Proper python wrapper #372

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Merged

pariterre merged 31 commits into pyomeca:master from pariterre:python_wrapper

Sep 25, 2025

.vscode/launch.json

            
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    @@ -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

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+Diff line change
@@ Expand Up / @@ -9,4 +9,10 @@ @@
         "[cpp]": {
             "editor.defaultFormatter": "ms-vscode.cpptools"
         },
+        "[python]": {
+            "editor.defaultFormatter": "ms-python.black-formatter",
+            "editor.rulers": [
+            ],
+        }
     }

CMakeLists.txt

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+Diff line change
@@ -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)
@@ Expand Down @@

README.md

            
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    @@ -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

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@@ Expand Up / @@ -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]*)*$")
@@ Expand Down @@

binding/python3/__init__.py

            
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    @@ -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

-Original file line number
+Diff line change
@@ -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__,
+    ]

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