catalinskh/compiler-ai
Question Answering
•
Updated
text
stringlengths 89
104k
| code_tokens
sequence | avg_line_len
float64 7.91
980
| score
float64 0
630
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|---|---|---|---|
def round(self, ndigits=0):
"""
Rounds the amount using the current ``Decimal`` rounding algorithm.
"""
if ndigits is None:
ndigits = 0
return self.__class__(
amount=self.amount.quantize(Decimal('1e' + str(-ndigits))),
currency=self.currency) | [
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def _make_input(self, action, old_quat):
"""
Helper function that returns a dictionary with keys dpos, rotation from a raw input
array. The first three elements are taken to be displacement in position, and a
quaternion indicating the change in rotation with respect to @old_quat.
"""
return {
"dpos": action[:3],
# IK controller takes an absolute orientation in robot base frame
"rotation": T.quat2mat(T.quat_multiply(old_quat, action[3:7])),
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def bump(args: argparse.Namespace) -> None:
"""
:args: An argparse.Namespace object.
This function is bound to the 'bump' sub-command. It increments the version
integer of the user's choice ('major', 'minor', or 'patch').
"""
try:
last_tag = last_git_release_tag(git_tags())
except NoGitTagsException:
print(SemVer(0, 1, 0))
exit(0)
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elif args.type == 'major':
print(last_ver.bump_major()) | [
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def stitch_block_rows(block_list):
'''
Stitches blocks together into a single block rowwise. These blocks are 2D tables usually
generated from tableproc. The final block will be of dimensions (sum(num_rows), max(num_cols)).
'''
stitched = list(itertools.chain(*block_list))
max_length = max(len(row) for row in stitched)
for row in stitched:
if len(row) < max_length:
row += [None] * (max_length - len(row))
return stitched | [
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def load_stock_links(self):
""" Read stock links into the model """
links = self.__get_session().query(dal.AssetClassStock).all()
for entity in links:
# log(DEBUG, f"adding {entity.symbol} to {entity.assetclassid}")
# mapping
stock: Stock = Stock(entity.symbol)
# find parent classes by id and assign children
parent: AssetClass = self.model.get_class_by_id(entity.assetclassid)
if parent:
# Assign to parent.
parent.stocks.append(stock)
# Add to index for easy reference
self.model.stocks.append(stock) | [
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def freeze(wait, force_kill):
'''Freeze manager.'''
if wait and force_kill:
print('You cannot use both --wait and --force-kill options '
'at the same time.', file=sys.stderr)
return
with Session() as session:
if wait:
while True:
resp = session.Manager.status()
active_sessions_num = resp['active_sessions']
if active_sessions_num == 0:
break
print_wait('Waiting for all sessions terminated... ({0} left)'
.format(active_sessions_num))
time.sleep(3)
print_done('All sessions are terminated.')
if force_kill:
print_wait('Killing all sessions...')
session.Manager.freeze(force_kill=force_kill)
if force_kill:
print_done('All sessions are killed.')
print('Manager is successfully frozen.') | [
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def read_tx_body(ptr, tx):
"""
Returns {'ins': [...], 'outs': [...]}
"""
_obj = {"ins": [], "outs": [], 'locktime': None}
# number of inputs
ins = read_var_int(ptr, tx)
# all inputs
for i in range(ins):
_obj["ins"].append({
"outpoint": {
"hash": read_bytes(ptr, tx, 32)[::-1],
"index": read_as_int(ptr, tx, 4)
},
"script": read_var_string(ptr, tx),
"sequence": read_as_int(ptr, tx, 4)
})
# number of outputs
outs = read_var_int(ptr, tx)
# all outputs
for i in range(outs):
_obj["outs"].append({
"value": read_as_int(ptr, tx, 8),
"script": read_var_string(ptr, tx)
})
return _obj | [
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def _try_b32_decode(v):
"""
Attempt to decode a b32-encoded username which is sometimes generated by
internal Globus components.
The expectation is that the string is a valid ID, username, or b32-encoded
name. Therefore, we can do some simple checking on it.
If it does not appear to be formatted correctly, return None.
"""
# should start with "u_"
if not v.startswith("u_"):
return None
# usernames have @ , we want to allow `[email protected]`
# b32 names never have @
if "@" in v:
return None
# trim "u_"
v = v[2:]
# wrong length
if len(v) != 26:
return None
# append padding and uppercase so that b32decode will work
v = v.upper() + (6 * "=")
# try to decode
try:
return str(uuid.UUID(bytes=base64.b32decode(v)))
# if it fails, I guess it's a username? Not much left to do
except ValueError:
return None | [
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def get_config_tuple_from_egrc(egrc_path):
"""
Create a Config named tuple from the values specified in the .egrc. Expands
any paths as necessary.
egrc_path must exist and point a file.
If not present in the .egrc, properties of the Config are returned as None.
"""
with open(egrc_path, 'r') as egrc:
try:
config = ConfigParser.RawConfigParser()
except AttributeError:
config = ConfigParser()
config.readfp(egrc)
# default to None
examples_dir = None
custom_dir = None
use_color = None
pager_cmd = None
squeeze = None
subs = None
editor_cmd = None
if config.has_option(DEFAULT_SECTION, EG_EXAMPLES_DIR):
examples_dir = config.get(DEFAULT_SECTION, EG_EXAMPLES_DIR)
examples_dir = get_expanded_path(examples_dir)
if config.has_option(DEFAULT_SECTION, CUSTOM_EXAMPLES_DIR):
custom_dir = config.get(DEFAULT_SECTION, CUSTOM_EXAMPLES_DIR)
custom_dir = get_expanded_path(custom_dir)
if config.has_option(DEFAULT_SECTION, USE_COLOR):
use_color_raw = config.get(DEFAULT_SECTION, USE_COLOR)
use_color = _parse_bool_from_raw_egrc_value(use_color_raw)
if config.has_option(DEFAULT_SECTION, PAGER_CMD):
pager_cmd_raw = config.get(DEFAULT_SECTION, PAGER_CMD)
pager_cmd = ast.literal_eval(pager_cmd_raw)
if config.has_option(DEFAULT_SECTION, EDITOR_CMD):
editor_cmd_raw = config.get(DEFAULT_SECTION, EDITOR_CMD)
editor_cmd = ast.literal_eval(editor_cmd_raw)
color_config = get_custom_color_config_from_egrc(config)
if config.has_option(DEFAULT_SECTION, SQUEEZE):
squeeze_raw = config.get(DEFAULT_SECTION, SQUEEZE)
squeeze = _parse_bool_from_raw_egrc_value(squeeze_raw)
if config.has_section(SUBSTITUTION_SECTION):
subs = get_substitutions_from_config(config)
return Config(
examples_dir=examples_dir,
custom_dir=custom_dir,
color_config=color_config,
use_color=use_color,
pager_cmd=pager_cmd,
editor_cmd=editor_cmd,
squeeze=squeeze,
subs=subs,
) | [
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def tag_autocomplete_js(format_string=None):
"""format_string should be ``app_label model counts``
renders 'tagging_ext/tag_autocomplete_js.html"""
if format_string:
context_list = format_string.split(' ')
context = {
'app_label':context_list[0],'model':context_list[1], 'counts':context_list[2]
}
else:
context = {}
return render_to_string('tagging_ext/tagging_autocomplete_js.html', context) | [
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def compute_integrated_acquisition_withGradients(acquisition,x):
'''
Used to compute the acquisition function with gradients when samples of the hyper-parameters have been generated (used in GP_MCMC model).
:param acquisition: acquisition function with GpyOpt model type GP_MCMC.
:param x: location where the acquisition is evaluated.
'''
acqu_x = 0
d_acqu_x = 0
for i in range(acquisition.model.num_hmc_samples):
acquisition.model.model.kern[:] = acquisition.model.hmc_samples[i,:]
acqu_x_sample, d_acqu_x_sample = acquisition.acquisition_function_withGradients(x)
acqu_x += acqu_x_sample
d_acqu_x += d_acqu_x_sample
acqu_x = acqu_x/acquisition.model.num_hmc_samples
d_acqu_x = d_acqu_x/acquisition.model.num_hmc_samples
return acqu_x, d_acqu_x | [
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def _render_item(self, depth, key, value = None, **settings):
"""
Format single list item.
"""
strptrn = self.INDENT * depth
lchar = self.lchar(settings[self.SETTING_LIST_STYLE])
s = self._es_text(settings, settings[self.SETTING_LIST_FORMATING])
lchar = self.fmt_text(lchar, **s)
strptrn = "{}"
if value is not None:
strptrn += ": {}"
s = self._es_text(settings, settings[self.SETTING_TEXT_FORMATING])
strptrn = self.fmt_text(strptrn.format(key, value), **s)
return '{} {} {}'.format(self.INDENT * depth, lchar, strptrn) | [
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def _expand_formula_(formula_string):
"""
Accounts for the many ways a user may write a formula string, and returns an expanded chemical formula string.
Assumptions:
-The Chemical Formula string it is supplied is well-written, and has no hanging parethneses
-The number of repeats occurs after the elemental symbol or ) ] character EXCEPT in the case of a hydrate where it is assumed to be in front of the first element
-All hydrates explicitly use the · symbol
-Only (, (,[, ], ., · are "important" symbols to intrepreting the string.
-IONS ARE NOT HANDLED
:param formula_string: a messy chemical formula string
:return: a non-emperical but expanded formula string
"""
formula_string = re.sub(r'[^A-Za-z0-9\(\)\[\]\·\.]+', '', formula_string)
hydrate_pos = formula_string.find('·')
if hydrate_pos >= 0:
formula_string = _expand_hydrate_(hydrate_pos, formula_string)
search_result = re.search(
r'(?:[\(\[]([A-Za-z0-9]+)[\)\]](\d*))',
formula_string)
if search_result is None:
return formula_string
this_start = search_result.start()
this_end = search_result.end()
this_string = search_result.group()
this_expansion_array = re.findall(
r'(?:[\(\[]([A-Za-z0-9]+)[\)\]](\d*))', this_string)
for a in this_expansion_array:
if a[1] == "":
a = (a[0], 1)
parenth_expanded = ""
multiplier = float(a[1])
element_array = re.findall('[A-Z][^A-Z]*', a[0])
for e in element_array:
occurance_array = re.findall('[0-9][^0-9]*', e)
if len(occurance_array) == 0:
occurance_array.append(1)
for o in occurance_array:
symbol = re.findall('[A-Z][a-z]*', e)
total_num = float(o) * multiplier
if total_num.is_integer():
total_num = int(total_num)
total_str = str(total_num)
if total_str == "1":
total_str = ""
new_string = symbol[0] + total_str
parenth_expanded += new_string
formula_string = formula_string[0:this_start] + \
parenth_expanded + formula_string[this_end:]
return _expand_formula_(formula_string) | [
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def run_location(self, value):
"""The run_location property.
Args:
value (string). the property value.
"""
if value == self._defaults['runLocation'] and 'runLocation' in self._values:
del self._values['runLocation']
else:
self._values['runLocation'] = value | [
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def compute_file_hashes(file_path, hashes=frozenset(['md5'])):
"""
Digests data read from file denoted by file_path.
"""
if not os.path.exists(file_path):
logging.warning("%s does not exist" % file_path)
return
else:
logging.debug("Computing [%s] hashes for file [%s]" % (','.join(hashes), file_path))
try:
with open(file_path, 'rb') as fd:
return compute_hashes(fd, hashes)
except (IOError, OSError) as e:
logging.warning("Error while calculating digest(s) for file %s: %s" % (file_path, str(e)))
raise | [
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def refresh_products(self, **kwargs):
"""
Refresh a product's cached info. Basically calls product_get
with the passed arguments, and tries to intelligently update
our product cache.
For example, if we already have cached info for product=foo,
and you pass in names=["bar", "baz"], the new cache will have
info for products foo, bar, baz. Individual product fields are
also updated.
"""
for product in self.product_get(**kwargs):
updated = False
for current in self._cache.products[:]:
if (current.get("id", -1) != product.get("id", -2) and
current.get("name", -1) != product.get("name", -2)):
continue
_nested_update(current, product)
updated = True
break
if not updated:
self._cache.products.append(product) | [
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def set_result(self, job_id, result):
"""Set the result for a job.
This will overwrite any existing results for the job.
Args:
job_id: The ID of the WorkItem to set the result for.
result: A WorkResult indicating the result of the job.
Raises:
KeyError: If there is no work-item with a matching job-id.
"""
with self._conn:
try:
self._conn.execute(
'''
REPLACE INTO results
VALUES (?, ?, ?, ?, ?)
''', _work_result_to_row(job_id, result))
except sqlite3.IntegrityError as exc:
raise KeyError('Can not add result with job-id {}'.format(
job_id)) from exc | [
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def ethnicities_clean():
""" Get dictionary of unformatted ethnicity types mapped to clean corresponding ethnicity strings """
eths_clean = {}
fname = pkg_resources.resource_filename(__name__, 'resources/Ethnicity_Groups.csv')
with open(fname, 'rU') as csvfile:
reader = csv.reader(csvfile, delimiter = ',')
first = []
for row in reader:
if first:
for i in range(len(first)):
if first[i] and row[i]:
eths_clean[first[i]] = row[i]
first = []
else:
first = deepcopy(row)
return eths_clean | [
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def generate_table_from(data):
"Output a nicely formatted ascii table"
table = Texttable(max_width=120)
table.add_row(["view", "method", "status", "count", "minimum", "maximum", "mean", "stdev", "queries", "querytime"])
table.set_cols_align(["l", "l", "l", "r", "r", "r", "r", "r", "r", "r"])
for item in sorted(data):
mean = round(sum(data[item]['times'])/data[item]['count'], 3)
mean_sql = round(sum(data[item]['sql'])/data[item]['count'], 3)
mean_sqltime = round(sum(data[item]['sqltime'])/data[item]['count'], 3)
sdsq = sum([(i - mean) ** 2 for i in data[item]['times']])
try:
stdev = '%.2f' % ((sdsq / (len(data[item]['times']) - 1)) ** .5)
except ZeroDivisionError:
stdev = '0.00'
minimum = "%.2f" % min(data[item]['times'])
maximum = "%.2f" % max(data[item]['times'])
table.add_row([data[item]['view'], data[item]['method'], data[item]['status'], data[item]['count'], minimum, maximum, '%.3f' % mean, stdev, mean_sql, mean_sqltime])
return table.draw() | [
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"]",
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".",
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"(",
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] | 46.565217 | 31.173913 |
def appliance_time_and_locale_configuration(self):
"""
Gets the ApplianceTimeAndLocaleConfiguration API client.
Returns:
ApplianceTimeAndLocaleConfiguration:
"""
if not self.__appliance_time_and_locale_configuration:
self.__appliance_time_and_locale_configuration = ApplianceTimeAndLocaleConfiguration(self.__connection)
return self.__appliance_time_and_locale_configuration | [
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] | 43.8 | 22.4 |
def tagReportCallback(llrpMsg):
"""Function to run each time the reader reports seeing tags."""
global tagReport
tags = llrpMsg.msgdict['RO_ACCESS_REPORT']['TagReportData']
if len(tags):
logger.info('saw tag(s): %s', pprint.pformat(tags))
else:
logger.info('no tags seen')
return
for tag in tags:
tagReport += tag['TagSeenCount'][0]
if "OpSpecResult" in tag:
# copy the binary data to the standard output stream
data = tag["OpSpecResult"].get("ReadData")
if data:
if sys.version_info.major < 3:
sys.stdout.write(data)
else:
sys.stdout.buffer.write(data) # bytes
logger.debug("hex data: %s", binascii.hexlify(data)) | [
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def _get_deltas(self, rake):
"""
Return the value of deltas (delta_R, delta_S, delta_V, delta_I),
as defined in "Table 5: Model 1" pag 198
"""
# delta_R = 1 for reverse focal mechanism (45<rake<135)
# and for interface events, 0 for all other events
# delta_S = 1 for Strike-slip focal mechanisms (0<=rake<=45) or
# (135<=rake<=180) or (-45<=rake<=0), 0 for all other events
# delta_V = 1 for TVZ events, 0 for all other events
# delta_I = 1 for interface events, 0 for all other events
# All deltas = 0 for Model 3: Deep Region, pag 198
delta_R, delta_S = 0, 0
delta_V, delta_I = 0, 0
if rake > 45.0 and rake < 135.0:
delta_R = 1
if (rake >= 0.0 and rake <= 45.0) or \
(rake >= 135 and rake <= 180.0) or \
(rake >= -180.0 and rake <= -135.0) or \
(rake >= -45.0 and rake < 0.0):
delta_S = 1
return delta_R, delta_S, delta_V, delta_I | [
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def minimize_matrix(self):
"""
This method finds and returns the permutations that produce the lowest
ewald sum calls recursive function to iterate through permutations
"""
if self._algo == EwaldMinimizer.ALGO_FAST or \
self._algo == EwaldMinimizer.ALGO_BEST_FIRST:
return self._recurse(self._matrix, self._m_list,
set(range(len(self._matrix)))) | [
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def save_as_plt(self, fname, pixel_array=None, vmin=None, vmax=None,
cmap=None, format=None, origin=None):
""" This method saves the image from a numpy array using matplotlib
:param fname: Location and name of the image file to be saved.
:param pixel_array: Numpy pixel array, i.e. ``numpy()`` return value
:param vmin: matplotlib vmin
:param vmax: matplotlib vmax
:param cmap: matplotlib color map
:param format: matplotlib format
:param origin: matplotlib origin
This method will return True if successful
"""
from matplotlib.backends.backend_agg \
import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
from pylab import cm
if pixel_array is None:
pixel_array = self.numpy
if cmap is None:
cmap = cm.bone
fig = Figure(figsize=pixel_array.shape[::-1], dpi=1, frameon=False)
canvas = FigureCanvas(fig)
fig.figimage(pixel_array, cmap=cmap, vmin=vmin,
vmax=vmax, origin=origin)
fig.savefig(fname, dpi=1, format=format)
return True | [
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def process_full_position(data, header, var_only=False):
"""
Return genetic data when all alleles called on same line.
Returns an array containing one item, a tuple of five items:
(string) chromosome
(string) start position (1-based)
(array of strings) matching dbSNP entries
(string) reference allele sequence
(array of strings) the genome's allele sequences
"""
feature_type = data[header['varType']]
# Skip unmatchable, uncovered, or pseudoautosomal-in-X
if (feature_type == 'no-ref' or feature_type.startswith('PAR-called-in-X')):
return None
if var_only and feature_type in ['no-call', 'ref']:
return None
filters = []
if feature_type == 'no-call':
filters.append('NOCALL')
if 'varQuality' in header:
if 'VQLOW' in data[header['varQuality']]:
filters.append('VQLOW')
else:
var_filter = data[header['varFilter']]
if var_filter and not var_filter == "PASS":
filters = filters + var_filter.split(';')
chrom = data[header['chromosome']]
start = data[header['begin']]
ref_allele = data[header['reference']]
alleles = [data[header['alleleSeq']]]
dbsnp_data = []
dbsnp_data = data[header['xRef']].split(';')
assert data[header['ploidy']] in ['1', '2']
if feature_type == 'ref' or feature_type == 'no-call':
return [{'chrom': chrom,
'start': start,
'dbsnp_data': dbsnp_data,
'ref_seq': ref_allele,
'alleles': alleles,
'allele_count': data[header['ploidy']],
'filters': filters,
'end': data[header['end']]}]
else:
return [{'chrom': chrom,
'start': start,
'dbsnp_data': dbsnp_data,
'ref_seq': ref_allele,
'alleles': alleles,
'allele_count': data[header['ploidy']],
'filters': filters}] | [
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",",
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":",
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":",
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",",
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":",
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":",
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"[",
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"[",
"'ploidy'",
"]",
"]",
",",
"'filters'",
":",
"filters",
"}",
"]"
] | 37.056604 | 12.264151 |
def diff_aff(self):
"""Symmetric diffusion affinity matrix
Return or calculate the symmetric diffusion affinity matrix
.. math:: A(x,y) = K(x,y) (d(x) d(y))^{-1/2}
where :math:`d` is the degrees (row sums of the kernel.)
Returns
-------
diff_aff : array-like, shape=[n_samples, n_samples]
symmetric diffusion affinity matrix defined as a
doubly-stochastic form of the kernel matrix
"""
row_degrees = np.array(self.kernel.sum(axis=1)).reshape(-1, 1)
col_degrees = np.array(self.kernel.sum(axis=0)).reshape(1, -1)
if sparse.issparse(self.kernel):
return self.kernel.multiply(1 / np.sqrt(row_degrees)).multiply(
1 / np.sqrt(col_degrees))
else:
return (self.kernel / np.sqrt(row_degrees)) / np.sqrt(col_degrees) | [
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] | 36.956522 | 23.869565 |
def seed_url(self):
"""A URL that can be used to open the page.
The URL is formatted from :py:attr:`URL_TEMPLATE`, which is then
appended to :py:attr:`base_url` unless the template results in an
absolute URL.
:return: URL that can be used to open the page.
:rtype: str
"""
url = self.base_url
if self.URL_TEMPLATE is not None:
url = urlparse.urljoin(
self.base_url, self.URL_TEMPLATE.format(**self.url_kwargs)
)
if not url:
return None
url_parts = list(urlparse.urlparse(url))
query = urlparse.parse_qsl(url_parts[4])
for k, v in self.url_kwargs.items():
if v is None:
continue
if "{{{}}}".format(k) not in str(self.URL_TEMPLATE):
for i in iterable(v):
query.append((k, i))
url_parts[4] = urlencode(query)
return urlparse.urlunparse(url_parts) | [
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def main(*argv):
""" main driver of program """
try:
adminUsername = argv[0]
adminPassword = argv[1]
siteURL = argv[2]
username = argv[3]
groupName = argv[4]
# Logic
#
# Connect to AGOL
#
sh = arcrest.AGOLTokenSecurityHandler(adminUsername, adminPassword)
admin = arcrest.manageorg.Administration(securityHandler=sh)
# Get the group ID
#
community = admin.community
groupId = community.getGroupIDs(groupNames=[groupName])[0]
# Add the User to the Group
#
groups = community.groups
res = groups.group(groupId=groupId).addUsersToGroups(users=username)
if len(res['notAdded'] ) == 0:
arcpy.SetParameterAsText(5, True)
else:
arcpy.SetParameterAsText(5, False)
except arcpy.ExecuteError:
line, filename, synerror = trace()
arcpy.AddError("error on line: %s" % line)
arcpy.AddError("error in file name: %s" % filename)
arcpy.AddError("with error message: %s" % synerror)
arcpy.AddError("ArcPy Error Message: %s" % arcpy.GetMessages(2))
except FunctionError, f_e:
messages = f_e.args[0]
arcpy.AddError("error in function: %s" % messages["function"])
arcpy.AddError("error on line: %s" % messages["line"])
arcpy.AddError("error in file name: %s" % messages["filename"])
arcpy.AddError("with error message: %s" % messages["synerror"])
arcpy.AddError("ArcPy Error Message: %s" % messages["arc"])
except:
line, filename, synerror = trace()
arcpy.AddError("error on line: %s" % line)
arcpy.AddError("error in file name: %s" % filename)
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def rows(self):
"""
Return/yield tuples or lists corresponding to each row to be inserted.
"""
with self.input().open('r') as fobj:
for line in fobj:
yield line.strip('\n').split('\t') | [
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def move_up(self):
"""Move up one level in the hierarchy, unless already on top."""
if self.current_item.parent is not None:
self.current_item = self.current_item.parent
for f in self._hooks["up"]:
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def get_time_index_range(self,
date_search_start=None,
date_search_end=None,
time_index_start=None,
time_index_end=None,
time_index=None):
"""
Generates a time index range based on time bounds given.
This is useful for subset data extraction.
Parameters
----------
date_search_start: :obj:`datetime.datetime`, optional
This is a datetime object with the date of the minimum date for
starting.
date_search_end: :obj:`datetime.datetime`, optional
This is a datetime object with the date of the maximum date
for ending.
time_index_start: int, optional
This is the index of the start of the time array subset.
Useful for the old file version.
time_index_end: int, optional
This is the index of the end of the time array subset.
Useful for the old file version.
time_index: int, optional
This is the index of time to return in the case that your
code only wants one index. Used internally.
Returns
-------
:obj:`numpy.array`:
This is an array of time indices used to extract a subset of data.
CF-Compliant Qout File Example:
.. code:: python
from datetime import datetime
from RAPIDpy import RAPIDDataset
path_to_rapid_qout = '/path/to/Qout.nc'
with RAPIDDataset(path_to_rapid_qout) as qout_nc:
time_index_range = qout_nc.get_time_index_range(
date_search_start=datetime(1980, 1, 1),
date_search_end=datetime(1980, 12, 11))
Legacy Qout File Example:
.. code:: python
from datetime import datetime
from RAPIDpy import RAPIDDataset
path_to_rapid_qout = '/path/to/Qout.nc'
with RAPIDDataset(path_to_rapid_qout,
datetime_simulation_start=datetime(1980, 1, 1),
simulation_time_step_seconds=3600) as qout_nc:
time_index_range = qout_nc.get_time_index_range(
date_search_start=datetime(1980, 1, 1),
date_search_end=datetime(1980, 12, 11))
"""
# get the range of time based on datetime range
time_range = None
if ((self.is_time_variable_valid() or self._is_legacy_time_valid()) and
(date_search_start is not None or
date_search_end is not None)):
log("Determining time range ({0} to {1})"
"...".format(date_search_start, date_search_end),
"INFO")
time_array = self.get_time_array()
if date_search_start is not None:
date_search_start_utc = date_search_start
if self.out_tzinfo is not None:
date_search_start_utc = self.out_tzinfo \
.localize(date_search_start) \
.astimezone(utc) \
.replace(tzinfo=None)
seconds_start = (date_search_start_utc -
datetime.datetime(1970, 1, 1)).total_seconds()
time_range = np.where(time_array >= seconds_start)[0]
if date_search_end is not None:
date_search_end_utc = date_search_end
if self.out_tzinfo is not None:
date_search_end_utc = self.out_tzinfo \
.localize(date_search_end) \
.astimezone(utc) \
.replace(tzinfo=None)
seconds_end = (date_search_end_utc -
datetime.datetime(1970, 1, 1)).total_seconds()
if time_range is not None:
time_range = np.intersect1d(time_range,
np.where(time_array <=
seconds_end)[0])
else:
time_range = np.where(time_array <= seconds_end)[0]
# get the range of time based on time index range
elif time_index_start is not None or time_index_end is not None:
if time_index_start is None:
time_index_start = 0
if time_index_end is None:
time_index_end = self.size_time
time_range = range(time_index_start, time_index_end)
# get only one time step
elif time_index is not None:
time_range = [time_index]
# return all
else:
time_range = range(self.size_time)
return time_range | [
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def deploy_app(self, site_folder, runtime_type=''):
''' a method to deploy a static html page to heroku using php '''
title = '%s.deploy_php' % self.__class__.__name__
# validate inputs
input_fields = {
'site_folder': site_folder,
'runtime_type': runtime_type
}
for key, value in input_fields.items():
if value:
object_title = '%s(%s=%s)' % (title, key, str(value))
self.fields.validate(value, '.%s' % key, object_title)
# verify app subdomain
if not self.subdomain:
raise Exception('You must access a subdomain before you can deploy to heroku. Try: %s.access()' % self.__class__.__name__)
# validate existence of site folder
from os import path
if not path.exists(site_folder):
raise ValueError('%s is not a valid path on localhost.' % site_folder)
# validate existence of proper runtime file
runtime_file = 'index.html'
static_build = False
if runtime_type == 'php':
runtime_file = 'index.php'
elif runtime_type in ('ruby', 'java', 'python', 'jingo'):
runtime_file = 'Procfile'
elif runtime_type == 'node':
runtime_file = 'package.json'
else:
runtime_type = 'html'
static_build = True
build_file = path.join(site_folder, runtime_file)
if not path.exists(build_file):
raise Exception('%s must contain an %s file to build a %s app.' % (site_folder, runtime_file, runtime_type))
if runtime_type == 'python':
req_file = path.join(site_folder, 'requirements.txt')
if not path.exists(req_file):
raise Exception('%s must contain a requirements.txt file to build a python app.' % site_folder)
if runtime_type == 'jingo':
req_file = path.join(site_folder, 'package.json')
if not path.exists(req_file):
raise Exception('%s must contain a package.json file to build a jingo app.' % site_folder)
# validate container plugin
from os import devnull
from subprocess import check_output
self.printer('Checking heroku plugin requirements ... ', flush=True)
sys_command = 'heroku plugins'
heroku_plugins = check_output(sys_command, shell=True, stderr=open(devnull, 'wb')).decode('utf-8')
if heroku_plugins.find('heroku-builds') == -1:
self.printer('ERROR')
raise Exception(
'heroku builds plugin required. Try: heroku plugins:install heroku-builds')
self.printer('done.')
# construct temporary folder
self.printer('Creating temporary files ... ', flush=True)
from shutil import copytree, move, ignore_patterns
from os import makedirs
from time import time
from labpack import __module__
from labpack.storage.appdata import appdataClient
client_kwargs = {
'collection_name': 'TempFiles',
'prod_name': __module__
}
tempfiles_client = appdataClient(**client_kwargs)
temp_folder = path.join(tempfiles_client.collection_folder, 'heroku%s' % time())
# define cleanup function
def _cleanup_temp():
self.printer('Cleaning up temporary files ... ', flush=True)
from shutil import rmtree
rmtree(temp_folder, ignore_errors=True)
self.printer('done.')
# copy site to temporary folder
try:
makedirs(temp_folder)
site_root, site_name = path.split(path.abspath(site_folder))
build_path = path.join(temp_folder, site_name)
copytree(site_folder, build_path, ignore=ignore_patterns('*node_modules/*','*.lab/*'))
if static_build:
index_path = path.join(build_path, 'index.html')
home_path = path.join(build_path, 'home.html')
compose_path = path.join(build_path, 'compose.json')
php_path = path.join(build_path, 'index.php')
with open(compose_path, 'wt') as f:
f.write('{}')
f.close()
with open(php_path, 'wt') as f:
f.write('<?php include_once("home.html"); ?>')
f.close()
move(index_path, home_path)
except:
self.printer('ERROR')
_cleanup_temp()
raise
self.printer('done.')
# deploy site to heroku
self.printer('Deploying %s to heroku ... ' % site_folder, flush=True)
try:
sys_command = 'cd %s; heroku builds:create -a %s' % (temp_folder, self.subdomain)
self._handle_command(sys_command, print_pipe=True)
except:
self.printer('ERROR')
raise
finally:
_cleanup_temp()
self.printer('Deployment complete.')
return True | [
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def resample(self, indexer: Optional[Mapping[Hashable, str]] = None,
skipna=None, closed: Optional[str] = None,
label: Optional[str] = None,
base: int = 0, keep_attrs: Optional[bool] = None,
loffset=None,
**indexer_kwargs: str):
"""Returns a Resample object for performing resampling operations.
Handles both downsampling and upsampling. If any intervals contain no
values from the original object, they will be given the value ``NaN``.
Parameters
----------
indexer : {dim: freq}, optional
Mapping from the dimension name to resample frequency.
skipna : bool, optional
Whether to skip missing values when aggregating in downsampling.
closed : 'left' or 'right', optional
Side of each interval to treat as closed.
label : 'left or 'right', optional
Side of each interval to use for labeling.
base : int, optional
For frequencies that evenly subdivide 1 day, the "origin" of the
aggregated intervals. For example, for '24H' frequency, base could
range from 0 through 23.
loffset : timedelta or str, optional
Offset used to adjust the resampled time labels. Some pandas date
offset strings are supported.
keep_attrs : bool, optional
If True, the object's attributes (`attrs`) will be copied from
the original object to the new one. If False (default), the new
object will be returned without attributes.
**indexer_kwargs : {dim: freq}
The keyword arguments form of ``indexer``.
One of indexer or indexer_kwargs must be provided.
Returns
-------
resampled : same type as caller
This object resampled.
Examples
--------
Downsample monthly time-series data to seasonal data:
>>> da = xr.DataArray(np.linspace(0, 11, num=12),
... coords=[pd.date_range('15/12/1999',
... periods=12, freq=pd.DateOffset(months=1))],
... dims='time')
>>> da
<xarray.DataArray (time: 12)>
array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11.])
Coordinates:
* time (time) datetime64[ns] 1999-12-15 2000-01-15 2000-02-15 ...
>>> da.resample(time="QS-DEC").mean()
<xarray.DataArray (time: 4)>
array([ 1., 4., 7., 10.])
Coordinates:
* time (time) datetime64[ns] 1999-12-01 2000-03-01 2000-06-01 2000-09-01
Upsample monthly time-series data to daily data:
>>> da.resample(time='1D').interpolate('linear')
<xarray.DataArray (time: 337)>
array([ 0. , 0.032258, 0.064516, ..., 10.935484, 10.967742, 11. ])
Coordinates:
* time (time) datetime64[ns] 1999-12-15 1999-12-16 1999-12-17 ...
Limit scope of upsampling method
>>> da.resample(time='1D').nearest(tolerance='1D')
<xarray.DataArray (time: 337)>
array([ 0., 0., nan, ..., nan, 11., 11.])
Coordinates:
* time (time) datetime64[ns] 1999-12-15 1999-12-16 ... 2000-11-15
References
----------
.. [1] http://pandas.pydata.org/pandas-docs/stable/timeseries.html#offset-aliases
""" # noqa
# TODO support non-string indexer after removing the old API.
from .dataarray import DataArray
from .resample import RESAMPLE_DIM
from ..coding.cftimeindex import CFTimeIndex
if keep_attrs is None:
keep_attrs = _get_keep_attrs(default=False)
# note: the second argument (now 'skipna') use to be 'dim'
if ((skipna is not None and not isinstance(skipna, bool))
or ('how' in indexer_kwargs and 'how' not in self.dims)
or ('dim' in indexer_kwargs and 'dim' not in self.dims)):
raise TypeError(
'resample() no longer supports the `how` or '
'`dim` arguments. Instead call methods on resample '
"objects, e.g., data.resample(time='1D').mean()")
indexer = either_dict_or_kwargs(indexer, indexer_kwargs, 'resample')
if len(indexer) != 1:
raise ValueError(
"Resampling only supported along single dimensions."
)
dim, freq = next(iter(indexer.items()))
dim_name = dim
dim_coord = self[dim]
if isinstance(self.indexes[dim_name], CFTimeIndex):
from .resample_cftime import CFTimeGrouper
grouper = CFTimeGrouper(freq, closed, label, base, loffset)
else:
# TODO: to_offset() call required for pandas==0.19.2
grouper = pd.Grouper(freq=freq, closed=closed, label=label,
base=base,
loffset=pd.tseries.frequencies.to_offset(
loffset))
group = DataArray(dim_coord, coords=dim_coord.coords,
dims=dim_coord.dims, name=RESAMPLE_DIM)
resampler = self._resample_cls(self, group=group, dim=dim_name,
grouper=grouper,
resample_dim=RESAMPLE_DIM)
return resampler | [
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def stop_button_click_handler(self):
"""Method to handle what to do when the stop button is pressed"""
self.stop_button.setDisabled(True)
# Interrupt computations or stop debugging
if not self.shellwidget._reading:
self.interrupt_kernel()
else:
self.shellwidget.write_to_stdin('exit') | [
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def follow(self, login):
"""Make the authenticated user follow login.
:param str login: (required), user to follow
:returns: bool
"""
resp = False
if login:
url = self._build_url('user', 'following', login)
resp = self._boolean(self._put(url), 204, 404)
return resp | [
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def create_metric_definition(self, metric_type, metric_id, **tags):
"""
Create metric definition with custom definition. **tags should be a set of tags, such as
units, env ..
:param metric_type: MetricType of the new definition
:param metric_id: metric_id is the string index of the created metric
:param tags: Key/Value tag values of the new metric
"""
item = { 'id': metric_id }
if len(tags) > 0:
# We have some arguments to pass..
data_retention = tags.pop('dataRetention', None)
if data_retention is not None:
item['dataRetention'] = data_retention
if len(tags) > 0:
item['tags'] = tags
json_data = json.dumps(item, indent=2)
try:
self._post(self._get_url(metric_type), json_data)
except HawkularError as e:
if e.code == 409:
return False
raise e
return True | [
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def set(self, key: Any, value: Any) -> None:
""" Sets the value of a key to a supplied value """
if key is not None:
self[key] = value | [
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async def send_heartbeat(self, name):
"""Send a heartbeat for a service.
Args:
name (string): The name of the service to send a heartbeat for
"""
await self.send_command(OPERATIONS.CMD_HEARTBEAT, {'name': name},
MESSAGES.HeartbeatResponse, timeout=5.0) | [
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def _brahmic(data, scheme_map, **kw):
"""Transliterate `data` with the given `scheme_map`. This function is used
when the source scheme is a Brahmic scheme.
:param data: the data to transliterate
:param scheme_map: a dict that maps between characters in the old scheme
and characters in the new scheme
"""
if scheme_map.from_scheme.name == northern.GURMUKHI:
data = northern.GurmukhiScheme.replace_tippi(text=data)
marks = scheme_map.marks
virama = scheme_map.virama
consonants = scheme_map.consonants
non_marks_viraama = scheme_map.non_marks_viraama
to_roman = scheme_map.to_scheme.is_roman
max_key_length_from_scheme = scheme_map.max_key_length_from_scheme
buf = []
i = 0
to_roman_had_consonant = found = False
append = buf.append
# logging.debug(pprint.pformat(scheme_map.consonants))
# We dont just translate each brAhmic character one after another in order to prefer concise transliterations when possible - for example ज्ञ -> jn in optitrans rather than j~n.
while i <= len(data):
# The longest token in the source scheme has length `max_key_length_from_scheme`. Iterate
# over `data` while taking `max_key_length_from_scheme` characters at a time. If we don`t
# find the character group in our scheme map, lop off a character and
# try again.
#
# If we've finished reading through `data`, then `token` will be empty
# and the loop below will be skipped.
token = data[i:i + max_key_length_from_scheme]
while token:
if len(token) == 1:
if token in marks:
append(marks[token])
found = True
elif token in virama:
append(virama[token])
found = True
else:
if to_roman_had_consonant:
append('a')
append(non_marks_viraama.get(token, token))
found = True
else:
if token in non_marks_viraama:
if to_roman_had_consonant:
append('a')
append(non_marks_viraama.get(token))
found = True
if found:
to_roman_had_consonant = to_roman and token in consonants
i += len(token)
break
else:
token = token[:-1]
# Continuing the outer while loop.
# We've exhausted the token; this must be some other character. Due to
# the implicit 'a', we must explicitly end any lingering consonants
# before we can handle the current token.
if not found:
if to_roman_had_consonant:
append(next(iter(virama.values())))
if i < len(data):
append(data[i])
to_roman_had_consonant = False
i += 1
found = False
if to_roman_had_consonant:
append('a')
return ''.join(buf) | [
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] | 34.064103 | 20.871795 |
def p_CommentOrEmptyLineList(p):
'''
CommentOrEmptyLineList :
| CommentOrEmptyLine
| CommentOrEmptyLineList CommentOrEmptyLine
'''
if len(p) <= 1:
p[0] = CommentOrEmptyLineList(None, None)
elif len(p) <= 2:
p[0] = CommentOrEmptyLineList(None, p[1])
else:
p[0] = CommentOrEmptyLineList(p[1], p[2]) | [
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def _compute_projection(self, X, W):
"""Compute the LPP projection matrix
Parameters
----------
X : array_like, (n_samples, n_features)
The input data
W : array_like or sparse matrix, (n_samples, n_samples)
The precomputed adjacency matrix
Returns
-------
P : ndarray, (n_features, self.n_components)
The matrix encoding the locality preserving projection
"""
# TODO: check W input; handle sparse case
X = check_array(X)
D = np.diag(W.sum(1))
L = D - W
evals, evecs = eigh_robust(np.dot(X.T, np.dot(L, X)),
np.dot(X.T, np.dot(D, X)),
eigvals=(0, self.n_components - 1))
return evecs | [
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def start_event_loop_qt4(app=None):
"""Start the qt4 event loop in a consistent manner."""
if app is None:
app = get_app_qt4([''])
if not is_event_loop_running_qt4(app):
app._in_event_loop = True
app.exec_()
app._in_event_loop = False
else:
app._in_event_loop = True | [
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def focusOutEvent( self, event ):
"""
Overloads the focus out event to cancel editing when the widget loses
focus.
:param event | <QFocusEvent>
"""
super(XNavigationEdit, self).focusOutEvent(event)
self.cancelEdit() | [
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def updateCurrentValue(self, value):
"""
Disables snapping during the current value update to ensure a smooth
transition for node animations. Since this can only be called via
code, we don't need to worry about snapping to the grid for a user.
"""
xsnap = None
ysnap = None
if value != self.endValue():
xsnap = self.targetObject().isXSnappedToGrid()
ysnap = self.targetObject().isYSnappedToGrid()
self.targetObject().setXSnapToGrid(False)
self.targetObject().setYSnapToGrid(False)
super(XNodeAnimation, self).updateCurrentValue(value)
if value != self.endValue():
self.targetObject().setXSnapToGrid(xsnap)
self.targetObject().setYSnapToGrid(ysnap) | [
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def get_votes_comment(self, *args, **kwargs):
""" :allowed_param: 'commentId'
"""
return bind_api(
api=self,
path='/comments/{commentId}/votes',
payload_type='vote',
payload_list=True,
allowed_param=['commentId']
)(*args, **kwargs) | [
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def pec(self, value):
"""True if Packet Error Codes (PEC) are enabled"""
pec = bool(value)
if pec != self._pec:
if ioctl(self._fd, SMBUS.I2C_PEC, pec):
raise IOError(ffi.errno)
self._pec = pec | [
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def other_set_producer(socket, which_set, image_archive, patch_archive,
groundtruth):
"""Push image files read from the valid/test set TAR to a socket.
Parameters
----------
socket : :class:`zmq.Socket`
PUSH socket on which to send images.
which_set : str
Which set of images is being processed. One of 'train', 'valid',
'test'. Used for extracting the appropriate images from the patch
archive.
image_archive : str or file-like object
The filename or file-handle for the TAR archive containing images.
patch_archive : str or file-like object
Filename or file handle for the TAR archive of patch images.
groundtruth : iterable
Iterable container containing scalar 0-based class index for each
image, sorted by filename.
"""
patch_images = extract_patch_images(patch_archive, which_set)
num_patched = 0
with tar_open(image_archive) as tar:
filenames = sorted(info.name for info in tar if info.isfile())
images = (load_from_tar_or_patch(tar, filename, patch_images)
for filename in filenames)
pathless_filenames = (os.path.split(fn)[-1] for fn in filenames)
image_iterator = equizip(images, pathless_filenames, groundtruth)
for (image_data, patched), filename, class_index in image_iterator:
if patched:
num_patched += 1
socket.send_pyobj((filename, class_index), zmq.SNDMORE)
socket.send(image_data, copy=False)
if num_patched != len(patch_images):
raise Exception | [
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def fill_key_info(self, key_info, signature_method):
"""
Fills the KeyInfo node
:param key_info: KeyInfo node
:type key_info: lxml.etree.Element
:param signature_method: Signature node to use
:type signature_method: str
:return: None
"""
x509_data = key_info.find('ds:X509Data', namespaces=constants.NS_MAP)
if x509_data is not None:
self.fill_x509_data(x509_data)
key_name = key_info.find('ds:KeyName', namespaces=constants.NS_MAP)
if key_name is not None and self.key_name is not None:
key_name.text = self.key_name
key_value = key_info.find('ds:KeyValue', namespaces=constants.NS_MAP)
if key_value is not None:
key_value.text = '\n'
signature = constants.TransformUsageSignatureMethod[
signature_method
]
key = self.public_key
if self.public_key is None:
key = self.private_key.public_key()
if not isinstance(
key, signature['method'].public_key_class
):
raise Exception('Key not compatible with signature method')
signature['method'].key_value(key_value, key) | [
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def kill(self, unique_id, configs=None):
""" Issues a kill -9 to the specified process
calls the deployers get_pid function for the process. If no pid_file/pid_keyword is specified
a generic grep of ps aux command is executed on remote machine based on process parameters
which may not be reliable if more process are running with similar name
:Parameter unique_id: the name of the process
"""
self._send_signal(unique_id, signal.SIGKILL, configs) | [
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def fit(self, values, bins):
"""
Fit the transform using the given values (in our case ic50s).
Parameters
----------
values : ic50 values
bins : bins for the cumulative distribution function
Anything that can be passed to numpy.histogram's "bins" argument
can be used here.
"""
assert self.cdf is None
assert self.bin_edges is None
assert len(values) > 0
(hist, self.bin_edges) = numpy.histogram(values, bins=bins)
self.cdf = numpy.ones(len(hist) + 3) * numpy.nan
self.cdf[0] = 0.0
self.cdf[1] = 0.0
self.cdf[-1] = 100.0
numpy.cumsum(hist * 100.0 / numpy.sum(hist), out=self.cdf[2:-1])
assert not numpy.isnan(self.cdf).any() | [
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def to_glyphs_background_image(self, ufo_glyph, layer):
"""Copy the background image from the UFO Glyph to the GSLayer."""
ufo_image = ufo_glyph.image
if ufo_image.fileName is None:
return
image = self.glyphs_module.GSBackgroundImage()
image.path = ufo_image.fileName
image.transform = Transform(*ufo_image.transformation)
if CROP_KEY in ufo_glyph.lib:
x, y, w, h = ufo_glyph.lib[CROP_KEY]
image.crop = Rect(Point(x, y), Size(w, h))
if LOCKED_KEY in ufo_glyph.lib:
image.locked = ufo_glyph.lib[LOCKED_KEY]
if ALPHA_KEY in ufo_glyph.lib:
image.alpha = ufo_glyph.lib[ALPHA_KEY]
layer.backgroundImage = image | [
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def items(self, folder_id, subfolder_id, ann_id=None):
'''Yields an unodered generator of items in a subfolder.
The generator yields items, which are represented by a tuple
of ``content_id`` and ``subtopic_id``. The format of these
identifiers is unspecified.
By default (with ``ann_id=None``), subfolders are shown for all
anonymous users. Optionally, ``ann_id`` can be set to a username,
which restricts the list to only subfolders owned by that user.
:param str folder_id: Folder id
:param str subfolder_id: Subfolder id
:param str ann_id: Username
:rtype: generator of ``(content_id, subtopic_id)``
'''
self.assert_valid_folder_id(folder_id)
self.assert_valid_folder_id(subfolder_id)
ann_id = self._annotator(ann_id)
folder_cid = self.wrap_folder_content_id(ann_id, folder_id)
subfolder_sid = self.wrap_subfolder_subtopic_id(subfolder_id)
ident = (folder_cid, subfolder_sid)
if self.store.get(folder_cid) is None:
raise KeyError(folder_id)
for lab in self.label_store.directly_connected(ident):
cid = lab.other(folder_cid)
subid = lab.subtopic_for(cid)
yield (cid, subid) | [
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def from_json(json):
"""Creates a Track from a JSON file.
No preprocessing is done.
Arguments:
json: map with the keys: name (optional) and segments.
Return:
A track instance
"""
segments = [Segment.from_json(s) for s in json['segments']]
return Track(json['name'], segments).compute_metrics() | [
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def phrase_replace(self, replace_dict):
"""
Replace phrases with single token, mapping defined in replace_dict
"""
def r(tokens):
text = ' ' + ' '.join(tokens)
for k, v in replace_dict.items():
text = text.replace(" " + k + " ", " " + v + " ")
return text.split()
self.stems = list(map(r, self.stems)) | [
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def unexpanduser(path):
r"""
Replaces home directory with '~'
"""
homedir = expanduser('~')
if path.startswith(homedir):
path = '~' + path[len(homedir):]
return path | [
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def load_segment(self, f, is_irom_segment=False):
""" Load the next segment from the image file """
file_offs = f.tell()
(offset, size) = struct.unpack('<II', f.read(8))
self.warn_if_unusual_segment(offset, size, is_irom_segment)
segment_data = f.read(size)
if len(segment_data) < size:
raise FatalError('End of file reading segment 0x%x, length %d (actual length %d)' % (offset, size, len(segment_data)))
segment = ImageSegment(offset, segment_data, file_offs)
self.segments.append(segment)
return segment | [
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def load_values(self):
"""
Go through the env var map, transferring the values to this object
as attributes.
:raises: RuntimeError if a required env var isn't defined.
"""
for config_name, evar in self.evar_defs.items():
if evar.is_required and evar.name not in os.environ:
raise RuntimeError((
"Missing required environment variable: {evar_name}\n"
"{help_txt}"
).format(evar_name=evar.name, help_txt=evar.help_txt))
# Env var is present. Transfer its value over.
if evar.name in os.environ:
self[config_name] = os.environ.get(evar.name)
else:
self[config_name] = evar.default_val
# Perform any validations or transformations.
for filter in evar.filters:
current_val = self.get(config_name)
new_val = filter(current_val, evar)
self[config_name] = new_val
# This is the top-level filter that is often useful for checking
# the values of related env vars (instead of individual validation).
self._filter_all() | [
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def _dispense_during_transfer(self, vol, loc, **kwargs):
"""
Performs a :any:`dispense` when running a :any:`transfer`, and
optionally a :any:`mix`, :any:`touch_tip`, and/or
:any:`blow_out` afterwards.
"""
mix_after = kwargs.get('mix_after', (0, 0))
rate = kwargs.get('rate', 1)
air_gap = kwargs.get('air_gap', 0)
well, _ = unpack_location(loc)
if air_gap:
self.dispense(air_gap, well.top(5), rate=rate)
self.dispense(vol, loc, rate=rate)
self._mix_during_transfer(mix_after, well, **kwargs) | [
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def cred_def_id(self, issuer_did: str, schema_seq_no: int) -> str:
"""
Return credential definition identifier for input issuer DID and schema sequence number.
:param issuer_did: DID of credential definition issuer
:param schema_seq_no: schema sequence number
:return: credential definition identifier
"""
return '{}:3:CL:{}{}'.format( # 3 marks indy cred def id, CL is sig type
issuer_did,
schema_seq_no,
self.cd_id_tag(True)) | [
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def apply_attribute(node: Node, attr: XmlAttr):
"""Maps xml attribute to instance node property and setups bindings"""
setter = get_setter(attr)
stripped_value = attr.value.strip() if attr.value else ''
if is_expression(stripped_value):
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binder().apply(binding_type, node=node, attr=attr, modifier=setter, expr_body=expr_body)
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setter(node, attr.name, attr.value) | [
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def check_auth(user):
'''
Check if the user should or shouldn't be inside the system:
- If the user is staff or superuser: LOGIN GRANTED
- If the user has a Person and it is not "disabled": LOGIN GRANTED
- Elsewhere: LOGIN DENIED
'''
# Initialize authentication
auth = None
person = None
# Check if there is an user
if user:
# It means that Django accepted the user and it is active
if user.is_staff or user.is_superuser:
# This is an administrator, let it in
auth = user
else:
# It is a normal user, check if there is a person behind
person = getattr(user, "person", None)
if not person:
# Check if there is related one
person_related = getattr(user, "people", None)
if person_related:
# Must be only one
if person_related.count() == 1:
person = person_related.get()
if person and ((person.disabled is None) or (person.disabled > timezone.now())):
# There is a person, no disabled found or the found one is fine to log in
auth = user
# Return back the final decision
return auth | [
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def _create_array(self, arr: np.ndarray) -> int:
"""Returns the handle of a RawArray created from the given numpy array.
Args:
arr: A numpy ndarray.
Returns:
The handle (int) of the array.
Raises:
ValueError: if arr is not a ndarray or of an unsupported dtype. If
the array is of an unsupported type, using a view of the array to
another dtype and then converting on get is often a work around.
"""
if not isinstance(arr, np.ndarray):
raise ValueError('Array is not a numpy ndarray.')
try:
c_arr = np.ctypeslib.as_ctypes(arr)
except (KeyError, NotImplementedError):
raise ValueError(
'Array has unsupported dtype {}.'.format(arr.dtype))
# pylint: disable=protected-access
raw_arr = RawArray(c_arr._type_, c_arr)
with self._lock:
if self._count >= len(self._arrays):
self._arrays += len(self._arrays) * [None]
self._get_next_free()
# Note storing the shape is a workaround for an issue encountered
# when upgrading to numpy 1.15.
# See https://github.com/numpy/numpy/issues/11636
self._arrays[self._current] = (raw_arr, arr.shape)
self._count += 1
return self._current | [
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"_count",
"+=",
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"return",
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".",
"_current"
] | 34.358974 | 21.333333 |
def collapse_focussed(self):
"""
Collapse currently focussed position; works only if the underlying
tree allows it.
"""
if implementsCollapseAPI(self._tree):
w, focuspos = self.get_focus()
self._tree.collapse(focuspos)
self._walker.clear_cache()
self.refresh() | [
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] | 33.9 | 8.7 |
def _send_bootstrap_request(self, request):
"""Make a request using an ephemeral broker connection
This routine is used to make broker-unaware requests to get the initial
cluster metadata. It cycles through the configured hosts, trying to
connect and send the request to each in turn. This temporary connection
is closed once a response is received.
Note that most Kafka APIs require requests be sent to a specific
broker. This method will only function for broker-agnostic requests
like:
* `Metadata <https://kafka.apache.org/protocol.html#The_Messages_Metadata>`_
* `FindCoordinator <https://kafka.apache.org/protocol.html#The_Messages_FindCoordinator>`_
:param bytes request:
The bytes of a Kafka `RequestMessage`_ structure. It must have
a unique (to this connection) correlation ID.
:returns: API response message for *request*
:rtype: Deferred[bytes]
:raises:
- `KafkaUnavailableError` when making the request of all known hosts
has failed.
- `twisted.internet.defer.TimeoutError` when connecting or making
a request exceeds the timeout.
"""
hostports = list(self._bootstrap_hosts)
random.shuffle(hostports)
for host, port in hostports:
ep = self._endpoint_factory(self.reactor, host, port)
try:
protocol = yield ep.connect(_bootstrapFactory)
except Exception as e:
log.debug("%s: bootstrap connect to %s:%s -> %s", self, host, port, e)
continue
try:
response = yield protocol.request(request).addTimeout(self.timeout, self.reactor)
except Exception:
log.debug("%s: bootstrap request to %s:%s failed", self, host, port, exc_info=True)
else:
returnValue(response)
finally:
protocol.transport.loseConnection()
raise KafkaUnavailableError("Failed to bootstrap from hosts {}".format(hostports)) | [
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def filter(self, dict_name, priority_min='-inf', priority_max='+inf',
start=0, limit=None):
'''Get a subset of a dictionary.
This retrieves only keys with priority scores greater than or
equal to `priority_min` and less than or equal to `priority_max`.
Of those keys, it skips the first `start` ones, and then returns
at most `limit` keys.
With default parameters, this retrieves the entire dictionary,
making it a more expensive version of :meth:`pull`. This can
be used to limit the dictionary by priority score, for instance
using the score as a time stamp and only retrieving values
before or after a specific time; or it can be used to get
slices of the dictionary if there are too many items to use
:meth:`pull`.
This is a read-only operation and does not require a session
lock, but if this is run in a session context, the lock will
be honored.
:param str dict_name: name of the dictionary to retrieve
:param float priority_min: lowest score to retrieve
:param float priority_max: highest score to retrieve
:param int start: number of items to skip
:param int limit: number of items to retrieve
:return: corresponding (partial) Python dictionary
:raise rejester.LockError: if the session lock timed out
'''
conn = redis.Redis(connection_pool=self.pool)
script = conn.register_script('''
if (ARGV[1] == "") or (redis.call("get", KEYS[1]) == ARGV[1])
then
-- find all the keys and priorities within range
local next_keys = redis.call("zrangebyscore", KEYS[3],
ARGV[2], ARGV[3],
"limit", ARGV[4], ARGV[5])
if not next_keys[1] then
return {}
end
local t = {}
for i = 1, #next_keys do
local next_val = redis.call("hget", KEYS[2], next_keys[i])
table.insert(t, next_keys[i])
table.insert(t, next_val)
end
return t
else
-- ERROR: No longer own the lock
return -1
end
''')
if limit is None: limit = -1
res = script(keys=[self._lock_name,
self._namespace(dict_name),
self._namespace(dict_name) + 'keys'],
args=[self._session_lock_identifier or '',
priority_min, priority_max, start, limit])
if res == -1:
raise LockError()
split_res = dict([(self._decode(res[i]),
self._decode(res[i+1]))
for i in xrange(0, len(res)-1, 2)])
return split_res | [
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"split_res"
] | 41.5 | 21.558824 |
def clip(dataset, normal='x', origin=None, invert=True):
"""
Clip a dataset by a plane by specifying the origin and normal. If no
parameters are given the clip will occur in the center of that dataset
Parameters
----------
normal : tuple(float) or str
Length 3 tuple for the normal vector direction. Can also be
specified as a string conventional direction such as ``'x'`` for
``(1,0,0)`` or ``'-x'`` for ``(-1,0,0)``, etc.
origin : tuple(float)
The center ``(x,y,z)`` coordinate of the plane on which the clip
occurs
invert : bool
Flag on whether to flip/invert the clip
"""
if isinstance(normal, str):
normal = NORMALS[normal.lower()]
# find center of data if origin not specified
if origin is None:
origin = dataset.center
# create the plane for clipping
plane = _generate_plane(normal, origin)
# run the clip
alg = vtk.vtkClipDataSet()
alg.SetInputDataObject(dataset) # Use the grid as the data we desire to cut
alg.SetClipFunction(plane) # the the cutter to use the plane we made
alg.SetInsideOut(invert) # invert the clip if needed
alg.Update() # Perfrom the Cut
return _get_output(alg) | [
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] | 39.029412 | 19.558824 |
def has_space(self, length=1, offset=0):
"""Returns boolean if self.pos + length < working string length."""
return self.pos + (length + offset) - 1 < self.length | [
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def script_post_save(model, os_path, contents_manager, **kwargs):
"""convert notebooks to Python script after save with nbconvert
replaces `ipython notebook --script`
"""
from nbconvert.exporters.script import ScriptExporter
if model['type'] != 'notebook':
return
global _script_exporter
if _script_exporter is None:
_script_exporter = ScriptExporter(parent=contents_manager)
log = contents_manager.log
base, ext = os.path.splitext(os_path)
# py_fname = base + '.py'
script, resources = _script_exporter.from_filename(os_path)
script_fname = base + resources.get('output_extension', '.txt')
log.info("Saving script /%s", to_api_path(script_fname, contents_manager.root_dir))
with io.open(script_fname, 'w', encoding='utf-8') as f:
f.write(script) | [
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def decorate(func, caller, extras=()):
"""
decorate(func, caller) decorates a function using a caller.
"""
evaldict = dict(_call_=caller, _func_=func)
es = ''
for i, extra in enumerate(extras):
ex = '_e%d_' % i
evaldict[ex] = extra
es += ex + ', '
fun = FunctionMaker.create(
func, "return _call_(_func_, %s%%(shortsignature)s)" % es,
evaldict, __wrapped__=func)
if hasattr(func, '__qualname__'):
fun.__qualname__ = func.__qualname__
return fun | [
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def update_access_key(self, access_key_id, status, user_name=None):
"""
Changes the status of the specified access key from Active to Inactive
or vice versa. This action can be used to disable a user's key as
part of a key rotation workflow.
If the user_name is not specified, the user_name is determined
implicitly based on the AWS Access Key ID used to sign the request.
:type access_key_id: string
:param access_key_id: The ID of the access key.
:type status: string
:param status: Either Active or Inactive.
:type user_name: string
:param user_name: The username of user (optional).
"""
params = {'AccessKeyId' : access_key_id,
'Status' : status}
if user_name:
params['UserName'] = user_name
return self.get_response('UpdateAccessKey', params) | [
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def _fix_call_activities_signavio(self, bpmn, filename):
"""
Signavio produces slightly invalid BPMN for call activity nodes... It
is supposed to put a reference to the id of the called process in to
the calledElement attribute. Instead it stores a string (which is the
name of the process - not its ID, in our interpretation) in an
extension tag.
This code gets the name of the 'subprocess reference', finds a process
with a matching name, and sets the calledElement attribute to the id of
the process.
"""
for node in xpath_eval(bpmn)(".//bpmn:callActivity"):
calledElement = node.get('calledElement', None)
if not calledElement:
signavioMetaData = xpath_eval(node, extra_ns={
'signavio': SIGNAVIO_NS})(
'.//signavio:signavioMetaData[@metaKey="entry"]')
if not signavioMetaData:
raise ValidationException(
'No Signavio "Subprocess reference" specified.',
node=node, filename=filename)
subprocess_reference = one(signavioMetaData).get('metaValue')
matches = []
for b in list(self.bpmn.values()):
for p in xpath_eval(b)(".//bpmn:process"):
if (p.get('name', p.get('id', None)) ==
subprocess_reference):
matches.append(p)
if not matches:
raise ValidationException(
"No matching process definition found for '%s'." %
subprocess_reference, node=node, filename=filename)
if len(matches) != 1:
raise ValidationException(
"More than one matching process definition "
" found for '%s'." % subprocess_reference, node=node,
filename=filename)
node.set('calledElement', matches[0].get('id')) | [
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"(",
"'id'",
")",
")"
] | 51.4 | 20.3 |
def _calc_hash_da(self, rs):
"""Compute hash of D and A timestamps for single-step D+A case.
"""
self.hash_d = hash_(rs.get_state())[:6]
self.hash_a = self.hash_d | [
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def host_domains(self, ip=None, limit=None, **kwargs):
"""Pass in an IP address."""
return self._results('reverse-ip', '/v1/{0}/host-domains'.format(ip), limit=limit, **kwargs) | [
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def print_cm(cm, labels, hide_zeroes=False, hide_diagonal=False, hide_threshold=None):
"""pretty print for confusion matrixes"""
columnwidth = max([len(x) for x in labels] + [5]) # 5 is value length
empty_cell = " " * columnwidth
# Print header
print(" " + empty_cell, end=" ")
for label in labels:
print("%{0}s".format(columnwidth) % label, end=" ")
print()
# Print rows
for i, label1 in enumerate(labels):
print(" %{0}s".format(columnwidth) % label1, end=" ")
for j in range(len(labels)):
cell = "%{0}.1f".format(columnwidth) % cm[i, j]
if hide_zeroes:
cell = cell if float(cm[i, j]) != 0 else empty_cell
if hide_diagonal:
cell = cell if i != j else empty_cell
if hide_threshold:
cell = cell if cm[i, j] > hide_threshold else empty_cell
print(cell, end=" ")
print() | [
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"(",
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] | 42.227273 | 17.454545 |
def segmentlistdict(self):
"""
A segmentlistdict object describing the instruments and
time spanned by this CacheEntry. A new object is
constructed each time this attribute is accessed (segments
are immutable so there is no reason to try to share a
reference to the CacheEntry's internal segment;
modifications of one would not be reflected in the other
anyway).
Example:
>>> c = CacheEntry(u"H1 S5 815901601 576.5 file://localhost/home/kipp/tmp/1/H1-815901601-576.xml")
>>> c.segmentlistdict
{u'H1': [segment(LIGOTimeGPS(815901601, 0), LIGOTimeGPS(815902177, 500000000))]}
The \"observatory\" column of the cache entry, which is
frequently used to store instrument names, is parsed into
instrument names for the dictionary keys using the same
rules as pycbc_glue.ligolw.lsctables.instrument_set_from_ifos().
Example:
>>> c = CacheEntry(u"H1H2, S5 815901601 576.5 file://localhost/home/kipp/tmp/1/H1H2-815901601-576.xml")
>>> c.segmentlistdict
{u'H1H2': [segment(LIGOTimeGPS(815901601, 0), LIGOTimeGPS(815902177, 500000000))]}
"""
# the import has to be done here to break the cyclic
# dependancy
from pycbc_glue.ligolw.lsctables import instrument_set_from_ifos
instruments = instrument_set_from_ifos(self.observatory) or (None,)
return segments.segmentlistdict((instrument, segments.segmentlist(self.segment is not None and [self.segment] or [])) for instrument in instruments) | [
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] | 43.90625 | 28.84375 |
def file_url(self, entity_id, filename, channel=None):
'''Generate a URL for a file in an archive without requesting it.
@param entity_id The ID of the entity to look up.
@param filename The name of the file in the archive.
@param channel Optional channel name.
'''
url = '{}/{}/archive/{}'.format(self.url, _get_path(entity_id),
filename)
return _add_channel(url, channel) | [
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"(",
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",",
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] | 46.1 | 19.9 |
def transform_value(self, value):
"""Convert the value to be stored.
This does nothing by default but subclasses can change this.
Then the index will be able to filter on the transformed value.
For example if the transform capitalizes some text, the filter
would be ``myfield__capitalized__eq='FOO'``
"""
if not self.transform:
return value
try:
# we store a staticmethod but we accept a method taking `self` and `value`
return self.transform(self, value)
except TypeError as e:
if 'argument' in str(e): # try to limit only to arguments error
return self.transform(value) | [
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] | 38.555556 | 21.277778 |
async def get_match(self, m_id, force_update=False) -> Match:
""" get a single match by id
|methcoro|
Args:
m_id: match id
force_update (default=False): True to force an update to the Challonge API
Returns:
Match
Raises:
APIException
"""
found_m = self._find_match(m_id)
if force_update or found_m is None:
await self.get_matches()
found_m = self._find_match(m_id)
return found_m | [
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] | 24.190476 | 21.285714 |
def smeft_evolve_leadinglog(C_in, scale_in, scale_out, newphys=True):
"""Solve the SMEFT RGEs in the leading log approximation.
Input C_in and output C_out are dictionaries of arrays."""
C_out = deepcopy(C_in)
b = beta.beta(C_out, newphys=newphys)
for k, C in C_out.items():
C_out[k] = C + b[k] / (16 * pi**2) * log(scale_out / scale_in)
return C_out | [
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] | 41.666667 | 16.444444 |
def _findrange(parlist,roots=['JUMP','DMXR1_','DMXR2_','DMX_','efac','log10_efac']):
"""Rewrite a list of parameters name by detecting ranges (e.g., JUMP1, JUMP2, ...)
and compressing them."""
rootdict = {root: [] for root in roots}
res = []
for par in parlist:
found = False
for root in roots:
if len(par) > len(root) and par[:len(root)] == root:
rootdict[root].append(int(par[len(root):]))
found = True
if not found:
res.append(par)
for root in roots:
if rootdict[root]:
if len(rootdict[root]) > 1:
rmin, rmax = min(rootdict[root]), max(rootdict[root])
res.append('{0}{{{1}-{2}}}{3}'.format(root,rmin,rmax,
'(incomplete)' if rmax - rmin != len(rootdict[root]) - 1 else ''))
else:
res.append('{0}{1}'.format(root,rootdict[root][0]))
return res | [
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"]",
")",
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def com_google_fonts_check_metadata_valid_filename_values(font,
family_metadata):
"""METADATA.pb font.filename field contains font name in right format?"""
expected = os.path.basename(font)
failed = True
for font_metadata in family_metadata.fonts:
if font_metadata.filename == expected:
failed = False
yield PASS, ("METADATA.pb filename field contains"
" font name in right format.")
break
if failed:
yield FAIL, ("None of the METADATA.pb filename fields match"
f" correct font name format (\"{expected}\").") | [
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def _init_map(self):
"""stub"""
super(edXAssetContentFormRecord, self)._init_map()
AssetContentTextFormRecord._init_map(self)
FilesFormRecord._init_map(self)
ProvenanceFormRecord._init_map(self) | [
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def single_request_timeout(self, value):
"""The timeout (seconds) for a single HTTP REST API request."""
check_type(value, int)
assert value is None or value > 0
self._single_request_timeout = value | [
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def logical_name(self):
"""The logical name of the seat.
This is an identifier to group sets of devices within the compositor.
Returns:
str: The logical name of this seat.
"""
pchar = self._libinput.libinput_seat_get_logical_name(self._handle)
return string_at(pchar).decode() | [
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def _data(self, asa=None):
"""
Returns the contents of the node: a dataframe or a file path, or passes
the node and its contents to a callable.
"""
if asa is not None:
if self._store is None or self._hashes is None:
msg = (
"Can only use asa functions with built dataframes."
" Build this package and try again."
)
raise ValueError(msg)
return asa(self, [self._store.object_path(obj) for obj in self._hashes])
else:
if self.__cached_data is None:
# TODO(dima): Temporary code.
if self._target() == TargetType.PANDAS:
self.__cached_data = self._store.load_dataframe(self._hashes)
elif self._target() == TargetType.NUMPY:
self.__cached_data = self._store.load_numpy(self._hashes)
else:
self.__cached_data = self._store.get_file(self._hashes)
return self.__cached_data | [
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] | 45.695652 | 18.565217 |
def _compute_grover_oracle_matrix(bitstring_map: Dict[str, int]) -> np.ndarray:
"""
Computes the unitary matrix that encodes the oracle function for Grover's algorithm
:param bitstring_map: dict with string keys corresponding to bitstrings,
and integer values corresponding to the desired phase on the output state.
:return: a numpy array corresponding to the unitary matrix for oracle for the given
bitstring_map
"""
n_bits = len(list(bitstring_map.keys())[0])
oracle_matrix = np.zeros(shape=(2 ** n_bits, 2 ** n_bits))
for b in range(2 ** n_bits):
pad_str = np.binary_repr(b, n_bits)
phase_factor = bitstring_map[pad_str]
oracle_matrix[b, b] = phase_factor
return oracle_matrix | [
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def _build_body_schema(serializer, body_parameters):
""" body is built differently, since it's a single argument no matter what. """
description = ""
if isinstance(body_parameters, Param):
schema = serializer.to_json_schema(body_parameters.arginfo.type)
description = body_parameters.description
required = True
else:
if len(body_parameters) == 0:
return None
required = set()
body_properties = {}
for name, param in body_parameters.items():
arginfo = param.arginfo
body_properties[name] = serializer.to_json_schema(arginfo.type)
body_properties[name]["description"] = param.description
if arginfo.default is NoDefault:
required.add(name)
schema = {
"type": "object",
"required": list(required),
"properties": body_properties,
}
required = len(required) > 0
return BodyParameter(
{
"name": "body",
"description": description,
"required": required,
"schema": schema,
}
) | [
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def phase_diff(self, phase):
'''Compute the phase differential along a given axis
Parameters
----------
phase : np.ndarray
Input phase (in radians)
Returns
-------
dphase : np.ndarray like `phase`
The phase differential.
'''
if self.conv is None:
axis = 0
elif self.conv in ('channels_last', 'tf'):
axis = 0
elif self.conv in ('channels_first', 'th'):
axis = 1
# Compute the phase differential
dphase = np.empty(phase.shape, dtype=phase.dtype)
zero_idx = [slice(None)] * phase.ndim
zero_idx[axis] = slice(1)
else_idx = [slice(None)] * phase.ndim
else_idx[axis] = slice(1, None)
zero_idx = tuple(zero_idx)
else_idx = tuple(else_idx)
dphase[zero_idx] = phase[zero_idx]
dphase[else_idx] = np.diff(np.unwrap(phase, axis=axis), axis=axis)
return dphase | [
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def insort_event_right(self, event, lo=0, hi=None):
"""Insert event in queue, and keep it sorted assuming queue is sorted.
If event is already in queue, insert it to the right of the rightmost
event (to keep FIFO order).
Optional args lo (default 0) and hi (default len(a)) bound the
slice of a to be searched.
Args:
event: a (time in sec since unix epoch, callback, args, kwds) tuple.
"""
if lo < 0:
raise ValueError('lo must be non-negative')
if hi is None:
hi = len(self.queue)
while lo < hi:
mid = (lo + hi) // 2
if event[0] < self.queue[mid][0]:
hi = mid
else:
lo = mid + 1
self.queue.insert(lo, event) | [
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def wait(self, *args, **kwargs):
"""Wait for the completion event to be set."""
if _debug: IOCB._debug("wait(%d) %r %r", self.ioID, args, kwargs)
# waiting from a non-daemon thread could be trouble
return self.ioComplete.wait(*args, **kwargs) | [
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def top_path(sources, sinks, net_flux):
"""
Use the Dijkstra algorithm for finding the shortest path
connecting a set of source states from a set of sink states.
Parameters
----------
sources : array_like, int
One-dimensional list of nodes to define the source states.
sinks : array_like, int
One-dimensional list of nodes to define the sink states.
net_flux : np.ndarray, shape = [n_states, n_states]
Net flux of the MSM
Returns
-------
top_path : np.ndarray
Array corresponding to the top path between sources and
sinks. It is an array of states visited along the path.
flux : float
Flux traveling through this path -- this is equal to the
minimum flux over edges in the path.
See Also
--------
msmbuilder.tpt.paths : function for calculating many high
flux paths through a network.
References
----------
.. [1] Weinan, E. and Vanden-Eijnden, E. Towards a theory of
transition paths. J. Stat. Phys. 123, 503-523 (2006).
.. [2] Metzner, P., Schutte, C. & Vanden-Eijnden, E.
Transition path theory for Markov jump processes.
Multiscale Model. Simul. 7, 1192-1219 (2009).
.. [3] Berezhkovskii, A., Hummer, G. & Szabo, A. Reactive
flux and folding pathways in network models of
coarse-grained protein dynamics. J. Chem. Phys.
130, 205102 (2009).
.. [4] Dijkstra, E. W. A Note on Two Problems in Connexion with Graphs.
Numeriche Mathematik 1, 269-271 (1959).
.. [5] Noe, Frank, et al. "Constructing the equilibrium ensemble of folding
pathways from short off-equilibrium simulations." PNAS 106.45 (2009):
19011-19016.
"""
sources = np.array(sources, dtype=np.int).reshape((-1,))
sinks = np.array(sinks, dtype=np.int).reshape((-1,))
n_states = net_flux.shape[0]
queue = list(sources)
# nodes to check (the "queue")
# going to use list.pop method so I can't keep it as an array
visited = np.zeros(n_states).astype(np.bool)
# have we already checked this node?
previous_node = np.ones(n_states).astype(np.int) * -1
# what node was found before finding this one
min_fluxes = np.ones(n_states) * -1 * np.inf
# what is the flux of the highest flux path
# from this node to the source set.
min_fluxes[sources] = np.inf
# source states are connected to the source
# so this distance is zero which means the flux is infinite
while len(queue) > 0: # iterate until there's nothing to check anymore
test_node = queue.pop(min_fluxes[queue].argmax())
# find the node in the queue that has the
# highest flux path to it from the source set
visited[test_node] = True
if np.all(visited[sinks]):
# if we've visited all of the sink states, then we just have to choose
# the path that goes to the sink state that is closest to the source
break
# if test_node in sinks: # I *think* we want to break ... or are there paths we still
# need to check?
# continue
# I think if sinks is more than one state we have to check everything
# now update the distances for each neighbor of the test_node:
neighbors = np.where(net_flux[test_node, :] > 0)[0]
if len(neighbors) == 0:
continue
new_fluxes = net_flux[test_node, neighbors].flatten()
# flux from test_node to each neighbor
new_fluxes[np.where(new_fluxes > min_fluxes[test_node])] = min_fluxes[test_node]
# previous step to get to test_node was lower flux, so that is still the path flux
ind = np.where((1 - visited[neighbors]) & (new_fluxes > min_fluxes[neighbors]))
min_fluxes[neighbors[ind]] = new_fluxes[ind]
previous_node[neighbors[ind]] = test_node
# each of these neighbors came from this test_node
# we don't want to update the nodes that have already been visited
queue.extend(neighbors[ind])
top_path = []
# populate the path in reverse
top_path.append(int(sinks[min_fluxes[sinks].argmax()]))
# find the closest sink state
while previous_node[top_path[-1]] != -1:
top_path.append(previous_node[top_path[-1]])
return np.array(top_path[::-1]), min_fluxes[top_path[0]] | [
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def peak_interval(data, alpha=_alpha, npoints=_npoints):
"""
Identify interval using Gaussian kernel density estimator.
"""
peak = kde_peak(data,npoints)
x = np.sort(data.flat); n = len(x)
# The number of entries in the interval
window = int(np.rint((1.0-alpha)*n))
# The start, stop, and width of all possible intervals
starts = x[:n-window]; ends = x[window:]
widths = ends - starts
# Just the intervals containing the peak
select = (peak >= starts) & (peak <= ends)
widths = widths[select]
if len(widths) == 0:
raise ValueError('Too few elements for interval calculation')
min_idx = np.argmin(widths)
lo = x[min_idx]
hi = x[min_idx+window]
return interval(peak,lo,hi) | [
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def deflections_from_grid(self, grid, **kwargs):
"""
Calculate the deflection angles at a given set of arc-second gridded coordinates.
Parameters
----------
grid : grids.RegularGrid
The grid of (y,x) arc-second coordinates the deflection angles are computed on.
"""
eta = np.multiply(1. / self.scale_radius, self.grid_to_grid_radii(grid))
deflection_grid = np.multiply((4. * self.kappa_s * self.scale_radius / eta), self.deflection_func_sph(eta))
return self.grid_to_grid_cartesian(grid, deflection_grid) | [
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def _replaces(self):
"""tge"""
return {concat(a, c, b[1:])
for a, b in self.slices[:-1]
for c in ALPHABET} | [
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def is_encodable(self, typ: TypeStr, arg: Any) -> bool:
"""
Determines if the python value ``arg`` is encodable as a value of the
ABI type ``typ``.
:param typ: A string representation for the ABI type against which the
python value ``arg`` will be checked e.g. ``'uint256'``,
``'bytes[]'``, ``'(int,int)'``, etc.
:param arg: The python value whose encodability should be checked.
:returns: ``True`` if ``arg`` is encodable as a value of the ABI type
``typ``. Otherwise, ``False``.
"""
encoder = self._registry.get_encoder(typ)
try:
encoder.validate_value(arg)
except EncodingError:
return False
except AttributeError:
try:
encoder(arg)
except EncodingError:
return False
return True | [
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def map_psmnrcol_to_quantcol(quantcols, psmcols, tablefn_map):
"""This function yields tuples of table filename, isobaric quant column
and if necessary number-of-PSM column"""
if not psmcols:
for fn in quantcols:
for qcol in quantcols[fn]:
yield (tablefn_map[fn], qcol)
else:
for fn in quantcols:
for qcol, psmcol in zip(quantcols[fn], psmcols[fn]):
yield (tablefn_map[fn], qcol, psmcol) | [
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def serialize_to_bundle(self, transformer, path, model_name, serialize_node=True):
"""
:type transformer: sklearn.tree.tree.BaseDecisionTree
:type path: str
:type model_name: str
:type serialize_node: bool
:param transformer:
:param path:
:param model_name:
:return:
"""
# Define attributes
attributes = list()
attributes.append(('num_features', transformer.n_features_))
if isinstance(transformer, DecisionTreeClassifier):
attributes.append(('num_classes', int(transformer.n_classes_)))
inputs = []
outputs = []
if serialize_node:
# define node inputs and outputs
inputs = [{
"name": transformer.input_features,
"port": "features"
}]
outputs = [{
"name": transformer.prediction_column,
"port": "prediction"
}]
self.serialize(transformer, path, model_name, attributes, inputs, outputs, node=serialize_node)
# Serialize tree.json
tree_path = "{}/{}.node/tree.json".format(path, model_name)
if not serialize_node:
tree_path = "{}/{}/tree.json".format(path, model_name)
with open(tree_path, 'w') as outfile:
self.serialize_tree(transformer, transformer.feature_names, outfile) | [
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def center_plot(self, ax):
"""
Centers and keep the aspect ratio in a 3D representation.
Created to help higher classes to manage cascade representation
of multiple lower objects.
:param ax: Axes to apply the method.
:type ax: mplot3d.Axes3D
:returns: None
"""
# Domain
domain = self.get_domain()
bound = np.max(domain[1]-domain[0])
centroid = self.get_centroid()
pos = np.vstack((centroid-bound/2, centroid+bound/2))
# Axis limits
ax.set_xlim3d(left=pos[0,0], right=pos[1,0])
ax.set_ylim3d(bottom=pos[0,1], top=pos[1,1])
ax.set_zlim3d(bottom=pos[0,2], top=pos[1,2]) | [
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def sys_mmap_pgoff(self, address, size, prot, flags, fd, offset):
"""Wrapper for mmap2"""
return self.sys_mmap2(address, size, prot, flags, fd, offset) | [
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def setParamValue(self, row, **kwargs):
"""Sets the arguments as field=val for parameter
indexed by *row*
:param row: the ith parameter number
:type row: int
"""
param = self._parameters[row]
for key, val in kwargs.items():
param[key] = val | [
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Size of downloaded dataset files:
398 MB
Size of the auto-converted Parquet files:
398 MB
Number of rows:
457,461
Models trained or fine-tuned on kejian/codesearchnet-python-linelen40-full