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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulationCell._tensors | def _tensors(cls, fluents: Sequence[FluentPair]) -> Iterable[tf.Tensor]:
'''Yields the `fluents`' tensors.'''
for _, fluent in fluents:
tensor = cls._output_size(fluent.tensor)
yield tensor | python | def _tensors(cls, fluents: Sequence[FluentPair]) -> Iterable[tf.Tensor]:
'''Yields the `fluents`' tensors.'''
for _, fluent in fluents:
tensor = cls._output_size(fluent.tensor)
yield tensor | [
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulationCell._dtype | def _dtype(cls, tensor: tf.Tensor) -> tf.Tensor:
'''Converts `tensor` to tf.float32 datatype if needed.'''
if tensor.dtype != tf.float32:
tensor = tf.cast(tensor, tf.float32)
return tensor | python | def _dtype(cls, tensor: tf.Tensor) -> tf.Tensor:
'''Converts `tensor` to tf.float32 datatype if needed.'''
if tensor.dtype != tf.float32:
tensor = tf.cast(tensor, tf.float32)
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulationCell._output | def _output(cls, fluents: Sequence[FluentPair]) -> Sequence[tf.Tensor]:
'''Returns output tensors for `fluents`.'''
return tuple(cls._dtype(t) for t in cls._tensors(fluents)) | python | def _output(cls, fluents: Sequence[FluentPair]) -> Sequence[tf.Tensor]:
'''Returns output tensors for `fluents`.'''
return tuple(cls._dtype(t) for t in cls._tensors(fluents)) | [
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulator.output_size | def output_size(self) -> Tuple[Sequence[Shape], Sequence[Shape], Sequence[Shape], int]:
'''Returns the simulation output size.'''
return self._cell.output_size | python | def output_size(self) -> Tuple[Sequence[Shape], Sequence[Shape], Sequence[Shape], int]:
'''Returns the simulation output size.'''
return self._cell.output_size | [
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulator.timesteps | def timesteps(self, horizon: int) -> tf.Tensor:
'''Returns the input tensor for the given `horizon`.'''
start, limit, delta = horizon - 1, -1, -1
timesteps_range = tf.range(start, limit, delta, dtype=tf.float32)
timesteps_range = tf.expand_dims(timesteps_range, -1)
batch_timestep... | python | def timesteps(self, horizon: int) -> tf.Tensor:
'''Returns the input tensor for the given `horizon`.'''
start, limit, delta = horizon - 1, -1, -1
timesteps_range = tf.range(start, limit, delta, dtype=tf.float32)
timesteps_range = tf.expand_dims(timesteps_range, -1)
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulator.trajectory | def trajectory(self,
horizon: int,
initial_state: Optional[StateTensor] = None) -> TrajectoryOutput:
'''Returns the ops for the trajectory generation with given `horizon`
and `initial_state`.
The simulation returns states, actions and interms as a
sequence of ten... | python | def trajectory(self,
horizon: int,
initial_state: Optional[StateTensor] = None) -> TrajectoryOutput:
'''Returns the ops for the trajectory generation with given `horizon`
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulator.run | def run(self,
horizon: int,
initial_state: Optional[StateTensor] = None) -> SimulationOutput:
'''Builds the MDP graph and simulates in batch the trajectories
with given `horizon`. Returns the non-fluents, states, actions, interms
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horizon: int,
initial_state: Optional[StateTensor] = None) -> SimulationOutput:
'''Builds the MDP graph and simulates in batch the trajectories
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/policy_simulator.py | PolicySimulator._output | def _output(cls,
tensors: Sequence[tf.Tensor],
dtypes: Sequence[tf.DType]) -> Sequence[tf.Tensor]:
'''Converts `tensors` to the corresponding `dtypes`.'''
outputs = []
for tensor, dtype in zip(tensors, dtypes):
tensor = tensor[0]
if tensor.dtype !=... | python | def _output(cls,
tensors: Sequence[tf.Tensor],
dtypes: Sequence[tf.DType]) -> Sequence[tf.Tensor]:
'''Converts `tensors` to the corresponding `dtypes`.'''
outputs = []
for tensor, dtype in zip(tensors, dtypes):
tensor = tensor[0]
if tensor.dtype !=... | [
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pgxcentre/geneparse | geneparse/readers/impute2.py | Impute2Reader._get_biallelic_variant | def _get_biallelic_variant(self, variant, info, _check_alleles=True):
"""Creates a bi-allelic variant."""
info = info.iloc[0, :]
assert not info.multiallelic
# Seeking and parsing the file
self._impute2_file.seek(info.seek)
genotypes = self._parse_impute2_line(self._impu... | python | def _get_biallelic_variant(self, variant, info, _check_alleles=True):
"""Creates a bi-allelic variant."""
info = info.iloc[0, :]
assert not info.multiallelic
# Seeking and parsing the file
self._impute2_file.seek(info.seek)
genotypes = self._parse_impute2_line(self._impu... | [
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pgxcentre/geneparse | geneparse/readers/impute2.py | Impute2Reader._fix_genotypes_object | def _fix_genotypes_object(self, genotypes, variant_info):
"""Fixes a genotypes object (variant name, multi-allelic value."""
# Checking the name (if there were duplications)
if self.has_index and variant_info.name != genotypes.variant.name:
if not variant_info.name.startswith(genotyp... | python | def _fix_genotypes_object(self, genotypes, variant_info):
"""Fixes a genotypes object (variant name, multi-allelic value."""
# Checking the name (if there were duplications)
if self.has_index and variant_info.name != genotypes.variant.name:
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pgxcentre/geneparse | geneparse/readers/plink.py | PlinkReader._normalize_missing | def _normalize_missing(g):
"""Normalize a plink genotype vector."""
g = g.astype(float)
g[g == -1.0] = np.nan
return g | python | def _normalize_missing(g):
"""Normalize a plink genotype vector."""
g = g.astype(float)
g[g == -1.0] = np.nan
return g | [
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255BITS/hyperchamber | examples/shared/cifar_utils.py | maybe_download_and_extract | def maybe_download_and_extract():
"""Download and extract the tarball from Alex's website."""
dest_directory = "/tmp/cifar"
if not os.path.exists(dest_directory):
os.makedirs(dest_directory)
filename = DATA_URL.split('/')[-1]
filepath = os.path.join(dest_directory, filename)
if not os.path.exists(filepa... | python | def maybe_download_and_extract():
"""Download and extract the tarball from Alex's website."""
dest_directory = "/tmp/cifar"
if not os.path.exists(dest_directory):
os.makedirs(dest_directory)
filename = DATA_URL.split('/')[-1]
filepath = os.path.join(dest_directory, filename)
if not os.path.exists(filepa... | [
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255BITS/hyperchamber | examples/shared/cifar_utils.py | plot | def plot(config, image, file):
""" Plot a single CIFAR image."""
image = np.squeeze(image)
print(file, image.shape)
imsave(file, image) | python | def plot(config, image, file):
""" Plot a single CIFAR image."""
image = np.squeeze(image)
print(file, image.shape)
imsave(file, image) | [
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | _get_seqtype_from_ext | def _get_seqtype_from_ext(handle):
'''Predict the filetype from a handle's name'''
if isinstance(handle, basestring):
name = handle
elif hasattr(handle, 'filename'):
name = handle.filename
elif hasattr(handle, 'name'):
name = handle.name
else:
raise ValueError("Unknow... | python | def _get_seqtype_from_ext(handle):
'''Predict the filetype from a handle's name'''
if isinstance(handle, basestring):
name = handle
elif hasattr(handle, 'filename'):
name = handle.filename
elif hasattr(handle, 'name'):
name = handle.name
else:
raise ValueError("Unknow... | [
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | _guess_seqtype_from_file | def _guess_seqtype_from_file(handle):
"Guess the sequence type from the file's contents"
if isinstance(handle, basestring):
handle = StringIO(handle)
for line in handle:
if not line.strip():
continue
if line.lstrip().split()[0] in ('LOCUS', 'FEATURES', 'source', 'CDS',
... | python | def _guess_seqtype_from_file(handle):
"Guess the sequence type from the file's contents"
if isinstance(handle, basestring):
handle = StringIO(handle)
for line in handle:
if not line.strip():
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... | [
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | _unzip_handle | def _unzip_handle(handle):
"""Transparently unzip the file handle"""
if isinstance(handle, basestring):
handle = _gzip_open_filename(handle)
else:
handle = _gzip_open_handle(handle)
return handle | python | def _unzip_handle(handle):
"""Transparently unzip the file handle"""
if isinstance(handle, basestring):
handle = _gzip_open_filename(handle)
else:
handle = _gzip_open_handle(handle)
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | sanity_check_insdcio | def sanity_check_insdcio(handle, id_marker, fake_id_line):
"""Sanity check for insdcio style files"""
found_id = False
found_end_marker = False
for line in handle:
line = line.strip()
if not line:
continue
if line.startswith(id_marker):
found_id = True
... | python | def sanity_check_insdcio(handle, id_marker, fake_id_line):
"""Sanity check for insdcio style files"""
found_id = False
found_end_marker = False
for line in handle:
line = line.strip()
if not line:
continue
if line.startswith(id_marker):
found_id = True
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | sanity_check_fasta | def sanity_check_fasta(handle):
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kblin/bioinf-helperlibs | helperlibs/bio/seqio.py | parse | def parse(handle, seqtype=None, robust=False):
'''Wrap SeqIO.parse'''
if seqtype is None:
seqtype = _get_seqtype_from_ext(handle)
if seqtype.startswith('gz-'):
handle = _unzip_handle(handle)
seqtype = seqtype[3:]
# False positive from pylint, both handles are fileobj-like
#... | python | def parse(handle, seqtype=None, robust=False):
'''Wrap SeqIO.parse'''
if seqtype is None:
seqtype = _get_seqtype_from_ext(handle)
if seqtype.startswith('gz-'):
handle = _unzip_handle(handle)
seqtype = seqtype[3:]
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Nic30/hwtGraph | hwtGraph/elk/containers/constants.py | PortConstraints.isOrderFixed | def isOrderFixed(self):
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testedminds/sand | sand/graph.py | _dicts_to_columns | def _dicts_to_columns(dicts):
"""
Given a List of Dictionaries with uniform keys, returns a single Dictionary
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[{'name': 'Field Museum', 'location': 'Chicago'},
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=>
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"""
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testedminds/sand | sand/graph.py | from_vertices_and_edges | def from_vertices_and_edges(vertices, edges, vertex_name_key='name', vertex_id_key='id',
edge_foreign_keys=('source', 'target'), directed=True):
"""
This representation assumes that vertices and edges are encoded in
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edge_foreign_keys=('source', 'target'), directed=True):
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testedminds/sand | sand/graph.py | from_edges | def from_edges(edges, source_key='source', target_key='target', weight_key='weight', directed=True):
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pgxcentre/geneparse | geneparse/utils.py | flip_alleles | def flip_alleles(genotypes):
"""Flip the alleles of an Genotypes instance."""
warnings.warn("deprecated: use 'Genotypes.flip_coded'", DeprecationWarning)
genotypes.reference, genotypes.coded = (genotypes.coded,
genotypes.reference)
genotypes.genotypes = 2 - ge... | python | def flip_alleles(genotypes):
"""Flip the alleles of an Genotypes instance."""
warnings.warn("deprecated: use 'Genotypes.flip_coded'", DeprecationWarning)
genotypes.reference, genotypes.coded = (genotypes.coded,
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pgxcentre/geneparse | geneparse/utils.py | code_minor | def code_minor(genotypes):
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In other words, this function can be used to make sure that the genotype
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pgxcentre/geneparse | geneparse/utils.py | maf | def maf(genotypes):
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"""
warnings.warn("deprecated: use 'Genotypes.maf'", DeprecationWarning)
g = genotypes.genotypes
maf = np.nansum(g) / (2 * np.sum(~np.isnan(g)))
if maf > 0.5:
... | python | def maf(genotypes):
"""Computes the MAF and returns a boolean indicating if the minor allele
is currently the coded allele.
"""
warnings.warn("deprecated: use 'Genotypes.maf'", DeprecationWarning)
g = genotypes.genotypes
maf = np.nansum(g) / (2 * np.sum(~np.isnan(g)))
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pgxcentre/geneparse | geneparse/utils.py | genotype_to_df | def genotype_to_df(g, samples, as_string=False):
"""Convert a genotype object to a pandas dataframe.
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name = g.variant.name if g.variant.name else "genotypes"
d... | python | def genotype_to_df(g, samples, as_string=False):
"""Convert a genotype object to a pandas dataframe.
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pgxcentre/geneparse | geneparse/utils.py | compute_ld | def compute_ld(cur_geno, other_genotypes, r2=False):
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cur_geno (Genotypes): The genotypes of the marker.
other_genotypes (list): A list of genotypes.
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"""Compute LD between a marker and a list of markers.
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cur_geno (Genotypes): The genotypes of the marker.
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pgxcentre/geneparse | geneparse/utils.py | normalize_genotypes | def normalize_genotypes(genotypes):
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Args:
genotypes (Genotypes): The genotypes to normalize.
Returns:
numpy.array: The normalized genotypes.
"""
genotypes = genotypes.genotypes
return (genotypes - np.nanmean(genotypes)) / np.nanstd(genotypes) | python | def normalize_genotypes(genotypes):
"""Normalize the genotypes.
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genotypes (Genotypes): The genotypes to normalize.
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numpy.array: The normalized genotypes.
"""
genotypes = genotypes.genotypes
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geophysics-ubonn/crtomo_tools | lib/crtomo/interface.py | crmod_interface._get_tdm | def _get_tdm(self, m):
"""For a given model, return a tdMan instance
Parameters
----------
m : ndarray
Model parameters (linear, ohm m)
"""
m = np.atleast_2d(m)
assert len(m.shape) == 2
tdm = crtomo.tdMan(grid=self.grid, tempdir=self.tempdir)
... | python | def _get_tdm(self, m):
"""For a given model, return a tdMan instance
Parameters
----------
m : ndarray
Model parameters (linear, ohm m)
"""
m = np.atleast_2d(m)
assert len(m.shape) == 2
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geophysics-ubonn/crtomo_tools | lib/crtomo/interface.py | crmod_interface.J | def J(self, log_sigma):
"""Return the sensitivity matrix
Parameters
----------
log_sigma : numpy.ndarray
log_e conductivities
"""
m = 1.0 / np.exp(log_sigma)
tdm = self._get_tdm(m)
tdm.model(
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# out... | python | def J(self, log_sigma):
"""Return the sensitivity matrix
Parameters
----------
log_sigma : numpy.ndarray
log_e conductivities
"""
m = 1.0 / np.exp(log_sigma)
tdm = self._get_tdm(m)
tdm.model(
sensitivities=True,
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"""
# TODO(Gonéri): ensure we adjust the correct node
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althonos/moclo | moclo/moclo/registry/_utils.py | find_resistance | def find_resistance(record):
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Arguments:
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Raises:
RuntimeError: when there's not exactly one resistance cassette.
"""
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labels =... | python | def find_resistance(record):
"""Infer the antibiotics resistance of the given record.
Arguments:
record (`~Bio.SeqRecord.SeqRecord`): an annotated sequence.
Raises:
RuntimeError: when there's not exactly one resistance cassette.
"""
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althonos/moclo | moclo/moclo/record.py | CircularRecord.reverse_complement | def reverse_complement(
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description=False,
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annotations=False,
letter_annotations=True,
dbxrefs=False,
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"""
return ... | python | def reverse_complement(
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description=False,
features=True,
annotations=False,
letter_annotations=True,
dbxrefs=False,
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redhat-openstack/python-tripleo-helper | tripleohelper/ssh.py | SshClient.load_private_key | def load_private_key(self, priv_key):
"""Register the SSH private key."""
with open(priv_key) as fd:
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"""Register the SSH private key."""
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redhat-openstack/python-tripleo-helper | tripleohelper/ssh.py | SshClient.start | def start(self):
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"""
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"""
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redhat-openstack/python-tripleo-helper | tripleohelper/ssh.py | SshClient._get_channel | def _get_channel(self):
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channel.get_pty()
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channel.get_pty()
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NJDFan/ctypes-bitfield | bitfield/__init__.py | print_fields | def print_fields(bf, *args, **kwargs):
"""
Print all the fields of a Bitfield object to stdout. This is
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"""
vals = {k: hex(v) for k, v in bf.items()}
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"""
Print all the fields of a Bitfield object to stdout. This is
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"""
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gebn/wood | wood/comparison.py | Comparison.new | def new(self, base: pathlib.PurePath = pathlib.PurePath(),
include_intermediates: bool = True) -> Iterator[str]:
"""
Find the list of new paths in this comparison.
:param base: The base directory to prepend to the right entity's name.
:param include_intermediates: Whether to... | python | def new(self, base: pathlib.PurePath = pathlib.PurePath(),
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gebn/wood | wood/comparison.py | Comparison.modified | def modified(self, base: pathlib.PurePath = pathlib.PurePath()) \
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gebn/wood | wood/comparison.py | Comparison.deleted | def deleted(self, base: pathlib.PurePath = pathlib.PurePath(),
include_children: bool = True,
include_directories: bool = True) -> Iterator[str]:
"""
Find the paths of entities deleted between the left and right entities
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gebn/wood | wood/comparison.py | Comparison.compare | def compare(left: Optional[L], right: Optional[R]) -> 'Comparison[L, R]':
"""
Calculate the comparison of two entities.
| left | right | Return Type |
|===========|===========|=========================|
| file | file | FileComparison |
... | python | def compare(left: Optional[L], right: Optional[R]) -> 'Comparison[L, R]':
"""
Calculate the comparison of two entities.
| left | right | Return Type |
|===========|===========|=========================|
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gebn/wood | wood/comparison.py | Comparison.print_hierarchy | def print_hierarchy(self, level: int = 0, file: IO[str] = sys.stdout) \
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gebn/wood | wood/comparison.py | FileComparison.is_modified | def is_modified(self) -> bool:
"""
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pgxcentre/geneparse | geneparse/index/impute2.py | generate_index | def generate_index(fn, cols=None, names=None, sep=" "):
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pgxcentre/geneparse | geneparse/index/impute2.py | get_open_func | def get_open_func(fn, return_fmt=False):
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pgxcentre/geneparse | geneparse/index/impute2.py | get_index | def get_index(fn, cols, names, sep):
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cols (list): a list containing column to keep (as int).
names (list): the name corresponding to the column to keep (as str).
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pgxcentre/geneparse | geneparse/index/impute2.py | write_index | def write_index(fn, index):
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index (pandas.DataFrame): the index.
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with open(fn, "wb") as o_file:
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rhayes777/PyAutoFit | autofit/tools/pipeline.py | make_path | def make_path(phase) -> str:
"""
Create the path to the folder at which the metadata and optimizer pickle should be saved
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return "{}/{}{}{}".format(conf.instance.output_path, phase.phase_path, phase.phase_name, phase.phase_tag) | python | def make_path(phase) -> str:
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rhayes777/PyAutoFit | autofit/tools/pipeline.py | save_optimizer_for_phase | def save_optimizer_for_phase(phase):
"""
Save the optimizer associated with the phase as a pickle
"""
with open(make_optimizer_pickle_path(phase), "w+b") as f:
f.write(pickle.dumps(phase.optimizer)) | python | def save_optimizer_for_phase(phase):
"""
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rhayes777/PyAutoFit | autofit/tools/pipeline.py | ResultsCollection.add | def add(self, phase_name, result):
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The result of that phase
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Add the result of a phase.
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Riminder/python-riminder-api | riminder/bytesutils.py | strtobytes | def strtobytes(input, encoding):
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py_version = sys.version_info[0]
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pgxcentre/geneparse | geneparse/index/__main__.py | index_impute2 | def index_impute2(fn):
"""Indexes an IMPUTE2 file.
Args:
fn (str): The name of the IMPUTE2 file.
"""
logger.info("Indexing {} (IMPUTE2)".format(fn))
impute2_index(fn, cols=[0, 1, 2], names=["chrom", "name", "pos"], sep=" ")
logger.info("Index generated") | python | def index_impute2(fn):
"""Indexes an IMPUTE2 file.
Args:
fn (str): The name of the IMPUTE2 file.
"""
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pgxcentre/geneparse | geneparse/index/__main__.py | index_bgen | def index_bgen(fn, legacy=False):
"""Indexes a BGEN file.
Args:
fn (str): The name of the BGEN file.
"""
logger.info("Indexing {} (BGEN) using 'bgenix'{}".format(
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))
command = ["bgenix", "-g", fn, "-index"]
if legacy:
command.... | python | def index_bgen(fn, legacy=False):
"""Indexes a BGEN file.
Args:
fn (str): The name of the BGEN file.
"""
logger.info("Indexing {} (BGEN) using 'bgenix'{}".format(
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unt-libraries/pyuntl | pyuntl/untl_structure.py | create_untl_xml_subelement | def create_untl_xml_subelement(parent, element, prefix=''):
"""Create a UNTL XML subelement."""
subelement = SubElement(parent, prefix + element.tag)
if element.content is not None:
subelement.text = element.content
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subelement.attrib["qualifier"] = eleme... | python | def create_untl_xml_subelement(parent, element, prefix=''):
"""Create a UNTL XML subelement."""
subelement = SubElement(parent, prefix + element.tag)
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subelement.text = element.content
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unt-libraries/pyuntl | pyuntl/untl_structure.py | add_missing_children | def add_missing_children(required_children, element_children):
"""Determine if there are elements not in the children
that need to be included as blank elements in the form.
"""
element_tags = [element.tag for element in element_children]
# Loop through the elements that should be in the form.
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"""Determine if there are elements not in the children
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Verifies the element is allowed to have a qualifier, and
throws an exception if not.
"""
if self.allows_qualifier:
self.qualifier = value.strip()
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"""Set the qualifier for the element.
Verifies the element is allowed to have a qualifier, and
throws an exception if not.
"""
if self.allows_qualifier:
self.qualifier = value.strip()
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unt-libraries/pyuntl | pyuntl/untl_structure.py | UNTLElement.add_form | def add_form(self, **kwargs):
"""Add the form attribute to the UNTL Python object."""
vocabularies = kwargs.get('vocabularies', None)
qualifier = kwargs.get('qualifier', None)
content = kwargs.get('content', None)
parent_tag = kwargs.get('parent_tag', None)
superuser = kw... | python | def add_form(self, **kwargs):
"""Add the form attribute to the UNTL Python object."""
vocabularies = kwargs.get('vocabularies', None)
qualifier = kwargs.get('qualifier', None)
content = kwargs.get('content', None)
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unt-libraries/pyuntl | pyuntl/untl_structure.py | UNTLElement.record_content_length | def record_content_length(self):
"""Calculate length of record, excluding metadata."""
untldict = py2dict(self)
untldict.pop('meta', None)
return len(str(untldict)) | python | def record_content_length(self):
"""Calculate length of record, excluding metadata."""
untldict = py2dict(self)
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unt-libraries/pyuntl | pyuntl/untl_structure.py | FormGenerator.create_form_data | def create_form_data(self, **kwargs):
"""Create groupings of form elements."""
# Get the specified keyword arguments.
children = kwargs.get('children', [])
sort_order = kwargs.get('sort_order', None)
solr_response = kwargs.get('solr_response', None)
superuser = kwargs.get... | python | def create_form_data(self, **kwargs):
"""Create groupings of form elements."""
# Get the specified keyword arguments.
children = kwargs.get('children', [])
sort_order = kwargs.get('sort_order', None)
solr_response = kwargs.get('solr_response', None)
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unt-libraries/pyuntl | pyuntl/untl_structure.py | FormGenerator.create_form_groupings | def create_form_groupings(self,
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element_list = []
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unt-libraries/pyuntl | pyuntl/untl_structure.py | FormGenerator.get_vocabularies | def get_vocabularies(self):
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# Timeout in seconds.
timeout = 15
socket.setdefaulttimeout(timeout)
# Create the ordered vocabulary URL.
vocab_url = VOCABULARIES_URL.replace('all', 'all-verbose')
# Request the v... | python | def get_vocabularies(self):
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# Timeout in seconds.
timeout = 15
socket.setdefaulttimeout(timeout)
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.create_xml_string | def create_xml_string(self):
"""Create a UNTL document in a string from a UNTL metadata
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untl_xml_string = metadata_root_object.create_xml_string()
"""
root = self.create_xml()
xml = '<?xml version="1.0" encoding="UTF-8"?>\n' + tostring(
root, pr... | python | def create_xml_string(self):
"""Create a UNTL document in a string from a UNTL metadata
root object.
untl_xml_string = metadata_root_object.create_xml_string()
"""
root = self.create_xml()
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.create_xml | def create_xml(self, useNamespace=False):
"""Create an ElementTree representation of the object."""
UNTL_NAMESPACE = 'http://digital2.library.unt.edu/untl/'
UNTL = '{%s}' % UNTL_NAMESPACE
NSMAP = {'untl': UNTL_NAMESPACE}
if useNamespace:
root = Element(UNTL + self.t... | python | def create_xml(self, useNamespace=False):
"""Create an ElementTree representation of the object."""
UNTL_NAMESPACE = 'http://digital2.library.unt.edu/untl/'
UNTL = '{%s}' % UNTL_NAMESPACE
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.create_element_dict | def create_element_dict(self):
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untl_dict = {}
# Loop through all UNTL elements in the Python object.
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# If an entry for the element list hasn't been made in the
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"""Convert a UNTL Python object into a UNTL Python dictionary."""
untl_dict = {}
# Loop through all UNTL elements in the Python object.
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.create_xml_file | def create_xml_file(self, untl_filename):
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Writes file to supplied file path.
"""
try:
f = open(untl_filename, 'w')
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Writes file to supplied file path.
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.sort_untl | def sort_untl(self, sort_structure):
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"""
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unt-libraries/pyuntl | pyuntl/untl_structure.py | Metadata.generate_form_data | def generate_form_data(self, **kwargs):
"""Create a form dictionary with the key being the element name
and the value being a list of form element objects.
"""
# Add elements that are missing from the form.
self.children = add_missing_children(
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unt-libraries/pyuntl | pyuntl/etd_ms_structure.py | contributor_director | def contributor_director(**kwargs):
"""Define the expanded qualifier name."""
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unt-libraries/pyuntl | pyuntl/etd_ms_structure.py | date_director | def date_director(**kwargs):
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unt-libraries/pyuntl | pyuntl/etd_ms_structure.py | ETD_MSElement.get_child_content | def get_child_content(self, children, element_name):
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geophysics-ubonn/crtomo_tools | src/td_residuals.py | shiftedColorMap | def shiftedColorMap(cmap, start=0, midpoint=0.5, stop=1.0, name='shiftedcmap'):
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Function to offset the "center" of a colormap. Useful for
data with a negative min and positive max and you want the
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'''
Function to offset the "center" of a colormap. Useful for
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cmap:
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geophysics-ubonn/crtomo_tools | src/td_residuals.py | read_lastmodfile | def read_lastmodfile(directory):
"""
Return the number of the final inversion result.
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filename = '{0}/exe/inv.lastmod'.format(directory)
# filename HAS to exist. Otherwise the inversion was not finished
if(not os.path.isfile(filename)):
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"""
Return the number of the final inversion result.
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Riminder/python-riminder-api | riminder/webhook.py | Webhook.setHandler | def setHandler(self, event_name, callback):
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Riminder/python-riminder-api | riminder/webhook.py | Webhook._get_fct_number_of_arg | def _get_fct_number_of_arg(self, fct):
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eventifyio/eventify | eventify/service.py | event_tracker | def event_tracker(func):
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KnightConan/sspdatatables | src/sspdatatables/utils/decorator.py | ensure_ajax | def ensure_ajax(valid_request_methods, error_response_context=None):
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KnightConan/sspdatatables | src/sspdatatables/utils/decorator.py | generate_error_json_response | def generate_error_json_response(error_dict, error_response_context=None):
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gofed/gofedlib | gofedlib/go/symbolsextractor/extractor.py | GoSymbolsExtractor._mergeGoSymbols | def _mergeGoSymbols(self, jsons = []):
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Assuming all files in the given package has mutual exclusive symbols.
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NikolayDachev/jadm | lib/paramiko-1.14.1/paramiko/_winapi.py | MemoryMap.read | def read(self, n):
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thiagopbueno/tf-rddlsim | tfrddlsim/simulation/transition_simulator.py | ActionSimulationCell._output | def _output(cls, fluents: Sequence[FluentPair]) -> Sequence[tf.Tensor]:
'''Converts `fluents` to tensors with datatype tf.float32.'''
output = []
for _, fluent in fluents:
tensor = fluent.tensor
if tensor.dtype != tf.float32:
tensor = tf.cast(tensor, tf.fl... | python | def _output(cls, fluents: Sequence[FluentPair]) -> Sequence[tf.Tensor]:
'''Converts `fluents` to tensors with datatype tf.float32.'''
output = []
for _, fluent in fluents:
tensor = fluent.tensor
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255BITS/hyperchamber | hyperchamber/selector.py | Selector.set | def set(self, key, value):
"""Sets a hyperparameter. Can be used to set an array of hyperparameters."""
self.store[key]=value
return self.store | python | def set(self, key, value):
"""Sets a hyperparameter. Can be used to set an array of hyperparameters."""
self.store[key]=value
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255BITS/hyperchamber | hyperchamber/selector.py | Selector.config_at | def config_at(self, i):
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sele... | python | def config_at(self, i):
"""Gets the ith config"""
selections = {}
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255BITS/hyperchamber | hyperchamber/selector.py | Selector.top | def top(self, sort_by):
"""Get the best results according to your custom sort method."""
sort = sorted(self.results, key=sort_by)
return sort | python | def top(self, sort_by):
"""Get the best results according to your custom sort method."""
sort = sorted(self.results, key=sort_by)
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255BITS/hyperchamber | hyperchamber/selector.py | Selector.load_or_create_config | def load_or_create_config(self, filename, config=None):
"""Loads a config from disk. Defaults to a random config if none is specified"""
os.makedirs(os.path.dirname(os.path.expanduser(filename)), exist_ok=True)
if os.path.exists(filename):
return self.load(filename)
if(conf... | python | def load_or_create_config(self, filename, config=None):
"""Loads a config from disk. Defaults to a random config if none is specified"""
os.makedirs(os.path.dirname(os.path.expanduser(filename)), exist_ok=True)
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redhat-openstack/python-tripleo-helper | tripleohelper/undercloud.py | Undercloud.configure | def configure(self, repositories):
"""Prepare the system to be ready for an undercloud installation.
"""
self.enable_repositories(repositories)
self.create_stack_user()
self.install_base_packages()
self.clean_system()
self.yum_update(allow_reboot=True)
sel... | python | def configure(self, repositories):
"""Prepare the system to be ready for an undercloud installation.
"""
self.enable_repositories(repositories)
self.create_stack_user()
self.install_base_packages()
self.clean_system()
self.yum_update(allow_reboot=True)
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redhat-openstack/python-tripleo-helper | tripleohelper/undercloud.py | Undercloud.openstack_undercloud_install | def openstack_undercloud_install(self):
"""Deploy an undercloud on the host.
"""
instack_undercloud_ver, _ = self.run('repoquery --whatprovides /usr/share/instack-undercloud/puppet-stack-config/puppet-stack-config.pp')
if instack_undercloud_ver.rstrip('\n') == 'instack-undercloud-0:2.2.0... | python | def openstack_undercloud_install(self):
"""Deploy an undercloud on the host.
"""
instack_undercloud_ver, _ = self.run('repoquery --whatprovides /usr/share/instack-undercloud/puppet-stack-config/puppet-stack-config.pp')
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redhat-openstack/python-tripleo-helper | tripleohelper/undercloud.py | Undercloud.create_flavor | def create_flavor(self, name):
"""Create a new baremetal flavor.
:param name: the name of the flavor
"""
self.add_environment_file(user='stack', filename='stackrc')
self.run('openstack flavor create --id auto --ram 4096 --disk 40 --vcpus 1 baremetal', user='stack', success_statu... | python | def create_flavor(self, name):
"""Create a new baremetal flavor.
:param name: the name of the flavor
"""
self.add_environment_file(user='stack', filename='stackrc')
self.run('openstack flavor create --id auto --ram 4096 --disk 40 --vcpus 1 baremetal', user='stack', success_statu... | [
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redhat-openstack/python-tripleo-helper | tripleohelper/undercloud.py | Undercloud.list_nodes | def list_nodes(self):
"""List the Ironic nodes UUID."""
self.add_environment_file(user='stack', filename='stackrc')
ret, _ = self.run("ironic node-list --fields uuid|awk '/-.*-/ {print $2}'", user='stack')
# NOTE(Gonéri): the good new is, the order of the nodes is preserved and follow th... | python | def list_nodes(self):
"""List the Ironic nodes UUID."""
self.add_environment_file(user='stack', filename='stackrc')
ret, _ = self.run("ironic node-list --fields uuid|awk '/-.*-/ {print $2}'", user='stack')
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redhat-openstack/python-tripleo-helper | tripleohelper/undercloud.py | Undercloud.set_flavor | def set_flavor(self, node, flavor):
"""Set a flavor to a given ironic node.
:param uuid: the ironic node UUID
:param flavor: the flavor name
"""
command = (
'ironic node-update {uuid} add '
'properties/capabilities=profile:{flavor},boot_option:local').for... | python | def set_flavor(self, node, flavor):
"""Set a flavor to a given ironic node.
:param uuid: the ironic node UUID
:param flavor: the flavor name
"""
command = (
'ironic node-update {uuid} add '
'properties/capabilities=profile:{flavor},boot_option:local').for... | [
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