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def is_valid_varname(self, name, item):
""" Valid variable name, checked against global context. """
check_valid_varname(name, self._custom_units, self._structs, self._constants, item)
if name in self._globals:
raise VariableDeclarationException(
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def openattachment(self, attachid):
"""
Get the contents of the attachment with the given attachment ID.
Returns a file-like object.
"""
attachments = self.get_attachments(None, attachid)
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def _get_revision(self, revision):
"""
For git backend we always return integer here. This way we ensure
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"""
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def total_capacity(self):
"""
Find the total task capacity available for this channel.
Query all the enabled hosts for this channel and sum up all the
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Each task has a "weight". Each task will be in "FREE" state until
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def add_macro(self,name,value):
"""
Add a variable (macro) for this node. This can be different for
each node in the DAG, even if they use the same CondorJob. Within
the CondorJob, the value of the macro can be referenced as
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def tree_sph(polar, azimuthal, n, standardization, symbolic=False):
"""Evaluate all spherical harmonics of degree at most `n` at angles `polar`,
`azimuthal`.
"""
cos = numpy.vectorize(sympy.cos) if symbolic else numpy.cos
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def read(author, kind):
"""
Attempts to read the cache to fetch missing arguments.
This method will attempt to find a '.license' file in the
'CACHE_DIRECTORY', to read any arguments that were not passed to the
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Arguments:
author (str): The author passed, if any.
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def get_chacra_repo(shaman_url):
"""
From a Shaman URL, get the chacra url for a repository, read the
contents that point to the repo and return it as a string.
"""
shaman_response = get_request(shaman_url)
chacra_url = shaman_response.geturl()
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def get_default_config(self):
"""
Returns the default collector settings
"""
config = super(NfsCollector, self).get_default_config()
config.update({
'path': 'nfs'
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def get_payroll_totals(month_work_entries, month_leave_entries):
"""Summarizes monthly work and leave totals, grouped by user.
Returns (labels, rows).
labels -> {'billable': [proj_labels], 'nonbillable': [proj_labels]}
rows -> [{
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def write_interactions(G, path, delimiter=' ', encoding='utf-8'):
"""Write a DyNetx graph in interaction list format.
Parameters
----------
G : graph
A DyNetx graph.
path : basestring
The desired output filename
delimiter : character
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def matches_sample(output, target, threshold, is_correct, actual_output):
"""
Check if a sample with the given network output, target output, and threshold
is the classification (is_correct, actual_output) like true positive or false negative
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def compare_table_cols(a, b):
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Return False if the two tables a and b have the same columns
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def get_extra(request):
"""Return information about a module / collection that cannot be cached."""
settings = get_current_registry().settings
exports_dirs = settings['exports-directories'].split()
args = request.matchdict
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def add_argument(self, *args, **kwargs):
"""
add_argument(dest, ..., name=value, ...)
add_argument(option_string, option_string, ..., name=value, ...)
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def get_assessment_taken_form_for_create(self, assessment_offered_id, assessment_taken_record_types):
"""Gets the assessment taken form for creating new assessments taken.
A new form should be requested for each create transaction.
arg: assessment_offered_id (osid.id.Id): the ``Id`` of the
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def update_user(self, user_id, **kwargs):
"""Update a user."""
body = self._formdata(kwargs, FastlyUser.FIELDS)
content = self._fetch("/user/%s" % user_id, method="PUT", body=body)
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def elapsed(self):
'''
Returns elapsed crawl time as a float in seconds.
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In contrast `Site.active_brozzling_time` only counts time when a
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def _merge_args_with_kwargs(args_dict, kwargs_dict):
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def matches_address(self, address):
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def remove_config_lock(name):
'''
Release config lock previously held.
name: The name of the module function to execute.
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panos/takelock:
panos.remove_config_lock
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def search_packages_info(query):
"""
Gather details from installed distributions. Print distribution name,
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def chunk(iterator, max_size):
"""Chunk a list/set/etc.
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def zadd(self, name, *args, **kwargs):
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Translate a relation node into SQLQuery.
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def _from_java(cls, java_stage):
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def revert_cnf(node):
"""Reverts a parse tree (RuleNode) to its original non-CNF form (Node)."""
if isinstance(node, T):
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def repository_factory(vcs_type, **kw):
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def move(self, dest, changelist=0, force=False):
"""Renames/moves the file to dest
:param dest: Destination to move the file to
:type dest: str
:param changelist: Changelist to add the move to
:type changelist: :class:`.Changelist`
:param force: Force the move to an exis... | [
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def sponsor_tagged_image(sponsor, tag):
"""returns the corresponding url from the tagged image list."""
if sponsor.files.filter(tag_name=tag).exists():
return sponsor.files.filter(tag_name=tag).first().tagged_file.item.url
return '' | [
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def addFeaturesSearchOptions(parser):
"""
Adds common options to a features search command line parser.
"""
addFeatureSetIdArgument(parser)
addFeaturesReferenceNameArgument(parser)
addStartArgument(parser)
addEndArgument(parser)
addParentFeatureIdArgument(parser)
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def sequence(values):
"""
Wrap a list of Python values as an Ibis sequence type
Parameters
----------
values : list
Should all be None or the same type
Returns
-------
seq : Sequence
"""
import ibis.expr.operations as ops
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def add_collection(self, path, c_name, c_type, c_doc, c_version="unknown",
c_scope="", c_namedargs="yes", c_doc_format="ROBOT"):
"""Insert data into the collection table"""
if path is not None:
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# dat... | [
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def gsum_(self, col: str, index_col: bool=True) -> "Ds":
"""
Group by and sum column
:param col: column to group
:type col: str
:param index_col:
:type index_col: bool
:return: a dataswim instance
:rtype: Ds
:example: ``ds2 = ds.gsum("Col 1")``
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def parse_datetime(dt_str, format):
"""Create a timezone-aware datetime object from a datetime string."""
t = time.strptime(dt_str, format)
return datetime(t[0], t[1], t[2], t[3], t[4], t[5], t[6], pytz.UTC) | [
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def get_requirements(self, reqts, extras=None, env=None):
"""
Base method to get dependencies, given a set of extras
to satisfy and an optional environment context.
:param reqts: A list of sometimes-wanted dependencies,
perhaps dependent on extras and environment.
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def render_noderef(self, ontol, n, query_ids=None, **args):
"""
Render a node object
"""
if query_ids is None:
query_ids = []
marker = ""
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def check_summary_health(summary_file, **kwargs):
"""Checks the health of a sample from the FastQC summary file.
Parses the FastQC summary file and tests whether the sample is good
or not. There are four categories that cannot fail, and two that
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def __convert_keys_2(header, d):
"""
Convert lpd to noaa keys for this one section
:param str header: Section header
:param dict d: Metadata
:return dict: Metadata w/ converted keys
"""
d_out = {}
try:
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tr... | [
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def _parse_cli_facter_results(facter_results):
'''Parse key value pairs printed with "=>" separators.
YAML is preferred output scheme for facter.
>>> list(_parse_cli_facter_results("""foo => bar
... baz => 1
... foo_bar => True"""))
[('foo', 'bar'), ('baz', '1'), ('foo_bar', 'True')]
>>> li... | [
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def blockstack_backup_restore(working_dir, block_number):
"""
Restore the database from a backup in the backups/ directory.
If block_number is None, then use the latest backup.
NOT THREAD SAFE
Return True on success
Raise an exception on error
"""
db = BlockstackDB.get_readwrite_instan... | [
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def load(self):
"""
Load the Certificate object from DigitalOcean.
Requires self.id to be set.
"""
data = self.get_data("certificates/%s" % self.id)
certificate = data["certificate"]
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def update_trial_stats(self, trial, result):
"""Update result for trial. Called after trial has finished
an iteration - will decrement iteration count.
TODO(rliaw): The other alternative is to keep the trials
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def eq_obj_contents(l, r):
"""
Compares object contents, supports slots
:param l:
:param r:
:return:
"""
if l.__class__ is not r.__class__:
return False
if hasattr(l, "__slots__"):
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def make_splice_junction_df(fn, type='gene'):
"""Read the Gencode gtf file and make a pandas dataframe describing the
splice junctions
Parameters
----------
filename : str of filename
Filename of the Gencode gtf file
Returns
-------
df : pandas.DataFrame
Dataframe of ... | [
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def vectorize(data, cloud=None, api_key=None, version=None, **kwargs):
"""
Support for raw features from the custom collections API
"""
batch = detect_batch(data)
data = data_preprocess(data, batch=batch)
url_params = {"batch": batch, "api_key": api_key, "version": version, "method": "vectorize"... | [
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def GET(self, courseid): # pylint: disable=arguments-differ
""" GET request """
course = self.get_course(courseid)
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def finalize(state, block):
"""Apply rewards and commit."""
if state.is_METROPOLIS():
br = state.config['BYZANTIUM_BLOCK_REWARD']
nr = state.config['BYZANTIUM_NEPHEW_REWARD']
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def get_event_discount(self, id, discount_id, **data):
"""
GET /events/:id/discounts/:discount_id/
Gets a :format:`discount` by ID as the key ``discount``.
"""
return self.get("/events/{0}/discounts/{0}/".format(id,discount_id), data=data) | [
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def get_mapping_actions(image=None, imageId=None, in_digests=[], bundle={}):
"""
Given an image, image_id, digests, and a bundle, determine which policies and whitelists to evaluate.
:param image: Image obj
:param imageId: image id string
:param in_digests: candidate digests
:param bundle:... | [
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def from_filepath(filepath, strict = True, parse_ligands = False):
'''A function to replace the old constructor call where a filename was passed in.'''
return PDB(read_file(filepath), strict = strict, parse_ligands = parse_ligands) | [
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def do_action_to_ancestors(analysis_request, transition_id):
"""Promotes the transitiion passed in to ancestors, if any
"""
parent_ar = analysis_request.getParentAnalysisRequest()
if parent_ar:
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def resize_img(fname, targ, path, new_path, fn=None):
"""
Enlarge or shrink a single image to scale, such that the smaller of the height or width dimension is equal to targ.
"""
if fn is None:
fn = resize_fn(targ)
dest = os.path.join(path_for(path, new_path, targ), fname)
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def visit_package(self, node):
"""visit an astroid.Package node
* optionally tag the node with a unique id
"""
if self.tag:
node.uid = self.generate_id()
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def rouge_2(hypotheses, references):
"""
Calculate ROUGE-2 F1, precision, recall scores
"""
rouge_2 = [
rouge_n([hyp], [ref], 2) for hyp, ref in zip(hypotheses, references)
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rouge_2_f, _, _ = map(np.mean, zip(*rouge_2))
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def iter_headers(self):
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headers = self._headers.iteritems()
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def _aload8(ins):
''' Loads an 8 bit value from a memory address
If 2nd arg. start with '*', it is always treated as
an indirect value.
'''
output = _addr(ins.quad[2])
output.append('ld a, (hl)')
output.append('push af')
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def get_filename(self, checksum):
"""
:param checksum: checksum
:return: filename no storage base part
"""
filename = None
for _filename, metadata in self._log.items():
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def indexFromItem(self, regItem, col=0):
""" Gets the index (with column=0) for the row that contains the regItem
If col is negative, it is counted from the end
"""
if col < 0:
col = len(self.attrNames) - col
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def kill(timeout=15):
'''
Kill the salt minion.
timeout
int seconds to wait for the minion to die.
If you have a monitor that restarts ``salt-minion`` when it dies then this is
a great way to restart after a minion upgrade.
CLI example::
>$ salt minion[12] minion.kill
... | [
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Helper function that makes an HTTP GET request to the given firebase
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`url`: The full URL of the firebase endpoint (DSN appended.)
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def _updateItemComboBoxIndex(self, item, column, num):
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def connect():
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def get_function_from_config(item):
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Import the function to get profile by handle.
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def Gregory_Scott(x, rhol, rhog):
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.. math::
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def serialize(self):
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def filter_by(zips=_zips, **kwargs):
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def interleave(*arrays,**kwargs):
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arr2 = ['a','b','c','d']
arr3 = ['@','#','%','*']
interleave(arr1,arr2,arr3)
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def generate_lambda_functions():
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def resume_trial(self, trial):
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# pylint: disable=too-many-nested-blocks,too-many-statements
# pylint: disable=too-many-branches, too-many-locals
"""Read and parse the Nagios legacy configuration files
and store their content into a StringIO object whi... | [
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def predict(self, x):
"""
This function calculates the new output value `y` from input array `x`.
**Args:**
* `x` : input vector (1 dimension array) in length of filter.
**Returns:**
* `y` : output value (float) calculated from input array.
"""
y = np... | [
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def media(self, uri):
"""Play a media file."""
try:
local_path, _ = urllib.request.urlretrieve(uri)
metadata = mutagen.File(local_path, easy=True)
if metadata.tags:
self._tags = metadata.tags
title = self._tags.get(TAG_TITLE, [])
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def _build_lv_grid(ding0_grid, network):
"""
Build eDisGo LV grid from Ding0 data
Parameters
----------
ding0_grid: ding0.MVGridDing0
Ding0 MV grid object
Returns
-------
list of LVGrid
LV grids
dict
Dictionary containing a mapping of LV stations in Ding0 to... | [
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... | 41.443609 | 0.000532 |
def apply_template(template, *args, **kw):
"""Applies every callable in any Mapping or Iterable"""
if six.callable(template):
return template(*args, **kw)
if isinstance(template, six.string_types):
return template
if isinstance(template, collections.Mapping):
return template.__cl... | [
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def compute(self, cost_matrix):
"""
Compute the indexes for the lowest-cost pairings between rows and
columns in the database. Returns a list of (row, column) tuples
that can be used to traverse the matrix.
:Parameters:
cost_matrix : list of lists
The... | [
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"cost... | 33.877193 | 0.005033 |
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