fmt: autoflake action

elastica/_calculus.py

@@ -1,7 +1,6 @@
 __doc__ = """ Quadrature and difference kernels """
 import numpy as np
 from numpy import zeros, empty
-import numba
 from numba import njit
 from elastica.reset_functions_for_block_structure._reset_ghost_vector_or_scalar import (
     _reset_vector_ghost,

elastica/_linalg.py

@@ -1,6 +1,5 @@
 __doc__ = """ Convenient linear algebra kernels """
 import numpy as np
-import numba
 from numba import njit
 from numpy import sqrt
 import functools

elastica/_rotations.py

@@ -9,7 +9,6 @@
 from numpy import sqrt
 from numpy import arccos
 
-import numba
 from numba import njit
 
 from elastica._linalg import _batch_matmul

elastica/boundary_conditions.py

@@ -15,7 +15,6 @@
 
 from abc import ABC, abstractmethod
 
-import numba
 from numba import njit
 
 from elastica._linalg import _batch_matvec, _batch_matrix_transpose

elastica/experimental/connection_contact_joint/generic_system_type_connection.py

@@ -4,7 +4,6 @@
 __all__ = ["GenericSystemTypeFreeJoint", "GenericSystemTypeFixedJoint"]
 from elastica.joint import FreeJoint, FixedJoint
 from elastica.typing import SystemType
-from elastica.utils import Tolerance, MaxDimension
 import numpy as np
 from typing import Optional
 

elastica/experimental/interaction.py

@@ -6,27 +6,16 @@
 
 import numpy as np
 from elastica.external_forces import NoForces
-from elastica.interaction import *
 from elastica.interaction import (
     find_slipping_elements,
     apply_normal_force_numba_rigid_body,
     InteractionPlaneRigidBody,
 )
 
-import numba
 from numba import njit
 from elastica._linalg import (
-    _batch_matmul,
-    _batch_matvec,
-    _batch_cross,
-    _batch_norm,
     _batch_dot,
-    _batch_product_i_k_to_ik,
-    _batch_product_i_ik_to_k,
     _batch_product_k_ik_to_ik,
-    _batch_vector_sum,
-    _batch_matrix_transpose,
-    _batch_vec_oneD_vec_cross,
 )
 
 

elastica/external_forces.py

@@ -15,7 +15,6 @@
 from elastica.typing import SystemType, RodType
 from elastica.utils import _bspline
 
-import numba
 from numba import njit
 from elastica._linalg import _batch_product_i_k_to_ik
 
@@ -52,9 +51,7 @@ def apply_forces(self, system: SystemType, time: np.float64 = 0.0):
         Returns
         -------
 
-
         """
-
         pass
 
     def apply_torques(self, system: SystemType, time: np.float64 = 0.0):

elastica/memory_block/memory_block_rigid_body.py

@@ -2,15 +2,10 @@
 import numpy as np
 from typing import Sequence
 
-from elastica.rigidbody import RigidBodyBase, Cylinder
+from elastica.rigidbody import RigidBodyBase
 
 # from elastica.rigidbody.rigid_body import RigidBody
 from elastica.rigidbody.data_structures import _RigidRodSymplecticStepperMixin
-from elastica.rod.data_structures import _RodSymplecticStepperMixin
-from elastica.reset_functions_for_block_structure import _reset_scalar_ghost
-from elastica.rod.cosserat_rod import CosseratRod
-from elastica.rigidbody import sphere, cylinder
-from elastica._linalg import _batch_matvec, _batch_cross
 
 
 class MemoryBlockRigidBody(RigidBodyBase, _RigidRodSymplecticStepperMixin):

elastica/modules/base_system.py

@@ -8,7 +8,6 @@
 from typing import Iterable, Callable, AnyStr
 
 from collections.abc import MutableSequence
-from itertools import chain
 
 from elastica.rod import RodBase
 from elastica.rigidbody import RigidBodyBase

elastica/modules/constraints.py

@@ -5,7 +5,6 @@
 Provides the constraints interface to enforce displacement boundary conditions (see `boundary_conditions.py`).
 """
 
-import numpy as np
 from elastica.boundary_conditions import ConstraintBase
 
 

elastica/reset_functions_for_block_structure/_reset_ghost_vector_or_scalar.py

@@ -1,7 +1,5 @@
 __doc__ = """Reset the ghost vectors or scalar variables using functions implemented in Numba"""
 
-import numpy as np
-import numba
 from numba import njit
 
 

elastica/rigidbody/data_structures.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from elastica._rotations import _get_rotation_matrix, _rotate
+from elastica._rotations import _get_rotation_matrix
 from elastica.rod.data_structures import _RodSymplecticStepperMixin
 
 """

elastica/rigidbody/rigid_body.py

@@ -1,9 +1,8 @@
 __doc__ = """"""
 
 import numpy as np
-from abc import ABC, abstractmethod
+from abc import ABC
 from elastica._linalg import _batch_matvec, _batch_cross
-from elastica.utils import MaxDimension
 
 
 class RigidBodyBase(ABC):

elastica/rod/cosserat_rod.py

@@ -1,7 +1,6 @@
 __doc__ = """ Rod classes and implementation details """
 __all__ = ["CosseratRod"]
 
-import typing
 
 import numpy as np
 import functools

elastica/rod/data_structures.py

@@ -8,7 +8,6 @@
     "_DynamicState",
 ]
 import numpy as np
-import numba
 from numba import njit
 from elastica._rotations import _get_rotation_matrix, _rotate
 from elastica._linalg import _batch_matmul

elastica/systems/analytical.py

@@ -1,12 +1,8 @@
 __doc__ = "Analytically integrable systems, used primarily for testing time-steppers of Elastica Numba implementation"
 
 import numpy as np
-import numba
-from elastica._rotations import _get_rotation_matrix, _rotate
-from elastica._linalg import _batch_matmul
+from elastica._rotations import _rotate
 from elastica.rod.data_structures import _RodSymplecticStepperMixin
-from elastica.rod.data_structures import _bootstrap_from_data
-from elastica.rod.data_structures import _KinematicState, _DynamicState
 
 
 class BaseStatefulSystem:

elastica/timestepper/_stepper_interface.py

@@ -1,7 +1,5 @@
 __doc__ = "Time stepper interface"
 
-import numpy as np
-
 
 class _TimeStepper:
     """Interface classes for all time-steppers"""

elastica/timestepper/symplectic_steppers.py

@@ -1,7 +1,6 @@
 __doc__ = """Symplectic time steppers and concepts for integrating the kinematic and dynamic equations of rod-like objects.  """
 
 import numpy as np
-import math
 
 # from elastica._elastica_numba._timestepper._symplectic_steppers import (
 #     SymplecticStepperTag,

examples/ExperimentalCases/GenericSystemConnectionCases/joint_cases_postprocessing.py

@@ -1,7 +1,6 @@
 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib.colors import to_rgb
-from mpl_toolkits import mplot3d
 from scipy.spatial.transform import Rotation
 
 from elastica.rigidbody import Cylinder

examples/HelicalBucklingCase/helicalbuckling_postprocessing.py

@@ -1,7 +1,5 @@
 import numpy as np
 from matplotlib import pyplot as plt
-from mpl_toolkits import mplot3d
-from matplotlib.colors import to_rgb
 from scipy.linalg import norm
 
 

examples/JointCases/joint_cases_postprocessing.py

@@ -1,7 +1,6 @@
 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib.colors import to_rgb
-from mpl_toolkits import mplot3d
 from scipy.spatial.transform import Rotation
 
 

examples/MuscularFlagella/connection_flagella.py

@@ -1,7 +1,6 @@
 __doc__ = """Muscular flagella connection class Numba implementation. """
 __all__ = ["MuscularFlagellaConnection"]
 import numpy as np
-import numba
 from numba import njit
 from elastica.joint import FreeJoint
 from elastica._linalg import _batch_matvec

examples/MuscularFlagella/post_processing.py

@@ -1,7 +1,5 @@
 import numpy as np
 from matplotlib import pyplot as plt
-from matplotlib.colors import to_rgb
-from matplotlib import cm
 from tqdm import tqdm
 
 from typing import Dict, Sequence
@@ -18,8 +16,6 @@ def plot_video(
 
     # 2d case <always 2d case for now>
     import matplotlib.animation as animation
-    from matplotlib.patches import Circle
-    from mpl_toolkits.mplot3d import proj3d, Axes3D
 
     # simulation time
     sim_time = np.array(rods_history[0]["time"])
@@ -130,7 +126,6 @@ def plot_video_2D(
 
     # 2d case <always 2d case for now>
     import matplotlib.animation as animation
-    from matplotlib.patches import Circle
 
     # simulation time
     sim_time = np.array(rods_history[0]["time"])

examples/MuscularSnake/muscle_forces.py

@@ -1,7 +1,6 @@
 __doc__ = """ Muscular snake muscle forces NumPy implementation """
 __all__ = ["MuscleForces"]
 import numpy as np
-import numba
 from numba import njit
 from elastica import NoForces
 from elastica._calculus import difference_kernel

examples/MuscularSnake/post_processing.py

@@ -5,7 +5,6 @@
 from matplotlib import pyplot as plt
 from matplotlib.colors import to_rgb
 from matplotlib import cm
-from mpl_toolkits.mplot3d import proj3d, Axes3D
 from tqdm import tqdm
 
 from typing import Dict, Sequence

examples/RigidBodyCases/RodRigidBodyContact/post_processing.py

@@ -55,7 +55,6 @@ def plot_video(
     dpi = 50
 
     # min_limits = np.roll(np.array([0.0, -0.5 * cylinder_height, 0.0]), _roll_key)
-    from mpl_toolkits.mplot3d import Axes3D
 
     fig = plt.figure(1, figsize=(10, 8), frameon=True, dpi=dpi)
     ax = plt.axes(projection="3d")  # fig.add_subplot(111)

examples/RodContactCase/RodSelfContact/PlectonemesCase/plectoneme_case.py

@@ -2,7 +2,6 @@
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,
-    plot_velocity,
     plot_link_writhe_twist,
 )
 

examples/RodContactCase/RodSelfContact/SolenoidsCase/solenoid_case.py

@@ -2,7 +2,6 @@
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,
-    plot_velocity,
     plot_link_writhe_twist,
 )
 

examples/RodContactCase/post_processing.py

@@ -1,7 +1,5 @@
 import numpy as np
 from matplotlib import pyplot as plt
-from matplotlib.colors import to_rgb
-from mpl_toolkits.mplot3d import proj3d, Axes3D
 from tqdm import tqdm
 
 from typing import Dict, Sequence

examples/Visualization/ContinuumSnakeVisualization/continuum_snake.py

@@ -5,7 +5,7 @@
 from elastica.external_forces import GravityForces, MuscleTorques
 from elastica.interaction import AnisotropicFrictionalPlane
 from elastica.callback_functions import CallBackBaseClass
-from elastica.timestepper.symplectic_steppers import PositionVerlet, PEFRL
+from elastica.timestepper.symplectic_steppers import PositionVerlet
 from elastica.timestepper import integrate
 
 

examples/Visualization/_povmacros.py

@@ -4,7 +4,6 @@
 
 """
 
-import os
 import subprocess
 from collections import defaultdict
 

examples/convergence_functions.py

@@ -1,6 +1,5 @@
 import numpy as np
 from matplotlib import pyplot as plt
-from mpl_toolkits import mplot3d
 from matplotlib.colors import to_rgb
 from scipy.linalg import norm
 

tests/test_boundary_conditions.py

@@ -1,5 +1,4 @@
 __doc__ = """ Test Boundary conditions for in Elastica implementation"""
-import sys
 
 # System imports
 import numpy as np

tests/test_callback_functions.py

@@ -1,10 +1,10 @@
 __doc__ = """ Call back functions for rod test module """
-import os, sys
+import os
 
 # System imports
 import logging
 import numpy as np
-from numpy.testing import assert_allclose, assert_array_equal
+from numpy.testing import assert_allclose
 from elastica.callback_functions import CallBackBaseClass, MyCallBack, ExportCallBack
 from elastica.utils import Tolerance
 import tempfile

tests/test_data_structures.py

@@ -1,9 +1,6 @@
 __doc__ = """ Data structures module import test"""
 
 # System imports
-import pytest
-import importlib
-import elastica
 
 
 if __name__ == "__main__":

tests/test_external_forces.py

@@ -1,9 +1,8 @@
 __doc__ = """ External forcing for rod test module for Elastica implementation"""
-import sys
 
 # System imports
 import numpy as np
-from numpy.testing import assert_allclose, assert_array_equal
+from numpy.testing import assert_allclose
 import pytest
 
 from elastica.external_forces import (

tests/test_math/test_governing_equations.py

@@ -18,7 +18,6 @@
     _compute_bending_twist_strains,
     _compute_damping_torques,
     _compute_internal_torques,
-    _update_accelerations,
     _get_z_vector,
 )
 import pytest

tests/test_math/test_rotation_non_numba_impls.py

@@ -16,8 +16,6 @@
     _skew_symmetrize_sq,  # noqa
 )
 
-from elastica.utils import Tolerance
-
 
 ###############################################################################
 ##################### Implementation tests start ##############################

tests/test_math/test_timestepper.py

@@ -396,7 +396,6 @@ class TestSteppersAgainstRodLikeSystems:
     def test_symplectics_against_ellipse_motion(self, symplectic_stepper):
         from elastica.systems.analytical import (
             make_simple_system_with_positions_directors,
-            SimpleSystemWithPositionsDirectors,
         )
 
         random_start_position = np.random.randn(3, 1)

tests/test_modules/test_callbacks.py

@@ -1,6 +1,5 @@
 __doc__ = """ Test modules for callback """
 import numpy as np
-from numpy.testing import assert_allclose
 import pytest
 
 from elastica.modules import CallBacks