test: fix unittest according to change in removing operator list

elastica/__init__.py

@@ -77,8 +77,6 @@
     integrate,
     PositionVerlet,
     PEFRL,
-    RungeKutta4,
-    EulerForward,
     extend_stepper_interface,
 )
 from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody

elastica/experimental/timestepper/explicit_steppers.py

@@ -13,7 +13,7 @@
     StateType,
 )
 from elastica.systems.protocol import ExplicitSystemProtocol
-from .protocol import ExplicitStepperProtocol, MemoryProtocol
+from elastica.timestepper.protocol import ExplicitStepperProtocol, MemoryProtocol
 
 
 """

elastica/experimental/timestepper/memory.py

@@ -1,6 +1,11 @@
 from typing import Iterator, TypeVar, Generic, Type
 from elastica.timestepper.protocol import ExplicitStepperProtocol
 from elastica.typing import SystemCollectionType
+from elastica.experimental.timestepper.explicit_steppers import (
+    RungeKutta4,
+    EulerForward,
+)
+
 
 from copy import copy
 
@@ -12,11 +17,6 @@ def make_memory_for_explicit_stepper(
 ) -> "MemoryCollection":
     # TODO Automated logic (class creation, memory management logic) agnostic of stepper details (RK, AB etc.)
 
-    from elastica.timestepper.explicit_steppers import (
-        RungeKutta4,
-        EulerForward,
-    )
-
     # is_this_system_a_collection = is_system_a_collection(system)
 
     memory_cls: Type

elastica/modules/base_system.py

@@ -247,7 +247,7 @@ def synchronize(self, time: np.float64) -> None:
         Features are registered in _feature_group_synchronize.
         """
         for func in self._feature_group_synchronize:
-            func(time)
+            func(time=time)
 
     @final
     def constrain_values(self, time: np.float64) -> None:
@@ -256,7 +256,7 @@ def constrain_values(self, time: np.float64) -> None:
         Features are registered in _feature_group_constrain_values.
         """
         for func in self._feature_group_constrain_values:
-            func(time)
+            func(time=time)
 
     @final
     def constrain_rates(self, time: np.float64) -> None:
@@ -265,7 +265,7 @@ def constrain_rates(self, time: np.float64) -> None:
         Features are registered in _feature_group_constrain_rates.
         """
         for func in self._feature_group_constrain_rates:
-            func(time)
+            func(time=time)
 
     @final
     def apply_callbacks(self, time: np.float64, current_step: int) -> None:
@@ -274,4 +274,4 @@ def apply_callbacks(self, time: np.float64, current_step: int) -> None:
         Features are registered in _feature_group_callback.
         """
         for func in self._feature_group_callback:
-            func(time, current_step)
+            func(time=time, current_step=current_step)

elastica/modules/protocol.py

@@ -1,4 +1,5 @@
 from typing import Protocol, Generator, TypeVar, Any, Type, overload
+from typing import TYPE_CHECKING
 from typing_extensions import Self  # python 3.11: from typing import Self
 
 from abc import abstractmethod
@@ -20,7 +21,8 @@
 
 import numpy as np
 
-from .operator_group import OperatorGroupFIFO
+if TYPE_CHECKING:
+    from .operator_group import OperatorGroupFIFO
 
 
 class MixinProtocol(Protocol):
@@ -55,28 +57,28 @@ def __getitem__(self, i: slice | int) -> "list[SystemType] | SystemType": ...
     @property
     def _feature_group_synchronize(
         self,
-    ) -> OperatorGroupFIFO[OperatorType, ModuleProtocol]: ...
+    ) -> "OperatorGroupFIFO[OperatorType, ModuleProtocol]": ...
 
     def synchronize(self, time: np.float64) -> None: ...
 
     @property
     def _feature_group_constrain_values(
         self,
-    ) -> OperatorGroupFIFO[OperatorType, ModuleProtocol]: ...
+    ) -> "OperatorGroupFIFO[OperatorType, ModuleProtocol]": ...
 
     def constrain_values(self, time: np.float64) -> None: ...
 
     @property
     def _feature_group_constrain_rates(
         self,
-    ) -> OperatorGroupFIFO[OperatorType, ModuleProtocol]: ...
+    ) -> "OperatorGroupFIFO[OperatorType, ModuleProtocol]": ...
 
     def constrain_rates(self, time: np.float64) -> None: ...
 
     @property
     def _feature_group_callback(
         self,
-    ) -> OperatorGroupFIFO[OperatorCallbackType, ModuleProtocol]: ...
+    ) -> "OperatorGroupFIFO[OperatorCallbackType, ModuleProtocol]": ...
 
     def apply_callbacks(self, time: np.float64, current_step: int) -> None: ...
 

elastica/timestepper/__init__.py

@@ -9,7 +9,6 @@
 from elastica.systems import is_system_a_collection
 
 from .symplectic_steppers import PositionVerlet, PEFRL
-from .explicit_steppers import RungeKutta4, EulerForward
 from .protocol import StepperProtocol, SymplecticStepperProtocol
 
 

tests/test_math/test_timestepper.py

@@ -15,7 +15,7 @@
 )
 from elastica.timestepper import integrate, extend_stepper_interface
 
-from elastica.timestepper.explicit_steppers import (
+from elastica.experimental.timestepper.explicit_steppers import (
     RungeKutta4,
     EulerForward,
     ExplicitStepperMixin,
@@ -245,7 +245,9 @@ def test_explicit_steppers(self, explicit_stepper):
 
         # Before stepping, let's extend the interface of the stepper
         # while providing memory slots
-        from elastica.systems.memory import make_memory_for_explicit_stepper
+        from elastica.experimental.timestepper.memory import (
+            make_memory_for_explicit_stepper,
+        )
 
         memory_collection = make_memory_for_explicit_stepper(stepper, collective_system)
         from elastica.timestepper import extend_stepper_interface

tests/test_modules/test_base_system.py

@@ -186,7 +186,16 @@ def test_constraint(self, load_collection, legal_constraint):
         simulator_class.finalize()
         # After finalize check if the created constrain object is instance of the class we have given.
         assert isinstance(
-            simulator_class._constraints_operators[-1][-1], legal_constraint
+            simulator_class._feature_group_constrain_values._operator_collection[-1][
+                -1
+            ].func.__self__,
+            legal_constraint,
+        )
+        assert isinstance(
+            simulator_class._feature_group_constrain_rates._operator_collection[-1][
+                -1
+            ].func.__self__,
+            legal_constraint,
         )
 
         # TODO: this is a dummy test for constrain values and rates find a better way to test them
@@ -225,7 +234,12 @@ def test_callback(self, load_collection, legal_callback):
         simulator_class.collect_diagnostics(rod).using(legal_callback)
         simulator_class.finalize()
         # After finalize check if the created callback object is instance of the class we have given.
-        assert isinstance(simulator_class._callback_operators[-1][-1], legal_callback)
+        assert isinstance(
+            simulator_class._feature_group_callback._operator_collection[-1][
+                -1
+            ].func.__self__,
+            legal_callback,
+        )
 
         # TODO: this is a dummy test for apply_callbacks find a better way to test them
         simulator_class.apply_callbacks(time=0, current_step=0)

tests/test_modules/test_callbacks.py

@@ -161,10 +161,13 @@ def mock_init(self, *args, **kwargs):
 
     def test_callback_finalize_correctness(self, load_rod_with_callbacks):
         scwc, callback_cls = load_rod_with_callbacks
+        callback_features = [d for d in scwc._callback_list]
 
         scwc._finalize_callback()
 
-        for x, y in scwc._callback_operators:
+        for _callback in callback_features:
+            x = _callback.id()
+            y = _callback.instantiate()
             assert type(x) is int
             assert type(y) is callback_cls
 

tests/test_modules/test_constraints.py

@@ -315,24 +315,20 @@ def constrain_rates(self, *args, **kwargs) -> None:
 
     def test_constrain_finalize_correctness(self, load_rod_with_constraints):
         scwc, bc_cls = load_rod_with_constraints
+        bc_features = [bc for bc in scwc._constraints_list]
 
         scwc._finalize_constraints()
+        assert not hasattr(scwc, "_constraints_list")
 
-        for x, y in scwc._constraints_operators:
-            assert type(x) is int
-            assert type(y) is bc_cls
+        for _constraint in bc_features:
+            x = _constraint.id()
+            y = _constraint.instantiate(scwc[x])
+            assert isinstance(x, int)
+            assert isinstance(y, bc_cls)
 
-    def test_constraint_properties(self, load_rod_with_constraints):
-        scwc, _ = load_rod_with_constraints
-        scwc._finalize_constraints()
-
-        for i in [0, 1, -1]:
-            x, y = scwc._constraints_operators[i]
-            mock_rod = scwc[i]
             # Test system
-            assert type(x) is int
-            assert type(y.system) is type(mock_rod)
-            assert y.system is mock_rod, f"{len(scwc)}"
+            assert type(y.system) is type(scwc[x])
+            assert y.system is scwc[x], f"{len(scwc)}"
             # Test node indices
             assert y.constrained_position_idx.size == 0
             # Test element indices. TODO: maybe add more generalized test

tests/test_modules/test_damping.py

@@ -180,26 +180,18 @@ def dampen_rates(self, *args, **kwargs) -> None:
 
         return scwd, MockDamper
 
-    def test_dampen_finalize_correctness(self, load_rod_with_dampers):
+    def test_dampen_finalize_clear_instances(self, load_rod_with_dampers):
         scwd, damper_cls = load_rod_with_dampers
+        damping_features = [d for d in scwd._damping_list]
 
         scwd._finalize_dampers()
+        assert not hasattr(scwd, "_damping_list")
 
-        for x, y in scwd._damping_operators:
-            assert type(x) is int
-            assert type(y) is damper_cls
-
-    def test_damper_properties(self, load_rod_with_dampers):
-        scwd, _ = load_rod_with_dampers
-        scwd._finalize_dampers()
-
-        for i in [0, 1, -1]:
-            x, y = scwd._damping_operators[i]
-            mock_rod = scwd[i]
-            # Test system
-            assert type(x) is int
-            assert type(y.system) is type(mock_rod)
-            assert y.system is mock_rod, f"{len(scwd)}"
+        for _damping in damping_features:
+            x = _damping.id()
+            y = _damping.instantiate(scwd[x])
+            assert isinstance(x, int)
+            assert isinstance(y, damper_cls)
 
     @pytest.mark.xfail
     def test_dampers_finalize_sorted(self, load_rod_with_dampers):

tests/test_rigid_body/test_rigid_body_data_structures.py

@@ -6,8 +6,6 @@
 from elastica.rigidbody.data_structures import _RigidRodSymplecticStepperMixin
 from elastica._rotations import _rotate
 from elastica.timestepper import (
-    RungeKutta4,
-    EulerForward,
     PEFRL,
     PositionVerlet,
     integrate,
@@ -92,7 +90,6 @@ def analytical_solution(self, type, time):
         return analytical_solution
 
 
-ExplicitSteppers = [EulerForward, RungeKutta4]
 SymplecticSteppers = [PositionVerlet, PEFRL]