Unnamed: 0 int64 0 389k | code stringlengths 26 79.6k | docstring stringlengths 1 46.9k |
|---|---|---|
9,200 | def featurecounts_stats_table(self):
headers = OrderedDict()
headers[] = {
: ,
: ,
: 100,
: 0,
: ,
:
}
headers[] = {
: .format(config.read_count_prefix),
: .format(config.read_count... | Take the parsed stats from the featureCounts report and add them to the
basic stats table at the top of the report |
9,201 | def argument_kind(args):
kinds = set(arg.kind for arg in args)
if len(kinds) != 1:
return None
return kinds.pop() | Return the kind of an argument, based on one or more descriptions of the argument.
Return None if every item does not have the same kind. |
9,202 | def slackbuild(self, name, sbo_file):
return URL(self.sbo_url + name + sbo_file).reading() | Read SlackBuild file |
9,203 | def _import_protobuf_from_file(grpc_pyfile, method_name, service_name = None):
prefix = grpc_pyfile[:-12]
pb2 = __import__("%s_pb2"%prefix)
pb2_grpc = __import__("%s_pb2_grpc"%prefix)
all_service_names = [stub_name[:-4] for stub_name in dir(pb2_grpc) if stub_name.endswith(... | helper function which try to import method from the given _pb2_grpc.py file
service_name should be provided only in case of name conflict
return (False, None) in case of failure
return (True, (stub_class, request_class, response_class)) in case of success |
9,204 | def get(self, request):
try:
consent_record = self.get_consent_record(request)
if consent_record is None:
return self.get_no_record_response(request)
except ConsentAPIRequestError as invalid_request:
return Response({: str(invalid_request)}, s... | GET /consent/api/v1/data_sharing_consent?username=bob&course_id=id&enterprise_customer_uuid=uuid
*username*
The edX username from whom to get consent.
*course_id*
The course for which consent is granted.
*enterprise_customer_uuid*
The UUID of the enterprise cu... |
9,205 | def _parse_proc_mount(self):
for line in fileops.readlines():
if not in line:
continue
items = line.split()
path = items[1]
opts = items[3].split()
name = None
for opt in opts:
if opt i... | Parse /proc/mounts |
9,206 | def _is_and_or_ternary(node):
return (
isinstance(node, astroid.BoolOp)
and node.op == "or"
and len(node.values) == 2
and isinstance(node.values[0], astroid.BoolOp)
and not isinstance(node.values[1], astroid.BoolOp)
and node.values... | Returns true if node is 'condition and true_value or false_value' form.
All of: condition, true_value and false_value should not be a complex boolean expression |
9,207 | def sort_layout(thread, listfile, column=0):
from jcvi.formats.base import DictFile
outfile = listfile.rsplit(".", 1)[0] + ".sorted.list"
threadorder = thread.order
fw = open(outfile, "w")
lt = DictFile(listfile, keypos=column, valuepos=None)
threaded = []
imported = set()
for t in... | Sort the syntelog table according to chromomomal positions. First orient the
contents against threadbed, then for contents not in threadbed, insert to
the nearest neighbor. |
9,208 | def construct_formset(self):
formset_class = self.get_formset()
if hasattr(self, ):
klass = type(self).__name__
raise DeprecationWarning(
.format(klass),
)
return formset_class(**self.get_formset_kwarg... | Returns an instance of the formset |
9,209 | def list_patterns(refresh=False, root=None):
*
if refresh:
refresh_db(root)
return _get_patterns(root=root) | List all known patterns from available repos.
refresh
force a refresh if set to True.
If set to False (default) it depends on zypper if a refresh is
executed.
root
operate on a different root directory.
CLI Examples:
.. code-block:: bash
salt '*' pkg.list_pat... |
9,210 | def attrs(self):
ret = dict(self.__dict__)
del ret["_matches"]
if self.type != c.COMPUTER:
del ret["difficulty"]
return ret | provide a copy of this player's attributes as a dictionary |
9,211 | def parse(expected, query):
return dict(
(key, parser(query.get(key, [])))
for key, parser in expected.items()) | Parse query parameters.
:type expected: `dict` mapping `bytes` to `callable`
:param expected: Mapping of query argument names to argument parsing
callables.
:type query: `dict` mapping `bytes` to `list` of `bytes`
:param query: Mapping of query argument names to lists of argument values,
... |
9,212 | def _linux_brdel(br):
brctl = _tool_path()
return __salt__[](.format(brctl, br),
python_shell=False) | Internal, deletes the bridge |
9,213 | def reset(self):
fetches = []
for processor in self.preprocessors:
fetches.extend(processor.reset() or [])
return fetches | Calls `reset` on all our Preprocessor objects.
Returns:
A list of tensors to be fetched. |
9,214 | def load_blotter_args(blotter_name=None, logger=None):
if logger is None:
logger = tools.createLogger(__name__, logging.WARNING)
if blotter_name is not None:
args_cache_file = tempfile.gettempdir() + "/" + blotter_name.lower() + ".qtpylib"
if not os.path.exists(args_cache_fi... | Load running blotter's settings (used by clients)
:Parameters:
blotter_name : str
Running Blotter's name (defaults to "auto-detect")
logger : object
Logger to be use (defaults to Blotter's)
:Returns:
args : dict
Running Blotter's arguments |
9,215 | def nlargest(n, mapping):
try:
it = mapping.iteritems()
except AttributeError:
it = iter(mapping.items())
pq = minpq()
try:
for i in range(n):
pq.additem(*next(it))
except StopIteration:
pass
try:
while it:
pq.pushpopitem(*next... | Takes a mapping and returns the n keys associated with the largest values
in descending order. If the mapping has fewer than n items, all its keys
are returned.
Equivalent to:
``next(zip(*heapq.nlargest(mapping.items(), key=lambda x: x[1])))``
Returns
-------
list of up to n keys from ... |
9,216 | def get_edge_type(self, edge_type):
edges = []
for e in self.edges():
if self.adj[e[0]][e[1]].get() == edge_type:
edges.append(e)
return edges | Returns all edges with the specified edge type.
Parameters
----------
edge_type : int
An integer specifying what type of edges to return.
Returns
-------
out : list of 2-tuples
A list of 2-tuples representing the edges in the graph
wi... |
9,217 | def get_hdulist_idx(self, ccdnum):
for (extno, hdu) in enumerate(self.hdulist):
if ccdnum == int(hdu.header.get(, -1)) or str(ccdnum) in hdu.header.get(, ):
return extno
raise ValueError("Failed to find requested CCD Number {} in cutout {}".format(ccdnum,
... | The SourceCutout is a list of HDUs, this method returns the index of the HDU that corresponds to the given
ccd number. CCDs are numbers from 0, but the first CCD (CCDNUM=0) is often in extension 1 of an MEF.
@param ccdnum: the number of the CCD in the MEF that is being referenced.
@return: the ... |
9,218 | def plot_cdf(fignum, data, xlab, sym, title, **kwargs):
fig = plt.figure(num=fignum)
sdata = []
for d in data:
sdata.append(d)
sdata.sort()
X, Y = [], []
color = ""
for j in range(len(sdata)):
Y.append(old_div(float(j), float(len(sdata))))
X.append(s... | Makes a plot of the cumulative distribution function.
Parameters
__________
fignum : matplotlib figure number
data : list of data to be plotted - doesn't need to be sorted
sym : matplotlib symbol for plotting, e.g., 'r--' for a red dashed line
**kwargs : optional dictionary with {'color': color... |
9,219 | def parse_django_adminopt_node(env, sig, signode):
from sphinx.domains.std import option_desc_re
count = 0
firstname =
for m in option_desc_re.finditer(sig):
optname, args = m.groups()
if count:
signode += addnodes.desc_addname(, )
signode += addnodes.desc_name(... | A copy of sphinx.directives.CmdoptionDesc.parse_signature() |
9,220 | def prime(self, key, value):
cache_key = self.get_cache_key(key)
if cache_key not in self._promise_cache:
if isinstance(value, Exception):
promise = Promise.reject(value)
else:
promise = Promise... | Adds the provied key and value to the cache. If the key already exists, no
change is made. Returns itself for method chaining. |
9,221 | def content(self):
answer_wrap = self.soup.find(, id=)
content = answer_wrap.find(, class_=)
content = answer_content_process(content)
return content | 以处理过的Html代码形式返回答案内容.
:return: 答案内容
:rtype: str |
9,222 | def enable(self):
logger.debug()
self.options.enabled = True
logger.info() | (Re)enable the cache |
9,223 | def fail(message, exception_data=None):
print(message, file=sys.stderr)
if exception_data:
print(repr(exception_data))
sys.exit(1) | Print a failure message and exit nonzero |
9,224 | def get_installed_distributions(local_only=True,
skip=stdlib_pkgs,
include_editables=True,
editables_only=False,
user_only=False):
if local_only:
local_test = dist_is_loc... | Return a list of installed Distribution objects.
If ``local_only`` is True (default), only return installations
local to the current virtualenv, if in a virtualenv.
``skip`` argument is an iterable of lower-case project names to
ignore; defaults to stdlib_pkgs
If ``include_editables`` is False, d... |
9,225 | def _fill_empty_sessions(self, fill_subjects, fill_visits):
if fill_subjects is None:
fill_subjects = [s.id for s in self.subjects]
if fill_visits is None:
fill_visits = [v.id for v in self.complete_visits]
for subject_id in fill_subjects:
try:
... | Fill in tree with additional empty subjects and/or visits to
allow the study to pull its inputs from external repositories |
9,226 | def _build_response(self):
responses = []
self.event_urls = []
for index, event in enumerate(self.events):
self.py3.threshold_get_color(index + 1, "event")
self.py3.threshold_get_color(index + 1, "time")
event_dict = {}
event_dict["summ... | Builds the composite reponse to be output by the module by looping
through all events and formatting the necessary strings.
Returns: A composite containing the individual response for each event. |
9,227 | def _source_info():
ofi = inspect.getouterframes(inspect.currentframe())[2]
try:
calling_class = ofi[0].f_locals[].__class__
except KeyError:
calling_class = None
return ofi[1], ofi[2], calling_class, ofi[3] | Get information from the user's code (two frames up)
to leave breadcrumbs for file, line, class and function. |
9,228 | def awd_lstm_lm_1150(dataset_name=None, vocab=None, pretrained=False, ctx=cpu(),
root=os.path.join(get_home_dir(), ), **kwargs):
r
predefined_args = {: 400,
: 1150,
: ,
: 3,
: True,
... | r"""3-layer LSTM language model with weight-drop, variational dropout, and tied weights.
Embedding size is 400, and hidden layer size is 1150.
Parameters
----------
dataset_name : str or None, default None
The dataset name on which the pre-trained model is trained.
Options are 'wikitex... |
9,229 | def workflow_script_reject(self):
if skip(self, "reject"):
return
workflow = self.portal_workflow
def copy_src_fields_to_dst(src, dst):
ignore_fields = [
,
,
,
,
,
... | Copy real analyses to RejectAnalysis, with link to real
create a new worksheet, with the original analyses, and new
duplicates and references to match the rejected
worksheet. |
9,230 | def multiglob_compile(globs, prefix=False):
if not globs:
return re.compile()
elif prefix:
globs = [x + for x in globs]
return re.compile(.join(fnmatch.translate(x) for x in globs)) | Generate a single "A or B or C" regex from a list of shell globs.
:param globs: Patterns to be processed by :mod:`fnmatch`.
:type globs: iterable of :class:`~__builtins__.str`
:param prefix: If ``True``, then :meth:`~re.RegexObject.match` will
perform prefix matching rather than exact string match... |
9,231 | def _compute_mean(self, C, mag, r):
mean = (C[] +
self._compute_term1(C, mag) +
self._compute_term2(C, mag, r))
return mean | Compute mean value according to equation 30, page 1021. |
9,232 | def updateUserTone(conversationPayload, toneAnalyzerPayload, maintainHistory):
emotionTone = None
writingTone = None
socialTone = None
if not in conversationPayload:
conversationPayload[] = {}
if not in conversationPayload[]:
conversationPayload[] = initUser()
... | updateUserTone processes the Tone Analyzer payload to pull out the emotion,
writing and social tones, and identify the meaningful tones (i.e.,
those tones that meet the specified thresholds).
The conversationPayload json object is updated to include these tones.
@param conversationPayload json object re... |
9,233 | def set_rich_menu_image(self, rich_menu_id, content_type, content, timeout=None):
self._post(
.format(rich_menu_id=rich_menu_id),
data=content,
headers={: content_type},
timeout=timeout
) | Call upload rich menu image API.
https://developers.line.me/en/docs/messaging-api/reference/#upload-rich-menu-image
Uploads and attaches an image to a rich menu.
:param str rich_menu_id: IDs of the richmenu
:param str content_type: image/jpeg or image/png
:param content: image... |
9,234 | def setRelay(self, seconds, relay, status, password="00000000"):
result = False
self.setContext("setRelay")
try:
self.clearCmdMsg()
if len(password) != 8:
self.writeCmdMsg("Invalid password length.")
self.setContext("")
... | Serial call to set relay.
Args:
seconds (int): Seconds to hold, ero is hold forever. See :class:`~ekmmeters.RelayInterval`.
relay (int): Selected relay, see :class:`~ekmmeters.Relay`.
status (int): Status to set, see :class:`~ekmmeters.RelayState`
password (str):... |
9,235 | def resolve_remote(self, uri):
try:
return super(LocalRefResolver, self).resolve_remote(uri)
except ValueError:
return super(LocalRefResolver, self).resolve_remote(
+ get_schema_path(uri.rsplit(, 1)[0])
) | Resolve a uri or relative path to a schema. |
9,236 | def _upload(param_dict, timeout, data):
param_dict[] =
param_dict[] =
param_dict[] =
result = util.callm(, param_dict, POST = True, socket_timeout = 300, data = data)
return _track_from_response(result, timeout) | Calls upload either with a local audio file,
or a url. Returns a track object. |
9,237 | def blame_incremental(self, rev, file, **kwargs):
data = self.git.blame(rev, , file, p=True, incremental=True, stdout_as_string=False, **kwargs)
commits = {}
stream = (line for line in data.split(b) if line)
while True:
try:
line = next(stream)
... | Iterator for blame information for the given file at the given revision.
Unlike .blame(), this does not return the actual file's contents, only
a stream of BlameEntry tuples.
:param rev: revision specifier, see git-rev-parse for viable options.
:return: lazy iterator of BlameEntry tupl... |
9,238 | def gen_image(img, width, height, outfile, img_type=):
assert len(img) == width * height or len(img) == width * height * 3
if img_type == :
misc.imsave(outfile, img.reshape(width, height))
elif img_type == :
misc.imsave(outfile, img.reshape(3, width, height)) | Save an image with the given parameters. |
9,239 | def sign(self, storepass=None, keypass=None, keystore=None, apk=None, alias=None, name=):
target = self.get_target()
build_tool = android_helper.get_highest_build_tool(target.split()[1])
if keystore is None:
(keystore, storepass, keypass, alias) = android_helper.get_default_keystore()
dist = ... | Signs (jarsign and zipalign) a target apk file based on keystore information, uses default debug keystore file by default.
:param storepass(str): keystore file storepass
:param keypass(str): keystore file keypass
:param keystore(str): keystore file path
:param apk(str): apk file path to be signed
:... |
9,240 | def validate(tool_class, model_class):
if not hasattr(tool_class, ):
raise ImproperlyConfigured("No attribute found for tool %s." % (
tool_class.__name__
))
if not hasattr(tool_class, ):
raise ImproperlyConfigured("No attribute found for tool %s." % (
tool... | Does basic ObjectTool option validation. |
9,241 | def run(self):
try:
language = self.arguments[0]
except IndexError:
language =
code = .join(self.content)
literal = docutils.nodes.literal_block(code, code)
literal[].append()
literal[] = language
return [literal] | Run directive. |
9,242 | def _setup_metric_group_definitions(self):
metric_group_definitions = dict()
for mg_info in self.properties[]:
mg_name = mg_info[]
mg_def = MetricGroupDefinition(
name=mg_name,
resource_class=_resource_class_from_group(mg_name),
... | Return the dict of MetricGroupDefinition objects for this metrics
context, by processing its 'metric-group-infos' property. |
9,243 | def register(device, data, facet):
if isinstance(data, string_types):
data = json.loads(data)
if data[] != VERSION:
raise ValueError( % data[])
app_id = data.get(, facet)
verify_facet(app_id, facet)
app_param = sha256(app_id.encode()).digest()
client_data = {
: ,... | Register a U2F device
data = {
"version": "U2F_V2",
"challenge": string, //b64 encoded challenge
"appId": string, //app_id
} |
9,244 | def convert_uen(pinyin):
return UN_RE.sub(lambda m: m.group(1) + UN_MAP[m.group(2)], pinyin) | uen 转换，还原原始的韵母
iou，uei，uen前面加声母的时候，写成iu，ui，un。
例如niu(牛)，gui(归)，lun(论)。 |
9,245 | def _buffer_decode(self, input, errors, final):
decoded_segments = []
position = 0
while True:
decoded, consumed = self._buffer_decode_step(
input[position:],
errors,
final
... | Decode bytes that may be arriving in a stream, following the Codecs
API.
`input` is the incoming sequence of bytes. `errors` tells us how to
handle errors, though we delegate all error-handling cases to the real
UTF-8 decoder to ensure correct behavior. `final` indicates whether
... |
9,246 | def staticproperty(func):
doc = func.__doc__
if not isinstance(func, staticmethod):
func = staticmethod(func)
return ClassPropertyDescriptor(func, doc) | Use as a decorator on a method definition to make it a class-level attribute (without binding).
This decorator can be applied to a method or a staticmethod. This decorator does not bind any
arguments.
Usage:
>>> other_x = 'value'
>>> class Foo(object):
... @staticproperty
... def x():
... retu... |
9,247 | def get(company=, company_uri=):
if not company and not company_uri:
raise Exception("glassdoor.gd.get(company=, company_uri=): "\
" company or company_uri required")
payload = {}
if not company_uri:
payload.update({: ,
: company
... | Performs a HTTP GET for a glassdoor page and returns json |
9,248 | def from_df(cls, ratings:DataFrame, valid_pct:float=0.2, user_name:Optional[str]=None, item_name:Optional[str]=None,
rating_name:Optional[str]=None, test:DataFrame=None, seed:int=None, path:PathOrStr=, bs:int=64,
val_bs:int=None, num_workers:int=defaults.cpus, dl_tfms:Optional[Collectio... | Create a `DataBunch` suitable for collaborative filtering from `ratings`. |
9,249 | def query_subdevice2index(self, ncfile) -> Subdevice2Index:
subdevices = self.query_subdevices(ncfile)
self._test_duplicate_exists(ncfile, subdevices)
subdev2index = {subdev: idx for (idx, subdev) in enumerate(subdevices)}
return Subdevice2Index(subdev2index, self.name, get_file... | Return a |Subdevice2Index| that maps the (sub)device names to
their position within the given NetCDF file.
Method |NetCDFVariableBase.query_subdevice2index| is based on
|NetCDFVariableBase.query_subdevices|. The returned
|Subdevice2Index| object remembers the NetCDF file the
(s... |
9,250 | def set_levels(self, levels):
assert_is_type(levels, [str])
return H2OFrame._expr(expr=ExprNode("setDomain", self, False, levels), cache=self._ex._cache) | Replace the levels of a categorical column.
New levels must be aligned with the old domain. This call has copy-on-write semantics.
:param List[str] levels: A list of strings specifying the new levels. The number of new
levels must match the number of old levels.
:returns: A single-... |
9,251 | def _to_power_basis_degree8(nodes1, nodes2):
r
evaluated = [
eval_intersection_polynomial(nodes1, nodes2, t_val) for t_val in _CHEB9
]
return polynomial.polyfit(_CHEB9, evaluated, 8) | r"""Compute the coefficients of an **intersection polynomial**.
Helper for :func:`to_power_basis` in the case that B |eacute| zout's
`theorem`_ tells us the **intersection polynomial** is degree
:math:`8`. This happens if the two curves have degrees one and eight
or have degrees two and four.
.. n... |
9,252 | def _raise_error_routes(iface, option, expected):
msg = _error_msg_routes(iface, option, expected)
log.error(msg)
raise AttributeError(msg) | Log and raise an error with a logical formatted message. |
9,253 | def convert_coordinates(coords, origin, wgs84, wrapped):
if isinstance(coords, list) or isinstance(coords, tuple):
try:
if isinstance(coords[0], list) or isinstance(coords[0], tuple):
return [convert_coordinates(list(c), origin, wgs84, wrapped) for c in coords]
e... | Convert coordinates from one crs to another |
9,254 | def stringify_summary(summary):
for index, suite_summary in enumerate(summary["details"]):
if not suite_summary.get("name"):
suite_summary["name"] = "testcase {}".format(index)
for record in suite_summary.get("records"):
meta_datas = record[]
__stringify_me... | stringify summary, in order to dump json file and generate html report. |
9,255 | def __rst2graph(self, rs3_xml_tree):
doc_root = rs3_xml_tree.getroot()
for segment in doc_root.iter():
self.__add_segment(segment)
for group in doc_root.iter():
self.__add_group(group) | Reads an RST tree (from an ElementTree representation of an RS3
XML file) and adds all segments (nodes representing text) and
groups (nonterminal nodes in an RST tree) as well as the
relationships that hold between them (typed edges) to this
RSTGraph.
Parameters
--------... |
9,256 | def _merge_meta(self, encoded_meta, meta):
new_meta = None
if meta:
_meta = self._decode_meta(encoded_meta)
for key, value in six.iteritems(meta):
if value is None:
_meta.pop(key, None)
else:
_meta[... | Merge new meta dict into encoded meta. Returns new encoded meta. |
9,257 | def modify(self, modification, parameters):
for src in self:
src.modify(modification, parameters) | Apply a modification to the underlying point sources, with the
same parameters for all sources |
9,258 | def insert(self, table, columns, values, execute=True):
cols, vals = get_col_val_str(columns)
statement = "INSERT INTO {0} ({1}) VALUES ({2})".format(wrap(table), cols, vals)
if execute:
self._cursor.execute(statement, values)
self._co... | Insert a single row into a table. |
9,259 | def get_random_user(self):
from provider.models import User
u = User.objects.order_by()[0]
return {"username": u.username, "password": u.password, "fullname": u.fullname} | Gets a random user from the provider
:returns: Dictionary |
9,260 | def pre_save(self, model_instance, add):
value = super(UserField, self).pre_save(model_instance, add)
if not value and not add:
value = self.get_os_username()
setattr(model_instance, self.attname, value)
return value
return v... | Updates username created on ADD only. |
9,261 | def ci(data, statfunction=None, alpha=0.05, n_samples=10000,
method=, output=, epsilon=0.001, multi=None,
_iter=True):
if np.iterable(alpha):
alphas = np.array(alpha)
else:
alphas = np.array([alpha/2, 1-alpha/2])
if multi is None:
if isinstance(data, tuple):... | Given a set of data ``data``, and a statistics function ``statfunction`` that
applies to that data, computes the bootstrap confidence interval for
``statfunction`` on that data. Data points are assumed to be delineated by
axis 0.
Parameters
----------
data: array_like, shape (N, ...) OR tuple of array_like all with sh... |
9,262 | def show(self):
off = 0
for n, i in enumerate(self.get_instructions()):
print("{:8d} (0x{:08x}) {:04x} {:30} {}".format(n, off, i.get_op_value(), i.get_name(), i.get_output(self.idx)))
off += i.get_length() | Display (with a pretty print) this object |
9,263 | def get_worksheet(self, index):
sheet_data = self.fetch_sheet_metadata()
try:
properties = sheet_data[][index][]
return Worksheet(self, properties)
except (KeyError, IndexError):
return None | Returns a worksheet with specified `index`.
:param index: An index of a worksheet. Indexes start from zero.
:type index: int
:returns: an instance of :class:`gsperad.models.Worksheet`
or `None` if the worksheet is not found.
Example. To get first worksheet of a sprea... |
9,264 | def as_params(self):
params = {}
if self.has_filters:
params[] = self.get_filters()
if self.has_order:
params[] = self.get_order()
if self.has_selects:
params[] = self.get_selects()
if self.has_expands:
params[] = self.get_... | Returns the filters, orders, select, expands and search as query parameters
:rtype: dict |
9,265 | def convert_sed_cols(tab):
for colname in list(tab.columns.keys()):
newname = colname.lower()
newname = newname.replace(, )
if tab.columns[colname].name == newname:
continue
tab.columns[colname].name = newname
return tab | Cast SED column names to lowercase. |
9,266 | def add(self, search):
ms = self._clone()
ms._searches.append(search)
return ms | Adds a new :class:`~elasticsearch_dsl.Search` object to the request::
ms = MultiSearch(index='my-index')
ms = ms.add(Search(doc_type=Category).filter('term', category='python'))
ms = ms.add(Search(doc_type=Blog)) |
9,267 | def _get_goid2dbids(associations):
go2ids = cx.defaultdict(set)
for ntd in associations:
go2ids[ntd.GO_ID].add(ntd.DB_ID)
return dict(go2ids) | Return gene2go data for user-specified taxids. |
9,268 | def _close_prepared_statement(self):
self.prepared_sql = None
self.flush_to_query_ready()
self.connection.write(messages.Close(, self.prepared_name))
self.connection.write(messages.Flush())
self._message = self.connection.read_expected_message(messages.CloseComplete)
... | Close the prepared statement on the server. |
9,269 | def delete_managed_disk(call=None, kwargs=None):
compconn = get_conn(client_type=)
try:
compconn.disks.delete(kwargs[], kwargs[])
except Exception as exc:
log.error(, kwargs.get(), six.text_type(exc))
return False
return True | Delete a managed disk from a resource group. |
9,270 | def distVersion():
from pkg_resources import parse_version
build_number = buildNumber()
parsedBaseVersion = parse_version(baseVersion)
if isinstance(parsedBaseVersion, tuple):
raise RuntimeError("Setuptools version 8.0 or newer required. Update by running "
"")
... | The distribution version identifying a published release on PyPI. |
9,271 | def region_size(im):
r
if im.dtype == bool:
im = spim.label(im)[0]
counts = sp.bincount(im.flatten())
counts[0] = 0
chords = counts[im]
return chords | r"""
Replace each voxel with size of region to which it belongs
Parameters
----------
im : ND-array
Either a boolean image wtih ``True`` indicating the features of
interest, in which case ``scipy.ndimage.label`` will be applied to
find regions, or a greyscale image with integer ... |
9,272 | def normalize_curves_eb(curves):
non_zero_curves = [(losses, poes)
for losses, poes in curves if losses[-1] > 0]
if not non_zero_curves:
return curves[0][0], numpy.array([poes for _losses, poes in curves])
else:
max_losses = [losses[-1] for losses, _poes ... | A more sophisticated version of normalize_curves, used in the event
based calculator.
:param curves: a list of pairs (losses, poes)
:returns: first losses, all_poes |
9,273 | def remote_mgmt_addr_uneq_store(self, remote_mgmt_addr):
if remote_mgmt_addr != self.remote_mgmt_addr:
self.remote_mgmt_addr = remote_mgmt_addr
return True
return False | This function saves the MGMT address, if different from stored. |
9,274 | def run(*steps):
if not steps:
return
task = None
run._sigint = False
loop = asyncio.get_event_loop()
def abort():
task.cancel()
run._sigint = True
added = False
try:
loop.add_signal_handler(signal.SIGINT, abort)
added = True
except (Valu... | Helper to run one or more async functions synchronously, with graceful
handling of SIGINT / Ctrl-C.
Returns the return value of the last function. |
9,275 | def NewOutputModule(cls, name, output_mediator):
output_class = cls.GetOutputClass(name)
return output_class(output_mediator) | Creates a new output module object for the specified output format.
Args:
name (str): name of the output module.
output_mediator (OutputMediator): output mediator.
Returns:
OutputModule: output module.
Raises:
KeyError: if there is no output class found with the supplied name.
... |
9,276 | def meth_set_acl(args):
acl_updates = [{"user": user, "role": args.role} \
for user in set(expand_fc_groups(args.users)) \
if user != fapi.whoami()]
id = args.snapshot_id
if not id:
r = fapi.list_repository_methods(namespace=args.namespace,
... | Assign an ACL role to a list of users for a workflow. |
9,277 | def p_example_multiline(self, p):
p[0] = AstExampleField(
self.path, p.lineno(1), p.lexpos(1), p[1], p[5]) | example_field : ID EQ NL INDENT ex_map NL DEDENT |
9,278 | def _CSI(self, cmd):
sys.stdout.write()
sys.stdout.write(cmd) | Control sequence introducer |
9,279 | def get_args_parser():
parser = argparse.ArgumentParser(
description=)
parser.add_argument(, ,
action=EnvDefault,
envvar=,
required=True,
help=)
parser.add_argument(, ,
action... | Return a parser for command line options. |
9,280 | def find_near_matches_no_deletions_ngrams(subsequence, sequence, search_params):
if not subsequence:
raise ValueError()
max_substitutions, max_insertions, max_deletions, max_l_dist = search_params.unpacked
max_substitutions = min(max_substitutions, max_l_dist)
max_insertions = min(max_ins... | search for near-matches of subsequence in sequence
This searches for near-matches, where the nearly-matching parts of the
sequence must meet the following limitations (relative to the subsequence):
* the maximum allowed number of character substitutions
* the maximum allowed number of new characters i... |
9,281 | def taskGroupCreationRequested(self, *args, **kwargs):
ref = {
: ,
: ,
: [
{
: ,
: False,
: ,
},
{
: False,
: ,
... | tc-gh requested the Queue service to create all the tasks in a group
supposed to signal that taskCreate API has been called for every task in the task group
for this particular repo and this particular organization
currently used for creating initial status indicators in GitHub UI using Statuse... |
9,282 | def pretty_print(self):
print colored.blue("-" * 40)
print colored.red("datacats: problem was encountered:")
print self.message
print colored.blue("-" * 40) | Print the error message to stdout with colors and borders |
9,283 | def unix_time(self, dt):
epoch = datetime.utcfromtimestamp(0)
delta = dt - epoch
return int(delta.total_seconds()) | Returns the number of seconds since the UNIX epoch for the given
datetime (dt).
PARAMETERS:
dt -- datetime |
9,284 | def ipv6_link_local(self, **kwargs):
int_type = kwargs.pop().lower()
ve_name = kwargs.pop()
rbridge_id = kwargs.pop(, )
callback = kwargs.pop(, self._callback)
valid_int_types = [, ]
if int_type not in valid_int_types:
raise ValueError( %
... | Configure ipv6 link local address on interfaces on vdx switches
Args:
int_type: Interface type on which the ipv6 link local needs to be
configured.
name: 'Ve' or 'loopback' interface name.
rbridge_id (str): rbridge-id for device.
get (bool): Get conf... |
9,285 | def getIdent(self, node):
ident = self.getRawIdent(node)
if ident is not None:
return ident
node = self.findNode(node)
if node is None:
return None
return node.graphident | Get the graph identifier for a node |
9,286 | def bbox_to_resolution(bbox, width, height):
utm_bbox = to_utm_bbox(bbox)
east1, north1 = utm_bbox.lower_left
east2, north2 = utm_bbox.upper_right
return abs(east2 - east1) / width, abs(north2 - north1) / height | Calculates pixel resolution in meters for a given bbox of a given width and height.
:param bbox: bounding box
:type bbox: geometry.BBox
:param width: width of bounding box in pixels
:type width: int
:param height: height of bounding box in pixels
:type height: int
:return: resolution east-w... |
9,287 | def mark_offer_as_lose(self, offer_id):
return self._create_put_request(
resource=OFFERS,
billomat_id=offer_id,
command=LOSE,
) | Mark offer as lose
:param offer_id: the offer id
:return Response |
9,288 | def run(self):
logger.debug("Starting execution of {0}{1}".format(self, " (backwards)" if self.backward_execution else ""))
self.setup_run()
try:
concurrency_history_item = self.setup_forward_or_backward_execution()
concurrency_queue = self.start_child_states(co... | This defines the sequence of actions that are taken when the preemptive concurrency state is executed
:return: |
9,289 | def taskdir(self):
return os.path.join(self.BASE, self.TAG, self.task_family) | Return the directory under which all artefacts are stored. |
9,290 | def get_required(self, name):
locator = self._locate(name)
if locator == None:
raise ReferenceException(None, name)
return self._references.get_required(locator) | Gets all required dependencies by their name.
At least one dependency must be present. If no dependencies was found it throws a [[ReferenceException]]
:param name: the dependency name to locate.
:return: a list with found dependencies. |
9,291 | def get_grouped_opcodes(self, n=3):
codes = self.get_opcodes()
if not codes:
codes = [("equal", 0, 1, 0, 1)]
if codes[0][0] == :
tag, i1, i2, j1, j2 = codes[0]
codes[0] = tag, max(i1, i2-n), i2, max(j1, j2-n), j2
if codes[-1][0] == :... | Isolate change clusters by eliminating ranges with no changes.
Return a generator of groups with up to n lines of context.
Each group is in the same format as returned by get_opcodes().
>>> from pprint import pprint
>>> a = map(str, range(1,40))
>>> b = a[:]
>>> b[8:8] ... |
9,292 | def get_managed(
name,
template,
source,
source_hash,
source_hash_name,
user,
group,
mode,
attrs,
saltenv,
context,
defaults,
skip_verify=False,
**kwargs):
*{hash_type: , : <md5sum>}755
sfn =
... | Return the managed file data for file.managed
name
location where the file lives on the server
template
template format
source
managed source file
source_hash
hash of the source file
source_hash_name
When ``source_hash`` refers to a remote file, this spec... |
9,293 | def load(self, name):
if self.reload:
self._maybe_purge_cache()
template = self.cache.get(name)
if template:
return template
path = self.resolve(name)
if not path:
raise OSError(errno.ENOENT, "File not found: %s" % name)
wi... | If not yet in the cache, load the named template and compiles it,
placing it into the cache.
If in cache, return the cached template. |
9,294 | def rst2md(text):
top_heading = re.compile(r, flags=re.M)
text = re.sub(top_heading, r, text)
math_eq = re.compile(r, flags=re.M)
text = re.sub(math_eq,
lambda match: r.format(match.group(1).strip()),
text)
inline_math = re.compile(r)
text = re.sub(inli... | Converts the RST text from the examples docstrigs and comments
into markdown text for the IPython notebooks |
9,295 | def field2choices(self, field, **kwargs):
attributes = {}
comparable = [
validator.comparable
for validator in field.validators
if hasattr(validator, "comparable")
]
if comparable:
attributes["enum"] = comparable
else:
... | Return the dictionary of OpenAPI field attributes for valid choices definition
:param Field field: A marshmallow field.
:rtype: dict |
9,296 | def md5sum(filename, blocksize=8192):
with open(filename, ) as fh:
m = hashlib.md5()
while True:
data = fh.read(blocksize)
if not data:
break
m.update(data)
return m.hexdigest() | Get the MD5 checksum of a file. |
9,297 | def init_default_config(self, path):
if not (os.path.exists(path) and os.path.isfile(path)):
raise AppConfigValueException(
.format(path))
cfl = open(path, )
data = json.load(cfl)
cfl.close()
for key in data.keys():
if == key:... | Initialize the config object and load the default configuration.
The path to the config file must be provided. The name of the
application is read from the config file.
The config file stores the description and the default values for
all configurations including the appl... |
9,298 | def check(text):
err = "airlinese.misc"
msg = u" is airlinese."
airlinese = [
"enplan(?:e|ed|ing|ement)",
"deplan(?:e|ed|ing|ement)",
"taking off momentarily",
]
return existence_check(text, airlinese, err, msg) | Check the text. |
9,299 | def create_sqlite_backup_db(audit_tables):
try:
Popen("rm %s"%(config.get(, )), shell=True)
logging.warn("Old sqlite backup DB removed")
except Exception as e:
logging.warn(e)
try:
aux_dir = config.get(, )
os.mkdir(aux_dir)
logging.warn("%s cre... | return an inspector object |
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