Merge pull request #341 from ankith26/more-typing

Typing: Add typehinting for `Rod` modules

elastica/_calculus.py

@@ -1,6 +1,8 @@
 __doc__ = """ Quadrature and difference kernels """
+from typing import Any, Union
 import numpy as np
 from numpy import zeros, empty
+from numpy.typing import NDArray
 from numba import njit
 from elastica.reset_functions_for_block_structure._reset_ghost_vector_or_scalar import (
     _reset_vector_ghost,
@@ -9,15 +11,17 @@
 
 
 @functools.lru_cache(maxsize=2)
-def _get_zero_array(dim, ndim):
+def _get_zero_array(dim: int, ndim: int) -> Union[float, NDArray[np.floating], None]:
     if ndim == 1:
         return 0.0
     if ndim == 2:
         return np.zeros((dim, 1))
 
+    return None
+
 
 @njit(cache=True)
-def _trapezoidal(array_collection):
+def _trapezoidal(array_collection: NDArray[np.floating]) -> NDArray[np.floating]:
     """
     Simple trapezoidal quadrature rule with zero at end-points, in a dimension agnostic way
 
@@ -63,7 +67,9 @@ def _trapezoidal(array_collection):
 
 
 @njit(cache=True)
-def _trapezoidal_for_block_structure(array_collection, ghost_idx):
+def _trapezoidal_for_block_structure(
+    array_collection: NDArray[np.floating], ghost_idx: NDArray[np.integer]
+) -> NDArray[np.floating]:
     """
     Simple trapezoidal quadrature rule with zero at end-points, in a dimension agnostic way. This form
     specifically for the block structure implementation and there is a reset function call, to reset
@@ -115,7 +121,9 @@ def _trapezoidal_for_block_structure(array_collection, ghost_idx):
 
 
 @njit(cache=True)
-def _two_point_difference(array_collection):
+def _two_point_difference(
+    array_collection: NDArray[np.floating],
+) -> NDArray[np.floating]:
     """
     This function does differentiation.
 
@@ -156,7 +164,9 @@ def _two_point_difference(array_collection):
 
 
 @njit(cache=True)
-def _two_point_difference_for_block_structure(array_collection, ghost_idx):
+def _two_point_difference_for_block_structure(
+    array_collection: NDArray[np.floating], ghost_idx: NDArray[np.integer]
+) -> NDArray[np.floating]:
     """
     This function does the differentiation, for Cosserat rod model equations. This form
     specifically for the block structure implementation and there is a reset function call, to
@@ -207,7 +217,7 @@ def _two_point_difference_for_block_structure(array_collection, ghost_idx):
 
 
 @njit(cache=True)
-def _difference(vector):
+def _difference(vector: NDArray[np.floating]) -> NDArray[np.floating]:
     """
     This function computes difference between elements of a batch vector.
 
@@ -238,7 +248,7 @@ def _difference(vector):
 
 
 @njit(cache=True)
-def _average(vector):
+def _average(vector: NDArray[np.floating]) -> NDArray[np.floating]:
     """
     This function computes the average between elements of a vector.
 
@@ -268,7 +278,9 @@ def _average(vector):
 
 
 @njit(cache=True)
-def _clip_array(input_array, vmin, vmax):
+def _clip_array(
+    input_array: NDArray[np.floating], vmin: np.floating, vmax: np.floating
+) -> NDArray[np.floating]:
     """
     This function clips an array values
     between user defined minimum and maximum
@@ -304,7 +316,7 @@ def _clip_array(input_array, vmin, vmax):
 
 
 @njit(cache=True)
-def _isnan_check(array):
+def _isnan_check(array: NDArray[Any]) -> bool:
     """
     This function checks if there is any nan inside the array.
     If there is nan, it returns True boolean.
@@ -324,7 +336,7 @@ def _isnan_check(array):
     Python version: 2.24 µs ± 96.1 ns per loop
     This version: 479 ns ± 6.49 ns per loop
     """
-    return np.isnan(array).any()
+    return bool(np.isnan(array).any())
 
 
 position_difference_kernel = _difference

elastica/_contact_functions.py

@@ -24,28 +24,29 @@
 )
 import numba
 import numpy as np
+from numpy.typing import NDArray
 
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_rod_cylinder(
-    x_collection_rod,
-    edge_collection_rod,
-    x_cylinder_center,
-    x_cylinder_tip,
-    edge_cylinder,
-    radii_sum,
-    length_sum,
-    internal_forces_rod,
-    external_forces_rod,
-    external_forces_cylinder,
-    external_torques_cylinder,
-    cylinder_director_collection,
-    velocity_rod,
-    velocity_cylinder,
-    contact_k,
-    contact_nu,
-    velocity_damping_coefficient,
-    friction_coefficient,
+    x_collection_rod: NDArray[np.floating],
+    edge_collection_rod: NDArray[np.floating],
+    x_cylinder_center: NDArray[np.floating],
+    x_cylinder_tip: NDArray[np.floating],
+    edge_cylinder: NDArray[np.floating],
+    radii_sum: NDArray[np.floating],
+    length_sum: NDArray[np.floating],
+    internal_forces_rod: NDArray[np.floating],
+    external_forces_rod: NDArray[np.floating],
+    external_forces_cylinder: NDArray[np.floating],
+    external_torques_cylinder: NDArray[np.floating],
+    cylinder_director_collection: NDArray[np.floating],
+    velocity_rod: NDArray[np.floating],
+    velocity_cylinder: NDArray[np.floating],
+    contact_k: np.floating,
+    contact_nu: np.floating,
+    velocity_damping_coefficient: np.floating,
+    friction_coefficient: np.floating,
 ) -> None:
     # We already pass in only the first n_elem x
     n_points = x_collection_rod.shape[1]
@@ -155,22 +156,22 @@ def _calculate_contact_forces_rod_cylinder(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_rod_rod(
-    x_collection_rod_one,
-    radius_rod_one,
-    length_rod_one,
-    tangent_rod_one,
-    velocity_rod_one,
-    internal_forces_rod_one,
-    external_forces_rod_one,
-    x_collection_rod_two,
-    radius_rod_two,
-    length_rod_two,
-    tangent_rod_two,
-    velocity_rod_two,
-    internal_forces_rod_two,
-    external_forces_rod_two,
-    contact_k,
-    contact_nu,
+    x_collection_rod_one: NDArray[np.floating],
+    radius_rod_one: NDArray[np.floating],
+    length_rod_one: NDArray[np.floating],
+    tangent_rod_one: NDArray[np.floating],
+    velocity_rod_one: NDArray[np.floating],
+    internal_forces_rod_one: NDArray[np.floating],
+    external_forces_rod_one: NDArray[np.floating],
+    x_collection_rod_two: NDArray[np.floating],
+    radius_rod_two: NDArray[np.floating],
+    length_rod_two: NDArray[np.floating],
+    tangent_rod_two: NDArray[np.floating],
+    velocity_rod_two: NDArray[np.floating],
+    internal_forces_rod_two: NDArray[np.floating],
+    external_forces_rod_two: NDArray[np.floating],
+    contact_k: np.floating,
+    contact_nu: np.floating,
 ) -> None:
     # We already pass in only the first n_elem x
     n_points_rod_one = x_collection_rod_one.shape[1]
@@ -272,14 +273,14 @@ def _calculate_contact_forces_rod_rod(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_self_rod(
-    x_collection_rod,
-    radius_rod,
-    length_rod,
-    tangent_rod,
-    velocity_rod,
-    external_forces_rod,
-    contact_k,
-    contact_nu,
+    x_collection_rod: NDArray[np.floating],
+    radius_rod: NDArray[np.floating],
+    length_rod: NDArray[np.floating],
+    tangent_rod: NDArray[np.floating],
+    velocity_rod: NDArray[np.floating],
+    external_forces_rod: NDArray[np.floating],
+    contact_k: np.floating,
+    contact_nu: np.floating,
 ) -> None:
     # We already pass in only the first n_elem x
     n_points_rod = x_collection_rod.shape[1]
@@ -360,24 +361,24 @@ def _calculate_contact_forces_self_rod(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_rod_sphere(
-    x_collection_rod,
-    edge_collection_rod,
-    x_sphere_center,
-    x_sphere_tip,
-    edge_sphere,
-    radii_sum,
-    length_sum,
-    internal_forces_rod,
-    external_forces_rod,
-    external_forces_sphere,
-    external_torques_sphere,
-    sphere_director_collection,
-    velocity_rod,
-    velocity_sphere,
-    contact_k,
-    contact_nu,
-    velocity_damping_coefficient,
-    friction_coefficient,
+    x_collection_rod: NDArray[np.floating],
+    edge_collection_rod: NDArray[np.floating],
+    x_sphere_center: NDArray[np.floating],
+    x_sphere_tip: NDArray[np.floating],
+    edge_sphere: NDArray[np.floating],
+    radii_sum: NDArray[np.floating],
+    length_sum: NDArray[np.floating],
+    internal_forces_rod: NDArray[np.floating],
+    external_forces_rod: NDArray[np.floating],
+    external_forces_sphere: NDArray[np.floating],
+    external_torques_sphere: NDArray[np.floating],
+    sphere_director_collection: NDArray[np.floating],
+    velocity_rod: NDArray[np.floating],
+    velocity_sphere: NDArray[np.floating],
+    contact_k: np.floating,
+    contact_nu: np.floating,
+    velocity_damping_coefficient: np.floating,
+    friction_coefficient: np.floating,
 ) -> None:
     # We already pass in only the first n_elem x
     n_points = x_collection_rod.shape[1]
@@ -486,18 +487,18 @@ def _calculate_contact_forces_rod_sphere(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_rod_plane(
-    plane_origin,
-    plane_normal,
-    surface_tol,
-    k,
-    nu,
-    radius,
-    mass,
-    position_collection,
-    velocity_collection,
-    internal_forces,
-    external_forces,
-):
+    plane_origin: NDArray[np.floating],
+    plane_normal: NDArray[np.floating],
+    surface_tol: np.floating,
+    k: np.floating,
+    nu: np.floating,
+    radius: NDArray[np.floating],
+    mass: NDArray[np.floating],
+    position_collection: NDArray[np.floating],
+    velocity_collection: NDArray[np.floating],
+    internal_forces: NDArray[np.floating],
+    external_forces: NDArray[np.floating],
+) -> tuple[NDArray[np.floating], NDArray[np.intp]]:
     """
     This function computes the plane force response on the element, in the
     case of contact. Contact model given in Eqn 4.8 Gazzola et. al. RSoS 2018 paper
@@ -571,30 +572,30 @@ def _calculate_contact_forces_rod_plane(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_rod_plane_with_anisotropic_friction(
-    plane_origin,
-    plane_normal,
-    surface_tol,
-    slip_velocity_tol,
-    k,
-    nu,
-    kinetic_mu_forward,
-    kinetic_mu_backward,
-    kinetic_mu_sideways,
-    static_mu_forward,
-    static_mu_backward,
-    static_mu_sideways,
-    radius,
-    mass,
-    tangents,
-    position_collection,
-    director_collection,
-    velocity_collection,
-    omega_collection,
-    internal_forces,
-    external_forces,
-    internal_torques,
-    external_torques,
-):
+    plane_origin: NDArray[np.floating],
+    plane_normal: NDArray[np.floating],
+    surface_tol: np.floating,
+    slip_velocity_tol: np.floating,
+    k: np.floating,
+    nu: np.floating,
+    kinetic_mu_forward: np.floating,
+    kinetic_mu_backward: np.floating,
+    kinetic_mu_sideways: np.floating,
+    static_mu_forward: np.floating,
+    static_mu_backward: np.floating,
+    static_mu_sideways: np.floating,
+    radius: NDArray[np.floating],
+    mass: NDArray[np.floating],
+    tangents: NDArray[np.floating],
+    position_collection: NDArray[np.floating],
+    director_collection: NDArray[np.floating],
+    velocity_collection: NDArray[np.floating],
+    omega_collection: NDArray[np.floating],
+    internal_forces: NDArray[np.floating],
+    external_forces: NDArray[np.floating],
+    internal_torques: NDArray[np.floating],
+    external_torques: NDArray[np.floating],
+) -> None:
     (
         plane_response_force_mag,
         no_contact_point_idx,
@@ -784,16 +785,16 @@ def _calculate_contact_forces_rod_plane_with_anisotropic_friction(
 
 @numba.njit(cache=True)
 def _calculate_contact_forces_cylinder_plane(
-    plane_origin,
-    plane_normal,
-    surface_tol,
-    k,
-    nu,
-    length,
-    position_collection,
-    velocity_collection,
-    external_forces,
-):
+    plane_origin: NDArray[np.floating],
+    plane_normal: NDArray[np.floating],
+    surface_tol: np.floating,
+    k: np.floating,
+    nu: np.floating,
+    length: NDArray[np.floating],
+    position_collection: NDArray[np.floating],
+    velocity_collection: NDArray[np.floating],
+    external_forces: NDArray[np.floating],
+) -> tuple[NDArray[np.floating], NDArray[np.intp]]:
 
     # Compute plane response force
     # total_forces = system.internal_forces + system.external_forces