From 4d6d315255a98a9306cbe98811936eb1b5ddc9e5 Mon Sep 17 00:00:00 2001
From: Seung Hyun Kim <skim0119@gmail.com>
Date: Sun, 30 Jun 2024 02:11:23 -0500
Subject: [PATCH] partially resolve #402: move analytical.py into tests

---
 Makefile                                      |  1 -
 elastica/__init__.py                          |  3 +-
 elastica/timestepper/symplectic_steppers.py   |  9 +++---
 pyproject.toml                                |  2 --
 {elastica/systems => tests}/analytical.py     |  0
 tests/test_math/test_timestepper.py           | 28 ++++++++-----------
 .../test_rigid_body_data_structures.py        |  4 +--
 7 files changed, 20 insertions(+), 27 deletions(-)
 rename {elastica/systems => tests}/analytical.py (100%)

diff --git a/Makefile b/Makefile
index 89b4b1799..3bce77a7a 100644
--- a/Makefile
+++ b/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
diff --git a/elastica/__init__.py b/elastica/__init__.py
index b5a1e8ea2..5f0703060 100644
--- a/elastica/__init__.py
+++ b/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
diff --git a/elastica/timestepper/symplectic_steppers.py b/elastica/timestepper/symplectic_steppers.py
index 9928997c8..6f2405074 100644
--- a/elastica/timestepper/symplectic_steppers.py
+++ b/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
diff --git a/pyproject.toml b/pyproject.toml
index bbd4e9ce4..eef6872b6 100644
--- a/pyproject.toml
+++ b/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",
 ]
diff --git a/elastica/systems/analytical.py b/tests/analytical.py
similarity index 100%
rename from elastica/systems/analytical.py
rename to tests/analytical.py
diff --git a/tests/test_math/test_timestepper.py b/tests/test_math/test_timestepper.py
index 6a6169856..62f79a453 100644
--- a/tests/test_math/test_timestepper.py
+++ b/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)
diff --git a/tests/test_rigid_body/test_rigid_body_data_structures.py b/tests/test_rigid_body/test_rigid_body_data_structures.py
index 844199529..0ede2bd89 100644
--- a/tests/test_rigid_body/test_rigid_body_data_structures.py
+++ b/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):