repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 | partition stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|
warrenspe/hconf | hconf/subparsers/cmdline.py | Cmdline.getArgumentParser | def getArgumentParser(self, configManager, config):
"""
May be overidden to provide custom functionality.
Constructs an argparse.ArgumentParser used to parse configuration options from the command line.
Inputs: configManager - Our parent ConfigManager instance which is constructing the ... | python | def getArgumentParser(self, configManager, config):
"""
May be overidden to provide custom functionality.
Constructs an argparse.ArgumentParser used to parse configuration options from the command line.
Inputs: configManager - Our parent ConfigManager instance which is constructing the ... | [
"def",
"getArgumentParser",
"(",
"self",
",",
"configManager",
",",
"config",
")",
":",
"argParser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"self",
".",
"description",
")",
"for",
"configName",
",",
"configDict",
"in",
"configManager",
".",
"configs",
".... | May be overidden to provide custom functionality.
Constructs an argparse.ArgumentParser used to parse configuration options from the command line.
Inputs: configManager - Our parent ConfigManager instance which is constructing the Config object.
config - The _Config object contai... | [
"May",
"be",
"overidden",
"to",
"provide",
"custom",
"functionality",
".",
"Constructs",
"an",
"argparse",
".",
"ArgumentParser",
"used",
"to",
"parse",
"configuration",
"options",
"from",
"the",
"command",
"line",
"."
] | 12074d15dc3641d3903488c95d89a507386a32d5 | https://github.com/warrenspe/hconf/blob/12074d15dc3641d3903488c95d89a507386a32d5/hconf/subparsers/cmdline.py#L41-L61 | train |
warrenspe/hconf | hconf/subparsers/cmdline.py | Cmdline.parse | def parse(self, configManager, config):
"""
Parses commandline arguments, given a series of configuration options.
Inputs: configManager - Our parent ConfigManager instance which is constructing the Config object.
config - The _Config object containing configuration optio... | python | def parse(self, configManager, config):
"""
Parses commandline arguments, given a series of configuration options.
Inputs: configManager - Our parent ConfigManager instance which is constructing the Config object.
config - The _Config object containing configuration optio... | [
"def",
"parse",
"(",
"self",
",",
"configManager",
",",
"config",
")",
":",
"argParser",
"=",
"self",
".",
"getArgumentParser",
"(",
"configManager",
",",
"config",
")",
"return",
"vars",
"(",
"argParser",
".",
"parse_args",
"(",
")",
")"
] | Parses commandline arguments, given a series of configuration options.
Inputs: configManager - Our parent ConfigManager instance which is constructing the Config object.
config - The _Config object containing configuration options populated thus far.
Outputs: A dictionary of new... | [
"Parses",
"commandline",
"arguments",
"given",
"a",
"series",
"of",
"configuration",
"options",
"."
] | 12074d15dc3641d3903488c95d89a507386a32d5 | https://github.com/warrenspe/hconf/blob/12074d15dc3641d3903488c95d89a507386a32d5/hconf/subparsers/cmdline.py#L63-L74 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.candidates | def candidates(text):
"""
Given a `text` string, get candidates and context for feature
extraction and classification
"""
for Pmatch in finditer(TARGET, text):
# the punctuation mark itself
P = Pmatch.group(1)
# is it a boundary?
B ... | python | def candidates(text):
"""
Given a `text` string, get candidates and context for feature
extraction and classification
"""
for Pmatch in finditer(TARGET, text):
# the punctuation mark itself
P = Pmatch.group(1)
# is it a boundary?
B ... | [
"def",
"candidates",
"(",
"text",
")",
":",
"for",
"Pmatch",
"in",
"finditer",
"(",
"TARGET",
",",
"text",
")",
":",
"# the punctuation mark itself",
"P",
"=",
"Pmatch",
".",
"group",
"(",
"1",
")",
"# is it a boundary?",
"B",
"=",
"bool",
"(",
"match",
... | Given a `text` string, get candidates and context for feature
extraction and classification | [
"Given",
"a",
"text",
"string",
"get",
"candidates",
"and",
"context",
"for",
"feature",
"extraction",
"and",
"classification"
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L105-L127 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.extract_one | def extract_one(self, L, P, R):
"""
Given left context `L`, punctuation mark `P`, and right context
R`, extract features. Probability distributions for any
quantile-based features will not be modified.
"""
yield "*bias*"
# L feature(s)
if match(QUOTE, L):
... | python | def extract_one(self, L, P, R):
"""
Given left context `L`, punctuation mark `P`, and right context
R`, extract features. Probability distributions for any
quantile-based features will not be modified.
"""
yield "*bias*"
# L feature(s)
if match(QUOTE, L):
... | [
"def",
"extract_one",
"(",
"self",
",",
"L",
",",
"P",
",",
"R",
")",
":",
"yield",
"\"*bias*\"",
"# L feature(s)",
"if",
"match",
"(",
"QUOTE",
",",
"L",
")",
":",
"L",
"=",
"QUOTE_TOKEN",
"elif",
"isnumberlike",
"(",
"L",
")",
":",
"L",
"=",
"NUM... | Given left context `L`, punctuation mark `P`, and right context
R`, extract features. Probability distributions for any
quantile-based features will not be modified. | [
"Given",
"left",
"context",
"L",
"punctuation",
"mark",
"P",
"and",
"right",
"context",
"R",
"extract",
"features",
".",
"Probability",
"distributions",
"for",
"any",
"quantile",
"-",
"based",
"features",
"will",
"not",
"be",
"modified",
"."
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L132-L173 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.fit | def fit(self, text, epochs=EPOCHS):
""" Given a string `text`, use it to train the segmentation classifier for `epochs` iterations.
"""
logger.debug("Extracting features and classifications.")
Phi = []
Y = []
for (L, P, R, gold, _) in Detector.candidates(text):
... | python | def fit(self, text, epochs=EPOCHS):
""" Given a string `text`, use it to train the segmentation classifier for `epochs` iterations.
"""
logger.debug("Extracting features and classifications.")
Phi = []
Y = []
for (L, P, R, gold, _) in Detector.candidates(text):
... | [
"def",
"fit",
"(",
"self",
",",
"text",
",",
"epochs",
"=",
"EPOCHS",
")",
":",
"logger",
".",
"debug",
"(",
"\"Extracting features and classifications.\"",
")",
"Phi",
"=",
"[",
"]",
"Y",
"=",
"[",
"]",
"for",
"(",
"L",
",",
"P",
",",
"R",
",",
"g... | Given a string `text`, use it to train the segmentation classifier for `epochs` iterations. | [
"Given",
"a",
"string",
"text",
"use",
"it",
"to",
"train",
"the",
"segmentation",
"classifier",
"for",
"epochs",
"iterations",
"."
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L177-L187 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.predict | def predict(self, L, P, R):
"""
Given an left context `L`, punctuation mark `P`, and right context
`R`, return True iff this observation is hypothesized to be a
sentence boundary.
"""
phi = self.extract_one(L, P, R)
return self.classifier.predict(phi) | python | def predict(self, L, P, R):
"""
Given an left context `L`, punctuation mark `P`, and right context
`R`, return True iff this observation is hypothesized to be a
sentence boundary.
"""
phi = self.extract_one(L, P, R)
return self.classifier.predict(phi) | [
"def",
"predict",
"(",
"self",
",",
"L",
",",
"P",
",",
"R",
")",
":",
"phi",
"=",
"self",
".",
"extract_one",
"(",
"L",
",",
"P",
",",
"R",
")",
"return",
"self",
".",
"classifier",
".",
"predict",
"(",
"phi",
")"
] | Given an left context `L`, punctuation mark `P`, and right context
`R`, return True iff this observation is hypothesized to be a
sentence boundary. | [
"Given",
"an",
"left",
"context",
"L",
"punctuation",
"mark",
"P",
"and",
"right",
"context",
"R",
"return",
"True",
"iff",
"this",
"observation",
"is",
"hypothesized",
"to",
"be",
"a",
"sentence",
"boundary",
"."
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L189-L196 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.segments | def segments(self, text):
"""
Given a string of `text`, return a generator yielding each
hypothesized sentence string
"""
start = 0
for (L, P, R, B, end) in Detector.candidates(text):
# if there's already a newline there, we have nothing to do
if B... | python | def segments(self, text):
"""
Given a string of `text`, return a generator yielding each
hypothesized sentence string
"""
start = 0
for (L, P, R, B, end) in Detector.candidates(text):
# if there's already a newline there, we have nothing to do
if B... | [
"def",
"segments",
"(",
"self",
",",
"text",
")",
":",
"start",
"=",
"0",
"for",
"(",
"L",
",",
"P",
",",
"R",
",",
"B",
",",
"end",
")",
"in",
"Detector",
".",
"candidates",
"(",
"text",
")",
":",
"# if there's already a newline there, we have nothing t... | Given a string of `text`, return a generator yielding each
hypothesized sentence string | [
"Given",
"a",
"string",
"of",
"text",
"return",
"a",
"generator",
"yielding",
"each",
"hypothesized",
"sentence",
"string"
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L198-L212 | train |
totalgood/pugnlp | src/pugnlp/detector_morse.py | Detector.evaluate | def evaluate(self, text):
"""
Given a string of `text`, compute confusion matrix for the
classification task.
"""
cx = BinaryConfusion()
for (L, P, R, gold, _) in Detector.candidates(text):
guess = self.predict(L, P, R)
cx.update(gold, guess)
... | python | def evaluate(self, text):
"""
Given a string of `text`, compute confusion matrix for the
classification task.
"""
cx = BinaryConfusion()
for (L, P, R, gold, _) in Detector.candidates(text):
guess = self.predict(L, P, R)
cx.update(gold, guess)
... | [
"def",
"evaluate",
"(",
"self",
",",
"text",
")",
":",
"cx",
"=",
"BinaryConfusion",
"(",
")",
"for",
"(",
"L",
",",
"P",
",",
"R",
",",
"gold",
",",
"_",
")",
"in",
"Detector",
".",
"candidates",
"(",
"text",
")",
":",
"guess",
"=",
"self",
".... | Given a string of `text`, compute confusion matrix for the
classification task. | [
"Given",
"a",
"string",
"of",
"text",
"compute",
"confusion",
"matrix",
"for",
"the",
"classification",
"task",
"."
] | c43445b14afddfdeadc5f3076675c9e8fc1ee67c | https://github.com/totalgood/pugnlp/blob/c43445b14afddfdeadc5f3076675c9e8fc1ee67c/src/pugnlp/detector_morse.py#L214-L227 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | scale | def scale(mask, mag_scale, outfile=None):
"""
Scale the completeness depth of a mask such that mag_new = mag + mag_scale.
Input is a full HEALPix map.
Optionally write out the scaled mask as an sparse HEALPix map.
"""
msg = "'mask.scale': ADW 2018-05-05"
DeprecationWarning(msg)
mask_new ... | python | def scale(mask, mag_scale, outfile=None):
"""
Scale the completeness depth of a mask such that mag_new = mag + mag_scale.
Input is a full HEALPix map.
Optionally write out the scaled mask as an sparse HEALPix map.
"""
msg = "'mask.scale': ADW 2018-05-05"
DeprecationWarning(msg)
mask_new ... | [
"def",
"scale",
"(",
"mask",
",",
"mag_scale",
",",
"outfile",
"=",
"None",
")",
":",
"msg",
"=",
"\"'mask.scale': ADW 2018-05-05\"",
"DeprecationWarning",
"(",
"msg",
")",
"mask_new",
"=",
"hp",
".",
"UNSEEN",
"*",
"np",
".",
"ones",
"(",
"len",
"(",
"m... | Scale the completeness depth of a mask such that mag_new = mag + mag_scale.
Input is a full HEALPix map.
Optionally write out the scaled mask as an sparse HEALPix map. | [
"Scale",
"the",
"completeness",
"depth",
"of",
"a",
"mask",
"such",
"that",
"mag_new",
"=",
"mag",
"+",
"mag_scale",
".",
"Input",
"is",
"a",
"full",
"HEALPix",
"map",
".",
"Optionally",
"write",
"out",
"the",
"scaled",
"mask",
"as",
"an",
"sparse",
"HEA... | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L1007-L1025 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | Mask.mask_roi_unique | def mask_roi_unique(self):
"""
Assemble a set of unique magnitude tuples for the ROI
"""
# There is no good inherent way in numpy to do this...
# http://stackoverflow.com/q/16970982/
# Also possible and simple:
#return np.unique(zip(self.mask_1.mask_roi_sparse,se... | python | def mask_roi_unique(self):
"""
Assemble a set of unique magnitude tuples for the ROI
"""
# There is no good inherent way in numpy to do this...
# http://stackoverflow.com/q/16970982/
# Also possible and simple:
#return np.unique(zip(self.mask_1.mask_roi_sparse,se... | [
"def",
"mask_roi_unique",
"(",
"self",
")",
":",
"# There is no good inherent way in numpy to do this...",
"# http://stackoverflow.com/q/16970982/",
"# Also possible and simple:",
"#return np.unique(zip(self.mask_1.mask_roi_sparse,self.mask_2.mask_roi_sparse))",
"A",
"=",
"np",
".",
"vst... | Assemble a set of unique magnitude tuples for the ROI | [
"Assemble",
"a",
"set",
"of",
"unique",
"magnitude",
"tuples",
"for",
"the",
"ROI"
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L55-L67 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | Mask.mask_roi_digi | def mask_roi_digi(self):
"""
Get the index of the unique magnitude tuple for each pixel in the ROI.
"""
# http://stackoverflow.com/q/24205045/#24206440
A = np.vstack([self.mask_1.mask_roi_sparse,self.mask_2.mask_roi_sparse]).T
B = self.mask_roi_unique
AA = np.asc... | python | def mask_roi_digi(self):
"""
Get the index of the unique magnitude tuple for each pixel in the ROI.
"""
# http://stackoverflow.com/q/24205045/#24206440
A = np.vstack([self.mask_1.mask_roi_sparse,self.mask_2.mask_roi_sparse]).T
B = self.mask_roi_unique
AA = np.asc... | [
"def",
"mask_roi_digi",
"(",
"self",
")",
":",
"# http://stackoverflow.com/q/24205045/#24206440",
"A",
"=",
"np",
".",
"vstack",
"(",
"[",
"self",
".",
"mask_1",
".",
"mask_roi_sparse",
",",
"self",
".",
"mask_2",
".",
"mask_roi_sparse",
"]",
")",
".",
"T",
... | Get the index of the unique magnitude tuple for each pixel in the ROI. | [
"Get",
"the",
"index",
"of",
"the",
"unique",
"magnitude",
"tuple",
"for",
"each",
"pixel",
"in",
"the",
"ROI",
"."
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L70-L87 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | Mask._fracRoiSparse | def _fracRoiSparse(self):
"""
Calculate an approximate pixel coverage fraction from the two masks.
We have no way to know a priori how much the coverage of the
two masks overlap in a give pixel. For example, masks that each
have frac = 0.5 could have a combined frac = [0.0 to 0.... | python | def _fracRoiSparse(self):
"""
Calculate an approximate pixel coverage fraction from the two masks.
We have no way to know a priori how much the coverage of the
two masks overlap in a give pixel. For example, masks that each
have frac = 0.5 could have a combined frac = [0.0 to 0.... | [
"def",
"_fracRoiSparse",
"(",
"self",
")",
":",
"self",
".",
"frac_roi_sparse",
"=",
"np",
".",
"min",
"(",
"[",
"self",
".",
"mask_1",
".",
"frac_roi_sparse",
",",
"self",
".",
"mask_2",
".",
"frac_roi_sparse",
"]",
",",
"axis",
"=",
"0",
")",
"return... | Calculate an approximate pixel coverage fraction from the two masks.
We have no way to know a priori how much the coverage of the
two masks overlap in a give pixel. For example, masks that each
have frac = 0.5 could have a combined frac = [0.0 to 0.5].
The limits will be:
ma... | [
"Calculate",
"an",
"approximate",
"pixel",
"coverage",
"fraction",
"from",
"the",
"two",
"masks",
"."
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L97-L113 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | Mask._pruneMMD | def _pruneMMD(self, minimum_solid_angle):
"""
Remove regions of magnitude-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
INPUTS:
solid_angle[1]: minimum solid angle (deg^2)
"""
logger.info('Pruning ma... | python | def _pruneMMD(self, minimum_solid_angle):
"""
Remove regions of magnitude-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
INPUTS:
solid_angle[1]: minimum solid angle (deg^2)
"""
logger.info('Pruning ma... | [
"def",
"_pruneMMD",
"(",
"self",
",",
"minimum_solid_angle",
")",
":",
"logger",
".",
"info",
"(",
"'Pruning mask based on minimum solid angle of %.2f deg^2'",
"%",
"(",
"minimum_solid_angle",
")",
")",
"solid_angle_mmd",
"=",
"self",
".",
"solid_angle_mmd",
"*",
"(",... | Remove regions of magnitude-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
INPUTS:
solid_angle[1]: minimum solid angle (deg^2) | [
"Remove",
"regions",
"of",
"magnitude",
"-",
"magnitude",
"space",
"where",
"the",
"unmasked",
"solid",
"angle",
"is",
"statistically",
"insufficient",
"to",
"estimate",
"the",
"background",
"."
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L135-L162 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | Mask._pruneCMD | def _pruneCMD(self, minimum_solid_angle):
"""
Remove regions of color-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
ADW: Why are we clipping at the bin center instead of edge?
INPUTS:
solid_angle[1]: minimum... | python | def _pruneCMD(self, minimum_solid_angle):
"""
Remove regions of color-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
ADW: Why are we clipping at the bin center instead of edge?
INPUTS:
solid_angle[1]: minimum... | [
"def",
"_pruneCMD",
"(",
"self",
",",
"minimum_solid_angle",
")",
":",
"logger",
".",
"info",
"(",
"'Pruning mask based on minimum solid angle of %.2f deg^2'",
"%",
"(",
"minimum_solid_angle",
")",
")",
"self",
".",
"solid_angle_cmd",
"*=",
"self",
".",
"solid_angle_c... | Remove regions of color-magnitude space where the unmasked solid angle is
statistically insufficient to estimate the background.
ADW: Why are we clipping at the bin center instead of edge?
INPUTS:
solid_angle[1]: minimum solid angle (deg^2) | [
"Remove",
"regions",
"of",
"color",
"-",
"magnitude",
"space",
"where",
"the",
"unmasked",
"solid",
"angle",
"is",
"statistically",
"insufficient",
"to",
"estimate",
"the",
"background",
"."
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L257-L294 | train |
DarkEnergySurvey/ugali | ugali/observation/mask.py | MaskBand.plot | def plot(self):
"""
Plot the magnitude depth.
"""
msg = "'%s.plot': ADW 2018-05-05"%self.__class__.__name__
DeprecationWarning(msg)
import ugali.utils.plotting
mask = hp.UNSEEN * np.ones(hp.nside2npix(self.nside))
mask[self.roi.pixels] = self.mask_roi_sp... | python | def plot(self):
"""
Plot the magnitude depth.
"""
msg = "'%s.plot': ADW 2018-05-05"%self.__class__.__name__
DeprecationWarning(msg)
import ugali.utils.plotting
mask = hp.UNSEEN * np.ones(hp.nside2npix(self.nside))
mask[self.roi.pixels] = self.mask_roi_sp... | [
"def",
"plot",
"(",
"self",
")",
":",
"msg",
"=",
"\"'%s.plot': ADW 2018-05-05\"",
"%",
"self",
".",
"__class__",
".",
"__name__",
"DeprecationWarning",
"(",
"msg",
")",
"import",
"ugali",
".",
"utils",
".",
"plotting",
"mask",
"=",
"hp",
".",
"UNSEEN",
"*... | Plot the magnitude depth. | [
"Plot",
"the",
"magnitude",
"depth",
"."
] | 21e890b4117fc810afb6fb058e8055d564f03382 | https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/observation/mask.py#L850-L865 | train |
stevearc/dynamo3 | dynamo3/connection.py | build_expected | def build_expected(dynamizer, expected):
""" Build the Expected parameters from a dict """
ret = {}
for k, v in six.iteritems(expected):
if is_null(v):
ret[k] = {
'Exists': False,
}
else:
ret[k] = {
'Exists': True,
... | python | def build_expected(dynamizer, expected):
""" Build the Expected parameters from a dict """
ret = {}
for k, v in six.iteritems(expected):
if is_null(v):
ret[k] = {
'Exists': False,
}
else:
ret[k] = {
'Exists': True,
... | [
"def",
"build_expected",
"(",
"dynamizer",
",",
"expected",
")",
":",
"ret",
"=",
"{",
"}",
"for",
"k",
",",
"v",
"in",
"six",
".",
"iteritems",
"(",
"expected",
")",
":",
"if",
"is_null",
"(",
"v",
")",
":",
"ret",
"[",
"k",
"]",
"=",
"{",
"'E... | Build the Expected parameters from a dict | [
"Build",
"the",
"Expected",
"parameters",
"from",
"a",
"dict"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L19-L32 | train |
stevearc/dynamo3 | dynamo3/connection.py | build_expression_values | def build_expression_values(dynamizer, expr_values, kwargs):
""" Build ExpresionAttributeValues from a value or kwargs """
if expr_values:
values = expr_values
return dynamizer.encode_keys(values)
elif kwargs:
values = dict(((':' + k, v) for k, v in six.iteritems(kwargs)))
re... | python | def build_expression_values(dynamizer, expr_values, kwargs):
""" Build ExpresionAttributeValues from a value or kwargs """
if expr_values:
values = expr_values
return dynamizer.encode_keys(values)
elif kwargs:
values = dict(((':' + k, v) for k, v in six.iteritems(kwargs)))
re... | [
"def",
"build_expression_values",
"(",
"dynamizer",
",",
"expr_values",
",",
"kwargs",
")",
":",
"if",
"expr_values",
":",
"values",
"=",
"expr_values",
"return",
"dynamizer",
".",
"encode_keys",
"(",
"values",
")",
"elif",
"kwargs",
":",
"values",
"=",
"dict"... | Build ExpresionAttributeValues from a value or kwargs | [
"Build",
"ExpresionAttributeValues",
"from",
"a",
"value",
"or",
"kwargs"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L35-L42 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.connect_to_host | def connect_to_host(cls, host='localhost', port=8000, is_secure=False,
session=None, access_key=None, secret_key=None,
**kwargs):
"""
Connect to a specific host.
This method has been deprecated in favor of :meth:`~.connect`
Parameters
... | python | def connect_to_host(cls, host='localhost', port=8000, is_secure=False,
session=None, access_key=None, secret_key=None,
**kwargs):
"""
Connect to a specific host.
This method has been deprecated in favor of :meth:`~.connect`
Parameters
... | [
"def",
"connect_to_host",
"(",
"cls",
",",
"host",
"=",
"'localhost'",
",",
"port",
"=",
"8000",
",",
"is_secure",
"=",
"False",
",",
"session",
"=",
"None",
",",
"access_key",
"=",
"None",
",",
"secret_key",
"=",
"None",
",",
"*",
"*",
"kwargs",
")",
... | Connect to a specific host.
This method has been deprecated in favor of :meth:`~.connect`
Parameters
----------
host : str, optional
Address of the host (default 'localhost')
port : int, optional
Connect to the host on this port (default 8000)
is... | [
"Connect",
"to",
"a",
"specific",
"host",
"."
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L121-L156 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.call | def call(self, command, **kwargs):
"""
Make a request to DynamoDB using the raw botocore API
Parameters
----------
command : str
The name of the Dynamo command to execute
**kwargs : dict
The parameters to pass up in the request
Raises
... | python | def call(self, command, **kwargs):
"""
Make a request to DynamoDB using the raw botocore API
Parameters
----------
command : str
The name of the Dynamo command to execute
**kwargs : dict
The parameters to pass up in the request
Raises
... | [
"def",
"call",
"(",
"self",
",",
"command",
",",
"*",
"*",
"kwargs",
")",
":",
"for",
"hook",
"in",
"self",
".",
"_hooks",
"[",
"'precall'",
"]",
":",
"hook",
"(",
"self",
",",
"command",
",",
"kwargs",
")",
"op",
"=",
"getattr",
"(",
"self",
"."... | Make a request to DynamoDB using the raw botocore API
Parameters
----------
command : str
The name of the Dynamo command to execute
**kwargs : dict
The parameters to pass up in the request
Raises
------
exc : :class:`~.DynamoDBError`
... | [
"Make",
"a",
"request",
"to",
"DynamoDB",
"using",
"the",
"raw",
"botocore",
"API"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L196-L254 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.subscribe | def subscribe(self, event, hook):
"""
Subscribe a callback to an event
Parameters
----------
event : str
Available events are 'precall', 'postcall', and 'capacity'.
precall is called with: (connection, command, query_kwargs)
postcall is called... | python | def subscribe(self, event, hook):
"""
Subscribe a callback to an event
Parameters
----------
event : str
Available events are 'precall', 'postcall', and 'capacity'.
precall is called with: (connection, command, query_kwargs)
postcall is called... | [
"def",
"subscribe",
"(",
"self",
",",
"event",
",",
"hook",
")",
":",
"if",
"hook",
"not",
"in",
"self",
".",
"_hooks",
"[",
"event",
"]",
":",
"self",
".",
"_hooks",
"[",
"event",
"]",
".",
"append",
"(",
"hook",
")"
] | Subscribe a callback to an event
Parameters
----------
event : str
Available events are 'precall', 'postcall', and 'capacity'.
precall is called with: (connection, command, query_kwargs)
postcall is called with: (connection, command, query_kwargs, response)
... | [
"Subscribe",
"a",
"callback",
"to",
"an",
"event"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L261-L276 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.unsubscribe | def unsubscribe(self, event, hook):
""" Unsubscribe a hook from an event """
if hook in self._hooks[event]:
self._hooks[event].remove(hook) | python | def unsubscribe(self, event, hook):
""" Unsubscribe a hook from an event """
if hook in self._hooks[event]:
self._hooks[event].remove(hook) | [
"def",
"unsubscribe",
"(",
"self",
",",
"event",
",",
"hook",
")",
":",
"if",
"hook",
"in",
"self",
".",
"_hooks",
"[",
"event",
"]",
":",
"self",
".",
"_hooks",
"[",
"event",
"]",
".",
"remove",
"(",
"hook",
")"
] | Unsubscribe a hook from an event | [
"Unsubscribe",
"a",
"hook",
"from",
"an",
"event"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L278-L281 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.add_rate_limit | def add_rate_limit(self, limiter):
""" Add a RateLimit to the connection """
if limiter not in self.rate_limiters:
self.subscribe('capacity', limiter.on_capacity)
self.rate_limiters.append(limiter) | python | def add_rate_limit(self, limiter):
""" Add a RateLimit to the connection """
if limiter not in self.rate_limiters:
self.subscribe('capacity', limiter.on_capacity)
self.rate_limiters.append(limiter) | [
"def",
"add_rate_limit",
"(",
"self",
",",
"limiter",
")",
":",
"if",
"limiter",
"not",
"in",
"self",
".",
"rate_limiters",
":",
"self",
".",
"subscribe",
"(",
"'capacity'",
",",
"limiter",
".",
"on_capacity",
")",
"self",
".",
"rate_limiters",
".",
"appen... | Add a RateLimit to the connection | [
"Add",
"a",
"RateLimit",
"to",
"the",
"connection"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L283-L287 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.remove_rate_limit | def remove_rate_limit(self, limiter):
""" Remove a RateLimit from the connection """
if limiter in self.rate_limiters:
self.unsubscribe('capacity', limiter.on_capacity)
self.rate_limiters.remove(limiter) | python | def remove_rate_limit(self, limiter):
""" Remove a RateLimit from the connection """
if limiter in self.rate_limiters:
self.unsubscribe('capacity', limiter.on_capacity)
self.rate_limiters.remove(limiter) | [
"def",
"remove_rate_limit",
"(",
"self",
",",
"limiter",
")",
":",
"if",
"limiter",
"in",
"self",
".",
"rate_limiters",
":",
"self",
".",
"unsubscribe",
"(",
"'capacity'",
",",
"limiter",
".",
"on_capacity",
")",
"self",
".",
"rate_limiters",
".",
"remove",
... | Remove a RateLimit from the connection | [
"Remove",
"a",
"RateLimit",
"from",
"the",
"connection"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L289-L293 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection._default_capacity | def _default_capacity(self, value):
""" Get the value for ReturnConsumedCapacity from provided value """
if value is not None:
return value
if self.default_return_capacity or self.rate_limiters:
return INDEXES
return NONE | python | def _default_capacity(self, value):
""" Get the value for ReturnConsumedCapacity from provided value """
if value is not None:
return value
if self.default_return_capacity or self.rate_limiters:
return INDEXES
return NONE | [
"def",
"_default_capacity",
"(",
"self",
",",
"value",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"return",
"value",
"if",
"self",
".",
"default_return_capacity",
"or",
"self",
".",
"rate_limiters",
":",
"return",
"INDEXES",
"return",
"NONE"
] | Get the value for ReturnConsumedCapacity from provided value | [
"Get",
"the",
"value",
"for",
"ReturnConsumedCapacity",
"from",
"provided",
"value"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L312-L318 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection._count | def _count(self, method, limit, keywords):
""" Do a scan or query and aggregate the results into a Count """
# The limit will be mutated, so copy it and leave the original intact
limit = limit.copy()
has_more = True
count = None
while has_more:
limit.set_reque... | python | def _count(self, method, limit, keywords):
""" Do a scan or query and aggregate the results into a Count """
# The limit will be mutated, so copy it and leave the original intact
limit = limit.copy()
has_more = True
count = None
while has_more:
limit.set_reque... | [
"def",
"_count",
"(",
"self",
",",
"method",
",",
"limit",
",",
"keywords",
")",
":",
"# The limit will be mutated, so copy it and leave the original intact",
"limit",
"=",
"limit",
".",
"copy",
"(",
")",
"has_more",
"=",
"True",
"count",
"=",
"None",
"while",
"... | Do a scan or query and aggregate the results into a Count | [
"Do",
"a",
"scan",
"or",
"query",
"and",
"aggregate",
"the",
"results",
"into",
"a",
"Count"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L320-L335 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.describe_table | def describe_table(self, tablename):
"""
Get the details about a table
Parameters
----------
tablename : str
Name of the table
Returns
-------
table : :class:`~dynamo3.fields.Table`
"""
try:
response = self.call(
... | python | def describe_table(self, tablename):
"""
Get the details about a table
Parameters
----------
tablename : str
Name of the table
Returns
-------
table : :class:`~dynamo3.fields.Table`
"""
try:
response = self.call(
... | [
"def",
"describe_table",
"(",
"self",
",",
"tablename",
")",
":",
"try",
":",
"response",
"=",
"self",
".",
"call",
"(",
"'describe_table'",
",",
"TableName",
"=",
"tablename",
")",
"[",
"'Table'",
"]",
"return",
"Table",
".",
"from_response",
"(",
"respon... | Get the details about a table
Parameters
----------
tablename : str
Name of the table
Returns
-------
table : :class:`~dynamo3.fields.Table` | [
"Get",
"the",
"details",
"about",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L354-L376 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.put_item | def put_item(self, tablename, item, expected=None, returns=NONE,
return_capacity=None, expect_or=False, **kwargs):
"""
Store an item, overwriting existing data
This uses the older version of the DynamoDB API.
See also: :meth:`~.put_item2`.
Parameters
--... | python | def put_item(self, tablename, item, expected=None, returns=NONE,
return_capacity=None, expect_or=False, **kwargs):
"""
Store an item, overwriting existing data
This uses the older version of the DynamoDB API.
See also: :meth:`~.put_item2`.
Parameters
--... | [
"def",
"put_item",
"(",
"self",
",",
"tablename",
",",
"item",
",",
"expected",
"=",
"None",
",",
"returns",
"=",
"NONE",
",",
"return_capacity",
"=",
"None",
",",
"expect_or",
"=",
"False",
",",
"*",
"*",
"kwargs",
")",
":",
"keywords",
"=",
"{",
"}... | Store an item, overwriting existing data
This uses the older version of the DynamoDB API.
See also: :meth:`~.put_item2`.
Parameters
----------
tablename : str
Name of the table to write
item : dict
Item data
expected : dict, optional
... | [
"Store",
"an",
"item",
"overwriting",
"existing",
"data"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L466-L513 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.delete_item2 | def delete_item2(self, tablename, key, expr_values=None, alias=None,
condition=None, returns=NONE, return_capacity=None,
return_item_collection_metrics=NONE, **kwargs):
"""
Delete an item from a table
For many parameters you will want to reference the D... | python | def delete_item2(self, tablename, key, expr_values=None, alias=None,
condition=None, returns=NONE, return_capacity=None,
return_item_collection_metrics=NONE, **kwargs):
"""
Delete an item from a table
For many parameters you will want to reference the D... | [
"def",
"delete_item2",
"(",
"self",
",",
"tablename",
",",
"key",
",",
"expr_values",
"=",
"None",
",",
"alias",
"=",
"None",
",",
"condition",
"=",
"None",
",",
"returns",
"=",
"NONE",
",",
"return_capacity",
"=",
"None",
",",
"return_item_collection_metric... | Delete an item from a table
For many parameters you will want to reference the DynamoDB API:
http://docs.aws.amazon.com/amazondynamodb/latest/APIReference/API_DeleteItem.html
Parameters
----------
tablename : str
Name of the table to update
key : dict
... | [
"Delete",
"an",
"item",
"from",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L695-L749 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.batch_write | def batch_write(self, tablename, return_capacity=None,
return_item_collection_metrics=NONE):
"""
Perform a batch write on a table
Parameters
----------
tablename : str
Name of the table to write to
return_capacity : {NONE, INDEXES, TOTAL},... | python | def batch_write(self, tablename, return_capacity=None,
return_item_collection_metrics=NONE):
"""
Perform a batch write on a table
Parameters
----------
tablename : str
Name of the table to write to
return_capacity : {NONE, INDEXES, TOTAL},... | [
"def",
"batch_write",
"(",
"self",
",",
"tablename",
",",
"return_capacity",
"=",
"None",
",",
"return_item_collection_metrics",
"=",
"NONE",
")",
":",
"return_capacity",
"=",
"self",
".",
"_default_capacity",
"(",
"return_capacity",
")",
"return",
"BatchWriter",
... | Perform a batch write on a table
Parameters
----------
tablename : str
Name of the table to write to
return_capacity : {NONE, INDEXES, TOTAL}, optional
INDEXES will return the consumed capacity for indexes, TOTAL will
return the consumed capacity for ... | [
"Perform",
"a",
"batch",
"write",
"on",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L751-L779 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.batch_get | def batch_get(self, tablename, keys, attributes=None, alias=None,
consistent=False, return_capacity=None):
"""
Perform a batch get of many items in a table
Parameters
----------
tablename : str
Name of the table to fetch from
keys : list or ... | python | def batch_get(self, tablename, keys, attributes=None, alias=None,
consistent=False, return_capacity=None):
"""
Perform a batch get of many items in a table
Parameters
----------
tablename : str
Name of the table to fetch from
keys : list or ... | [
"def",
"batch_get",
"(",
"self",
",",
"tablename",
",",
"keys",
",",
"attributes",
"=",
"None",
",",
"alias",
"=",
"None",
",",
"consistent",
"=",
"False",
",",
"return_capacity",
"=",
"None",
")",
":",
"keys",
"=",
"[",
"self",
".",
"dynamizer",
".",
... | Perform a batch get of many items in a table
Parameters
----------
tablename : str
Name of the table to fetch from
keys : list or iterable
List or iterable of primary key dicts that specify the hash key and
the optional range key of each item to fetch... | [
"Perform",
"a",
"batch",
"get",
"of",
"many",
"items",
"in",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L781-L811 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.update_item | def update_item(self, tablename, key, updates, returns=NONE,
return_capacity=None, expect_or=False, **kwargs):
"""
Update a single item in a table
This uses the older version of the DynamoDB API.
See also: :meth:`~.update_item2`.
Parameters
---------... | python | def update_item(self, tablename, key, updates, returns=NONE,
return_capacity=None, expect_or=False, **kwargs):
"""
Update a single item in a table
This uses the older version of the DynamoDB API.
See also: :meth:`~.update_item2`.
Parameters
---------... | [
"def",
"update_item",
"(",
"self",
",",
"tablename",
",",
"key",
",",
"updates",
",",
"returns",
"=",
"NONE",
",",
"return_capacity",
"=",
"None",
",",
"expect_or",
"=",
"False",
",",
"*",
"*",
"kwargs",
")",
":",
"key",
"=",
"self",
".",
"dynamizer",
... | Update a single item in a table
This uses the older version of the DynamoDB API.
See also: :meth:`~.update_item2`.
Parameters
----------
tablename : str
Name of the table to update
key : dict
Primary key dict specifying the hash key and, if appli... | [
"Update",
"a",
"single",
"item",
"in",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L813-L880 | train |
stevearc/dynamo3 | dynamo3/connection.py | DynamoDBConnection.query | def query(self, tablename, attributes=None, consistent=False, count=False,
index=None, limit=None, desc=False, return_capacity=None,
filter=None, filter_or=False, exclusive_start_key=None, **kwargs):
"""
Perform an index query on a table
This uses the older version o... | python | def query(self, tablename, attributes=None, consistent=False, count=False,
index=None, limit=None, desc=False, return_capacity=None,
filter=None, filter_or=False, exclusive_start_key=None, **kwargs):
"""
Perform an index query on a table
This uses the older version o... | [
"def",
"query",
"(",
"self",
",",
"tablename",
",",
"attributes",
"=",
"None",
",",
"consistent",
"=",
"False",
",",
"count",
"=",
"False",
",",
"index",
"=",
"None",
",",
"limit",
"=",
"None",
",",
"desc",
"=",
"False",
",",
"return_capacity",
"=",
... | Perform an index query on a table
This uses the older version of the DynamoDB API.
See also: :meth:`~.query2`.
Parameters
----------
tablename : str
Name of the table to query
attributes : list
If present, only fetch these attributes from the ite... | [
"Perform",
"an",
"index",
"query",
"on",
"a",
"table"
] | f897c40ece28586272dbcab8f0d99a14a1831dda | https://github.com/stevearc/dynamo3/blob/f897c40ece28586272dbcab8f0d99a14a1831dda/dynamo3/connection.py#L1099-L1178 | train |
etal/biofrills | biofrills/logoutils.py | read_logodata | def read_logodata(handle):
"""Get weblogo data for a sequence alignment.
Returns a list of tuples: (posn, letter_counts, entropy, weight)
"""
seqs = weblogolib.read_seq_data(handle,
alphabet=unambiguous_protein_alphabet)
ldata = weblogolib.LogoData.from_seqs(seqs... | python | def read_logodata(handle):
"""Get weblogo data for a sequence alignment.
Returns a list of tuples: (posn, letter_counts, entropy, weight)
"""
seqs = weblogolib.read_seq_data(handle,
alphabet=unambiguous_protein_alphabet)
ldata = weblogolib.LogoData.from_seqs(seqs... | [
"def",
"read_logodata",
"(",
"handle",
")",
":",
"seqs",
"=",
"weblogolib",
".",
"read_seq_data",
"(",
"handle",
",",
"alphabet",
"=",
"unambiguous_protein_alphabet",
")",
"ldata",
"=",
"weblogolib",
".",
"LogoData",
".",
"from_seqs",
"(",
"seqs",
")",
"letter... | Get weblogo data for a sequence alignment.
Returns a list of tuples: (posn, letter_counts, entropy, weight) | [
"Get",
"weblogo",
"data",
"for",
"a",
"sequence",
"alignment",
"."
] | 36684bb6c7632f96215e8b2b4ebc86640f331bcd | https://github.com/etal/biofrills/blob/36684bb6c7632f96215e8b2b4ebc86640f331bcd/biofrills/logoutils.py#L9-L25 | train |
etal/biofrills | biofrills/logoutils.py | aln2logodata | def aln2logodata(aln):
"""Get weblogo data for an alignment object.
Returns a list of tuples: (posn, letter_counts, entropy, weight)
"""
handle = StringIO(aln.format('fasta'))
logodata = read_logodata(handle)
handle.close()
return logodata | python | def aln2logodata(aln):
"""Get weblogo data for an alignment object.
Returns a list of tuples: (posn, letter_counts, entropy, weight)
"""
handle = StringIO(aln.format('fasta'))
logodata = read_logodata(handle)
handle.close()
return logodata | [
"def",
"aln2logodata",
"(",
"aln",
")",
":",
"handle",
"=",
"StringIO",
"(",
"aln",
".",
"format",
"(",
"'fasta'",
")",
")",
"logodata",
"=",
"read_logodata",
"(",
"handle",
")",
"handle",
".",
"close",
"(",
")",
"return",
"logodata"
] | Get weblogo data for an alignment object.
Returns a list of tuples: (posn, letter_counts, entropy, weight) | [
"Get",
"weblogo",
"data",
"for",
"an",
"alignment",
"object",
"."
] | 36684bb6c7632f96215e8b2b4ebc86640f331bcd | https://github.com/etal/biofrills/blob/36684bb6c7632f96215e8b2b4ebc86640f331bcd/biofrills/logoutils.py#L28-L36 | train |
etal/biofrills | biofrills/logoutils.py | letter_scales | def letter_scales(counts):
"""Convert letter counts to frequencies, sorted increasing."""
try:
scale = 1.0 / sum(counts.values())
except ZeroDivisionError:
# This logo is all gaps, nothing can be done
return []
freqs = [(aa, cnt*scale) for aa, cnt in counts.iteritems() if cnt]
... | python | def letter_scales(counts):
"""Convert letter counts to frequencies, sorted increasing."""
try:
scale = 1.0 / sum(counts.values())
except ZeroDivisionError:
# This logo is all gaps, nothing can be done
return []
freqs = [(aa, cnt*scale) for aa, cnt in counts.iteritems() if cnt]
... | [
"def",
"letter_scales",
"(",
"counts",
")",
":",
"try",
":",
"scale",
"=",
"1.0",
"/",
"sum",
"(",
"counts",
".",
"values",
"(",
")",
")",
"except",
"ZeroDivisionError",
":",
"# This logo is all gaps, nothing can be done",
"return",
"[",
"]",
"freqs",
"=",
"... | Convert letter counts to frequencies, sorted increasing. | [
"Convert",
"letter",
"counts",
"to",
"frequencies",
"sorted",
"increasing",
"."
] | 36684bb6c7632f96215e8b2b4ebc86640f331bcd | https://github.com/etal/biofrills/blob/36684bb6c7632f96215e8b2b4ebc86640f331bcd/biofrills/logoutils.py#L46-L55 | train |
johnnoone/json-spec | src/jsonspec/operations/__init__.py | replace | def replace(doc, pointer, value):
"""Replace element from sequence, member from mapping.
:param doc: the document base
:param pointer: the path to search in
:param value: the new value
:return: the new object
.. note::
This operation is functionally identical to a "remove" operation f... | python | def replace(doc, pointer, value):
"""Replace element from sequence, member from mapping.
:param doc: the document base
:param pointer: the path to search in
:param value: the new value
:return: the new object
.. note::
This operation is functionally identical to a "remove" operation f... | [
"def",
"replace",
"(",
"doc",
",",
"pointer",
",",
"value",
")",
":",
"return",
"Target",
"(",
"doc",
")",
".",
"replace",
"(",
"pointer",
",",
"value",
")",
".",
"document"
] | Replace element from sequence, member from mapping.
:param doc: the document base
:param pointer: the path to search in
:param value: the new value
:return: the new object
.. note::
This operation is functionally identical to a "remove" operation for
a value, followed immediately ... | [
"Replace",
"element",
"from",
"sequence",
"member",
"from",
"mapping",
"."
] | f91981724cea0c366bd42a6670eb07bbe31c0e0c | https://github.com/johnnoone/json-spec/blob/f91981724cea0c366bd42a6670eb07bbe31c0e0c/src/jsonspec/operations/__init__.py#L49-L64 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.set_options | def set_options(self, **kw):
r"""Set Parser options.
.. seealso::
``kw`` argument have the same meaning as in :func:`lazyxml.loads`
"""
for k, v in kw.iteritems():
if k in self.__options:
self.__options[k] = v | python | def set_options(self, **kw):
r"""Set Parser options.
.. seealso::
``kw`` argument have the same meaning as in :func:`lazyxml.loads`
"""
for k, v in kw.iteritems():
if k in self.__options:
self.__options[k] = v | [
"def",
"set_options",
"(",
"self",
",",
"*",
"*",
"kw",
")",
":",
"for",
"k",
",",
"v",
"in",
"kw",
".",
"iteritems",
"(",
")",
":",
"if",
"k",
"in",
"self",
".",
"__options",
":",
"self",
".",
"__options",
"[",
"k",
"]",
"=",
"v"
] | r"""Set Parser options.
.. seealso::
``kw`` argument have the same meaning as in :func:`lazyxml.loads` | [
"r",
"Set",
"Parser",
"options",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L39-L47 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.xml2object | def xml2object(self, content):
r"""Convert xml content to python object.
:param content: xml content
:rtype: dict
.. versionadded:: 1.2
"""
content = self.xml_filter(content)
element = ET.fromstring(content)
tree = self.parse(element) if self.__options['... | python | def xml2object(self, content):
r"""Convert xml content to python object.
:param content: xml content
:rtype: dict
.. versionadded:: 1.2
"""
content = self.xml_filter(content)
element = ET.fromstring(content)
tree = self.parse(element) if self.__options['... | [
"def",
"xml2object",
"(",
"self",
",",
"content",
")",
":",
"content",
"=",
"self",
".",
"xml_filter",
"(",
"content",
")",
"element",
"=",
"ET",
".",
"fromstring",
"(",
"content",
")",
"tree",
"=",
"self",
".",
"parse",
"(",
"element",
")",
"if",
"s... | r"""Convert xml content to python object.
:param content: xml content
:rtype: dict
.. versionadded:: 1.2 | [
"r",
"Convert",
"xml",
"content",
"to",
"python",
"object",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L64-L80 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.xml_filter | def xml_filter(self, content):
r"""Filter and preprocess xml content
:param content: xml content
:rtype: str
"""
content = utils.strip_whitespace(content, True) if self.__options['strip'] else content.strip()
if not self.__options['encoding']:
encoding = sel... | python | def xml_filter(self, content):
r"""Filter and preprocess xml content
:param content: xml content
:rtype: str
"""
content = utils.strip_whitespace(content, True) if self.__options['strip'] else content.strip()
if not self.__options['encoding']:
encoding = sel... | [
"def",
"xml_filter",
"(",
"self",
",",
"content",
")",
":",
"content",
"=",
"utils",
".",
"strip_whitespace",
"(",
"content",
",",
"True",
")",
"if",
"self",
".",
"__options",
"[",
"'strip'",
"]",
"else",
"content",
".",
"strip",
"(",
")",
"if",
"not",... | r"""Filter and preprocess xml content
:param content: xml content
:rtype: str | [
"r",
"Filter",
"and",
"preprocess",
"xml",
"content"
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L82-L100 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.guess_xml_encoding | def guess_xml_encoding(self, content):
r"""Guess encoding from xml header declaration.
:param content: xml content
:rtype: str or None
"""
matchobj = self.__regex['xml_encoding'].match(content)
return matchobj and matchobj.group(1).lower() | python | def guess_xml_encoding(self, content):
r"""Guess encoding from xml header declaration.
:param content: xml content
:rtype: str or None
"""
matchobj = self.__regex['xml_encoding'].match(content)
return matchobj and matchobj.group(1).lower() | [
"def",
"guess_xml_encoding",
"(",
"self",
",",
"content",
")",
":",
"matchobj",
"=",
"self",
".",
"__regex",
"[",
"'xml_encoding'",
"]",
".",
"match",
"(",
"content",
")",
"return",
"matchobj",
"and",
"matchobj",
".",
"group",
"(",
"1",
")",
".",
"lower"... | r"""Guess encoding from xml header declaration.
:param content: xml content
:rtype: str or None | [
"r",
"Guess",
"encoding",
"from",
"xml",
"header",
"declaration",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L102-L109 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.parse | def parse(self, element):
r"""Parse xml element.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
"""
values = {}
for child in element:
node = self.get_node(child)
subs = self.parse(child)
value = subs o... | python | def parse(self, element):
r"""Parse xml element.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
"""
values = {}
for child in element:
node = self.get_node(child)
subs = self.parse(child)
value = subs o... | [
"def",
"parse",
"(",
"self",
",",
"element",
")",
":",
"values",
"=",
"{",
"}",
"for",
"child",
"in",
"element",
":",
"node",
"=",
"self",
".",
"get_node",
"(",
"child",
")",
"subs",
"=",
"self",
".",
"parse",
"(",
"child",
")",
"value",
"=",
"su... | r"""Parse xml element.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict | [
"r",
"Parse",
"xml",
"element",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L119-L136 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.parse_full | def parse_full(self, element):
r"""Parse xml element include the node attributes.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
.. versionadded:: 1.2.1
"""
values = collections.defaultdict(dict)
for child in element:
... | python | def parse_full(self, element):
r"""Parse xml element include the node attributes.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
.. versionadded:: 1.2.1
"""
values = collections.defaultdict(dict)
for child in element:
... | [
"def",
"parse_full",
"(",
"self",
",",
"element",
")",
":",
"values",
"=",
"collections",
".",
"defaultdict",
"(",
"dict",
")",
"for",
"child",
"in",
"element",
":",
"node",
"=",
"self",
".",
"get_node",
"(",
"child",
")",
"subs",
"=",
"self",
".",
"... | r"""Parse xml element include the node attributes.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
.. versionadded:: 1.2.1 | [
"r",
"Parse",
"xml",
"element",
"include",
"the",
"node",
"attributes",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L138-L158 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.get_node | def get_node(self, element):
r"""Get node info.
Parse element and get the element tag info. Include tag name, value, attribute, namespace.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
"""
ns, tag = self.split_namespace(element.tag)
... | python | def get_node(self, element):
r"""Get node info.
Parse element and get the element tag info. Include tag name, value, attribute, namespace.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict
"""
ns, tag = self.split_namespace(element.tag)
... | [
"def",
"get_node",
"(",
"self",
",",
"element",
")",
":",
"ns",
",",
"tag",
"=",
"self",
".",
"split_namespace",
"(",
"element",
".",
"tag",
")",
"return",
"{",
"'tag'",
":",
"tag",
",",
"'value'",
":",
"(",
"element",
".",
"text",
"or",
"''",
")",... | r"""Get node info.
Parse element and get the element tag info. Include tag name, value, attribute, namespace.
:param element: an :class:`~xml.etree.ElementTree.Element` instance
:rtype: dict | [
"r",
"Get",
"node",
"info",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L160-L169 | train |
heronotears/lazyxml | lazyxml/parser.py | Parser.split_namespace | def split_namespace(self, tag):
r"""Split tag namespace.
:param tag: tag name
:return: a pair of (namespace, tag)
:rtype: tuple
"""
matchobj = self.__regex['xml_ns'].search(tag)
return matchobj.groups() if matchobj else ('', tag) | python | def split_namespace(self, tag):
r"""Split tag namespace.
:param tag: tag name
:return: a pair of (namespace, tag)
:rtype: tuple
"""
matchobj = self.__regex['xml_ns'].search(tag)
return matchobj.groups() if matchobj else ('', tag) | [
"def",
"split_namespace",
"(",
"self",
",",
"tag",
")",
":",
"matchobj",
"=",
"self",
".",
"__regex",
"[",
"'xml_ns'",
"]",
".",
"search",
"(",
"tag",
")",
"return",
"matchobj",
".",
"groups",
"(",
")",
"if",
"matchobj",
"else",
"(",
"''",
",",
"tag"... | r"""Split tag namespace.
:param tag: tag name
:return: a pair of (namespace, tag)
:rtype: tuple | [
"r",
"Split",
"tag",
"namespace",
"."
] | e3f1ebd3f34cfa03d022ddec90e17d60c1c81953 | https://github.com/heronotears/lazyxml/blob/e3f1ebd3f34cfa03d022ddec90e17d60c1c81953/lazyxml/parser.py#L171-L179 | train |
LISE-B26/pylabcontrol | build/lib/pylabcontrol/src/core/loading.py | instantiate_probes | def instantiate_probes(probes, instruments):
"""
Creates instances of the probes inputed;
Args:
probes: probes is a nested dictionary with
(key, sub_dict ) = (name of the probe, {'probe_name': value_probe, 'instrument_name': value_inst}),
where value_probe is a valid name... | python | def instantiate_probes(probes, instruments):
"""
Creates instances of the probes inputed;
Args:
probes: probes is a nested dictionary with
(key, sub_dict ) = (name of the probe, {'probe_name': value_probe, 'instrument_name': value_inst}),
where value_probe is a valid name... | [
"def",
"instantiate_probes",
"(",
"probes",
",",
"instruments",
")",
":",
"probe_instances",
"=",
"{",
"}",
"for",
"name",
",",
"sub_dict",
"in",
"probes",
".",
"items",
"(",
")",
":",
"assert",
"isinstance",
"(",
"sub_dict",
",",
"dict",
")",
"assert",
... | Creates instances of the probes inputed;
Args:
probes: probes is a nested dictionary with
(key, sub_dict ) = (name of the probe, {'probe_name': value_probe, 'instrument_name': value_inst}),
where value_probe is a valid name of a probe in intrument with name value_inst
for... | [
"Creates",
"instances",
"of",
"the",
"probes",
"inputed",
";"
] | 67482e5157fcd1c40705e5c2cacfb93564703ed0 | https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/core/loading.py#L22-L58 | train |
emre/lightsteem | lightsteem/broadcast/key_objects.py | PublicKey.compressed | def compressed(self):
""" Derive compressed public key """
order = ecdsa.SECP256k1.generator.order()
p = ecdsa.VerifyingKey.from_string(
compat_bytes(self), curve=ecdsa.SECP256k1).pubkey.point
x_str = ecdsa.util.number_to_string(p.x(), order)
# y_str = ecdsa.util.numb... | python | def compressed(self):
""" Derive compressed public key """
order = ecdsa.SECP256k1.generator.order()
p = ecdsa.VerifyingKey.from_string(
compat_bytes(self), curve=ecdsa.SECP256k1).pubkey.point
x_str = ecdsa.util.number_to_string(p.x(), order)
# y_str = ecdsa.util.numb... | [
"def",
"compressed",
"(",
"self",
")",
":",
"order",
"=",
"ecdsa",
".",
"SECP256k1",
".",
"generator",
".",
"order",
"(",
")",
"p",
"=",
"ecdsa",
".",
"VerifyingKey",
".",
"from_string",
"(",
"compat_bytes",
"(",
"self",
")",
",",
"curve",
"=",
"ecdsa"... | Derive compressed public key | [
"Derive",
"compressed",
"public",
"key"
] | 0fc29a517c20d881cbdbb15b43add4bcf3af242e | https://github.com/emre/lightsteem/blob/0fc29a517c20d881cbdbb15b43add4bcf3af242e/lightsteem/broadcast/key_objects.py#L106-L116 | train |
emre/lightsteem | lightsteem/broadcast/key_objects.py | PublicKey.unCompressed | def unCompressed(self):
""" Derive uncompressed key """
public_key = repr(self._pk)
prefix = public_key[0:2]
if prefix == "04":
return public_key
assert prefix == "02" or prefix == "03"
x = int(public_key[2:], 16)
y = self._derive_y_from_x(x, (prefix =... | python | def unCompressed(self):
""" Derive uncompressed key """
public_key = repr(self._pk)
prefix = public_key[0:2]
if prefix == "04":
return public_key
assert prefix == "02" or prefix == "03"
x = int(public_key[2:], 16)
y = self._derive_y_from_x(x, (prefix =... | [
"def",
"unCompressed",
"(",
"self",
")",
":",
"public_key",
"=",
"repr",
"(",
"self",
".",
"_pk",
")",
"prefix",
"=",
"public_key",
"[",
"0",
":",
"2",
"]",
"if",
"prefix",
"==",
"\"04\"",
":",
"return",
"public_key",
"assert",
"prefix",
"==",
"\"02\""... | Derive uncompressed key | [
"Derive",
"uncompressed",
"key"
] | 0fc29a517c20d881cbdbb15b43add4bcf3af242e | https://github.com/emre/lightsteem/blob/0fc29a517c20d881cbdbb15b43add4bcf3af242e/lightsteem/broadcast/key_objects.py#L118-L128 | train |
emre/lightsteem | lightsteem/broadcast/key_objects.py | PrivateKey.compressedpubkey | def compressedpubkey(self):
""" Derive uncompressed public key """
secret = unhexlify(repr(self._wif))
order = ecdsa.SigningKey.from_string(
secret, curve=ecdsa.SECP256k1).curve.generator.order()
p = ecdsa.SigningKey.from_string(
secret, curve=ecdsa.SECP256k1).ver... | python | def compressedpubkey(self):
""" Derive uncompressed public key """
secret = unhexlify(repr(self._wif))
order = ecdsa.SigningKey.from_string(
secret, curve=ecdsa.SECP256k1).curve.generator.order()
p = ecdsa.SigningKey.from_string(
secret, curve=ecdsa.SECP256k1).ver... | [
"def",
"compressedpubkey",
"(",
"self",
")",
":",
"secret",
"=",
"unhexlify",
"(",
"repr",
"(",
"self",
".",
"_wif",
")",
")",
"order",
"=",
"ecdsa",
".",
"SigningKey",
".",
"from_string",
"(",
"secret",
",",
"curve",
"=",
"ecdsa",
".",
"SECP256k1",
")... | Derive uncompressed public key | [
"Derive",
"uncompressed",
"public",
"key"
] | 0fc29a517c20d881cbdbb15b43add4bcf3af242e | https://github.com/emre/lightsteem/blob/0fc29a517c20d881cbdbb15b43add4bcf3af242e/lightsteem/broadcast/key_objects.py#L174-L189 | train |
emre/lightsteem | lightsteem/broadcast/key_objects.py | PasswordKey.get_private | def get_private(self):
""" Derive private key from the brain key and the current sequence
number
"""
a = compat_bytes(self.account + self.role + self.password, 'utf8')
s = hashlib.sha256(a).digest()
return PrivateKey(hexlify(s).decode('ascii')) | python | def get_private(self):
""" Derive private key from the brain key and the current sequence
number
"""
a = compat_bytes(self.account + self.role + self.password, 'utf8')
s = hashlib.sha256(a).digest()
return PrivateKey(hexlify(s).decode('ascii')) | [
"def",
"get_private",
"(",
"self",
")",
":",
"a",
"=",
"compat_bytes",
"(",
"self",
".",
"account",
"+",
"self",
".",
"role",
"+",
"self",
".",
"password",
",",
"'utf8'",
")",
"s",
"=",
"hashlib",
".",
"sha256",
"(",
"a",
")",
".",
"digest",
"(",
... | Derive private key from the brain key and the current sequence
number | [
"Derive",
"private",
"key",
"from",
"the",
"brain",
"key",
"and",
"the",
"current",
"sequence",
"number"
] | 0fc29a517c20d881cbdbb15b43add4bcf3af242e | https://github.com/emre/lightsteem/blob/0fc29a517c20d881cbdbb15b43add4bcf3af242e/lightsteem/broadcast/key_objects.py#L224-L230 | train |
lreis2415/PyGeoC | pygeoc/hydro.py | D8Util.downstream_index | def downstream_index(dir_value, i, j, alg='taudem'):
"""find downslope coordinate for D8 direction."""
assert alg.lower() in FlowModelConst.d8_deltas
delta = FlowModelConst.d8_deltas.get(alg.lower())
drow, dcol = delta[int(dir_value)]
return i + drow, j + dcol | python | def downstream_index(dir_value, i, j, alg='taudem'):
"""find downslope coordinate for D8 direction."""
assert alg.lower() in FlowModelConst.d8_deltas
delta = FlowModelConst.d8_deltas.get(alg.lower())
drow, dcol = delta[int(dir_value)]
return i + drow, j + dcol | [
"def",
"downstream_index",
"(",
"dir_value",
",",
"i",
",",
"j",
",",
"alg",
"=",
"'taudem'",
")",
":",
"assert",
"alg",
".",
"lower",
"(",
")",
"in",
"FlowModelConst",
".",
"d8_deltas",
"delta",
"=",
"FlowModelConst",
".",
"d8_deltas",
".",
"get",
"(",
... | find downslope coordinate for D8 direction. | [
"find",
"downslope",
"coordinate",
"for",
"D8",
"direction",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/hydro.py#L130-L135 | train |
heinzK1X/pylibconfig2 | pylibconfig2/parsing.py | convert_group | def convert_group(tokens):
"""Converts parseResult from to ConfGroup type."""
tok = tokens.asList()
dic = dict(tok)
if not (len(dic) == len(tok)):
raise ParseFatalException("Names in group must be unique: %s" % tokens)
return ConfGroup(dic) | python | def convert_group(tokens):
"""Converts parseResult from to ConfGroup type."""
tok = tokens.asList()
dic = dict(tok)
if not (len(dic) == len(tok)):
raise ParseFatalException("Names in group must be unique: %s" % tokens)
return ConfGroup(dic) | [
"def",
"convert_group",
"(",
"tokens",
")",
":",
"tok",
"=",
"tokens",
".",
"asList",
"(",
")",
"dic",
"=",
"dict",
"(",
"tok",
")",
"if",
"not",
"(",
"len",
"(",
"dic",
")",
"==",
"len",
"(",
"tok",
")",
")",
":",
"raise",
"ParseFatalException",
... | Converts parseResult from to ConfGroup type. | [
"Converts",
"parseResult",
"from",
"to",
"ConfGroup",
"type",
"."
] | f3a851ac780da28a42264c24aac51b54fbd63f81 | https://github.com/heinzK1X/pylibconfig2/blob/f3a851ac780da28a42264c24aac51b54fbd63f81/pylibconfig2/parsing.py#L64-L70 | train |
LISE-B26/pylabcontrol | build/lib/pylabcontrol/src/gui/qt_b26_load_dialog.py | LoadDialog.load_elements | def load_elements(self, filename):
"""
loads the elements from file filename
"""
input_data = load_b26_file(filename)
if isinstance(input_data, dict) and self.elements_type in input_data:
return input_data[self.elements_type]
else:
return {} | python | def load_elements(self, filename):
"""
loads the elements from file filename
"""
input_data = load_b26_file(filename)
if isinstance(input_data, dict) and self.elements_type in input_data:
return input_data[self.elements_type]
else:
return {} | [
"def",
"load_elements",
"(",
"self",
",",
"filename",
")",
":",
"input_data",
"=",
"load_b26_file",
"(",
"filename",
")",
"if",
"isinstance",
"(",
"input_data",
",",
"dict",
")",
"and",
"self",
".",
"elements_type",
"in",
"input_data",
":",
"return",
"input_... | loads the elements from file filename | [
"loads",
"the",
"elements",
"from",
"file",
"filename"
] | 67482e5157fcd1c40705e5c2cacfb93564703ed0 | https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/gui/qt_b26_load_dialog.py#L178-L186 | train |
LISE-B26/pylabcontrol | build/lib/pylabcontrol/src/gui/qt_b26_load_dialog.py | LoadDialog.add_script_sequence | def add_script_sequence(self):
"""
creates a script sequence based on the script iterator type selected and the selected scripts and sends it to the tree
self.tree_loaded
"""
def empty_tree(tree_model):
# COMMENT_ME
def add_children_to_list(item, somelis... | python | def add_script_sequence(self):
"""
creates a script sequence based on the script iterator type selected and the selected scripts and sends it to the tree
self.tree_loaded
"""
def empty_tree(tree_model):
# COMMENT_ME
def add_children_to_list(item, somelis... | [
"def",
"add_script_sequence",
"(",
"self",
")",
":",
"def",
"empty_tree",
"(",
"tree_model",
")",
":",
"# COMMENT_ME",
"def",
"add_children_to_list",
"(",
"item",
",",
"somelist",
")",
":",
"if",
"item",
".",
"hasChildren",
"(",
")",
":",
"for",
"rownum",
... | creates a script sequence based on the script iterator type selected and the selected scripts and sends it to the tree
self.tree_loaded | [
"creates",
"a",
"script",
"sequence",
"based",
"on",
"the",
"script",
"iterator",
"type",
"selected",
"and",
"the",
"selected",
"scripts",
"and",
"sends",
"it",
"to",
"the",
"tree",
"self",
".",
"tree_loaded"
] | 67482e5157fcd1c40705e5c2cacfb93564703ed0 | https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/gui/qt_b26_load_dialog.py#L247-L295 | train |
moonso/ped_parser | ped_parser/parser.py | cli | def cli(family_file, family_type, to_json, to_madeline, to_ped, to_dict,
outfile, logfile, loglevel):
"""Cli for testing the ped parser."""
from pprint import pprint as pp
my_parser = FamilyParser(family_file, family_type)
if to_json:
if outfile:
outfile.write(my_p... | python | def cli(family_file, family_type, to_json, to_madeline, to_ped, to_dict,
outfile, logfile, loglevel):
"""Cli for testing the ped parser."""
from pprint import pprint as pp
my_parser = FamilyParser(family_file, family_type)
if to_json:
if outfile:
outfile.write(my_p... | [
"def",
"cli",
"(",
"family_file",
",",
"family_type",
",",
"to_json",
",",
"to_madeline",
",",
"to_ped",
",",
"to_dict",
",",
"outfile",
",",
"logfile",
",",
"loglevel",
")",
":",
"from",
"pprint",
"import",
"pprint",
"as",
"pp",
"my_parser",
"=",
"FamilyP... | Cli for testing the ped parser. | [
"Cli",
"for",
"testing",
"the",
"ped",
"parser",
"."
] | a7393e47139532782ea3c821aabea33d46f94323 | https://github.com/moonso/ped_parser/blob/a7393e47139532782ea3c821aabea33d46f94323/ped_parser/parser.py#L641-L668 | train |
moonso/ped_parser | ped_parser/parser.py | FamilyParser.check_line_length | def check_line_length(self, splitted_line, expected_length):
"""
Check if the line is correctly formated. Throw a SyntaxError if it is not.
"""
if len(splitted_line) != expected_length:
raise WrongLineFormat(
message='WRONG FORMATED PED LINE!',
... | python | def check_line_length(self, splitted_line, expected_length):
"""
Check if the line is correctly formated. Throw a SyntaxError if it is not.
"""
if len(splitted_line) != expected_length:
raise WrongLineFormat(
message='WRONG FORMATED PED LINE!',
... | [
"def",
"check_line_length",
"(",
"self",
",",
"splitted_line",
",",
"expected_length",
")",
":",
"if",
"len",
"(",
"splitted_line",
")",
"!=",
"expected_length",
":",
"raise",
"WrongLineFormat",
"(",
"message",
"=",
"'WRONG FORMATED PED LINE!'",
",",
"ped_line",
"... | Check if the line is correctly formated. Throw a SyntaxError if it is not. | [
"Check",
"if",
"the",
"line",
"is",
"correctly",
"formated",
".",
"Throw",
"a",
"SyntaxError",
"if",
"it",
"is",
"not",
"."
] | a7393e47139532782ea3c821aabea33d46f94323 | https://github.com/moonso/ped_parser/blob/a7393e47139532782ea3c821aabea33d46f94323/ped_parser/parser.py#L195-L203 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | deck_vote_tag | def deck_vote_tag(deck: Deck) -> str:
'''deck vote tag address'''
if deck.id is None:
raise Exception("deck.id is required")
deck_vote_tag_privkey = sha256(unhexlify(deck.id) + b"vote_init").hexdigest()
deck_vote_tag_address = Kutil(network=deck.network, privkey=bytearray.fromhex(deck_vote_tag... | python | def deck_vote_tag(deck: Deck) -> str:
'''deck vote tag address'''
if deck.id is None:
raise Exception("deck.id is required")
deck_vote_tag_privkey = sha256(unhexlify(deck.id) + b"vote_init").hexdigest()
deck_vote_tag_address = Kutil(network=deck.network, privkey=bytearray.fromhex(deck_vote_tag... | [
"def",
"deck_vote_tag",
"(",
"deck",
":",
"Deck",
")",
"->",
"str",
":",
"if",
"deck",
".",
"id",
"is",
"None",
":",
"raise",
"Exception",
"(",
"\"deck.id is required\"",
")",
"deck_vote_tag_privkey",
"=",
"sha256",
"(",
"unhexlify",
"(",
"deck",
".",
"id"... | deck vote tag address | [
"deck",
"vote",
"tag",
"address"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L14-L22 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | parse_vote_info | def parse_vote_info(protobuf: bytes) -> dict:
'''decode vote init tx op_return protobuf message and validate it.'''
vote = pavoteproto.Vote()
vote.ParseFromString(protobuf)
assert vote.version > 0, {"error": "Vote info incomplete, version can't be 0."}
assert vote.start_block < vote.end_block, {"e... | python | def parse_vote_info(protobuf: bytes) -> dict:
'''decode vote init tx op_return protobuf message and validate it.'''
vote = pavoteproto.Vote()
vote.ParseFromString(protobuf)
assert vote.version > 0, {"error": "Vote info incomplete, version can't be 0."}
assert vote.start_block < vote.end_block, {"e... | [
"def",
"parse_vote_info",
"(",
"protobuf",
":",
"bytes",
")",
"->",
"dict",
":",
"vote",
"=",
"pavoteproto",
".",
"Vote",
"(",
")",
"vote",
".",
"ParseFromString",
"(",
"protobuf",
")",
"assert",
"vote",
".",
"version",
">",
"0",
",",
"{",
"\"error\"",
... | decode vote init tx op_return protobuf message and validate it. | [
"decode",
"vote",
"init",
"tx",
"op_return",
"protobuf",
"message",
"and",
"validate",
"it",
"."
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L101-L118 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | vote_init | def vote_init(vote: Vote, inputs: dict, change_address: str) -> bytes:
'''initialize vote transaction, must be signed by the deck_issuer privkey'''
network_params = net_query(vote.deck.network)
deck_vote_tag_address = deck_vote_tag(vote.deck)
tx_fee = network_params.min_tx_fee # settle for min tx fee... | python | def vote_init(vote: Vote, inputs: dict, change_address: str) -> bytes:
'''initialize vote transaction, must be signed by the deck_issuer privkey'''
network_params = net_query(vote.deck.network)
deck_vote_tag_address = deck_vote_tag(vote.deck)
tx_fee = network_params.min_tx_fee # settle for min tx fee... | [
"def",
"vote_init",
"(",
"vote",
":",
"Vote",
",",
"inputs",
":",
"dict",
",",
"change_address",
":",
"str",
")",
"->",
"bytes",
":",
"network_params",
"=",
"net_query",
"(",
"vote",
".",
"deck",
".",
"network",
")",
"deck_vote_tag_address",
"=",
"deck_vot... | initialize vote transaction, must be signed by the deck_issuer privkey | [
"initialize",
"vote",
"transaction",
"must",
"be",
"signed",
"by",
"the",
"deck_issuer",
"privkey"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L121-L140 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | find_vote_inits | def find_vote_inits(provider: Provider, deck: Deck) -> Iterable[Vote]:
'''find vote_inits on this deck'''
vote_ints = provider.listtransactions(deck_vote_tag(deck))
for txid in vote_ints:
try:
raw_vote = provider.getrawtransaction(txid)
vote = parse_vote_info(read_tx_opretu... | python | def find_vote_inits(provider: Provider, deck: Deck) -> Iterable[Vote]:
'''find vote_inits on this deck'''
vote_ints = provider.listtransactions(deck_vote_tag(deck))
for txid in vote_ints:
try:
raw_vote = provider.getrawtransaction(txid)
vote = parse_vote_info(read_tx_opretu... | [
"def",
"find_vote_inits",
"(",
"provider",
":",
"Provider",
",",
"deck",
":",
"Deck",
")",
"->",
"Iterable",
"[",
"Vote",
"]",
":",
"vote_ints",
"=",
"provider",
".",
"listtransactions",
"(",
"deck_vote_tag",
"(",
"deck",
")",
")",
"for",
"txid",
"in",
"... | find vote_inits on this deck | [
"find",
"vote_inits",
"on",
"this",
"deck"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L143-L157 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | vote_cast | def vote_cast(vote: Vote, choice_index: int, inputs: dict,
change_address: str) -> bytes:
'''vote cast transaction'''
network_params = net_query(vote.deck.network)
vote_cast_addr = vote.vote_choice_address[choice_index]
tx_fee = network_params.min_tx_fee # settle for min tx fee for now
... | python | def vote_cast(vote: Vote, choice_index: int, inputs: dict,
change_address: str) -> bytes:
'''vote cast transaction'''
network_params = net_query(vote.deck.network)
vote_cast_addr = vote.vote_choice_address[choice_index]
tx_fee = network_params.min_tx_fee # settle for min tx fee for now
... | [
"def",
"vote_cast",
"(",
"vote",
":",
"Vote",
",",
"choice_index",
":",
"int",
",",
"inputs",
":",
"dict",
",",
"change_address",
":",
"str",
")",
"->",
"bytes",
":",
"network_params",
"=",
"net_query",
"(",
"vote",
".",
"deck",
".",
"network",
")",
"v... | vote cast transaction | [
"vote",
"cast",
"transaction"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L160-L179 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | find_vote_casts | def find_vote_casts(provider: Provider, vote: Vote, choice_index: int) -> Iterable[VoteCast]:
'''find and verify vote_casts on this vote_choice_address'''
vote_casts = provider.listtransactions(vote.vote_choice_address[choice_index])
for tx in vote_casts:
raw_tx = provider.getrawtransaction(tx, 1)
... | python | def find_vote_casts(provider: Provider, vote: Vote, choice_index: int) -> Iterable[VoteCast]:
'''find and verify vote_casts on this vote_choice_address'''
vote_casts = provider.listtransactions(vote.vote_choice_address[choice_index])
for tx in vote_casts:
raw_tx = provider.getrawtransaction(tx, 1)
... | [
"def",
"find_vote_casts",
"(",
"provider",
":",
"Provider",
",",
"vote",
":",
"Vote",
",",
"choice_index",
":",
"int",
")",
"->",
"Iterable",
"[",
"VoteCast",
"]",
":",
"vote_casts",
"=",
"provider",
".",
"listtransactions",
"(",
"vote",
".",
"vote_choice_ad... | find and verify vote_casts on this vote_choice_address | [
"find",
"and",
"verify",
"vote_casts",
"on",
"this",
"vote_choice_address"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L207-L217 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | Vote.to_protobuf | def to_protobuf(self) -> str:
'''encode vote into protobuf'''
vote = pavoteproto.Vote()
vote.version = self.version
vote.description = self.description
vote.count_mode = vote.MODE.Value(self.count_mode)
vote.start_block = self.start_block
vote.end_block = self.en... | python | def to_protobuf(self) -> str:
'''encode vote into protobuf'''
vote = pavoteproto.Vote()
vote.version = self.version
vote.description = self.description
vote.count_mode = vote.MODE.Value(self.count_mode)
vote.start_block = self.start_block
vote.end_block = self.en... | [
"def",
"to_protobuf",
"(",
"self",
")",
"->",
"str",
":",
"vote",
"=",
"pavoteproto",
".",
"Vote",
"(",
")",
"vote",
".",
"version",
"=",
"self",
".",
"version",
"vote",
".",
"description",
"=",
"self",
".",
"description",
"vote",
".",
"count_mode",
"=... | encode vote into protobuf | [
"encode",
"vote",
"into",
"protobuf"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L44-L65 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | Vote.to_dict | def to_dict(self) -> dict:
'''vote info as dict'''
return {
"version": self.version,
"description": self.description,
"count_mode": self.count_mode,
"start_block": self.start_block,
"end_block": self.end_block,
"choices": self.choi... | python | def to_dict(self) -> dict:
'''vote info as dict'''
return {
"version": self.version,
"description": self.description,
"count_mode": self.count_mode,
"start_block": self.start_block,
"end_block": self.end_block,
"choices": self.choi... | [
"def",
"to_dict",
"(",
"self",
")",
"->",
"dict",
":",
"return",
"{",
"\"version\"",
":",
"self",
".",
"version",
",",
"\"description\"",
":",
"self",
".",
"description",
",",
"\"count_mode\"",
":",
"self",
".",
"count_mode",
",",
"\"start_block\"",
":",
"... | vote info as dict | [
"vote",
"info",
"as",
"dict"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L68-L79 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | Vote.vote_choice_address | def vote_choice_address(self) -> List[str]:
'''calculate the addresses on which the vote is casted.'''
if self.vote_id is None:
raise Exception("vote_id is required")
addresses = []
vote_init_txid = unhexlify(self.vote_id)
for choice in self.choices:
vo... | python | def vote_choice_address(self) -> List[str]:
'''calculate the addresses on which the vote is casted.'''
if self.vote_id is None:
raise Exception("vote_id is required")
addresses = []
vote_init_txid = unhexlify(self.vote_id)
for choice in self.choices:
vo... | [
"def",
"vote_choice_address",
"(",
"self",
")",
"->",
"List",
"[",
"str",
"]",
":",
"if",
"self",
".",
"vote_id",
"is",
"None",
":",
"raise",
"Exception",
"(",
"\"vote_id is required\"",
")",
"addresses",
"=",
"[",
"]",
"vote_init_txid",
"=",
"unhexlify",
... | calculate the addresses on which the vote is casted. | [
"calculate",
"the",
"addresses",
"on",
"which",
"the",
"vote",
"is",
"casted",
"."
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L82-L98 | train |
PeerAssets/pypeerassets | pypeerassets/voting.py | VoteCast.is_valid | def is_valid(self) -> bool:
'''check if VoteCast is valid'''
if not (self.blocknum >= self.vote.start_block and
self.blocknum <= self.vote.end_block):
return False
if not self.confirmations >= 6:
return False
return True | python | def is_valid(self) -> bool:
'''check if VoteCast is valid'''
if not (self.blocknum >= self.vote.start_block and
self.blocknum <= self.vote.end_block):
return False
if not self.confirmations >= 6:
return False
return True | [
"def",
"is_valid",
"(",
"self",
")",
"->",
"bool",
":",
"if",
"not",
"(",
"self",
".",
"blocknum",
">=",
"self",
".",
"vote",
".",
"start_block",
"and",
"self",
".",
"blocknum",
"<=",
"self",
".",
"vote",
".",
"end_block",
")",
":",
"return",
"False"... | check if VoteCast is valid | [
"check",
"if",
"VoteCast",
"is",
"valid"
] | 8927b4a686887f44fe2cd9de777e2c827c948987 | https://github.com/PeerAssets/pypeerassets/blob/8927b4a686887f44fe2cd9de777e2c827c948987/pypeerassets/voting.py#L194-L204 | train |
nmdp-bioinformatics/SeqAnn | seqann/models/reference_data.py | ReferenceData.search_refdata | def search_refdata(self, seq, locus):
"""
This checks to see if a sequence already exists in the reference data. If it does, then it'll return the known annotation.
:return: The Annotation of associated with the input sequence
:rtype: :ref:`ann`
Example:
>>> from B... | python | def search_refdata(self, seq, locus):
"""
This checks to see if a sequence already exists in the reference data. If it does, then it'll return the known annotation.
:return: The Annotation of associated with the input sequence
:rtype: :ref:`ann`
Example:
>>> from B... | [
"def",
"search_refdata",
"(",
"self",
",",
"seq",
",",
"locus",
")",
":",
"# TODO: ONLY MAKE ONE CONNECTION",
"# TODO: add try statement",
"# TODO: take password from environment variable",
"if",
"self",
".",
"server_avail",
":",
"hla",
",",
"loc",
"=",
"locus",
".",
... | This checks to see if a sequence already exists in the reference data. If it does, then it'll return the known annotation.
:return: The Annotation of associated with the input sequence
:rtype: :ref:`ann`
Example:
>>> from Bio.Seq import Seq
>>> from seqann.models.refer... | [
"This",
"checks",
"to",
"see",
"if",
"a",
"sequence",
"already",
"exists",
"in",
"the",
"reference",
"data",
".",
"If",
"it",
"does",
"then",
"it",
"ll",
"return",
"the",
"known",
"annotation",
"."
] | 5ce91559b0a4fbe4fb7758e034eb258202632463 | https://github.com/nmdp-bioinformatics/SeqAnn/blob/5ce91559b0a4fbe4fb7758e034eb258202632463/seqann/models/reference_data.py#L621-L679 | train |
LISE-B26/pylabcontrol | build/lib/pylabcontrol/src/core/parameter.py | Parameter.update | def update(self, *args):
"""
updates the values of the parameter, just as a regular dictionary
"""
for d in args:
for (key, value) in d.items():
self.__setitem__(key, value) | python | def update(self, *args):
"""
updates the values of the parameter, just as a regular dictionary
"""
for d in args:
for (key, value) in d.items():
self.__setitem__(key, value) | [
"def",
"update",
"(",
"self",
",",
"*",
"args",
")",
":",
"for",
"d",
"in",
"args",
":",
"for",
"(",
"key",
",",
"value",
")",
"in",
"d",
".",
"items",
"(",
")",
":",
"self",
".",
"__setitem__",
"(",
"key",
",",
"value",
")"
] | updates the values of the parameter, just as a regular dictionary | [
"updates",
"the",
"values",
"of",
"the",
"parameter",
"just",
"as",
"a",
"regular",
"dictionary"
] | 67482e5157fcd1c40705e5c2cacfb93564703ed0 | https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/core/parameter.py#L110-L116 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.error | def error(msg, log_file=None):
"""Print, output error message and raise RuntimeError."""
UtilClass.print_msg(msg + os.linesep)
if log_file is not None:
UtilClass.writelog(log_file, msg, 'append')
raise RuntimeError(msg) | python | def error(msg, log_file=None):
"""Print, output error message and raise RuntimeError."""
UtilClass.print_msg(msg + os.linesep)
if log_file is not None:
UtilClass.writelog(log_file, msg, 'append')
raise RuntimeError(msg) | [
"def",
"error",
"(",
"msg",
",",
"log_file",
"=",
"None",
")",
":",
"UtilClass",
".",
"print_msg",
"(",
"msg",
"+",
"os",
".",
"linesep",
")",
"if",
"log_file",
"is",
"not",
"None",
":",
"UtilClass",
".",
"writelog",
"(",
"log_file",
",",
"msg",
",",... | Print, output error message and raise RuntimeError. | [
"Print",
"output",
"error",
"message",
"and",
"raise",
"RuntimeError",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L96-L101 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.log | def log(lines, log_file=None):
"""Output log message."""
err = False
for line in lines:
print(line)
if log_file is not None:
UtilClass.writelog(log_file, line, 'append')
if 'BAD TERMINATION' in line.upper():
err = True
... | python | def log(lines, log_file=None):
"""Output log message."""
err = False
for line in lines:
print(line)
if log_file is not None:
UtilClass.writelog(log_file, line, 'append')
if 'BAD TERMINATION' in line.upper():
err = True
... | [
"def",
"log",
"(",
"lines",
",",
"log_file",
"=",
"None",
")",
":",
"err",
"=",
"False",
"for",
"line",
"in",
"lines",
":",
"print",
"(",
"line",
")",
"if",
"log_file",
"is",
"not",
"None",
":",
"UtilClass",
".",
"writelog",
"(",
"log_file",
",",
"... | Output log message. | [
"Output",
"log",
"message",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L104-L115 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.write_time_log | def write_time_log(logfile, time):
"""Write time log."""
if os.path.exists(logfile):
log_status = open(logfile, 'a', encoding='utf-8')
else:
log_status = open(logfile, 'w', encoding='utf-8')
log_status.write('Function Name\tRead Time\tCompute Time\tWrite Time\... | python | def write_time_log(logfile, time):
"""Write time log."""
if os.path.exists(logfile):
log_status = open(logfile, 'a', encoding='utf-8')
else:
log_status = open(logfile, 'w', encoding='utf-8')
log_status.write('Function Name\tRead Time\tCompute Time\tWrite Time\... | [
"def",
"write_time_log",
"(",
"logfile",
",",
"time",
")",
":",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"logfile",
")",
":",
"log_status",
"=",
"open",
"(",
"logfile",
",",
"'a'",
",",
"encoding",
"=",
"'utf-8'",
")",
"else",
":",
"log_status",
... | Write time log. | [
"Write",
"time",
"log",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L118-L130 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.check_infile_and_wp | def check_infile_and_wp(curinf, curwp):
"""Check the existence of the given file and directory path.
1. Raise Runtime exception of both not existed.
2. If the ``curwp`` is None, the set the base folder of ``curinf`` to it.
"""
if not os.path.exists(curinf):
if c... | python | def check_infile_and_wp(curinf, curwp):
"""Check the existence of the given file and directory path.
1. Raise Runtime exception of both not existed.
2. If the ``curwp`` is None, the set the base folder of ``curinf`` to it.
"""
if not os.path.exists(curinf):
if c... | [
"def",
"check_infile_and_wp",
"(",
"curinf",
",",
"curwp",
")",
":",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"curinf",
")",
":",
"if",
"curwp",
"is",
"None",
":",
"TauDEM",
".",
"error",
"(",
"'You must specify one of the workspace and the '",
"'... | Check the existence of the given file and directory path.
1. Raise Runtime exception of both not existed.
2. If the ``curwp`` is None, the set the base folder of ``curinf`` to it. | [
"Check",
"the",
"existence",
"of",
"the",
"given",
"file",
"and",
"directory",
"path",
".",
"1",
".",
"Raise",
"Runtime",
"exception",
"of",
"both",
"not",
"existed",
".",
"2",
".",
"If",
"the",
"curwp",
"is",
"None",
"the",
"set",
"the",
"base",
"fold... | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L163-L180 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.pitremove | def pitremove(np, dem, filleddem, workingdir=None, mpiexedir=None, exedir=None, log_file=None,
runtime_file=None, hostfile=None):
"""Run pit remove using the flooding approach """
fname = TauDEM.func_name('pitremove')
return TauDEM.run(FileClass.get_executable_fullpath(fname, e... | python | def pitremove(np, dem, filleddem, workingdir=None, mpiexedir=None, exedir=None, log_file=None,
runtime_file=None, hostfile=None):
"""Run pit remove using the flooding approach """
fname = TauDEM.func_name('pitremove')
return TauDEM.run(FileClass.get_executable_fullpath(fname, e... | [
"def",
"pitremove",
"(",
"np",
",",
"dem",
",",
"filleddem",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
",",
"hostfile",
"=",
"None",
")",
... | Run pit remove using the flooding approach | [
"Run",
"pit",
"remove",
"using",
"the",
"flooding",
"approach"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L377-L386 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.d8flowdir | def d8flowdir(np, filleddem, flowdir, slope, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D8 flow direction"""
fname = TauDEM.func_name('d8flowdir')
return TauDEM.run(FileClass.get_executable_fullpath(fname, exedir),
... | python | def d8flowdir(np, filleddem, flowdir, slope, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D8 flow direction"""
fname = TauDEM.func_name('d8flowdir')
return TauDEM.run(FileClass.get_executable_fullpath(fname, exedir),
... | [
"def",
"d8flowdir",
"(",
"np",
",",
"filleddem",
",",
"flowdir",
",",
"slope",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
",",
"hostfile",
"... | Run D8 flow direction | [
"Run",
"D8",
"flow",
"direction"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L389-L398 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.dinfflowdir | def dinfflowdir(np, filleddem, flowangle, slope, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Dinf flow direction"""
fname = TauDEM.func_name('dinfflowdir')
return TauDEM.run(FileClass.get_executable_fullpath(fname, ex... | python | def dinfflowdir(np, filleddem, flowangle, slope, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Dinf flow direction"""
fname = TauDEM.func_name('dinfflowdir')
return TauDEM.run(FileClass.get_executable_fullpath(fname, ex... | [
"def",
"dinfflowdir",
"(",
"np",
",",
"filleddem",
",",
"flowangle",
",",
"slope",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
",",
"hostfile",... | Run Dinf flow direction | [
"Run",
"Dinf",
"flow",
"direction"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L401-L410 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.aread8 | def aread8(np, flowdir, acc, outlet=None, streamskeleton=None, edgecontaimination=False,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Accumulate area according to D8 flow direction"""
# -nc means do not consider edge... | python | def aread8(np, flowdir, acc, outlet=None, streamskeleton=None, edgecontaimination=False,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Accumulate area according to D8 flow direction"""
# -nc means do not consider edge... | [
"def",
"aread8",
"(",
"np",
",",
"flowdir",
",",
"acc",
",",
"outlet",
"=",
"None",
",",
"streamskeleton",
"=",
"None",
",",
"edgecontaimination",
"=",
"False",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
... | Run Accumulate area according to D8 flow direction | [
"Run",
"Accumulate",
"area",
"according",
"to",
"D8",
"flow",
"direction"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L413-L428 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.areadinf | def areadinf(np, angfile, sca, outlet=None, wg=None, edgecontaimination=False,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Accumulate area according to Dinf flow direction"""
# -nc means do not consider edge con... | python | def areadinf(np, angfile, sca, outlet=None, wg=None, edgecontaimination=False,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run Accumulate area according to Dinf flow direction"""
# -nc means do not consider edge con... | [
"def",
"areadinf",
"(",
"np",
",",
"angfile",
",",
"sca",
",",
"outlet",
"=",
"None",
",",
"wg",
"=",
"None",
",",
"edgecontaimination",
"=",
"False",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"lo... | Run Accumulate area according to Dinf flow direction | [
"Run",
"Accumulate",
"area",
"according",
"to",
"Dinf",
"flow",
"direction"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L431-L446 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.connectdown | def connectdown(np, p, acc, outlet, wtsd=None, workingdir=None, mpiexedir=None,
exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Reads an ad8 contributing area file,
identifies the location of the largest ad8 value as the outlet of the largest watershed"""
# ... | python | def connectdown(np, p, acc, outlet, wtsd=None, workingdir=None, mpiexedir=None,
exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Reads an ad8 contributing area file,
identifies the location of the largest ad8 value as the outlet of the largest watershed"""
# ... | [
"def",
"connectdown",
"(",
"np",
",",
"p",
",",
"acc",
",",
"outlet",
",",
"wtsd",
"=",
"None",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",... | Reads an ad8 contributing area file,
identifies the location of the largest ad8 value as the outlet of the largest watershed | [
"Reads",
"an",
"ad8",
"contributing",
"area",
"file",
"identifies",
"the",
"location",
"of",
"the",
"largest",
"ad8",
"value",
"as",
"the",
"outlet",
"of",
"the",
"largest",
"watershed"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L449-L465 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.threshold | def threshold(np, acc, stream_raster, threshold=100., workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run threshold for stream raster"""
fname = TauDEM.func_name('threshold')
return TauDEM.run(FileClass.get_executable_fullpath(... | python | def threshold(np, acc, stream_raster, threshold=100., workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run threshold for stream raster"""
fname = TauDEM.func_name('threshold')
return TauDEM.run(FileClass.get_executable_fullpath(... | [
"def",
"threshold",
"(",
"np",
",",
"acc",
",",
"stream_raster",
",",
"threshold",
"=",
"100.",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
"... | Run threshold for stream raster | [
"Run",
"threshold",
"for",
"stream",
"raster"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L480-L489 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.moveoutletstostrm | def moveoutletstostrm(np, flowdir, streamRaster, outlet, modifiedOutlet,
workingdir=None, mpiexedir=None,
exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run move the given outlets to stream"""
fname = TauDEM.func_name('moveoutletstos... | python | def moveoutletstostrm(np, flowdir, streamRaster, outlet, modifiedOutlet,
workingdir=None, mpiexedir=None,
exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run move the given outlets to stream"""
fname = TauDEM.func_name('moveoutletstos... | [
"def",
"moveoutletstostrm",
"(",
"np",
",",
"flowdir",
",",
"streamRaster",
",",
"outlet",
",",
"modifiedOutlet",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
... | Run move the given outlets to stream | [
"Run",
"move",
"the",
"given",
"outlets",
"to",
"stream"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L507-L518 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.convertdistmethod | def convertdistmethod(method_str):
"""Convert distance method to h, v, p, and s."""
if StringClass.string_match(method_str, 'Horizontal'):
return 'h'
elif StringClass.string_match(method_str, 'Vertical'):
return 'v'
elif StringClass.string_match(method_str, 'Pytha... | python | def convertdistmethod(method_str):
"""Convert distance method to h, v, p, and s."""
if StringClass.string_match(method_str, 'Horizontal'):
return 'h'
elif StringClass.string_match(method_str, 'Vertical'):
return 'v'
elif StringClass.string_match(method_str, 'Pytha... | [
"def",
"convertdistmethod",
"(",
"method_str",
")",
":",
"if",
"StringClass",
".",
"string_match",
"(",
"method_str",
",",
"'Horizontal'",
")",
":",
"return",
"'h'",
"elif",
"StringClass",
".",
"string_match",
"(",
"method_str",
",",
"'Vertical'",
")",
":",
"r... | Convert distance method to h, v, p, and s. | [
"Convert",
"distance",
"method",
"to",
"h",
"v",
"p",
"and",
"s",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L521-L534 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.convertstatsmethod | def convertstatsmethod(method_str):
"""Convert statistics method to ave, min, and max."""
if StringClass.string_match(method_str, 'Average'):
return 'ave'
elif StringClass.string_match(method_str, 'Maximum'):
return 'max'
elif StringClass.string_match(method_str, ... | python | def convertstatsmethod(method_str):
"""Convert statistics method to ave, min, and max."""
if StringClass.string_match(method_str, 'Average'):
return 'ave'
elif StringClass.string_match(method_str, 'Maximum'):
return 'max'
elif StringClass.string_match(method_str, ... | [
"def",
"convertstatsmethod",
"(",
"method_str",
")",
":",
"if",
"StringClass",
".",
"string_match",
"(",
"method_str",
",",
"'Average'",
")",
":",
"return",
"'ave'",
"elif",
"StringClass",
".",
"string_match",
"(",
"method_str",
",",
"'Maximum'",
")",
":",
"re... | Convert statistics method to ave, min, and max. | [
"Convert",
"statistics",
"method",
"to",
"ave",
"min",
"and",
"max",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L537-L548 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.d8hdisttostrm | def d8hdisttostrm(np, p, src, dist, thresh, workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run D8 horizontal distance down to stream.
"""
fname = TauDEM.func_name('d8hdisttostrm')
return TauDEM.run(FileClass.get_ex... | python | def d8hdisttostrm(np, p, src, dist, thresh, workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Run D8 horizontal distance down to stream.
"""
fname = TauDEM.func_name('d8hdisttostrm')
return TauDEM.run(FileClass.get_ex... | [
"def",
"d8hdisttostrm",
"(",
"np",
",",
"p",
",",
"src",
",",
"dist",
",",
"thresh",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
",",
"host... | Run D8 horizontal distance down to stream. | [
"Run",
"D8",
"horizontal",
"distance",
"down",
"to",
"stream",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L551-L562 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.d8distdowntostream | def d8distdowntostream(np, p, fel, src, dist, distancemethod, thresh, workingdir=None,
mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D8 distance down to stream by different method for distance.
This function is... | python | def d8distdowntostream(np, p, fel, src, dist, distancemethod, thresh, workingdir=None,
mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D8 distance down to stream by different method for distance.
This function is... | [
"def",
"d8distdowntostream",
"(",
"np",
",",
"p",
",",
"fel",
",",
"src",
",",
"dist",
",",
"distancemethod",
",",
"thresh",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
... | Run D8 distance down to stream by different method for distance.
This function is extended from d8hdisttostrm by Liangjun.
Please clone `TauDEM by lreis2415`_ and compile for this program.
.. _TauDEM by lreis2415:
https://github.com/lreis2415/TauDEM | [
"Run",
"D8",
"distance",
"down",
"to",
"stream",
"by",
"different",
"method",
"for",
"distance",
".",
"This",
"function",
"is",
"extended",
"from",
"d8hdisttostrm",
"by",
"Liangjun",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L565-L583 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.dinfdistdown | def dinfdistdown(np, ang, fel, slp, src, statsm, distm, edgecontamination, wg, dist,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D-inf distance down to stream"""
in_params = {'-m': '%s %s' % (TauDEM.conv... | python | def dinfdistdown(np, ang, fel, slp, src, statsm, distm, edgecontamination, wg, dist,
workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run D-inf distance down to stream"""
in_params = {'-m': '%s %s' % (TauDEM.conv... | [
"def",
"dinfdistdown",
"(",
"np",
",",
"ang",
",",
"fel",
",",
"slp",
",",
"src",
",",
"statsm",
",",
"distm",
",",
"edgecontamination",
",",
"wg",
",",
"dist",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None"... | Run D-inf distance down to stream | [
"Run",
"D",
"-",
"inf",
"distance",
"down",
"to",
"stream"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L586-L601 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.peukerdouglas | def peukerdouglas(np, fel, streamSkeleton, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run peuker-douglas function"""
fname = TauDEM.func_name('peukerdouglas')
return TauDEM.run(FileClass.get_executable_fullpath(fname, ... | python | def peukerdouglas(np, fel, streamSkeleton, workingdir=None, mpiexedir=None, exedir=None,
log_file=None, runtime_file=None, hostfile=None):
"""Run peuker-douglas function"""
fname = TauDEM.func_name('peukerdouglas')
return TauDEM.run(FileClass.get_executable_fullpath(fname, ... | [
"def",
"peukerdouglas",
"(",
"np",
",",
"fel",
",",
"streamSkeleton",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exedir",
"=",
"None",
",",
"log_file",
"=",
"None",
",",
"runtime_file",
"=",
"None",
",",
"hostfile",
"=",
"None",... | Run peuker-douglas function | [
"Run",
"peuker",
"-",
"douglas",
"function"
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L604-L613 | train |
lreis2415/PyGeoC | pygeoc/TauDEM.py | TauDEM.dropanalysis | def dropanalysis(np, fel, p, ad8, ssa, outlet, minthresh, maxthresh, numthresh,
logspace, drp, workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Drop analysis for optimal threshold for extracting stream."""
parstr... | python | def dropanalysis(np, fel, p, ad8, ssa, outlet, minthresh, maxthresh, numthresh,
logspace, drp, workingdir=None,
mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None):
"""Drop analysis for optimal threshold for extracting stream."""
parstr... | [
"def",
"dropanalysis",
"(",
"np",
",",
"fel",
",",
"p",
",",
"ad8",
",",
"ssa",
",",
"outlet",
",",
"minthresh",
",",
"maxthresh",
",",
"numthresh",
",",
"logspace",
",",
"drp",
",",
"workingdir",
"=",
"None",
",",
"mpiexedir",
"=",
"None",
",",
"exe... | Drop analysis for optimal threshold for extracting stream. | [
"Drop",
"analysis",
"for",
"optimal",
"threshold",
"for",
"extracting",
"stream",
"."
] | 9a92d1a229bb74298e3c57f27c97079980b5f729 | https://github.com/lreis2415/PyGeoC/blob/9a92d1a229bb74298e3c57f27c97079980b5f729/pygeoc/TauDEM.py#L616-L632 | train |
johnnoone/json-spec | src/jsonspec/reference/bases.py | Registry.resolve | def resolve(self, pointer):
"""Resolve from documents.
:param pointer: foo
:type pointer: DocumentPointer
"""
dp = DocumentPointer(pointer)
obj, fetcher = self.prototype(dp)
for token in dp.pointer:
obj = token.extract(obj, bypass_ref=True)
... | python | def resolve(self, pointer):
"""Resolve from documents.
:param pointer: foo
:type pointer: DocumentPointer
"""
dp = DocumentPointer(pointer)
obj, fetcher = self.prototype(dp)
for token in dp.pointer:
obj = token.extract(obj, bypass_ref=True)
... | [
"def",
"resolve",
"(",
"self",
",",
"pointer",
")",
":",
"dp",
"=",
"DocumentPointer",
"(",
"pointer",
")",
"obj",
",",
"fetcher",
"=",
"self",
".",
"prototype",
"(",
"dp",
")",
"for",
"token",
"in",
"dp",
".",
"pointer",
":",
"obj",
"=",
"token",
... | Resolve from documents.
:param pointer: foo
:type pointer: DocumentPointer | [
"Resolve",
"from",
"documents",
"."
] | f91981724cea0c366bd42a6670eb07bbe31c0e0c | https://github.com/johnnoone/json-spec/blob/f91981724cea0c366bd42a6670eb07bbe31c0e0c/src/jsonspec/reference/bases.py#L37-L52 | train |
nmdp-bioinformatics/SeqAnn | seqann/align.py | count_diffs | def count_diffs(align, feats, inseq, locus, cutoff,
verbose=False, verbosity=0):
"""
count_diffs - Counts the number of mismatches, gaps, and insertions and then determines if those are within an acceptable range.
:param align: The alignment
:type align: ``List``
:param feats: Dicto... | python | def count_diffs(align, feats, inseq, locus, cutoff,
verbose=False, verbosity=0):
"""
count_diffs - Counts the number of mismatches, gaps, and insertions and then determines if those are within an acceptable range.
:param align: The alignment
:type align: ``List``
:param feats: Dicto... | [
"def",
"count_diffs",
"(",
"align",
",",
"feats",
",",
"inseq",
",",
"locus",
",",
"cutoff",
",",
"verbose",
"=",
"False",
",",
"verbosity",
"=",
"0",
")",
":",
"nfeats",
"=",
"len",
"(",
"feats",
".",
"keys",
"(",
")",
")",
"mm",
"=",
"0",
"insr... | count_diffs - Counts the number of mismatches, gaps, and insertions and then determines if those are within an acceptable range.
:param align: The alignment
:type align: ``List``
:param feats: Dictonary of the features
:type feats: ``dict``
:param locus: The gene locus associated with the sequence.... | [
"count_diffs",
"-",
"Counts",
"the",
"number",
"of",
"mismatches",
"gaps",
"and",
"insertions",
"and",
"then",
"determines",
"if",
"those",
"are",
"within",
"an",
"acceptable",
"range",
"."
] | 5ce91559b0a4fbe4fb7758e034eb258202632463 | https://github.com/nmdp-bioinformatics/SeqAnn/blob/5ce91559b0a4fbe4fb7758e034eb258202632463/seqann/align.py#L394-L480 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_stop | def cmd_stop(self, argv, help):
"""Stops the instance"""
parser = argparse.ArgumentParser(
prog="%s stop" % self.progname,
description=help,
)
instances = self.get_instances(command='stop')
parser.add_argument("instance", nargs=1,
... | python | def cmd_stop(self, argv, help):
"""Stops the instance"""
parser = argparse.ArgumentParser(
prog="%s stop" % self.progname,
description=help,
)
instances = self.get_instances(command='stop')
parser.add_argument("instance", nargs=1,
... | [
"def",
"cmd_stop",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s stop\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"instances",
"=",
"self",
".... | Stops the instance | [
"Stops",
"the",
"instance"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L219-L232 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_terminate | def cmd_terminate(self, argv, help):
"""Terminates the instance"""
from ploy.common import yesno
parser = argparse.ArgumentParser(
prog="%s terminate" % self.progname,
description=help,
)
instances = self.get_instances(command='terminate')
parser.a... | python | def cmd_terminate(self, argv, help):
"""Terminates the instance"""
from ploy.common import yesno
parser = argparse.ArgumentParser(
prog="%s terminate" % self.progname,
description=help,
)
instances = self.get_instances(command='terminate')
parser.a... | [
"def",
"cmd_terminate",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"from",
"ploy",
".",
"common",
"import",
"yesno",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s terminate\"",
"%",
"self",
".",
"progname",
",",
"descripti... | Terminates the instance | [
"Terminates",
"the",
"instance"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L234-L252 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_start | def cmd_start(self, argv, help):
"""Starts the instance"""
parser = argparse.ArgumentParser(
prog="%s start" % self.progname,
description=help,
)
instances = self.get_instances(command='start')
parser.add_argument("instance", nargs=1,
... | python | def cmd_start(self, argv, help):
"""Starts the instance"""
parser = argparse.ArgumentParser(
prog="%s start" % self.progname,
description=help,
)
instances = self.get_instances(command='start')
parser.add_argument("instance", nargs=1,
... | [
"def",
"cmd_start",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s start\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"instances",
"=",
"self",
... | Starts the instance | [
"Starts",
"the",
"instance"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L270-L293 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_annotate | def cmd_annotate(self, argv, help):
"""Prints annotated config"""
parser = argparse.ArgumentParser(
prog="%s annotate" % self.progname,
description=help,
)
parser.parse_args(argv)
list(self.instances.values()) # trigger instance augmentation
for g... | python | def cmd_annotate(self, argv, help):
"""Prints annotated config"""
parser = argparse.ArgumentParser(
prog="%s annotate" % self.progname,
description=help,
)
parser.parse_args(argv)
list(self.instances.values()) # trigger instance augmentation
for g... | [
"def",
"cmd_annotate",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s annotate\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"parser",
".",
"parse_... | Prints annotated config | [
"Prints",
"annotated",
"config"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L295-L310 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_debug | def cmd_debug(self, argv, help):
"""Prints some debug info for this script"""
parser = argparse.ArgumentParser(
prog="%s debug" % self.progname,
description=help,
)
instances = self.instances
parser.add_argument("instance", nargs=1,
... | python | def cmd_debug(self, argv, help):
"""Prints some debug info for this script"""
parser = argparse.ArgumentParser(
prog="%s debug" % self.progname,
description=help,
)
instances = self.instances
parser.add_argument("instance", nargs=1,
... | [
"def",
"cmd_debug",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s debug\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"instances",
"=",
"self",
... | Prints some debug info for this script | [
"Prints",
"some",
"debug",
"info",
"for",
"this",
"script"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L312-L375 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_list | def cmd_list(self, argv, help):
"""Return a list of various things"""
parser = argparse.ArgumentParser(
prog="%s list" % self.progname,
description=help,
)
parser.add_argument("list", nargs=1,
metavar="listname",
... | python | def cmd_list(self, argv, help):
"""Return a list of various things"""
parser = argparse.ArgumentParser(
prog="%s list" % self.progname,
description=help,
)
parser.add_argument("list", nargs=1,
metavar="listname",
... | [
"def",
"cmd_list",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s list\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"parser",
".",
"add_argument",... | Return a list of various things | [
"Return",
"a",
"list",
"of",
"various",
"things"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L377-L393 | train |
ployground/ploy | ploy/__init__.py | Controller.cmd_ssh | def cmd_ssh(self, argv, help):
"""Log into the instance with ssh using the automatically generated known hosts"""
parser = argparse.ArgumentParser(
prog="%s ssh" % self.progname,
description=help,
)
instances = self.get_instances(command='init_ssh_key')
pa... | python | def cmd_ssh(self, argv, help):
"""Log into the instance with ssh using the automatically generated known hosts"""
parser = argparse.ArgumentParser(
prog="%s ssh" % self.progname,
description=help,
)
instances = self.get_instances(command='init_ssh_key')
pa... | [
"def",
"cmd_ssh",
"(",
"self",
",",
"argv",
",",
"help",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"prog",
"=",
"\"%s ssh\"",
"%",
"self",
".",
"progname",
",",
"description",
"=",
"help",
",",
")",
"instances",
"=",
"self",
".",... | Log into the instance with ssh using the automatically generated known hosts | [
"Log",
"into",
"the",
"instance",
"with",
"ssh",
"using",
"the",
"automatically",
"generated",
"known",
"hosts"
] | 9295b5597c09c434f170afbfd245d73f09affc39 | https://github.com/ployground/ploy/blob/9295b5597c09c434f170afbfd245d73f09affc39/ploy/__init__.py#L395-L445 | train |
mivade/tornadose | tornadose/handlers.py | BaseHandler.initialize | def initialize(self, store):
"""Common initialization of handlers happens here. If additional
initialization is required, this method must either be called with
``super`` or the child class must assign the ``store`` attribute and
register itself with the store.
"""
... | python | def initialize(self, store):
"""Common initialization of handlers happens here. If additional
initialization is required, this method must either be called with
``super`` or the child class must assign the ``store`` attribute and
register itself with the store.
"""
... | [
"def",
"initialize",
"(",
"self",
",",
"store",
")",
":",
"assert",
"isinstance",
"(",
"store",
",",
"stores",
".",
"BaseStore",
")",
"self",
".",
"messages",
"=",
"Queue",
"(",
")",
"self",
".",
"store",
"=",
"store",
"self",
".",
"store",
".",
"reg... | Common initialization of handlers happens here. If additional
initialization is required, this method must either be called with
``super`` or the child class must assign the ``store`` attribute and
register itself with the store. | [
"Common",
"initialization",
"of",
"handlers",
"happens",
"here",
".",
"If",
"additional",
"initialization",
"is",
"required",
"this",
"method",
"must",
"either",
"be",
"called",
"with",
"super",
"or",
"the",
"child",
"class",
"must",
"assign",
"the",
"store",
... | d220e0e3040d24c98997eee7a8a236602b4c5159 | https://github.com/mivade/tornadose/blob/d220e0e3040d24c98997eee7a8a236602b4c5159/tornadose/handlers.py#L22-L32 | train |
mivade/tornadose | tornadose/handlers.py | EventSource.prepare | def prepare(self):
"""Log access."""
request_time = 1000.0 * self.request.request_time()
access_log.info(
"%d %s %.2fms", self.get_status(),
self._request_summary(), request_time) | python | def prepare(self):
"""Log access."""
request_time = 1000.0 * self.request.request_time()
access_log.info(
"%d %s %.2fms", self.get_status(),
self._request_summary(), request_time) | [
"def",
"prepare",
"(",
"self",
")",
":",
"request_time",
"=",
"1000.0",
"*",
"self",
".",
"request",
".",
"request_time",
"(",
")",
"access_log",
".",
"info",
"(",
"\"%d %s %.2fms\"",
",",
"self",
".",
"get_status",
"(",
")",
",",
"self",
".",
"_request_... | Log access. | [
"Log",
"access",
"."
] | d220e0e3040d24c98997eee7a8a236602b4c5159 | https://github.com/mivade/tornadose/blob/d220e0e3040d24c98997eee7a8a236602b4c5159/tornadose/handlers.py#L69-L74 | train |
mivade/tornadose | tornadose/handlers.py | EventSource.publish | async def publish(self, message):
"""Pushes data to a listener."""
try:
self.write('data: {}\n\n'.format(message))
await self.flush()
except StreamClosedError:
self.finished = True | python | async def publish(self, message):
"""Pushes data to a listener."""
try:
self.write('data: {}\n\n'.format(message))
await self.flush()
except StreamClosedError:
self.finished = True | [
"async",
"def",
"publish",
"(",
"self",
",",
"message",
")",
":",
"try",
":",
"self",
".",
"write",
"(",
"'data: {}\\n\\n'",
".",
"format",
"(",
"message",
")",
")",
"await",
"self",
".",
"flush",
"(",
")",
"except",
"StreamClosedError",
":",
"self",
"... | Pushes data to a listener. | [
"Pushes",
"data",
"to",
"a",
"listener",
"."
] | d220e0e3040d24c98997eee7a8a236602b4c5159 | https://github.com/mivade/tornadose/blob/d220e0e3040d24c98997eee7a8a236602b4c5159/tornadose/handlers.py#L76-L82 | train |
mivade/tornadose | tornadose/handlers.py | WebSocketSubscriber.open | async def open(self):
"""Register with the publisher."""
self.store.register(self)
while not self.finished:
message = await self.messages.get()
await self.publish(message) | python | async def open(self):
"""Register with the publisher."""
self.store.register(self)
while not self.finished:
message = await self.messages.get()
await self.publish(message) | [
"async",
"def",
"open",
"(",
"self",
")",
":",
"self",
".",
"store",
".",
"register",
"(",
"self",
")",
"while",
"not",
"self",
".",
"finished",
":",
"message",
"=",
"await",
"self",
".",
"messages",
".",
"get",
"(",
")",
"await",
"self",
".",
"pub... | Register with the publisher. | [
"Register",
"with",
"the",
"publisher",
"."
] | d220e0e3040d24c98997eee7a8a236602b4c5159 | https://github.com/mivade/tornadose/blob/d220e0e3040d24c98997eee7a8a236602b4c5159/tornadose/handlers.py#L102-L107 | train |
mivade/tornadose | tornadose/handlers.py | WebSocketSubscriber.publish | async def publish(self, message):
"""Push a new message to the client. The data will be
available as a JSON object with the key ``data``.
"""
try:
self.write_message(dict(data=message))
except WebSocketClosedError:
self._close() | python | async def publish(self, message):
"""Push a new message to the client. The data will be
available as a JSON object with the key ``data``.
"""
try:
self.write_message(dict(data=message))
except WebSocketClosedError:
self._close() | [
"async",
"def",
"publish",
"(",
"self",
",",
"message",
")",
":",
"try",
":",
"self",
".",
"write_message",
"(",
"dict",
"(",
"data",
"=",
"message",
")",
")",
"except",
"WebSocketClosedError",
":",
"self",
".",
"_close",
"(",
")"
] | Push a new message to the client. The data will be
available as a JSON object with the key ``data``. | [
"Push",
"a",
"new",
"message",
"to",
"the",
"client",
".",
"The",
"data",
"will",
"be",
"available",
"as",
"a",
"JSON",
"object",
"with",
"the",
"key",
"data",
"."
] | d220e0e3040d24c98997eee7a8a236602b4c5159 | https://github.com/mivade/tornadose/blob/d220e0e3040d24c98997eee7a8a236602b4c5159/tornadose/handlers.py#L116-L124 | train |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.