Merge branch 'update-0.3.0' of https://github.com/GazzolaLab/PyElastica…

… into update-0.3.0

.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools: {python: "3.10"}
+  jobs:
+    pre_create_environment:
+      - asdf plugin add poetry
+      - asdf install poetry latest
+      - asdf global poetry latest
+      - poetry config virtualenvs.create false  # Key
+    post_install:
+      - poetry install -E docs
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  #fail_on_warning: true

docs/api/simulator.rst

@@ -1,26 +1,26 @@
 Simulator
 =========
 
-.. automodule:: elastica.wrappers.base_system
+.. automodule:: elastica.modules.base_system
    :members:
    :exclude-members: __weakref__, __init__, __str__, insert
 
-.. automodule:: elastica.wrappers.callbacks
+.. automodule:: elastica.modules.callbacks
    :members:
    :exclude-members: __weakref__, __init__, _callbacks, _CallBack
 
-.. automodule:: elastica.wrappers.connections
+.. automodule:: elastica.modules.connections
    :members:
    :exclude-members: __weakref__, __init__, __call__, _Connect
 
-.. automodule:: elastica.wrappers.constraints
+.. automodule:: elastica.modules.constraints
    :members:
    :exclude-members: __weakref__, __init__, _Constraint
 
-.. automodule:: elastica.wrappers.forcing
+.. automodule:: elastica.modules.forcing
    :members:
    :exclude-members: __weakref__, __init__, __call__, _ExtForceTorque 
 
-.. automodule:: elastica.wrappers.damping
+.. automodule:: elastica.modules.damping
    :members:
-   :exclude-members: __weakref__, __init__, __call__, _Damper
+   :exclude-members: __weakref__, __init__, __call__, _Damper

docs/guide/workflow.md

@@ -9,7 +9,7 @@ When using PyElastica, users will setup a simulation in which they define a syst
 <h2>1. Setup Simulation</h2>
 
 ```python
-from elastica.wrappers import (
+from elastica.modules import (
     BaseSystemCollection,
     Connections,
     Constraints,
@@ -28,7 +28,7 @@ class SystemSimulator(
 ):
     pass
 ```
-This simply combines all the wrappers previously imported together. If a wrapper is not needed for the simulation, it does not need to be added here.
+This simply combines all the modules previously imported together. If a module is not needed for the simulation, it does not need to be added here.
 
 Available components are:
 

elastica/__init__.py

@@ -1,5 +1,5 @@
 from collections import defaultdict
-from elastica.wrappers import *
+from elastica.modules import *
 from elastica.rod.cosserat_rod import *
 from elastica.rod.knot_theory import *
 from elastica.rigidbody import *

elastica/boundary_conditions.py

@@ -2,9 +2,7 @@
 __all__ = [
     "ConstraintBase",
     "FreeBC",
-    "FreeRod",  # Deprecated: remove v0.3.0
     "OneEndFixedBC",
-    "OneEndFixedRod",  # Deprecated: remove v0.3.0
     "GeneralConstraint",
     "FixedConstraint",
     "HelicalBucklingBC",

elastica/wrappers/__init__.py → elastica/modules/__init__.py

@@ -1,5 +1,5 @@
 __doc__ = """
-Wrappers are simple objects that you can subclass to provide extended
+Modules are simple objects that you can subclass to provide extended
 functionality to the simulation, such as adding an environment, joints, controllers, etc.
 """
 

elastica/wrappers/base_system.py → elastica/modules/base_system.py

@@ -12,7 +12,7 @@
 
 from elastica.rod import RodBase
 from elastica.rigidbody import RigidBodyBase
-from elastica.wrappers.memory_block import construct_memory_block_structures
+from elastica.modules.memory_block import construct_memory_block_structures
 
 
 class BaseSystemCollection(MutableSequence):

elastica/wrappers/callbacks.py → elastica/modules/callbacks.py

@@ -10,7 +10,7 @@
 
 class CallBacks:
     """
-    CallBacks class is a wrapper for calling callback functions, set by the user. If the user
+    CallBacks class is a module for calling callback functions, set by the user. If the user
     wants to collect data from the simulation, the simulator class has to be derived
     from the CallBacks class.
 
@@ -80,7 +80,7 @@ def _callback_execution(self, time, current_step: int, *args, **kwargs):
 
 class _CallBack:
     """
-    CallBack wrapper private class
+    CallBack module private class
 
         Attributes
         ----------
@@ -107,7 +107,7 @@ def __init__(self, sys_idx: int):
 
     def using(self, callback_cls, *args, **kwargs):
         """
-        This method is a wrapper to set which callback class is used to collect data
+        This method is a module to set which callback class is used to collect data
         from user defined rod-like object.
 
         Parameters

elastica/wrappers/connections.py → elastica/modules/connections.py

@@ -11,7 +11,7 @@
 
 class Connections:
     """
-    The Connections class is a wrapper for connecting rod-like objects using joints selected
+    The Connections class is a module for connecting rod-like objects using joints selected
     by the user. To connect two rod-like objects, the simulator class must be derived from
     the Connections class.
 
@@ -106,7 +106,7 @@ def _call_connections(self, *args, **kwargs):
 
 class _Connect:
     """
-    Connect wrapper private class
+    Connect module private class
 
     Attributes
     ----------
@@ -231,7 +231,7 @@ def set_index(self, first_idx, second_idx):
 
     def using(self, connect_cls, *args, **kwargs):
         """
-        This method is a wrapper to set which joint class is used to connect
+        This method is a module to set which joint class is used to connect
         user defined rod-like objects.
 
         Parameters

elastica/wrappers/constraints.py → elastica/modules/constraints.py

@@ -11,7 +11,7 @@
 
 class Constraints:
     """
-    The Constraints class is a wrapper for enforcing displacement boundary conditions.
+    The Constraints class is a module for enforcing displacement boundary conditions.
     To enforce boundary conditions on rod-like objects, the simulator class
     must be derived from Constraints class.
 
@@ -87,7 +87,7 @@ def _constrain_rates(self, time, *args, **kwargs):
 
 class _Constraint:
     """
-    Constraint wrapper private class
+    Constraint module private class
 
     Attributes
     ----------
@@ -114,7 +114,7 @@ def __init__(self, sys_idx: int):
 
     def using(self, bc_cls, *args, **kwargs):
         """
-        This method is a wrapper to set which boundary condition class is used to
+        This method is a module to set which boundary condition class is used to
         enforce boundary condition from user defined rod-like objects.
 
         Parameters

elastica/wrappers/damping.py → elastica/modules/damping.py

@@ -14,7 +14,7 @@
 
 class Damping:
     """
-    The Damping class is a wrapper for applying damping
+    The Damping class is a module for applying damping
     on rod-like objects, the simulator class must be derived from
     Damping class.
 
@@ -76,7 +76,7 @@ def _dampen_rates(self, time, *args, **kwargs):
 
 class _Damper:
     """
-    Damper wrapper private class
+    Damper module private class
 
     Attributes
     ----------
@@ -103,7 +103,7 @@ def __init__(self, sys_idx: int):
 
     def using(self, damper_cls, *args, **kwargs):
         """
-        This method is a wrapper to set which damper class is used to
+        This method is a module to set which damper class is used to
         enforce damping from user defined rod-like objects.
 
         Parameters

elastica/wrappers/forcing.py → elastica/modules/forcing.py

@@ -10,7 +10,7 @@
 
 class Forcing:
     """
-    The Forcing class is a wrapper for applying boundary conditions that
+    The Forcing class is a module for applying boundary conditions that
     consist of applied external forces. To apply forcing on rod-like objects,
     the simulator class must be derived from the Forcing class.
 
@@ -89,7 +89,7 @@ def _call_ext_forces_torques(self, time, *args, **kwargs):
 
 class _ExtForceTorque:
     """
-    Forcing wrapper private class
+    Forcing module private class
 
     Attributes
     ----------
@@ -115,7 +115,7 @@ def __init__(self, sys_idx: int):
 
     def using(self, forcing_cls, *args, **kwargs):
         """
-        This method is a wrapper to set which forcing class is used to apply forcing
+        This method is a module to set which forcing class is used to apply forcing
         to user defined rod-like objects.
 
         Parameters

elastica/wrappers/memory_block.py → elastica/modules/memory_block.py

@@ -1,5 +1,5 @@
 __doc__ = """
-This function is a wrapper to construct memory blocks for different types of systems, such as
+This function is a module to construct memory blocks for different types of systems, such as
 Cosserat Rods, Rigid Body etc.
 """
 

elastica/systems/__init__.py

@@ -30,7 +30,7 @@ def is_system_a_collection(system):
     evolve as the interface evolves. Then we can add those
     requirements on the interface here.
     """
-    from elastica.wrappers import BaseSystemCollection
+    from elastica.modules import BaseSystemCollection
 
     __sys_get_item = getattr(system, "__getitem__", None)
     return issubclass(system.__class__, BaseSystemCollection) or callable(

elastica/wrappers.py

@@ -0,0 +1,21 @@
+import warnings
+
+__all__ = [
+    "BaseSystemCollection",
+    "Connections",
+    "Constraints",
+    "Forcing",
+    "CallBacks",
+    "Damping",
+]
+from elastica.modules.base_system import BaseSystemCollection
+from elastica.modules.connections import Connections
+from elastica.modules.constraints import Constraints
+from elastica.modules.forcing import Forcing
+from elastica.modules.callbacks import CallBacks
+from elastica.modules.damping import Damping
+
+warnings.warn(
+    "elastica.wrappers is refactored to elastica.modules in version 0.3.0.",
+    DeprecationWarning,
+)

examples/Binder/1_Timoshenko_Beam.ipynb

@@ -15,7 +15,7 @@
     "![timoshenko_beam_figure.png](../../assets/timoshenko_beam_figure.png)\n",
     "\n",
     "## Getting Started\n",
-    "To set up the simulation, the first thing you need to do is import the necessary classes. Here we will only import the classes that we need. The `elastica.wrappers` classes make it easy to construct different simulation systems. Along with these wrappers, we need to import a rod class, classes for the boundary conditions, and time-stepping functions. As a note, this method of explicitly importing all classes can be a bit cumbersome. Future releases will simplify this step."
+    "To set up the simulation, the first thing you need to do is import the necessary classes. Here we will only import the classes that we need. The `elastica.modules` classes make it easy to construct different simulation systems. Along with these modules, we need to import a rod class, classes for the boundary conditions, and time-stepping functions. As a note, this method of explicitly importing all classes can be a bit cumbersome. Future releases will simplify this step."
    ]
   },
   {
@@ -41,8 +41,8 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "# Import Wrappers\n",
-    "from elastica.wrappers import BaseSystemCollection, Constraints, Forcing, Damping\n",
+    "# Import modules\n",
+    "from elastica.modules import BaseSystemCollection, Constraints, Forcing, Damping\n",
     "\n",
     "# Import Cosserat Rod Class\n",
     "from elastica.rod.cosserat_rod import CosseratRod\n",
@@ -67,7 +67,7 @@
     }
    },
    "source": [
-    "Now that we have imported all the necessary classes, we want to create our beam system. We do this by combining all the wrappers we need to represent the physics that we to include in the simulation. In this case, that is the `BaseSystemCollection`, `Constraint`, `Forcings` and `Damping` because the simulation will consider a rod that is fixed in place on one end, and subject to an applied force on the other end."
+    "Now that we have imported all the necessary classes, we want to create our beam system. We do this by combining all the modules we need to represent the physics that we to include in the simulation. In this case, that is the `BaseSystemCollection`, `Constraint`, `Forcings` and `Damping` because the simulation will consider a rod that is fixed in place on one end, and subject to an applied force on the other end."
    ]
   },
   {

examples/Binder/2_Slithering_Snake.ipynb

@@ -16,7 +16,7 @@
     "\n",
     "\n",
     "## Getting Started\n",
-    "To set up the simulation, the first thing you need to do is import the necessary classes. As with the Timoshenko bean, we need to import wrapper functions which allow us to more easily construct different simulation systems. We also need to import a rod class, all the necessary forces to be applied, timestepping functions, and callback classes. "
+    "To set up the simulation, the first thing you need to do is import the necessary classes. As with the Timoshenko bean, we need to import modules which allow us to more easily construct different simulation systems. We also need to import a rod class, all the necessary forces to be applied, timestepping functions, and callback classes. "
    ]
   },
   {
@@ -31,8 +31,8 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "# import wrappers\n",
-    "from elastica.wrappers import BaseSystemCollection, Constraints, Forcing, CallBacks, Damping\n",
+    "# import modules\n",
+    "from elastica.modules import BaseSystemCollection, Constraints, Forcing, CallBacks, Damping\n",
     "\n",
     "# import rod class, damping and forces to be applied\n",
     "from elastica.rod.cosserat_rod import CosseratRod\n",
@@ -58,7 +58,7 @@
    },
    "source": [
     "## Initialize System and Add Rod\n",
-    "The first thing to do is initialize the simulator class by combining all the imported wrappers. After initializing, we will generate a rod and add it to the simulation. "
+    "The first thing to do is initialize the simulator class by combining all the imported modules. After initializing, we will generate a rod and add it to the simulation. "
    ]
   },
   {

examples/Visualization/ContinuumSnakeVisualization/continuum_snake.py

@@ -1,6 +1,6 @@
 import numpy as np
 from collections import defaultdict
-from elastica.wrappers import BaseSystemCollection, Constraints, Forcing, CallBacks
+from elastica.modules import BaseSystemCollection, Constraints, Forcing, CallBacks
 from elastica.rod.cosserat_rod import CosseratRod
 from elastica.external_forces import GravityForces, MuscleTorques
 from elastica.interaction import AnisotropicFrictionalPlane

tests/test_wrappers/test_base_system.py → tests/test_modules/test_base_system.py

@@ -1,9 +1,9 @@
-__doc__ = """ Test wrappers for base systems """
+__doc__ = """ Test modules for base systems """
 
 import pytest
 import numpy as np
 
-from elastica.wrappers import (
+from elastica.modules import (
     BaseSystemCollection,
     Constraints,
     Forcing,

tests/test_wrappers/test_callbacks.py → tests/test_modules/test_callbacks.py

@@ -1,10 +1,10 @@
-__doc__ = """ Test wrappers for callback """
+__doc__ = """ Test modules for callback """
 import numpy as np
 from numpy.testing import assert_allclose
 import pytest
 
-from elastica.wrappers import CallBacks
-from elastica.wrappers.callbacks import _CallBack
+from elastica.modules import CallBacks
+from elastica.modules.callbacks import _CallBack
 
 
 class TestCallBacks:
@@ -61,7 +61,7 @@ def mock_init(self, *args, **kwargs):
 
 
 class TestCallBacksMixin:
-    from elastica.wrappers import BaseSystemCollection
+    from elastica.modules import BaseSystemCollection
 
     class SystemCollectionWithCallBacksMixedin(BaseSystemCollection, CallBacks):
         pass