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328,300 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/DiporderPlanar.py | maicos.modules.DiporderPlanar.DiporderPlanar | import logging
import MDAnalysis as mda
from ..core import ProfilePlanarBase
from ..lib.weights import diporder_weights
from ..lib.util import render_docs, unit_vectors_planar
@render_docs
class DiporderPlanar(ProfilePlanarBase):
"""Cartesian dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATIO... | @render_docs
class DiporderPlanar(ProfilePlanarBase):
'''Cartesian dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATION_INFO_PLANAR}
Parameters
----------
${ATOMGROUP_PARAMETER}
${ORDER_PARAMETER_PARAMETER}
${PDIM_PLANAR_PARAMETER}
${PROFILE_PLANAR_CLASS_PARAMETERS}
${... | 5 | 1 | 19 | 1 | 18 | 0 | 1 | 0.27 | 1 | 5 | 0 | 0 | 2 | 1 | 2 | 31 | 75 | 9 | 52 | 24 | 30 | 14 | 10 | 6 | 6 | 2 | 4 | 0 | 4 |
328,301 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/DiporderSphere.py | maicos.modules.DiporderSphere.DiporderSphere | from ..lib.weights import diporder_weights
from ..core import ProfileSphereBase
import MDAnalysis as mda
from ..lib.util import render_docs, unit_vectors_sphere
import logging
@render_docs
class DiporderSphere(ProfileSphereBase):
"""Spherical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATIO... | @render_docs
class DiporderSphere(ProfileSphereBase):
'''Spherical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${ATOMGROUP_PARAMETER}
${ORDER_PARAMETER_PARAMETER}
${PROFILE_SPHERE_CLASS_PARAMETERS}
${OUTPUT_PARAMETER}
Attribu... | 5 | 1 | 17 | 1 | 16 | 0 | 1 | 0.29 | 1 | 5 | 0 | 0 | 2 | 0 | 2 | 30 | 67 | 9 | 45 | 20 | 26 | 13 | 9 | 5 | 5 | 2 | 4 | 0 | 4 |
328,302 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/DiporderStructureFactor.py | maicos.modules.DiporderStructureFactor.DiporderStructureFactor | from ..lib.weights import diporder_weights
from ..lib.math import structure_factor
from ..core import AnalysisBase
from ..lib.util import get_center, render_docs, unit_vectors_planar
import numpy as np
import MDAnalysis as mda
import logging
@render_docs
class DiporderStructureFactor(AnalysisBase):
"""Structure fa... | @render_docs
class DiporderStructureFactor(AnalysisBase):
'''Structure factor for dipoles.
Extension the standard structure factor :math:`S(q)` by weighting it with different
the normalized dipole moment :math:`\hat{\boldsymbol{\mu}}` of a ``group`` according
to
.. math::
S(q)_{\hat{\boldsym... | 9 | 2 | 20 | 2 | 17 | 1 | 1 | 0.32 | 1 | 8 | 0 | 0 | 5 | 9 | 5 | 17 | 155 | 26 | 98 | 45 | 74 | 31 | 42 | 26 | 35 | 2 | 2 | 2 | 7 |
328,303 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/KineticEnergy.py | maicos.modules.KineticEnergy.KineticEnergy | from ..lib.util import get_compound, render_docs
import numpy as np
from ..core import AnalysisBase
import MDAnalysis as mda
import logging
@render_docs
class KineticEnergy(AnalysisBase):
"""Kinetic energy timeseries.
The kinetic energy function computes the translational and rotational kinetic energy
wit... | @render_docs
class KineticEnergy(AnalysisBase):
'''Kinetic energy timeseries.
The kinetic energy function computes the translational and rotational kinetic energy
with respect to molecular center (center of mass, center of charge) of a molecular
dynamics simulation trajectory.
The analysis can be ap... | 8 | 3 | 16 | 1 | 14 | 1 | 2 | 0.38 | 1 | 6 | 0 | 0 | 5 | 8 | 5 | 17 | 118 | 17 | 73 | 28 | 56 | 28 | 31 | 17 | 25 | 3 | 2 | 1 | 8 |
328,304 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/PDFCylinder.py | maicos.modules.PDFCylinder.PDFCylinder | import MDAnalysis as mda
import logging
from MDAnalysis.lib.distances import capped_distance
import numpy as np
from ..core import CylinderBase
from ..lib.math import transform_cylinder
from ..lib.util import get_center, get_compound, render_docs
@render_docs
class PDFCylinder(CylinderBase):
"""Shell-wise one-dime... | @render_docs
class PDFCylinder(CylinderBase):
'''Shell-wise one-dimensional (cylindrical) pair distribution functions.
The one-dimensional pair distribution functions :math:`g_{\text{1d}}(\phi)`
and :math:`g_{\text{1d}}(z)` describes the pair distribution to particles
which lie on the same cylinder alon... | 8 | 2 | 63 | 7 | 51 | 6 | 3 | 0.34 | 1 | 8 | 0 | 0 | 5 | 16 | 5 | 28 | 392 | 52 | 257 | 78 | 226 | 87 | 99 | 53 | 93 | 8 | 4 | 2 | 17 |
328,305 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/PDFPlanar.py | maicos.modules.PDFPlanar.PDFPlanar | from MDAnalysis.lib.distances import capped_distance
import numpy as np
from ..lib.util import get_center, get_compound, render_docs
import logging
from ..core import PlanarBase
import MDAnalysis as mda
@render_docs
class PDFPlanar(PlanarBase):
"""Slab-wise planar 2D pair distribution functions.
The pair dist... | @render_docs
class PDFPlanar(PlanarBase):
'''Slab-wise planar 2D pair distribution functions.
The pair distribution function :math:`g_\mathrm{2D}(r)` describes the
spatial correlation between atoms in :math:`g_1` and atoms in
:math:`g_2`, which lie in the same plane.
It gives the average number dens... | 8 | 2 | 37 | 4 | 30 | 3 | 3 | 0.53 | 1 | 8 | 0 | 0 | 5 | 14 | 5 | 23 | 273 | 42 | 151 | 64 | 125 | 80 | 75 | 43 | 69 | 6 | 3 | 2 | 13 |
328,306 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/RDFDiporder.py | maicos.modules.RDFDiporder.RDFDiporder | import logging
import numpy as np
import MDAnalysis as mda
from ..core import AnalysisBase
from ..lib.util import get_center, render_docs
from MDAnalysis.lib import distances
from ..lib.weights import diporder_pair_weights
@render_docs
class RDFDiporder(AnalysisBase):
"""Spherical Radial Distribution function betw... | @render_docs
class RDFDiporder(AnalysisBase):
'''Spherical Radial Distribution function between dipoles.
The implementation is heavily inspired by :class:`MDAnalysis.analysis.rdf.InterRDF`
and is according to :footcite:t:`zhang_dipolar_2014` given by
.. math::
g_\mathrm{\hat{\boldsymbol{\mu}}, \... | 8 | 2 | 25 | 3 | 21 | 1 | 3 | 0.37 | 1 | 6 | 0 | 0 | 5 | 10 | 5 | 17 | 173 | 29 | 105 | 47 | 82 | 39 | 54 | 30 | 48 | 4 | 2 | 2 | 13 |
328,307 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/Saxs.py | maicos.modules.Saxs.Saxs | from ..lib.util import render_docs
import numpy as np
from ..lib.math import atomic_form_factor, structure_factor
import logging
import MDAnalysis as mda
from ..core import AnalysisBase
@render_docs
class Saxs(AnalysisBase):
"""Small angle X-Ray scattering intensities (SAXS).
This module computes the structur... | @render_docs
class Saxs(AnalysisBase):
'''Small angle X-Ray scattering intensities (SAXS).
This module computes the structure factor :math:`S(q)`, the scattering intensity
(sometimes also called scattering factor) :math:`I(q)` and their corresponding
scattering vectors :math:`q`. For a system containing... | 8 | 2 | 49 | 6 | 42 | 2 | 4 | 0.33 | 1 | 11 | 0 | 0 | 5 | 15 | 5 | 17 | 326 | 46 | 212 | 57 | 190 | 71 | 110 | 41 | 104 | 6 | 2 | 2 | 20 |
328,308 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/TemperaturePlanar.py | maicos.modules.TemperaturePlanar.TemperaturePlanar | import MDAnalysis as mda
from ..lib.util import render_docs
import logging
from ..lib.weights import temperature_weights
from ..core import ProfilePlanarBase
@render_docs
class TemperaturePlanar(ProfilePlanarBase):
"""Temperature profiles in a cartesian geometry.
Currently only atomistic temperature profiles ... | @render_docs
class TemperaturePlanar(ProfilePlanarBase):
'''Temperature profiles in a cartesian geometry.
Currently only atomistic temperature profiles are supported. Therefore grouping per
molecule, segment, residue, or fragment is not possible.
${CORRELATION_INFO_PLANAR}
Parameters
----------
... | 4 | 1 | 22 | 1 | 22 | 0 | 2 | 0.3 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 31 | 65 | 8 | 44 | 20 | 25 | 13 | 9 | 4 | 6 | 2 | 4 | 1 | 3 |
328,309 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/VelocityCylinder.py | maicos.modules.VelocityCylinder.VelocityCylinder | import logging
from ..lib.util import render_docs
from ..lib.weights import velocity_weights
from ..core import ProfileCylinderBase
import MDAnalysis as mda
@render_docs
class VelocityCylinder(ProfileCylinderBase):
"""Cartesian velocity profile across a cylinder.
Reads in coordinates and velocities from a tra... | @render_docs
class VelocityCylinder(ProfileCylinderBase):
'''Cartesian velocity profile across a cylinder.
Reads in coordinates and velocities from a trajectory and calculates a velocity
:math:`[\mathrm{Å/ps}]` or a flux per unit area :math:`[\mathrm{Å^{-2}\,ps^{-1}}]`
profile along a given axis.
Th... | 4 | 1 | 24 | 1 | 24 | 0 | 2 | 0.42 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 36 | 77 | 9 | 48 | 24 | 26 | 20 | 10 | 5 | 7 | 3 | 5 | 1 | 4 |
328,310 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/VelocityPlanar.py | maicos.modules.VelocityPlanar.VelocityPlanar | from ..core import ProfilePlanarBase
import logging
from ..lib.util import render_docs
import MDAnalysis as mda
from ..lib.weights import velocity_weights
@render_docs
class VelocityPlanar(ProfilePlanarBase):
"""Velocity profiles in a cartesian geometry.
Reads in coordinates and velocities from a trajectory a... | @render_docs
class VelocityPlanar(ProfilePlanarBase):
'''Velocity profiles in a cartesian geometry.
Reads in coordinates and velocities from a trajectory and calculates a velocity
:math:`[\mathrm{Å/ps}]` or a flux per unit area :math:`[\mathrm{Å^{-2}\,ps^{-1}}]`
profile along a given axis.
The ``gro... | 4 | 1 | 24 | 1 | 24 | 0 | 2 | 0.5 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 31 | 81 | 9 | 48 | 24 | 26 | 24 | 10 | 5 | 7 | 3 | 4 | 1 | 4 |
328,311 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/densitycylinder.py | maicos.modules.densitycylinder.DensityCylinder | from ..lib.weights import density_weights
from ..lib.util import render_docs
import logging
import MDAnalysis as mda
from ..core import ProfileCylinderBase
@render_docs
class DensityCylinder(ProfileCylinderBase):
"""Cylindrical partial density profiles.
${DENSITY_CYLINDER_DESCRIPTION}
${CORRELATION_INFO_... | @render_docs
class DensityCylinder(ProfileCylinderBase):
'''Cylindrical partial density profiles.
${DENSITY_CYLINDER_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${ATOMGROUP_PARAMETER}
${DENS_PARAMETER}
${PROFILE_CYLINDER_CLASS_PARAMETERS}
${OUTPUT_PARAMETER}
Att... | 4 | 1 | 22 | 0 | 22 | 0 | 1 | 0.3 | 1 | 5 | 0 | 0 | 2 | 1 | 2 | 36 | 64 | 7 | 44 | 22 | 23 | 13 | 7 | 4 | 4 | 1 | 5 | 0 | 2 |
328,312 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/densityplanar.py | maicos.modules.densityplanar.DensityPlanar | from ..lib.weights import density_weights
import MDAnalysis as mda
import logging
from ..lib.util import render_docs
from ..core import ProfilePlanarBase
@render_docs
class DensityPlanar(ProfilePlanarBase):
"""Cartesian partial density profiles.
${DENSITY_PLANAR_DESCRIPTION}
${CORRELATION_INFO_PLANAR}
... | @render_docs
class DensityPlanar(ProfilePlanarBase):
'''Cartesian partial density profiles.
${DENSITY_PLANAR_DESCRIPTION}
${CORRELATION_INFO_PLANAR}
Parameters
----------
${ATOMGROUP_PARAMETER}
${DENS_PARAMETER}
${PROFILE_PLANAR_CLASS_PARAMETERS}
${OUTPUT_PARAMETER}
Attributes
... | 4 | 1 | 21 | 0 | 21 | 0 | 1 | 0.42 | 1 | 5 | 0 | 0 | 2 | 1 | 2 | 31 | 69 | 8 | 43 | 21 | 23 | 18 | 7 | 4 | 4 | 1 | 4 | 0 | 2 |
328,313 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/densitysphere.py | maicos.modules.densitysphere.DensitySphere | import MDAnalysis as mda
from ..lib.weights import density_weights
from ..core import ProfileSphereBase
import logging
from ..lib.util import render_docs
@render_docs
class DensitySphere(ProfileSphereBase):
"""Spherical partial density profiles.
${DENSITY_SPHERE_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
... | @render_docs
class DensitySphere(ProfileSphereBase):
'''Spherical partial density profiles.
${DENSITY_SPHERE_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${ATOMGROUP_PARAMETER}
${DENS_PARAMETER}
${PROFILE_SPHERE_CLASS_PARAMETERS}
${OUTPUT_PARAMETER}
Attributes
... | 4 | 1 | 19 | 0 | 19 | 0 | 1 | 0.34 | 1 | 5 | 0 | 0 | 2 | 1 | 2 | 30 | 58 | 7 | 38 | 19 | 20 | 13 | 7 | 4 | 4 | 1 | 4 | 0 | 2 |
328,314 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dielectriccylinder.py | maicos.modules.dielectriccylinder.DielectricCylinder | import numpy as np
import logging
import MDAnalysis as mda
from ..lib.util import charge_neutral, citation_reminder, get_compound, render_docs
import scipy.constants
from ..core import CylinderBase
@render_docs
@charge_neutral(filter='error')
class DielectricCylinder(CylinderBase):
"""Cylindrical dielectric profil... | @render_docs
@charge_neutral(filter='error')
class DielectricCylinder(CylinderBase):
'''Cylindrical dielectric profiles.
Computes the axial :math:`\varepsilon_z(r)` and inverse radial
:math:`\varepsilon_r^{-1}(r)` components of the cylindrical dielectric tensor
:math:`\varepsilon`. The components are bi... | 9 | 2 | 39 | 5 | 29 | 5 | 1 | 0.45 | 1 | 5 | 0 | 0 | 5 | 8 | 5 | 28 | 248 | 38 | 145 | 52 | 120 | 65 | 66 | 33 | 60 | 2 | 4 | 1 | 7 |
328,315 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dielectricplanar.py | maicos.modules.dielectricplanar.DielectricPlanar | from ..core import PlanarBase
import numpy as np
from ..lib.math import symmetrize
from ..lib.util import charge_neutral, citation_reminder, get_compound, render_docs
import MDAnalysis as mda
import scipy.constants
import logging
@render_docs
@charge_neutral(filter='error')
class DielectricPlanar(PlanarBase):
"""P... | @render_docs
@charge_neutral(filter='error')
class DielectricPlanar(PlanarBase):
'''Planar dielectric profiles.
Computes the parallel :math:`\varepsilon_\parallel(z)` and inverse perpendicular
(:math:`\varepsilon_\perp^{-1}(r)`) components of the planar dielectric tensor
:math:`\varepsilon`. The compone... | 9 | 2 | 56 | 9 | 43 | 5 | 2 | 0.37 | 1 | 6 | 0 | 0 | 5 | 10 | 5 | 23 | 350 | 56 | 215 | 61 | 191 | 79 | 116 | 43 | 110 | 3 | 3 | 1 | 9 |
328,316 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dielectricspectrum.py | maicos.modules.dielectricspectrum.DielectricSpectrum | import numpy as np
from ..lib.util import bin, charge_neutral, citation_reminder, get_compound, render_docs
from ..core import AnalysisBase
from pathlib import Path
import MDAnalysis as mda
import scipy.constants
from ..lib.math import FT, iFT
import logging
@render_docs
@charge_neutral(filter='error')
class Dielectri... | @render_docs
@charge_neutral(filter='error')
class DielectricSpectrum(AnalysisBase):
'''Linear dielectric spectrum.
This module, given a molecular dynamics trajectory, produces a `.txt` file
containing the complex dielectric function as a function of the (linear, not radial
- i.e., :math:`\nu` or :math:... | 9 | 2 | 43 | 6 | 33 | 4 | 3 | 0.35 | 1 | 8 | 0 | 0 | 5 | 14 | 5 | 17 | 266 | 40 | 167 | 47 | 145 | 59 | 87 | 29 | 81 | 7 | 2 | 2 | 13 |
328,317 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dielectricsphere.py | maicos.modules.dielectricsphere.DielectricSphere | import scipy.constants
from ..lib.util import charge_neutral, citation_reminder, get_compound, render_docs
import numpy as np
from ..core import SphereBase
import MDAnalysis as mda
import logging
@render_docs
@charge_neutral(filter='error')
class DielectricSphere(SphereBase):
"""Spherical dielectric profiles.
... | @render_docs
@charge_neutral(filter='error')
class DielectricSphere(SphereBase):
'''Spherical dielectric profiles.
Computes the inverse radial :math:`\varepsilon_r^{-1}(r)` component of the
spherical dielectric tensor :math:`\varepsilon`. The center of the sphere is either
located at the center of the s... | 9 | 2 | 23 | 3 | 18 | 3 | 1 | 0.43 | 1 | 5 | 0 | 0 | 5 | 7 | 5 | 22 | 157 | 28 | 90 | 35 | 70 | 39 | 39 | 21 | 33 | 2 | 3 | 1 | 6 |
328,318 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dipoleangle.py | maicos.modules.dipoleangle.DipoleAngle | from ..lib.weights import diporder_weights
from ..lib.util import get_compound, render_docs, unit_vectors_planar
import MDAnalysis as mda
from ..core import AnalysisBase
import numpy as np
import logging
@render_docs
class DipoleAngle(AnalysisBase):
"""Angle timeseries of dipole moments with respect to an axis.
... | @render_docs
class DipoleAngle(AnalysisBase):
'''Angle timeseries of dipole moments with respect to an axis.
The analysis can be applied to study the orientational dynamics of water molecules
during an excitation pulse. For more details read
:footcite:t:`elgabartyEnergyTransferHydrogen2020`.
Paramet... | 9 | 2 | 13 | 1 | 12 | 0 | 1 | 0.33 | 1 | 5 | 0 | 0 | 5 | 11 | 5 | 17 | 106 | 13 | 70 | 33 | 51 | 23 | 32 | 20 | 25 | 1 | 2 | 0 | 6 |
328,319 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dipordercylinder.py | maicos.modules.dipordercylinder.DiporderCylinder | from ..lib.weights import diporder_weights
import logging
from ..core import ProfileCylinderBase
import MDAnalysis as mda
from ..lib.util import render_docs, unit_vectors_cylinder
@render_docs
class DiporderCylinder(ProfileCylinderBase):
"""Cylindrical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${... | @render_docs
class DiporderCylinder(ProfileCylinderBase):
'''Cylindrical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${ATOMGROUP_PARAMETER}
${ORDER_PARAMETER_PARAMETER}
${PDIM_RADIAL_PARAMETER}
${PROFILE_CYLINDER_CLASS_PARAMETERS... | 5 | 1 | 22 | 1 | 21 | 0 | 1 | 0.25 | 1 | 5 | 0 | 0 | 2 | 0 | 2 | 36 | 79 | 9 | 56 | 24 | 33 | 14 | 9 | 5 | 5 | 2 | 5 | 0 | 4 |
328,320 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/diporderplanar.py | maicos.modules.diporderplanar.DiporderPlanar | import logging
from ..lib.util import render_docs, unit_vectors_planar
import MDAnalysis as mda
from ..lib.weights import diporder_weights
from ..core import ProfilePlanarBase
@render_docs
class DiporderPlanar(ProfilePlanarBase):
"""Cartesian dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATIO... | @render_docs
class DiporderPlanar(ProfilePlanarBase):
'''Cartesian dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATION_INFO_PLANAR}
Parameters
----------
${ATOMGROUP_PARAMETER}
${ORDER_PARAMETER_PARAMETER}
${PDIM_PLANAR_PARAMETER}
${PROFILE_PLANAR_CLASS_PARAMETERS}
${... | 5 | 1 | 19 | 1 | 18 | 0 | 1 | 0.27 | 1 | 5 | 0 | 0 | 2 | 1 | 2 | 31 | 75 | 9 | 52 | 24 | 30 | 14 | 10 | 6 | 6 | 2 | 4 | 0 | 4 |
328,321 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/dipordersphere.py | maicos.modules.dipordersphere.DiporderSphere | from ..lib.util import render_docs, unit_vectors_sphere
from ..lib.weights import diporder_weights
import logging
import MDAnalysis as mda
from ..core import ProfileSphereBase
@render_docs
class DiporderSphere(ProfileSphereBase):
"""Spherical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATIO... | @render_docs
class DiporderSphere(ProfileSphereBase):
'''Spherical dipolar order parameters.
${DIPORDER_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${ATOMGROUP_PARAMETER}
${ORDER_PARAMETER_PARAMETER}
${PROFILE_SPHERE_CLASS_PARAMETERS}
${OUTPUT_PARAMETER}
Attribu... | 5 | 1 | 17 | 1 | 16 | 0 | 1 | 0.29 | 1 | 5 | 0 | 0 | 2 | 0 | 2 | 30 | 67 | 9 | 45 | 20 | 26 | 13 | 9 | 5 | 5 | 2 | 4 | 0 | 4 |
328,322 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/diporderstructurefactor.py | maicos.modules.diporderstructurefactor.DiporderStructureFactor | import MDAnalysis as mda
from ..lib.weights import diporder_weights
import numpy as np
from ..lib.util import get_center, render_docs, unit_vectors_planar
from ..core import AnalysisBase
from ..lib.math import structure_factor
import logging
@render_docs
class DiporderStructureFactor(AnalysisBase):
"""Structure fa... | @render_docs
class DiporderStructureFactor(AnalysisBase):
'''Structure factor for dipoles.
Extension the standard structure factor :math:`S(q)` by weighting it with different
the normalized dipole moment :math:`\hat{\boldsymbol{\mu}}` of a ``group`` according
to
.. math::
S(q)_{\hat{\boldsym... | 9 | 2 | 20 | 2 | 17 | 1 | 1 | 0.32 | 1 | 8 | 0 | 0 | 5 | 9 | 5 | 17 | 155 | 26 | 98 | 45 | 74 | 31 | 42 | 26 | 35 | 2 | 2 | 2 | 7 |
328,323 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/kineticenergy.py | maicos.modules.kineticenergy.KineticEnergy | from ..core import AnalysisBase
import logging
from ..lib.util import get_compound, render_docs
import MDAnalysis as mda
import numpy as np
@render_docs
class KineticEnergy(AnalysisBase):
"""Kinetic energy timeseries.
The kinetic energy function computes the translational and rotational kinetic energy
wit... | @render_docs
class KineticEnergy(AnalysisBase):
'''Kinetic energy timeseries.
The kinetic energy function computes the translational and rotational kinetic energy
with respect to molecular center (center of mass, center of charge) of a molecular
dynamics simulation trajectory.
The analysis can be ap... | 8 | 3 | 16 | 1 | 14 | 1 | 2 | 0.38 | 1 | 6 | 0 | 0 | 5 | 8 | 5 | 17 | 118 | 17 | 73 | 28 | 56 | 28 | 31 | 17 | 25 | 3 | 2 | 1 | 8 |
328,324 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/pdfcylinder.py | maicos.modules.pdfcylinder.PDFCylinder | from MDAnalysis.lib.distances import capped_distance
import numpy as np
import MDAnalysis as mda
import logging
from ..lib.math import transform_cylinder
from ..lib.util import get_center, get_compound, render_docs
from ..core import CylinderBase
@render_docs
class PDFCylinder(CylinderBase):
"""Shell-wise one-dime... | @render_docs
class PDFCylinder(CylinderBase):
'''Shell-wise one-dimensional (cylindrical) pair distribution functions.
The one-dimensional pair distribution functions :math:`g_{\text{1d}}(\phi)`
and :math:`g_{\text{1d}}(z)` describes the pair distribution to particles
which lie on the same cylinder alon... | 8 | 2 | 63 | 7 | 51 | 6 | 3 | 0.34 | 1 | 8 | 0 | 0 | 5 | 16 | 5 | 28 | 392 | 52 | 257 | 78 | 226 | 87 | 99 | 53 | 93 | 8 | 4 | 2 | 17 |
328,325 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/pdfplanar.py | maicos.modules.pdfplanar.PDFPlanar | from MDAnalysis.lib.distances import capped_distance
from ..core import PlanarBase
import numpy as np
import logging
import MDAnalysis as mda
from ..lib.util import get_center, get_compound, render_docs
@render_docs
class PDFPlanar(PlanarBase):
"""Slab-wise planar 2D pair distribution functions.
The pair dist... | @render_docs
class PDFPlanar(PlanarBase):
'''Slab-wise planar 2D pair distribution functions.
The pair distribution function :math:`g_\mathrm{2D}(r)` describes the
spatial correlation between atoms in :math:`g_1` and atoms in
:math:`g_2`, which lie in the same plane.
It gives the average number dens... | 8 | 2 | 37 | 4 | 30 | 3 | 3 | 0.53 | 1 | 8 | 0 | 0 | 5 | 14 | 5 | 23 | 273 | 42 | 151 | 64 | 125 | 80 | 75 | 43 | 69 | 6 | 3 | 2 | 13 |
328,326 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/rdfdiporder.py | maicos.modules.rdfdiporder.RDFDiporder | from ..lib.util import get_center, render_docs
from ..lib.weights import diporder_pair_weights
import MDAnalysis as mda
from MDAnalysis.lib import distances
import logging
from ..core import AnalysisBase
import numpy as np
@render_docs
class RDFDiporder(AnalysisBase):
"""Spherical Radial Distribution function betw... | @render_docs
class RDFDiporder(AnalysisBase):
'''Spherical Radial Distribution function between dipoles.
The implementation is heavily inspired by :class:`MDAnalysis.analysis.rdf.InterRDF`
and is according to :footcite:t:`zhang_dipolar_2014` given by
.. math::
g_\mathrm{\hat{\boldsymbol{\mu}}, \... | 8 | 2 | 25 | 3 | 21 | 1 | 3 | 0.37 | 1 | 6 | 0 | 0 | 5 | 10 | 5 | 17 | 173 | 29 | 105 | 47 | 82 | 39 | 54 | 30 | 48 | 4 | 2 | 2 | 13 |
328,327 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/saxs.py | maicos.modules.saxs.Saxs | from ..lib.util import render_docs
import logging
import MDAnalysis as mda
from ..core import AnalysisBase
import numpy as np
from ..lib.math import atomic_form_factor, structure_factor
@render_docs
class Saxs(AnalysisBase):
"""Small angle X-Ray scattering intensities (SAXS).
This module computes the structur... | @render_docs
class Saxs(AnalysisBase):
'''Small angle X-Ray scattering intensities (SAXS).
This module computes the structure factor :math:`S(q)`, the scattering intensity
(sometimes also called scattering factor) :math:`I(q)` and their corresponding
scattering vectors :math:`q`. For a system containing... | 8 | 2 | 49 | 6 | 42 | 2 | 4 | 0.33 | 1 | 11 | 0 | 0 | 5 | 15 | 5 | 17 | 326 | 46 | 212 | 57 | 190 | 71 | 110 | 41 | 104 | 6 | 2 | 2 | 20 |
328,328 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/temperatureplanar.py | maicos.modules.temperatureplanar.TemperaturePlanar | import MDAnalysis as mda
from ..core import ProfilePlanarBase
from ..lib.weights import temperature_weights
from ..lib.util import render_docs
import logging
@render_docs
class TemperaturePlanar(ProfilePlanarBase):
"""Temperature profiles in a cartesian geometry.
Currently only atomistic temperature profiles ... | @render_docs
class TemperaturePlanar(ProfilePlanarBase):
'''Temperature profiles in a cartesian geometry.
Currently only atomistic temperature profiles are supported. Therefore grouping per
molecule, segment, residue, or fragment is not possible.
${CORRELATION_INFO_PLANAR}
Parameters
----------
... | 4 | 1 | 22 | 1 | 22 | 0 | 2 | 0.3 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 31 | 65 | 8 | 44 | 20 | 25 | 13 | 9 | 4 | 6 | 2 | 4 | 1 | 3 |
328,329 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/velocitycylinder.py | maicos.modules.velocitycylinder.VelocityCylinder | from ..lib.util import render_docs
from ..lib.weights import velocity_weights
import logging
import MDAnalysis as mda
from ..core import ProfileCylinderBase
@render_docs
class VelocityCylinder(ProfileCylinderBase):
"""Cartesian velocity profile across a cylinder.
Reads in coordinates and velocities from a tra... | @render_docs
class VelocityCylinder(ProfileCylinderBase):
'''Cartesian velocity profile across a cylinder.
Reads in coordinates and velocities from a trajectory and calculates a velocity
:math:`[\mathrm{Å/ps}]` or a flux per unit area :math:`[\mathrm{Å^{-2}\,ps^{-1}}]`
profile along a given axis.
Th... | 4 | 1 | 24 | 1 | 24 | 0 | 2 | 0.42 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 36 | 77 | 9 | 48 | 24 | 26 | 20 | 10 | 5 | 7 | 3 | 5 | 1 | 4 |
328,330 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/src/maicos/modules/velocityplanar.py | maicos.modules.velocityplanar.VelocityPlanar | from ..core import ProfilePlanarBase
import MDAnalysis as mda
import logging
from ..lib.util import render_docs
from ..lib.weights import velocity_weights
@render_docs
class VelocityPlanar(ProfilePlanarBase):
"""Velocity profiles in a cartesian geometry.
Reads in coordinates and velocities from a trajectory a... | @render_docs
class VelocityPlanar(ProfilePlanarBase):
'''Velocity profiles in a cartesian geometry.
Reads in coordinates and velocities from a trajectory and calculates a velocity
:math:`[\mathrm{Å/ps}]` or a flux per unit area :math:`[\mathrm{Å^{-2}\,ps^{-1}}]`
profile along a given axis.
The ``gro... | 4 | 1 | 24 | 1 | 24 | 0 | 2 | 0.5 | 1 | 6 | 0 | 0 | 2 | 1 | 2 | 31 | 81 | 9 | 48 | 24 | 26 | 24 | 10 | 5 | 7 | 3 | 4 | 1 | 4 |
328,331 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/versioneer.py | versioneer.NotThisMethod | class NotThisMethod(Exception):
"""Exception raised if a method is not valid for the current scenario.""" | class NotThisMethod(Exception):
'''Exception raised if a method is not valid for the current scenario.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 3 | 0 | 0 |
328,332 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/versioneer.py | versioneer.VersioneerBadRootError | class VersioneerBadRootError(Exception):
"""The project root directory is unknown or missing key files.""" | class VersioneerBadRootError(Exception):
'''The project root directory is unknown or missing key files.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 3 | 0 | 0 |
328,333 | maicos-devel/maicos | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/maicos-devel_maicos/versioneer.py | versioneer.VersioneerConfig | from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union
class VersioneerConfig:
"""Container for Versioneer configuration parameters."""
VCS: str
style: str
tag_prefix: str
versionfile_source: str
versionfile_build: Optional[str]
parentdir_prefix: Optional[str]
verbos... |
class VersioneerConfig:
'''Container for Versioneer configuration parameters.'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 1 | 8 | 1 | 7 | 1 | 8 | 1 | 7 | 0 | 0 | 0 | 0 |
328,334 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Lucia/Bot/__init__.py | Bot.SilentXBot | from typing import Union, Optional, AsyncGenerator
from pyrogram import Client
class SilentXBot(Client):
def __init__(self):
super().__init__(name=SESSION, api_id=API_ID, api_hash=API_HASH, bot_token=BOT_TOKEN, workers=50, plugins={'root': 'plugins'}, sleep_threshold=5)
async def iter_messages(self, ... |
class SilentXBot(Client):
def __init__(self):
pass
async def iter_messages(self, chat_id: Union[int, str], limit: int, offset: int=0) -> Optional[AsyncGenerator['types.Message', None]]:
'''Iterate through a chat sequentially.
This convenience method does the same as repeatedly calling... | 3 | 1 | 24 | 1 | 13 | 11 | 3 | 0.81 | 1 | 5 | 0 | 0 | 2 | 0 | 2 | 2 | 49 | 2 | 26 | 12 | 18 | 21 | 13 | 7 | 10 | 4 | 1 | 2 | 5 |
328,335 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Script.py | Script.script | class script(object):
START_TXT = '<b>\u200b\u200b\u200bʜɪɪ {} 👋, \nɪ ᴀᴍ ᴛʜᴇ ᴍᴏꜱᴛ ᴘᴏᴡᴇʀꜰᴜʟʟ ᴍᴇᴅɪᴀ ᴘʀᴏᴠɪᴅᴇʀ ʙᴏᴛ. ɪ ᴄᴀɴ ᴘʀᴏᴠɪᴅᴇᴅ ᴀʟʟ ʟᴀᴛᴇꜱᴛ ᴍᴏᴠɪᴇꜱ ᴏʀ ꜱᴇʀɪᴇꜱ. ᴊᴜꜱᴛ ꜱᴇɴᴅ ᴍᴇ ᴛʜᴇ ᴄᴏʀʀᴇᴄᴛ ɴᴀᴍᴇ .</b>'
FEATURES_TXT = '<b>ʜᴇʀᴇ ɪꜱ ᴀʟʟ ᴍʏ ꜰᴜɴᴛɪᴏɴꜱ.</b>'
ABOUT_TXT = "<b>╭────[ ᴍʏ ᴅᴇᴛᴀɪʟs ]────⍟\n├⍟ ᴍʏ ɴᴀᴍᴇ : <a href=ht... | class script(object):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0.03 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 324 | 95 | 224 | 39 | 223 | 7 | 39 | 39 | 38 | 0 | 1 | 0 | 0 |
328,336 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Lucia/util/config_parser.py | config_parser.TokenParser | from os import environ
from typing import Dict, Optional
class TokenParser:
def __init__(self, config_file: Optional[str]=None):
self.tokens = {}
self.config_file = config_file
def parse_from_env(self) -> Dict[int, str]:
self.tokens = dict(((c + 1, t) for c, (_, t) in enumerate(filter... |
class TokenParser:
def __init__(self, config_file: Optional[str]=None):
pass
def parse_from_env(self) -> Dict[int, str]:
pass | 3 | 0 | 7 | 0 | 7 | 0 | 1 | 0 | 0 | 5 | 0 | 0 | 2 | 2 | 2 | 2 | 15 | 1 | 14 | 6 | 11 | 0 | 7 | 5 | 4 | 1 | 0 | 0 | 2 |
328,337 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Lucia/util/custom_dl.py | custom_dl.ByteStreamer | from pyrogram import Client, utils, raw
from pyrogram.session import Session, Auth
from pyrogram.file_id import FileId, FileType, ThumbnailSource
from Lucia.Bot import work_loads
from Lucia.server.exceptions import FIleNotFound
from pyrogram.errors import AuthBytesInvalid
from typing import Dict, Union
from .file_prope... |
class ByteStreamer:
def __init__(self, client: Client):
'''A custom class that holds the cache of a specific client and class functions.
attributes:
client: the client that the cache is for.
cached_file_ids: a dict of cached file IDs.
cached_file_properties: a d... | 9 | 7 | 30 | 2 | 23 | 5 | 3 | 0.23 | 0 | 6 | 1 | 0 | 6 | 3 | 7 | 7 | 217 | 21 | 160 | 36 | 140 | 36 | 87 | 24 | 79 | 9 | 0 | 4 | 24 |
328,338 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Lucia/server/exceptions.py | exceptions.FIleNotFound | class FIleNotFound(Exception):
message = 'File Not Found' | class FIleNotFound(Exception):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 2 | 0 | 2 | 2 | 1 | 0 | 2 | 2 | 1 | 0 | 3 | 0 | 0 |
328,339 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/Lucia/server/exceptions.py | exceptions.InvalidHash | class InvalidHash(Exception):
message = 'Invalid Hash' | class InvalidHash(Exception):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | 2 | 0 | 2 | 2 | 1 | 0 | 2 | 2 | 1 | 0 | 3 | 0 | 0 |
328,340 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/database/ia_filterdb.py | ia_filterdb.Media | from umongo import Instance, Document, fields
@instance.register
class Media(Document):
file_id = fields.StrField(attribute='_id')
file_ref = fields.StrField(allow_none=True)
file_name = fields.StrField(required=True)
file_size = fields.IntField(required=True)
file_type = fields.StrField(allow_none... | null | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 0 | 11 | 11 | 9 | 0 | 11 | 11 | 9 | 0 | 1 | 0 | 0 |
328,341 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/database/ia_filterdb.py | ia_filterdb.Media2 | from umongo import Instance, Document, fields
@instance2.register
class Media2(Document):
file_id = fields.StrField(attribute='_id')
file_ref = fields.StrField(allow_none=True)
file_name = fields.StrField(required=True)
file_size = fields.IntField(required=True)
file_type = fields.StrField(allow_no... | null | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 11 | 0 | 11 | 11 | 9 | 0 | 11 | 11 | 9 | 0 | 1 | 0 | 0 |
328,342 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/database/refer.py | refer.UserTracker | class UserTracker:
def __init__(self):
self.user_collection = mydb['referusers']
self.refer_collection = mydb['refers']
def add_user(self, user_id):
if not self.is_user_in_list(user_id):
self.user_collection.insert_one({'user_id': user_id})
def remove_user(self, user_i... | class UserTracker:
def __init__(self):
pass
def add_user(self, user_id):
pass
def remove_user(self, user_id):
pass
def is_user_in_list(self, user_id):
pass
def add_refer_points(self, user_id: int, points: int):
pass
def get_refer_points(self, user_id... | 7 | 0 | 3 | 0 | 3 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 6 | 2 | 6 | 6 | 25 | 5 | 20 | 10 | 13 | 0 | 16 | 10 | 9 | 2 | 0 | 1 | 8 |
328,343 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/database/topdb.py | topdb.Database | from motor.motor_asyncio import AsyncIOMotorClient
class Database:
def __init__(self, uri, db_name):
self.client = AsyncIOMotorClient(uri)
self.db = self.client[db_name]
self.col = self.db.user
async def update_top_messages(self, user_id, message_text):
user = await self.col.f... |
class Database:
def __init__(self, uri, db_name):
pass
async def update_top_messages(self, user_id, message_text):
pass
async def get_top_messages(self, limit=30):
pass
async def delete_all_messages(self):
pass | 5 | 0 | 7 | 0 | 7 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 3 | 4 | 4 | 33 | 4 | 29 | 11 | 24 | 0 | 16 | 11 | 11 | 2 | 0 | 1 | 5 |
328,344 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/database/users_chats_db.py | users_chats_db.Database | import pytz
from datetime import timedelta
import datetime
import motor.motor_asyncio
import time
class Database:
def __init__(self, uri, database_name):
self._client = motor.motor_asyncio.AsyncIOMotorClient(uri)
self.db = self._client[database_name]
self.col = self.db.users
self.g... |
class Database:
def __init__(self, uri, database_name):
pass
async def find_join_req(self, id, chnl):
pass
async def add_join_req(self, id, chnl):
pass
async def del_join_req(self):
pass
def new_user(self, id, name):
pass
def new_group(self, id, tit... | 57 | 0 | 6 | 0 | 6 | 0 | 2 | 0.01 | 0 | 7 | 0 | 0 | 56 | 10 | 56 | 56 | 414 | 58 | 354 | 147 | 297 | 2 | 274 | 145 | 217 | 5 | 0 | 2 | 84 |
328,345 | NBBotz/Auto-Filter-Bot | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/NBBotz_Auto-Filter-Bot/utils.py | utils.temp | import os
class temp(object):
BANNED_USERS = []
BANNED_CHATS = []
SETTINGS = {}
ME = None
CURRENT = int(os.environ.get('SKIP', 2))
CANCEL = False
B_USERS_CANCEL = False
B_GROUPS_CANCEL = False
MELCOW = {}
U_NAME = None
B_NAME = None
B_LINK = None
GETALL = {}
SHOR... |
class temp(object):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 17 | 0 | 17 | 17 | 16 | 0 | 17 | 17 | 16 | 0 | 1 | 0 | 0 |
328,346 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/AssetDownloadResult.py | prefect_managedfiletransfer.AssetDownloadResult.AssetDownloadResult | from pathlib import Path
from datetime import datetime
class AssetDownloadResult:
"""
Represents the result of an asset download operation.
"""
def __init__(self, success: bool, file_path: Path | None, download_skipped: bool=False, last_modified: datetime | None=None, size: int=0, error: str | None=No... |
class AssetDownloadResult:
'''
Represents the result of an asset download operation.
'''
def __init__(self, success: bool, file_path: Path | None, download_skipped: bool=False, last_modified: datetime | None=None, size: int=0, error: str | None=None):
'''
Represents the result of an as... | 3 | 2 | 15 | 1 | 11 | 4 | 2 | 0.45 | 0 | 6 | 0 | 0 | 2 | 6 | 2 | 2 | 36 | 4 | 22 | 17 | 11 | 10 | 14 | 9 | 11 | 2 | 0 | 1 | 4 |
328,347 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/FileMatcher.py | prefect_managedfiletransfer.FileMatcher.FileMatcher | from pathlib import Path
from prefect_managedfiletransfer.SortFilesBy import SortFilesBy
from datetime import timedelta
from pydantic import BaseModel, Field
class FileMatcher(BaseModel):
"""
Represents a file matcher with a source path and a pattern to match files.
This is used to find files in a director... |
class FileMatcher(BaseModel):
'''
Represents a file matcher with a source path and a pattern to match files.
This is used to find files in a directory that match a specific pattern.
'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.14 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 82 | 34 | 1 | 29 | 8 | 28 | 4 | 8 | 8 | 7 | 0 | 5 | 0 | 0 |
328,348 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/FileToFolderMapping.py | prefect_managedfiletransfer.FileToFolderMapping.FileToFolderMapping | from pydantic import BaseModel, Field
from prefect_managedfiletransfer.RemoteAsset import RemoteAsset
from pathlib import Path
class FileToFolderMapping(BaseModel):
source_path_pattern_to_match: str = Field(default='*', description="Pattern to match files against in the source directory. Supports glob patterns. E.... |
class FileToFolderMapping(BaseModel):
def is_match(self, file_path: Path) -> bool:
'''
Check if the given file path matches the source path pattern.
'''
pass
def __init__(self, source_path_pattern_to_match: str='*', destination_folder: str='.'):
pass
@staticmethod
... | 5 | 1 | 22 | 3 | 18 | 1 | 4 | 0.08 | 1 | 7 | 1 | 0 | 2 | 0 | 3 | 85 | 81 | 13 | 63 | 19 | 50 | 5 | 30 | 10 | 26 | 7 | 5 | 4 | 11 |
328,349 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/PathUtil.py | prefect_managedfiletransfer.PathUtil.PathUtil | from prefect_managedfiletransfer.RemoteConnectionType import RemoteConnectionType
from pathlib import Path
class PathUtil:
@staticmethod
def resolve_path(path_type: RemoteConnectionType, basepath: Path | str | None, path: Path | str) -> Path:
if path_type == RemoteConnectionType.LOCAL:
rem... |
class PathUtil:
@staticmethod
def resolve_path(path_type: RemoteConnectionType, basepath: Path | str | None, path: Path | str) -> Path:
pass
@staticmethod
def _local_resolve_path(basepath: str | Path | None, path: str | Path, validate: bool=False) -> Path:
pass
@staticmethod
de... | 7 | 0 | 24 | 3 | 21 | 1 | 5 | 0.05 | 0 | 5 | 1 | 0 | 0 | 0 | 3 | 3 | 79 | 10 | 66 | 19 | 51 | 3 | 33 | 8 | 29 | 8 | 0 | 2 | 16 |
328,350 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RCloneCommandBuilder.py | prefect_managedfiletransfer.RCloneCommandBuilder.RCloneCommandBuilder | from pathlib import Path
import platform
import subprocess
from prefect_managedfiletransfer.RCloneConfig import RCloneConfig
import importlib
import importlib.resources
class RCloneCommandBuilder:
def __init__(self, rclone_config_file: Path | None=None, rclone_config: RCloneConfig | None=None):
self.rclon... |
class RCloneCommandBuilder:
def __init__(self, rclone_config_file: Path | None=None, rclone_config: RCloneConfig | None=None):
pass
def uploadTo(self, source_file, destination_file: Path, update_only_if_newer_mode=False) -> 'RCloneCommandBuilder':
pass
def downloadTo(self, source_file, d... | 9 | 1 | 25 | 3 | 21 | 1 | 3 | 0.05 | 0 | 7 | 1 | 0 | 8 | 4 | 8 | 8 | 206 | 32 | 170 | 38 | 142 | 9 | 77 | 19 | 68 | 9 | 0 | 1 | 20 |
328,351 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RCloneConfig.py | prefect_managedfiletransfer.RCloneConfig.RCloneConfig | class RCloneConfig:
def __init__(self, remote_name: str):
self.remote_name = remote_name
self._config_contents: str
def get_config(self):
return self._config_contents
async def update_config(self, config_contents: str):
self._config_contents = config_contents | class RCloneConfig:
def __init__(self, remote_name: str):
pass
def get_config(self):
pass
async def update_config(self, config_contents: str):
pass | 4 | 0 | 2 | 0 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 3 | 2 | 3 | 3 | 10 | 2 | 8 | 6 | 4 | 0 | 8 | 6 | 4 | 1 | 0 | 0 | 3 |
328,352 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RCloneConfigFileBlock.py | prefect_managedfiletransfer.RCloneConfigFileBlock.RCloneConfigFileBlock | from pydantic import Field
from prefect.blocks.core import Block
class RCloneConfigFileBlock(Block):
"""
Block for storing RClone configuration file contents.
This block is used to store the contents of an RClone configuration file, which can be used to configure RClone for file transfers.
The block is... |
class RCloneConfigFileBlock(Block):
'''
Block for storing RClone configuration file contents.
This block is used to store the contents of an RClone configuration file, which can be used to configure RClone for file transfers.
The block is updated with tokends when they are refreshed, allowing for dynam... | 3 | 2 | 16 | 1 | 12 | 3 | 1 | 1.32 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 65 | 8 | 25 | 9 | 22 | 33 | 9 | 8 | 7 | 1 | 1 | 0 | 1 |
328,353 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RCloneConfigSavedInPrefect.py | prefect_managedfiletransfer.RCloneConfigSavedInPrefect.RCloneConfigSavedInPrefect | from prefect_managedfiletransfer import RCloneConfigFileBlock
from prefect_managedfiletransfer.RCloneConfig import RCloneConfig
class RCloneConfigSavedInPrefect(RCloneConfig):
"""
RCloneDynamicConfig that uses a Prefect block to store the rclone config file contents. Is saved after sucessful uploads to update ... |
class RCloneConfigSavedInPrefect(RCloneConfig):
'''
RCloneDynamicConfig that uses a Prefect block to store the rclone config file contents. Is saved after sucessful uploads to update the token when it is refreshed
'''
def __init__(self, block: RCloneConfigFileBlock):
pass
def get_config(s... | 4 | 1 | 3 | 0 | 3 | 0 | 1 | 0.33 | 1 | 1 | 0 | 0 | 3 | 2 | 3 | 6 | 15 | 3 | 9 | 6 | 5 | 3 | 9 | 6 | 5 | 1 | 1 | 0 | 3 |
328,354 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RemoteAsset.py | prefect_managedfiletransfer.RemoteAsset.RemoteAsset | from datetime import datetime
from pathlib import Path
class RemoteAsset:
"""
Represents a remote asset with its path and last modified time.
"""
def __init__(self, path: Path, last_modified: datetime, size: int | None=None):
self.path: Path = path
self.last_modified: datetime = last_m... |
class RemoteAsset:
'''
Represents a remote asset with its path and last modified time.
'''
def __init__(self, path: Path, last_modified: datetime, size: int | None=None):
pass
def __repr__(self):
pass | 3 | 1 | 3 | 0 | 3 | 0 | 1 | 0.43 | 0 | 3 | 0 | 0 | 2 | 3 | 2 | 2 | 12 | 2 | 7 | 6 | 4 | 3 | 7 | 6 | 4 | 1 | 0 | 0 | 2 |
328,355 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/RemoteConnectionType.py | prefect_managedfiletransfer.RemoteConnectionType.RemoteConnectionType | from enum import Enum
class RemoteConnectionType(Enum):
LOCAL = 'local'
SFTP = 'sftp'
RCLONE = 'rclone' |
class RemoteConnectionType(Enum):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 49 | 4 | 0 | 4 | 4 | 3 | 0 | 4 | 4 | 3 | 0 | 4 | 0 | 0 |
328,356 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/ServerWithBasicAuthBlock.py | prefect_managedfiletransfer.ServerWithBasicAuthBlock.ServerWithBasicAuthBlock | from prefect_managedfiletransfer.constants import CONSTANTS
from pydantic import Field, SecretStr
from prefect.blocks.core import Block
from typing import Optional
class ServerWithBasicAuthBlock(Block):
"""
A connection to a remote server with basic authentication.
Attributes:
username (str): The ... |
class ServerWithBasicAuthBlock(Block):
'''
A connection to a remote server with basic authentication.
Attributes:
username (str): The username for authentication.
password (SecretStr): The password for authentication.
host (str): The host of the server.
port (int): The port ... | 4 | 3 | 10 | 0 | 8 | 2 | 1 | 0.58 | 1 | 2 | 0 | 0 | 1 | 0 | 2 | 2 | 57 | 6 | 33 | 12 | 29 | 19 | 13 | 11 | 10 | 1 | 1 | 0 | 2 |
328,357 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/ServerWithPublicKeyAuthBlock.py | prefect_managedfiletransfer.ServerWithPublicKeyAuthBlock.ServerWithPublicKeyAuthBlock | from pydantic import Field
from pydantic import SecretStr
from prefect.blocks.core import Block
from prefect_managedfiletransfer.constants import CONSTANTS
class ServerWithPublicKeyAuthBlock(Block):
"""
Block for storing SFTP server details with public key authentication.
Attributes:
username: The ... |
class ServerWithPublicKeyAuthBlock(Block):
'''
Block for storing SFTP server details with public key authentication.
Attributes:
username: The username for SFTP authentication.
private_key: The private key for SFTP authentication, stored as a SecretStr.
host: The hostname or IP addr... | 5 | 4 | 9 | 0 | 6 | 3 | 1 | 0.94 | 1 | 3 | 1 | 0 | 2 | 0 | 3 | 3 | 72 | 7 | 34 | 13 | 29 | 32 | 15 | 12 | 11 | 1 | 1 | 0 | 3 |
328,358 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/ServerWithPublicKeyAuthBlock.py | prefect_managedfiletransfer.ServerWithPublicKeyAuthBlock._TemporaryKeyFile | import tempfile
import logging
from pydantic import SecretStr
from pathlib import Path
class _TemporaryKeyFile:
def __init__(self, private_key: SecretStr):
self.private_key = private_key
self._tempfile = None
def __enter__(self):
self._tempfile = tempfile.NamedTemporaryFile('w')
... |
class _TemporaryKeyFile:
def __init__(self, private_key: SecretStr):
pass
def __enter__(self):
pass
def __exit__(self, exc, value, tb):
pass
def close(self):
pass
def get_path(self):
pass | 6 | 0 | 5 | 0 | 4 | 0 | 1 | 0 | 0 | 3 | 0 | 0 | 5 | 2 | 5 | 5 | 28 | 6 | 22 | 9 | 16 | 0 | 22 | 9 | 16 | 2 | 0 | 1 | 7 |
328,359 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/SortFilesBy.py | prefect_managedfiletransfer.SortFilesBy.SortFilesBy | from enum import Enum
class SortFilesBy(Enum):
PATH_ASC = 'path_asc'
PATH_DESC = 'path_desc'
SIZE_ASC = 'size_asc'
SIZE_DESC = 'size_desc'
DATE_ASC = 'date_asc'
DATE_DESC = 'date_desc'
def get_sort_by_lambda_tuple(self) -> tuple:
"""
Returns a tuple of (lambda function, rev... |
class SortFilesBy(Enum):
def get_sort_by_lambda_tuple(self) -> tuple:
'''
Returns a tuple of (lambda function, reverse boolean) for sorting.
The lambda function is used to extract the attribute to sort by,
and the boolean indicates whether to sort in reverse order.
'''
... | 2 | 1 | 15 | 0 | 10 | 5 | 1 | 0.29 | 1 | 1 | 0 | 0 | 1 | 0 | 1 | 50 | 23 | 1 | 17 | 9 | 15 | 5 | 10 | 9 | 8 | 1 | 4 | 0 | 1 |
328,360 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/TransferType.py | prefect_managedfiletransfer.TransferType.TransferType | from enum import Enum
class TransferType(str, Enum):
Copy = 'COPY'
Move = 'MOVE' |
class TransferType(str, Enum):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 115 | 3 | 0 | 3 | 3 | 2 | 0 | 3 | 3 | 2 | 0 | 4 | 0 | 0 |
328,361 | ImperialCollegeLondon/prefect-managedfiletransfer | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/ImperialCollegeLondon_prefect-managedfiletransfer/prefect_managedfiletransfer/constants.py | prefect_managedfiletransfer.constants.CONSTANTS | class CONSTANTS:
SKIPPED_STATE_NAME = 'Skipped'
SERVER_LOGO_URL = 'https://cdn.sanity.io/images/3ugk85nk/production/fb3f4debabcda1c5a3aeea4f5b3f94c28845e23e-250x250.png'
ONE_GIGABYTE = 1024 * 1024 * 1024
class ENV_VAR_NAMES:
PMFTUPLOAD_USERNAME = 'PMFTUPLOAD_USERNAME'
PMFTUPLOAD_PASSWOR... | null | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 18 | 3 | 15 | 15 | 11 | 0 | 15 | 15 | 11 | 0 | 0 | 0 | 0 |
328,362 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/interface.py | gloria.interface.Gloria | from matplotlib.dates import AutoDateFormatter, AutoDateLocator
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
from gloria.utilities.constants import _DELIM, _DTYPE_KIND, _FIT_DEFAULTS, _GLORIA_DEFAULTS, _LOAD_DATA_DEFAULTS, _PREDICT_DEFAULTS, _T_INT
import numpy as np
from gloria.utilit... |
class Gloria(BaseModel):
'''
The Gloria forecaster object is the central hub for the entire modeling
workflow.
Gloria objects are initialized with parameters controlling the fit and
prediction behaviour. Features such as ``seasonalities``, ``external
regressors``, and ``events`` (or collection ... | 37 | 27 | 77 | 9 | 35 | 32 | 5 | 0.95 | 1 | 28 | 9 | 0 | 21 | 14 | 27 | 109 | 2,219 | 280 | 999 | 249 | 857 | 949 | 464 | 136 | 433 | 17 | 5 | 4 | 128 |
328,363 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Beta | from typing_extensions import Self, TypeAlias
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
import numpy as np
class Beta(ModelBackendBase):
"""
Implementation of model backend for beta distribution
... |
class Beta(ModelBackendBase):
'''
Implementation of model backend for beta distribution
'''
def quant_func(self: Self, level: float, yhat: np.ndarray, scale: float=1, **kwargs: Any) -> np.ndarray:
'''
Quantile function of the underlying distribution
Parameters
---------... | 3 | 3 | 36 | 6 | 11 | 20 | 1 | 1.88 | 1 | 5 | 2 | 0 | 2 | 2 | 2 | 36 | 85 | 14 | 25 | 18 | 14 | 47 | 15 | 10 | 12 | 1 | 5 | 0 | 2 |
328,364 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.BetaBinomial | import numpy as np
from typing_extensions import Self, TypeAlias
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
class BetaBinomial(ModelBackendBase):
"""
Implementation of model backend for beta-binomi... |
class BetaBinomial(ModelBackendBase):
'''
Implementation of model backend for beta-binomial distribution
'''
def yhat_func(self: Self, linked_arg: np.ndarray, scale: float=1, capacity_vec: Optional[np.ndarray]=None, **kwargs: Any) -> np.ndarray:
'''
Produces the predicted values yhat
... | 4 | 4 | 51 | 7 | 20 | 25 | 2 | 1.26 | 1 | 9 | 3 | 0 | 3 | 2 | 3 | 37 | 169 | 24 | 65 | 37 | 40 | 82 | 26 | 16 | 22 | 3 | 5 | 1 | 7 |
328,365 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Binomial | import numpy as np
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from typing_extensions import Self, TypeAlias
class Binomial(ModelBackendBase):
"""
Implementation of model backend for binomial distri... |
class Binomial(ModelBackendBase):
'''
Implementation of model backend for binomial distribution
'''
def yhat_func(self: Self, linked_arg: np.ndarray, capacity_vec: Optional[np.ndarray]=None, **kwargs: Any) -> np.ndarray:
'''
Produces the predicted values yhat
Parameters
... | 4 | 4 | 45 | 5 | 17 | 23 | 2 | 1.4 | 1 | 9 | 3 | 0 | 3 | 2 | 3 | 37 | 149 | 19 | 55 | 31 | 32 | 77 | 19 | 12 | 15 | 2 | 5 | 1 | 6 |
328,366 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.BinomialCapacity | from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
class BinomialCapacity(BaseModel):
"""
Configuration parameters used by the augment_data method of the model
BinomialConstantN and BetaBinomialC... |
class BinomialCapacity(BaseModel):
'''
Configuration parameters used by the augment_data method of the model
BinomialConstantN and BetaBinomialConstantN to determine the capacity
size.
'''
@field_validator('value')
@classmethod
def validate_value(cls, value: Union[int, float], info) -> ... | 6 | 2 | 28 | 1 | 24 | 3 | 6 | 0.19 | 1 | 3 | 0 | 0 | 0 | 0 | 2 | 84 | 69 | 5 | 54 | 10 | 46 | 10 | 26 | 6 | 23 | 8 | 5 | 2 | 12 |
328,367 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Gamma | import numpy as np
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
from typing_extensions import Self, TypeAlias
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
class Gamma(ModelBackendBase):
"""
Implementation of model backend for gamma distribution... |
class Gamma(ModelBackendBase):
'''
Implementation of model backend for gamma distribution
'''
def quant_func(self: Self, level: float, yhat: np.ndarray, scale: float=1, **kwargs: Any) -> np.ndarray:
'''
Quantile function of the underlying distribution
Parameters
-------... | 3 | 3 | 33 | 6 | 10 | 18 | 1 | 1.91 | 1 | 5 | 2 | 0 | 2 | 2 | 2 | 36 | 80 | 14 | 23 | 16 | 12 | 44 | 13 | 8 | 10 | 1 | 5 | 0 | 2 |
328,368 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.LinkPair | from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
import numpy as np
from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
class LinkPair(BaseModel):
"""
Link function pairs connection the expectation value to Stan's GLM
predictors
link = tran... |
class LinkPair(BaseModel):
'''
Link function pairs connection the expectation value to Stan's GLM
predictors
link = transforming expectation value to predictor
inverse = transforming predictor to expectation value
'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 82 | 11 | 2 | 3 | 1 | 2 | 6 | 3 | 1 | 2 | 0 | 5 | 0 | 0 |
328,369 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.ModelBackendBase | from pathlib import Path
from scipy.optimize import minimize
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from gloria.utilities.errors import NotFittedError
from gloria.utilities.logging import get_logger
import logging
from scipy.stats import beta, betabinom, binom, gamma, nbinom, no... |
class ModelBackendBase(ABC):
'''
Abstract base clase for the model backend.
The model backend is in charge of passing data and model parameters to the
stan code as well as distribution model dependent prediction
'''
def yhat_func(self: Self, linked_arg: np.ndarray, **kwargs: Any) -> np.ndarray... | 17 | 16 | 57 | 6 | 26 | 26 | 2 | 1.02 | 1 | 15 | 4 | 7 | 14 | 9 | 14 | 34 | 866 | 111 | 379 | 164 | 309 | 388 | 200 | 110 | 184 | 9 | 4 | 2 | 37 |
328,370 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.ModelInputData | import numpy as np
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
class ModelInputData(BaseModel):
"""
A container for... |
class ModelInputData(BaseModel):
'''
A container for the input data of each model. Additional model-dependent
parameters have to be added within the model
'''
@field_validator('S')
@classmethod
def validate_S(cls, S: int, info: ValidationInfo) -> int:
pass
@field_validator('y')
... | 19 | 1 | 10 | 0 | 10 | 0 | 3 | 0.22 | 1 | 3 | 0 | 0 | 0 | 0 | 6 | 88 | 104 | 8 | 88 | 36 | 59 | 19 | 54 | 20 | 47 | 5 | 5 | 1 | 20 |
328,371 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.ModelParams | from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
import numpy as np
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
class ModelParams(BaseModel):
"""
A container for the fitting parameter of each model. Additional model-
dependent parameters ha... |
class ModelParams(BaseModel):
'''
A container for the fitting parameter of each model. Additional model-
dependent parameters have to be added within the model
'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1.11 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 82 | 17 | 2 | 9 | 6 | 8 | 10 | 6 | 6 | 5 | 0 | 5 | 0 | 0 |
328,372 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.NegativeBinomial | import numpy as np
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from typing_extensions import Self, TypeAlias
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
class NegativeBinomial(ModelBackendBase):
"""
Implementation of model backend for negativ... |
class NegativeBinomial(ModelBackendBase):
'''
Implementation of model backend for negative binomial distribution
'''
def quant_func(self: Self, level: float, yhat: np.ndarray, scale: float=1, **kwargs: Any) -> np.ndarray:
'''
Quantile function of the underlying distribution
Par... | 3 | 3 | 35 | 6 | 10 | 20 | 1 | 1.96 | 1 | 5 | 2 | 0 | 2 | 2 | 2 | 36 | 84 | 14 | 24 | 17 | 13 | 47 | 14 | 9 | 11 | 1 | 5 | 0 | 2 |
328,373 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Normal | import numpy as np
from typing_extensions import Self, TypeAlias
from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
class Normal(ModelBackendBase):
"""
Implementation of model backend for normal distributi... |
class Normal(ModelBackendBase):
'''
Implementation of model backend for normal distribution
'''
def quant_func(self: Self, level: float, yhat: np.ndarray, scale: float=1, **kwargs: Any) -> np.ndarray:
'''
Quantile function of the underlying distribution
Parameters
-----... | 3 | 3 | 34 | 6 | 10 | 18 | 1 | 1.83 | 1 | 5 | 2 | 0 | 2 | 2 | 2 | 36 | 82 | 15 | 24 | 17 | 13 | 44 | 14 | 9 | 11 | 1 | 5 | 0 | 2 |
328,374 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Poisson | from scipy.stats import beta, betabinom, binom, gamma, nbinom, norm, poisson
import numpy as np
from typing import Any, Callable, Literal, Mapping, Optional, Type, Union, cast
from typing_extensions import Self, TypeAlias
class Poisson(ModelBackendBase):
"""
Implementation of model backend for poisson distribu... |
class Poisson(ModelBackendBase):
'''
Implementation of model backend for poisson distribution
'''
def quant_func(self: Self, level: float, yhat: np.ndarray, **kwargs: Any) -> np.ndarray:
'''
Quantile function of the underlying distribution
Parameters
----------
... | 3 | 3 | 31 | 6 | 8 | 18 | 1 | 2.32 | 1 | 5 | 2 | 0 | 2 | 2 | 2 | 36 | 76 | 14 | 19 | 12 | 12 | 44 | 13 | 8 | 10 | 1 | 5 | 0 | 2 |
328,375 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/models.py | gloria.models.Uncertainty | import numpy as np
from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
class Uncertainty(BaseModel):
"""
Small container class for holding trend uncertainties
"""
model_config = ConfigDict(arbitrary_types_allowed=True)
lower: np.ndarray
upper: np.ndarray |
class Uncertainty(BaseModel):
'''
Small container class for holding trend uncertainties
'''
pass | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0.67 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 82 | 12 | 2 | 6 | 2 | 5 | 4 | 4 | 2 | 3 | 0 | 5 | 0 | 0 |
328,376 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/profiles.py | gloria.profiles.BoxCar | from typing_extensions import Self
from typing import Any, Type
import pandas as pd
from gloria.utilities.types import Timedelta
class BoxCar(Profile):
"""
A BoxCar shaped profile.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \\left\\{
\\begin{array}... |
class BoxCar(Profile):
'''
A BoxCar shaped profile.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \left\{
\begin{array}{ll}
1 & t_0 \le t < t_0 + w \\
0 & \text{otherwise}
\end{array}
\right.
with ... | 5 | 4 | 19 | 2 | 4 | 13 | 1 | 4.47 | 1 | 5 | 0 | 0 | 2 | 0 | 3 | 90 | 98 | 16 | 15 | 9 | 8 | 67 | 12 | 6 | 8 | 1 | 6 | 0 | 3 |
328,377 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/profiles.py | gloria.profiles.Cauchy | from gloria.utilities.types import Timedelta
import pandas as pd
from typing_extensions import Self
from typing import Any, Type
class Cauchy(Profile):
"""
A Cauchy shaped profile.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \\frac{1}{4\\cdot \\left(t-t_0 \\rig... |
class Cauchy(Profile):
'''
A Cauchy shaped profile.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \frac{1}{4\cdot \left(t-t_0 \right)^2 / w^2 + 1}
with ``width=w`` being a constructor parameter as well as ``t_anchor=t_0``
the input of :meth:`~gloria.Cauchy... | 5 | 4 | 20 | 2 | 4 | 14 | 1 | 3.93 | 1 | 5 | 0 | 0 | 2 | 0 | 3 | 90 | 92 | 18 | 15 | 9 | 8 | 59 | 12 | 6 | 8 | 1 | 6 | 0 | 3 |
328,378 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/profiles.py | gloria.profiles.Exponential | from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
from gloria.utilities.types import Timedelta
from typing import Any, Type
from typing_extensions import Self
import pandas as pd
import numpy as np
class Exponential(Profile):
"""
A two-sided exponential decay shaped profile.
... |
class Exponential(Profile):
'''
A two-sided exponential decay shaped profile.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \exp\left(
-\log 2 \left|\frac{t-t_0}{w\left(t\right)}\right|
\right).
Here, :math:`w\left(t\right) = w_\text{lead}` ... | 11 | 6 | 25 | 3 | 11 | 11 | 2 | 1.3 | 1 | 7 | 0 | 0 | 2 | 0 | 5 | 92 | 172 | 27 | 63 | 26 | 41 | 82 | 39 | 15 | 30 | 3 | 6 | 1 | 10 |
328,379 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/profiles.py | gloria.profiles.Gaussian | from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
from typing import Any, Type
import numpy as np
from typing_extensions import Self
import pandas as pd
from gloria.utilities.types import Timedelta
class Gaussian(Profile):
"""
A Gaussian shaped profile with ``order`` parameter ... |
class Gaussian(Profile):
'''
A Gaussian shaped profile with ``order`` parameter for generating flat-top
Gaussians.
For a given time :math:`t` the profile can be described by
.. math::
f(t) = \exp\left(-\left(
\frac{\left(t-t_0\right)^2}{2\sigma^2}
\right)^n\right)
w... | 5 | 4 | 21 | 3 | 4 | 14 | 1 | 4 | 1 | 5 | 0 | 0 | 2 | 0 | 3 | 90 | 104 | 19 | 17 | 10 | 10 | 68 | 14 | 7 | 10 | 1 | 6 | 0 | 3 |
328,380 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/profiles.py | gloria.profiles.Profile | from typing import Any, Type
import pandas as pd
from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator
from typing_extensions import Self
from abc import ABC, abstractmethod
class Profile(BaseModel, ABC):
"""
Abstract base class for all profiles
"""
model_config = ConfigDic... |
class Profile(BaseModel, ABC):
'''
Abstract base class for all profiles
'''
@property
def _profile_type(self: Self):
'''
Returns name of the profile class.
'''
pass
@abstractmethod
def generate(self: Self, timestamps: pd.Series, t_anchor: pd.Timestamp) ->... | 11 | 6 | 17 | 1 | 5 | 10 | 1 | 1.57 | 2 | 6 | 0 | 4 | 3 | 0 | 5 | 87 | 103 | 13 | 35 | 20 | 20 | 55 | 17 | 11 | 11 | 2 | 5 | 1 | 6 |
328,381 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/protocols/calendric.py | gloria.protocols.calendric.CalendricData | from gloria.utilities.misc import infer_sampling_period
import numpy as np
from gloria.profiles import BoxCar, Profile
from gloria.utilities.constants import _HOLIDAY
from gloria.utilities.logging import get_logger
from typing_extensions import Self
from gloria.protocols.protocol_base import Protocol
from typing import... |
class CalendricData(Protocol):
'''
Manage calendar-driven seasonal cycles and public-holiday effects for a
:class:`Gloria` forecaster.
The protocol contributes:
* **Seasonalities** - yearly, quarterly, monthly, weekly, and daily terms.
* **Holidays** - :class:`Holiday` event regressors for ever... | 12 | 7 | 43 | 4 | 21 | 18 | 4 | 1.22 | 1 | 11 | 1 | 0 | 3 | 0 | 6 | 94 | 365 | 45 | 144 | 46 | 122 | 176 | 74 | 32 | 67 | 10 | 6 | 3 | 24 |
328,382 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/protocols/calendric.py | gloria.protocols.calendric.Holiday | from gloria.utilities.constants import _HOLIDAY
import pandas as pd
from gloria.profiles import BoxCar, Profile
from typing_extensions import Self
from gloria.regressors import IntermittentEvent
from typing import TYPE_CHECKING, Any, Optional, Type, Union, cast
class Holiday(IntermittentEvent):
"""
A regressor... |
class Holiday(IntermittentEvent):
'''
A regressor to model events coinciding with public holidays.
The regressor is added to the :class:`Gloria` model either using
:meth:`~Gloria.add_event` or by adding the :class:`CalendricData` protocoll
via :meth:`Gloria.add_protocol` and does not need to be han... | 7 | 6 | 27 | 3 | 7 | 16 | 1 | 2.95 | 1 | 9 | 1 | 0 | 4 | 1 | 5 | 98 | 184 | 26 | 40 | 17 | 31 | 118 | 28 | 14 | 22 | 2 | 8 | 1 | 6 |
328,383 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/protocols/protocol_base.py | gloria.protocols.protocol_base.Protocol | from abc import ABC, abstractmethod
import pandas as pd
from typing import TYPE_CHECKING, Any, Type
from pydantic import BaseModel, ConfigDict
from typing_extensions import Self
class Protocol(ABC, BaseModel):
"""
Protocols can be added to Gloria models in order to configure them based
on the type of data ... |
class Protocol(ABC, BaseModel):
'''
Protocols can be added to Gloria models in order to configure them based
on the type of data that the model is supposed to fit.
This abstract base class defines the Protocol interface and some basic
functionalities
'''
@property
def _protocol_type(sel... | 13 | 7 | 17 | 2 | 5 | 10 | 1 | 1.69 | 2 | 6 | 0 | 1 | 4 | 0 | 6 | 88 | 123 | 18 | 39 | 22 | 22 | 66 | 19 | 12 | 12 | 2 | 5 | 1 | 7 |
328,384 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.EventRegressor | import pandas as pd
from typing import Any, Optional, Type
from typing_extensions import Self
from abc import ABC, abstractmethod
from gloria.profiles import Profile
class EventRegressor(Regressor):
"""
A base class used to create a regressor based on an event
"""
profile: Profile
def to_dict(self... |
class EventRegressor(Regressor):
'''
A base class used to create a regressor based on an event
'''
def to_dict(self: Self) -> dict[str, Any]:
'''
Converts the EventRegressor to a serializable dictionary.
Returns
-------
dict[str, Any]
Dictionary ... | 4 | 3 | 10 | 1 | 3 | 6 | 1 | 1.78 | 1 | 6 | 0 | 2 | 2 | 0 | 2 | 89 | 29 | 4 | 9 | 5 | 5 | 16 | 8 | 4 | 5 | 1 | 6 | 0 | 2 |
328,385 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.ExternalRegressor | import pandas as pd
from typing import Any, Optional, Type
from gloria.utilities.constants import _DELIM
from typing_extensions import Self
class ExternalRegressor(Regressor):
"""
A regressor based on user-provided data.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_exte... |
class ExternalRegressor(Regressor):
'''
A regressor based on user-provided data.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_external_regressor` and does not need to be handled
directly by the user. Instead of synthesizing the regressor data, they must
be provid... | 4 | 3 | 29 | 4 | 8 | 17 | 2 | 2.72 | 1 | 7 | 0 | 0 | 1 | 0 | 2 | 89 | 78 | 11 | 18 | 9 | 12 | 49 | 12 | 6 | 9 | 3 | 6 | 1 | 4 |
328,386 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.IntermittentEvent | from gloria.profiles import Profile
from typing_extensions import Self
from typing import Any, Optional, Type
from gloria.utilities.types import Timestamp
from gloria.utilities.constants import _DELIM
import pandas as pd
class IntermittentEvent(EventRegressor):
"""
A regressor to model reoccuring events at giv... |
class IntermittentEvent(EventRegressor):
'''
A regressor to model reoccuring events at given times.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_event` and does not need to be handled
directly by the user.
Parameters
----------
name : str
A descri... | 6 | 5 | 30 | 4 | 10 | 17 | 2 | 2.1 | 1 | 11 | 1 | 1 | 3 | 0 | 4 | 93 | 154 | 24 | 42 | 17 | 34 | 88 | 29 | 13 | 24 | 3 | 7 | 2 | 8 |
328,387 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.PeriodicEvent | from typing_extensions import Self
from gloria.utilities.constants import _DELIM
import pandas as pd
from gloria.profiles import Profile
from typing import Any, Optional, Type
class PeriodicEvent(SingleEvent):
"""
A regressor to model periodically recurring events.
The regressor is added to the :class:`Gl... |
class PeriodicEvent(SingleEvent):
'''
A regressor to model periodically recurring events.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_event` and does not need to be handled
directly by the user.
Parameters
----------
name : str
A descriptive, uni... | 7 | 6 | 29 | 4 | 8 | 16 | 1 | 2.43 | 1 | 10 | 1 | 0 | 4 | 0 | 5 | 98 | 181 | 30 | 44 | 22 | 35 | 107 | 34 | 19 | 28 | 2 | 8 | 1 | 7 |
328,388 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.Regressor | from typing import Any, Optional, Type
from typing_extensions import Self
from abc import ABC, abstractmethod
import pandas as pd
from pydantic import BaseModel, ConfigDict, Field
class Regressor(BaseModel, ABC):
"""
Base class for adding regressors to the Gloria model and creating the
respective feature m... |
class Regressor(BaseModel, ABC):
'''
Base class for adding regressors to the Gloria model and creating the
respective feature matrix
Parameters
----------
name : str
A descriptive, unique name to identify the regressor
prior_scale : float
Parameter modulating the strength of... | 11 | 6 | 19 | 2 | 6 | 11 | 1 | 1.79 | 2 | 7 | 0 | 3 | 3 | 0 | 5 | 87 | 127 | 18 | 39 | 21 | 24 | 70 | 20 | 12 | 14 | 2 | 5 | 1 | 6 |
328,389 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.Seasonality | import pandas as pd
from itertools import product
from pydantic import BaseModel, ConfigDict, Field
from gloria.utilities.constants import _DELIM
import numpy as np
from typing import Any, Optional, Type
from typing_extensions import Self
class Seasonality(Regressor):
"""
A regressor to model seasonality featu... |
class Seasonality(Regressor):
'''
A regressor to model seasonality features from Fourier components.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_seasonality` and does not need to be handled
directly by the user. The feature matrix produced by
:meth:`~Seasonality... | 7 | 5 | 33 | 4 | 9 | 20 | 1 | 3.02 | 1 | 11 | 0 | 0 | 2 | 0 | 4 | 91 | 190 | 29 | 40 | 21 | 29 | 121 | 21 | 15 | 16 | 1 | 6 | 0 | 4 |
328,390 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/regressors.py | gloria.regressors.SingleEvent | from typing_extensions import Self
from gloria.profiles import Profile
from gloria.utilities.types import Timestamp
import pandas as pd
from gloria.utilities.constants import _DELIM
from typing import Any, Optional, Type
class SingleEvent(EventRegressor):
"""
A regressor to model a single occurrence of an even... |
class SingleEvent(EventRegressor):
'''
A regressor to model a single occurrence of an event.
The regressor is added to the :class:`Gloria` model using
:meth:`~Gloria.add_event` and does not need to be handled
directly by the user.
Parameters
----------
name : str
A descriptive, ... | 6 | 5 | 23 | 3 | 6 | 15 | 1 | 3.08 | 1 | 8 | 1 | 1 | 3 | 0 | 4 | 93 | 125 | 19 | 26 | 13 | 18 | 80 | 18 | 10 | 13 | 1 | 7 | 0 | 4 |
328,391 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/constants.py | gloria.utilities.constants.FitDefaults | from typing import Literal, Optional, TypedDict
class FitDefaults(TypedDict):
optimize_mode: Literal['MAP', 'MLE']
use_laplace: bool
capacity: Optional[int]
capacity_mode: Optional[str]
capacity_value: Optional[float] |
class FitDefaults(TypedDict):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 6 | 1 | 5 | 0 | 6 | 1 | 5 | 0 | 1 | 0 | 0 |
328,392 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/constants.py | gloria.utilities.constants.LoadDataDefaults | from typing import Literal, Optional, TypedDict
from gloria.utilities.types import DTypeKind
class LoadDataDefaults(TypedDict):
source: str
dtype_kind: DTypeKind |
class LoadDataDefaults(TypedDict):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 3 | 1 | 2 | 0 | 3 | 1 | 2 | 0 | 1 | 0 | 0 |
328,393 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/constants.py | gloria.utilities.constants.PredictDefaults | from typing import Literal, Optional, TypedDict
class PredictDefaults(TypedDict):
periods: int
include_history: bool |
class PredictDefaults(TypedDict):
pass | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 3 | 1 | 2 | 0 | 3 | 1 | 2 | 0 | 1 | 0 | 0 |
328,394 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/errors.py | gloria.utilities.errors.FittedError | from typing_extensions import Self
from typing import Optional
class FittedError(RuntimeError):
"""
Raised when an operation expects an unfitted Gloria instance but got a
fitted one.
"""
def __init__(self: Self, message: Optional[str]=None) -> None:
if message is None:
message ... |
class FittedError(RuntimeError):
'''
Raised when an operation expects an unfitted Gloria instance but got a
fitted one.
'''
def __init__(self: Self, message: Optional[str]=None) -> None:
pass | 2 | 1 | 4 | 0 | 4 | 0 | 2 | 0.8 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 10 | 1 | 5 | 2 | 3 | 4 | 5 | 2 | 3 | 2 | 4 | 1 | 2 |
328,395 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/errors.py | gloria.utilities.errors.NotFittedError | from typing import Optional
from typing_extensions import Self
class NotFittedError(RuntimeError):
"""
Raised when an operation expects a fitted Gloria instance but got an
unfitted one.
"""
def __init__(self: Self, message: Optional[str]=None) -> None:
if message is None:
messa... |
class NotFittedError(RuntimeError):
'''
Raised when an operation expects a fitted Gloria instance but got an
unfitted one.
'''
def __init__(self: Self, message: Optional[str]=None) -> None:
pass | 2 | 1 | 4 | 0 | 4 | 0 | 2 | 0.8 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 12 | 10 | 1 | 5 | 2 | 3 | 4 | 5 | 2 | 3 | 2 | 4 | 1 | 2 |
328,396 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/gloria/utilities/logging.py | gloria.utilities.logging.LoggingConfig | from typing import Any, Callable, Union
from gloria.utilities.constants import _GLORIA_PATH, _RUN_TIMESTAMP
from pathlib import Path
from pydantic import BaseModel, ConfigDict, field_validator
from gloria.utilities.types import LogLevel
class LoggingConfig(BaseModel):
model_config = ConfigDict(validate_assignment=... |
class LoggingConfig(BaseModel):
@field_validator('log_path', mode='before')
@classmethod
def validate_log_path(cls, log_path: Union[Path, str]) -> Path:
pass | 4 | 0 | 8 | 0 | 8 | 0 | 2 | 0.06 | 1 | 4 | 0 | 0 | 0 | 0 | 1 | 83 | 21 | 2 | 18 | 9 | 14 | 1 | 12 | 7 | 10 | 2 | 5 | 1 | 2 |
328,397 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/setup.py | setup.BuildModels | import os
from setuptools.command.build_ext import build_ext
class BuildModels(build_ext):
"""Custom build command to pre-compile Stan models."""
def run(self) -> None:
if not self.dry_run:
target_dir = os.path.join(self.build_lib, MODEL_DIR)
self.mkpath(target_dir)
... |
class BuildModels(build_ext):
'''Custom build command to pre-compile Stan models.'''
def run(self) -> None:
pass | 2 | 1 | 5 | 0 | 5 | 0 | 2 | 0.17 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 70 | 8 | 1 | 6 | 3 | 4 | 1 | 6 | 3 | 4 | 2 | 3 | 1 | 2 |
328,398 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/setup.py | setup.CleanModels | import os
from distutils.command.clean import clean
class CleanModels(clean):
"""Custom clean command to remove pre-compile Stan models."""
def run(self) -> None:
if not self.dry_run:
target_dir = os.path.join(self.build_lib, MODEL_DIR)
clean_models(target_dir)
clea... |
class CleanModels(clean):
'''Custom clean command to remove pre-compile Stan models.'''
def run(self) -> None:
pass | 2 | 1 | 6 | 0 | 6 | 0 | 2 | 0.14 | 1 | 1 | 0 | 0 | 1 | 0 | 1 | 34 | 9 | 1 | 7 | 3 | 5 | 1 | 7 | 3 | 5 | 2 | 2 | 1 | 2 |
328,399 | e-dyn/gloria | /Users/umroot/Documents/PhD_works/PhD-Core-Contents/Class-level-dataset-curation/unseen_data/git_repos_for_analysis/e-dyn_gloria/setup.py | setup.WheelABINone | from wheel.bdist_wheel import bdist_wheel
from typing import Tuple
class WheelABINone(bdist_wheel):
def finalize_options(self) -> None:
bdist_wheel.finalize_options(self)
self.root_is_pure = False
def get_tag(self) -> Tuple[str, str, str]:
_, _, plat = bdist_wheel.get_tag(self)
... |
class WheelABINone(bdist_wheel):
def finalize_options(self) -> None:
pass
def get_tag(self) -> Tuple[str, str, str]:
pass | 3 | 0 | 3 | 0 | 3 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 2 | 1 | 2 | 11 | 8 | 1 | 7 | 5 | 4 | 0 | 7 | 5 | 4 | 1 | 2 | 0 | 2 |
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