partially resolve GazzolaLab#402: move analytical.py into tests

Makefile

@@ -50,7 +50,6 @@ flake8:
 .PHONY: autoflake-check
 autoflake-check:
 	poetry run autoflake --version
-	poetry run autoflake $(AUTOFLAKE_ARGS) elastica tests examples
 	poetry run autoflake --check $(AUTOFLAKE_ARGS) elastica tests examples
 
 .PHONY: autoflake-format

elastica/__init__.py

@@ -75,10 +75,9 @@
 from elastica.utils import isqrt
 from elastica.timestepper import (
     integrate,
-    PositionVerlet,
-    PEFRL,
     extend_stepper_interface,
 )
+from elastica.timestepper.symplectic_steppers import PositionVerlet, PEFRL
 from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody
 from elastica.memory_block.memory_block_rod import MemoryBlockCosseratRod
 from elastica.restart import save_state, load_state

elastica/timestepper/symplectic_steppers.py

@@ -1,14 +1,11 @@
 __doc__ = """Symplectic time steppers and concepts for integrating the kinematic and dynamic equations of rod-like objects.  """
 
-from typing import Any, Final
+from typing import TYPE_CHECKING, Any
 
 from itertools import zip_longest
 
 from elastica.typing import (
-    SystemType,
     SystemCollectionType,
-    # StepOperatorType,
-    # PrefactorOperatorType,
     StepType,
     SteppersOperatorsType,
 )
@@ -308,3 +305,7 @@ def _third_kinematic_step(
             System.omega_collection,
         )
         # System.kinematic_states += prefac * System.kinematic_rates(time, prefac)
+
+
+if TYPE_CHECKING:
+    pass

pyproject.toml

@@ -145,7 +145,6 @@ warn_unused_configs = true
 warn_unused_ignores = false
 
 exclude = [
-    "elastica/systems/analytical.py",
     "elastica/experimental/*",
 ]
 
@@ -183,7 +182,6 @@ branch = true
 omit = [
     "*/.local/*",
 	"setup.py",
-    "elastica/systems/analytical.py",
     "elastica/experimental/*",
     "elastica/**/protocol.py",
 ]

tests/test_math/test_timestepper.py

@@ -3,18 +3,7 @@
 import pytest
 from numpy.testing import assert_allclose
 
-from elastica.systems.analytical import (
-    ScalarExponentialDecaySystem,
-    # UndampedSimpleHarmonicOscillatorSystem,
-    SymplecticUndampedSimpleHarmonicOscillatorSystem,
-    # DampedSimpleHarmonicOscillatorSystem,
-    # MultipleFrameRotationSystem,
-    # SecondOrderHybridSystem,
-    SymplecticUndampedHarmonicOscillatorCollectiveSystem,
-    ScalarExponentialDampedHarmonicOscillatorCollectiveSystem,
-)
 from elastica.timestepper import integrate, extend_stepper_interface
-
 from elastica.experimental.timestepper.explicit_steppers import (
     RungeKutta4,
     EulerForward,
@@ -25,10 +14,20 @@
     PEFRL,
     SymplecticStepperMixin,
 )
-
-
 from elastica.utils import Tolerance
 
+from tests.analytical import (
+    ScalarExponentialDecaySystem,
+    # UndampedSimpleHarmonicOscillatorSystem,
+    SymplecticUndampedSimpleHarmonicOscillatorSystem,
+    # DampedSimpleHarmonicOscillatorSystem,
+    # MultipleFrameRotationSystem,
+    # SecondOrderHybridSystem,
+    SymplecticUndampedHarmonicOscillatorCollectiveSystem,
+    ScalarExponentialDampedHarmonicOscillatorCollectiveSystem,
+    make_simple_system_with_positions_directors,
+)
+
 
 class TestExtendStepperInterface:
     """TODO add documentation"""
@@ -309,9 +308,6 @@ class TestSteppersAgainstRodLikeSystems:
 
     @pytest.mark.parametrize("symplectic_stepper", SymplecticSteppers)
     def test_symplectics_against_ellipse_motion(self, symplectic_stepper):
-        from elastica.systems.analytical import (
-            make_simple_system_with_positions_directors,
-        )
 
         random_start_position = np.random.randn(3, 1)
         random_end_position = np.random.randn(3, 1)

tests/test_rigid_body/test_rigid_body_data_structures.py

@@ -5,11 +5,11 @@
 from elastica.utils import Tolerance
 from elastica.rigidbody.data_structures import _RigidRodSymplecticStepperMixin
 from elastica._rotations import _rotate
-from elastica.timestepper import (
+from elastica.timestepper.symplectic_steppers import (
     PEFRL,
     PositionVerlet,
-    integrate,
 )
+from elastica.timestepper import integrate
 
 
 def make_simple_system_with_positions_directors(start_position, start_director):