Merge pull request #238 from AsadNizami/master

(#119) Wildcard imports removed
GazzolaLab · Apr 6, 2023 · 0ff189f · 0ff189f
2 parents bb0d16f + 530387b
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 <div align='center'>
 <h1> PyElastica </h1>
 
-[![Build_status][badge-travis]][link-travis] [![CI][badge-CI]][link-CI] [![Documentation Status][badge-docs-status]][link-docs-status] [![codecov][badge-codecov]][link-codecov] [![Downloads][badge-pepy-download-count]][link-pepy-download-count] [![Binder][badge-binder]][link-binder] [![Gitter][badge-gitter]][link-gitter]
+[![Build_status][badge-travis]][link-travis] [![CI][badge-CI]][link-CI] [![Documentation Status][badge-docs-status]][link-docs-status] [![codecov][badge-codecov]][link-codecov] [![Downloads][badge-pepy-download-count]][link-pepy-download-count] [![DOI][badge-doi]][link-doi] [![Binder][badge-binder]][link-binder] [![Gitter][badge-gitter]][link-gitter]
  </div>
 
 PyElastica is the python implementation of **Elastica**: an *open-source* project for simulating assemblies of slender, one-dimensional structures using Cosserat Rod theory.
@@ -26,12 +26,25 @@ Documentation of PyElastica is available [here][link-docs-website].
 We ask that any publications which use Elastica cite as following:
 
 ```
-@misc{tekinalp2022pyelastica,
-  title={PyElastica: A computational framework for Cosserat rod assemblies},
-  author={Tekinalp, Arman and Kim, Seung Hyun and Parthasarathy, Tejaswin and Bhosale, Yashraj},
-  journal={https://github.com/GazzolaLab/PyElastica},
-  year={2022},
-  publisher={GitHub}
+@software{arman_tekinalp_2023_7658872,
+  author       = {Arman Tekinalp and
+                  Seung Hyun Kim and
+                  Yashraj Bhosale and
+                  Tejaswin Parthasarathy and
+                  Noel Naughton and
+                  Maximilian Stölzle and
+                  Zhi Dou and
+                  Chia-Hsien (Cathy) Shih and
+                  Mattia Gazzola},
+  title        = {{PyElastica: Open-source software for the 
+                   simulation of assemblies of slender, one-
+                   dimensional structures using Cosserat Rod theory}},
+  month        = feb,
+  year         = 2023,
+  publisher    = {Zenodo},
+  version      = {v0.3.0.post1},
+  doi          = {10.5281/zenodo.7658872},
+  url          = {https://doi.org/10.5281/zenodo.7658872}
 }
 ```
 
@@ -91,6 +104,7 @@ _Names arranged alphabetically_
 [badge-pepy-download-count]: https://pepy.tech/badge/pyelastica
 [badge-codecov]: https://codecov.io/gh/GazzolaLab/PyElastica/branch/master/graph/badge.svg
 [badge-gitter]: https://badges.gitter.im/PyElastica/community.svg
+[badge-doi]: https://zenodo.org/badge/254172891.svg
 [link-pypi]: https://badge.fury.io/py/pyelastica
 [link-travis]: https://travis-ci.com/github/GazzolaLab/PyElastica
 [link-CI]: https://github.com/GazzolaLab/PyElastica/actions
@@ -101,3 +115,4 @@ _Names arranged alphabetically_
 [badge-binder-tutorial]: https://img.shields.io/badge/Launch-PyElastica%20Tutorials-579ACA.svg?logo=data:image/png;base64,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
 [link-binder]: https://mybinder.org/v2/gh/GazzolaLab/PyElastica/master?filepath=examples%2FBinder%2F0_PyElastica_Tutorials_Overview.ipynb
 [link-gitter]: https://gitter.im/PyElastica/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+[link-doi]: https://zenodo.org/badge/latestdoi/254172891
diff --git a/elastica/__init__.py b/elastica/__init__.py
@@ -1,15 +1,73 @@
 from collections import defaultdict
-from elastica.modules import *
-from elastica.rod.cosserat_rod import *
-from elastica.rod.knot_theory import *
-from elastica.rigidbody import *
-from elastica.boundary_conditions import *
-from elastica.external_forces import *
-from elastica.callback_functions import *
-from elastica.dissipation import *
-from elastica.interaction import *
-from elastica.joint import *
-from elastica.timestepper import *
-from elastica.restart import *
-from elastica.reset_functions_for_block_structure import *
-from elastica.typing import *
+from elastica.rod.knot_theory import KnotTheory, KnotTheoryCompatibleProtocol
+from elastica.rod.rod_base import RodBase
+from elastica.rod.cosserat_rod import CosseratRod
+from elastica.rigidbody.rigid_body import RigidBodyBase
+from elastica.rigidbody.cylinder import Cylinder
+from elastica.rigidbody.sphere import Sphere
+from elastica.boundary_conditions import (
+    ConstraintBase,
+    FreeBC,
+    OneEndFixedBC,
+    GeneralConstraint,
+    FixedConstraint,
+    HelicalBucklingBC,
+    FreeRod,
+    OneEndFixedRod,
+)
+from elastica.external_forces import (
+    NoForces,
+    EndpointForces,
+    GravityForces,
+    UniformForces,
+    UniformTorques,
+    MuscleTorques,
+    EndpointForcesSinusoidal,
+)
+from elastica.interaction import (
+    AnisotropicFrictionalPlane,
+    InteractionPlane,
+    SlenderBodyTheory,
+)
+from elastica.joint import (
+    FreeJoint,
+    ExternalContact,
+    FixedJoint,
+    HingeJoint,
+    SelfContact,
+)
+from elastica.callback_functions import CallBackBaseClass, ExportCallBack, MyCallBack
+from elastica.dissipation import (
+    DamperBase,
+    AnalyticalLinearDamper,
+    LaplaceDissipationFilter,
+)
+from elastica.modules.base_system import BaseSystemCollection
+from elastica.modules.callbacks import CallBacks
+from elastica.modules.connections import Connections
+from elastica.modules.constraints import Constraints
+from elastica.modules.forcing import Forcing
+from elastica.modules.damping import Damping
+from elastica.transformations import inv_skew_symmetrize
+from elastica.transformations import rotate
+from elastica._calculus import (
+    position_difference_kernel,
+    position_average,
+    quadrature_kernel,
+    difference_kernel,
+    quadrature_kernel_for_block_structure,
+    difference_kernel_for_block_structure,
+)
+from elastica._linalg import levi_civita_tensor
+from elastica.utils import isqrt
+from elastica.typing import RodType, SystemType
+from elastica.timestepper import (
+    integrate,
+    PositionVerlet,
+    PEFRL,
+    RungeKutta4,
+    EulerForward,
+    extend_stepper_interface,
+)
+from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody
+from elastica.memory_block.memory_block_rod import MemoryBlockCosseratRod
diff --git a/elastica/boundary_conditions.py b/elastica/boundary_conditions.py
@@ -1,12 +1,4 @@
 __doc__ = """ Built-in boundary condition implementationss """
-__all__ = [
-    "ConstraintBase",
-    "FreeBC",
-    "OneEndFixedBC",
-    "GeneralConstraint",
-    "FixedConstraint",
-    "HelicalBucklingBC",
-]
 
 import warnings
 from typing import Optional

diff --git a/elastica/callback_functions.py b/elastica/callback_functions.py
@@ -1,5 +1,4 @@
 __doc__ = """ Module contains callback classes to save simulation data for rod-like objects """
-__all__ = ["CallBackBaseClass", "MyCallBack", "ExportCallBack"]
 
 import os
 import sys

diff --git a/elastica/dissipation.py b/elastica/dissipation.py
@@ -3,11 +3,7 @@
 
 Built in damper module implementations
 """
-__all__ = [
-    "DamperBase",
-    "AnalyticalLinearDamper",
-    "LaplaceDissipationFilter",
-]
+
 from abc import ABC, abstractmethod
 
 from elastica.typing import RodType, SystemType

diff --git a/elastica/experimental/connection_contact_joint/generic_system_type_connection.py b/elastica/experimental/connection_contact_joint/generic_system_type_connection.py
@@ -1,7 +1,6 @@
 __doc__ = (
     """ Module containing joint classes to connect rods and rigid bodies together. """
 )
-__all__ = ["GenericSystemTypeFreeJoint", "GenericSystemTypeFixedJoint"]
 from elastica.joint import FreeJoint, FixedJoint
 from elastica.typing import SystemType
 import numpy as np

diff --git a/elastica/experimental/interaction.py b/elastica/experimental/interaction.py
@@ -1,7 +1,4 @@
 __doc__ = """ Experimental interaction implementation."""
-__all__ = [
-    "AnisotropicFrictionalPlaneRigidBody",
-]
 
 
 import numpy as np

diff --git a/elastica/external_forces.py b/elastica/external_forces.py
@@ -1,14 +1,6 @@
 __doc__ = """ Numba implementation module for boundary condition implementations that apply
 external forces to the system."""
-__all__ = [
-    "NoForces",
-    "GravityForces",
-    "EndpointForces",
-    "UniformTorques",
-    "UniformForces",
-    "MuscleTorques",
-    "EndpointForcesSinusoidal",
-]
+
 
 import numpy as np
 from elastica._linalg import _batch_matvec

diff --git a/elastica/interaction.py b/elastica/interaction.py
@@ -1,10 +1,4 @@
 __doc__ = """ Numba implementation module containing interactions between a rod and its environment."""
-__all__ = [
-    "AnisotropicFrictionalPlane",
-    "InteractionPlane",
-    "InteractionPlaneRigidBody",
-    "SlenderBodyTheory",
-]
 
 
 import numpy as np

diff --git a/elastica/joint.py b/elastica/joint.py
@@ -1,5 +1,5 @@
 __doc__ = """ Module containing joint classes to connect multiple rods together. """
-__all__ = ["FreeJoint", "HingeJoint", "FixedJoint", "ExternalContact", "SelfContact"]
+
 from elastica._linalg import _batch_product_k_ik_to_ik
 from elastica._rotations import _inv_rotate
 from elastica.typing import SystemType, RodType

diff --git a/elastica/memory_block/__init__.py b/elastica/memory_block/__init__.py
@@ -1,7 +1,2 @@
-__all__ = [
-    "MemoryBlockCosseratRod",
-    "MemoryBlockRigidBody",
-]
-
-from elastica.memory_block.memory_block_rod import MemoryBlockCosseratRod
-from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody
+from .memory_block_rigid_body import MemoryBlockRigidBody
+from .memory_block_rod import MemoryBlockCosseratRod
diff --git a/elastica/modules/__init__.py b/elastica/modules/__init__.py
@@ -4,14 +4,6 @@
 """
 
 
-__all__ = [
-    "BaseSystemCollection",
-    "Connections",
-    "Constraints",
-    "Forcing",
-    "CallBacks",
-    "Damping",
-]
 from .base_system import BaseSystemCollection
 from .connections import Connections
 from .constraints import Constraints

diff --git a/elastica/reset_functions_for_block_structure/__init__.py b/elastica/reset_functions_for_block_structure/__init__.py
@@ -1,8 +1,3 @@
-__all__ = [
-    "_reset_scalar_ghost",
-    "_reset_vector_ghost",
-]
-
 from elastica.reset_functions_for_block_structure._reset_ghost_vector_or_scalar import (
     _reset_scalar_ghost,
     _reset_vector_ghost,

diff --git a/elastica/restart.py b/elastica/restart.py
@@ -1,5 +1,5 @@
 __doc__ = """Generate or load restart file implementations."""
-__all__ = ["save_state", "load_state"]
+
 import numpy as np
 import os
 from itertools import groupby

diff --git a/elastica/rigidbody/__init__.py b/elastica/rigidbody/__init__.py
@@ -1,4 +1,3 @@
-__all__ = ["RigidBodyBase", "Cylinder", "Sphere"]
 from .rigid_body import RigidBodyBase
 from .cylinder import Cylinder
 from .sphere import Sphere
diff --git a/elastica/rigidbody/cylinder.py b/elastica/rigidbody/cylinder.py
@@ -1,5 +1,4 @@
 __doc__ = """"""
-__all__ = ["Cylinder"]
 
 import numpy as np
 

diff --git a/elastica/rigidbody/sphere.py b/elastica/rigidbody/sphere.py
@@ -1,5 +1,4 @@
 __doc__ = """"""
-__all__ = ["Sphere"]
 
 import numpy as np
 

diff --git a/elastica/rod/__init__.py b/elastica/rod/__init__.py
@@ -1,6 +1,12 @@
 __doc__ = """Rod classes and its data structures """
 
 
-from elastica.rod.knot_theory import *
-from elastica.rod.data_structures import *
+from elastica.rod.knot_theory import KnotTheory
 from elastica.rod.rod_base import RodBase
+from elastica.rod.data_structures import (
+    _RodSymplecticStepperMixin,
+    _State,
+    _DerivativeState,
+    _KinematicState,
+    _DynamicState,
+)
diff --git a/elastica/rod/cosserat_rod.py b/elastica/rod/cosserat_rod.py
@@ -1,5 +1,4 @@
 __doc__ = """ Rod classes and implementation details """
-__all__ = ["CosseratRod"]
 
 
 import numpy as np

diff --git a/elastica/rod/data_structures.py b/elastica/rod/data_structures.py
@@ -1,12 +1,5 @@
 __doc__ = "Data structure wrapper for rod components"
-__all__ = [
-    "_RodSymplecticStepperMixin",
-    "_bootstrap_from_data",
-    "_State",
-    "_DerivativeState",
-    "_KinematicState",
-    "_DynamicState",
-]
+
 import numpy as np
 from numba import njit
 from elastica._rotations import _get_rotation_matrix, _rotate

diff --git a/elastica/rod/factory_function.py b/elastica/rod/factory_function.py
@@ -1,5 +1,4 @@
 __doc__ = """ Factory function to allocate variables for Cosserat Rod"""
-__all__ = ["allocate"]
 from typing import Optional, Tuple
 import logging
 import numpy as np

diff --git a/elastica/rod/knot_theory.py b/elastica/rod/knot_theory.py
@@ -9,13 +9,6 @@
 
 The details discussion is included in `N Charles et. al. PRL (2019) <https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.123.208003>`_.
 """
-__all__ = [
-    "KnotTheoryCompatibleProtocol",
-    "KnotTheory",
-    "compute_twist",
-    "compute_link",
-    "compute_writhe",
-]
 
 import sys
 

diff --git a/elastica/timestepper/__init__.py b/elastica/timestepper/__init__.py
@@ -1,12 +1,5 @@
 __doc__ = """Timestepping utilities to be used with Rod and RigidBody classes"""
-__all__ = [
-    "integrate",
-    "PositionVerlet",
-    "PEFRL",
-    "RungeKutta4",
-    "EulerForward",
-    "extend_stepper_interface",
-]
+
 
 import numpy as np
 from tqdm import tqdm

diff --git a/elastica/transformations.py b/elastica/transformations.py
@@ -1,5 +1,4 @@
 __doc__ = """ Rotation interface functions"""
-__all__ = ["skew_symmetrize", "inv_skew_symmetrize", "rotate"]
 
 import numpy as np
 

diff --git a/elastica/utils.py b/elastica/utils.py
@@ -1,6 +1,6 @@
 """ Handy utilities
 """
-__all__ = ["isqrt"]
+
 import functools
 import numpy as np
 from numpy import finfo, float64

diff --git a/elastica/wrappers.py b/elastica/wrappers.py
@@ -8,13 +8,15 @@
     "CallBacks",
     "Damping",
 ]
+
 from elastica.modules.base_system import BaseSystemCollection
 from elastica.modules.connections import Connections
 from elastica.modules.constraints import Constraints
 from elastica.modules.forcing import Forcing
 from elastica.modules.callbacks import CallBacks
 from elastica.modules.damping import Damping
 
+
 warnings.warn(
     "elastica.wrappers is refactored to elastica.modules in version 0.3.0.",
     DeprecationWarning,