text stringlengths 75 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 0.18 |
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def magick_to_rio(convert_opts):
"""Translate a limited subset of imagemagick convert commands
to rio color operations
Parameters
----------
convert_opts: String, imagemagick convert options
Returns
-------
operations string, ordered rio color operations
"""
ops = []
bands ... | [
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def nt_db_search(self, files, base, unpack, euk_check,
search_method, maximum_range, threads, evalue):
'''
Nucleotide database search pipeline - pipeline where reads are searched
as nucleotides, and hits are identified using nhmmer searches
Parameters
------... | [
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def AnnotateBED(bed, GTF, genome_file, bedcols=None, promoter=[1000,200]):
"""
Annotates a bed file.
:param bed: either a /path/to/file.bed or a Pandas dataframe in bed format. /path/to/file.bed implies bedcols.
:param GTF: /path/to/file.gtf
:param genome_file: /path/to/file.genome - a tab separate... | [
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def _handle_tag_definetext2(self):
"""Handle the DefineText2 tag."""
obj = _make_object("DefineText2")
self._generic_definetext_parser(obj, self._get_struct_rgba)
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def click_info_switch(f):
"""Decorator to create eager Click info switch option, as described in:
http://click.pocoo.org/6/options/#callbacks-and-eager-options.
Takes a no-argument function and abstracts the boilerplate required by
Click (value checking, exit on done).
Example:
@click.opt... | [
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def _add_loss_summaries(total_loss):
"""Add summaries for losses in CIFAR-10 model.
Generates moving average for all losses and associated summaries for
visualizing the performance of the network.
Args:
total_loss: Total loss from loss().
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def applyTransformOnGroup(self, transform, group):
"""Apply an SVG transformation to a RL Group shape.
The transformation is the value of an SVG transform attribute
like transform="scale(1, -1) translate(10, 30)".
rotate(<angle> [<cx> <cy>]) is equivalent to:
translate(<cx> <... | [
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def annual_frequency_of_exceedence(poe, t_haz):
"""
:param poe: array of probabilities of exceedence
:param t_haz: hazard investigation time
:returns: array of frequencies (with +inf values where poe=1)
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# avoid R... | [
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def values(self, *args: str, **kwargs: str) -> "ValuesQuery":
"""
Make QuerySet return dicts instead of objects.
"""
fields_for_select = {} # type: Dict[str, str]
for field in args:
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def pop_events(self, regex_pattern, timeout):
"""Pop events whose names match a regex pattern.
If such event(s) exist, pop one event from each event queue that
satisfies the condition. Otherwise, wait for an event that satisfies
the condition to occur, with timeout.
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def getConfiguration(configPath = None):
"""
Reading the configuration file to look for where the different gates are running.
:return: A json containing the information stored in the .cfg file.
"""
if configPath == None:
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def add_one(self, url: str,
url_properties: Optional[URLProperties]=None,
url_data: Optional[URLData]=None):
'''Add a single URL to the table.
Args:
url: The URL to be added
url_properties: Additional values to be saved
url_data: Addit... | [
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def run_validators(self, value):
"""
Test the given value against all the validators on the field,
and either raise a `ValidationError` or simply return.
"""
errors = []
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def to_dot_file(self, fname: str):
"""
write a '.dot' file.
"""
with open(fname, 'w') as f:
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def plot_ts(fignum, dates, ts):
"""
plot the geomagnetic polarity time scale
Parameters
__________
fignum : matplotlib figure number
dates : bounding dates for plot
ts : time scale ck95, gts04, or gts12
"""
vertical_plot_init(fignum, 10, 3)
TS, Chrons = pmag.get_ts(ts)
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def get_parent(self, el, no_iframe=False):
"""Get parent."""
parent = el.parent
if no_iframe and parent is not None and self.is_iframe(parent):
parent = None
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def cluster_sample1():
"Start with wrong number of clusters."
start_centers = [[3.7, 5.5]]
template_clustering(start_centers, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, criterion = splitting_type.BAYESIAN_INFORMATION_CRITERION)
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def omega_mixture(omegas, zs, CASRNs=None, Method=None,
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r'''This function handles the calculation of a mixture's acentric factor.
Calculation is based on the omegas provided for each pure component. Will
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def write_json(f: TextIO, deja_vu_sans_path: str,
measurer: text_measurer.TextMeasurer,
encodings: Iterable[str]) -> None:
"""Write the data required by PrecalculatedTextMeasurer to a stream."""
supported_characters = list(
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def filtmask(sp, fmin=0.02, fmax=0.15, debugplot=0):
"""Filter spectrum in Fourier space and apply cosine bell.
Parameters
----------
sp : numpy array
Spectrum to be filtered and masked.
fmin : float
Minimum frequency to be employed.
fmax : float
Maximum frequency to be ... | [
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def apply_link_ref(offset: int, length: int, value: bytes, bytecode: bytes) -> bytes:
"""
Returns the new bytecode with `value` put into the location indicated by `offset` and `length`.
"""
try:
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def get_slide_vars(self, slide_src, source=None):
""" Computes a single slide template vars from its html source code.
Also extracts slide informations for the table of contents.
"""
presenter_notes = None
find = re.search(r'<h\d[^>]*>presenter notes</h\d>', slide_src,
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def list(self, **params):
"""
Retrieve all products
Returns all products available to the user according to the parameters provided
:calls: ``get /products``
:param dict params: (optional) Search options.
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def posterior_predictive_to_xarray(self):
"""Convert posterior_predictive samples to xarray."""
data = {k: np.expand_dims(v, 0) for k, v in self.posterior_predictive.items()}
return dict_to_dataset(data, library=self.pymc3, coords=self.coords, dims=self.dims) | [
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def update(self, data={}, options={}):
"""
Update the configuration with new data.
This can be passed either or both `data` and `options`.
`options` is a dict of keypath/value pairs like this (similar to
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def _overlap(y,yr,psd):
""" returns the detector noise weighted inner product """
yyr = _inner_product(y,yr,psd)
yy = _inner_product(y,y,psd)
yryr = _inner_product(yr,yr,psd)
olap = yyr/np.sqrt(yy*yryr)
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def histogram(self, tag, values, bins, step=None):
"""Saves histogram of values.
Args:
tag: str: label for this data
values: ndarray: will be flattened by this routine
bins: number of bins in histogram, or array of bins for onp.histogram
step: int: training step
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def valid_sequences(self):
"""Returns list"""
valid_sets = [[x] for x in self.possible_items if x['left'] == 0]
change = True
niter = 200
while change and niter > 0:
change = False
niter -=1
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def draw(self, **kwargs):
"""
Draws the heatmap of the ranking matrix of variables.
"""
# Set the axes aspect to be equal
self.ax.set_aspect("equal")
# Generate a mask for the upper triangle
mask = np.zeros_like(self.ranks_, dtype=np.bool)
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def compose_schemas(*schemas):
"""
Returns a single three-ple of the following for all provided schemas:
- a map of attribute names to attributes for all related schema
attributes
- a set of names of all related required schema attributes
- a set of names of all related default s... | [
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def calc_max_flexural_wavelength(self):
"""
Returns the approximate maximum flexural wavelength
This is important when padding of the grid is required: in Flexure (this
code), grids are padded out to one maximum flexural wavelength, but in any
case, the flexural wavelength is a good character... | [
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def find_file(self, path, tgt_env='base', **kwargs): # pylint: disable=W0613
'''
Find the first file to match the path and ref, read the file out of git
and send the path to the newly cached file
'''
fnd = {'path': '',
'rel': ''}
if os.path.isabs(path) or ... | [
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def logProbability(self, distn):
"""Form of distribution must be an array of counts in order of self.keys."""
x = numpy.asarray(distn)
n = x.sum()
return (logFactorial(n) - numpy.sum([logFactorial(k) for k in x]) +
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def btc_tx_get_hash( tx_serialized, hashcode=None ):
"""
Make a transaction hash (txid) from a hex tx, optionally along with a sighash.
This DOES NOT WORK for segwit transactions
"""
if btc_tx_is_segwit(tx_serialized):
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def _transliterate (self, text, outFormat):
""" Transliterate the text to the target transliteration scheme."""
result = []
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result.append(self[c].equivalents[outFormat.name])
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def bulk_remove(self, named_graph, add, size=DEFAULT_CHUNK_SIZE):
"""
Remove batches of statements in n-sized chunks.
"""
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def _parse_common(text, **options):
"""
Tries to parse the string as a common datetime format.
:param text: The string to parse.
:type text: str
:rtype: dict or None
"""
m = COMMON.match(text)
has_date = False
year = 0
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day = 1
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def guess_url_vcs(url):
"""
Given a url, try to guess what kind of VCS it's for. Return None if we
can't make a good guess.
"""
parsed = urllib.parse.urlsplit(url)
if parsed.scheme in ('git', 'svn'):
return parsed.scheme
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def update_many(path,points):
"""update_many(path,points)
path is a string
points is a list of (timestamp,value) points
"""
if not points: return
points = [ (int(t),float(v)) for (t,v) in points]
points.sort(key=lambda p: p[0],reverse=True) #order points by timestamp, newest first
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def _add_conversation(self, conversation):
"""
Add the conversation and fire the :meth:`on_conversation_added` event.
:param conversation: The conversation object to add.
:type conversation: :class:`~.AbstractConversation`
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def _parse_header_params(self,header_param_lines):
'''解析头部参数'''
headers = {}
for line in header_param_lines:
if line.strip(): # 跳过空行
key,val = line.split(':', 1)
headers[key.lower()] = val.strip()
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def _convert_from(data):
"""Internal function that will be hooked to the native `json.loads`
Find the right deserializer for a given value, taking into account
the internal deserializer registry.
"""
try:
module, klass_name = data['__class__'].rsplit('.', 1)
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def _restoreDPFromArchive(self):
"""Callback for item menu."""
dp = self._dp_menu_on
if dp and dp.archived:
dp.restore_from_archive(parent=self) | [
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def get_child_classes(cls, slot, page, instance=None):
"""Restrict child classes of Card to one of each: Header, Body and Footer"""
child_classes = super(BootstrapCardPlugin, cls).get_child_classes(slot, page, instance)
# allow only one child of type Header, Body, Footer
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def _free_shortcut(self, shortcut):
"""
Replace the shortcut of elements, that has the shortcut passed.
:param shortcut: The shortcut.
:type shortcut: str
"""
alpha_numbers = '1234567890abcdefghijklmnopqrstuvwxyz'
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def image_display(element, max_frames, fmt):
"""
Used to render elements to an image format (svg or png) if requested
in the display formats.
"""
if fmt not in Store.display_formats:
return None
info = process_object(element)
if info:
display(HTML(info))
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def evaluate():
"""Get Policy and Value for each network, for each position
Usage:
python3 sharp_positions.py evaluate --sgf_dir data/s --model_dir models/
"""
def short_str(v):
if isinstance(v, float):
return "{.3f}".format(v)
return str(v)
# Load positons
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def _check_module_attrs(self, node, module, module_names):
"""check that module_names (list of string) are accessible through the
given module
if the latest access name corresponds to a module, return it
"""
assert isinstance(module, astroid.Module), module
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def create_address(kwargs=None, call=None):
'''
Create a static address in a region.
CLI Example:
.. code-block:: bash
salt-cloud -f create_address gce name=my-ip region=us-central1 address=IP
'''
if call != 'function':
raise SaltCloudSystemExit(
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def release(path, repository):
"""Create a new release upgrade recipe, for developers."""
upgrader = InvenioUpgrader()
logger = upgrader.get_logger()
try:
endpoints = upgrader.find_endpoints()
if not endpoints:
logger.error("No upgrades found.")
click.Abort()
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def _iter_serial_enum_member(eid, value, bitmask):
"""Iterate serial and CID of enum members with given value and bitmask.
Here only valid values are returned, as `idaapi.BADNODE` always indicates
an invalid member.
"""
cid, serial = idaapi.get_first_serial_enum_member(eid, value, bitmask)
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def best_buy_2(self):
"""量縮價不跌
"""
result = self.data.capacity[-1] < self.data.capacity[-2] and \
self.data.price[-1] > self.data.price[-2]
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def applyTimeCalMs1(msrunContainer, specfile, correctionData, **kwargs):
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def reset(self, initial_document=None, append_to_history=False):
"""
:param append_to_history: Append current input to history first.
"""
assert initial_document is None or isinstance(initial_document, Document)
if append_to_history:
self.append_to_history()
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def _read_requirements(metadata, extras):
"""Read wheel metadata to know what it depends on.
The `run_requires` attribute contains a list of dict or str specifying
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def oauth_connect(self, provider, action):
"""
This endpoint doesn't check if user is logged in, because it has two functions
1. If the user is not logged in, it will try to signup the user
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def searchTag(self,HTAG="#python"):
"""Set Twitter search or stream criteria for the selection of tweets"""
self.t = Twython(app_key =self.app_key ,
app_secret =self.app_secret ,
oauth_token =self.oauth_token ... | [
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def run(self, lines):
""" Match and generate dot code blocks."""
text = "\n".join(lines)
while 1:
m = BLOCK_RE.search(text)
if m:
command = m.group('command')
# Whitelist command, prevent command injection.
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def makeParser(self):
"""Generate the argparse parser object containing the bootloader
accepted parameters
"""
self.parser = argparse.ArgumentParser(description='Starts the executable.',
prog=("{0} -m scoop.bootstrap"
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def values(self, values):
"""The values for insert ,
it can be a dict row or list tuple row.
"""
if isinstance(values, dict):
l = []
for column in self._columns:
l.append(values[column])
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async def set_passport_data_errors(self,
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Informs a user that some of the Telegram Passport elements they provided contains errors.
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def try_unbuffered_file(file, _alreadyopen={}):
""" Try re-opening a file in an unbuffered mode and return it.
If that fails, just return the original file.
This function remembers the file descriptors it opens, so it
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def beacon(config):
'''
Broadcast values via zeroconf
If the announced values are static, it is advised to set run_once: True
(do not poll) on the beacon configuration.
The following are required configuration settings:
- ``servicetype`` - The service type to announce
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n_items : int
Number of panels required
rows : int
Number of rows
cols : int
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def get_path_for_termid(self,termid):
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def VerifierMiddleware(verifier):
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def quit(self, *args, **kwargs): # real signature unknown
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quit the instrument thread
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def set_account_username(self, account, old_username, new_username):
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def parse_coordinates(variant, category):
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def log(**data):
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def parse(self, data=None, table_name=None):
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def client_args_for_bank(bank_info, ofx_version):
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def _compute_iso_line(self):
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level_index = []
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def _proxy(self):
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Generate an instance context for the instance, the context is capable of
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:rtype: twilio.rest.fax.v1.fax.FaxContext
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def addVariantOld(self,
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var = Variant(literal=literal,
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def draw_text(img, pos, text, color, font_scale=0.4):
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def dump_with_fn(dump_fn, data, stream, **options):
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file-like object 'stream'.
:param dump_fn: Callable to dump data
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def execute(self, input_data):
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def close(self):
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def get_example():
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and -1 otherwise; and features is a list of letters.
"""
features = random.sample(string.ascii_letters, NUM_SAMPLES)
num_capitalized = l... | [
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"string... | 46 | 0.011475 |
def _add_team_features(df):
"""Adds extra convenience features based on teams with and without
possession, with the precondition that the there are 'team' and 'opp'
specified in row.
:df: A DataFrame representing a game's play-by-play data after
_clean_features has been called and 'team' and 'o... | [
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def log_level(level):
"""
Attempt to convert the given argument into a log level.
Log levels are represented as integers, where higher values are more
severe. If the given level is already an integer, it is simply returned.
If the given level is a string that can be converted into an integer, i... | [
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... | 37.125 | 0.010941 |
def put(self, prompt):
"""
Puts prompt in each downstream inbox (an actual queue).
"""
for queue in self.downstream_inboxes.values():
queue.put(prompt) | [
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] | 31.666667 | 0.010256 |
def convert(data):
"""
Convert from unicode to native ascii
"""
try:
st = basestring
except NameError:
st = str
if isinstance(data, st):
return str(data)
elif isinstance(data, Mapping):
return dict(map(convert, data.iteritems()))
elif isinstance(data, Iter... | [
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... | 24.1875 | 0.002488 |
def setParameter(self, name, index, value):
"""
Overrides :meth:`nupic.bindings.regions.PyRegion.PyRegion.setParameter`.
"""
if name == "learningMode":
self.learningMode = bool(int(value))
self._epoch = 0
elif name == "inferenceMode":
self._epoch = 0
if int(value) and not sel... | [
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