Merge branch 'update-0.3.1' into 169_update_visualization_example

.github/workflows/main.yml

@@ -20,15 +20,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
         os: [ubuntu-latest, macos-latest] #, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
         include:
           - os: ubuntu-latest
             path: ~/.cache/pip
           - os: macos-latest
             path: ~/Library/Caches/pip
-#          - os: windows-latest
-#            path: ~\AppData\Local\pip\Cache
+          #- os: windows-latest
+          #  path: ~\AppData\Local\pip\Cache
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -102,6 +102,6 @@ jobs:
         run: |
           make test_coverage_xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

Makefile

@@ -1,6 +1,7 @@
 #* Variables
 PYTHON := python3
 PYTHONPATH := `pwd`
+AUTOFLAKE8_ARGS := -r --exclude '__init__.py' --keep-pass-after-docstring
 #* Poetry
 .PHONY: poetry-download
 poetry-download:
@@ -46,6 +47,17 @@ flake8:
 	poetry run flake8 --version
 	poetry run flake8 elastica tests
 
+.PHONY: autoflake8-check
+autoflake8-check:
+	poetry run autoflake8 --version
+	poetry run autoflake8 $(AUTOFLAKE8_ARGS) elastica tests examples
+	poetry run autoflake8 --check $(AUTOFLAKE8_ARGS) elastica tests examples
+
+.PHONY: autoflake8-format
+autoflake8-format:
+	poetry run autoflake8 --version
+	poetry run autoflake8 --in-place $(AUTOFLAKE8_ARGS) elastica tests examples
+
 .PHONY: format-codestyle
 format-codestyle: black flake8
 
@@ -62,7 +74,7 @@ test_coverage_xml:
 	NUMBA_DISABLE_JIT=1 poetry run pytest --cov=elastica --cov-report=xml
 
 .PHONY: check-codestyle
-check-codestyle: black-check flake8
+check-codestyle: black-check flake8 autoflake8-check
 
 .PHONY: formatting
 formatting: format-codestyle

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

@@ -9,20 +9,17 @@
 ]
 
 import warnings
-from typing import Optional, Type, Union
+from typing import Optional
 
 import numpy as np
 
 from abc import ABC, abstractmethod
 
-import numba
 from numba import njit
 
 from elastica._linalg import _batch_matvec, _batch_matrix_transpose
 from elastica._rotations import _get_rotation_matrix
-from elastica.rod import RodBase
-from elastica.rigidbody import RigidBodyBase
-from elastica.typing import SystemType
+from elastica.typing import SystemType, RodType
 
 
 class ConstraintBase(ABC):
@@ -41,7 +38,7 @@ class ConstraintBase(ABC):
 
     """
 
-    _system: Union[Type[RodBase], Type[RigidBodyBase]]
+    _system: SystemType
     _constrained_position_idx: np.ndarray
     _constrained_director_idx: np.ndarray
 
@@ -61,7 +58,7 @@ def __init__(self, *args, **kwargs):
             )
 
     @property
-    def system(self) -> Union[Type[RodBase], Type[RigidBodyBase]]:
+    def system(self) -> SystemType:
         """get system (rod or rigid body) reference"""
         return self._system
 
@@ -78,33 +75,29 @@ def constrained_director_idx(self) -> Optional[np.ndarray]:
         return self._constrained_director_idx
 
     @abstractmethod
-    def constrain_values(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_values(self, system: SystemType, time: float) -> None:
         # TODO: In the future, we can remove rod and use self.system
         """
         Constrain values (position and/or directors) of a rod object.
 
         Parameters
         ----------
-        rod : Union[Type[RodBase], Type[RigidBodyBase]]
+        system : SystemType
             Rod or rigid-body object.
         time : float
             The time of simulation.
         """
         pass
 
     @abstractmethod
-    def constrain_rates(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_rates(self, system: SystemType, time: float) -> None:
         # TODO: In the future, we can remove rod and use self.system
         """
         Constrain rates (velocity and/or omega) of a rod object.
 
         Parameters
         ----------
-        rod : Union[Type[RodBase], Type[RigidBodyBase]]
+        system : SystemType
             Rod or rigid-body object.
         time : float
             The time of simulation.
@@ -121,15 +114,11 @@ class FreeBC(ConstraintBase):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
-    def constrain_values(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_values(self, system: SystemType, time: float) -> None:
         """In FreeBC, this routine simply passes."""
         pass
 
-    def constrain_rates(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_rates(self, system: SystemType, time: float) -> None:
         """In FreeBC, this routine simply passes."""
         pass
 
@@ -178,26 +167,22 @@ def __init__(self, fixed_position, fixed_directors, **kwargs):
         self.fixed_position_collection = np.array(fixed_position)
         self.fixed_directors_collection = np.array(fixed_directors)
 
-    def constrain_values(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
-        # rod.position_collection[..., 0] = self.fixed_position
-        # rod.director_collection[..., 0] = self.fixed_directors
+    def constrain_values(self, system: SystemType, time: float) -> None:
+        # system.position_collection[..., 0] = self.fixed_position
+        # system.director_collection[..., 0] = self.fixed_directors
         self.compute_constrain_values(
-            rod.position_collection,
+            system.position_collection,
             self.fixed_position_collection,
-            rod.director_collection,
+            system.director_collection,
             self.fixed_directors_collection,
         )
 
-    def constrain_rates(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
-        # rod.velocity_collection[..., 0] = 0.0
-        # rod.omega_collection[..., 0] = 0.0
+    def constrain_rates(self, system: SystemType, time: float) -> None:
+        # system.velocity_collection[..., 0] = 0.0
+        # system.omega_collection[..., 0] = 0.0
         self.compute_constrain_rates(
-            rod.velocity_collection,
-            rod.omega_collection,
+            system.velocity_collection,
+            system.omega_collection,
         )
 
     @staticmethod
@@ -270,7 +255,7 @@ class GeneralConstraint(ConstraintBase):
     --------
     How to fix all translational and rotational dof except allowing twisting around the z-axis in an inertial frame:
 
-    >>> simulator.constrain(rod).using(
+    >>> simulator.constrain(system).using(
     ...    GeneralConstraint,
     ...    constrained_position_idx=(0,),
     ...    constrained_director_idx=(0,),
@@ -531,33 +516,29 @@ def __init__(self, *args, **kwargs):
             **kwargs,
         )
 
-    def constrain_values(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_values(self, system: SystemType, time: float) -> None:
         if self.constrained_position_idx.size:
             self.nb_constrain_translational_values(
-                rod.position_collection,
+                system.position_collection,
                 self.fixed_positions,
                 self.constrained_position_idx,
             )
         if self.constrained_director_idx.size:
             self.nb_constraint_rotational_values(
-                rod.director_collection,
+                system.director_collection,
                 self.fixed_directors,
                 self.constrained_director_idx,
             )
 
-    def constrain_rates(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_rates(self, system: SystemType, time: float) -> None:
         if self.constrained_position_idx.size:
             self.nb_constrain_translational_rates(
-                rod.velocity_collection,
+                system.velocity_collection,
                 self.constrained_position_idx,
             )
         if self.constrained_director_idx.size:
             self.nb_constrain_rotational_rates(
-                rod.omega_collection,
+                system.omega_collection,
                 self.constrained_director_idx,
             )
 
@@ -745,19 +726,15 @@ def __init__(
             @ director_end
         )  # rotation_matrix wants vectors 3,1
 
-    def constrain_values(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_values(self, rod: RodType, time: float) -> None:
         if time > self.twisting_time:
             rod.position_collection[..., 0] = self.final_start_position
             rod.position_collection[..., -1] = self.final_end_position
 
             rod.director_collection[..., 0] = self.final_start_directors
             rod.director_collection[..., -1] = self.final_end_directors
 
-    def constrain_rates(
-        self, rod: Union[Type[RodBase], Type[RigidBodyBase]], time: float
-    ) -> None:
+    def constrain_rates(self, rod: RodType, time: float) -> None:
         if time > self.twisting_time:
             rod.velocity_collection[..., 0] = 0.0
             rod.omega_collection[..., 0] = 0.0

elastica/dissipation.py

@@ -56,15 +56,15 @@ def system(self):  # -> SystemType: (Return type is not parsed with sphinx book.
         return self._system
 
     @abstractmethod
-    def dampen_rates(self, rod: SystemType, time: float):
+    def dampen_rates(self, system: SystemType, time: float):
         # TODO: In the future, we can remove rod and use self.system
         """
         Dampen rates (velocity and/or omega) of a rod object.
 
         Parameters
         ----------
-        rod : Union[Type[RodBase], Type[RigidBodyBase]]
-            Rod or rigid-body object.
+        system : SystemType
+            System (rod or rigid-body) object.
         time : float
             The time of simulation.
 
@@ -144,7 +144,7 @@ def __init__(self, damping_constant, time_step, **kwargs):
             * np.diagonal(self._system.inv_mass_second_moment_of_inertia).T
         )
 
-    def dampen_rates(self, rod: SystemType, time: float):
+    def dampen_rates(self, rod: RodType, time: float):
         rod.velocity_collection[:] = (
             rod.velocity_collection * self.translational_damping_coefficient
         )

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,
 )