code stringlengths 51 2.34k | sequence stringlengths 186 3.94k | docstring stringlengths 11 171 |
|---|---|---|
def _get_files_variantcall(sample):
out = []
algorithm = sample["config"]["algorithm"]
out = _maybe_add_summary(algorithm, sample, out)
out = _maybe_add_alignment(algorithm, sample, out)
out = _maybe_add_callable(sample, out)
out = _maybe_add_disambiguate(algorithm, sample, out)
out = _maybe... | module function_definition identifier parameters identifier block expression_statement assignment identifier list expression_statement assignment identifier subscript subscript identifier string string_start string_content string_end string string_start string_content string_end expression_statement assignment identifi... | Return output files for the variant calling pipeline. |
def validate_json(file):
max_file_size = current_app.config.get(
'PREVIEWER_MAX_FILE_SIZE_BYTES', 1 * 1024 * 1024)
if file.size > max_file_size:
return False
with file.open() as fp:
try:
json.loads(fp.read().decode('utf-8'))
return True
except:
... | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end binary_operator binary_operator integer integer integer if_statement comparison_operator attr... | Validate a JSON file. |
def wsgi_app(self, environ, start_response):
@_LOCAL_MANAGER.middleware
def _wrapped_app(environ, start_response):
request = Request(environ)
setattr(_local, _CURRENT_REQUEST_KEY, request)
response = self._dispatch_request(request)
return response(environ,... | module function_definition identifier parameters identifier identifier identifier block decorated_definition decorator attribute identifier identifier function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list identifier expression_stat... | A basic WSGI app |
def __parse_email_to_employer_line(self, raw_email, raw_enrollment):
e = re.match(self.EMAIL_ADDRESS_REGEX, raw_email, re.UNICODE)
if not e and self.email_validation:
cause = "invalid email format: '%s'" % raw_email
raise InvalidFormatError(cause=cause)
if self.email_vali... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier identifier attribute identifier identifier if_statement boolean_operator not_operator identifier attribute... | Parse email to employer lines |
def data(self, data):
self._data = {det: d.copy() for (det, d) in data.items()} | module function_definition identifier parameters identifier identifier block expression_statement assignment attribute identifier identifier dictionary_comprehension pair identifier call attribute identifier identifier argument_list for_in_clause tuple_pattern identifier identifier call attribute identifier identifier ... | Store a copy of the data. |
def fetch_build_egg(self, req):
from setuptools.command.easy_install import easy_install
dist = self.__class__({'script_args': ['easy_install']})
opts = dist.get_option_dict('easy_install')
opts.clear()
opts.update(
(k, v)
for k, v in self.get_option_dict(... | module function_definition identifier parameters identifier identifier block import_from_statement dotted_name identifier identifier identifier dotted_name identifier expression_statement assignment identifier call attribute identifier identifier argument_list dictionary pair string string_start string_content string_e... | Fetch an egg needed for building |
def range(cls, dataset, dimension):
dim = dataset.get_dimension(dimension, strict=True)
values = dataset.dimension_values(dim.name, False)
return (np.nanmin(values), np.nanmax(values)) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier keyword_argument identifier true expression_statement assignment identifier call attribute identifier identifier argument_list ... | Computes the range along a particular dimension. |
def tempfile(self, mode='wb', **args):
"write the contents of the file to a tempfile and return the tempfile filename"
tf = tempfile.NamedTemporaryFile(mode=mode)
self.write(tf.name, mode=mode, **args)
return tfn | module function_definition identifier parameters identifier default_parameter identifier string string_start string_content string_end dictionary_splat_pattern identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier call attribute identifier identif... | write the contents of the file to a tempfile and return the tempfile filename |
def create_reference_server_flask_app(cfg):
app = Flask(__name__)
Flask.secret_key = "SECRET_HERE"
app.debug = cfg.debug
client_prefixes = dict()
for api_version in cfg.api_versions:
handler_config = Config(cfg)
handler_config.api_version = api_version
handler_config.klass_na... | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment attribute identifier identifier string string_start string_content string_end expression_statement assignment attribute identifier identif... | Create referece server Flask application with one or more IIIF handlers. |
def incident_path(cls, project, incident):
return google.api_core.path_template.expand(
"projects/{project}/incidents/{incident}",
project=project,
incident=incident,
) | module function_definition identifier parameters identifier identifier identifier block return_statement call attribute attribute attribute identifier identifier identifier identifier argument_list string string_start string_content string_end keyword_argument identifier identifier keyword_argument identifier identifie... | Return a fully-qualified incident string. |
def current_reading(self) -> Optional[Union[int, float]]:
return self._get_field_value(SpecialDevice.PROP_CURRENT_READING) | module function_definition identifier parameters identifier type generic_type identifier type_parameter type generic_type identifier type_parameter type identifier type identifier block return_statement call attribute identifier identifier argument_list attribute identifier identifier | Current reading for a special sensor. |
def layer(command=None, *args):
'hints the start of a new layer'
if not command:
return eval([['hint', 'layer']])
else:
lst = [['layer']]
for arg in args:
lst.append([command, arg])
lst.append(['layer'])
return eval(lst) | module function_definition identifier parameters default_parameter identifier none list_splat_pattern identifier block expression_statement string string_start string_content string_end if_statement not_operator identifier block return_statement call identifier argument_list list list string string_start string_content... | hints the start of a new layer |
async def handle_agent_job_ssh_debug(self, _, message: AgentJobSSHDebug):
await ZMQUtils.send_with_addr(self._client_socket, message.job_id[0], BackendJobSSHDebug(message.job_id[1], message.host, message.port,
messa... | module function_definition identifier parameters identifier identifier typed_parameter identifier type identifier block expression_statement await call attribute identifier identifier argument_list attribute identifier identifier subscript attribute identifier identifier integer call identifier argument_list subscript ... | Handle an AgentJobSSHDebug message. Send the data back to the client |
def _replace_bbox_none(self, bbox):
(bb_top, bb_left), (bb_bottom, bb_right) = bbox
if bb_top is None:
bb_top = 0
if bb_left is None:
bb_left = 0
if bb_bottom is None:
bb_bottom = self.code_array.shape[0] - 1
if bb_right is None:
bb... | module function_definition identifier parameters identifier identifier block expression_statement assignment pattern_list tuple_pattern identifier identifier tuple_pattern identifier identifier identifier if_statement comparison_operator identifier none block expression_statement assignment identifier integer if_statem... | Returns bbox, in which None is replaced by grid boundaries |
def _check_jointcaller(data):
allowed = set(joint.get_callers() + [None, False])
cs = data["algorithm"].get("jointcaller", [])
if not isinstance(cs, (tuple, list)):
cs = [cs]
problem = [x for x in cs if x not in allowed]
if len(problem) > 0:
raise ValueError("Unexpected algorithm 'jo... | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list binary_operator call attribute identifier identifier argument_list list none false expression_statement assignment identifier call attribute subscript identifier string string_start... | Ensure specified jointcaller is valid. |
def crossover(self, gene2):
assert self.key == gene2.key
new_gene = self.__class__(self.key)
for a in self._gene_attributes:
if random() > 0.5:
setattr(new_gene, a.name, getattr(self, a.name))
else:
setattr(new_gene, a.name, getattr(gene2, ... | module function_definition identifier parameters identifier identifier block assert_statement comparison_operator attribute identifier identifier attribute identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier for_statement id... | Creates a new gene randomly inheriting attributes from its parents. |
def stop(self):
LOGGER.info('Shutting down controller')
self.set_state(self.STATE_STOP_REQUESTED)
signal.setitimer(signal.ITIMER_PROF, 0, 0)
self._mcp.stop_processes()
if self._mcp.is_running:
LOGGER.info('Waiting up to 3 seconds for MCP to shut things down')
... | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_list attribute identifier identifier expression_statement call attrib... | Shutdown the MCP and child processes cleanly |
def write_xml(self, xmlfile, config=None):
root = ElementTree.Element('source_library')
root.set('title', 'source_library')
for s in self._srcs:
s.write_xml(root)
if config is not None:
srcs = self.create_diffuse_srcs(config)
diffuse_srcs = {s.name: s ... | module function_definition identifier parameters identifier identifier default_parameter identifier none block expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_li... | Save the ROI model as an XML file. |
def getboolean_config(section, option, default=False):
try:
return config.getboolean(section, option) or default
except ConfigParser.NoSectionError:
return default | module function_definition identifier parameters identifier identifier default_parameter identifier false block try_statement block return_statement boolean_operator call attribute identifier identifier argument_list identifier identifier identifier except_clause attribute identifier identifier block return_statement i... | Get data from configs which store boolean records |
def build_conversion_table(self, dataframes):
self.data = pd.DataFrame(dataframes)
tmp_pairs = [s.split("/") for s in self.data.columns]
self.data.columns = pd.MultiIndex.from_tuples(tmp_pairs) | module function_definition identifier parameters identifier identifier block expression_statement assignment attribute identifier identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier list_comprehension call attribute identifier identifier argument_list stri... | Build conversion table from a dictionary of dataframes |
def title(self):
return (u'[{}] {}>>'.format(
os.path.split(os.path.abspath('.'))[-1],
u' '.join(self.command))).encode('utf8') | module function_definition identifier parameters identifier block return_statement call attribute parenthesized_expression call attribute string string_start string_content string_end identifier argument_list subscript call attribute attribute identifier identifier identifier argument_list call attribute attribute iden... | Returns the UTF-8 encoded title |
def bullet_ant():
locals().update(default())
import pybullet_envs
env = 'AntBulletEnv-v0'
max_length = 1000
steps = 3e7
update_every = 60
return locals() | module function_definition identifier parameters block expression_statement call attribute call identifier argument_list identifier argument_list call identifier argument_list import_statement dotted_name identifier expression_statement assignment identifier string string_start string_content string_end expression_stat... | Configuration for PyBullet's ant task. |
def token(config, token):
if not token:
info_out(
"To generate a personal API token, go to:\n\n\t"
"https://github.com/settings/tokens\n\n"
"To read more about it, go to:\n\n\t"
"https://help.github.com/articles/creating-an-access"
"-token-for-comm... | module function_definition identifier parameters identifier identifier block if_statement not_operator identifier block expression_statement call identifier argument_list concatenated_string string string_start string_content escape_sequence escape_sequence escape_sequence string_end string string_start string_content ... | Store and fetch a GitHub access token |
def head(self, wg_uuid, uuid):
url = "%(base)s/%(wg_uuid)s/nodes/%(uuid)s" % {
'base': self.local_base_url,
'wg_uuid': wg_uuid,
'uuid': uuid
}
try:
return self.core.get(url)
except LinShareException:
return False | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier binary_operator string string_start string_content string_end dictionary pair string string_start string_content string_end attribute identifier identifier pair string string_start string_c... | Get one workgroup node. |
def _asdict(self):
retval = {key: self._declarations[key].default_value for
key in self._declarations if self._declarations[key].has_default}
retval.update(self._loaded_values)
for key, value in self._modules['six'].iteritems(self._flag_values):
if key in self._declarations:
retv... | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary_comprehension pair identifier attribute subscript attribute identifier identifier identifier identifier for_in_clause identifier attribute identifier identifier if_clause attribute subscript attribute... | Create a dictionary snapshot of the current config values. |
def _doAtomicFileCreation(filePath):
try:
_os.close(_os.open(filePath, _os.O_CREAT | _os.O_EXCL))
return True
except OSError as e:
if e.errno == _errno.EEXIST:
return False
else:
raise e | module function_definition identifier parameters identifier block try_statement block expression_statement call attribute identifier identifier argument_list call attribute identifier identifier argument_list identifier binary_operator attribute identifier identifier attribute identifier identifier return_statement tru... | Tries to atomically create the requested file. |
def _get_parent_classes_transparent(cls, slot, page, instance=None):
parent_classes = super(CascadePluginBase, cls).get_parent_classes(slot, page, instance)
if parent_classes is None:
if cls.get_require_parent(slot, page) is False:
return
parent_classes = []
... | module function_definition identifier parameters identifier identifier identifier default_parameter identifier none block expression_statement assignment identifier call attribute call identifier argument_list identifier identifier identifier argument_list identifier identifier identifier if_statement comparison_operat... | Return all parent classes including those marked as "transparent". |
def _serialize(self, include_run_logs=False, strict_json=False):
try:
topo_sorted = self.topological_sort()
t = [self.tasks[task]._serialize(include_run_logs=include_run_logs,
strict_json=strict_json)
for task in topo_sorted]
... | module function_definition identifier parameters identifier default_parameter identifier false default_parameter identifier false block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment identifier list_comprehension call att... | Serialize a representation of this Job to a Python dict object. |
def next_token(self):
if self.lookahead:
self.current_token = self.lookahead.popleft()
return self.current_token
self.current_token = self._parse_next_token()
return self.current_token | module function_definition identifier parameters identifier block if_statement attribute identifier identifier block expression_statement assignment attribute identifier identifier call attribute attribute identifier identifier identifier argument_list return_statement attribute identifier identifier expression_stateme... | Returns the next logical token, advancing the tokenizer. |
def all_subclasses(cls):
for s in cls.__subclasses__():
yield s
for c in s.all_subclasses():
yield c | module function_definition identifier parameters identifier block for_statement identifier call attribute identifier identifier argument_list block expression_statement yield identifier for_statement identifier call attribute identifier identifier argument_list block expression_statement yield identifier | An iterator over all subclasses of `cls`. |
def getAggregator(cls, instanceId, name):
parent = cls.parentMap.get(instanceId)
while parent:
stat = cls.getStat(parent, name)
if stat:
return stat, parent
parent = cls.parentMap.get(statsId(parent)) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier while_statement identifier block expression_statement assignment identifier call attribute identifier iden... | Gets the aggregate stat for the given stat. |
def format_list(data):
if isinstance(data, (list, tuple)):
to_clean = ['[', ']', '(', ')', "'"]
for item in to_clean:
data = str(data).replace("u\"", "\"").replace("u\'", "\'")
data = str(data).replace(item, '')
return data | module function_definition identifier parameters identifier block if_statement call identifier argument_list identifier tuple identifier identifier block expression_statement assignment identifier list string string_start string_content string_end string string_start string_content string_end string string_start string... | Remove useless characters to output a clean list. |
def matches(self, client, event_data):
for f in self.filters:
if not f(client, event_data):
return False
return True | module function_definition identifier parameters identifier identifier identifier block for_statement identifier attribute identifier identifier block if_statement not_operator call identifier argument_list identifier identifier block return_statement false return_statement true | True if all filters are matching. |
def _do_timeout_for_leave(self, timeout, datapath, dst, in_port):
parser = datapath.ofproto_parser
dpid = datapath.id
hub.sleep(timeout)
outport = self._to_querier[dpid]['port']
if self._to_hosts[dpid][dst]['ports'][in_port]['out']:
return
del self._to_hosts[d... | module function_definition identifier parameters identifier identifier identifier identifier identifier block expression_statement assignment identifier attribute identifier identifier expression_statement assignment identifier attribute identifier identifier expression_statement call attribute identifier identifier ar... | the process when the QUERY from the switch timeout expired. |
def _interpolate_with_fill(self, method='pad', axis=0, inplace=False,
limit=None, fill_value=None, coerce=False,
downcast=None):
inplace = validate_bool_kwarg(inplace, 'inplace')
if coerce:
if not self._can_hold_na:
... | module function_definition identifier parameters identifier default_parameter identifier string string_start string_content string_end default_parameter identifier integer default_parameter identifier false default_parameter identifier none default_parameter identifier none default_parameter identifier false default_pa... | fillna but using the interpolate machinery |
def append_sources_from(self, other):
self_aliases = self[self._KEYS.SOURCE].split(',')
other_aliases = other[self._KEYS.SOURCE].split(',')
self[self._KEYS.SOURCE] = uniq_cdl(self_aliases + other_aliases)
return | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute subscript identifier attribute attribute identifier identifier identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifi... | Merge the source alias lists of two CatDicts. |
def process_tags(self, tag=None):
if self.downloaded is False:
raise serror("Track not downloaded, can't process tags..")
filetype = magic.from_file(self.filepath, mime=True)
if filetype != "audio/mpeg":
raise serror("Cannot process tags for file type %s." % filetype)
... | module function_definition identifier parameters identifier default_parameter identifier none block if_statement comparison_operator attribute identifier identifier false block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier call att... | Process ID3 Tags for mp3 files. |
def _check_import(module_names):
diagnostics = {}
for module_name in module_names:
try:
__import__(module_name)
res = 'ok'
except ImportError as err:
res = str(err)
diagnostics[module_name] = res
return diagnostics | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary for_statement identifier identifier block try_statement block expression_statement call identifier argument_list identifier expression_statement assignment identifier string string_start string_conten... | Import the specified modules and provide status. |
def add_semantic_hub_layout(cx, hub):
graph = cx_to_networkx(cx)
hub_node = get_node_by_name(graph, hub)
node_classes = classify_nodes(graph, hub_node)
layout_aspect = get_layout_aspect(hub_node, node_classes)
cx['cartesianLayout'] = layout_aspect | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement assignment identifier call identifier argum... | Attach a layout aspect to a CX network given a hub node. |
def streamy_download_file(context, path):
bio = io.BytesIO()
ok, metadata = mitogen.service.FileService.get(context, path, bio)
return {
'success': ok,
'metadata': metadata,
'size': len(bio.getvalue()),
} | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment pattern_list identifier identifier call attribute attribute attribute identifier identifier identifier identifier arg... | Fetch a file from the FileService hosted by `context`. |
def xview(self, *args):
self.after_idle(self.__updateWnds)
ttk.Treeview.xview(self, *args) | module function_definition identifier parameters identifier list_splat_pattern identifier block expression_statement call attribute identifier identifier argument_list attribute identifier identifier expression_statement call attribute attribute identifier identifier identifier argument_list identifier list_splat ident... | Update inplace widgets position when doing horizontal scroll |
def namer(cls, imageUrl, pageUrl):
imgname = imageUrl.split('/')[-1]
imgbase = imgname.rsplit('-', 1)[0]
imgext = imgname.rsplit('.', 1)[1]
return '%s.%s' % (imgbase, imgext) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier subscript call attribute identifier identifier argument_list string string_start string_content string_end unary_operator integer expression_statement assignment identifier subscript call a... | Remove random junk from image names. |
def _timesheet_url(url_name, pk, date=None):
url = reverse(url_name, args=(pk,))
if date:
params = {'month': date.month, 'year': date.year}
return '?'.join((url, urlencode(params)))
return url | module function_definition identifier parameters identifier identifier default_parameter identifier none block expression_statement assignment identifier call identifier argument_list identifier keyword_argument identifier tuple identifier if_statement identifier block expression_statement assignment identifier diction... | Utility to create a time sheet URL with optional date parameters. |
def updateColumnWidths(tag, cw, options):
longforms = {"med": "median",
"ave": "average",
"min": "min",
"total": "total",
"max": "max",}
for category in ["time", "clock", "wait", "memory"]:
if category in options.categories:
... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier dictionary pair string string_start string_content string_end string string_start string_content string_end pair string string_start string_content string_end string string_start string_con... | Update the column width attributes for this tag's fields. |
def _reset_flood_offenders(self, *args):
offenders = []
for offender, offence_time in self._flooding.items():
if time() - offence_time < 10:
self.log('Removed offender from flood list:', offender)
offenders.append(offender)
for offender in offenders:
... | module function_definition identifier parameters identifier list_splat_pattern identifier block expression_statement assignment identifier list for_statement pattern_list identifier identifier call attribute attribute identifier identifier identifier argument_list block if_statement comparison_operator binary_operator ... | Resets the list of flood offenders on event trigger |
def _validate_lattice_vectors(self, lattice_vectors):
dataType = np.float64
if lattice_vectors is None:
lattice_vectors = np.identity(self.dimension, dtype=dataType)
else:
lattice_vectors = np.asarray(lattice_vectors, dtype=dataType)
if (self.dimension, se... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier attribute identifier identifier if_statement comparison_operator identifier none block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifie... | Ensure that the lattice_vectors are reasonable inputs. |
def destroy(self, folder=None, as_coro=False):
async def _destroy(folder):
ret = self.save_info(folder)
await self.stop_slaves()
if self._pool is not None:
self._pool.terminate()
self._pool.join()
await self._env.shutdown(as_coro=Tr... | module function_definition identifier parameters identifier default_parameter identifier none default_parameter identifier false block function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement ... | Destroy the multiprocessing environment and its slave environments. |
def send_theme_file(self, filename):
cache_timeout = self.get_send_file_max_age(filename)
return send_from_directory(self.config['THEME_STATIC_FOLDER'], filename,
cache_timeout=cache_timeout) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier return_statement call identifier argument_list subscript attribute identifier identifier string string_start string_content string_end ide... | Function used to send static theme files from the theme folder to the browser. |
def file_pour(filepath, block_size=10240, *args, **kwargs):
def opener(archive_res):
_LOGGER.debug("Opening from file (file_pour): %s", filepath)
_archive_read_open_filename(archive_res, filepath, block_size)
return _pour(opener, *args, flags=0, **kwargs) | module function_definition identifier parameters identifier default_parameter identifier integer list_splat_pattern identifier dictionary_splat_pattern identifier block function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list string string_start ... | Write physical files from entries. |
def enable_evb(self):
if self.is_ncb:
self.run_lldptool(["-T", "-i", self.port_name, "-g", "ncb",
"-V", "evb", "enableTx=yes"])
ret = self.enable_gpid()
return ret
else:
LOG.error("EVB cannot be set on NB")
return... | module function_definition identifier parameters identifier block if_statement attribute identifier identifier block expression_statement call attribute identifier identifier argument_list list string string_start string_content string_end string string_start string_content string_end attribute identifier identifier st... | Function to enable EVB on the interface. |
def bind(self) -> None:
self.base.metadata.bind = self.engine
self.base.query = self.session.query_property() | module function_definition identifier parameters identifier type none block expression_statement assignment attribute attribute attribute identifier identifier identifier identifier attribute identifier identifier expression_statement assignment attribute attribute identifier identifier identifier call attribute attrib... | Bind the metadata to the engine and session. |
def i2osp(self, long_integer, block_size):
'Convert a long integer into an octet string.'
hex_string = '%X' % long_integer
if len(hex_string) > 2 * block_size:
raise ValueError('integer %i too large to encode in %i octets' % (long_integer, block_size))
return a2b_hex(hex_stri... | module function_definition identifier parameters identifier identifier identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier binary_operator string string_start string_content string_end identifier if_statement comparison_operator call identifier ... | Convert a long integer into an octet string. |
def hook(self, *hook_names):
def wrapper(decorated):
for hook_name in hook_names:
self.register(hook_name, decorated)
else:
self.register(decorated.__name__, decorated)
if '_' in decorated.__name__:
self.register(
... | module function_definition identifier parameters identifier list_splat_pattern identifier block function_definition identifier parameters identifier block for_statement identifier identifier block expression_statement call attribute identifier identifier argument_list identifier identifier else_clause block expression_... | Decorator, registering them as hooks |
def languages2marc(self, key, value):
return {'a': pycountry.languages.get(alpha_2=value).name.lower()} | module function_definition identifier parameters identifier identifier identifier block return_statement dictionary pair string string_start string_content string_end call attribute attribute call attribute attribute identifier identifier identifier argument_list keyword_argument identifier identifier identifier identi... | Populate the ``041`` MARC field. |
def process_kill(pid, sig=None):
sig = sig or signal.SIGTERM
os.kill(pid, sig) | module function_definition identifier parameters identifier default_parameter identifier none block expression_statement assignment identifier boolean_operator identifier attribute identifier identifier expression_statement call attribute identifier identifier argument_list identifier identifier | Send signal to process. |
def _rts_from_ra(ra, tspan, labels, block=True):
def _convert(a, tspan, labels):
from nsim import Timeseries
return Timeseries(a, tspan, labels)
return distob.call(
_convert, ra, tspan, labels, prefer_local=False, block=block) | module function_definition identifier parameters identifier identifier identifier default_parameter identifier true block function_definition identifier parameters identifier identifier identifier block import_from_statement dotted_name identifier dotted_name identifier return_statement call identifier argument_list id... | construct a RemoteTimeseries from a RemoteArray |
def _dry_message_received(self, msg):
for callback in self._dry_wet_callbacks:
callback(LeakSensorState.DRY)
self._update_subscribers(0x11) | module function_definition identifier parameters identifier identifier block for_statement identifier attribute identifier identifier block expression_statement call identifier argument_list attribute identifier identifier expression_statement call attribute identifier identifier argument_list integer | Report a dry state. |
def rlmb_grid(rhp):
rhp.set_categorical("loop.game", ["breakout", "pong", "freeway"])
base = 100000
medium = base // 2
small = medium // 2
rhp.set_discrete("loop.num_real_env_frames", [base, medium, small])
rhp.set_discrete("model.moe_loss_coef", list(range(5))) | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end list string string_start string_content string_end string string_start string_content string_end string string_start string_content stri... | Grid over games and frames, and 5 runs each for variance. |
def filter_record(self, record):
if len(record) >= self.max_length:
return record[:self.max_length]
else:
return record | module function_definition identifier parameters identifier identifier block if_statement comparison_operator call identifier argument_list identifier attribute identifier identifier block return_statement subscript identifier slice attribute identifier identifier else_clause block return_statement identifier | Filter record, truncating any over some maximum length |
def _uncheck_descendant(self, item):
children = self.get_children(item)
for iid in children:
self.change_state(iid, "unchecked")
self._uncheck_descendant(iid) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier for_statement identifier identifier block expression_statement call attribute identifier identifier argument_list identifier string string... | Uncheck the boxes of item's descendant. |
def dataSetElementType(h5Dataset):
dtype = h5Dataset.dtype
if dtype.names:
return '<structured>'
else:
if dtype.metadata and 'vlen' in dtype.metadata:
vlen_type = dtype.metadata['vlen']
try:
return "<vlen {}>".format(vlen_type.__name__)
ex... | module function_definition identifier parameters identifier block expression_statement assignment identifier attribute identifier identifier if_statement attribute identifier identifier block return_statement string string_start string_content string_end else_clause block if_statement boolean_operator attribute identif... | Returns a string describing the element type of the dataset |
def meta(self):
if not self._pv.meta_data_property or not self._meta_target:
return {}
return getattr(self._meta_target, self._pv.meta_data_property) | module function_definition identifier parameters identifier block if_statement boolean_operator not_operator attribute attribute identifier identifier identifier not_operator attribute identifier identifier block return_statement dictionary return_statement call identifier argument_list attribute identifier identifier ... | Value of the bound meta-property on the target. |
def reboot(self):
reboot_msg = self.message_factory.command_long_encode(
0, 0,
mavutil.mavlink.MAV_CMD_PREFLIGHT_REBOOT_SHUTDOWN,
0,
1,
0,
0,
0,
0, 0, 0)
self.send_mavlink(reboot_msg) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list integer integer attribute attribute identifier identifier identifier integer integer integer integer integer integer integer integer expres... | Requests an autopilot reboot by sending a ``MAV_CMD_PREFLIGHT_REBOOT_SHUTDOWN`` command. |
def save_shortcuts(self):
self.check_shortcuts()
for shortcut in self.source_model.shortcuts:
shortcut.save() | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list for_statement identifier attribute attribute identifier identifier identifier block expression_statement call attribute identifier identifier argument_list | Save shortcuts from table model. |
def _check_command_result(self):
if self.commandResult.startswith('/bin/bash'):
raise UtilError('%s' % self.commandResult.split(' ', 1)[1])
if self.commandResult.startswith('/bin/mv'):
raise UtilError('%s' % self.commandResult.split(' ', 1)[1])
if self.commandResult.start... | module function_definition identifier parameters identifier block if_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end block raise_statement call identifier argument_list binary_operator string string_start string_content string_end subscript... | If command result exists run these checks. |
def turn_on(self):
if self.device_status != 'on':
body = helpers.req_body(self.manager, 'devicestatus')
body['uuid'] = self.uuid
body['status'] = 'on'
head = helpers.req_headers(self.manager)
r, _ = helpers.call_api('/131airPurifier/v1/device/deviceSta... | module function_definition identifier parameters identifier block if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier string stri... | Turn Air Purifier on |
def peek_step(self, val: ObjectValue,
sn: "DataNode") -> Tuple[None, "DataNode"]:
cn = sn.get_child(self.name, self.namespace)
return (None, cn) | module function_definition identifier parameters identifier typed_parameter identifier type identifier typed_parameter identifier type string string_start string_content string_end type generic_type identifier type_parameter type none type string string_start string_content string_end block expression_statement assignm... | Fail because there is no action instance. |
def items(self):
return [(k, unidecode.unidecode(v))
for k, v in self.identity_dict.items()] | module function_definition identifier parameters identifier block return_statement list_comprehension tuple identifier call attribute identifier identifier argument_list identifier for_in_clause pattern_list identifier identifier call attribute attribute identifier identifier identifier argument_list | Return a copy of identity_dict items. |
def sep_dist_clay(ConcClay, material):
return ((material.Density/ConcClay)*((np.pi
* material.Diameter ** 3)/6))**(1/3) | module function_definition identifier parameters identifier identifier block return_statement binary_operator parenthesized_expression binary_operator parenthesized_expression binary_operator attribute identifier identifier identifier parenthesized_expression binary_operator parenthesized_expression binary_operator att... | Return the separation distance between clay particles. |
def reset(self):
self.info(self.tr("About to reset.."))
models = self.data["models"]
models["instances"].store_checkstate()
models["plugins"].store_checkstate()
models["instances"].ids = []
for m in models.values():
m.reset()
for b in self.data["button... | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list call attribute identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifier subscript attribute identifier identifier ... | Prepare GUI for reset |
def shuffle_records(fname):
tf.logging.info("Shuffling records in file %s" % fname)
tmp_fname = fname + ".unshuffled"
tf.gfile.Rename(fname, tmp_fname)
reader = tf.python_io.tf_record_iterator(tmp_fname)
records = []
for record in reader:
records.append(record)
if len(records) % 100000 == 0:
t... | module function_definition identifier parameters identifier block expression_statement call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end identifier expression_statement assignment identifier binary_operator identifier string string_star... | Shuffle records in a single file. |
def _patch_original_class(self):
cls = self._cls
base_names = self._base_names
if self._delete_attribs:
for name in self._attr_names:
if (
name not in base_names
and getattr(cls, name, None) is not None
):
... | module function_definition identifier parameters identifier block expression_statement assignment identifier attribute identifier identifier expression_statement assignment identifier attribute identifier identifier if_statement attribute identifier identifier block for_statement identifier attribute identifier identif... | Apply accumulated methods and return the class. |
def page_next(self):
window_start = (self.parent.value('window_start') +
self.parent.value('window_length'))
self.parent.overview.update_position(window_start) | module function_definition identifier parameters identifier block expression_statement assignment identifier parenthesized_expression binary_operator call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end call attribute attribute identifier identifier ident... | Go to the next page. |
def run(
paths,
output=_I_STILL_HATE_EVERYTHING,
recurse=core.flat,
sort_by=None,
ls=core.ls,
stdout=stdout,
):
if output is _I_STILL_HATE_EVERYTHING:
output = core.columnized if stdout.isatty() else core.one_per_line
if sort_by is None:
if output == core.as_tree:
... | module function_definition identifier parameters identifier default_parameter identifier identifier default_parameter identifier attribute identifier identifier default_parameter identifier none default_parameter identifier attribute identifier identifier default_parameter identifier identifier block if_statement compa... | Project-oriented directory and file information lister. |
def authenticate_peer(self, auth_data, peer_id, message):
logger.debug('message: {}'.format(dump(message)))
signed_octets = message + self.Ni + prf(self.SK_pr, peer_id._data)
auth_type = const.AuthenticationType(struct.unpack(const.AUTH_HEADER, auth_data[:4])[0])
assert auth_type == cons... | module function_definition identifier parameters identifier identifier identifier identifier block expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list call identifier argument_list identifier expression_statement a... | Verifies the peers authentication. |
def on_batch_end(self, iteration:int, smooth_loss:TensorOrNumber, **kwargs:Any)->None:
"Determine if loss has runaway and we should stop."
if iteration==0 or smooth_loss < self.best_loss: self.best_loss = smooth_loss
self.opt.lr = self.sched.step()
if self.sched.is_done or (self.stop_div... | module function_definition identifier parameters identifier typed_parameter identifier type identifier typed_parameter identifier type identifier typed_parameter dictionary_splat_pattern identifier type identifier type none block expression_statement string string_start string_content string_end if_statement boolean_op... | Determine if loss has runaway and we should stop. |
def modules(self):
defmodule = lib.EnvGetNextDefmodule(self._env, ffi.NULL)
while defmodule != ffi.NULL:
yield Module(self._env, defmodule)
defmodule = lib.EnvGetNextDefmodule(self._env, defmodule) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier attribute identifier identifier while_statement comparison_operator identifier attribute identifier identifier block expression_... | Iterates over the defined Modules. |
def trial(request):
job_id = request.GET.get("job_id")
trial_id = request.GET.get("trial_id")
recent_trials = TrialRecord.objects \
.filter(job_id=job_id) \
.order_by("-start_time")
recent_results = ResultRecord.objects \
.filter(trial_id=trial_id) \
.order_by("-date")[0:... | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifier call attribute attribute identifier identifier ide... | View for a single trial. |
def content_type(self) -> str:
raw = self._headers.get(hdrs.CONTENT_TYPE)
if self._stored_content_type != raw:
self._parse_content_type(raw)
return self._content_type | module function_definition identifier parameters identifier type identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier if_statement comparison_operator attribute identifier identifier identifier block expressio... | The value of content part for Content-Type HTTP header. |
def poll(poll, msg, server):
poll = remove_smart_quotes(poll.replace(u"\u2014", u"--"))
try:
args = ARGPARSE.parse_args(shlex.split(poll)).poll
except ValueError:
return ERROR_INVALID_FORMAT
if not 2 < len(args) < len(POLL_EMOJIS) + 1:
return ERROR_WRONG_NUMBER_OF_ARGUMENTS
r... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call identifier argument_list call attribute identifier identifier argument_list string string_start string_content escape_sequence string_end string string_start string_content string_end ... | Given a question and answers, present a poll |
def empty(self):
for k in list(self.children.keys()):
self.remove_child(self.children[k]) | module function_definition identifier parameters identifier block for_statement identifier call identifier argument_list call attribute attribute identifier identifier identifier argument_list block expression_statement call attribute identifier identifier argument_list subscript attribute identifier identifier identif... | remove all children from the widget |
def run(arguments: typing.List[str] = None):
initialize()
from cauldron.invoke import parser
from cauldron.invoke import invoker
args = parser.parse(arguments)
exit_code = invoker.run(args.get('command'), args)
sys.exit(exit_code) | module function_definition identifier parameters typed_default_parameter identifier type subscript attribute identifier identifier identifier none block expression_statement call identifier argument_list import_from_statement dotted_name identifier identifier dotted_name identifier import_from_statement dotted_name ide... | Executes the cauldron command |
def StopToTuple(stop):
return (stop.stop_id, stop.stop_name, float(stop.stop_lat),
float(stop.stop_lon), stop.location_type) | module function_definition identifier parameters identifier block return_statement tuple attribute identifier identifier attribute identifier identifier call identifier argument_list attribute identifier identifier call identifier argument_list attribute identifier identifier attribute identifier identifier | Return tuple as expected by javascript function addStopMarkerFromList |
def insertions_from_masked(seq):
insertions = []
prev = True
for i, base in enumerate(seq):
if base.isupper() and prev is True:
insertions.append([])
prev = False
elif base.islower():
insertions[-1].append(i)
prev = True
return [[min(i), ma... | module function_definition identifier parameters identifier block expression_statement assignment identifier list expression_statement assignment identifier true for_statement pattern_list identifier identifier call identifier argument_list identifier block if_statement boolean_operator call attribute identifier identi... | get coordinates of insertions from insertion-masked sequence |
def _set_other(self):
if self.dst.style['in'] == 'numpydoc':
if self.docs['in']['raw'] is not None:
self.docs['out']['post'] = self.dst.numpydoc.get_raw_not_managed(self.docs['in']['raw'])
elif 'post' not in self.docs['out'] or self.docs['out']['post'] is None:
... | module function_definition identifier parameters identifier block if_statement comparison_operator subscript attribute attribute identifier identifier identifier string string_start string_content string_end string string_start string_content string_end block if_statement comparison_operator subscript subscript attribu... | Sets other specific sections |
def klm(p, q):
p, q = flatten(p), flatten(q)
return max(abs(p * np.nan_to_num(np.log(p / q)))) | module function_definition identifier parameters identifier identifier block expression_statement assignment pattern_list identifier identifier expression_list call identifier argument_list identifier call identifier argument_list identifier return_statement call identifier argument_list call identifier argument_list b... | Compute the KLM divergence. |
def from_shakemap(cls, shakemap_array):
self = object.__new__(cls)
self.complete = self
n = len(shakemap_array)
dtype = numpy.dtype([(p, site_param_dt[p])
for p in 'sids lon lat depth vs30'.split()])
self.array = arr = numpy.zeros(n, dtype)
ar... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment attribute identifier identifier identifier expression_statement assignment identifier call identifier argu... | Build a site collection from a shakemap array |
def clean(self, *args, **kwargs):
if not self.pk:
if self.node.participation_settings.voting_allowed is not True:
raise ValidationError("Voting not allowed for this node")
if 'nodeshot.core.layers' in settings.INSTALLED_APPS:
layer = self.node.layer
... | module function_definition identifier parameters identifier list_splat_pattern identifier dictionary_splat_pattern identifier block if_statement not_operator attribute identifier identifier block if_statement comparison_operator attribute attribute attribute identifier identifier identifier identifier true block raise_... | Check if votes can be inserted for parent node or parent layer |
def print_all_signals(self):
for o in dir(self):
obj= getattr(self, o)
div = False
for c in dir(obj):
cobj = getattr(obj, c)
if isinstance(cobj, Signal):
print('def _on_{}__{}(self):'.format(o, c))
div = ... | module function_definition identifier parameters identifier block for_statement identifier call identifier argument_list identifier block expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement assignment identifier false for_statement identifier call identifi... | Prints out every signal available for this widget and childs. |
def visit_set(self, node):
return "{%s}" % ", ".join(child.accept(self) for child in node.elts) | module function_definition identifier parameters identifier identifier block return_statement binary_operator string string_start string_content string_end call attribute string string_start string_content string_end identifier generator_expression call attribute identifier identifier argument_list identifier for_in_cl... | return an astroid.Set node as string |
def create_api_v4_virtual_interface(self):
return ApiV4VirtualInterface(
self.networkapi_url,
self.user,
self.password,
self.user_ldap) | module function_definition identifier parameters identifier block return_statement call identifier argument_list attribute identifier identifier attribute identifier identifier attribute identifier identifier attribute identifier identifier | Get an instance of Api Virtual Interface services facade. |
def _prepare_bam_file(bam_file, tmp_dir, config):
sort_mode = _get_sort_order(bam_file, config)
if sort_mode != "queryname":
bam_file = sort(bam_file, config, "queryname")
return bam_file | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call identifier argument_list identifier identifier if_statement comparison_operator identifier string string_start string_content string_end block expression_statement assignment identifie... | Pipe sort by name cmd in case sort by coordinates |
def reset (self):
super(FtpUrl, self).reset()
self.files = []
self.filename = None
self.filename_encoding = 'iso-8859-1' | module function_definition identifier parameters identifier block expression_statement call attribute call identifier argument_list identifier identifier identifier argument_list expression_statement assignment attribute identifier identifier list expression_statement assignment attribute identifier identifier none exp... | Initialize FTP url data. |
def gen_encode(data):
"A generator for unsynchronizing a byte iterable."
sync = False
for b in data:
if sync and (b == 0x00 or b & 0xE0):
yield 0x00
yield b
sync = (b == 0xFF)
if sync:
yield 0x00 | module function_definition identifier parameters identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier false for_statement identifier identifier block if_statement boolean_operator identifier parenthesized_expression boolean_operator comparison_op... | A generator for unsynchronizing a byte iterable. |
def load_entities():
path = os.path.join(TOPDIR, 'entities.json')
entities = json.load(open(path))
names = [i['name'] for i in entities]
try:
assert len(set(names)) == len(entities)
except AssertionError:
raise Exception('Entities with same name: %s' % [i for i in names if
... | module function_definition identifier parameters block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier string string_start string_content string_end expression_statement assignment identifier call attribute identifier identifier argument_list... | Load entities from JSON file. |
def validator(ch):
global screen_needs_update
try:
if screen_needs_update:
curses.doupdate()
screen_needs_update = False
return ch
finally:
winlock.release()
sleep(0.01)
winlock.acquire() | module function_definition identifier parameters identifier block global_statement identifier try_statement block if_statement identifier block expression_statement call attribute identifier identifier argument_list expression_statement assignment identifier false return_statement identifier finally_clause block expres... | Update screen if necessary and release the lock so receiveThread can run |
def send(self, cmd, timeout, wait_for_string, password):
return self.target_device.send(cmd, timeout=timeout, wait_for_string=wait_for_string, password=password) | module function_definition identifier parameters identifier identifier identifier identifier identifier block return_statement call attribute attribute identifier identifier identifier argument_list identifier keyword_argument identifier identifier keyword_argument identifier identifier keyword_argument identifier iden... | Send command to the target device. |
def output_callback(self, line, kill_switch):
self.notifications += line + "\n"
if "Initialization Sequence Completed" in line:
self.started = True
if "ERROR:" in line or "Cannot resolve host address:" in line:
self.error = True
if "process exiting" in line:
... | module function_definition identifier parameters identifier identifier identifier block expression_statement augmented_assignment attribute identifier identifier binary_operator identifier string string_start string_content escape_sequence string_end if_statement comparison_operator string string_start string_content s... | Set status of openvpn according to what we process |
def split_markers_from_line(line):
if not any(line.startswith(uri_prefix) for uri_prefix in SCHEME_LIST):
marker_sep = ";"
else:
marker_sep = "; "
markers = None
if marker_sep in line:
line, markers = line.split(marker_sep, 1)
markers = markers.strip() if markers else Non... | module function_definition identifier parameters identifier block if_statement not_operator call identifier generator_expression call attribute identifier identifier argument_list identifier for_in_clause identifier identifier block expression_statement assignment identifier string string_start string_content string_en... | Split markers from a dependency |
def hybrid_forward(self, F, a, b):
tilde_a = self.f(a)
tilde_b = self.f(b)
e = F.batch_dot(tilde_a, tilde_b, transpose_b=True)
beta = F.batch_dot(e.softmax(), tilde_b)
alpha = F.batch_dot(e.transpose([0, 2, 1]).softmax(), tilde_a)
feature1 = self.g(F.concat(tilde_a, beta,... | module function_definition identifier parameters identifier identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_... | Forward of Decomposable Attention layer |
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