatter:
out["plot... | [
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def Glyph(actor, glyphObj, orientationArray="",
scaleByVectorSize=False, c=None, alpha=1):
"""
At each vertex of a mesh, another mesh - a `'glyph'` - is shown with
various orientation options and coloring.
Color can be specfied as a colormap which maps the size of the orientation
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def romanNumeral(n):
"""
>>> romanNumeral(13)
'XIII'
>>> romanNumeral(2944)
'MMCMXLIV'
"""
if 0 > n > 4000: raise ValueError('``n`` must lie between 1 and 3999: %d' % n)
roman = 'I IV V IX X XL L XC C CD D CM M'.split()
arabic = [1, 4, 5, 9, 10, 40, 50, 90, 10... | [
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def get_gecko_params(request, uid=None, days_back=0, cumulative=True,
frequency=settings.STATISTIC_FREQUENCY_DAILY, min_val=0, max_val=100,
chart_type='standard', percentage='show', sort=False):
"""
Returns the default GET parameters for a particular Geckoboard
view request.
"""
return {
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def genre(self):
""" Cette routine convertit les indications morphologiques, données dans le fichier lemmes.la, pour exprimer le genre du mot dans la langue courante.
:return: Genre
:rtype: str
"""
_genre = ""
if " m." in self._indMorph:
_genre += "m"
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def set_alias(self, alias_hosted_zone_id, alias_dns_name):
"""Make this an alias resource record set"""
self.alias_hosted_zone_id = alias_hosted_zone_id
self.alias_dns_name = alias_dns_name | [
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def validate_metadata_sign(xml, cert=None, fingerprint=None, fingerprintalg='sha1', validatecert=False, debug=False):
"""
Validates a signature of a EntityDescriptor.
:param xml: The element we should validate
:type: string | Document
:param cert: The pubic cert
:type: ... | [
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def get_user(self, validated_token):
"""
Attempts to find and return a user using the given validated token.
"""
try:
user_id = validated_token[api_settings.USER_ID_CLAIM]
except KeyError:
raise InvalidToken(_('Token contained no recognizable user identifi... | [
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def count(self):
"""
Return the number of hits matching the query and filters. Note that
only the actual number is returned.
"""
if hasattr(self, '_response'):
return self._response.hits.total
es = connections.get_connection(self._using)
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def has_special_char(p_str, check_style=charChinese):
"""
检查字符串是否含有指定类型字符
:param:
* p_str: (string) 需要判断的字符串
* check_style: (string) 需要判断的字符类型，默认为 charChinese (编码仅支持utf-8), 支持 charNum，该参数向后兼容
:return:
* True 含有指定类型字符
* False 不含有指定类型字符
举例如下::
print('--- has... | [
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def check_s3_url(self, s3url):
"""
Check if an S3 URL exists
:param s3url: S3 url
:type s3url: str
:rtype: bool
"""
bucket, key = S3Hook.parse_s3_url(s3url)
if not self.s3_hook.check_for_bucket(bucket_name=bucket):
raise AirflowException(
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def deregister():
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Remove pandas' formatters and converters
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def _writeblocks(cls, blocks, available, cont_size, padding_func):
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def thanks(year=None):
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def add_identity(self,item_name,item_category=None,item_type=None):
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".",... | 45.416667 | 26.916667 |
def Print(self, output_writer):
"""Prints a human readable version of the filter.
Args:
output_writer (CLIOutputWriter): output writer.
"""
if self._extensions:
output_writer.Write('\textensions: {0:s}\n'.format(
', '.join(self._extensions))) | [
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"(",
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")"
] | 30.333333 | 14.111111 |
def rmdup(args):
"""
%prog rmdup *.bam > rmdup.cmds
Remove PCR duplicates from BAM files, generate a list of commands.
"""
p = OptionParser(rmdup.__doc__)
p.add_option("-S", default=False, action="store_true",
help="Treat PE reads as SE in rmdup")
opts, args = p.parse_args(... | [
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"\"Treat PE reads as SE in rmdu... | 25.92 | 16.96 |
def whitespace_before_parameters(logical_line, tokens):
r"""Avoid extraneous whitespace.
Avoid extraneous whitespace in the following situations:
- before the open parenthesis that starts the argument list of a
function call.
- before the open parenthesis that starts an indexing or slicing.
... | [
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"(",
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... | 38.133333 | 16.833333 |
def get_temp_url_key(self, cached=True):
"""
Returns the current TempURL key, or None if it has not been set.
By default the value returned is cached. To force an API call to get
the current value on the server, pass `cached=False`.
"""
meta = self._cached_temp_url_key
... | [
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"get_account_metadata",... | 38.076923 | 14.076923 |
def convert(self, value):
"""Convert self value."""
try:
return convert_to_format(value, self._format)
except (ValueError, TypeError):
return value | [
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def delete_fields(self, form_id, field_ids):
"""
Remove fields from a form
:param form_id: int
:param field_ids: list|tuple
:return: dict|str
"""
response = self._client.session.delete(
'{url}/{form_id}/fields/delete'.format(
url=self... | [
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".",
"endpoint_url",
",",... | 28 | 13.625 |
def save_config_variables(self):
"""Save the configuration variables in non-volatile memory. This method
should be used in conjuction with *write_config_variables*.
:rtype: boolean
:Example:
>>> alpha.save_config_variables()
True
"""
command = 0x43
... | [
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"save_config_variables",
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"0x43",
",",
"0x3F",
",",
"0x3C",
",",
"0x3F",
... | 26.774194 | 20.064516 |
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