code stringlengths 114 1.05M | path stringlengths 3 312 | quality_prob float64 0.5 0.99 | learning_prob float64 0.2 1 | filename stringlengths 3 168 | kind stringclasses 1
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**Important project update (April 2022):** scikit-bio is currently in maintenance mode. Due to limited developer bandwidth, we are focusing on keeping scikit-bio up-to-date with Python and Python scientific computing libraries. We plan to do this through two annual releases of scikit-bio. At this time, we have less ava... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/README.rst | 0.762778 | 0.654177 | README.rst | pypi |
# scikit-bio changelog
## Version 0.5.9
### Features
* Adding Variance log ratio estimators in `skbio.stats.composition.vlr` and `skbio.stats.composition.pairwise_vlr` ([#1803](https://github.com/biocore/scikit-bio/pull/1803))
* Added `skbio.stats.composition.tree_basis` to construct ILR bases from `TreeNode` object... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/CHANGELOG.md | 0.897793 | 0.961929 | CHANGELOG.md | pypi |
import collections.abc
import numpy as np
import pandas as pd
from skbio.tree import DuplicateNodeError, MissingNodeError
from skbio.diversity._phylogenetic import _nodes_by_counts
def _validate_counts_vector(counts, suppress_cast=False):
"""Validate and convert input to an acceptable counts vector type.
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/diversity/_util.py | 0.734976 | 0.509093 | _util.py | pypi |
from skbio.util._decorator import experimental
from skbio.diversity._util import (_validate_counts_vector,
_validate_otu_ids_and_tree,
_vectorize_counts_and_tree)
def _faith_pd(counts_by_node, branch_lengths):
return (branch_lengths * (counts_... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/diversity/alpha/_faith_pd.py | 0.965438 | 0.729857 | _faith_pd.py | pypi |
import numpy as np
from scipy.special import gammaln
from scipy.optimize import fmin_powell, minimize_scalar
from skbio.stats import subsample_counts
from skbio.util._decorator import experimental
from skbio.diversity._util import _validate_counts_vector
@experimental(as_of="0.4.0")
def berger_parker_d(counts):
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/diversity/alpha/_base.py | 0.952783 | 0.642601 | _base.py | pypi |
import numpy as np
from skbio.diversity._util import _validate_counts_vector
from skbio.util._decorator import experimental
@experimental(as_of="0.4.0")
def gini_index(data, method='rectangles'):
r"""Calculate the Gini index.
The Gini index is defined as
.. math::
G=\frac{A}{A+B}
where :m... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/diversity/alpha/_gini.py | 0.949983 | 0.766053 | _gini.py | pypi |
import numpy as np
from skbio.diversity._util import _validate_counts_vector
from skbio.util._decorator import experimental
@experimental(as_of="0.4.0")
def ace(counts, rare_threshold=10):
r"""Calculate the ACE metric (Abundance-based Coverage Estimator).
The ACE metric is defined as:
.. math::
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/diversity/alpha/_ace.py | 0.940946 | 0.825273 | _ace.py | pypi |
from warnings import warn
from itertools import product
import numpy as np
from skbio.alignment import TabularMSA
from skbio.alignment._ssw_wrapper import StripedSmithWaterman
from skbio.sequence import DNA, RNA, Protein
from skbio.sequence import GrammaredSequence
from skbio.util import EfficiencyWarning
from skbio... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/alignment/_pairwise.py | 0.466846 | 0.369002 | _pairwise.py | pypi |
import math
from skbio.util._misc import chunk_str
from skbio.metadata._repr import _MetadataReprBuilder
class _SequenceReprBuilder(_MetadataReprBuilder):
"""Build a ``Sequence`` repr.
Parameters
----------
seq : Sequence
Sequence to repr.
width : int
Maximum width of the repr.
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_repr.py | 0.908344 | 0.411998 | _repr.py | pypi |
from abc import ABCMeta, abstractproperty
from itertools import product
import re
import numpy as np
from skbio.util._decorator import (classproperty, overrides, stable,
deprecated, experimental)
from skbio.util._misc import MiniRegistry
from ._sequence import Sequence
class Gram... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_grammared_sequence.py | 0.594198 | 0.320688 | _grammared_sequence.py | pypi |
import skbio
from skbio.util._decorator import classproperty, overrides
from skbio.util._decorator import stable
from ._nucleotide_mixin import NucleotideMixin, _motifs as _parent_motifs
from ._grammared_sequence import GrammaredSequence, DisableSubclassingMeta
class DNA(GrammaredSequence, NucleotideMixin,
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_dna.py | 0.914946 | 0.568685 | _dna.py | pypi |
import skbio
from skbio.util._decorator import classproperty, overrides
from skbio.util._decorator import stable
from ._nucleotide_mixin import NucleotideMixin, _motifs as _parent_motifs
from ._grammared_sequence import GrammaredSequence, DisableSubclassingMeta
class RNA(GrammaredSequence, NucleotideMixin,
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_rna.py | 0.916615 | 0.579728 | _rna.py | pypi |
import numpy as np
import scipy.spatial.distance
import skbio
from skbio.util._decorator import experimental
@experimental(as_of='0.4.2')
def hamming(seq1, seq2):
"""Compute Hamming distance between two sequences.
The Hamming distance between two equal-length sequences is the proportion
of differing ch... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/distance.py | 0.936807 | 0.747201 | distance.py | pypi |
from abc import ABCMeta, abstractproperty
import numpy as np
from skbio.util._decorator import classproperty, stable
from ._grammared_sequence import _motifs as parent_motifs
class NucleotideMixin(metaclass=ABCMeta):
"""Mixin for adding funtionality for working with sequences of nucleotides.
This is an ab... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_nucleotide_mixin.py | 0.851845 | 0.379091 | _nucleotide_mixin.py | pypi |
import numpy as np
from skbio.util._decorator import classproperty, overrides
from skbio.util._decorator import stable
from ._grammared_sequence import (GrammaredSequence, DisableSubclassingMeta,
_motifs as parent_motifs)
class Protein(GrammaredSequence, metaclass=DisableSubclassin... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/sequence/_protein.py | 0.924649 | 0.737796 | _protein.py | pypi |
import io
def is_binary_file(file):
return isinstance(file, (io.BufferedReader, io.BufferedWriter,
io.BufferedRandom))
# Everything beyond this point will be some kind of hack needed to make
# everything work. It's not pretty and it doesn't make great sense much
# of the time. I am ... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/_fileobject.py | 0.515376 | 0.182007 | _fileobject.py | pypi |
class IOSourceError(Exception):
"""Raised when a file source cannot be resolved."""
pass
class FileFormatError(Exception):
"""Raised when a file cannot be parsed."""
pass
class UnrecognizedFormatError(FileFormatError):
"""Raised when a file's format is unknown, ambiguous, or unidentifiable."""... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/_exception.py | 0.850903 | 0.321407 | _exception.py | pypi |
import re
import warnings
import numpy as np
from skbio.util import cardinal_to_ordinal
_whitespace_regex = re.compile(r'\s')
_newline_regex = re.compile(r'\n')
def _decode_qual_to_phred(qual_str, variant=None, phred_offset=None):
phred_offset, phred_range = _get_phred_offset_and_range(
variant, phred... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/_base.py | 0.601828 | 0.3068 | _base.py | pypi |
import functools
import contextlib
import pandas as pd
_possible_columns = {'qseqid': str, 'qgi': float, 'qacc': str, 'qaccver': str,
'qlen': float, 'sseqid': str, 'sallseqid': str,
'sgi': float, 'sallgi': float, 'sacc': str,
'saccver': str, 'sallacc': s... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/_blast.py | 0.616936 | 0.250411 | _blast.py | pypi |
import csv
import numpy as np
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
from skbio.io import create_format, LSMatFormatError
lsmat = create_format('lsmat')
@lsmat.sniffer()
def _lsmat_sniffer(fh):
header = _find_header(fh)
if header is not None:
try:
dialec... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/lsmat.py | 0.541409 | 0.54825 | lsmat.py | pypi |
from skbio.alignment import TabularMSA
from skbio.io import create_format, PhylipFormatError
from skbio.util._misc import chunk_str
phylip = create_format('phylip')
@phylip.sniffer()
def _phylip_sniffer(fh):
# Strategy:
# Read the header and a single sequence; verify that the sequence length
# matc... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/phylip.py | 0.711331 | 0.440229 | phylip.py | pypi |
import pandas as pd
from skbio.io import create_format, BLAST7FormatError
from skbio.io.format._blast import _parse_blast_data
blast7 = create_format('blast+7')
column_converter = {'query id': 'qseqid', 'query gi': 'qgi',
'query acc.': 'qacc', 'query acc.ver': 'qaccver',
'que... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/blast7.py | 0.584983 | 0.191517 | blast7.py | pypi |
import h5py
from skbio.io import create_format
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
binary_dm = create_format('binary_dm', encoding='binary')
_vlen_dtype = h5py.special_dtype(vlen=str)
@binary_dm.sniffer()
def _binary_dm_sniffer(fh):
try:
f = h5py.File(fh, 'r')
exce... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/binary_dm.py | 0.470737 | 0.310041 | binary_dm.py | pypi |
from collections import OrderedDict
from skbio.alignment import TabularMSA
from skbio.sequence._grammared_sequence import GrammaredSequence
from skbio.io import create_format, StockholmFormatError
stockholm = create_format('stockholm')
_REFERENCE_TAGS = frozenset({'RM', 'RT', 'RA', 'RL', 'RC'})
@stockholm.sniffer(... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/io/format/stockholm.py | 0.817756 | 0.299995 | stockholm.py | pypi |
import hashlib
import inspect
from types import FunctionType
from ._decorator import experimental
def resolve_key(obj, key):
"""Resolve key given an object and key."""
if callable(key):
return key(obj)
elif hasattr(obj, 'metadata'):
return obj.metadata[key]
raise TypeError("Could not... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/util/_misc.py | 0.881373 | 0.23709 | _misc.py | pypi |
import numpy as np
import pandas as pd
from scipy.linalg import svd, lstsq
from ._ordination_results import OrdinationResults
from ._utils import corr, svd_rank, scale
from skbio.util._decorator import experimental
@experimental(as_of="0.4.0")
def cca(y, x, scaling=1):
r"""Compute canonical (also known as const... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/ordination/_canonical_correspondence_analysis.py | 0.917799 | 0.715772 | _canonical_correspondence_analysis.py | pypi |
import functools
import numpy as np
from IPython.core.pylabtools import print_figure
from IPython.core.display import Image, SVG
from skbio._base import SkbioObject
from skbio.stats._misc import _pprint_strs
from skbio.util._decorator import experimental
class OrdinationResults(SkbioObject):
"""Store ordinatio... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/ordination/_ordination_results.py | 0.860867 | 0.558688 | _ordination_results.py | pypi |
import numpy as np
from skbio.util._decorator import experimental
from ._cutils import center_distance_matrix_cy
@experimental(as_of="0.4.0")
def mean_and_std(a, axis=None, weights=None, with_mean=True, with_std=True,
ddof=0):
"""Compute the weighted average and standard deviation along the
... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/ordination/_utils.py | 0.955496 | 0.736329 | _utils.py | pypi |
import numpy as np
from scipy.stats import pearsonr
from skbio import DistanceMatrix
from skbio.util._decorator import experimental
@experimental(as_of="0.4.0")
def hommola_cospeciation(host_dist, par_dist, interaction, permutations=999):
"""Perform Hommola et al (2009) host/parasite cospeciation test.
Thi... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/evolve/_hommola.py | 0.942195 | 0.778733 | _hommola.py | pypi |
from itertools import combinations
import numpy as np
import pandas as pd
from scipy.spatial.distance import pdist
from scipy.stats import spearmanr
from skbio.stats.distance import DistanceMatrix
from skbio.util._decorator import experimental
@experimental(as_of="0.4.0")
def bioenv(distance_matrix, data_frame, co... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/distance/_bioenv.py | 0.935043 | 0.776242 | _bioenv.py | pypi |
from functools import partial
import numpy as np
from ._base import (_preprocess_input_sng, _run_monte_carlo_stats,
_build_results, DistanceMatrix)
from skbio.util._decorator import experimental
from ._cutils import permanova_f_stat_sW_cy
@experimental(as_of="0.4.0")
def permanova(distance_matr... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/stats/distance/_permanova.py | 0.922813 | 0.749408 | _permanova.py | pypi |
import abc
import copy
import pandas as pd
from skbio.util._decorator import stable, experimental
from skbio.metadata import IntervalMetadata
class MetadataMixin(metaclass=abc.ABCMeta):
@property
@stable(as_of="0.4.0")
def metadata(self):
"""``dict`` containing metadata which applies to the ent... | /scikit-bio-0.5.9.tar.gz/scikit-bio-0.5.9/skbio/metadata/_mixin.py | 0.883488 | 0.296957 | _mixin.py | pypi |
from __future__ import annotations
from abc import ABC, abstractmethod
from typing import Callable, Optional, Tuple
import numpy as np
from scipy.optimize import minimize
from sklearn.base import BaseEstimator, RegressorMixin
from sklearn.utils.validation import (
_check_sample_weight,
check_array,
check_... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/linear_model/_scipy_regressors.py | 0.976858 | 0.681329 | _scipy_regressors.py | pypi |
from __future__ import annotations
from typing import Any
import numpy as np
from sklearn.base import BaseEstimator, RegressorMixin, clone
from sklearn.tree import DecisionTreeRegressor
from sklearn.utils.validation import (
check_X_y,
check_is_fitted,
check_array,
_check_sample_weight,
)
class Expl... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/meta/_explainable_regressor.py | 0.936814 | 0.573977 | _explainable_regressor.py | pypi |
from __future__ import annotations
from typing import Any
import numpy as np
from sklearn.base import (
BaseEstimator,
RegressorMixin,
clone,
is_regressor,
is_classifier,
)
from sklearn.exceptions import NotFittedError
from sklearn.utils.validation import check_is_fitted, check_X_y, check_array
... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/meta/_zero_inflated_regressor.py | 0.963959 | 0.795618 | _zero_inflated_regressor.py | pypi |
from __future__ import annotations
from abc import ABC, abstractmethod
import numpy as np
from scipy.signal import convolve2d
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils import check_array
from sklearn.utils.validation import check_is_fitted
class Smoother(BaseEstimator, Transformer... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/timeseries/smoothing.py | 0.977586 | 0.643735 | smoothing.py | pypi |
from __future__ import annotations
from typing import Optional, Union
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.covariance import EllipticEnvelope
from sklearn.utils.validation import check_is_fitted
class SpikeRemover(BaseEstimator, TransformerMixin):
"""
Thi... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/timeseries/outliers.py | 0.969771 | 0.689623 | outliers.py | pypi |
from __future__ import annotations
from abc import ABC, abstractmethod
import numpy as np
from sklearn.base import BaseEstimator, OutlierMixin
from sklearn.utils.validation import check_array, check_is_fitted
class BoxEnvelope(BaseEstimator, OutlierMixin, ABC):
"""
Detect if a data point is an outlier via ... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/outlier/naive.py | 0.974374 | 0.73659 | naive.py | pypi |
from __future__ import annotations
from typing import List, Tuple, Optional
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.validation import check_array, check_is_fitted
class CyclicalEncoder(BaseEstimator, TransformerMixin):
"""
Break each cyclic feature int... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/preprocessing/time.py | 0.958333 | 0.759091 | time.py | pypi |
from __future__ import annotations
from abc import ABC, abstractmethod
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.validation import check_is_fitted, check_array
class Saturation(BaseEstimator, TransformerMixin, ABC):
"""Base class for all saturations, such as... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/preprocessing/saturation.py | 0.975202 | 0.588446 | saturation.py | pypi |
from __future__ import annotations
import pandas as pd
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.preprocessing import OneHotEncoder as ScikitLearnOneHotEncoder
from sklearn.utils.validation import check_is_fitted, check_array
class OneHotEncoderWithNames(ScikitLearnOneHotEncoder):
""... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/pandas/preprocessing.py | 0.969914 | 0.816589 | preprocessing.py | pypi |
import numpy as np
import pandas as pd
def explode_date(
df: pd.DataFrame,
start_column: str,
end_column: str,
result_column: str = "Date",
frequency: str = "d",
drop: bool = True,
) -> pd.DataFrame:
"""
Transform a pandas dataframe with columns (*, start_date, end_date) into a longer... | /scikit_bonus-0.1.12-py3-none-any.whl/skbonus/pandas/time_utils.py | 0.916536 | 0.588002 | time_utils.py | pypi |
import numpy as np
from numba.extending import overload, register_jitable
from numba.np.unsafe.ndarray import to_fixed_tuple
from numba import types
from numpy.typing import ArrayLike
@overload(np.moveaxis)
def moveaxis(a: np.ndarray, source, destination) -> np.ndarray:
"""Move axes of an array to new positions.
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/_numba_overloads.py | 0.857097 | 0.762468 | _numba_overloads.py | pypi |
from abc import ABC, abstractmethod
import numpy as np
from numpy.typing import ArrayLike
from .affine import Rotation, Translation
from .utils3d import RotvecRotation
class Joint(ABC):
"""Abstract Joint.
This class is used to define the joint interface and to create a common base
class that joints can... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/joints.py | 0.970785 | 0.614307 | joints.py | pypi |
from numpy.typing import ArrayLike
from typing import List, Tuple, Union, Callable
import numpy as np
from dataclasses import dataclass, field
from queue import PriorityQueue
import warnings
def DepthFirst(frames: Tuple["Frame"], links: Tuple["Link"]) -> float:
"""Depth-first search metric for Frame.chain_between... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/base.py | 0.975589 | 0.610773 | base.py | pypi |
from math import sqrt
from .base import Link
from .affine import Rotation
from numpy.typing import ArrayLike
import numpy as np
class Rotation2D(Rotation):
"""Rotation in 2D.
A convenient way of initializing a rotation in 2D.
Parameters
----------
angle : ArrayLike
The magnitude of the r... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/utils2d.py | 0.941385 | 0.820433 | utils2d.py | pypi |
from numpy.typing import ArrayLike
from typing import List
import numpy as np
from .base import Frame, Link, InvertLink
from ._utils import vector_project, angle_between
from .functions import translate, rotate, as_affine_matrix
class AffineLink(Link):
"""A link representing a affine transformation.
This is... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/affine.py | 0.966976 | 0.682031 | affine.py | pypi |
from typing import List
from .base import CompundLink, Link, InvertLink
from .affine import AffineCompound, Translation, Rotation
from .joints import Joint
import numpy as np
def simplify_links(
links: List[Link],
*,
keep_links: List[Link] = None,
keep_joints: bool = False,
eps: float = 1e-16
) ->... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/simplfy.py | 0.884489 | 0.426083 | simplfy.py | pypi |
import numpy as np
from numpy.typing import ArrayLike
from .base import Frame
from ._utils import vector_project
def scale(vector: ArrayLike, scalar: ArrayLike) -> np.ndarray:
"""Scale each dimension of a vector.
Multiplies each dimension of ``vector`` with the matching dimension of
``scalar``. If neces... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/functions.py | 0.957288 | 0.925027 | functions.py | pypi |
from math import tan
import numpy as np
from numpy.typing import ArrayLike
from scipy.spatial.transform import Rotation as scipy_rotation
from .base import Link
from .projections import PerspectiveProjection
from .affine import AffineCompound, Translation, Rotation
from ._utils import angle_between, vector_project
c... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/utils3d.py | 0.950583 | 0.617282 | utils3d.py | pypi |
from math import tan
from typing import Tuple
import numpy as np
from numpy.typing import ArrayLike
from .affine import AffineLink
from ._utils import scalar_project
class PerspectiveProjection(AffineLink):
"""Perspective projection in N-D.
This link projects a N dimensional frame onto an M dimensional fra... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/transform/projections.py | 0.960869 | 0.899608 | projections.py | pypi |
from .. import transform as tf
from ..transform._utils import scalar_project, angle_between
from numpy.typing import ArrayLike
from typing import List, Callable
import numpy as np
from scipy.optimize import minimize_scalar
from scipy.optimize import OptimizeResult
from .targets import Target, PositionTarget, RotationTa... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/inverse_kinematics/cyclic_coordinate_descent.py | 0.953891 | 0.581184 | cyclic_coordinate_descent.py | pypi |
from numpy.typing import ArrayLike
from typing import Callable, List, Union
import numpy as np
from .. import transform as tf
class Target:
"""Abstract IK target.
.. versionadded:: 0.10.0
Parameters
----------
static_frame : tf.Frame
The frame in which the objective is constant.
dyna... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/inverse_kinematics/targets.py | 0.96893 | 0.65846 | targets.py | pypi |
import numpy as np
from scipy.interpolate import splprep, splev
from numpy.typing import ArrayLike
from typing import Optional
def spline_trajectory(
t: ArrayLike,
control_points: ArrayLike,
*,
t_control: Optional[ArrayLike] = None,
degree: int = 3,
t_min: float = 0,
t_max: float = 1,
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/trajectory/spline.py | 0.944408 | 0.757817 | spline.py | pypi |
import numpy as np
from numpy.typing import ArrayLike
def integral(control_points: ArrayLike, t: ArrayLike, *, axis: int = 0) -> float:
"""Estimate the integral along a curve.
Estimates the integral of a time-parameterized curve along the chosen axis.
The curve is given by a sequence of control points an... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/trajectory/utils.py | 0.94049 | 0.888081 | utils.py | pypi |
import numpy as np
from scipy.interpolate import interp1d
from numpy.typing import ArrayLike
from typing import Optional
def linear_trajectory(
t: ArrayLike,
control_points: ArrayLike,
*,
t_control: Optional[ArrayLike] = None,
t_min: float = 0,
t_max: float = 1
) -> np.ndarray:
"""Evaluate... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/trajectory/linear.py | 0.952695 | 0.76921 | linear.py | pypi |
from xml.etree import ElementTree
from scipy.spatial.transform import Rotation
from typing import Dict, List, Tuple
import numpy as np
from ... import transform as rtf
def create_frame_graph(urdf: str) -> Tuple[Dict[str, rtf.Frame], Dict[str, rtf.Link]]:
"""Create a frame graph from a URDF string.
Parameter... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ros/generic/urdf.py | 0.90241 | 0.547162 | urdf.py | pypi |
import zmq
import subprocess
import socket
import os
import getpass
from . import messages
class Subscriber:
"""Subscribe and listen to Ignition messages.
Ignition uses ZMQ_ to pass around protocol buffers as means of
communication. This subscriber enabels python to receive copies of these
buffers. ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/subscriber.py | 0.695545 | 0.321487 | subscriber.py | pypi |
from urllib.parse import quote
import cachetools
import requests
from cachetools import TTLCache
from zipfile import ZipFile
from io import BytesIO
from pathlib import Path
from dataclasses import dataclass, field
from typing import List, Optional, Callable, Union
class InternalCache:
"""Simple Caching structure... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/fuel.py | 0.883494 | 0.227126 | fuel.py | pypi |
from xml.etree import ElementTree
from xsdata.formats.dataclass import parsers
from xsdata.formats.dataclass.context import XmlContext
from xsdata.formats.dataclass.parsers import XmlParser
from xsdata.formats.dataclass.parsers.config import ParserConfig
from xsdata.formats.dataclass.serializers import XmlSerializer
fr... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/sdformat.py | 0.897246 | 0.240462 | sdformat.py | pypi |
from typing import Union, List, Tuple, Dict
from itertools import chain
from ... import transform as tf
from .load_as_generic import loads_generic
from .generic_sdf.world import World
def to_frame_graph(
sdf: str,
*,
unwrap: bool = True,
insert_world_frame: bool = True,
shape: Tuple[int] = (3,),
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/transform_factory.py | 0.95996 | 0.703569 | transform_factory.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
from .geometry import Geometry
__NAMESPACE__ = "sdformat/v1.2/collision.xsd"
@dataclass
class Collision:
"""The collision properties of a link.
Note that this can be different from the visual properties of a
link, for example, simpler ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/collision.py | 0.945901 | 0.466116 | collision.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.2/light.xsd"
@dataclass
class Light:
"""
The light element describes a light source.
Parameters
----------
cast_shadows: When true, the light will cast shadows.
pose: A position and orientation ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/light.py | 0.947137 | 0.471649 | light.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.2/scene.xsd"
@dataclass
class Scene:
"""
Specifies the look of the environment.
Parameters
----------
ambient: Color of the ambient light.
background: Color of the background.
sky: Propertie... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/scene.py | 0.9342 | 0.460228 | scene.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
from .geometry import Geometry
__NAMESPACE__ = "sdformat/v1.2/visual.xsd"
@dataclass
class Visual:
"""The visual properties of the link.
This element specifies the shape of the object (box, cylinder, etc.)
for visualization purposes.
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/visual.py | 0.922469 | 0.507507 | visual.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .collision import Collision
from .sensor import Sensor
from .visual import Visual
__NAMESPACE__ = "sdformat/v1.2/link.xsd"
@dataclass
class Link:
"""A physical link with inertia, collision, and visual properties.
A link must be ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/link.py | 0.945876 | 0.603815 | link.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.2/joint.xsd"
@dataclass
class Joint:
"""
A joint connections two links with kinematic and dynamic properties.
Parameters
----------
parent: Name of the parent link
child: Name of the child link
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/joint.py | 0.968194 | 0.629789 | joint.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .actor import Actor
from .joint import Joint
from .light import Light
from .model import Model
from .physics import Physics
from .scene import Scene
from .state import State
__NAMESPACE__ = "sdformat/v1.2/world.xsd"
@dataclass
class Worl... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/world.py | 0.930797 | 0.41947 | world.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.2/state.xsd"
@dataclass
class State:
"""
Parameters
----------
time: Time stamp of the state [seconds nanoseconds]
model: Model state
world_name: Name of the world this state applies to
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/state.py | 0.892438 | 0.475788 | state.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.2/physics.xsd"
@dataclass
class Physics:
"""
The physics tag specifies the type and properties of the dynamics engine.
Parameters
----------
update_rate: Rate at which to update the physics engine
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/physics.py | 0.943996 | 0.475849 | physics.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.2/model.xsd"
@dataclass
class Model:
"""
The model element defines a complete robot or any other physical object.
Parameters
----------
static: ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/model.py | 0.945045 | 0.54698 | model.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.2/actor.xsd"
@dataclass
class Actor:
"""
Parameters
----------
pose: Origin of the actor
skin:
animation:
script:
link: A physical li... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/actor.py | 0.908582 | 0.416381 | actor.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.2/geometry.xsd"
@dataclass
class Geometry:
"""
The shape of the visual or collision object.
Parameters
----------
box: Box shape
sphere: Sphere shape
cylinder: Cylinder shape
mesh:... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v12/geometry.py | 0.951301 | 0.592637 | geometry.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.6/material.xsd"
@dataclass
class Material:
"""
The material of the visual element.
Parameters
----------
script: Name of material from an installed script file. This will
override the ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/material.py | 0.944472 | 0.46952 | material.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .geometry import Geometry
__NAMESPACE__ = "sdformat/v1.6/collision.xsd"
@dataclass
class Collision:
"""The collision properties of a link.
Note that this can be different from the visual properties of a
link, for example, si... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/collision.py | 0.953902 | 0.532668 | collision.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.6/light.xsd"
@dataclass
class Light:
"""
The light element describes a light source.
Parameters
----------
cast_shadows: When true, the light will cast shadows.
diffuse: Diffuse light colo... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/light.py | 0.935854 | 0.48182 | light.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.6/scene.xsd"
@dataclass
class Scene:
"""
Specifies the look of the environment.
Parameters
----------
ambient: Color of the ambient light.
background: Color of the background.
sky: Propertie... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/scene.py | 0.921675 | 0.460774 | scene.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .geometry import Geometry
from .material import Material
__NAMESPACE__ = "sdformat/v1.6/visual.xsd"
@dataclass
class Visual:
"""The visual properties of the link.
This element specifies the shape of the object (box, cylinder, et... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/visual.py | 0.943543 | 0.524456 | visual.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .collision import Collision
from .light import Light
from .material import Material
from .sensor import Sensor
from .visual import Visual
__NAMESPACE__ = "sdformat/v1.6/link.xsd"
@dataclass
class Link:
"""A physical link with inertia... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/link.py | 0.955878 | 0.552057 | link.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .sensor import Sensor
__NAMESPACE__ = "sdformat/v1.6/joint.xsd"
@dataclass
class Joint:
"""A joint connects two links with kinematic and dynamic properties.
By default, the pose of a joint is expressed in the child link
fram... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/joint.py | 0.956665 | 0.653766 | joint.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .actor import Actor
from .joint import Joint
from .light import Light
from .material import Material
from .model import Model
from .physics import Physics
from .scene import Scene
from .state import State
__NAMESPACE__ = "sdformat/v1.6/wor... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/world.py | 0.938505 | 0.492859 | world.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .light import Light
from .model import Model as ModelModel
__NAMESPACE__ = "sdformat/v1.6/state.xsd"
@dataclass
class Model:
"""
Model state.
Parameters
----------
joint: Joint angle
model: A nested model state e... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/state.py | 0.948728 | 0.47993 | state.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.6/physics.xsd"
@dataclass
class Physics:
"""
The physics tag specifies the type and properties of the dynamics engine.
Parameters
----------
max_step_size: Maximum time step size at which every syst... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/physics.py | 0.955961 | 0.531209 | physics.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.6/model.xsd"
@dataclass
class Model:
"""
The model element defines a complete robot or any other physical object.
Parameters
----------
static: ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/model.py | 0.939755 | 0.519278 | model.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.6/actor.xsd"
@dataclass
class Actor:
"""A special kind of model which can have a scripted motion.
This includes both global waypoint type animations and ske... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/actor.py | 0.95511 | 0.419113 | actor.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.6/geometry.xsd"
@dataclass
class Geometry:
"""
The shape of the visual or collision object.
Parameters
----------
empty: You can use the empty tag to make empty geometries.
box: Box shape
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v16/geometry.py | 0.949983 | 0.563258 | geometry.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.5/material.xsd"
@dataclass
class Material:
"""
The material of the visual element.
Parameters
----------
script: Name of material from an installed script file. This will
override the ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/material.py | 0.9287 | 0.453141 | material.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .geometry import Geometry
__NAMESPACE__ = "sdformat/v1.5/collision.xsd"
@dataclass
class Collision:
"""The collision properties of a link.
Note that this can be different from the visual properties of a
link, for example, si... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/collision.py | 0.96086 | 0.585516 | collision.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.5/light.xsd"
@dataclass
class Light:
"""
The light element describes a light source.
Parameters
----------
cast_shadows: When true, the light will cast shadows.
diffuse: Diffuse light colo... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/light.py | 0.941654 | 0.472014 | light.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.5/scene.xsd"
@dataclass
class Scene:
"""
Specifies the look of the environment.
Parameters
----------
ambient: Color of the ambient light.
background: Color of the background.
sky: Propertie... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/scene.py | 0.921891 | 0.461563 | scene.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .geometry import Geometry
from .material import Material
__NAMESPACE__ = "sdformat/v1.5/visual.xsd"
@dataclass
class Visual:
"""The visual properties of the link.
This element specifies the shape of the object (box, cylinder, et... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/visual.py | 0.943608 | 0.524943 | visual.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .collision import Collision
from .sensor import Sensor
from .visual import Visual
__NAMESPACE__ = "sdformat/v1.5/link.xsd"
@dataclass
class Link:
"""A physical link with inertia, collision, and visual properties.
A link must be ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/link.py | 0.956289 | 0.608885 | link.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .sensor import Sensor
__NAMESPACE__ = "sdformat/v1.5/joint.xsd"
@dataclass
class Joint:
"""
A joint connections two links with kinematic and dynamic properties.
Parameters
----------
parent: Name of the parent link
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/joint.py | 0.953827 | 0.787584 | joint.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .actor import Actor
from .joint import Joint
from .light import Light
from .material import Material
from .model import Model
from .physics import Physics
from .scene import Scene
from .state import State
__NAMESPACE__ = "sdformat/v1.5/wor... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/world.py | 0.932492 | 0.511961 | world.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .model import Model as ModelModel
__NAMESPACE__ = "sdformat/v1.5/state.xsd"
@dataclass
class Model:
"""
Model state.
Parameters
----------
joint: Joint angle
model: A nested model state element
frame: A frame... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/state.py | 0.941007 | 0.535584 | state.py | pypi |
from dataclasses import dataclass, field
from typing import Optional
__NAMESPACE__ = "sdformat/v1.5/physics.xsd"
@dataclass
class Physics:
"""
The physics tag specifies the type and properties of the dynamics engine.
Parameters
----------
max_step_size: Maximum time step size at which every syst... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/physics.py | 0.945349 | 0.670028 | physics.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.5/model.xsd"
@dataclass
class Model:
"""
The model element defines a complete robot or any other physical object.
Parameters
----------
static: ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/model.py | 0.947296 | 0.464355 | model.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
from .joint import Joint
from .link import Link
__NAMESPACE__ = "sdformat/v1.5/actor.xsd"
@dataclass
class Actor:
"""
Parameters
----------
static: Actors should be static, in terms of physics simulation.
skin:
animati... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/actor.py | 0.921375 | 0.409368 | actor.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.5/geometry.xsd"
@dataclass
class Geometry:
"""
The shape of the visual or collision object.
Parameters
----------
empty: You can use the empty tag to make empty geometries.
box: Box shape
... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v15/geometry.py | 0.944267 | 0.627523 | geometry.py | pypi |
from dataclasses import dataclass, field
from typing import List, Optional
__NAMESPACE__ = "sdformat/v1.8/material.xsd"
@dataclass
class Material:
"""
The material of the visual element.
Parameters
----------
script: Name of material from an installed script file. This will
override the ... | /scikit-bot-0.14.0.tar.gz/scikit-bot-0.14.0/skbot/ignition/sdformat/bindings/v18/material.py | 0.939206 | 0.581244 | material.py | pypi |
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