code stringlengths 75 104k | docstring stringlengths 1 46.9k |
|---|---|
def _gamma_factorial(self, expr, n):
r"""
Compute :math:`\frac {(\alpha)_m = (\alpha + m - 1)!}{(\alpha - 1)!}`
See Eq. 3 in Gamma moment closure Lakatos 2014 unpublished
:param expr: a symbolic expression
:type expr:
:param n:
:type n: `int`
:return: a ... | r"""
Compute :math:`\frac {(\alpha)_m = (\alpha + m - 1)!}{(\alpha - 1)!}`
See Eq. 3 in Gamma moment closure Lakatos 2014 unpublished
:param expr: a symbolic expression
:type expr:
:param n:
:type n: `int`
:return: a symbolic expression |
def get_options_for_id(options: Dict[str, Dict[str, Any]], identifier: str):
"""
Helper method, from the full options dict of dicts, to return either the options related to this parser or an
empty dictionary. It also performs all the var type checks
:param options:
:param identifier:
:return:
... | Helper method, from the full options dict of dicts, to return either the options related to this parser or an
empty dictionary. It also performs all the var type checks
:param options:
:param identifier:
:return: |
def from_cwl(cls, data, __reference__=None):
"""Return an instance from CWL data."""
class_name = data.get('class', None)
cls = cls.registry.get(class_name, cls)
if __reference__:
with with_reference(__reference__):
self = cls(
**{k: v
... | Return an instance from CWL data. |
def accumulate(self, axis: AxisIdentifier) -> HistogramBase:
"""Calculate cumulative frequencies along a certain axis.
Returns
-------
new_hist: Histogram of the same type & size
"""
# TODO: Merge with Histogram1D.cumulative_frequencies
# TODO: Deal with errors a... | Calculate cumulative frequencies along a certain axis.
Returns
-------
new_hist: Histogram of the same type & size |
def move(self, x, y):
"""Move the virtual cursor.
Args:
x (int): x-coordinate to place the cursor.
y (int): y-coordinate to place the cursor.
.. seealso:: :any:`get_cursor`, :any:`print_str`, :any:`write`
"""
self._cursor = self._normalizePoint(x, y) | Move the virtual cursor.
Args:
x (int): x-coordinate to place the cursor.
y (int): y-coordinate to place the cursor.
.. seealso:: :any:`get_cursor`, :any:`print_str`, :any:`write` |
def setDefaults(configObj={}):
""" Return a dictionary of the default parameters
which also been updated with the user overrides.
"""
paramDict = {
'gain': 7, # Detector gain, e-/ADU
'grow': 1, # Radius around CR pixel to mask [default=1 for
... | Return a dictionary of the default parameters
which also been updated with the user overrides. |
def as_doc(self):
"""Get the SON document representation of this DBRef.
Generally not needed by application developers
"""
doc = SON([("$ref", self.collection),
("$id", self.id)])
if self.database is not None:
doc["$db"] = self.database
doc... | Get the SON document representation of this DBRef.
Generally not needed by application developers |
def get_subpackages(name):
"""Return subpackages of package *name*"""
splist = []
for dirpath, _dirnames, _filenames in os.walk(name):
if osp.isfile(osp.join(dirpath, '__init__.py')):
splist.append(".".join(dirpath.split(os.sep)))
return splist | Return subpackages of package *name* |
def merge_user_commits(cls, commits):
"""Merge all the commits for the user.
Aggregate line counts, and use the most recent commit (by date/time)
as the representative commit for the user.
"""
user = None
for commit in commits:
if not user:
us... | Merge all the commits for the user.
Aggregate line counts, and use the most recent commit (by date/time)
as the representative commit for the user. |
def imsave(filename, data, maxval=None, pam=False):
"""Write image data to Netpbm file.
Examples
--------
>>> image = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16)
>>> imsave('_tmp.pgm', image)
"""
try:
netpbm = NetpbmFile(data, maxval=maxval)
netpbm.write(filena... | Write image data to Netpbm file.
Examples
--------
>>> image = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16)
>>> imsave('_tmp.pgm', image) |
def _extract_proxies(self, ajax_endpoint):
''' request the xml object '''
proxy_xml = requests.get(ajax_endpoint)
print(proxy_xml.content)
root = etree.XML(proxy_xml.content)
quote = root.xpath('quote')[0]
''' extract the raw text from the body of the quote ... | request the xml object |
def _zforce(self,R,z,phi=0.,t=0.):
"""
NAME:
_zforce
PURPOSE:
evaluate the vertical force for this potential
INPUT:
R - Galactocentric cylindrical radius
z - vertical height
phi - azimuth
t - time
OUTPUT:
... | NAME:
_zforce
PURPOSE:
evaluate the vertical force for this potential
INPUT:
R - Galactocentric cylindrical radius
z - vertical height
phi - azimuth
t - time
OUTPUT:
the vertical force
HISTORY:
... |
def unpack(self, obs):
"""Return a correctly shaped numpy array for this feature."""
planes = getattr(obs.feature_layer_data, self.layer_set)
plane = getattr(planes, self.name)
return self.unpack_layer(plane) | Return a correctly shaped numpy array for this feature. |
def customize(self, customize):
"""
Special handling for opcodes, such as those that take a variable number
of arguments -- we add a new entry for each in TABLE_R.
"""
for k, v in list(customize.items()):
if k in TABLE_R:
continue
op = k[ :... | Special handling for opcodes, such as those that take a variable number
of arguments -- we add a new entry for each in TABLE_R. |
def is_(self, value):
"""
Sets the operator type to Query.Op.Is and sets the
value to the inputted value.
:param value <variant>
:return <Query>
:sa __eq__
:usage |>>> from orb import Query as Q
... | Sets the operator type to Query.Op.Is and sets the
value to the inputted value.
:param value <variant>
:return <Query>
:sa __eq__
:usage |>>> from orb import Query as Q
|>>> query = Q('test').is_(... |
def _read(self, ti, try_number, metadata=None):
"""
Read logs of given task instance and try_number from Wasb remote storage.
If failed, read the log from task instance host machine.
:param ti: task instance object
:param try_number: task instance try_number to read logs from
... | Read logs of given task instance and try_number from Wasb remote storage.
If failed, read the log from task instance host machine.
:param ti: task instance object
:param try_number: task instance try_number to read logs from
:param metadata: log metadata,
can be ... |
def rpc_get_account_balance(self, address, token_type, **con_info):
"""
Get the balance of an address for a particular token type
Returns the value on success
Returns 0 if the balance is 0, or if there is no address
"""
if not check_account_address(address):
r... | Get the balance of an address for a particular token type
Returns the value on success
Returns 0 if the balance is 0, or if there is no address |
def handle_friday(next_date: Datum, period: str, mult: int, start_date: Datum):
""" Extracted the calculation for when the next_day is Friday """
assert isinstance(next_date, Datum)
assert isinstance(start_date, Datum)
# Starting from line 220.
tmp_sat = next_date.clone()
tmp_sat.add_days(1)
... | Extracted the calculation for when the next_day is Friday |
def get_existing_pipelines(self):
"""Get existing pipeline configs for specific application.
Returns:
str: Pipeline config json
"""
url = "{0}/applications/{1}/pipelineConfigs".format(API_URL, self.app_name)
resp = requests.get(url, verify=GATE_CA_BUNDLE, cert=GATE_... | Get existing pipeline configs for specific application.
Returns:
str: Pipeline config json |
def accel_next(self, *args):
"""Callback to go to the next tab. Called by the accel key.
"""
if self.get_notebook().get_current_page() + 1 == self.get_notebook().get_n_pages():
self.get_notebook().set_current_page(0)
else:
self.get_notebook().next_page()
r... | Callback to go to the next tab. Called by the accel key. |
def _installed_packages(self) -> Generator[str, None, None]:
"""Extract installed packages as list from `package.json`."""
with (self._build_dir / 'package.json').open('r') as f:
packages = json.load(f)
yield from packages['dependencies'].keys() | Extract installed packages as list from `package.json`. |
def handle(dispatcher, *accept_args, **accept_kwargs):
"""
:param dispatcher: dispatcher to recieve events from
:param accept_args: args to match on
:param accept_kwargs: kwargs to match on
Creates an MNDFunction instance which containing the
argspec and adds the function to the dispatcher.
... | :param dispatcher: dispatcher to recieve events from
:param accept_args: args to match on
:param accept_kwargs: kwargs to match on
Creates an MNDFunction instance which containing the
argspec and adds the function to the dispatcher. |
def main():
""" Parses the command-line args, and calls run. """
parser = argparse.ArgumentParser(
description='A pipeline that generates analysis pipelines.')
parser.add_argument('input', nargs='?',
help='A valid metapipe configuration file.')
parser.add_argument('-o', '--out... | Parses the command-line args, and calls run. |
def _pack_image(filename, max_size, form_field='image', f=None):
"""Pack image from file into multipart-formdata post body"""
# image must be less than 700kb in size
if f is None:
try:
if os.path.getsize(filename) > (max_size * 1024):
raise TweepEr... | Pack image from file into multipart-formdata post body |
def do_global_lock(self, args):
'''read (or clear) the global lock'''
if args.purge:
self.task_master.registry.force_clear_lock()
else:
owner = self.task_master.registry.read_lock()
if owner:
heartbeat = self.task_master.get_heartbeat(owner)
... | read (or clear) the global lock |
def daterange(start, stop, step=1, inclusive=False):
"""In the spirit of :func:`range` and :func:`xrange`, the `daterange`
generator that yields a sequence of :class:`~datetime.date`
objects, starting at *start*, incrementing by *step*, until *stop*
is reached.
When *inclusive* is True, the final d... | In the spirit of :func:`range` and :func:`xrange`, the `daterange`
generator that yields a sequence of :class:`~datetime.date`
objects, starting at *start*, incrementing by *step*, until *stop*
is reached.
When *inclusive* is True, the final date may be *stop*, **if**
*step* falls evenly on it. By ... |
def get_consistent_set_and_saxis(magmoms, saxis=None):
"""
Method to ensure a list of magmoms use the same spin axis.
Returns a tuple of a list of Magmoms and their global spin axis.
:param magmoms: list of magmoms (Magmoms, scalars or vectors)
:param saxis: can provide a specif... | Method to ensure a list of magmoms use the same spin axis.
Returns a tuple of a list of Magmoms and their global spin axis.
:param magmoms: list of magmoms (Magmoms, scalars or vectors)
:param saxis: can provide a specific global spin axis
:return: (list of Magmoms, global spin axis) tu... |
def html(self) -> str:
"""Get whole html representation of this node."""
if self._inner_element:
return self.start_tag + self._inner_element.html + self.end_tag
return super().html | Get whole html representation of this node. |
def to_dict(self):
"""
Return dict representation of public key to embed in DID document.
"""
return {
'id': self.id,
'type': str(self.type.ver_type),
'controller': canon_ref(self.did, self.controller),
**self.type.specification(self.value... | Return dict representation of public key to embed in DID document. |
def host_diskpool_get_info(self, disk_pool=None):
""" Retrieve diskpool information.
:param str disk_pool: the disk pool info. It use ':' to separate
disk pool type and pool name, eg "ECKD:eckdpool" or "FBA:fbapool"
:returns: Dictionary describing disk pool usage info
"""
... | Retrieve diskpool information.
:param str disk_pool: the disk pool info. It use ':' to separate
disk pool type and pool name, eg "ECKD:eckdpool" or "FBA:fbapool"
:returns: Dictionary describing disk pool usage info |
def sync_counts(**kwargs):
"""
Iterates over registered recipes and denormalizes ``Badge.users.count()``
into ``Badge.users_count`` field.
"""
badges = kwargs.get('badges')
excluded = kwargs.get('exclude_badges')
instances = registry.get_recipe_instances(badges=badges, excluded=excluded)
... | Iterates over registered recipes and denormalizes ``Badge.users.count()``
into ``Badge.users_count`` field. |
def discover():
"""
Automatically discover the paths to various data folders in this project
and compose a Project instance.
Returns:
A constructed Project object.
Raises:
ValueError: if the paths could not be figured out automatically.
I... | Automatically discover the paths to various data folders in this project
and compose a Project instance.
Returns:
A constructed Project object.
Raises:
ValueError: if the paths could not be figured out automatically.
In this case, you have to create a Pr... |
def cropcenter(sz, img=None):
"""
if no img, then return crop function
:param sz:
:param img:
:return:
"""
l = len(sz)
sz = np.array(sz)
def wrapped(im):
imsz = np.array(im.shape)
s = (imsz[:l] - sz) / 2 # start index
to = s + sz # end index
# img[... | if no img, then return crop function
:param sz:
:param img:
:return: |
def add_bool_option(self, *args, **kwargs):
""" Add a boolean option.
@keyword help: Option description.
"""
dest = [o for o in args if o.startswith("--")][0].replace("--", "").replace("-", "_")
self.parser.add_option(dest=dest, action="store_true", default=False,
... | Add a boolean option.
@keyword help: Option description. |
def parse_setup(options: Union[List, str]) -> str:
"""Convert potentially a list of commands into a single string.
This creates a single string with newlines between each element of the list
so that they will all run after each other in a bash script.
"""
if isinstance(options, str):
retur... | Convert potentially a list of commands into a single string.
This creates a single string with newlines between each element of the list
so that they will all run after each other in a bash script. |
def remove_readonly(func, path, _):
"Clear the readonly bit and reattempt the removal"
os.chmod(path, stat.S_IWRITE)
func(path) | Clear the readonly bit and reattempt the removal |
def token_at_cursor(code, pos=0):
"""
Find the token present at the passed position in the code buffer
:return (tuple): a pair (token, start_position)
"""
l = len(code)
end = start = pos
# Go forwards while we get alphanumeric chars
while end < l and code[end].isalpha():
end += ... | Find the token present at the passed position in the code buffer
:return (tuple): a pair (token, start_position) |
def image_data(image):
"""Get components and bytes for an image"""
# NOTE: We might want to check the actual image.mode
# and convert to an acceptable format.
# At the moment we load the data as is.
data = image.tobytes()
components = len(data) // (image.size[0] * image.size[1]... | Get components and bytes for an image |
def alleles_to_retrieve(df):
"""Alleles to retrieve from genome fasta
Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be
retrieved from the genome contig.
Args:
df (pandas.DataFrame): blastn results dataframe
Returns:
{str:... | Alleles to retrieve from genome fasta
Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be
retrieved from the genome contig.
Args:
df (pandas.DataFrame): blastn results dataframe
Returns:
{str:[pandas.Series]}: dict of contig tit... |
def _parse(self, fname):
"""Parse a processed.top GROMACS topology file
The function reads in the file line-by-line, and it's a bunch of 'elif' statements,
writing parameter/atom line to current section/molecule.
ParamTypes are added to self.xyztypes (AtomType goes to self.atomtypes).
... | Parse a processed.top GROMACS topology file
The function reads in the file line-by-line, and it's a bunch of 'elif' statements,
writing parameter/atom line to current section/molecule.
ParamTypes are added to self.xyztypes (AtomType goes to self.atomtypes).
Params are added to current ... |
def generate_default_filename(infile_path, is_cropped_file=True):
"""Generate the name of the default output file from the name of the input
file. The is_cropped_file boolean is used to indicate that the file has been
(or will be) cropped, to determine which filename-modification string to
use. Functi... | Generate the name of the default output file from the name of the input
file. The is_cropped_file boolean is used to indicate that the file has been
(or will be) cropped, to determine which filename-modification string to
use. Function assumes that args has been set globally by argparse. |
def search_rule_by_id(self, ruleID) -> Rule:
""" searches a rule by given id
Args:
ruleID(str): the rule to search for
Returns
the rule object or None if it couldn't find a rule
"""
for r in self.rules:
if r.id == ruleID... | searches a rule by given id
Args:
ruleID(str): the rule to search for
Returns
the rule object or None if it couldn't find a rule |
def io_priority(self):
"""
IO priority for this instance.
"""
return (
self._iocb.aio_reqprio
if self._iocb.u.c.flags & libaio.IOCB_FLAG_IOPRIO else
None
) | IO priority for this instance. |
def get_built_image_info(self):
"""
query docker about built image
:return dict
"""
logger.info("getting information about built image '%s'", self.image)
image_info = self.tasker.get_image_info_by_image_name(self.image)
items_count = len(image_info)
if it... | query docker about built image
:return dict |
def _generic_convert_string(v, from_type, to_type, encoding):
"""
Generic method to convert any argument type (string type, list, set, tuple, dict) to an equivalent,
with string values converted to given 'to_type' (str or unicode).
This method must be used with Python 2 interpreter only.
:param v: ... | Generic method to convert any argument type (string type, list, set, tuple, dict) to an equivalent,
with string values converted to given 'to_type' (str or unicode).
This method must be used with Python 2 interpreter only.
:param v: The value to convert
:param from_type: The original string type to con... |
def generic_modis5kmto1km(*data5km):
"""Getting 1km data for modis from 5km tiepoints.
"""
cols5km = np.arange(2, 1354, 5)
cols1km = np.arange(1354)
lines = data5km[0].shape[0] * 5
rows5km = np.arange(2, lines, 5)
rows1km = np.arange(lines)
along_track_order = 1
cross_track_order = ... | Getting 1km data for modis from 5km tiepoints. |
def draw_strip_text(self, text_lines, location, pid):
"""
Create a background patch and put a label on it
"""
ax = self.axs[pid]
themeable = self.figure._themeable
dim = self.strip_dimensions(text_lines, location, pid)
if location == 'right':
rotation... | Create a background patch and put a label on it |
def get_next_character(self):
"""
Returns the character after the cursor.
:return: Next cursor character.
:rtype: QString
"""
cursor = self.textCursor()
cursor.movePosition(QTextCursor.NextCharacter, QTextCursor.KeepAnchor)
return cursor.selectedText() | Returns the character after the cursor.
:return: Next cursor character.
:rtype: QString |
def get_job_details(self, job_id):
"""
Gets all details for existing job
:param job_id: job_id as returned by 'create_operation_job(...)'
:return: job info as xml
"""
response = requests.get(self._get_job_details_url(job_id))
response.raise_for_status()
... | Gets all details for existing job
:param job_id: job_id as returned by 'create_operation_job(...)'
:return: job info as xml |
def _temp_exists(method, ip):
'''
Checks if the ip exists as a temporary rule based
on the method supplied, (tempallow, tempdeny).
'''
_type = method.replace('temp', '').upper()
cmd = "csf -t | awk -v code=1 -v type=_type -v ip=ip '$1==type && $2==ip {{code=0}} END {{exit code}}'".format(_type=_... | Checks if the ip exists as a temporary rule based
on the method supplied, (tempallow, tempdeny). |
def install_setuptools(python_cmd='python', use_sudo=True):
"""
Install the latest version of `setuptools`_.
::
import burlap
burlap.python_setuptools.install_setuptools()
"""
setuptools_version = package_version('setuptools', python_cmd)
distribute_version = package_version... | Install the latest version of `setuptools`_.
::
import burlap
burlap.python_setuptools.install_setuptools() |
def _check_for_slash_endings(self, readnames):
'''
Provide a list of read names to be checked for the /1 or /2 endings
which cause troubles downstream when working with paired reads. This
function checks the list for ANY read ending in /1 or /2. The reads are
first stripped of an... | Provide a list of read names to be checked for the /1 or /2 endings
which cause troubles downstream when working with paired reads. This
function checks the list for ANY read ending in /1 or /2. The reads are
first stripped of any comment lines, using the 'split' function
Parameters
... |
def routes(self):
""" Retrieves the main routes of the DTS Collection
Response format expected :
{
"@context": "/dts/api/contexts/EntryPoint.jsonld",
"@id": "/dts/api/",
"@type": "EntryPoint",
"collections": "/dts/api/collections/",
... | Retrieves the main routes of the DTS Collection
Response format expected :
{
"@context": "/dts/api/contexts/EntryPoint.jsonld",
"@id": "/dts/api/",
"@type": "EntryPoint",
"collections": "/dts/api/collections/",
"documents": "/dts... |
async def import_image(self, data, stream: bool = False):
"""
Import tarball of image to docker.
Args:
data: tarball data of image to be imported
Returns:
Tarball of the image
"""
headers = {"Content-Type": "application/x-tar"}
response =... | Import tarball of image to docker.
Args:
data: tarball data of image to be imported
Returns:
Tarball of the image |
def update_cache_for_instance(
model_name, instance_pk, instance=None, version=None):
"""Update the cache for an instance, with cascading updates."""
cache = SampleCache()
invalid = cache.update_instance(model_name, instance_pk, instance, version)
for invalid_name, invalid_pk, invalid_version in... | Update the cache for an instance, with cascading updates. |
def find_lc_timegroups(lctimes, mingap=4.0):
'''This finds the time gaps in the light curve, so we can figure out which
times are for consecutive observations and which represent gaps
between seasons.
Parameters
----------
lctimes : np.array
This is the input array of times, assumed to... | This finds the time gaps in the light curve, so we can figure out which
times are for consecutive observations and which represent gaps
between seasons.
Parameters
----------
lctimes : np.array
This is the input array of times, assumed to be in some form of JD.
mingap : float
... |
def update_opdocs(self, checksum, opdocs, revision=None):
"""
Modifies the internal state based a change to the content and returns
the sets of words added and removed.
:Parameters:
checksum : `hashable`
A checksum generated from the text of a revision
... | Modifies the internal state based a change to the content and returns
the sets of words added and removed.
:Parameters:
checksum : `hashable`
A checksum generated from the text of a revision
opdocs : `iterable` ( `dict` )
A sequence of operations ... |
def transform_sequence(f):
"""
A decorator to take a function operating on a point and
turn it into a function returning a callable operating on a sequence.
The functions passed to this decorator must define a kwarg called "point",
or have point be the last positional argument
"""
@wraps(f)
... | A decorator to take a function operating on a point and
turn it into a function returning a callable operating on a sequence.
The functions passed to this decorator must define a kwarg called "point",
or have point be the last positional argument |
def to_literal(self):
"""
Convert the node into a literal Python object
"""
if not self.nodes:
return (self.tag, self.attrib, self.text, [])
else:
return (self.tag, self.attrib, self.text,
list(map(to_literal, self.nodes))) | Convert the node into a literal Python object |
def spt(points, max_dist_error, max_speed_error):
""" A combination of both `td_sp` and `td_tr`
Detailed in,
Spatiotemporal Compression Techniques for Moving Point Objects,
Nirvana Meratnia and Rolf A. de By, 2004,
in Advances in Database Technology - EDBT 2004: 9th
Internationa... | A combination of both `td_sp` and `td_tr`
Detailed in,
Spatiotemporal Compression Techniques for Moving Point Objects,
Nirvana Meratnia and Rolf A. de By, 2004,
in Advances in Database Technology - EDBT 2004: 9th
International Conference on Extending Database Technology,
Her... |
def create_committee_member(self, url="", account=None, **kwargs):
""" Create a committee member
:param str url: URL to read more about the worker
:param str account: (optional) the account to allow access
to (defaults to ``default_account``)
"""
if not a... | Create a committee member
:param str url: URL to read more about the worker
:param str account: (optional) the account to allow access
to (defaults to ``default_account``) |
def merge(arg, *rest, **kwargs):
"""Merge a collection, with functions as items, into a single function
that takes a collection and maps its items through corresponding functions.
:param arg: A collection of functions, such as list, tuple, or dictionary
:param default: Optional default function to use ... | Merge a collection, with functions as items, into a single function
that takes a collection and maps its items through corresponding functions.
:param arg: A collection of functions, such as list, tuple, or dictionary
:param default: Optional default function to use for items
within mer... |
def create_config():
"""Initiates process to generate configuration file."""
file_exists = exists(CONFIG_FILE)
if not file_exists:
# Set directories
config.add_section('Directories')
defaults = [
('AbstractRetrieval', expanduser('~/.scopus/abstract_retrieval')),
... | Initiates process to generate configuration file. |
def get_info(self, code):
"""Return a dict of information about the currency"""
currency = self.get_currency(code)
info = {}
users = list(filter(None, currency['users'].split(',')))
if users:
info['Users'] = users
alt = list(filter(None, currency['alternativ... | Return a dict of information about the currency |
def wait_event(self, filter: Callable[[T_Event], bool] = None) -> Awaitable[T_Event]:
"""Shortcut for calling :func:`wait_event` with this signal in the first argument."""
return wait_event([self], filter) | Shortcut for calling :func:`wait_event` with this signal in the first argument. |
def new_dataset(data, identifier=None):
"""Initialize a new RT-DC dataset
Parameters
----------
data:
can be one of the following:
- dict
- .tdms file
- .rtdc file
- subclass of `RTDCBase`
(will create a hierarchy child)
identifier: str
A u... | Initialize a new RT-DC dataset
Parameters
----------
data:
can be one of the following:
- dict
- .tdms file
- .rtdc file
- subclass of `RTDCBase`
(will create a hierarchy child)
identifier: str
A unique identifier for this dataset. If set to `N... |
def _maybe_host_form_to_py_ast(
_: GeneratorContext, node: MaybeHostForm
) -> GeneratedPyAST:
"""Generate a Python AST node for accessing a potential Python module
variable name with a namespace."""
assert node.op == NodeOp.MAYBE_HOST_FORM
return GeneratedPyAST(
node=_load_attr(
... | Generate a Python AST node for accessing a potential Python module
variable name with a namespace. |
def pad_matrix(self, matrix, pad_value=0):
"""
Pad a possibly non-square matrix to make it square.
:Parameters:
matrix : list of lists
matrix to pad
pad_value : int
value to use to pad the matrix
:rtype: list of lists
:re... | Pad a possibly non-square matrix to make it square.
:Parameters:
matrix : list of lists
matrix to pad
pad_value : int
value to use to pad the matrix
:rtype: list of lists
:return: a new, possibly padded, matrix |
def find_key(self, regex):
"""Attempts to find a single S3 key based on the passed regex
Given a regular expression, this method searches the S3 bucket
for a matching key, and returns it if exactly 1 key matches.
Otherwise, None is returned.
:param regex: (str) Regular expressi... | Attempts to find a single S3 key based on the passed regex
Given a regular expression, this method searches the S3 bucket
for a matching key, and returns it if exactly 1 key matches.
Otherwise, None is returned.
:param regex: (str) Regular expression for an S3 key
:return: (str... |
def label_sectors(
*,
labels=["I", "II", "IV", "VI", "V", "III"],
ax=None,
lw=2,
lc="k",
cs=None,
c_zlevel=2,
c_alpha=0.5,
fontsize=40
):
"""Label the six time-orderings in a three-pulse experiment.
Parameters
----------
labels : list of strings
Labels to pla... | Label the six time-orderings in a three-pulse experiment.
Parameters
----------
labels : list of strings
Labels to place within sectors, starting in the upper left and
proceeding clockwise. Default is ['I', 'II', 'IV', 'VI', 'V', 'III'].
ax : matplotlib axis object (optional)
Ax... |
def derive_source_offset(self, offset, is_end=False):
"""
Given a post-preprocessed coordinate, derives the corresponding coordinate
in the original source file.
Returns result in the following tuple:
(src_offset, src_path, include_ref)
where:
- src_offse... | Given a post-preprocessed coordinate, derives the corresponding coordinate
in the original source file.
Returns result in the following tuple:
(src_offset, src_path, include_ref)
where:
- src_offset is the translated coordinate
If the input offset lands o... |
def start(self):
"""Start the channel"""
# observers for this channel only need to wait for one value
self._observer_params.update(dict(once=True))
super(CurrentResourceValue, self).start()
self._api.ensure_notifications_thread()
self._api._mds_rpc_post(
devic... | Start the channel |
def get_line_number(line_map, offset):
"""Find a line number, given a line map and a character offset."""
for lineno, line_offset in enumerate(line_map, start=1):
if line_offset > offset:
return lineno
return -1 | Find a line number, given a line map and a character offset. |
def delete_interconnect(self, enclosure_uri, bay, timeout=-1):
"""
Deletes an interconnect from a location.
Warning:
This won't delete the LOGICAL INTERCONNECT itself and might cause inconsistency between the enclosure
and Logical Interconnect Group.
Args:
... | Deletes an interconnect from a location.
Warning:
This won't delete the LOGICAL INTERCONNECT itself and might cause inconsistency between the enclosure
and Logical Interconnect Group.
Args:
enclosure_uri: URI of the Enclosure
bay: Bay
timeout... |
def revise(self, data, ignore_none=True):
"""
Revise attributes value with dictionary data.
:type data: dict
:type ignore_none: bool
**中文文档**
将一个字典中的数据更新到本条文档。当且仅当数据值不为None时。
"""
if not isinstance(data, dict):
raise TypeError("`data` has to ... | Revise attributes value with dictionary data.
:type data: dict
:type ignore_none: bool
**中文文档**
将一个字典中的数据更新到本条文档。当且仅当数据值不为None时。 |
def _trim_and_decode(ids, subtokenizer):
"""Trim EOS and PAD tokens from ids, and decode to return a string."""
try:
index = list(ids).index(tokenizer.EOS_ID)
return subtokenizer.decode(ids[:index])
except ValueError: # No EOS found in sequence
return subtokenizer.decode(ids) | Trim EOS and PAD tokens from ids, and decode to return a string. |
def _write_images(self, name:str, images:[Tensor])->None:
"Writes list of images as tensors to Tensorboard."
tag = self.ds_type.name + ' ' + name
self.tbwriter.add_image(tag=tag, img_tensor=vutils.make_grid(images, normalize=True), global_step=self.iteration) | Writes list of images as tensors to Tensorboard. |
def mask_file(regionfile, infile, outfile, negate=False):
"""
Created a masked version of file, using a region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The image will be masked according to this region.
infile... | Created a masked version of file, using a region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The image will be masked according to this region.
infile : str
Input FITS image.
outfile : str
Output FIT... |
def get_trade_histories(self, symbol):
"""List the latest trades for a symbol
https://docs.kucoin.com/#get-trade-histories
:param symbol: Name of symbol e.g. KCS-BTC
:type symbol: string
.. code:: python
orders = client.get_trade_histories('KCS-BTC')
:ret... | List the latest trades for a symbol
https://docs.kucoin.com/#get-trade-histories
:param symbol: Name of symbol e.g. KCS-BTC
:type symbol: string
.. code:: python
orders = client.get_trade_histories('KCS-BTC')
:returns: ApiResponse
.. code:: python
... |
def _get_x_axis(self):
"""See http://www.gdal.org/gdal_datamodel.html for details."""
# 0,0 is top/left top top/left pixel. Actual x/y coord of that pixel are (.5,.5).
x_centers = np.linspace(.5, self.x_size - .5, self.x_size)
y_centers = x_centers * 0
return (self.geotransform[0... | See http://www.gdal.org/gdal_datamodel.html for details. |
def close(self):
"""Send CLOSE command to device."""
close_command = StandardSend(self._address,
COMMAND_LIGHT_OFF_0X13_0X00)
self._send_method(close_command, self._close_message_received) | Send CLOSE command to device. |
def params(dirnames, param_func, t_steady=None):
"""Calculate a parameter of a set of model output directories,
for a measure function which returns an associated uncertainty.
Parameters
----------
dirnames: list[str]
Model output directory paths.
param_func: function
Function w... | Calculate a parameter of a set of model output directories,
for a measure function which returns an associated uncertainty.
Parameters
----------
dirnames: list[str]
Model output directory paths.
param_func: function
Function which takes a :class:`Model` instance as a single argumen... |
def clean(self):
''' priorDays is required for Generic Repeated Expenses to avoid infinite loops '''
if not self.priorDays and not self.startDate:
raise ValidationError(_(
'Either a start date or an "up to __ days in the past" limit is required ' +
'for repeat... | priorDays is required for Generic Repeated Expenses to avoid infinite loops |
def _coerce_type(self, field_type, value):
"""Returns unicode(value) after trying to coerce it into the Solr field type.
@param field_type(string) The Solr field type for the value
@param value(any) The value that is to be represented as Unicode text.
"""
if value is None:
... | Returns unicode(value) after trying to coerce it into the Solr field type.
@param field_type(string) The Solr field type for the value
@param value(any) The value that is to be represented as Unicode text. |
def run(self, gin):
"""
Run GULP using the gin as input
Args:
gin: GULP input string
Returns:
gout: GULP output string
"""
with ScratchDir("."):
p = subprocess.Popen(
self._gulp_cmd, stdout=subprocess.PIPE,
... | Run GULP using the gin as input
Args:
gin: GULP input string
Returns:
gout: GULP output string |
def _convolve_spatial2(im, hs,
mode = "constant",
grid_dim = None,
pad_factor = 2,
plan = None,
return_plan = False):
"""
spatial varying convolution of an 2d image with a 2d grid of psfs
shape(im_... | spatial varying convolution of an 2d image with a 2d grid of psfs
shape(im_ = (Ny,Nx)
shape(hs) = (Gy,Gx, Hy,Hx)
the input image im is subdivided into (Gy,Gx) blocks
hs[j,i] is the psf at the center of each block (i,j)
as of now each image dimension has to be divisible by the grid dim, i.e.
N... |
def dedent(text):
"""Equivalent of textwrap.dedent that ignores unindented first line.
This means it will still dedent strings like:
'''foo
is a bar
'''
For use in wrap_paragraphs.
"""
if text.startswith('\n'):
# text starts with blank line, don't ignore the first line
... | Equivalent of textwrap.dedent that ignores unindented first line.
This means it will still dedent strings like:
'''foo
is a bar
'''
For use in wrap_paragraphs. |
def loadmask(self, filename: str) -> np.ndarray:
"""Load a mask file."""
mask = scipy.io.loadmat(self.find_file(filename, what='mask'))
maskkey = [k for k in mask.keys() if not (k.startswith('_') or k.endswith('_'))][0]
return mask[maskkey].astype(np.bool) | Load a mask file. |
def texto_decimal(valor, remover_zeros=True):
"""Converte um valor :py:class:`decimal.Decimal` para texto, com a opção de
remover os zeros à direita não significativos. A conversão para texto irá
considerar o :py:module:`locale` para converter o texto pronto para
apresentação.
:param decimal.Decima... | Converte um valor :py:class:`decimal.Decimal` para texto, com a opção de
remover os zeros à direita não significativos. A conversão para texto irá
considerar o :py:module:`locale` para converter o texto pronto para
apresentação.
:param decimal.Decimal valor: Valor a converter para texto.
:param boo... |
def __init_from_list_np2d(self, mats, params_str, ref_dataset):
"""Initialize data from a list of 2-D numpy matrices."""
ncol = mats[0].shape[1]
nrow = np.zeros((len(mats),), np.int32)
if mats[0].dtype == np.float64:
ptr_data = (ctypes.POINTER(ctypes.c_double) * len(mats))()
... | Initialize data from a list of 2-D numpy matrices. |
def write_multiple_registers(slave_id, starting_address, values):
""" Return ADU for Modbus function code 16: Write Multiple Registers.
:param slave_id: Number of slave.
:return: Byte array with ADU.
"""
function = WriteMultipleRegisters()
function.starting_address = starting_address
functi... | Return ADU for Modbus function code 16: Write Multiple Registers.
:param slave_id: Number of slave.
:return: Byte array with ADU. |
def scale(self, selections, factor):
'''Scale the objects represented by *selections* up to a
certain *factor*.
'''
if 'atoms' in selections:
atms = selections['atoms'].mask
if factor is None:
self.scale_factors[atms] = 1.0
else:
... | Scale the objects represented by *selections* up to a
certain *factor*. |
def get_min_distance(self, mesh):
"""
For each point in ``mesh`` compute the minimum distance to each
surface element and return the smallest value.
See :meth:`superclass method
<.base.BaseSurface.get_min_distance>`
for spec of input and result values.
"""
... | For each point in ``mesh`` compute the minimum distance to each
surface element and return the smallest value.
See :meth:`superclass method
<.base.BaseSurface.get_min_distance>`
for spec of input and result values. |
def is_dxlink(x):
'''
:param x: A potential DNAnexus link
Returns whether *x* appears to be a DNAnexus link (is a dict with
key ``"$dnanexus_link"``) with a referenced data object.
'''
if not isinstance(x, dict):
return False
if '$dnanexus_link' not in x:
return False
li... | :param x: A potential DNAnexus link
Returns whether *x* appears to be a DNAnexus link (is a dict with
key ``"$dnanexus_link"``) with a referenced data object. |
def share(self, project, to_user, force_send, auth_role, user_message):
"""
Send mail and give user specified access to the project.
:param project: RemoteProject project to share
:param to_user: RemoteUser user to receive email/access
:param auth_role: str project role eg 'proje... | Send mail and give user specified access to the project.
:param project: RemoteProject project to share
:param to_user: RemoteUser user to receive email/access
:param auth_role: str project role eg 'project_admin' to give to the user
:param user_message: str message to be sent with the s... |
def get_queryset(self): # pylint: disable=method-hidden
"""Return queryset."""
if self.request and self.request.query_params.get('hydrate_data', False):
return self.queryset.prefetch_related('data__entity_set')
return self.queryset | Return queryset. |
def repmd(instr, marker, value, sigdig):
"""
Replace a marker with a double precision number.
http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/repmd_c.html
:param instr: Input string.
:type instr: str
:param marker: Marker to be replaced.
:type marker: str
:param value: Replacem... | Replace a marker with a double precision number.
http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/repmd_c.html
:param instr: Input string.
:type instr: str
:param marker: Marker to be replaced.
:type marker: str
:param value: Replacement value.
:type value: float
:param sigdig: ... |
def run(self):
"""Parse the script file.
:rtype: :py:class:`~turberfield.dialogue.model.Model`
"""
model = Model(self.fP, self.doc)
self.doc.walkabout(model)
return model | Parse the script file.
:rtype: :py:class:`~turberfield.dialogue.model.Model` |
def lsdirs(root=".", **kwargs):
"""
Return only subdirectories from a directory listing.
Arguments:
root (str): Path to directory. Can be relative or absolute.
**kwargs: Any additional arguments to be passed to ls().
Returns:
list of str: A list of directory paths.
Raise... | Return only subdirectories from a directory listing.
Arguments:
root (str): Path to directory. Can be relative or absolute.
**kwargs: Any additional arguments to be passed to ls().
Returns:
list of str: A list of directory paths.
Raises:
OSError: If root directory does ... |
def delete_password(self, service, username):
"""Delete the password for the username of the service.
"""
if not self.connected(service):
# the user pressed "cancel" when prompted to unlock their keyring.
raise PasswordDeleteError("Cancelled by user")
if not self.... | Delete the password for the username of the service. |
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