Merge pull request #372 from pariterre/python_wrapper

Proper python wrapper

Author: pariterre

.vscode/launch.json

@@ -5,13 +5,22 @@
     "version": "0.2.0",
     "configurations": [
         {
-            "name": "Forward dynamics Python example",
+            "name": "Python: Current example file",
             "type": "debugpy",
             "request": "launch",
-            "program": "${workspaceFolder}/examples/python3/forward_dynamics.py",
+            "program": "${file}",
             "cwd": "${workspaceFolder}/examples/python3",
             "console": "integratedTerminal",
-            "justMyCode": false,
+            "justMyCode": false
+        },
+        {
+            "name": "Python: Current test file",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "cwd": "${workspaceFolder}/test/binding/python3",
+            "console": "integratedTerminal",
+            "justMyCode": false
         }
     ]
 }

.vscode/settings.json

@@ -9,4 +9,10 @@
     "[cpp]": {
         "editor.defaultFormatter": "ms-vscode.cpptools"
     },
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.rulers": [
+            120
+        ],
+    }
 }

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.17)
 
-project(biorbd VERSION 1.11.3)
+project(biorbd VERSION 1.12.0)
 set(BIORBD_ROOT_FOLDER ${PROJECT_SOURCE_DIR})
 set (BIORBD_NAME_NO_SUFFIX ${PROJECT_NAME})
 set (CMAKE_CXX_STANDARD 11)

README.md

@@ -649,10 +649,10 @@ The tag `r` represented the width of the curve based of the torque-angle relatio
 ...
 
 ## Convert from OpenSim models
-For users who have well-established models in OpenSim and wish to convert them to a `.bioMod`, there's a handy tool called Osim_to_biomod. 
+For users who have well-established models in OpenSim and wish to convert them to a `.bioMod`, there's a handy tool called BioBuddy. 
 This package facilitates the conversion process, ensuring that OpenSim models can be seamlessly integrated into our ecosystem.
 
-To get started with the Osim_to_biomod package, please refer to its documentation and source code available at [Osim_to_biomod](https://github.com/pyomeca/osim_to_biomod) GitHub Repository.
+To get started with the BioBuddy package, please refer to its documentation and source code available at [BioBuddy](https://github.com/pyomeca/biobuddy) GitHub Repository.
 
 Let us know if you'd like any further modifications!
 

binding/python3/CMakeLists.txt

@@ -108,6 +108,10 @@ file(GLOB PYTHON_FILES "${CMAKE_CURRENT_SOURCE_DIR}/*.py")
 INSTALL(FILES ${PYTHON_FILES}
     DESTINATION "${Python3_SITELIB_INSTALL}/${BIORBD_PYTHON_DIR}"
 )
+file(GLOB PYTHON_FILES "${CMAKE_CURRENT_SOURCE_DIR}/wrapper/*.py")
+INSTALL(FILES ${PYTHON_FILES}
+    DESTINATION "${Python3_SITELIB_INSTALL}/${BIORBD_PYTHON_DIR}/wrapper"
+)
 
 # Check if swig has its version 3 or 4, to choose the right place to put the library
 if(${SWIG_VERSION} MATCHES "^3(\.[0-9]*)*$")

binding/python3/__init__.py

@@ -1,28 +1,45 @@
-import numpy as np
 from . import biorbd  # This is created while installing using CMake
 from .biorbd import *
 from ._version import __version__
 from .surface_max_torque_actuator import *
 from .rigid_body import *
 from .utils import *
+from .wrapper import *
+from .wrapper import has_static_optimization, has_extended_kalman_filter
 
 
-if biorbd.currentLinearAlgebraBackend() == 1:
-    from casadi import Function, MX, SX, horzcat
+if biorbd.currentLinearAlgebraBackend() == biorbd.CASADI:
+    from casadi import MX, SX, Function, horzcat
 
-    def to_casadi_func(name, func, *all_param, expand=True):
+    backend = biorbd.CASADI
+
+    def to_casadi_func(name, func, *all_param, expand=True, **kwargs):
         cx_param = []
         for p in all_param:
             if isinstance(p, (MX, SX)):
                 cx_param.append(p)
+        for value in kwargs.values():
+            if isinstance(value, (MX, SX)):
+                cx_param.append(value)
 
         if isinstance(func, (MX, SX, Function)):
-            func_evaluated = func
+            func_evaluated = [func]
         else:
-            func_evaluated = func(*all_param)
+            func_evaluated = func(*all_param, **kwargs)
             if isinstance(func_evaluated, (list, tuple)):
-                func_evaluated = horzcat(*[val if isinstance(val, MX) else val.to_mx() for val in func_evaluated])
+                func_evaluated = [val if isinstance(val, MX) else val.to_mx() for val in func_evaluated]
             elif not isinstance(func_evaluated, MX):
-                func_evaluated = func_evaluated.to_mx()
-        func = Function(name, cx_param, [func_evaluated])
+                func_evaluated = [func_evaluated.to_mx()]
+            else:
+                func_evaluated = [func_evaluated]
+        func = Function(name, cx_param, func_evaluated)
         return func.expand() if expand else func
+
+elif biorbd.currentLinearAlgebraBackend() == biorbd.EIGEN3:
+    backend = biorbd.EIGEN3
+
+    def to_casadi_func(name, func, *all_param, expand=True):
+        raise RuntimeError("to_casadi_func is only available with the CASADI backend")
+
+else:
+    raise RuntimeError("Unknown backend")

binding/python3/wrapper/__init__.py

@@ -0,0 +1,19 @@
+from .biorbd_model import Biorbd
+from .extended_kalman_filter import ExtendedKalmanFilterMarkers, has_extended_kalman_filter
+from .external_force_set import ExternalForceSet
+from .marker import Marker
+from .muscle import Muscle
+from .segment_frame import SegmentFrame
+from .segment import Segment
+from .static_optimization import StaticOptimization, has_static_optimization
+
+__all__ = [
+    Biorbd.__name__,
+    ExtendedKalmanFilterMarkers.__name__,
+    ExternalForceSet.__name__,
+    Marker.__name__,
+    Muscle.__name__,
+    SegmentFrame.__name__,
+    Segment.__name__,
+    StaticOptimization.__name__,
+]