text stringlengths 75 104k | code_tokens list | avg_line_len float64 7.91 980 | score float64 0 0.18 |
|---|---|---|---|
def to_html(self, **kwargs):
"""Render as html
Args:
None
Returns:
Str the html representation
Raises:
Errors are propagated
We pass the kwargs on to the base class so an exception is raised
if invalid keywords were passed. See:
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def fetch(
self, request: Union["HTTPRequest", str], **kwargs: Any
) -> "HTTPResponse":
"""Executes a request, returning an `HTTPResponse`.
The request may be either a string URL or an `HTTPRequest` object.
If it is a string, we construct an `HTTPRequest` using any additional
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def upload_feature_value_file(self, mapobject_type_name, plate_name,
well_name, well_pos_y, well_pos_x, tpoint, filename, index_col):
'''Uploads feature values for the given
:class:`MapobjectType <tmlib.models.mapobject.MapobjectType>` at the
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def parse_http_scheme(uri):
"""
match on http scheme if no match is found will assume http
"""
regex = re.compile(
r'^(?:http)s?://',
flags=re.IGNORECASE
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match = regex.match(uri)
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def set_default_unit(self, twig=None, unit=None, **kwargs):
"""
TODO: add documentation
"""
if twig is not None and unit is None:
# then try to support value as the first argument if no matches with twigs
if isinstance(unit, u.Unit) or not isinstance(twig, str):
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def to_tex(self, text_size='large', table_width=5, clear_pages = False):
"""
Write the program information to a .tex file, which can be
rendered to .pdf running pdflatex. The program can then be
printed and brought to the gym.
Parameters
----------
text_size
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def addDataModels(self, mods):
'''
Adds a model definition (same format as input to Model.addDataModels and output of Model.getModelDef).
'''
# Load all the universal properties
for _, mdef in mods:
for univname, _, _ in mdef.get('univs', ()):
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def find_ask():
"""
Find our instance of Ask, navigating Local's and possible blueprints.
Note: This only supports returning a reference to the first instance
of Ask found.
"""
if hasattr(current_app, 'ask'):
return getattr(current_app, 'ask')
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def _classify_load_constant(self, regs_init, regs_fini, mem_fini, written_regs, read_regs):
"""Classify load-constant gadgets.
"""
matches = []
# Check for "dst_reg <- constant" pattern.
for dst_reg, dst_val in regs_fini.items():
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def _read_json(self, path, name):
"""
Load a json into a dictionary from a file.
:param path: path to file
:param name: name of file
:return: dict
"""
with open(os.path.join(path, name), 'r') as fil:
output = json.load(fil)
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def spawn_containers(addrs, env_cls=Environment,
env_params=None,
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"""Spawn environments in a multiprocessing :class:`multiprocessing.Pool`.
Arguments and keyword arguments are passed down to the created environments
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def process_text(text, save_xml_name='trips_output.xml', save_xml_pretty=True,
offline=False, service_endpoint='drum'):
"""Return a TripsProcessor by processing text.
Parameters
----------
text : str
The text to be processed.
save_xml_name : Optional[str]
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def set_file(path, saltenv='base', **kwargs):
'''
Set answers to debconf questions from a file.
CLI Example:
.. code-block:: bash
salt '*' debconf.set_file salt://pathto/pkg.selections
'''
if '__env__' in kwargs:
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def savepysyn(self,wave,flux,fname,units=None):
""" Cannot ever use the .writefits() method, because the array is
frequently just sampled at the synphot waveset; plus, writefits
is smart and does things like tapering."""
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def __global_logging_exception_handler(exc_type, exc_value, exc_traceback):
'''
This function will log all un-handled python exceptions.
'''
if exc_type.__name__ == "KeyboardInterrupt":
# Do not log the exception or display the traceback on Keyboard Interrupt
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def array_to_hdf5(a, parent, name, **kwargs):
"""Write a Numpy array to an HDF5 dataset.
Parameters
----------
a : ndarray
Data to write.
parent : string or h5py group
Parent HDF5 file or group. If a string, will be treated as HDF5 file
name.
name : string
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def _get_metadata_for_region(region_code):
"""The metadata needed by this class is the same for all regions
sharing the same country calling code. Therefore, we return the
metadata for "main" region for this country calling code."""
country_calling_code = country_code_for_region(region_code)
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def _fix_pooling(self, op_name, inputs, new_attr):
"""onnx pooling operator supports asymmetrical padding
Adding pad operator before pooling in mxnet to work with onnx"""
pool_type = 'avg' if op_name == 'AveragePool' else 'max'
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def get_archive_part_value(self, part):
"""Return archive part for today"""
parts_dict = {'year': '%Y',
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'day': '%d'}
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def _compute_hamming_matrix(N):
"""Compute and store a Hamming matrix for |N| nodes.
Hamming matrices have the following sizes::
N MBs
== ===
9 2
10 8
11 32
12 128
13 512
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def _set_link_fault_signaling(self, v, load=False):
"""
Setter method for link_fault_signaling, mapped from YANG variable /interface/ethernet/link_fault_signaling (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_link_fault_signaling is considered as a private
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def modelAdoptNextOrphan(self, jobId, maxUpdateInterval):
""" Look through the models table for an orphaned model, which is a model
that is not completed yet, whose _eng_last_update_time is more than
maxUpdateInterval seconds ago.
If one is found, change its _eng_worker_conn_id to the current worker's
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def update(self, client=None):
"""API call: update the project via a ``PUT`` request.
See
https://cloud.google.com/resource-manager/reference/rest/v1beta1/projects/update
:type client: :class:`google.cloud.resource_manager.client.Client` or
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def unlock(self, time=3):
"""
unlock the door\n
thanks to https://github.com/SoftwareHouseMerida/pyzk/
:param time: define delay in seconds
:return: bool
"""
command = const.CMD_UNLOCK
command_string = pack("I",int(time)*10)
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def rename_key(d: Dict[str, Any], old: str, new: str) -> None:
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Rename a key in dictionary ``d`` from ``old`` to ``new``, in place.
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def config(host, seq, option, value):
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def _trj_backup_trajectory(self, traj, backup_filename=None):
"""Backs up a trajectory.
:param traj: Trajectory that should be backed up
:param backup_filename:
Path and filename of backup file. If None is specified the storage service
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def _lerp(x, x0, x1, y0, y1):
"""Affinely map from [x0, x1] onto [y0, y1]."""
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def _validate_compose_list(destination_file, file_list,
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"""Validates the file_list and merges the file_list, files_metadata.
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destination: Path to the file (ie. /destination_bucket/destination_file).
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def pretty_print(source, dest):
"""
Pretty print the XML file
"""
parser = etree.XMLParser(remove_blank_text=True)
if not isinstance(source, str):
source = str(source)
tree = etree.parse(source, parser)
docinfo = tree.docinfo
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def delete(self, uuid):
# type: (UUID) -> None
"""Delete file with given uuid.
:param:uuid: :class:`UUID` instance
:raises:KeyError if file does not exists
"""
dest = self.abs_path(uuid)
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def delete_repository_from_recycle_bin(self, project, repository_id):
"""DeleteRepositoryFromRecycleBin.
[Preview API] Destroy (hard delete) a soft-deleted Git repository.
:param str project: Project ID or project name
:param str repository_id: The ID of the repository.
"""
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def _check_connectivity(self, err):
''' a method to check connectivity as source of error '''
try:
import requests
requests.get(self.uptime_ssl)
except:
from requests import Request
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def jstimestamp(dte):
'''Convert a date or datetime object into a javsacript timestamp.'''
days = date(dte.year, dte.month, 1).toordinal() - _EPOCH_ORD + dte.day - 1
hours = days*24
if isinstance(dte,datetime):
hours += dte.hour
minutes = hours*60 + dte.minute
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def create_group(self, group):
"""
Creates a new group and set group privileges.
:param group: The group object to be created.
:type group: ``dict``
"""
data = json.dumps(self._create_group_dict(group))
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def get_link(href, value=None, **kwargs):
"""
Returns a well-formed link. If href is None/empty, returns an empty string
:param href: value to be set for attribute href
:param value: the text to be displayed. If None, the href itself is used
:param kwargs: additional attributes and values
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def _get_tokens_for_line_func(self, cli, document):
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Create a function that returns the tokens for a given line.
"""
# Cache using `document.text`.
def get_tokens_for_line():
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def latex(self):
"""Return LaTeX representation of the abstract."""
s = ('{authors}, \\textit{{{title}}}, {journal}, {volissue}, '
'{pages}, ({date}). {doi}, {scopus_url}.')
if len(self.authors) > 1:
authors = ', '.join([str(a.given_name) +
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def total_seconds(offset):
"""Backport of offset.total_seconds() from python 2.7+."""
seconds = offset.days * 24 * 60 * 60 + offset.seconds
microseconds = seconds * 10**6 + offset.microseconds
return microseconds / (10**6 * 1.0) | [
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def set_xlabels(self, label=None, **kwargs):
"""Label the x axis on the bottom row of the grid."""
if label is None:
label = label_from_attrs(self.data[self._x_var])
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ax.set_xlabel(label, **kwargs)
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def get(self, request, bot_id, id, format=None):
"""
Get list of source state of a handler
---
serializer: StateSerializer
responseMessages:
- code: 401
message: Not authenticated
"""
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def handleException(exception):
"""
Handles an exception that occurs somewhere in the process of handling
a request.
"""
serverException = exception
if not isinstance(exception, exceptions.BaseServerException):
with app.test_request_context():
app.log_exception(exception)
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def simxReadProximitySensor(clientID, sensorHandle, operationMode):
'''
Please have a look at the function description/documentation in the V-REP user manual
'''
detectionState = ct.c_ubyte()
detectedObjectHandle = ct.c_int()
detectedPoint = (ct.c_float*3)()
detectedSurfaceNormalVector = (... | [
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def replace_grist (features, new_grist):
""" Replaces the grist of a string by a new one.
Returns the string with the new grist.
"""
assert is_iterable_typed(features, basestring) or isinstance(features, basestring)
assert isinstance(new_grist, basestring)
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def setRoute(self, vehID, edgeList):
"""
setRoute(string, list) -> None
changes the vehicle route to given edges list.
The first edge in the list has to be the one that the vehicle is at at the moment.
example usage:
setRoute('1', ['1', '2', '4', '6', '7'])
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def mknod(name,
ntype,
major=0,
minor=0,
user=None,
group=None,
mode='0600'):
'''
.. versionadded:: 0.17.0
Create a block device, character device, or fifo pipe.
Identical to the gnu mknod.
CLI Examples:
.. code-block:: bash
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def copy_snapshot(kwargs=None, call=None):
'''
Copy a snapshot
'''
if call != 'function':
log.error(
'The copy_snapshot function must be called with -f or --function.'
)
return False
if 'source_region' not in kwargs:
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def tensor_components_to_use(mrr, mtt, mpp, mrt, mrp, mtp):
'''
Converts components to Up, South, East definition::
USE = [[mrr, mrt, mrp],
[mtt, mtt, mtp],
[mrp, mtp, mpp]]
'''
return np.array([[mrr, mrt, mrp], [mrt, mtt, mtp], [mrp, mtp, mpp]]) | [
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def primers(self, tm=60):
'''Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
:type tm: float
:returns: Primer list (the output of coral.design.primers).
:rtype: list
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def _doCascadeFetch(obj):
'''
_doCascadeFetch - Takes an object and performs a cascading fetch on all foreign links, and all theirs, and so on.
@param obj <IndexedRedisModel> - A fetched model
'''
obj.validateModel()
if not obj.foreignFields:
return
# NOTE: Currently this fetches using one trans... | [
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def _check_log_scale(base, sides, scales, coord):
"""
Check the log transforms
Parameters
----------
base : float or None
Base of the logarithm in which the ticks will be
calculated. If ``None``, the base of the log transform
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def load_from_tar_or_patch(tar, image_filename, patch_images):
"""Do everything necessary to process an image inside a TAR.
Parameters
----------
tar : `TarFile` instance
The tar from which to read `image_filename`.
image_filename : str
Fully-qualified path inside of `tar` from whic... | [
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def visit(self, node):
""" Replace the placeholder if it is one or continue. """
if isinstance(node, Placeholder):
return self.placeholders[node.id]
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def _resolve_children(self, ldap_user, groups):
"""
Generates the query result for each child.
"""
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def get_dataset(self, key, info):
"""Get the dataset refered to by `key`."""
angles = self._get_coarse_dataset(key, info)
if angles is None:
return
# Fill gaps at edges of swath
darr = DataArray(angles, dims=['y', 'x'])
darr = darr.bfill('x')
darr = ... | [
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def _get_credentials_from_settings(self):
"""Get the stored credentials if any."""
remember_me = CONF.get('main', 'report_error/remember_me')
remember_token = CONF.get('main', 'report_error/remember_token')
username = CONF.get('main', 'report_error/username', '')
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def get_grading_standards_for_course(self, course_id):
"""
List the grading standards available to a course
https://canvas.instructure.com/doc/api/grading_standards.html#method.grading_standards_api.context_index
"""
url = COURSES_API.format(course_id) + "/grading_standards"
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def update(self):
"""Update the IRQ stats."""
# Init new stats
stats = self.get_init_value()
# IRQ plugin only available on GNU/Linux
if not LINUX:
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def estimate_achievable_tmid_precision(snr, t_ingress_min=10,
t_duration_hr=2.14):
'''Using Carter et al. 2009's estimate, calculate the theoretical optimal
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def step(self, action):
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for i in range(self._skip):
obs, reward, done, info = self.env.step(action)
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def context(root, project=""):
"""Produce the be environment
The environment is an exact replica of the active
environment of the current process, with a few
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"""
environment = os.environ.copy()
environment.update({
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def render(self, doc, context=None, math_option=False, img_path='',
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"""Start thread to render a given documentation"""
# If the thread is already running wait for it to finish before
# starting it again.
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def list_security_groups(self, retrieve_all=True, **_params):
"""Fetches a list of all security groups for a project."""
return self.list('security_groups', self.security_groups_path,
retrieve_all, **_params) | [
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def _to_dict(objects):
'''
Potentially interprets a string as JSON for usage with mongo
'''
try:
if isinstance(objects, six.string_types):
objects = salt.utils.json.loads(objects)
except ValueError as err:
log.error("Could not parse objects: %s", err)
raise err
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def insert(self, song):
"""在当前歌曲后插入一首歌曲"""
if song in self._songs:
return
if self._current_song is None:
self._songs.append(song)
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def stop(self):
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self.stop_flag.value = True
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def getReadGroupSet(self, id_):
"""
Returns the readgroup set with the specified ID.
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataset(compoundId.dataset_id)
return dataset.getReadGroupSet(id_) | [
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def __main(draft, directory, project_name, project_version, project_date, answer_yes):
"""
The main entry point.
"""
directory = os.path.abspath(directory)
config = load_config(directory)
to_err = draft
click.echo("Loading template...", err=to_err)
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def _make_info(self, name, stat_result, namespaces):
"""Create an `Info` object from a stat result.
"""
info = {
'basic': {
'name': name,
'is_dir': stat.S_ISDIR(stat_result.st_mode)
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def render_source(self):
"""Render the sourcecode."""
return SOURCE_TABLE_HTML % u'\n'.join(line.render() for line in
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def avail_locations(call=None):
'''
List all available locations
'''
if call == 'action':
raise SaltCloudSystemExit(
'The avail_locations function must be called with '
'-f or --function, or with the --list-locations option'
)
ret = {}
conn = get_conn()
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def stop_timer(self, timer_id):
"""
Stop a timer.
If the timer is not active, nothing happens.
"""
self._logger.debug('Stop timer {} in stm {}'.format(timer_id, self.id))
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def send_media_group(self, chat_id, media, disable_notification=None, reply_to_message_id=None):
"""
Use this method to send a group of photos or videos as an album. On success, an array of the sent Messages is returned.
https://core.telegram.org/bots/api#sendmediagroup
Parameters:
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def register(linter):
"""
Registering additional checkers.
"""
# add all of the checkers
register_checkers(linter)
# register any checking fiddlers
try:
from pylint_django.augmentations import apply_augmentations
apply_augmentations(linter)
except ImportError:
# ... | [
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def resolve_blobs(self, iter_blobs):
"""Resolve the blobs given in blob iterator. This will effectively remove the
index entries of the respective path at all non-null stages and add the given
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For each path there may only be one blob, otherwise a ValueError ... | [
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def read_mm_uic2(fd, byte_order, dtype, count):
"""Read MM_UIC2 tag from file and return as dictionary."""
result = {'number_planes': count}
values = numpy.fromfile(fd, byte_order+'I', 6*count)
result['z_distance'] = values[0::6] // values[1::6]
#result['date_created'] = tuple(values[2::6])
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def mission_start_date_as_string(self) -> str:
"""
Returns: mission start date as string
"""
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def infer_typing_namedtuple_class(class_node, context=None):
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# Check if it has the corresponding bases
annassigns_fields = [
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def find_atoms_near_atom(self, source_atom, search_radius, atom_hit_cache = set(), atom_names_to_include = set(), atom_names_to_exclude = set(), restrict_to_CA = False):
'''It is advisable to set up and use an atom hit cache object. This reduces the number of distance calculations and gives better performance.
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def add(event, reactors, saltenv='base', test=None):
'''
Add a new reactor
CLI Example:
.. code-block:: bash
salt-run reactor.add 'salt/cloud/*/destroyed' reactors='/srv/reactor/destroy/*.sls'
'''
if isinstance(reactors, string_types):
reactors = [reactors]
sevent = salt.... | [
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def _run(self, thread_n):
"""The thread function."""
try:
logger.debug("{0!r}: entering thread #{1}"
.format(self, thread_n))
resolver = self._make_resolver()
while True:
request = self.queue.get()
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def get_primitive_structure(self, tolerance=0.25, use_site_props=False,
constrain_latt=None):
"""
This finds a smaller unit cell than the input. Sometimes it doesn"t
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def run(self):
""" Run the server. Returns with system error code. """
normalized = os.path.normpath(self.path) + ("/" if self.path.endswith("/") else "")
if self.path != normalized:
sys.stderr.write("Please use full path '%s'" % (normalized,))
return -1
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def _uninstall(action='remove', name=None, pkgs=None, **kwargs):
'''
remove and purge do identical things but with different pacman commands,
this function performs the common logic.
'''
try:
pkg_params = __salt__['pkg_resource.parse_targets'](name, pkgs)[0]
except MinionError as exc:
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def getFullPathToSnapshot(self, n):
"""Get the full path to snapshot n."""
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def ufo_create_background_layer_for_all_glyphs(ufo_font):
# type: (defcon.Font) -> None
"""Create a background layer for all glyphs in ufo_font if not present to
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if "public.background" in ufo_font.layers:
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def _setup_tls_files(self, files):
"""Initiates TLSFIle objects with the paths given to this bundle"""
for file_type in TLSFileType:
if file_type.value in files:
file_path = files[file_type.value]
setattr(self, file_type.value,
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def _finish_transaction_with_retry(self, command_name, explict_retry):
"""Run commit or abort with one retry after any retryable error.
:Parameters:
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def _find_next(server):
"""Finds the name of the next repository to run based on the *current*
state of the database.
"""
from datetime import datetime
#Re-load the database in case we have multiple instances of the script
#running in memory.
_load_db()
result = None
visited = []
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def clean(args):
"""
%prog clean fastafile
Remove irregular chars in FASTA seqs.
"""
p = OptionParser(clean.__doc__)
p.add_option("--fancy", default=False, action="store_true",
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p.add_option("--canonical", default=False, ... | [
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async def spawn_n(self, agent_cls, n, *args, **kwargs):
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def from_dict(d):
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query_params_match = d.get('@query_params_match')
query_person_match = d.get('@query_person_match')
valid_since = d.get('@valid_since')
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def run(path, code=None, params=None, **meta):
"""Check code with mypy.
:return list: List of errors.
"""
args = [path, '--follow-imports=skip', '--show-column-numbers']
stdout, stderr, status = api.run(args)
messages = []
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async def shutdown(self, force = False, connmark = -1):
'''
Can call without delegate
'''
if connmark is None:
connmark = self.connmark
self.scheduler.emergesend(ConnectionControlEvent(self, ConnectionControlEvent.SHUTDOWN, force, connmark)) | [
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"emergesend",
"(",
"ConnectionC... | 41 | 0.023891 |
def batch(args):
"""
%prog batch all.cds *.anchors
Compute Ks values for a set of anchors file. This will generate a bunch of
work directories for each comparisons. The anchorsfile should be in the form
of specie1.species2.anchors.
"""
from jcvi.apps.grid import MakeManager
p = OptionP... | [
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... | 31.363636 | 0.003749 |
def _set_igmps_static_group(self, v, load=False):
"""
Setter method for igmps_static_group, mapped from YANG variable /bridge_domain/ip/bd_ip_igmp/snooping/igmps_static_group (list)
If this variable is read-only (config: false) in the
source YANG file, then _set_igmps_static_group is considered as a pri... | [
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"(",
"v",
","... | 131.454545 | 0.003776 |
def update(self, value=None):
"""
Update progress bar via the console or notebook accordingly.
"""
# Update self.value
if value is None:
value = self._current_value + 1
self._current_value = value
# Choose the appropriate environment
if self.... | [
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"# Choose the appropriate environmen... | 27.5 | 0.003906 |
def expand_curlys(s):
"""Takes string and returns list of options:
Example
-------
>>> expand_curlys("py{26, 27}")
["py26", "py27"]
"""
from functools import reduce
curleys = list(re.finditer(r"{[^{}]*}", s))
return reduce(_replace_curly, reversed(curleys), [s]) | [
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... | 24.083333 | 0.003333 |
def id(self, opts_id):
"""Handles tracking and cleanup of custom ids."""
old_id = self._id
self._id = opts_id
if old_id is not None:
cleanup_custom_options(old_id)
if opts_id is not None and opts_id != old_id:
if opts_id not in Store._weakrefs:
... | [
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"... | 42.818182 | 0.004158 |
def create_multi_weather(df, rename_dc):
"""Create a list of oemof weather objects if the given geometry is a polygon
"""
weather_list = []
# Create a pandas.DataFrame with the time series of the weather data set
# for each data set and append them to a list.
for gid in df.gid.unique():
... | [
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"uni... | 40.727273 | 0.004367 |
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