update: remove sys append calls in examples

examples/AxialStretchingCase/axial_stretching.py

@@ -23,13 +23,6 @@
 
     isort:skip_file
 """
-# FIXME without appending sys.path make it more generic
-import sys
-
-sys.path.append("../../")  # isort:skip
-
-# from collections import defaultdict
-
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/BoundaryConditionsCases/bc_cases_postprocessing.py

@@ -1,12 +1,7 @@
 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
-from elastica._linalg import _batch_matvec
-
 
 def plot_position(
     plot_params_rod1: dict,

examples/BoundaryConditionsCases/general_constraint_allow_yaw.py

@@ -1,11 +1,6 @@
 __doc__ = """Fixed joint example, for detailed explanation refer to Zhang et. al. Nature Comm.  methods section."""
 
-import matplotlib.pyplot as plt
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.BoundaryConditionsCases.bc_cases_postprocessing import (
     plot_position,
@@ -37,7 +32,7 @@ class GeneralConstraintSimulator(
 shear_modulus = E / (poisson_ratio + 1.0)
 
 # setting up timestepper and video
-final_time = 10
+final_time = 1
 dl = base_length / n_elem
 dt = 1e-5
 total_steps = int(final_time / dt)

examples/ButterflyCase/butterfly.py

@@ -1,10 +1,3 @@
-# FIXME without appending sys.path make it more generic
-import sys
-
-sys.path.append("../")
-sys.path.append("../../")
-
-# from collections import defaultdict
 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib.colors import to_rgb

examples/ContinuumFlagellaCase/continuum_flagella.py

@@ -2,10 +2,6 @@
 section 5.2.1 """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 import os
 from elastica import *
 from examples.ContinuumFlagellaCase.continuum_flagella_postprocessing import (

examples/ContinuumSnakeCase/continuum_snake.py

@@ -1,10 +1,7 @@
 __doc__ = """Snake friction case from X. Zhang et. al. Nat. Comm. 2021"""
 
-import sys
 import os
 import numpy as np
-
-sys.path.append("../../")
 from elastica import *
 
 from examples.ContinuumSnakeCase.continuum_snake_postprocessing import (

examples/ExperimentalCases/ParallelConnectionExample/parallel_connection_example.py

@@ -1,10 +1,6 @@
 __doc__ = """Parallel connection example"""
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../../")
 from elastica import *
 from elastica.experimental.connection_contact_joint.parallel_connection import (
     get_connection_vector_straight_straight_rod,

examples/FlexibleSwingingPendulumCase/flexible_swinging_pendulum.py

@@ -1,13 +1,6 @@
 """ Flexible swinging pendulum test-case
     isort:skip_file
 """
-# FIXME without appending sys.path make it more generic
-import sys
-
-sys.path.append("../../")  # isort:skip
-
-# from collections import defaultdict
-
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/FrictionValidationCases/axial_friction.py

@@ -1,10 +1,6 @@
-__doc__ = """Axial friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018  
+__doc__ = """Axial friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018
 section 4.1.4 and Appendix G """
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_axial_friction_validation,

examples/FrictionValidationCases/friction_validation_postprocessing.py

@@ -1,4 +1,3 @@
-import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib.colors import to_rgb
 

examples/FrictionValidationCases/rolling_friction_initial_velocity.py

@@ -1,11 +1,7 @@
-__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018  
+__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018
 section 4.1.4 and Appendix G """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/FrictionValidationCases/rolling_friction_on_inclined_plane.py

@@ -1,11 +1,7 @@
-__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018  
+__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018
 section 4.1.4 and Appendix G """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/FrictionValidationCases/rolling_friction_torque.py

@@ -1,11 +1,7 @@
-__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018  
+__doc__ = """Rolling friction validation, for detailed explanation refer to Gazzola et. al. R. Soc. 2018
 section 4.1.4 and Appendix G """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/HelicalBucklingCase/convergence_helicalbuckling.py

@@ -2,10 +2,6 @@
   section 3.4.1 """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.HelicalBucklingCase.helicalbuckling_postprocessing import (
     analytical_solution,

examples/HelicalBucklingCase/helicalbuckling.py

@@ -1,11 +1,7 @@
-__doc__ = """Helical buckling validation case, for detailed explanation refer to 
+__doc__ = """Helical buckling validation case, for detailed explanation refer to
 Gazzola et. al. R. Soc. 2018  section 3.4.1 """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.HelicalBucklingCase.helicalbuckling_postprocessing import (
     plot_helicalbuckling,

examples/JointCases/fixed_joint.py

@@ -1,10 +1,6 @@
 __doc__ = """Fixed joint example, for detailed explanation refer to Zhang et. al. Nature Comm.  methods section."""
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.JointCases.joint_cases_postprocessing import (
     plot_position,

examples/JointCases/fixed_joint_torsion.py

@@ -1,11 +1,6 @@
 __doc__ = """Fixed joint example, for detailed explanation refer to Zhang et. al. Nature Comm.  methods section."""
 
-import matplotlib.pyplot as plt
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from elastica.joint import get_relative_rotation_two_systems
 from examples.JointCases.joint_cases_postprocessing import (

examples/JointCases/hinge_joint.py

@@ -1,10 +1,6 @@
 __doc__ = """Hinge joint example, for detailed explanation refer to Zhang et. al. Nature Comm.  methods section."""
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.JointCases.joint_cases_postprocessing import (
     plot_position,

examples/JointCases/spherical_joint.py

@@ -1,11 +1,7 @@
-__doc__ = """Spherical(Free) joint example, for detailed explanation refer to Zhang et. al. Nature Comm.  
+__doc__ = """Spherical(Free) joint example, for detailed explanation refer to Zhang et. al. Nature Comm.
 methods section."""
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.JointCases.joint_cases_postprocessing import (
     plot_position,

examples/MuscularFlagella/muscular_flagella.py

@@ -1,10 +1,6 @@
 __doc__ = """Muscular flagella example from Zhang et. al. Nature Comm 2019 paper."""
 
-import sys
 import numpy as np
-
-sys.path.append("../../")
-
 from elastica import *
 from examples.MuscularFlagella.post_processing import (
     plot_video_2D,

examples/MuscularSnake/muscular_snake.py

@@ -1,8 +1,5 @@
 __doc__ = """Muscular snake example from Zhang et. al. Nature Comm 2019 paper."""
-import sys
 import numpy as np
-
-sys.path.append("../../")
 from elastica import *
 from examples.MuscularSnake.post_processing import (
     plot_video_with_surface,
@@ -94,7 +91,7 @@ class MuscularSnakeSimulator(
 # Muscle group 1 and 3, define two antagonistic muscle pairs
 n_elem_muscle_group_one_to_three = 13 * 3
 base_length_muscle = 0.39
-"""  
+"""
 In our simulation, we lump many biological tendons into one computational
 tendon. As a result, our computational tendon is bigger in size, set as elements other than 4-8
 below.

examples/RestartExample/restart_example.py

@@ -2,10 +2,7 @@
 This script is an example to how to use Pyelastica restart functionality.
 """
 
-import sys
 import numpy as np
-
-sys.path.append("../../")
 from elastica import *
 
 

examples/RigidBodyCases/RodRigidBodyContact/rod_cylinder_contact.py

@@ -1,7 +1,4 @@
 import numpy as np
-import sys
-
-sys.path.append("../../../")
 from elastica import *
 from post_processing import plot_velocity, plot_video_with_surface
 

examples/RigidBodyCases/RodRigidBodyContact/rod_cylinder_contact_friction.py

@@ -1,7 +1,4 @@
 import numpy as np
-import sys
-
-sys.path.append("../../../")
 from elastica import *
 from post_processing import plot_velocity, plot_video_with_surface
 

examples/RigidBodyCases/RodRigidBodyContact/rod_cylinder_contact_validation.py

@@ -1,9 +1,4 @@
 import numpy as np
-
-# FIXME without appending sys.path make it more generic
-import sys
-
-sys.path.append("../../../")
 from elastica import *
 from post_processing import plot_video, plot_cylinder_rod_position
 

examples/RigidBodyCases/RodRigidBodyContact/rod_cylinder_contact_with_y_normal.py

@@ -1,9 +1,4 @@
 import numpy as np
-
-# FIXME without appending sys.path make it more generic
-import sys
-
-sys.path.append("../../../")
 from elastica import *
 from post_processing import plot_video, plot_cylinder_rod_position
 

examples/RigidBodyCases/rigid_cylinder_rotational_motion_case.py

@@ -1,8 +1,4 @@
-import sys
 import numpy as np
-
-sys.path.append("../../")
-
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/RigidBodyCases/rigid_cylinder_translational_motion_case.py

@@ -1,8 +1,4 @@
-import sys
 import numpy as np
-
-sys.path.append("../../")
-
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/RigidBodyCases/rigid_sphere_rotational_motion_case.py

@@ -1,8 +1,4 @@
-import sys
 import numpy as np
-
-sys.path.append("../../")
-
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/RigidBodyCases/rigid_sphere_translational_motion_case.py

@@ -1,8 +1,4 @@
-import sys
 import numpy as np
-
-sys.path.append("../../")
-
 from elastica import *
 from examples.FrictionValidationCases.friction_validation_postprocessing import (
     plot_friction_validation,

examples/RodContactCase/RodRodContact/rod_rod_contact_inclined_validation.py

@@ -1,8 +1,4 @@
 import numpy as np
-import sys
-import numpy as np
-
-sys.path.append("../../../")
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,

examples/RodContactCase/RodRodContact/rod_rod_contact_parallel_validation.py

@@ -1,8 +1,4 @@
 import numpy as np
-import sys
-import numpy as np
-
-sys.path.append("../../../")
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,

examples/RodContactCase/RodSelfContact/PlectonemesCase/plectoneme_case.py

@@ -1,8 +1,4 @@
 import numpy as np
-import sys
-import numpy as np
-
-sys.path.append("../../../../")
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,

examples/RodContactCase/RodSelfContact/SolenoidsCase/solenoid_case.py

@@ -1,8 +1,4 @@
 import numpy as np
-import sys
-import numpy as np
-
-sys.path.append("../../../../")
 from elastica import *
 from examples.RodContactCase.post_processing import (
     plot_video_with_surface,

examples/TimoshenkoBeamCase/convergence_timoshenko.py

@@ -1,11 +1,7 @@
-__doc__ = """Timoshenko beam convergence study, for detailed explanation refer to 
+__doc__ = """Timoshenko beam convergence study, for detailed explanation refer to
 Gazzola et. al. R. Soc. 2018  section 3.4.3 """
 
 import numpy as np
-import sys
-
-# FIXME without appending sys.path make it more generic
-sys.path.append("../../")
 from elastica import *
 from examples.TimoshenkoBeamCase.timoshenko_postprocessing import (
     plot_timoshenko,