text stringlengths 78 104k | score float64 0 0.18 |
|---|---|
def set_duration(self, dur):
"""See :meth:`AbstractCalibrationRunner<sparkle.run.calibration_runner.AbstractCalibrationRunner.set_duration>`"""
# this may be set at any time, and is not checked before run, so set
# all stim components
for comp in self.stim_components:
comp.se... | 0.008065 |
def local_check (self):
"""
Warn about empty host names. Else call super.local_check().
"""
if not self.host:
self.set_result(_("Host is empty"), valid=False)
return
super(TelnetUrl, self).local_check() | 0.011278 |
def set_widgets(self):
"""Set widgets on the LayerMode tab."""
self.clear_further_steps()
# Set widgets
self.lblBandSelector.setText(tr(
'Please select which band that contains the data that you want to '
'use for this layer.'))
self.lstBands.clear()
... | 0.002328 |
def getScreenRGB(self,screen_data=None):
"""This function fills screen_data with the data
screen_data MUST be a numpy array of uint32/int32. This can be initialized like so:
screen_data = np.array(w*h,dtype=np.uint32)
Notice, it must be width*height in size also
If it is None, th... | 0.009077 |
def hook_output (module:nn.Module, detach:bool=True, grad:bool=False)->Hook:
"Return a `Hook` that stores activations of `module` in `self.stored`"
return Hook(module, _hook_inner, detach=detach, is_forward=not grad) | 0.044643 |
def from_path(klass, path, tabix_path=None, record_checks=None, parsed_samples=None):
"""Create new :py:class:`Reader` from path
.. note::
If you use the ``parsed_samples`` feature and you write out
records then you must not change the ``FORMAT`` of the record.
:param p... | 0.002349 |
def get_labels(filename, logger=None):
"""Returns a dictionary of alternative sequence labels, or None
- filename - path to file containing tab-separated table of labels
Input files should be formatted as <key>\t<label>, one pair per line.
"""
labeldict = {}
if filename is not None:
if... | 0.001011 |
def get_identity_changes(self, identity_sequence_id, group_sequence_id, organization_identity_sequence_id=None, page_size=None, scope_id=None):
"""GetIdentityChanges.
:param int identity_sequence_id:
:param int group_sequence_id:
:param int organization_identity_sequence_id:
:par... | 0.00615 |
def _construct_connector(self, pos):
"""
build widget to be used as "connector" bit between the vertical bar
between siblings and their respective horizontal bars leading to the
arrow tip
"""
# connector symbol, either L or |- shaped.
connectorw = None
con... | 0.00232 |
def refresh(self):
"""刷新 Question object 的属性.
例如回答数增加了, 先调用 ``refresh()``
再访问 answer_num 属性, 可获得更新后的答案数量.
:return: None
"""
super().refresh()
self._html = None
self._title = None
self._details = None
self._answer_num = None
... | 0.011416 |
def build(self, message, status, detailed_status=None):
"""Function builds and signs an AS2 MDN message.
:param message: The received AS2 message for which this is an MDN.
:param status: The status of processing of the received AS2 message.
:param detailed_status:
The opti... | 0.000392 |
def get_product_value(self, value_name, wanted_type=None):
'''
For the product section of the registry return the name value.
Args:
value_name (str): Registry value name.
wanted_type (str):
The type of value wanted if the type does not match
... | 0.00246 |
def optimise_xy(xy, *args):
"""Return negative pore diameter for x and y coordinates optimisation."""
z, elements, coordinates = args
window_com = np.array([xy[0], xy[1], z])
return -pore_diameter(elements, coordinates, com=window_com)[0] | 0.003937 |
def rate_limited(num_calls=1, every=1.0):
"""
Source: https://github.com/tomasbasham/ratelimit/tree/0ca5a616fa6d184fa180b9ad0b6fd0cf54c46936
Need to make a few changes that included having num_calls be a float
Prevent a method from being called
if it was previously called before
a time widows h... | 0.003243 |
def delete(self, docids):
"""Delete documents (specified by their ids) from the index."""
logger.debug("deleting %i documents from %s" % (len(docids), self))
deleted = 0
for docid in docids:
try:
del self.id2pos[docid]
deleted += 1
... | 0.005545 |
def connect(self, *args, **kwargs):
""" Proxy to DynamoDBConnection.connect. """
self.connection = DynamoDBConnection.connect(*args, **kwargs)
self._session = kwargs.get("session")
if self._session is None:
self._session = botocore.session.get_session() | 0.006734 |
def remove_handler():
"""Remove the user, group and policies for Blockade."""
logger.debug("[#] Removing user, group and permissions for Blockade")
client = boto3.client("iam", region_name=PRIMARY_REGION)
iam = boto3.resource('iam')
account_id = iam.CurrentUser().arn.split(':')[4]
try:
... | 0.002971 |
def get_coords(data):
"""Retrieve coordinates of genes of interest for prioritization.
Can read from CIViC input data or a supplied BED file of chrom, start, end
and gene information.
"""
for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}),
("amplification", {"... | 0.001825 |
def asDigraph(self):
"""
Generate a L{graphviz.Digraph} that represents this machine's
states and transitions.
@return: L{graphviz.Digraph} object; for more information, please
see the documentation for
U{graphviz<https://graphviz.readthedocs.io/>}
"""
... | 0.003221 |
def read_maxquant(f, header=0, index_col='id', **kwargs):
"""
Load the quantified table output from MaxQuant run, e.g.
- Proteingroups.txt
- Phospho (STY)Sites.txt
:param f: Source file
:return: Pandas dataframe of imported data
"""
df = pd.read_csv(f, delimiter='\t', header=he... | 0.005391 |
def _new_conn(self):
"""
Return a fresh :class:`httplib.HTTPConnection`.
"""
self.num_connections += 1
log.info("Starting new HTTP connection (%d): %s" %
(self.num_connections, self.host))
return HTTPConnection(host=self.host, port=self.port) | 0.006515 |
def build_from_developer_settings(api_name: str, api_version: str):
"""
:param api_name: Example hello
:param api_version: Example v1, v2alpha
:return: ApiClient
"""
developer_settings = read_developer_settings()
api_host = "http://" + api_name + ".apis.devision.... | 0.003165 |
def config(self):
"""
A `dict` containing the options this `_Bootstrapper` was configured
with.
"""
return dict((optname, getattr(self, optname))
for optname, _ in CFG_OPTIONS if hasattr(self, optname)) | 0.007605 |
def send_theme_file(self, filename):
"""
Function used to send static theme files from the theme folder to the browser.
"""
cache_timeout = self.get_send_file_max_age(filename)
return send_from_directory(self.config['THEME_STATIC_FOLDER'], filename,
... | 0.011331 |
def merge_moments(m_a, m_a2, m_a3, m_a4, n_a, m_b, m_b2, m_b3, m_b4, n_b):
'''
Merge moments of two samples A and B.
parameters are
m_a, ..., m_a4 = first through fourth moment of sample A
n_a = size of sample A
m_b, ..., m_b4 = first through fourth moment of sample B
n_b = size of s... | 0.005297 |
def InitUI(self):
"""
Initialize interface for drop down menu
"""
if self.data_type in ['orient', 'ages']:
belongs_to = []
else:
parent_table_name = self.parent_type + "s"
if parent_table_name in self.contribution.tables:
belong... | 0.002946 |
def deep_convert_dict(value):
"""Converts any OrderedDict elements in a value to
ordinary dictionaries, safe for storage in QSettings
:param value: value to convert
:type value: Union[dict,OrderedDict]
:return: dict
"""
to_ret = value
if isinstance(value, OrderedDict):
to_ret =... | 0.002075 |
def get_ladder_matches(session, ladder_id, from_timestamp=None, limit=LADDER_MATCH_LIMIT):
"""Get recently played ladder matches."""
if not from_timestamp:
from_timestamp = datetime.datetime.now() - datetime.timedelta(days=1)
matches = []
page_id = 0
done = False
i = 0
while not done... | 0.003469 |
def import_type(dest, src, name, api=None, filter_symbol=None):
"""Import Type `name` and its dependencies from Registry `src`
to Registry `dest`.
:param Registry dest: Destination Registry
:param Registry src: Source Registry
:param str name: Name of type to import
:param str api: Prefer to im... | 0.001116 |
def _resolve_and_add(nodes1, s_val, final_s, nodes2, t_val, final_t):
"""Resolve a computed intersection and add to lists.
We perform one Newton step to deal with any residual issues of
high-degree polynomial solves (one of which depends on the already
approximate ``x_val, y_val``).
Args:
... | 0.000883 |
def find_critical(self, crit=True):
"""
Return list of critical extensions (or list of non-cricital, if
optional second argument is False
"""
if crit:
flag = 1
else:
flag = 0
found = []
end = len(self)
index = -1
whi... | 0.00339 |
def get_tunnel_info_input_filter_type_filter_by_adm_state_admin_state(self, **kwargs):
"""Auto Generated Code
"""
config = ET.Element("config")
get_tunnel_info = ET.Element("get_tunnel_info")
config = get_tunnel_info
input = ET.SubElement(get_tunnel_info, "input")
... | 0.004505 |
async def commission(
self, *, enable_ssh: bool = None, skip_networking: bool = None,
skip_storage: bool = None,
commissioning_scripts: typing.Sequence[str] = None,
testing_scripts: typing.Sequence[str] = None,
wait: bool = False, wait_interval: int = 5):
... | 0.00061 |
def to_python(self, data):
"""
Convert a data to python format.
"""
if data is None:
return u''
if isinstance(data, unicode):
return data
else:
return unicode(data, DEFAULT_ENCODING) | 0.007519 |
def getfnc_qual_ev(self):
"""Keep annotaion if it passes potentially modified selection."""
fnc_key = (
self.nd_not2desc[(self._keep_nd, self._keep_not)],
self.incexc2num[(
self.include_evcodes is not None,
self.exclude_evcodes is not None)],
... | 0.00551 |
def get_restbase(self, endpoint='/page/',
show=True, proxy=None, timeout=0):
"""
GET RESTBase /page/ endpoints needing only {title}
https://en.wikipedia.org/api/rest_v1/
for example:
/page/
/page/html/{title}
/page/summary/{title}... | 0.001755 |
def OpenKey(key, sub_key):
"""This calls the Windows OpenKeyEx function in a Unicode safe way."""
regopenkeyex = advapi32["RegOpenKeyExW"]
regopenkeyex.restype = ctypes.c_long
regopenkeyex.argtypes = [
ctypes.c_void_p, ctypes.c_wchar_p, ctypes.c_ulong, ctypes.c_ulong,
ctypes.POINTER(ctypes.c_void_p)... | 0.01548 |
def block_offset_bounds(self, namespace):
"""Get the minimum and maximum block offset for the specified
namespace"""
cursor = self.cursor
cursor.execute('SELECT MIN("offset"), MAX("offset") '
'FROM gauged_statistics WHERE namespace = %s',
(na... | 0.00551 |
def load_fasta_file(filename):
"""Load a FASTA file and return the sequences as a list of SeqRecords
Args:
filename (str): Path to the FASTA file to load
Returns:
list: list of all sequences in the FASTA file as Biopython SeqRecord objects
"""
with open(filename, "r") as handle:
... | 0.005115 |
def image_summary(predictions, targets, hparams):
"""Reshapes predictions and passes it to tensorboard.
Args:
predictions : The predicted image (logits).
targets : The ground truth.
hparams: model hparams.
Returns:
summary_proto: containing the summary images.
weights: A Tensor of zeros of t... | 0.013025 |
def run(files, temp_folder, arg=None):
"Check coding convention of the code base."
try:
import pylint
except ImportError:
return NO_PYLINT_MSG
# set default level of threshold
arg = arg or SCORE
py_files = filter_python_files(files)
if not py_files:
return False
... | 0.008197 |
def add_user(self, user, group):
""" Adds user to a group """
if self.is_user_in(user, group):
raise UserAlreadyInAGroup
self.new_groups.add(group, user) | 0.010582 |
def set(self, key, *args):
"""Hash the key and set it in the cache"""
return self.cache.set(self._hashed(key), *args) | 0.015038 |
def hashed_download(url, temp, digest):
"""Download ``url`` to ``temp``, make sure it has the SHA-256 ``digest``,
and return its path."""
# Based on pip 1.4.1's URLOpener but with cert verification removed
def opener():
opener = build_opener(HTTPSHandler())
# Strip out HTTPHandler to pre... | 0.000909 |
def assert_element_not_visible(self, selector, by=By.CSS_SELECTOR,
timeout=settings.SMALL_TIMEOUT):
""" Similar to wait_for_element_not_visible() - returns nothing.
As above, will raise an exception if the element stays visible.
Returns True if successf... | 0.005137 |
def _makeini(self, w, v):
"""C initializer string for a wire with a given value."""
pieces = []
for n in range(self._limbs(w)):
pieces.append(hex(v & ((1 << 64)-1)))
v >>= 64
return ','.join(pieces).join('{}') | 0.007547 |
def set_model(self, model):
"""Set the model the item belongs to
A TreeItem can only belong to one model.
:param model: the model the item belongs to
:type model: :class:`Treemodel`
:returns: None
:rtype: None
:raises: None
"""
self._model = mode... | 0.005181 |
def page(self, number=None):
"""
If page is given, modify the URL correspondingly, return the current
page otherwise.
"""
if number is None:
return int(self.url.page)
self.url.page = str(number) | 0.007874 |
def transform(self, textual):
"""Transform an object from textual form to `PyObject`"""
if textual is None:
return None
type = textual[0]
try:
method = getattr(self, type + '_to_pyobject')
return method(textual)
except AttributeError:
... | 0.005988 |
def windows_intersection(windows):
"""Given a list of (beginning, ending), return another describing where they overlap.
:rtype: list
"""
def intersect2(left, right):
if left == right:
return left
elif left is (None, None):
return right
elif right is (No... | 0.000956 |
def load_h5(self, filepath):
"""Load a Hdf5 file to the main dataframe
:param filepath: url of the csv file to load,
can be absolute if it starts with ``/``
or relative if it starts with ``./``
:type filepath: str... | 0.004854 |
def loadNetworkbyID(self, id, callback=None, errback=None):
"""
Load an existing Network by ID into a high level Network object
:param int id: id of an existing Network
"""
import ns1.ipam
network = ns1.ipam.Network(self.config, id=id)
return network.load(callbac... | 0.005747 |
def get_indices():
"""
Return a list of 3 integers representing EU indices for yesterday, today
and tomorrow.
"""
doc = BeautifulSoup(urlopen(BASEURL))
divs = doc.select('.indices_txt')
if not divs:
return None
sibling = divs[1].nextSibling
if not sibling:
return No... | 0.001835 |
def input(name, default=None, foreach=None):
"""Decorator to declare input for a node.
Plain inputs, that is plain python objects, are directly passed to
the node. Whereas streams generated by other nodes are requested
and once the handles of all input streams are available the node
is instantiated... | 0.001461 |
def broadcast_dimension_size(
variables: List[Variable],
) -> 'OrderedDict[Any, int]':
"""Extract dimension sizes from a dictionary of variables.
Raises ValueError if any dimensions have different sizes.
"""
dims = OrderedDict() # type: OrderedDict[Any, int]
for var in variables:
for d... | 0.001942 |
def assemble_phi5_author_filepaths():
"""Reads PHI5 index and builds a list of absolute filepaths.
"""
plaintext_dir_rel = '~/cltk_data/latin/text/phi5/plaintext/'
plaintext_dir = os.path.expanduser(plaintext_dir_rel)
filepaths = [os.path.join(plaintext_dir, x + '.TXT') for x in PHI5_INDEX]
retu... | 0.003012 |
def remove_insignificant_text_nodes(dom):
"""
For html elements that should not have text nodes inside them, remove all
whitespace. For elements that may have text, collapse multiple spaces to a
single space.
"""
nodes_to_remove = []
for node in walk_dom(dom):
if is_text(node):
... | 0.001689 |
def _get_hmm_from_alignment(self, alignment, hmm_filename, output_alignment_filename):
'''Return a HMM file and alignment of sequences to that HMM
Parameters
----------
alignment: str
path to aligned proteins
hmm_filename: str
write the hmm to this file p... | 0.004751 |
def t_RP(self, t):
r'[])]'
if t.value != ']' and OPTIONS.bracket.value:
t.type = 'RPP'
return t | 0.015267 |
def community_post_subscription_show(self, post_id, id, **kwargs):
"https://developer.zendesk.com/rest_api/docs/help_center/subscriptions#show-post-subscription"
api_path = "/api/v2/community/posts/{post_id}/subscriptions/{id}.json"
api_path = api_path.format(post_id=post_id, id=id)
retu... | 0.008523 |
def rollback(cls, resource, background=False):
""" Rollback a disk from a snapshot. """
disk_id = cls.usable_id(resource)
result = cls.call('hosting.disk.rollback_from', disk_id)
if background:
return result
cls.echo('Disk rollback in progress.')
cls.display... | 0.005571 |
def diff_jid(jid, config='root'):
'''
Returns the changes applied by a `jid`
jid
The job id to lookup
config
Configuration name.
CLI Example:
.. code-block:: bash
salt '*' snapper.diff_jid jid=20160607130930720112
'''
pre_snapshot, post_snapshot = _get_jid_sn... | 0.002398 |
def get_tile(tile_number):
"""
Returns a crop of `img` based on a sequence number `tile_number`.
:param int tile_number: Number of the tile between 0 and `max_tiles`^2.
:raises TileOutOfBoundsError: When `tile_number` exceeds `max_tiles`^2
:rtype PIL.Image:
"""
tile_number = int(tile_number... | 0.001144 |
def parse_exception(line):
'''Parse the first line of a Cartouche exception description.
Args:
line (str): A single line Cartouche exception description.
Returns:
A 2-tuple containing the exception type and the first line of the description.
'''
m = RAISES_REGEX.match(line)
if ... | 0.006237 |
def __choicebox(msg, title, choices):
"""
internal routine to support choicebox() and multchoicebox()
"""
global boxRoot, __choiceboxResults, choiceboxWidget, defaultText
global choiceboxWidget, choiceboxChoices
# -------------------------------------------------------------------
# If choic... | 0.000537 |
def group_by(self, by):
"""
Return a new ``GroupBy`` object using this frame and the desired grouping columns.
The returned groups are sorted by the natural group-by column sort.
:param by: The columns to group on (either a single column name, or a list of column names, or
... | 0.009091 |
def get_camera_imageseries(self, number_of_imageseries=10, offset=0):
""" Get smartcam image series
Args:
number_of_imageseries (int): number of image series to get
offset (int): skip offset amount of image series
"""
response = None
try:
resp... | 0.00197 |
def process_chat(self, chat: types.Chat):
"""
Generate chat data
:param chat:
:return:
"""
if not chat:
return
yield 'chat_id', chat.id
yield 'chat_type', chat.type
if self.include_content:
yield 'chat_title', chat.full_na... | 0.004914 |
def _reload_maybe(self):
"""
Reload the config if the config\
model has been updated. This is called\
once on every request by the middleware.\
Should not be called directly.
"""
ConfigModel = apps.get_model('djconfig.Config')
data = dict(
Con... | 0.005329 |
def list_task_definitions(self):
"""
Filtering not implemented
"""
task_arns = []
for task_definition_list in self.task_definitions.values():
task_arns.extend(
[task_definition.arn for task_definition in task_definition_list])
return task_arns | 0.009404 |
def types(**requirements):
"""
Specify a precondition based on the types of the function's
arguments.
"""
def predicate(args):
for name, kind in sorted(requirements.items()):
assert hasattr(args, name), "missing required argument `%s`" % name
if not isinstance(kind,... | 0.001776 |
def articles(self):
"""
articles getter
"""
if self._articles is None:
self._articles = []
for doc in self.docs:
# ensure all fields in the "fl" are in the doc to address
# issue #38
for k in set(self.fl).difference(... | 0.004444 |
def evaluate_hull(x,hull):
"""evaluate_hull: evaluate h_u(x) and (optional) h_l(x)
Input:
x - abcissa
hull - the hull (see setup_hull for a definition)
Output:
hu(x) (optional), hl(x)
History:
2009-05-21 - Written - Bovy (NYU)
"""
#Find in which [z_{i-1},z_i] i... | 0.015572 |
def run_in_memory(args, edges):
"""Run OSLOM with an in-memory list of edges, return in-memory results."""
# Create an OSLOM runner with a temporary working directory
oslom_runner = OslomRunner(tempfile.mkdtemp())
# Write temporary edges file with re-mapped Ids
logging.info("writing temporary edges... | 0.001523 |
def get_ajax_url(self):
"""Get ajax url"""
if self.ajax_url:
return self.ajax_url
return reverse('trionyx:model-list-ajax', kwargs=self.kwargs) | 0.011173 |
def part_datasheet(self, part, command=None, path=None):
'''
downloads and/or shows the datasheet of a given part
command: if set will use it to open the datasheet.
path: if set will download the file under that path.
if path is given alone, the file will only get downloaded,
... | 0.001833 |
def base_install():
"""Generates configuration setting for required functionality of ISAMBARD."""
# scwrl
scwrl = {}
print('{BOLD}{HEADER}Generating configuration files for ISAMBARD.{END_C}\n'
'All required input can use tab completion for paths.\n'
'{BOLD}Setting up SCWRL 4.0 (Recom... | 0.0044 |
def mission_request_send(self, target_system, target_component, seq, force_mavlink1=False):
'''
Request the information of the mission item with the sequence number
seq. The response of the system to this message should
be a MISSION_ITEM message.
... | 0.006887 |
def remove_named_query(self, alias, afterwards=None):
"""
remove a named query from the notmuch database.
:param alias: name of shortcut
:type alias: str
:param afterwards: callback to trigger after adding the alias
:type afterwards: callable or None
"""
... | 0.004474 |
def get_remote_url(path, remote="origin"):
"""
Run git config --get remote.<remote>.url in path.
:param path: Path where git is to be run
:param remote: Remote name
:return: str or None
"""
path = get_path(path)
cmd = ["config", "--get", "remote.%s.url" % remote]
return __run_git(cm... | 0.003021 |
def assert_condition_md5(self):
"""If the ``Content-MD5`` request header is present in the request
it's verified against the MD5 hash of the request body. If they don't
match, a 400 HTTP response is returned.
:raises: :class:`webob.exceptions.ResponseException` of status 400 if
... | 0.00316 |
def print_results(converter, ofx, ledger, txns, args):
"""
This function is the final common pathway of program:
Print initial balance if requested;
Print transactions surviving de-duplication filter;
Print balance assertions if requested;
Print commodity prices obtained from position statement... | 0.001656 |
def get(self, object_id):
"""
根据 objectId 查询。
:param object_id: 要查询对象的 objectId
:return: 查询结果
:rtype: Object
"""
if not object_id:
raise LeanCloudError(code=101, error='Object not found.')
obj = self._query_class.create_without_data(object_id)... | 0.004988 |
def read_user_dict(var_name, default_value):
"""Prompt the user to provide a dictionary of data.
:param str var_name: Variable as specified in the context
:param default_value: Value that will be returned if no input is provided
:return: A Python dictionary to use in the context.
"""
# Please s... | 0.001318 |
def _restore_constructor(self, cls):
"""
Restore the original constructor, lose track of class.
"""
cls.__init__ = self._observers[cls].init
del self._observers[cls] | 0.009756 |
def FindMatchingPolys(self, start_point, end_point, max_radius=150):
"""
Returns a list of polylines in the collection that have endpoints
within max_radius of the given start and end points.
"""
matches = []
for shape in self._name_to_shape.itervalues():
if start_point.GetDistanceMeters(s... | 0.004211 |
def send_keys(self, *keys_to_send):
"""
Sends keys to current focused element.
:Args:
- keys_to_send: The keys to send. Modifier keys constants can be found in the
'Keys' class.
"""
typing = keys_to_typing(keys_to_send)
if self._driver.w3c:
... | 0.005181 |
def satisfyVersionFromSearchPaths(name, version_required, search_paths, update=False, type='module', inherit_shrinkwrap=None):
''' returns a Component/Target for the specified version, if found in the
list of search paths. If `update' is True, then also check for newer
versions of the found componen... | 0.004815 |
def translate_func(name, block, args):
"""Translates functions and all nested functions to Python code.
name - name of that function (global functions will be available under var while
inline will be available directly under this name )
block - code of the function (*with* brackets {} )
... | 0.002232 |
def new():
"""Create new group."""
form = GroupForm(request.form)
if form.validate_on_submit():
try:
group = Group.create(admins=[current_user], **form.data)
flash(_('Group "%(name)s" created', name=group.name), 'success')
return redirect(url_for(".index"))
... | 0.002037 |
def simple_mult(A, B, start):
""" Builds a slow, small multiplier using the simple shift-and-add algorithm.
Requires very small area (it uses only a single adder), but has long delay
(worst case is len(A) cycles). start is a one-bit input to indicate inputs are ready.
done is a one-bit output signal rai... | 0.002078 |
def _get_maxcov_downsample(data):
"""Calculate maximum coverage downsampling for whole genome samples.
Returns None if we're not doing downsampling.
"""
from bcbio.bam import ref
from bcbio.ngsalign import alignprep, bwa
from bcbio.variation import coverage
fastq_file = data["files"][0]
... | 0.003189 |
def collect_program_info(self, fname):
"""
gets details on the program, size, date, list of functions
and produces a Markdown file for documentation
"""
md = '#AIKIF Technical details\n'
md += 'Autogenerated list of programs with comments and progress\n'
md += '\n... | 0.006711 |
def from_git_rev_read(path):
"""Retrieve given file path contents of certain Git revision."""
if ":" not in path:
raise ValueError("Path identifier must start with a revision hash.")
cmd = "git", "show", "-t", path
try:
return subprocess.check_output(cmd).rstrip().decode("utf-8")
ex... | 0.002632 |
def listDevices(self, interface_id):
"""The CCU / Homegear asks for devices known to our XML-RPC server. We respond to that request using this method."""
LOG.debug("RPCFunctions.listDevices: interface_id = %s, _devices_raw = %s" % (
interface_id, str(self._devices_raw)))
remote = int... | 0.00708 |
def whichrestype(atom):
"""Returns the residue name of an Pybel or OpenBabel atom."""
atom = atom if not isinstance(atom, Atom) else atom.OBAtom # Convert to OpenBabel Atom
return atom.GetResidue().GetName() if atom.GetResidue() is not None else None | 0.011407 |
def _store_outputs_in_object_store(self, object_ids, outputs):
"""Store the outputs of a remote function in the local object store.
This stores the values that were returned by a remote function in the
local object store. If any of the return values are object IDs, then
these object IDs... | 0.001115 |
def videoWrite(path, imgs, levels=None, shape=None, frames=15,
annotate_names=None,
lut=None, updateFn=None):
'''
TODO
'''
frames = int(frames)
if annotate_names is not None:
assert len(annotate_names) == len(imgs)
if levels is None:
if i... | 0.000479 |
def attr(prev, attr_name):
"""attr pipe can extract attribute value of object.
:param prev: The previous iterator of pipe.
:type prev: Pipe
:param attr_name: The name of attribute
:type attr_name: str
:returns: generator
"""
for obj in prev:
if hasattr(obj, attr_name):
... | 0.002841 |
def set_auth_field(self, user_field, biz_field):
"""
设置授权页字段信息
详情请参考
https://mp.weixin.qq.com/wiki?id=mp1497082828_r1cI2
:param user_field: 授权页个人发票字段
:type user_field: dict
:param biz_field: 授权页单位发票字段
:type biz_field: dict
"""
return self.... | 0.003241 |
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