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adafruit/Adafruit_Python_GPIO | Adafruit_GPIO/FT232H.py | https://github.com/adafruit/Adafruit_Python_GPIO/blob/a92a23d6b5869663b2bc1ccf78bb11585076a9c4/Adafruit_GPIO/FT232H.py#L364-L370 | def output(self, pin, value):
"""Set the specified pin the provided high/low value. Value should be
either HIGH/LOW or a boolean (true = high)."""
if pin < 0 or pin > 15:
raise ValueError('Pin must be between 0 and 15 (inclusive).')
self._output_pin(pin, value)
self.mpsse_write_gpio() | [
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sorgerlab/indra | indra/util/statement_presentation.py | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/util/statement_presentation.py#L40-L109 | def group_and_sort_statements(stmt_list, ev_totals=None):
"""Group statements by type and arguments, and sort by prevalence.
Parameters
----------
stmt_list : list[Statement]
A list of INDRA statements.
ev_totals : dict{int: int}
A dictionary, keyed by statement hash (shallow) with counts of total
evidence as the values. Including this will allow statements to be
better sorted.
Returns
-------
sorted_groups : list[tuple]
A list of tuples containing a sort key, the statement type, and a list
of statements, also sorted by evidence count, for that key and type.
The sort key contains a count of statements with those argument, the
arguments (normalized strings), the count of statements with those
arguements and type, and then the statement type.
"""
def _count(stmt):
if ev_totals is None:
return len(stmt.evidence)
else:
return ev_totals[stmt.get_hash()]
stmt_rows = defaultdict(list)
stmt_counts = defaultdict(lambda: 0)
arg_counts = defaultdict(lambda: 0)
for key, s in _get_keyed_stmts(stmt_list):
# Update the counts, and add key if needed.
stmt_rows[key].append(s)
# Keep track of the total evidence counts for this statement and the
# arguments.
stmt_counts[key] += _count(s)
# Add up the counts for the arguments, pairwise for Complexes and
# Conversions. This allows, for example, a complex between MEK, ERK,
# and something else to lend weight to the interactions between MEK
# and ERK.
if key[0] == 'Conversion':
subj = key[1]
for obj in key[2] + key[3]:
arg_counts[(subj, obj)] += _count(s)
else:
arg_counts[key[1:]] += _count(s)
# Sort the rows by count and agent names.
def process_rows(stmt_rows):
for key, stmts in stmt_rows.items():
verb = key[0]
inps = key[1:]
sub_count = stmt_counts[key]
arg_count = arg_counts[inps]
if verb == 'Complex' and sub_count == arg_count and len(inps) <= 2:
if all([len(set(ag.name for ag in s.agent_list())) > 2
for s in stmts]):
continue
new_key = (arg_count, inps, sub_count, verb)
stmts = sorted(stmts,
key=lambda s: _count(s) + 1/(1+len(s.agent_list())),
reverse=True)
yield new_key, verb, stmts
sorted_groups = sorted(process_rows(stmt_rows),
key=lambda tpl: tpl[0], reverse=True)
return sorted_groups | [
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ev_totals : dict{int: int}
A dictionary, keyed by statement hash (shallow) with counts of total
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dcaune/perseus-lib-python-common | majormode/perseus/model/geolocation.py | https://github.com/dcaune/perseus-lib-python-common/blob/ba48fe0fd9bb4a75b53e7d10c41ada36a72d4496/majormode/perseus/model/geolocation.py#L205-L234 | def great_circle_distance(self, other):
"""
Return the great-circle distance, in meters, from this geographic
coordinates to the specified other point, i.e., the shortest distance
over the earth’s surface, ‘as-the-crow-flies’ distance between the
points, ignoring any natural elevations of the ground.
Haversine formula::
R = earth’s radius (mean radius = 6,371km)
Δlat = lat2 − lat1
Δlong = long2 − long1
a = sin²(Δlat / 2) + cos(lat1).cos(lat2).sin²(Δlong/2)
c = 2.atan2(√a, √(1−a))
d = R.c
@param other: a ``GeoPoint`` instance.
@return: the great-circle distance, in meters, between this geographic
coordinates to the specified other point.
"""
distance_latitude = math.radians(abs(self.latitude - other.latitude))
distance_longitude = math.radians(abs(self.longitude - other.longitude))
a = math.sin(distance_latitude / 2) * math.sin(distance_latitude / 2) \
+ math.cos(math.radians(self.latitude)) \
* math.cos(math.radians(other.latitude)) \
* math.sin(distance_longitude / 2) \
* math.sin(distance_longitude / 2)
c = 2 * math.atan2(math.sqrt(a), math.sqrt(1 - a))
return GeoPoint.EARTH_RADIUS_METERS * c | [
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mlperf/training | translation/tensorflow/transformer/utils/metrics.py | https://github.com/mlperf/training/blob/1c6ae725a81d15437a2b2df05cac0673fde5c3a4/translation/tensorflow/transformer/utils/metrics.py#L112-L130 | def get_eval_metrics(logits, labels, params):
"""Return dictionary of model evaluation metrics."""
metrics = {
"accuracy": _convert_to_eval_metric(padded_accuracy)(logits, labels),
"accuracy_top5": _convert_to_eval_metric(padded_accuracy_top5)(
logits, labels),
"accuracy_per_sequence": _convert_to_eval_metric(
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"rouge_L_fscore": _convert_to_eval_metric(rouge_l_fscore)(logits, labels),
}
# Prefix each of the metric names with "metrics/". This allows the metric
# graphs to display under the "metrics" category in TensorBoard.
metrics = {"metrics/%s" % k: v for k, v in six.iteritems(metrics)}
return metrics | [
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cokelaer/spectrum | src/spectrum/window.py | https://github.com/cokelaer/spectrum/blob/bad6c32e3f10e185098748f67bb421b378b06afe/src/spectrum/window.py#L464-L506 | def enbw(data):
r"""Computes the equivalent noise bandwidth
.. math:: ENBW = N \frac{\sum_{n=1}^{N} w_n^2}{\left(\sum_{n=1}^{N} w_n \right)^2}
.. doctest::
>>> from spectrum import create_window, enbw
>>> w = create_window(64, 'rectangular')
>>> enbw(w)
1.0
The following table contains the ENBW values for some of the
implemented windows in this module (with N=16384). They have been
double checked against litterature (Source: [Harris]_, [Marple]_).
If not present, it means that it has not been checked.
=================== ============ =============
name ENBW litterature
=================== ============ =============
rectangular 1. 1.
triangle 1.3334 1.33
Hann 1.5001 1.5
Hamming 1.3629 1.36
blackman 1.7268 1.73
kaiser 1.7
blackmanharris,4 2.004 2.
riesz 1.2000 1.2
riemann 1.32 1.3
parzen 1.917 1.92
tukey 0.25 1.102 1.1
bohman 1.7858 1.79
poisson 2 1.3130 1.3
hanningpoisson 0.5 1.609 1.61
cauchy 1.489 1.48
lanczos 1.3
=================== ============ =============
"""
N = len(data)
return N * np.sum(data**2) / np.sum(data)**2 | [
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>>> from spectrum import create_window, enbw
>>> w = create_window(64, 'rectangular')
>>> enbw(w)
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lanczos 1.3
=================== ============ ============= | [
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janpipek/physt | physt/special.py | https://github.com/janpipek/physt/blob/6dd441b073514e7728235f50b2352d56aacf38d4/physt/special.py#L380-L412 | def spherical_histogram(data=None, radial_bins="numpy", theta_bins=16, phi_bins=16, transformed=False, *args, **kwargs):
"""Facade construction function for the SphericalHistogram.
"""
dropna = kwargs.pop("dropna", True)
data = _prepare_data(data, transformed=transformed, klass=SphericalHistogram, dropna=dropna)
if isinstance(theta_bins, int):
theta_range = (0, np.pi)
if "theta_range" in "kwargs":
theta_range = kwargs["theta_range"]
elif "range" in "kwargs":
theta_range = kwargs["range"][1]
theta_range = list(theta_range) + [theta_bins + 1]
theta_bins = np.linspace(*theta_range)
if isinstance(phi_bins, int):
phi_range = (0, 2 * np.pi)
if "phi_range" in "kwargs":
phi_range = kwargs["phi_range"]
elif "range" in "kwargs":
phi_range = kwargs["range"][2]
phi_range = list(phi_range) + [phi_bins + 1]
phi_bins = np.linspace(*phi_range)
bin_schemas = binnings.calculate_bins_nd(data, [radial_bins, theta_bins, phi_bins], *args,
check_nan=not dropna, **kwargs)
weights = kwargs.pop("weights", None)
frequencies, errors2, missed = histogram_nd.calculate_frequencies(data, ndim=3,
binnings=bin_schemas,
weights=weights)
return SphericalHistogram(binnings=bin_schemas, frequencies=frequencies, errors2=errors2, missed=missed) | [
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apache/incubator-mxnet | python/mxnet/contrib/onnx/onnx2mx/import_onnx.py | https://github.com/apache/incubator-mxnet/blob/1af29e9c060a4c7d60eeaacba32afdb9a7775ba7/python/mxnet/contrib/onnx/onnx2mx/import_onnx.py#L41-L74 | def _convert_operator(self, node_name, op_name, attrs, inputs):
"""Convert from onnx operator to mxnet operator.
The converter must specify conversions explicitly for incompatible name, and
apply handlers to operator attributes.
Parameters
----------
:param node_name : str
name of the node to be translated.
:param op_name : str
Operator name, such as Convolution, FullyConnected
:param attrs : dict
Dict of operator attributes
:param inputs: list
list of inputs to the operator
Returns
-------
:return mxnet_sym
Converted mxnet symbol
"""
if op_name in convert_map:
op_name, new_attrs, inputs = convert_map[op_name](attrs, inputs, self)
else:
raise NotImplementedError("Operator {} not implemented.".format(op_name))
if isinstance(op_name, string_types):
new_op = getattr(symbol, op_name, None)
if not new_op:
raise RuntimeError("Unable to map op_name {} to sym".format(op_name))
if node_name is None:
mxnet_sym = new_op(*inputs, **new_attrs)
else:
mxnet_sym = new_op(name=node_name, *inputs, **new_attrs)
return mxnet_sym
return op_name | [
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mbedmicro/pyOCD | pyocd/coresight/cortex_m.py | https://github.com/mbedmicro/pyOCD/blob/41a174718a9739f3cbe785c2ba21cb7fd1310c6f/pyocd/coresight/cortex_m.py#L467-L476 | def default_software_reset_type(self, reset_type):
"""! @brief Modify the default software reset method.
@param self
@param reset_type Must be one of the software reset types: Target.ResetType.SW_SYSRESETREQ,
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assert isinstance(reset_type, Target.ResetType)
assert reset_type in (Target.ResetType.SW_SYSRESETREQ, Target.ResetType.SW_VECTRESET,
Target.ResetType.SW_EMULATED)
self._default_software_reset_type = reset_type | [
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zetaops/pyoko | pyoko/model.py | https://github.com/zetaops/pyoko/blob/236c509ad85640933ac0f89ad8f7ed95f62adf07/pyoko/model.py#L169-L183 | def get_choices_for(self, field):
"""
Get the choices for the given fields.
Args:
field (str): Name of field.
Returns:
List of tuples. [(name, value),...]
"""
choices = self._fields[field].choices
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return choices | [
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pyca/pyopenssl | src/OpenSSL/crypto.py | https://github.com/pyca/pyopenssl/blob/1fbe064c50fd030948141d7d630673761525b0d0/src/OpenSSL/crypto.py#L1628-L1648 | def set_time(self, vfy_time):
"""
Set the time against which the certificates are verified.
Normally the current time is used.
.. note::
For example, you can determine if a certificate was valid at a given
time.
.. versionadded:: 17.0.0
:param datetime vfy_time: The verification time to set on this store.
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"""
param = _lib.X509_VERIFY_PARAM_new()
param = _ffi.gc(param, _lib.X509_VERIFY_PARAM_free)
_lib.X509_VERIFY_PARAM_set_time(param, int(vfy_time.strftime('%s')))
_openssl_assert(_lib.X509_STORE_set1_param(self._store, param) != 0) | [
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mozilla/mozilla-django-oidc | mozilla_django_oidc/auth.py | https://github.com/mozilla/mozilla-django-oidc/blob/e780130deacccbafc85a92f48d1407e042f5f955/mozilla_django_oidc/auth.py#L30-L46 | def default_username_algo(email):
"""Generate username for the Django user.
:arg str/unicode email: the email address to use to generate a username
:returns: str/unicode
"""
# bluntly stolen from django-browserid
# store the username as a base64 encoded sha224 of the email address
# this protects against data leakage because usernames are often
# treated as public identifiers (so we can't use the email address).
username = base64.urlsafe_b64encode(
hashlib.sha1(force_bytes(email)).digest()
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return smart_text(username) | [
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datosgobar/pydatajson | pydatajson/federation.py | https://github.com/datosgobar/pydatajson/blob/3141082ffbaa295e2deaf6ffbbc5a59f5859960e/pydatajson/federation.py#L347-L369 | def push_new_themes(catalog, portal_url, apikey):
"""Toma un catálogo y escribe los temas de la taxonomía que no están
presentes.
Args:
catalog (DataJson): El catálogo de origen que contiene la
taxonomía.
portal_url (str): La URL del portal CKAN de destino.
apikey (str): La apikey de un usuario con los permisos que le
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Returns:
str: Los ids de los temas creados.
"""
ckan_portal = RemoteCKAN(portal_url, apikey=apikey)
existing_themes = ckan_portal.call_action('group_list')
new_themes = [theme['id'] for theme in catalog[
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pushed_names = []
for new_theme in new_themes:
name = push_theme_to_ckan(
catalog, portal_url, apikey, identifier=new_theme)
pushed_names.append(name)
return pushed_names | [
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pymc-devs/pymc | pymc/gp/GPutils.py | https://github.com/pymc-devs/pymc/blob/c6e530210bff4c0d7189b35b2c971bc53f93f7cd/pymc/gp/GPutils.py#L150-L159 | def vecs_to_datmesh(x, y):
"""
Converts input arguments x and y to a 2d meshgrid,
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"""
x, y = meshgrid(x, y)
out = zeros(x.shape + (2,), dtype=float)
out[:, :, 0] = x
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joestump/python-oauth2 | oauth2/__init__.py | https://github.com/joestump/python-oauth2/blob/b94f69b1ad195513547924e380d9265133e995fa/oauth2/__init__.py#L388-L391 | def get_nonoauth_parameters(self):
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return dict([(k, v) for k, v in self.items()
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elifesciences/proofreader-python | proofreader/utils/print_table.py | https://github.com/elifesciences/proofreader-python/blob/387b3c65ee7777e26b3a7340179dc4ed68f24f58/proofreader/utils/print_table.py#L64-L86 | def _row_to_str(self, row):
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e.g.
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_row_text = ''
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l_pad, r_pad = self._split_int(width - len(row[col]))
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agoragames/haigha | haigha/classes/basic_class.py | https://github.com/agoragames/haigha/blob/7b004e1c0316ec14b94fec1c54554654c38b1a25/haigha/classes/basic_class.py#L96-L106 | def qos(self, prefetch_size=0, prefetch_count=0, is_global=False):
'''
Set QoS on this channel.
'''
args = Writer()
args.write_long(prefetch_size).\
write_short(prefetch_count).\
write_bit(is_global)
self.send_frame(MethodFrame(self.channel_id, 60, 10, args))
self.channel.add_synchronous_cb(self._recv_qos_ok) | [
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kajala/django-jutil | jutil/admin.py | https://github.com/kajala/django-jutil/blob/2abd93ebad51042744eaeb1ee1074ed0eb55ad0c/jutil/admin.py#L65-L73 | def kw_changelist_view(self, request: HttpRequest, extra_context=None, **kw):
"""
Changelist view which allow key-value arguments.
:param request: HttpRequest
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bitesofcode/projexui | projexui/widgets/xviewwidget/xviewprofiletoolbar.py | https://github.com/bitesofcode/projexui/blob/f18a73bec84df90b034ca69b9deea118dbedfc4d/projexui/widgets/xviewwidget/xviewprofiletoolbar.py#L461-L493 | def setCurrentProfile(self, prof):
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Sets the current profile for this toolbar to the inputed profile.
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self.clearActive()
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self._currentProfile = profile
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flo-compbio/goparser | goparser/parser.py | https://github.com/flo-compbio/goparser/blob/5e27d7d04a26a70a1d9dc113357041abff72be3f/goparser/parser.py#L305-L318 | def clear_annotation_data(self):
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Parameters
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oscarlazoarjona/fast | fast/inhomo.py | https://github.com/oscarlazoarjona/fast/blob/3e5400672af2a7b7cc616e7f4aa10d7672720222/fast/inhomo.py#L442-L496 | def fast_maxwell_boltzmann(mass, file_name=None,
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>>> from fast import Atom
>>> mass = Atom("Rb", 87).mass
>>> f = fast_maxwell_boltzmann(mass)
>>> print f(0, 273.15+20)
0.00238221482739
>>> import numpy as np
>>> v = np.linspace(-600, 600, 101)
>>> dist = f(v, 273.15+20)
>>> dv = v[1]-v[0]
>>> print sum(dist)*dv
0.999704711134
"""
# We get the mass of the atom.
code = ""
code = "def maxwell_boltzmann(v, T):\n"
code += ' r"""A fast calculation of the'
code += ' Maxwell-Boltzmann distribution."""\n'
code += " if hasattr(v, 'shape'):\n"
code += " d = 1\n"
code += " m = %s\n" % mass
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code += " f = f * np.exp(-m*v**2/2/k_B_num/T)\n"
code += " return f\n"
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code += " vsquare = sum([v[i]**2 for i in range(d)])\n"
code += " f = f * np.exp(-m*vsquare/2/k_B_num/T)\n"
code += " return f\n"
code += " else:\n"
code += " d = 1\n"
code += " m = %s\n" % mass
code += " f = np.sqrt(m/2/np.pi/k_B_num/T)**d\n"
code += " f = f * np.exp(-m*v**2/2/k_B_num/T)\n"
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f = file(file_name+".py", "w")
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>>> print f(0, 273.15+20)
0.00238221482739
>>> import numpy as np
>>> v = np.linspace(-600, 600, 101)
>>> dist = f(v, 273.15+20)
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0.999704711134 | [
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scieloorg/porteira | porteira/porteira.py | https://github.com/scieloorg/porteira/blob/e61f7d248b16848e63b2f85f37125aa77aba0366/porteira/porteira.py#L75-L79 | def deserialize(self, xml_input, *args, **kwargs):
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cohorte/cohorte-herald | python/snippets/herald_irc/bonus.py | https://github.com/cohorte/cohorte-herald/blob/bb3445d0031c8b3abad71e6219cc559b49faa3ee/python/snippets/herald_irc/bonus.py#L20-L27 | def cmd_join(self, connection, sender, target, payload):
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ga4gh/ga4gh-server | ga4gh/server/sqlite_backend.py | https://github.com/ga4gh/ga4gh-server/blob/1aa18922ef136db8604f6f098cb1732cba6f2a76/ga4gh/server/sqlite_backend.py#L13-L21 | def sqliteRowsToDicts(sqliteRows):
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gwastro/pycbc | pycbc/inject/inject.py | https://github.com/gwastro/pycbc/blob/7a64cdd104d263f1b6ea0b01e6841837d05a4cb3/pycbc/inject/inject.py#L660-L699 | def make_strain_from_inj_object(self, inj, delta_t, detector_name,
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"""Make a h(t) strain time-series from an injection object as read from
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Parameters
-----------
inj : injection object
The injection object to turn into a strain h(t).
delta_t : float
Sample rate to make injection at.
detector_name : string
Name of the detector used for projecting injections.
distance_scale: float, optional
Factor to scale the distance of an injection with. The default (=1)
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signal : float
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detector = Detector(detector_name)
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hc._epoch += inj['tc']
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hp /= distance_scale
hc /= distance_scale
# compute the detector response and add it to the strain
signal = detector.project_wave(hp, hc,
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return signal | [
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mmcauliffe/Conch-sounds | conch/main.py | https://github.com/mmcauliffe/Conch-sounds/blob/e05535fd08e4b0e47e37a77ef521d05eff1d6bc5/conch/main.py#L76-L130 | def acoustic_similarity_directories(directories, analysis_function, distance_function, stop_check=None, call_back=None, multiprocessing=True):
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Analyze many directories.
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SuLab/WikidataIntegrator | wikidataintegrator/wdi_fastrun.py | https://github.com/SuLab/WikidataIntegrator/blob/8ceb2ed1c08fec070ec9edfcf7db7b8691481b62/wikidataintegrator/wdi_fastrun.py#L504-L510 | def clear(self):
"""
convinience function to empty this fastrun container
"""
self.prop_dt_map = dict()
self.prop_data = dict()
self.rev_lookup = defaultdict(set) | [
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aio-libs/aiomcache | aiomcache/client.py | https://github.com/aio-libs/aiomcache/blob/75d44b201aea91bc2856b10940922d5ebfbfcd7b/aiomcache/client.py#L415-L422 | def flush_all(self, conn):
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tanghaibao/jcvi | jcvi/algorithms/formula.py | https://github.com/tanghaibao/jcvi/blob/d2e31a77b6ade7f41f3b321febc2b4744d1cdeca/jcvi/algorithms/formula.py#L96-L114 | def spearmanr(x, y):
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>>> x = [5.05, 6.75, 3.21, 2.66]
>>> y = [1.65, 26.5, -5.93, 7.96]
>>> z = [1.65, 2.64, 2.64, 6.95]
>>> round(spearmanr(x, y), 4)
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>>> round(spearmanr(x, z), 4)
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if not x or not y:
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corr, pvalue = stats.spearmanr(x, y)
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pyokagan/pyglreg | glreg.py | https://github.com/pyokagan/pyglreg/blob/68fa5a6c6cee8667879840fbbcc7d30f52852915/glreg.py#L355-L362 | def get_profiles(self):
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out = set(x.profile for x in self.requires if x.profile)
out.update(x.profile for x in self.removes if x.profile)
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theirc/rapidsms-multitenancy | multitenancy/views.py | https://github.com/theirc/rapidsms-multitenancy/blob/121bd0a628e691a88aade2e10045cba43af2dfcb/multitenancy/views.py#L24-L40 | def group_dashboard(request, group_slug):
"""Dashboard for managing a TenantGroup."""
groups = get_user_groups(request.user)
group = get_object_or_404(groups, slug=group_slug)
tenants = get_user_tenants(request.user, group)
can_edit_group = request.user.has_perm('multitenancy.change_tenantgroup', group)
count = len(tenants)
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return redirect(tenants[0])
context = {
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'tenants': tenants,
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return render(request, 'multitenancy/group-detail.html', context) | [
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Hackerfleet/hfos | hfos/ui/clientmanager.py | https://github.com/Hackerfleet/hfos/blob/b6df14eacaffb6be5c844108873ff8763ec7f0c9/hfos/ui/clientmanager.py#L405-L443 | def broadcast(self, event):
"""Broadcasts an event either to all users or clients, depending on
event flag"""
try:
if event.broadcasttype == "users":
if len(self._users) > 0:
self.log("Broadcasting to all users:",
event.content, lvl=network)
for useruuid in self._users.keys():
self.fireEvent(
send(useruuid, event.content, sendtype="user"))
# else:
# self.log("Not broadcasting, no users connected.",
# lvl=debug)
elif event.broadcasttype == "clients":
if len(self._clients) > 0:
self.log("Broadcasting to all clients: ",
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for client in self._clients.values():
self.fireEvent(write(client.sock, event.content),
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# self.log("Not broadcasting, no clients
# connected.",
# lvl=debug)
elif event.broadcasttype == "socks":
if len(self._sockets) > 0:
self.log("Emergency?! Broadcasting to all sockets: ",
event.content)
for sock in self._sockets:
self.fireEvent(write(sock, event.content), "wsserver")
# else:
# self.log("Not broadcasting, no sockets
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# lvl=debug)
except Exception as e:
self.log("Error during broadcast: ", e, type(e), lvl=critical) | [
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trailofbits/manticore | manticore/native/cpu/x86.py | https://github.com/trailofbits/manticore/blob/54c5a15b1119c523ae54c09972413e8b97f11629/manticore/native/cpu/x86.py#L4085-L4112 | def BTC(cpu, dest, src):
"""
Bit test and complement.
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the bit base) at the bit-position designated by the bit offset operand
(second operand), stores the value of the bit in the CF flag, and complements
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:param cpu: current CPU.
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:param src: bit offset operand.
"""
if dest.type == 'register':
value = dest.read()
pos = src.read() % dest.size
cpu.CF = value & (1 << pos) == 1 << pos
dest.write(value ^ (1 << pos))
elif dest.type == 'memory':
addr, pos = cpu._getMemoryBit(dest, src)
base, size, ty = cpu.get_descriptor(cpu.DS)
addr += base
value = cpu.read_int(addr, 8)
cpu.CF = value & (1 << pos) == 1 << pos
value = value ^ (1 << pos)
cpu.write_int(addr, value, 8)
else:
raise NotImplementedError(f"Unknown operand for BTC: {dest.type}") | [
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trickvi/economics | economics/cpi.py | https://github.com/trickvi/economics/blob/18da5ce7169472ca1ba6022272a389b933f76edd/economics/cpi.py#L69-L86 | def get(self, date=datetime.date.today(), country=None):
"""
Get the CPI value for a specific time. Defaults to today. This uses
the closest method internally but sets limit to one day.
"""
if not country:
country = self.country
if country == "all":
raise ValueError("You need to specify a country")
if not isinstance(date, str) and not isinstance(date, int):
date = date.year
cpi = self.data.get(country.upper(), {}).get(str(date))
if not cpi:
raise ValueError("Missing CPI data for {} for {}".format(
country, date))
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jhorman/pledge | pledge/__init__.py | https://github.com/jhorman/pledge/blob/062ba5b788aeb15e68c85a329374a50b4618544d/pledge/__init__.py#L171-L183 | def check(f):
"""
Wraps the function with a decorator that runs all of the
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if hasattr(f, 'wrapped_fn'):
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HewlettPackard/python-hpOneView | hpOneView/resources/settings/firmware_bundles.py | https://github.com/HewlettPackard/python-hpOneView/blob/3c6219723ef25e6e0c83d44a89007f89bc325b89/hpOneView/resources/settings/firmware_bundles.py#L48-L62 | def upload(self, file_path, timeout=-1):
"""
Upload an SPP ISO image file or a hotfix file to the appliance.
The API supports upload of one hotfix at a time into the system.
For the successful upload of a hotfix, ensure its original name and extension are not altered.
Args:
file_path: Full path to firmware.
timeout: Timeout in seconds. Wait for task completion by default. The timeout does not abort the operation
in OneView; it just stops waiting for its completion.
Returns:
dict: Information about the updated firmware bundle.
"""
return self._client.upload(file_path, timeout=timeout) | [
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sorgerlab/indra | indra/preassembler/ontology_mapper.py | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/preassembler/ontology_mapper.py#L102-L215 | def _load_wm_map(exclude_auto=None):
"""Load an ontology map for world models.
exclude_auto : None or list[tuple]
A list of ontology mappings for which automated mappings should be
excluded, e.g. [(HUME, UN)] would result in not using mappings
from HUME to UN.
"""
exclude_auto = [] if not exclude_auto else exclude_auto
path_here = os.path.dirname(os.path.abspath(__file__))
ontomap_file = os.path.join(path_here, '../resources/wm_ontomap.tsv')
mappings = {}
def make_hume_prefix_map():
hume_ont = os.path.join(path_here, '../sources/hume/hume_ontology.rdf')
graph = rdflib.Graph()
graph.parse(os.path.abspath(hume_ont), format='nt')
entry_map = {}
for node in graph.all_nodes():
entry = node.split('#')[1]
# Handle "event" and other top-level entries
if '/' not in entry:
entry_map[entry] = None
continue
parts = entry.split('/')
prefix, real_entry = parts[0], '/'.join(parts[1:])
entry_map[real_entry] = prefix
return entry_map
hume_prefix_map = make_hume_prefix_map()
def add_hume_prefix(hume_entry):
"""We need to do this because the HUME prefixes are missing"""
prefix = hume_prefix_map[hume_entry]
return '%s/%s' % (prefix, hume_entry)
def map_entry(reader, entry):
"""Remap the readers and entries to match our internal standards."""
if reader == 'eidos':
namespace = 'UN'
entry = entry.replace(' ', '_')
entry_id = entry
elif reader == 'BBN':
namespace = 'HUME'
entry = entry.replace(' ', '_')
entry_id = add_hume_prefix(entry)
elif reader == 'sofia':
namespace = 'SOFIA'
# First chop off the Event/Entity prefix
parts = entry.split('/')[1:]
# Now we split each part by underscore and capitalize
# each piece of each part
parts = ['_'.join([p.capitalize() for p in part.split('_')])
for part in parts]
# Finally we stick the entry back together separated by slashes
entry_id = '/'.join(parts)
else:
return reader, entry
return namespace, entry_id
with open(ontomap_file, 'r') as fh:
for line in fh.readlines():
# Get each entry from the line
s, se, t, te, score = line.strip().split('\t')
score = float(score)
# Map the entries to our internal naming standards
s, se = map_entry(s, se)
t, te = map_entry(t, te)
# Skip automated mappings when they should be excluded
if (s, t) not in exclude_auto:
# We first do the forward mapping
if (s, se, t) in mappings:
if mappings[(s, se, t)][1] < score:
mappings[(s, se, t)] = ((t, te), score)
else:
mappings[(s, se, t)] = ((t, te), score)
# Then we add the reverse mapping
if (t, s) not in exclude_auto:
if (t, te, s) in mappings:
if mappings[(t, te, s)][1] < score:
mappings[(t, te, s)] = ((s, se), score)
else:
mappings[(t, te, s)] = ((s, se), score)
ontomap = []
for s, ts in mappings.items():
ontomap.append(((s[0], s[1]), ts[0], ts[1]))
# Now apply the Hume -> Eidos override
override_file = os.path.join(path_here, '../resources/wm_ontomap.bbn.tsv')
override_mappings = []
with open(override_file, 'r') as fh:
for row in fh.readlines():
if 'BBN' not in row:
continue
# Order is target first, source second
_, te, _, se = row.strip().split('\t')
# Map the entries to our internal naming standards
s = 'HUME'
t = 'UN'
se = se.replace(' ', '_')
te = te.replace(' ', '_')
if se.startswith('/'):
se = se[1:]
override_mappings.append((s, se, t, te))
for s, se, t, te in override_mappings:
found = False
for idx, ((so, seo), (eo, teo), score) in enumerate(ontomap):
if (s, se, t) == (so, seo, eo):
# Override when a match is found
ontomap[idx] = ((s, se), (t, te), 1.0)
found = True
if not found:
ontomap.append(((s, se), (t, te), 1.0))
return ontomap | [
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PyCQA/astroid | astroid/transforms.py | https://github.com/PyCQA/astroid/blob/e0a298df55b15abcb77c2a93253f5ab7be52d0fb/astroid/transforms.py#L79-L81 | def unregister_transform(self, node_class, transform, predicate=None):
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cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/prompts.py | https://github.com/cloud9ers/gurumate/blob/075dc74d1ee62a8c6b7a8bf2b271364f01629d1e/environment/lib/python2.7/site-packages/IPython/core/prompts.py#L219-L234 | def cwd_filt2(depth):
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linkedin/pyexchange | pyexchange/exchange2010/__init__.py | https://github.com/linkedin/pyexchange/blob/d568f4edd326adb451b915ddf66cf1a37820e3ca/pyexchange/exchange2010/__init__.py#L338-L353 | def cancel(self):
"""
Cancels an event in Exchange. ::
event = service.calendar().get_event(id='KEY HERE')
event.cancel()
This will send notifications to anyone who has not declined the meeting.
"""
if not self.id:
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self.refresh_change_key()
self.service.send(soap_request.delete_event(self))
# TODO rsanders high - check return status to make sure it was actually sent
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elastic/elasticsearch-dsl-py | elasticsearch_dsl/index.py | https://github.com/elastic/elasticsearch-dsl-py/blob/874b52472fc47b601de0e5fa0e4300e21aff0085/elasticsearch_dsl/index.py#L509-L517 | def recovery(self, using=None, **kwargs):
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Any additional keyword arguments will be passed to
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portfors-lab/sparkle | sparkle/gui/stim/component_label.py | https://github.com/portfors-lab/sparkle/blob/5fad1cf2bec58ec6b15d91da20f6236a74826110/sparkle/gui/stim/component_label.py#L37-L48 | def getLabelByName(self, name):
"""Gets a label widget by it component name
:param name: name of the AbstractStimulusComponent which this label is named after
:type name: str
:returns: :class:`DragLabel<sparkle.gui.drag_label.DragLabel>`
"""
name = name.lower()
if name in self.stimLabels:
return self.stimLabels[name]
else:
return None | [
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Chilipp/psyplot | psyplot/project.py | https://github.com/Chilipp/psyplot/blob/75a0a15a9a1dd018e79d2df270d56c4bf5f311d5/psyplot/project.py#L1976-L1995 | def _gen_doc(cls, summary, full_name, identifier, example_call, doc_str,
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"""Generate the documentation docstring for a PlotMethod"""
# leave out the first argument
example_call = ', '.join(map(str.strip, example_call.split(',')[1:]))
ret = docstrings.dedents("""
%s
This plotting method adds data arrays and plots them via
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To plot a variable in this dataset, type::
>>> ds.psy.plot.%s(%s)
%s""" % (summary, full_name, identifier, example_call, doc_str))
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andy-z/ged4py | ged4py/detail/name.py | https://github.com/andy-z/ged4py/blob/d0e0cceaadf0a84cbf052705e3c27303b12e1757/ged4py/detail/name.py#L38-L85 | def parse_name_altree(record):
"""Parse NAME structure assuming ALTREE dialect.
In ALTREE dialect maiden name (if present) is saved as SURN sub-record
and is also appended to family name in parens. Given name is saved in
GIVN sub-record. Few examples:
No maiden name:
1 NAME John /Smith/
2 GIVN John
With maiden name:
1 NAME Jane /Smith (Ivanova)/
2 GIVN Jane
2 SURN Ivanova
No maiden name
1 NAME Mers /Daimler (-Benz)/
2 GIVN Mers
Because family name can also contain parens it's not enough to parse
family name and guess maiden name from it, we also have to check for
SURN record.
ALTREE also replaces empty names with question mark, we undo that too.
:param record: NAME record
:return: tuple with 3 or 4 elements, first three elements of tuple are
the same as returned from :py:meth:`split_name` method, fourth element
(if present) denotes maiden name.
"""
name_tuple = split_name(record.value)
if name_tuple[1] == '?':
name_tuple = (name_tuple[0], '', name_tuple[2])
maiden = record.sub_tag_value("SURN")
if maiden:
# strip "(maiden)" from family name
ending = '(' + maiden + ')'
surname = name_tuple[1]
if surname.endswith(ending):
surname = surname[:-len(ending)].rstrip()
if surname == '?':
surname = ''
name_tuple = (name_tuple[0], surname, name_tuple[2], maiden)
return name_tuple | [
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OpenTreeOfLife/peyotl | peyotl/collections_store/collections_umbrella.py | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/collections_store/collections_umbrella.py#L269-L280 | def _coerce_json_to_collection(self, json_repr):
"""Use to ensure that a JSON string (if found) is parsed to the equivalent dict in python.
If the incoming value is already parsed, do nothing. If a string fails to parse, return None."""
if isinstance(json_repr, dict):
collection = json_repr
else:
try:
collection = anyjson.loads(json_repr)
except:
_LOG.warn('> invalid JSON (failed anyjson parsing)')
return None
return collection | [
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bitesofcode/xqt | xqt/gui/xfiledialog.py | https://github.com/bitesofcode/xqt/blob/befa649a2f2104a20d49c8c78ffdba5907fd94d2/xqt/gui/xfiledialog.py#L24-L39 | def getDirectory(*args):
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"""
result = QtGui.QFileDialog.getDirectory(*args)
# PyQt4 returns just a string
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gbiggs/rtsprofile | rtsprofile/component.py | https://github.com/gbiggs/rtsprofile/blob/fded6eddcb0b25fe9808b1b12336a4413ea00905/rtsprofile/component.py#L529-L540 | def get_configuration_set_by_id(self, id):
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hyperledger/indy-plenum | plenum/server/node.py | https://github.com/hyperledger/indy-plenum/blob/dcd144e238af7f17a869ffc9412f13dc488b7020/plenum/server/node.py#L3403-L3421 | def onBatchRejected(self, ledger_id):
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A batch of requests has been rejected, if stateRoot is None, reject
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:param ledger_id:
:param stateRoot: state root after the batch was created
:return:
"""
if ledger_id == POOL_LEDGER_ID:
if isinstance(self.poolManager, TxnPoolManager):
self.get_req_handler(POOL_LEDGER_ID).onBatchRejected()
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self.audit_handler.post_batch_rejected(ledger_id)
self.execute_hook(NodeHooks.POST_BATCH_REJECTED, ledger_id) | [
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archman/beamline | beamline/mathutils.py | https://github.com/archman/beamline/blob/417bc5dc13e754bc89d246427984590fced64d07/beamline/mathutils.py#L437-L447 | def getR(self, i=5, j=6):
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fprimex/zdesk | zdesk/zdesk_api.py | https://github.com/fprimex/zdesk/blob/851611c13b4d530e9df31390b3ec709baf0a0188/zdesk/zdesk_api.py#L1150-L1154 | def dynamic_content_item_variant_delete(self, item_id, id, **kwargs):
"https://developer.zendesk.com/rest_api/docs/core/dynamic_content#delete-variant"
api_path = "/api/v2/dynamic_content/items/{item_id}/variants/{id}.json"
api_path = api_path.format(item_id=item_id, id=id)
return self.call(api_path, method="DELETE", **kwargs) | [
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/GettextCommon.py | https://github.com/iotile/coretools/blob/2d794f5f1346b841b0dcd16c9d284e9bf2f3c6ec/iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/GettextCommon.py#L131-L151 | def _read_linguas_from_files(env, linguas_files=None):
""" Parse `LINGUAS` file and return list of extracted languages """
import SCons.Util
import SCons.Environment
global _re_comment
global _re_lang
if not SCons.Util.is_List(linguas_files) \
and not SCons.Util.is_String(linguas_files) \
and not isinstance(linguas_files, SCons.Node.FS.Base) \
and linguas_files:
# If, linguas_files==True or such, then read 'LINGUAS' file.
linguas_files = ['LINGUAS']
if linguas_files is None:
return []
fnodes = env.arg2nodes(linguas_files)
linguas = []
for fnode in fnodes:
contents = _re_comment.sub("", fnode.get_text_contents())
ls = [l for l in _re_lang.findall(contents) if l]
linguas.extend(ls)
return linguas | [
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pmorissette/ffn | ffn/core.py | https://github.com/pmorissette/ffn/blob/ef09f28b858b7ffcd2627ce6a4dc618183a6bc8a/ffn/core.py#L2084-L2095 | def winsorize(x, axis=0, limits=0.01):
"""
`Winsorize <https://en.wikipedia.org/wiki/Winsorizing>`_ values based on limits
"""
# operate on copy
x = x.copy()
if isinstance(x, pd.DataFrame):
return x.apply(_winsorize_wrapper, axis=axis, args=(limits, ))
else:
return pd.Series(_winsorize_wrapper(x, limits).values,
index=x.index) | [
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google/grr | grr/core/grr_response_core/lib/rdfvalues/paths.py | https://github.com/google/grr/blob/5cef4e8e2f0d5df43ea4877e9c798e0bf60bfe74/grr/core/grr_response_core/lib/rdfvalues/paths.py#L201-L261 | def AFF4Path(self, client_urn):
"""Returns the AFF4 URN this pathspec will be stored under.
Args:
client_urn: A ClientURN.
Returns:
A urn that corresponds to this pathspec.
Raises:
ValueError: If pathspec is not of the correct type.
"""
# If the first level is OS and the second level is TSK its probably a mount
# point resolution. We map it into the tsk branch. For example if we get:
# path: \\\\.\\Volume{1234}\\
# pathtype: OS
# mount_point: /c:/
# nested_path {
# path: /windows/
# pathtype: TSK
# }
# We map this to aff4://client_id/fs/tsk/\\\\.\\Volume{1234}\\/windows/
if not self.HasField("pathtype"):
raise ValueError("Can't determine AFF4 path without a valid pathtype.")
first_component = self[0]
dev = first_component.path
if first_component.HasField("offset"):
# We divide here just to get prettier numbers in the GUI
dev += ":{}".format(first_component.offset // 512)
if (len(self) > 1 and first_component.pathtype == PathSpec.PathType.OS and
self[1].pathtype == PathSpec.PathType.TSK):
result = [self.AFF4_PREFIXES[PathSpec.PathType.TSK], dev]
# Skip the top level pathspec.
start = 1
else:
# For now just map the top level prefix based on the first pathtype
result = [self.AFF4_PREFIXES[first_component.pathtype]]
start = 0
for p in self[start]:
component = p.path
# The following encode different pathspec properties into the AFF4 path in
# such a way that unique files on the client are mapped to unique URNs in
# the AFF4 space. Note that this transformation does not need to be
# reversible since we always use the PathSpec when accessing files on the
# client.
if p.HasField("offset"):
component += ":{}".format(p.offset // 512)
# Support ADS names.
if p.HasField("stream_name"):
component += ":" + p.stream_name
result.append(component)
return client_urn.Add("/".join(result)) | [
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saltstack/salt | salt/states/boto_asg.py | https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/states/boto_asg.py#L822-L892 | def absent(
name,
force=False,
region=None,
key=None,
keyid=None,
profile=None,
remove_lc=False):
'''
Ensure the named autoscale group is deleted.
name
Name of the autoscale group.
force
Force deletion of autoscale group.
remove_lc
Delete the launch config as well.
region
The region to connect to.
key
Secret key to be used.
keyid
Access key to be used.
profile
A dict with region, key and keyid, or a pillar key (string)
that contains a dict with region, key and keyid.
'''
ret = {'name': name, 'result': True, 'comment': '', 'changes': {}}
asg = __salt__['boto_asg.get_config'](name, region, key, keyid, profile)
if asg is None:
ret['result'] = False
ret['comment'] = 'Failed to check autoscale group existence.'
elif asg:
if __opts__['test']:
ret['comment'] = 'Autoscale group set to be deleted.'
ret['result'] = None
if remove_lc:
msg = 'Launch configuration {0} is set to be deleted.'.format(asg['launch_config_name'])
ret['comment'] = ' '.join([ret['comment'], msg])
return ret
deleted = __salt__['boto_asg.delete'](name, force, region, key, keyid,
profile)
if deleted:
if remove_lc:
lc_deleted = __salt__['boto_asg.delete_launch_configuration'](asg['launch_config_name'],
region,
key,
keyid,
profile)
if lc_deleted:
if 'launch_config' not in ret['changes']:
ret['changes']['launch_config'] = {}
ret['changes']['launch_config']['deleted'] = asg['launch_config_name']
else:
ret['result'] = False
ret['comment'] = ' '.join([ret['comment'], 'Failed to delete launch configuration.'])
ret['changes']['old'] = asg
ret['changes']['new'] = None
ret['comment'] = 'Deleted autoscale group.'
else:
ret['result'] = False
ret['comment'] = 'Failed to delete autoscale group.'
else:
ret['comment'] = 'Autoscale group does not exist.'
return ret | [
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name
Name of the autoscale group.
force
Force deletion of autoscale group.
remove_lc
Delete the launch config as well.
region
The region to connect to.
key
Secret key to be used.
keyid
Access key to be used.
profile
A dict with region, key and keyid, or a pillar key (string)
that contains a dict with region, key and keyid. | [
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calston/tensor | tensor/utils.py | https://github.com/calston/tensor/blob/7c0c99708b5dbff97f3895f705e11996b608549d/tensor/utils.py#L254-L261 | def getBody(self, url, method='GET', headers={}, data=None, socket=None):
"""Make an HTTP request and return the body
"""
if not 'User-Agent' in headers:
headers['User-Agent'] = ['Tensor HTTP checker']
return self.request(url, method, headers, data, socket) | [
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phoebe-project/phoebe2 | phoebe/parameters/constraint.py | https://github.com/phoebe-project/phoebe2/blob/e64b8be683977064e2d55dd1b3ac400f64c3e379/phoebe/parameters/constraint.py#L989-L1026 | def requiv_contact_min(b, component, solve_for=None, **kwargs):
"""
Create a constraint to determine the critical (at L1) value of
requiv at which a constact will underflow. This will only be used
for contacts for requiv_min
:parameter b: the :class:`phoebe.frontend.bundle.Bundle`
:parameter str component: the label of the star in which this
constraint should be built
:parameter str solve_for: if 'requiv_max' should not be the derived/constrained
parameter, provide which other parameter should be derived
:returns: lhs (Parameter), rhs (ConstraintParameter), args (list of arguments
that were passed to this function)
"""
hier = b.get_hierarchy()
if not len(hier.get_value()):
# TODO: change to custom error type to catch in bundle.add_component
# TODO: check whether the problem is 0 hierarchies or more than 1
raise NotImplementedError("constraint for requiv_contact_min requires hierarchy")
component_ps = _get_system_ps(b, component)
parentorbit = hier.get_parent_of(component)
parentorbit_ps = _get_system_ps(b, parentorbit)
requiv_min = component_ps.get_parameter(qualifier='requiv_min')
q = parentorbit_ps.get_parameter(qualifier='q')
sma = parentorbit_ps.get_parameter(qualifier='sma')
if solve_for in [None, requiv_min]:
lhs = requiv_min
rhs = roche_requiv_contact_L1(q, sma, hier.get_primary_or_secondary(component, return_ind=True))
else:
raise NotImplementedError("requiv_contact_min can only be solved for requiv_min")
return lhs, rhs, {'component': component} | [
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fr33jc/bang | bang/providers/hpcloud/__init__.py | https://github.com/fr33jc/bang/blob/8f000713f88d2a9a8c1193b63ca10a6578560c16/bang/providers/hpcloud/__init__.py#L136-L193 | def authenticate(self):
"""
Authenticate against the HP Cloud Identity Service. This is the first
step in any hpcloud.com session, although this method is automatically
called when accessing higher-level methods/attributes.
**Examples of Credentials Configuration**
- Bare minimum for authentication using HP API keys:
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
access_key_id: MZOFIE9S83FOS248FIE3
secret_access_key: EU859vjksor73gkY378f9gkslbkrabcxwfyW2loo
- With multiple *compute* availability zones activated, the region must
also be specified (due to current limitations in the OpenStack client
libraries):
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
access_key_id: MZOFIE9S83FOS248FIE3
secret_access_key: EU859vjksor73gkY378f9gkslbkrabcxwfyW2loo
region_name: az-1.region-a.geo-1
- Using ``username`` and ``password`` is also allowed, but
discouraged:
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
username: farley.mowat
password: NeverCryW0lf
When both API keys and ``username+password`` are specified, the API
keys are used.
"""
log.info("Authenticating to HP Cloud...")
creds = self.creds
access_key_id = creds.get('access_key_id', '')
secret_access_key = creds.get('secret_access_key', '')
# prefer api key + secret key, but fallback to username + password
if access_key_id and secret_access_key:
self.nova_client.client.os_access_key_id = access_key_id
self.nova_client.client.os_secret_key = secret_access_key
self.nova_client.authenticate() | [
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] | Authenticate against the HP Cloud Identity Service. This is the first
step in any hpcloud.com session, although this method is automatically
called when accessing higher-level methods/attributes.
**Examples of Credentials Configuration**
- Bare minimum for authentication using HP API keys:
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
access_key_id: MZOFIE9S83FOS248FIE3
secret_access_key: EU859vjksor73gkY378f9gkslbkrabcxwfyW2loo
- With multiple *compute* availability zones activated, the region must
also be specified (due to current limitations in the OpenStack client
libraries):
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
access_key_id: MZOFIE9S83FOS248FIE3
secret_access_key: EU859vjksor73gkY378f9gkslbkrabcxwfyW2loo
region_name: az-1.region-a.geo-1
- Using ``username`` and ``password`` is also allowed, but
discouraged:
.. code-block:: yaml
deployer_credentials:
hpcloud:
auth_url: https://region-a.geo-1.identity.hpcloudsvc.com:35357/v2.0/
tenant_name: farley.mowat-tenant1
username: farley.mowat
password: NeverCryW0lf
When both API keys and ``username+password`` are specified, the API
keys are used. | [
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] | python | train | 38.862069 |
tanghaibao/jcvi | jcvi/formats/contig.py | https://github.com/tanghaibao/jcvi/blob/d2e31a77b6ade7f41f3b321febc2b4744d1cdeca/jcvi/formats/contig.py#L90-L146 | def frombed(args):
"""
%prog frombed bedfile contigfasta readfasta
Convert read placement to contig format. This is useful before running BAMBUS.
"""
from jcvi.formats.fasta import Fasta
from jcvi.formats.bed import Bed
from jcvi.utils.cbook import fill
p = OptionParser(frombed.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, contigfasta, readfasta = args
prefix = bedfile.rsplit(".", 1)[0]
contigfile = prefix + ".contig"
idsfile = prefix + ".ids"
contigfasta = Fasta(contigfasta)
readfasta = Fasta(readfasta)
bed = Bed(bedfile)
checksum = "00000000 checksum."
fw_ids = open(idsfile, "w")
fw = open(contigfile, "w")
for ctg, reads in bed.sub_beds():
ctgseq = contigfasta[ctg]
ctgline = "##{0} {1} {2} bases, {3}".format(\
ctg, len(reads), len(ctgseq), checksum)
print(ctg, file=fw_ids)
print(ctgline, file=fw)
print(fill(ctgseq.seq), file=fw)
for b in reads:
read = b.accn
strand = b.strand
readseq = readfasta[read]
rc = " [RC]" if strand == "-" else ""
readlen = len(readseq)
rstart, rend = 1, readlen
if strand == "-":
rstart, rend = rend, rstart
readrange = "{{{0} {1}}}".format(rstart, rend)
conrange = "<{0} {1}>".format(b.start, b.end)
readline = "#{0}(0){1} {2} bases, {3} {4} {5}".format(\
read, rc, readlen, checksum, readrange, conrange)
print(readline, file=fw)
print(fill(readseq.seq), file=fw)
logging.debug("Mapped contigs written to `{0}`.".format(contigfile))
logging.debug("Contig IDs written to `{0}`.".format(idsfile)) | [
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] | %prog frombed bedfile contigfasta readfasta
Convert read placement to contig format. This is useful before running BAMBUS. | [
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] | python | train | 31.385965 |
ActivisionGameScience/assertpy | assertpy/assertpy.py | https://github.com/ActivisionGameScience/assertpy/blob/08d799cdb01f9a25d3e20672efac991c7bc26d79/assertpy/assertpy.py#L231-L244 | def is_instance_of(self, some_class):
"""Asserts that val is an instance of the given class."""
try:
if not isinstance(self.val, some_class):
if hasattr(self.val, '__name__'):
t = self.val.__name__
elif hasattr(self.val, '__class__'):
t = self.val.__class__.__name__
else:
t = 'unknown'
self._err('Expected <%s:%s> to be instance of class <%s>, but was not.' % (self.val, t, some_class.__name__))
except TypeError:
raise TypeError('given arg must be a class')
return self | [
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StackStorm/pybind | pybind/slxos/v17r_1_01a/mpls_state/__init__.py | https://github.com/StackStorm/pybind/blob/44c467e71b2b425be63867aba6e6fa28b2cfe7fb/pybind/slxos/v17r_1_01a/mpls_state/__init__.py#L1150-L1173 | def _set_autobw_threshold_table_summary(self, v, load=False):
"""
Setter method for autobw_threshold_table_summary, mapped from YANG variable /mpls_state/autobw_threshold_table_summary (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_autobw_threshold_table_summary is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_autobw_threshold_table_summary() directly.
YANG Description: MPLS Auto Bandwidth Threshold TableSummary
"""
if hasattr(v, "_utype"):
v = v._utype(v)
try:
t = YANGDynClass(v,base=autobw_threshold_table_summary.autobw_threshold_table_summary, is_container='container', presence=False, yang_name="autobw-threshold-table-summary", rest_name="autobw-threshold-table-summary", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mpls-autobw-threshold-table-summary', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mpls-operational', defining_module='brocade-mpls-operational', yang_type='container', is_config=False)
except (TypeError, ValueError):
raise ValueError({
'error-string': """autobw_threshold_table_summary must be of a type compatible with container""",
'defined-type': "container",
'generated-type': """YANGDynClass(base=autobw_threshold_table_summary.autobw_threshold_table_summary, is_container='container', presence=False, yang_name="autobw-threshold-table-summary", rest_name="autobw-threshold-table-summary", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'callpoint': u'mpls-autobw-threshold-table-summary', u'cli-suppress-show-path': None}}, namespace='urn:brocade.com:mgmt:brocade-mpls-operational', defining_module='brocade-mpls-operational', yang_type='container', is_config=False)""",
})
self.__autobw_threshold_table_summary = t
if hasattr(self, '_set'):
self._set() | [
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CityOfZion/neo-python | neo/Implementations/Notifications/LevelDB/NotificationDB.py | https://github.com/CityOfZion/neo-python/blob/fe90f62e123d720d4281c79af0598d9df9e776fb/neo/Implementations/Notifications/LevelDB/NotificationDB.py#L302-L320 | def get_token(self, hash):
"""
Looks up a token by hash
Args:
hash (UInt160): The token to look up
Returns:
SmartContractEvent: A smart contract event with a contract that is an NEP5 Token
"""
tokens_snapshot = self.db.prefixed_db(NotificationPrefix.PREFIX_TOKEN).snapshot()
try:
val = tokens_snapshot.get(hash.ToBytes())
if val:
event = SmartContractEvent.FromByteArray(val)
return event
except Exception as e:
logger.error("Smart contract event with contract hash %s not found: %s " % (hash.ToString(), e))
return None | [
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log2timeline/plaso | plaso/storage/sqlite/merge_reader.py | https://github.com/log2timeline/plaso/blob/9c564698d2da3ffbe23607a3c54c0582ea18a6cc/plaso/storage/sqlite/merge_reader.py#L99-L116 | def _AddEvent(self, event):
"""Adds an event.
Args:
event (EventObject): event.
"""
if hasattr(event, 'event_data_row_identifier'):
event_data_identifier = identifiers.SQLTableIdentifier(
self._CONTAINER_TYPE_EVENT_DATA,
event.event_data_row_identifier)
lookup_key = event_data_identifier.CopyToString()
event_data_identifier = self._event_data_identifier_mappings[lookup_key]
event.SetEventDataIdentifier(event_data_identifier)
# TODO: add event identifier mappings for event tags.
self._storage_writer.AddEvent(event) | [
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Gorialis/jishaku | jishaku/repl/compilation.py | https://github.com/Gorialis/jishaku/blob/fc7c479b9d510ede189a929c8aa6f7c8ef7f9a6e/jishaku/repl/compilation.py#L150-L164 | async def traverse(self, func):
"""
Traverses an async function or generator, yielding each result.
This function is private. The class should be used as an iterator instead of using this method.
"""
# this allows the reference to be stolen
async_executor = self
if inspect.isasyncgenfunction(func):
async for result in func(*async_executor.args):
yield result
else:
yield await func(*async_executor.args) | [
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bodylabs/lace | lace/texture.py | https://github.com/bodylabs/lace/blob/b68f4a60a4cac66c0607ffbae38ef9d07d37f459/lace/texture.py#L56-L69 | def load_texture(self, texture_version):
'''
Expect a texture version number as an integer, load the texture version from /is/ps/shared/data/body/template/texture_coordinates/.
Currently there are versions [0, 1, 2, 3] availiable.
'''
import numpy as np
lowres_tex_template = 's3://bodylabs-korper-assets/is/ps/shared/data/body/template/texture_coordinates/textured_template_low_v%d.obj' % texture_version
highres_tex_template = 's3://bodylabs-korper-assets/is/ps/shared/data/body/template/texture_coordinates/textured_template_high_v%d.obj' % texture_version
from lace.mesh import Mesh
from lace.cache import sc
mesh_with_texture = Mesh(filename=sc(lowres_tex_template))
if not np.all(mesh_with_texture.f.shape == self.f.shape):
mesh_with_texture = Mesh(filename=sc(highres_tex_template))
self.transfer_texture(mesh_with_texture) | [
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bioidiap/gridtk | gridtk/script/jman.py | https://github.com/bioidiap/gridtk/blob/9e3291b8b50388682908927231b2730db1da147d/gridtk/script/jman.py#L198-L201 | def list(args):
"""Lists the jobs in the given database."""
jm = setup(args)
jm.list(job_ids=get_ids(args.job_ids), print_array_jobs=args.print_array_jobs, print_dependencies=args.print_dependencies, status=args.status, long=args.long, print_times=args.print_times, ids_only=args.ids_only, names=args.names) | [
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wal-e/wal-e | wal_e/blobstore/file/file_util.py | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/blobstore/file/file_util.py#L36-L59 | def do_lzop_get(creds, url, path, decrypt, do_retry):
"""
Get and decompress a URL
This streams the content directly to lzop; the compressed version
is never stored on disk.
"""
assert url.endswith('.lzo'), 'Expect an lzop-compressed file'
with files.DeleteOnError(path) as decomp_out:
key = _uri_to_key(creds, url)
with get_download_pipeline(PIPE, decomp_out.f, decrypt) as pl:
g = gevent.spawn(write_and_return_error, key, pl.stdin)
exc = g.get()
if exc is not None:
raise exc
logger.info(
msg='completed download and decompression',
detail='Downloaded and decompressed "{url}" to "{path}"'
.format(url=url, path=path))
return True | [
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estnltk/estnltk | estnltk/text.py | https://github.com/estnltk/estnltk/blob/28ae334a68a0673072febc318635f04da0dcc54a/estnltk/text.py#L1296-L1315 | def split_by(self, layer, sep=' '):
"""Split the text into multiple instances defined by elements of given layer.
The spans for layer elements are extracted and feed to :py:meth:`~estnltk.text.Text.split_given_spans`
method.
Parameters
----------
layer: str
String determining the layer that is used to define the start and end positions of resulting splits.
sep: str (default: ' ')
The separator to use to join texts of multilayer elements.
Returns
-------
list of Text
"""
if not self.is_tagged(layer):
self.tag(layer)
return self.split_given_spans(self.spans(layer), sep=sep) | [
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layer: str
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cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/utils/path.py | https://github.com/cloud9ers/gurumate/blob/075dc74d1ee62a8c6b7a8bf2b271364f01629d1e/environment/lib/python2.7/site-packages/IPython/utils/path.py#L322-L333 | def locate_profile(profile='default'):
"""Find the path to the folder associated with a given profile.
I.e. find $IPYTHONDIR/profile_whatever.
"""
from IPython.core.profiledir import ProfileDir, ProfileDirError
try:
pd = ProfileDir.find_profile_dir_by_name(get_ipython_dir(), profile)
except ProfileDirError:
# IOError makes more sense when people are expecting a path
raise IOError("Couldn't find profile %r" % profile)
return pd.location | [
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gabstopper/smc-python | smc/elements/helpers.py | https://github.com/gabstopper/smc-python/blob/e027b8a5dcfaf884eada32d113d41c1e56b32457/smc/elements/helpers.py#L45-L59 | def zone_helper(zone):
"""
Zone finder by name. If zone doesn't exist, create it and
return the href
:param str zone: name of zone (if href, will be returned as is)
:return str href: href of zone
"""
if zone is None:
return None
elif isinstance(zone, Zone):
return zone.href
elif zone.startswith('http'):
return zone
return Zone.get_or_create(name=zone).href | [
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iotile/coretools | transport_plugins/native_ble/iotile_transport_native_ble/device_adapter.py | https://github.com/iotile/coretools/blob/2d794f5f1346b841b0dcd16c9d284e9bf2f3c6ec/transport_plugins/native_ble/iotile_transport_native_ble/device_adapter.py#L218-L226 | def stop_scan(self):
"""Stop to scan."""
try:
self.bable.stop_scan(sync=True)
except bable_interface.BaBLEException:
# If we errored our it is because we were not currently scanning
pass
self.scanning = False | [
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minhhoit/yacms | yacms/utils/docs.py | https://github.com/minhhoit/yacms/blob/2921b706b7107c6e8c5f2bbf790ff11f85a2167f/yacms/utils/docs.py#L288-L302 | def build_requirements(docs_path, package_name="yacms"):
"""
Updates the requirements file with yacms's version number.
"""
mezz_string = "yacms=="
project_path = os.path.join(docs_path, "..")
requirements_file = os.path.join(project_path, package_name,
"project_template", "requirements.txt")
with open(requirements_file, "r") as f:
requirements = f.readlines()
with open(requirements_file, "w") as f:
f.write("yacms==%s\n" % __version__)
for requirement in requirements:
if requirement.strip() and not requirement.startswith(mezz_string):
f.write(requirement) | [
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HazyResearch/fonduer | src/fonduer/learning/disc_models/sparse_lstm.py | https://github.com/HazyResearch/fonduer/blob/4520f86a716f03dcca458a9f4bddac75b4e7068f/src/fonduer/learning/disc_models/sparse_lstm.py#L25-L64 | def forward(self, X):
"""Forward function.
:param X: The input (batch) of the model contains word sequences for lstm,
features and feature weights.
:type X: For word sequences: a list of torch.Tensor pair (word sequence
and word mask) of shape (batch_size, sequence_length).
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For feature weights: torch.Tensor of shape
(batch_size, sparse_feature_size).
:return: The output of LSTM layer.
:rtype: torch.Tensor of shape (batch_size, num_classes)
"""
s = X[:-2]
f = X[-2]
w = X[-1]
batch_size = len(f)
# Generate lstm weight indices
x_idx = self._cuda(
torch.as_tensor(np.arange(1, self.settings["lstm_dim"] + 1)).repeat(
batch_size, 1
)
)
outputs = self._cuda(torch.Tensor([]))
# Calculate textual features from LSTMs
for i in range(len(s)):
state_word = self.lstms[0].init_hidden(batch_size)
output = self.lstms[0].forward(s[i][0], s[i][1], state_word)
outputs = torch.cat((outputs, output), 1)
# Concatenate textual features with multi-modal features
feaures = torch.cat((x_idx, f), 1)
weights = torch.cat((outputs, w), 1)
return self.sparse_linear(feaures, weights) | [
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UCBerkeleySETI/blimpy | blimpy/waterfall.py | https://github.com/UCBerkeleySETI/blimpy/blob/b8822d3e3e911944370d84371a91fa0c29e9772e/blimpy/waterfall.py#L195-L212 | def info(self):
""" Print header information and other derived information. """
print("\n--- File Info ---")
for key, val in self.file_header.items():
if key == 'src_raj':
val = val.to_string(unit=u.hour, sep=':')
if key == 'src_dej':
val = val.to_string(unit=u.deg, sep=':')
print("%16s : %32s" % (key, val))
print("\n%16s : %32s" % ("Num ints in file", self.n_ints_in_file))
print("%16s : %32s" % ("File shape", self.file_shape))
print("--- Selection Info ---")
print("%16s : %32s" % ("Data selection shape", self.selection_shape))
print("%16s : %32s" % ("Minimum freq (MHz)", self.container.f_start))
print("%16s : %32s" % ("Maximum freq (MHz)", self.container.f_stop)) | [
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] | python | test | 44.333333 |
praekeltfoundation/seed-control-interface | ci/utils.py | https://github.com/praekeltfoundation/seed-control-interface/blob/32ddad88b5bc2f8f4d80b848361899da2e081636/ci/utils.py#L162-L185 | def get_page_of_iterator(iterator, page_size, page_number):
"""
Get a page from an interator, handling invalid input from the page number
by defaulting to the first page.
"""
try:
page_number = validate_page_number(page_number)
except (PageNotAnInteger, EmptyPage):
page_number = 1
start = (page_number - 1) * page_size
# End 1 more than we need, so that we can see if there's another page
end = (page_number * page_size) + 1
skipped_items = list(islice(iterator, start))
items = list(islice(iterator, end))
if len(items) == 0 and page_number != 1:
items = skipped_items
page_number = 1
has_next = len(items) > page_size
items = items[:page_size]
return NoCountPage(items, page_number, page_size, has_next) | [
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] | python | test | 32.458333 |
lucasmaystre/choix | choix/mm.py | https://github.com/lucasmaystre/choix/blob/05a57a10bb707338113a9d91601ca528ead7a881/choix/mm.py#L149-L183 | def mm_top1(
n_items, data, initial_params=None, alpha=0.0,
max_iter=10000, tol=1e-8):
"""Compute the ML estimate of model parameters using the MM algorithm.
This function computes the maximum-likelihood (ML) estimate of model
parameters given top-1 data (see :ref:`data-top1`), using the
minorization-maximization (MM) algorithm [Hun04]_, [CD12]_.
If ``alpha > 0``, the function returns the maximum a-posteriori (MAP)
estimate under a (peaked) Dirichlet prior. See :ref:`regularization` for
details.
Parameters
----------
n_items : int
Number of distinct items.
data : list of lists
Top-1 data.
initial_params : array_like, optional
Parameters used to initialize the iterative procedure.
alpha : float, optional
Regularization parameter.
max_iter : int, optional
Maximum number of iterations allowed.
tol : float, optional
Maximum L1-norm of the difference between successive iterates to
declare convergence.
Returns
-------
params : numpy.ndarray
The ML estimate of model parameters.
"""
return _mm(n_items, data, initial_params, alpha, max_iter, tol, _mm_top1) | [
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minorization-maximization (MM) algorithm [Hun04]_, [CD12]_.
If ``alpha > 0``, the function returns the maximum a-posteriori (MAP)
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Parameters
----------
n_items : int
Number of distinct items.
data : list of lists
Top-1 data.
initial_params : array_like, optional
Parameters used to initialize the iterative procedure.
alpha : float, optional
Regularization parameter.
max_iter : int, optional
Maximum number of iterations allowed.
tol : float, optional
Maximum L1-norm of the difference between successive iterates to
declare convergence.
Returns
-------
params : numpy.ndarray
The ML estimate of model parameters. | [
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] | python | train | 34.085714 |
atlassian-api/atlassian-python-api | atlassian/jira.py | https://github.com/atlassian-api/atlassian-python-api/blob/540d269905c3e7547b666fe30c647b2d512cf358/atlassian/jira.py#L652-L669 | def update_issue_remote_link_by_id(self, issue_key, link_id, url, title, global_id=None, relationship=None):
"""
Update existing Remote Link on Issue
:param issue_key: str
:param link_id: str
:param url: str
:param title: str
:param global_id: str, OPTIONAL:
:param relationship: str, Optional. Default by built-in method: 'Web Link'
"""
data = {'object': {'url': url, 'title': title}}
if global_id:
data['globalId'] = global_id
if relationship:
data['relationship'] = relationship
url = 'rest/api/2/issue/{issue_key}/remotelink/{link_id}'.format(issue_key=issue_key, link_id=link_id)
return self.put(url, data=data) | [
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:param link_id: str
:param url: str
:param title: str
:param global_id: str, OPTIONAL:
:param relationship: str, Optional. Default by built-in method: 'Web Link' | [
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] | python | train | 41.333333 |
erdc/RAPIDpy | RAPIDpy/rapid.py | https://github.com/erdc/RAPIDpy/blob/50e14e130554b254a00ff23b226cd7e4c6cfe91a/RAPIDpy/rapid.py#L342-L427 | def update_reach_number_data(self):
"""
Update the reach number data for the namelist based on input files.
.. warning:: You need to make sure you set *rapid_connect_file*
and *riv_bas_id_file* before running this function.
Example:
.. code:: python
from RAPIDpy import RAPID
rapid_manager = RAPID(
rapid_connect_file='../rapid-io/input/rapid_connect.csv',
riv_bas_id_file='../rapid-io/input/riv_bas_id.csv',
)
rapid_manager.update_reach_number_data()
Example with forcing data:
.. code:: python
from RAPIDpy import RAPID
rapid_manager = RAPID(
rapid_connect_file='../rapid-io/input/rapid_connect.csv',
riv_bas_id_file='../rapid-io/input/riv_bas_id.csv',
Qfor_file='../rapid-io/input/qfor_file.csv',
for_tot_id_file='../rapid-io/input/for_tot_id_file.csv',
for_use_id_file='../rapid-io/input/for_use_id_file.csv',
ZS_dtF=3*60*60,
BS_opt_for=True
)
rapid_manager.update_reach_number_data()
"""
if not self.rapid_connect_file:
log("Missing rapid_connect_file. "
"Please set before running this function ...",
"ERROR")
if not self.riv_bas_id_file:
log("Missing riv_bas_id_file. "
"Please set before running this function ...",
"ERROR")
# get rapid connect info
rapid_connect_table = np.loadtxt(self.rapid_connect_file,
ndmin=2, delimiter=",", dtype=int)
self.IS_riv_tot = int(rapid_connect_table.shape[0])
self.IS_max_up = int(rapid_connect_table[:, 2].max())
# get riv_bas_id info
riv_bas_id_table = np.loadtxt(self.riv_bas_id_file,
ndmin=1, delimiter=",",
usecols=(0,), dtype=int)
self.IS_riv_bas = int(riv_bas_id_table.size)
# add the forcing files
if not self.for_tot_id_file:
self.IS_for_tot = 0
log("Missing for_tot_id_file. Skipping ...",
"WARNING")
else:
# get riv_bas_id info
for_tot_id_table = np.loadtxt(self.for_tot_id_file,
ndmin=1, delimiter=",",
usecols=(0,), dtype=int)
self.IS_for_tot = int(for_tot_id_table.size)
if not self.for_use_id_file:
self.IS_for_use = 0
log("Missing for_use_id_file. Skipping ...",
"WARNING")
else:
# get riv_bas_id info
for_use_id_table = np.loadtxt(self.for_use_id_file,
ndmin=1, delimiter=",",
usecols=(0,), dtype=int)
self.IS_for_use = int(for_use_id_table.size) | [
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.. warning:: You need to make sure you set *rapid_connect_file*
and *riv_bas_id_file* before running this function.
Example:
.. code:: python
from RAPIDpy import RAPID
rapid_manager = RAPID(
rapid_connect_file='../rapid-io/input/rapid_connect.csv',
riv_bas_id_file='../rapid-io/input/riv_bas_id.csv',
)
rapid_manager.update_reach_number_data()
Example with forcing data:
.. code:: python
from RAPIDpy import RAPID
rapid_manager = RAPID(
rapid_connect_file='../rapid-io/input/rapid_connect.csv',
riv_bas_id_file='../rapid-io/input/riv_bas_id.csv',
Qfor_file='../rapid-io/input/qfor_file.csv',
for_tot_id_file='../rapid-io/input/for_tot_id_file.csv',
for_use_id_file='../rapid-io/input/for_use_id_file.csv',
ZS_dtF=3*60*60,
BS_opt_for=True
)
rapid_manager.update_reach_number_data() | [
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ellisonleao/pyshorteners | pyshorteners/shorteners/adfly.py | https://github.com/ellisonleao/pyshorteners/blob/116155751c943f8d875c819d5a41db10515db18d/pyshorteners/shorteners/adfly.py#L79-L118 | def expand(self, url):
"""Expand implementation for Adf.ly
Args:
url: the URL you want to expand
Returns:
A string containing the expanded URL
Raises:
BadAPIResponseException: If the data is malformed or we got a bad
status code on API response
ShorteningErrorException: If the API Returns an error as response
"""
url = self.clean_url(url)
expand_url = f'{self.api_url}v1/expand'
payload = {
'domain': getattr(self, 'domain', 'adf.ly'),
'advert_type': getattr(self, 'type', 'int'),
'group_id': getattr(self, 'group_id', None),
'key': self.api_key,
'user_id': self.user_id,
'url': url,
}
response = self._post(expand_url, data=payload)
if not response.ok:
raise BadAPIResponseException(response.content)
try:
data = response.json()
except json.decoder.JSONDecodeError:
raise BadAPIResponseException('API response could not be decoded')
if data.get('errors'):
errors = ','.join(i['msg'] for i in data['errors'])
raise ShorteningErrorException(errors)
if not data.get('data'):
raise BadAPIResponseException(response.content)
return data['data'][0]['url'] | [
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Raises:
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status code on API response
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JelteF/PyLaTeX | pylatex/tikz.py | https://github.com/JelteF/PyLaTeX/blob/62d9d9912ce8445e6629cdbcb80ad86143a1ed23/pylatex/tikz.py#L249-L263 | def get_anchor_point(self, anchor_name):
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markovmodel/msmtools | msmtools/analysis/api.py | https://github.com/markovmodel/msmtools/blob/54dc76dd2113a0e8f3d15d5316abab41402941be/msmtools/analysis/api.py#L1259-L1350 | def correlation(T, obs1, obs2=None, times=(1), maxtime=None, k=None, ncv=None, return_times=False):
r"""Time-correlation for equilibrium experiment.
Parameters
----------
T : (M, M) ndarray or scipy.sparse matrix
Transition matrix
obs1 : (M,) ndarray
Observable, represented as vector on state space
obs2 : (M,) ndarray (optional)
Second observable, for cross-correlations
times : array-like of int (optional), default=(1)
List of times (in tau) at which to compute correlation
maxtime : int, optional, default=None
Maximum time step to use. Equivalent to . Alternative to times.
k : int (optional)
Number of eigenvalues and eigenvectors to use for computation
ncv : int (optional)
The number of Lanczos vectors generated, `ncv` must be greater than k;
it is recommended that ncv > 2*k
Returns
-------
correlations : ndarray
Correlation values at given times
times : ndarray, optional
time points at which the correlation was computed (if return_times=True)
References
----------
.. [1] Noe, F, S Doose, I Daidone, M Loellmann, M Sauer, J D
Chodera and J Smith. 2010. Dynamical fingerprints for probing
individual relaxation processes in biomolecular dynamics with
simulations and kinetic experiments. PNAS 108 (12): 4822-4827.
Notes
-----
**Auto-correlation**
The auto-correlation of an observable :math:`a(x)` for a system in
equilibrium is
.. math:: \mathbb{E}_{\mu}[a(x,0)a(x,t)]=\sum_x \mu(x) a(x, 0) a(x, t)
:math:`a(x,0)=a(x)` is the observable at time :math:`t=0`. It can
be propagated forward in time using the t-step transition matrix
:math:`p^{t}(x, y)`.
The propagated observable at time :math:`t` is :math:`a(x,
t)=\sum_y p^t(x, y)a(y, 0)`.
Using the eigenvlaues and eigenvectors of the transition matrix
the autocorrelation can be written as
.. math:: \mathbb{E}_{\mu}[a(x,0)a(x,t)]=\sum_i \lambda_i^t \langle a, r_i\rangle_{\mu} \langle l_i, a \rangle.
**Cross-correlation**
The cross-correlation of two observables :math:`a(x)`,
:math:`b(x)` is similarly given
.. math:: \mathbb{E}_{\mu}[a(x,0)b(x,t)]=\sum_x \mu(x) a(x, 0) b(x, t)
Examples
--------
>>> import numpy as np
>>> from msmtools.analysis import correlation
>>> T = np.array([[0.9, 0.1, 0.0], [0.5, 0.0, 0.5], [0.0, 0.1, 0.9]])
>>> a = np.array([1.0, 0.0, 0.0])
>>> times = np.array([1, 5, 10, 20])
>>> corr = correlation(T, a, times=times)
>>> corr
array([ 0.40909091, 0.34081364, 0.28585667, 0.23424263])
"""
# check if square matrix and remember size
T = _types.ensure_ndarray_or_sparse(T, ndim=2, uniform=True, kind='numeric')
n = T.shape[0]
obs1 = _types.ensure_ndarray(obs1, ndim=1, size=n, kind='numeric')
obs2 = _types.ensure_ndarray_or_None(obs2, ndim=1, size=n, kind='numeric')
times = _types.ensure_int_vector(times, require_order=True)
# check input
# go
if _issparse(T):
return sparse.fingerprints.correlation(T, obs1, obs2=obs2, times=times, k=k, ncv=ncv)
else:
return dense.fingerprints.correlation(T, obs1, obs2=obs2, times=times, k=k) | [
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Transition matrix
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Observable, represented as vector on state space
obs2 : (M,) ndarray (optional)
Second observable, for cross-correlations
times : array-like of int (optional), default=(1)
List of times (in tau) at which to compute correlation
maxtime : int, optional, default=None
Maximum time step to use. Equivalent to . Alternative to times.
k : int (optional)
Number of eigenvalues and eigenvectors to use for computation
ncv : int (optional)
The number of Lanczos vectors generated, `ncv` must be greater than k;
it is recommended that ncv > 2*k
Returns
-------
correlations : ndarray
Correlation values at given times
times : ndarray, optional
time points at which the correlation was computed (if return_times=True)
References
----------
.. [1] Noe, F, S Doose, I Daidone, M Loellmann, M Sauer, J D
Chodera and J Smith. 2010. Dynamical fingerprints for probing
individual relaxation processes in biomolecular dynamics with
simulations and kinetic experiments. PNAS 108 (12): 4822-4827.
Notes
-----
**Auto-correlation**
The auto-correlation of an observable :math:`a(x)` for a system in
equilibrium is
.. math:: \mathbb{E}_{\mu}[a(x,0)a(x,t)]=\sum_x \mu(x) a(x, 0) a(x, t)
:math:`a(x,0)=a(x)` is the observable at time :math:`t=0`. It can
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The propagated observable at time :math:`t` is :math:`a(x,
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Using the eigenvlaues and eigenvectors of the transition matrix
the autocorrelation can be written as
.. math:: \mathbb{E}_{\mu}[a(x,0)a(x,t)]=\sum_i \lambda_i^t \langle a, r_i\rangle_{\mu} \langle l_i, a \rangle.
**Cross-correlation**
The cross-correlation of two observables :math:`a(x)`,
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.. math:: \mathbb{E}_{\mu}[a(x,0)b(x,t)]=\sum_x \mu(x) a(x, 0) b(x, t)
Examples
--------
>>> import numpy as np
>>> from msmtools.analysis import correlation
>>> T = np.array([[0.9, 0.1, 0.0], [0.5, 0.0, 0.5], [0.0, 0.1, 0.9]])
>>> a = np.array([1.0, 0.0, 0.0])
>>> times = np.array([1, 5, 10, 20])
>>> corr = correlation(T, a, times=times)
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PMEAL/OpenPNM | openpnm/algorithms/InvasionPercolation.py | https://github.com/PMEAL/OpenPNM/blob/0547b5724ffedc0a593aae48639d36fe10e0baed/openpnm/algorithms/InvasionPercolation.py#L103-L143 | def setup(self, phase, entry_pressure='', pore_volume='', throat_volume=''):
r"""
Set up the required parameters for the algorithm
Parameters
----------
phase : OpenPNM Phase object
The phase to be injected into the Network. The Phase must have the
capillary entry pressure values for the system.
entry_pressure : string
The dictionary key to the capillary entry pressure. If none is
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pore_volume : string
The dictionary key to the pore volume. If none is supplied then
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The dictionary key to the throat volume. If none is supplied then
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"""
self.settings['phase'] = phase.name
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if throat_volume:
self.settings['throat_volume'] = throat_volume
if entry_pressure:
self.settings['entry_pressure'] = entry_pressure
# Setup arrays and info
self['throat.entry_pressure'] = phase[self.settings['entry_pressure']]
# Indices into t_entry giving a sorted list
self['throat.sorted'] = sp.argsort(self['throat.entry_pressure'], axis=0)
self['throat.order'] = 0
self['throat.order'][self['throat.sorted']] = sp.arange(0, self.Nt)
self['throat.invasion_sequence'] = -1
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self._tcount = 0 | [
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entry_pressure : string
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JasonKessler/scattertext | scattertext/TermDocMatrixWithoutCategories.py | https://github.com/JasonKessler/scattertext/blob/cacf1f687d218ee8cae3fc05cc901db824bb1b81/scattertext/TermDocMatrixWithoutCategories.py#L471-L488 | def add_metadata(self, metadata_matrix, meta_index_store):
'''
Returns a new corpus with a the metadata matrix and index store integrated.
:param metadata_matrix: scipy.sparse matrix (# docs, # metadata)
:param meta_index_store: IndexStore of metadata values
:return: TermDocMatrixWithoutCategories
'''
assert isinstance(meta_index_store, IndexStore)
assert len(metadata_matrix.shape) == 2
assert metadata_matrix.shape[0] == self.get_num_docs()
return self._make_new_term_doc_matrix(new_X=self._X,
new_y=None,
new_category_idx_store=None,
new_y_mask=np.ones(self.get_num_docs()).astype(bool),
new_mX=metadata_matrix,
new_term_idx_store=self._term_idx_store,
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mikeboers/Flask-ACL | flask_acl/extension.py | https://github.com/mikeboers/Flask-ACL/blob/7339b89f96ad8686d1526e25c138244ad912e12d/flask_acl/extension.py#L101-L114 | def permission_set(self, name, func=None):
"""Define a new permission set (directly, or as a decorator).
E.g.::
@authz.permission_set('HTTP')
def is_http_perm(perm):
return perm.startswith('http.')
"""
if func is None:
return functools.partial(self.predicate, name)
self.permission_sets[name] = func
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Othernet-Project/ndb-utils | ndb_utils/models.py | https://github.com/Othernet-Project/ndb-utils/blob/7804a5e305a4ed280742e22dad1dd10756cbe695/ndb_utils/models.py#L130-L144 | def clean(self):
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senaite/senaite.core | bika/lims/browser/widgets/referenceresultswidget.py | https://github.com/senaite/senaite.core/blob/7602ce2ea2f9e81eb34e20ce17b98a3e70713f85/bika/lims/browser/widgets/referenceresultswidget.py#L133-L180 | def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
url = api.get_url(obj)
title = api.get_title(obj)
# get the category
if self.show_categories_enabled():
category = obj.getCategoryTitle()
if category not in self.categories:
self.categories.append(category)
item["category"] = category
rr = self.referenceresults.get(uid, {})
item["Title"] = title
item["replace"]["Title"] = get_link(url, value=title)
item["allow_edit"] = self.get_editable_columns()
item["required"] = self.get_required_columns()
item["selected"] = rr and True or False
item["result"] = rr.get("result", "")
item["min"] = rr.get("min", "")
item["max"] = rr.get("max", "")
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image(
"accredited.png", title=_("Accredited"))
if obj.getAttachmentOption() == "r":
after_icons += get_image(
"attach_reqd.png", title=_("Attachment required"))
if obj.getAttachmentOption() == "n":
after_icons += get_image(
"attach_no.png", title=_("Attachment not permitted"))
if after_icons:
item["after"]["Title"] = after_icons
return item | [
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gwastro/pycbc-glue | pycbc_glue/iterutils.py | https://github.com/gwastro/pycbc-glue/blob/a3e906bae59fbfd707c3ff82e5d008d939ec5e24/pycbc_glue/iterutils.py#L218-L240 | def inplace_filter(func, sequence):
"""
Like Python's filter() builtin, but modifies the sequence in place.
Example:
>>> l = range(10)
>>> inplace_filter(lambda x: x > 5, l)
>>> l
[6, 7, 8, 9]
Performance considerations: the function iterates over the
sequence, shuffling surviving members down and deleting whatever
top part of the sequence is left empty at the end, so sequences
whose surviving members are predominantly at the bottom will be
processed faster.
"""
target = 0
for source in xrange(len(sequence)):
if func(sequence[source]):
sequence[target] = sequence[source]
target += 1
del sequence[target:] | [
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bunq/sdk_python | bunq/sdk/model/generated/object_.py | https://github.com/bunq/sdk_python/blob/da6c9b83e6d83ee8062617f53c6eb7293c0d863d/bunq/sdk/model/generated/object_.py#L4337-L4369 | def is_all_field_none(self):
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if self._MasterCardAction is not None:
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dwavesystems/dwave-system | dwave/embedding/polynomialembedder.py | https://github.com/dwavesystems/dwave-system/blob/86a1698f15ccd8b0ece0ed868ee49292d3f67f5b/dwave/embedding/polynomialembedder.py#L291-L319 | def biclique(self, xmin, xmax, ymin, ymax):
"""Compute a maximum-sized complete bipartite graph contained in the
rectangle defined by ``xmin, xmax, ymin, ymax`` where each chain of
qubits is either a vertical line or a horizontal line.
INPUTS:
xmin,xmax,ymin,ymax: integers defining the bounds of a rectangle
where we look for unbroken chains. These ranges include both
endpoints.
OUTPUT:
(A_side, B_side): a tuple of two lists containing lists of qubits.
the lists found in ``A_side`` and ``B_side`` are chains of qubits.
These lists of qubits are arranged so that
>>> [zip(chain,chain[1:]) for chain in A_side]
and
>>> [zip(chain,chain[1:]) for chain in B_side]
are lists of valid couplers.
"""
Aside = sum((self.maximum_hline_bundle(y, xmin, xmax)
for y in range(ymin, ymax + 1)), [])
Bside = sum((self.maximum_vline_bundle(x, ymin, ymax)
for x in range(xmin, xmax + 1)), [])
return Aside, Bside | [
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pytroll/trollimage | trollimage/utilities.py | https://github.com/pytroll/trollimage/blob/d35a7665ad475ff230e457085523e21f2cd3f454/trollimage/utilities.py#L52-L73 | def _make_cmap(colors, position=None, bit=False):
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bit_rgb = np.linspace(0,1,256)
if position == None:
position = np.linspace(0,1,len(colors))
else:
if len(position) != len(colors):
sys.exit("position length must be the same as colors")
elif position[0] != 0 or position[-1] != 1:
sys.exit("position must start with 0 and end with 1")
palette = [(i, (float(r), float(g), float(b), float(a))) for
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cmap = Colormap(*palette)
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openid/python-openid | openid/consumer/discover.py | https://github.com/openid/python-openid/blob/f7e13536f0d1828d3cef5ae7a7b55cabadff37fc/openid/consumer/discover.py#L221-L231 | def fromOPEndpointURL(cls, op_endpoint_url):
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@param op_endpoint_url: The URL of the endpoint
@rtype: OpenIDServiceEndpoint
"""
service = cls()
service.server_url = op_endpoint_url
service.type_uris = [OPENID_IDP_2_0_TYPE]
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rfarley3/Kibana | kibana/mapping.py | https://github.com/rfarley3/Kibana/blob/3df1e13be18edfb39ec173d8d2bbe9e90be61022/kibana/mapping.py#L256-L278 | def get_field_mappings(self, field):
"""Converts ES field mappings to .kibana field mappings"""
retdict = {}
retdict['indexed'] = False
retdict['analyzed'] = False
for (key, val) in iteritems(field):
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JoelBender/bacpypes | py25/bacpypes/netservice.py | https://github.com/JoelBender/bacpypes/blob/4111b8604a16fa2b7f80d8104a43b9f3e28dfc78/py25/bacpypes/netservice.py#L234-L253 | def bind(self, server, net=None, address=None):
"""Create a network adapter object and bind."""
if _debug: NetworkServiceAccessPoint._debug("bind %r net=%r address=%r", server, net, address)
# make sure this hasn't already been called with this network
if net in self.adapters:
raise RuntimeError("already bound")
# create an adapter object, add it to our map
adapter = NetworkAdapter(self, net)
self.adapters[net] = adapter
if _debug: NetworkServiceAccessPoint._debug(" - adapters[%r]: %r", net, adapter)
# if the address was given, make it the "local" one
if address and not self.local_address:
self.local_adapter = adapter
self.local_address = address
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bind(adapter, server) | [
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belbio/bel | bel/edge/edges.py | https://github.com/belbio/bel/blob/60333e8815625b942b4836903f3b618cf44b3771/bel/edge/edges.py#L199-L217 | def extract_ast_species(ast):
"""Extract species from ast.species set of tuples (id, label)"""
species_id = "None"
species_label = "None"
species = [
(species_id, species_label) for (species_id, species_label) in ast.species if species_id
]
if len(species) == 1:
(species_id, species_label) = species[0]
if not species_id:
species_id = "None"
species_label = "None"
log.debug(f"AST Species: {ast.species} Species: {species} SpeciesID: {species_id}")
return (species_id, species_label) | [
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mwshinn/paranoidscientist | paranoid/decorators.py | https://github.com/mwshinn/paranoidscientist/blob/a5e9198bc40b0a985174ad643cc5d6d0c46efdcd/paranoid/decorators.py#L176-L217 | def accepts(*argtypes, **kwargtypes):
"""A function decorator to specify argument types of the function.
Types may be specified either in the order that they appear in the
function or via keyword arguments (just as if you were calling the
function).
Example usage:
| @accepts(Positive0)
| def square_root(x):
| ...
"""
theseargtypes = [T.TypeFactory(a) for a in argtypes]
thesekwargtypes = {k : T.TypeFactory(a) for k,a in kwargtypes.items()}
def _decorator(func):
# @accepts decorator
f = func.__wrapped__ if hasattr(func, "__wrapped__") else func
try:
argtypes = inspect.getcallargs(f, *theseargtypes, **thesekwargtypes)
argtypes = {k: v if issubclass(type(v), T.Type) else T.Constant(v)
for k,v in argtypes.items()}
except TypeError:
raise E.ArgumentTypeError("Invalid argument specification to @accepts in %s" % func.__qualname__)
# Support keyword arguments. Find the name of the **kwargs
# parameter (not necessarily "kwargs") and set it to be a
# dictionary of unspecified types.
kwargname = U.get_func_kwargs_name(func)
if kwargname in argtypes.keys():
argtypes[kwargname] = T.KeywordArguments()
# Support positional arguments. Find the name of the *args
# parameter (not necessarily "args") and set it to be an
# unspecified type.
posargname = U.get_func_posargs_name(func)
if posargname in argtypes.keys():
argtypes[posargname] = T.PositionalArguments() # TODO merge with actual argument names
if U.has_fun_prop(func, "argtypes"):
raise ValueError("Cannot set argument types twice")
U.set_fun_prop(func, "argtypes", argtypes)
return _wrap(func)
return _decorator | [
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ElementAI/greensim | greensim/__init__.py | https://github.com/ElementAI/greensim/blob/f160e8b57d69f6ef469f2e991cc07b7721e08a91/greensim/__init__.py#L301-L313 | def add_at(self, moment: float, fn_process: Callable, *args: Any, **kwargs: Any) -> 'Process':
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Adds a process to the simulation, which is made to start at the given exact time on the simulated clock. Note
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delay = moment - self.now()
if delay < 0.0:
raise ValueError(
f"The given moment to start the process ({moment:f}) is in the past (now is {self.now():f})."
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return self.add_in(delay, fn_process, *args, **kwargs) | [
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secdev/scapy | scapy/asn1fields.py | https://github.com/secdev/scapy/blob/3ffe757c184017dd46464593a8f80f85abc1e79a/scapy/asn1fields.py#L74-L101 | def m2i(self, pkt, s):
"""
The good thing about safedec is that it may still decode ASN1
even if there is a mismatch between the expected tag (self.ASN1_tag)
and the actual tag; the decoded ASN1 object will simply be put
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"""
diff_tag, s = BER_tagging_dec(s, hidden_tag=self.ASN1_tag,
implicit_tag=self.implicit_tag,
explicit_tag=self.explicit_tag,
safe=self.flexible_tag)
if diff_tag is not None:
# this implies that flexible_tag was True
if self.implicit_tag is not None:
self.implicit_tag = diff_tag
elif self.explicit_tag is not None:
self.explicit_tag = diff_tag
codec = self.ASN1_tag.get_codec(pkt.ASN1_codec)
if self.flexible_tag:
return codec.safedec(s, context=self.context)
else:
return codec.dec(s, context=self.context) | [
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pyrogram/pyrogram | pyrogram/client/filters/filters.py | https://github.com/pyrogram/pyrogram/blob/e7258a341ba905cfa86264c22040654db732ec1c/pyrogram/client/filters/filters.py#L275-L292 | def regex(pattern, flags: int = 0):
"""Filter messages that match a given RegEx pattern.
Args:
pattern (``str``):
The RegEx pattern as string, it will be applied to the text of a message. When a pattern matches,
all the `Match Objects <https://docs.python.org/3/library/re.html#match-objects>`_
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flags (``int``, *optional*):
RegEx flags.
"""
def f(_, m):
m.matches = [i for i in _.p.finditer(m.text or m.caption or "")]
return bool(m.matches)
return create("Regex", f, p=re.compile(pattern, flags)) | [
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sethmlarson/virtualbox-python | virtualbox/library.py | https://github.com/sethmlarson/virtualbox-python/blob/706c8e3f6e3aee17eb06458e73cbb4bc2d37878b/virtualbox/library.py#L30553-L30574 | def create_aggregator(self, subordinates):
"""Creates an aggregator event source, collecting events from multiple sources.
This way a single listener can listen for events coming from multiple sources,
using a single blocking :py:func:`get_event` on the returned aggregator.
in subordinates of type :class:`IEventSource`
Subordinate event source this one aggregates.
return result of type :class:`IEventSource`
Event source aggregating passed sources.
"""
if not isinstance(subordinates, list):
raise TypeError("subordinates can only be an instance of type list")
for a in subordinates[:10]:
if not isinstance(a, IEventSource):
raise TypeError(
"array can only contain objects of type IEventSource")
result = self._call("createAggregator",
in_p=[subordinates])
result = IEventSource(result)
return result | [
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singularityhub/sregistry-cli | sregistry/utils/fileio.py | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/utils/fileio.py#L283-L297 | def write_json(json_obj, filename, mode="w", print_pretty=True):
'''write_json will (optionally,pretty print) a json object to file
Parameters
==========
json_obj: the dict to print to json
filename: the output file to write to
pretty_print: if True, will use nicer formatting
'''
with open(filename, mode) as filey:
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filey.writelines(print_json(json_obj))
else:
filey.writelines(json.dumps(json_obj))
return filename | [
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openai/baselines | baselines/common/cmd_util.py | https://github.com/openai/baselines/blob/3301089b48c42b87b396e246ea3f56fa4bfc9678/baselines/common/cmd_util.py#L88-L102 | def make_mujoco_env(env_id, seed, reward_scale=1.0):
"""
Create a wrapped, monitored gym.Env for MuJoCo.
"""
rank = MPI.COMM_WORLD.Get_rank()
myseed = seed + 1000 * rank if seed is not None else None
set_global_seeds(myseed)
env = gym.make(env_id)
logger_path = None if logger.get_dir() is None else os.path.join(logger.get_dir(), str(rank))
env = Monitor(env, logger_path, allow_early_resets=True)
env.seed(seed)
if reward_scale != 1.0:
from baselines.common.retro_wrappers import RewardScaler
env = RewardScaler(env, reward_scale)
return env | [
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ray-project/ray | python/ray/tune/trial_runner.py | https://github.com/ray-project/ray/blob/4eade036a0505e244c976f36aaa2d64386b5129b/python/ray/tune/trial_runner.py#L247-L256 | def is_finished(self):
"""Returns whether all trials have finished running."""
if self._total_time > self._global_time_limit:
logger.warning("Exceeded global time limit {} / {}".format(
self._total_time, self._global_time_limit))
return True
trials_done = all(trial.is_finished() for trial in self._trials)
return trials_done and self._search_alg.is_finished() | [
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] | python | train | 42.5 |
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