biobuddy 0.1.0__tar.gz

biobuddy-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 pyomeca
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

biobuddy-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: biobuddy
+Version: 0.1.0
+Summary: A generic interface to generate a virtual buddy
+Home-page: https://github.com/pyomeca/biobuddy
+Author: Eve Charbonneau
+Author-email: EveCharbie <eve.charbie@gmail.com>, Pariterre <pariterre@hotmail.com>
+Project-URL: Documentation, https://github.com/pyomeca/biobuddy/tree/main#readme
+Project-URL: Source, https://github.com/pyomeca/biobuddy
+Project-URL: Tracker, https://github.com/pyomeca/biobuddy/issues
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: ezc3d
+Requires-Dist: lxml
+Requires-Dist: scipy
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: black; extra == "test"
+Requires-Dist: opensim; extra == "test"
+Requires-Dist: biorbd; extra == "test"
+Requires-Dist: pyorerun; extra == "test"
+Requires-Dist: deepdiff; extra == "test"
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+
+
+![biobuddy](https://github.com/user-attachments/assets/c8689155-0b26-4e13-835c-cdb6696e1acb)
+
+`BioBuddy` is an open-source tool for [translating](#model-translation), [creating](#model-creation) and [personalizing](#model-personalization) musculoskeletal models across different formats (e.g., .osim, .bioMod). By enabling reliable interoperability between modeling environments, BioBuddy allows researchers to focus on scientific questions rather than technical constraints.
+
+<!---
+[![Actions Status](https://github.com/pyomeca/biobuddy/workflows/CI/badge.svg)](https://github.com/pyomeca/biobuddy/actions)
+[![PyPI](https://anaconda.org/conda-forge/biobuddy/badges/latest_release_date.svg)](https://pypi.org/project/biobuddy/)
+--->
+
+[![codecov](https://codecov.io/gh/pyomeca/biobuddy/branch/main/graph/badge.svg)](https://codecov.io/gh/pyomeca/biobuddy)
+[![Discord](https://img.shields.io/discord/1340640457327247460.svg?label=chat&logo=discord&color=7289DA)](https://discord.gg/Ux7BkdjQFW)
+
+# How to install 
+Currently, the only way to install `BioBuddy` is from source. But it will be available on conda-forge and pip in the near future.
+
+If you are a user, you can set up your environment with minimal dependencies.
+```bash
+conda install -c conda-forge python=3.11.11 pip
+pip install scipy==1.15.1 numpy==1.25.2 lxml ezc3d
+```
+Note: On mac, you might need to add `conda install conda-forge::libcxx`
+
+However, if you are a developer and want to contribute, you will need to set up your environment using the following command:
+Due to the OpenSim dependency used only in BioBuddy's tests, we recommend using python=3.11.
+```bash
+pip install pytest pytest-cov codecov
+conda install -c opensim-org opensim=4.5.1
+conda install -c conda-forge biorbd=1.11.2 deepdiff
+```
+
+# Model translation
+You can load the original model using one of the `BiomechanicalModelReal().from_[format]` methods, and then export it 
+into another format using the `BiomechanicalModelReal.to_[format]` method (see [example](examples/read_and_write_models.py)).
+```python3
+from biobuddy import BiomechanicalModelReal
+
+# Read an .osim file
+model = BiomechanicalModelReal().from_osim(
+    filepath=osim_filepath,
+    # Other optional parameters here
+)
+
+# Translate it into a .bioMod file
+model.to_biomod(biomod_filepath)
+```
+
+# Model creation
+A model can also be created from scratch using the `BiomechanicalModel`. In this generic model, everything can be defined 
+through functions (i.e., without numerical values). The subject specific model (a `BiomechanicalModelReal`) can then be 
+generated by evaluating the generic model with a motion capture trial. This feature is especially useful for kinematic 
+models where the joint centers are defined based on anatomical marker placement (like in the plug in gait, see full 
+[example](examples/create_model_from_c3d.py)). 
+
+Here is a simple example of how to add components to such a model:
+```python3
+
+# Create the model
+model = BiomechanicalModel()
+de_leva = DeLevaTable(total_mass=60, sex=Sex.FEMALE)
+
+# Add components to build the kinematic chain
+model.add_segment(
+    Segment(
+        name="HEAD",
+        parent_name="TRUNK",
+        segment_coordinate_system=SegmentCoordinateSystem(
+            "BOTTOM_HEAD",
+            first_axis=Axis(name=Axis.Name.Z, start="BOTTOM_HEAD", end="HEAD_Z"),
+            second_axis=Axis(name=Axis.Name.X, start="BOTTOM_HEAD", end="HEAD_XZ"),
+            axis_to_keep=Axis.Name.Z,
+        ),
+        mesh=Mesh(("BOTTOM_HEAD", "TOP_HEAD", "HEAD_Z", "HEAD_XZ", "BOTTOM_HEAD")),
+        inertia_parameters=de_leva[SegmentName.HEAD],
+    )
+)
+model.segments["HEAD"].add_marker(Marker("BOTTOM_HEAD"))
+model.segments["HEAD"].add_marker(Marker("TOP_HEAD"))
+model.segments["HEAD"].add_marker(Marker("HEAD_Z"))
+model.segments["HEAD"].add_marker(Marker("HEAD_XZ"))
+
+# Evaluate the model with a motion capture trial
+model_real = model.to_real(C3dData(c3d_filepath))
+```
+
+There are many different components available to build a model (see this [example](examples/create_model.py) to see how to add those components to your model).
+
+![Build_segment](docs/images/Build_segment.png)
+
+# Model personalization/modification
+The current version of BioBuddy allows you to modify your `BiomechanicalModelReal` to personalize it to your subjects by:
+- [Scaling](###scaling)
+- [Identifying joint centers](###joint-center-identification)
+- [Merging segments](#merging-segments)
+- [Modifying the kinematic chain](#modifying-the-kinematic-chain)
+
+### Scaling:
+The scaling is performed by the `ScaleTool` which can be initialized from scratch like this:
+```python3
+original_model = BiomechanicalModelReal()
+
+# Create the scaling configuration
+scaling_configuration = ScaleTool(original_model)
+
+# Add a scaling segment for the pelvis
+scaling_configuration.add_scaling_segment(
+    SegmentScaling(
+        name="pelvis",
+        scaling_type= SegmentWiseScaling(
+            axis=Translations.XYZ,
+            marker_pairs=[
+                ["RASIS", "LASIS"],
+                ["RPSIS", "LPSIS"],
+            ]
+        )
+    )
+)
+
+# Add marker weights for the pelvis segment
+scaling_configuration.add_marker_weight(MarkerWeight(name="RASIS", weight=1.0))
+scaling_configuration.add_marker_weight(MarkerWeight(name="LASIS", weight=1.0))
+scaling_configuration.add_marker_weight(MarkerWeight(name="RPSIS", weight=0.5))
+scaling_configuration.add_marker_weight(MarkerWeight(name="LPSIS", weight=0.5))
+```
+or by reading from an existing file (e.g., `.xml` or `.biomod`) using the appropriate `ScaleTool.from_[format]` method.
+Once the scaling configuration is set up, you can scale your model based on a static trial (`.c3d` file) and the total 
+mass of your participant using the `ScaleTool.scale` like this:
+```python3
+# Performing the scaling based on a static trial
+scale_tool = ScaleTool.from_biomod(biomod_filepath)
+scaled_model = scale_tool.scale(static_c3d=C3dData(filepath), mass=mass)
+```
+
+For now, there are three scaling methods available:
+- `BodyWiseScaling`: scales the entire body based on the total height of the participant.
+- `SegmentWiseScaling`: scales the segment based on the distance between marker pairs.
+- `AxisWiseScaling`: scales each axis of the segment independently based on the distance between marker pairs.
+![scaling_types](docs/images/Scaling_with_names.png)
+
+### Joint center identification:
+The `JointCenterTool` allows you to identify the joint centers of your model based on the movement of segments during 
+functional trials.
+First, you need to define the joint center configuration using `JointCenterTool.add()` method to define the joint 
+you want to modify.
+Then, you can use the `JointCenterTool.replace_joint_centers()` method to modify each joint.
+```python3
+from biobuddy import JointCenterTool
+
+# Set up the joint center identification tool
+joint_center_tool = JointCenterTool(scaled_model)
+# Example for the right hip
+joint_center_tool.add(
+    Score(
+        functional_c3d=C3dData(c3d_filepath, first_frame=100, last_frame=900),
+        parent_name="pelvis",
+        child_name="femur_r",
+        parent_marker_names=["RASIS", "LASIS", "LPSIS", "RPSIS"],
+        child_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg", "RMFE", "RLFE"],
+    )
+)
+# Example for the right knee
+joint_center_tool.add(
+    Sara(
+        functional_c3d=C3dData(c3d_filepath),
+        parent_name="femur_r",
+        child_name="tibia_r",
+        parent_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg"],
+        child_marker_names=["RATT", "RUB_Tib", "RDF_Tib", "RDB_Tib", "RSPH", "RLM"],
+    )
+)
+
+# Perform the joint center identification
+modified_model = joint_center_tool.replace_joint_centers()
+```
+For now, two algorithms were implemented `SCoRE` to locate the position of the joint center and `SARA` 
+to identify the joint axis of rotation. Please note that in both cases, all segment components stay the same, only the 
+joint position and axis are modified.
+
+![SCoRE_SARA](docs/images/SCoRE_SARA.png)
+
+### Merging segments:
+The `MergeSegmentTool` allows you to merge two segments into one (including inertial parameters and all the components on the segment).
+You can define which segments you want to merge using `SegmentMerge`, which requires the names of the segments to merge and the name of the new segment.
+```python3
+merge_tool = MergeSegmentsTool(original_model)
+# By default, segments merge together setting the new segment coordinate as the mean of the old coordinates
+merge_tool.add(
+   SegmentMerge(
+      name="LOWER_ARMS", 
+      first_segment_name="L_LOWER_ARM", 
+      second_segment_name="R_LOWER_ARM",
+   )
+)
+# But you can also merge one segment on top of another one by specifying the segment coordinate system to keep
+merge_tool.add(
+   SegmentMerge(
+      name="R_LOWER_ARM_AND_HAND", 
+      first_segment_name="R_LOWER_ARM", 
+      second_segment_name="R_HAND", 
+      merged_origin_name="R_LOWER_ARM",
+   )
+)
+modified_model = merge_tool.merge()
+```
+
+![merge_segments](docs/images/merge_segments.png)
+
+### Modifying the kinematic chain:
+The `ModifyKinematicChainTool` allows you to modify the kinematic chain of your model.
+For now, the only modification available is to change which segment is the first segment of the kinematic chain (`ChangeFirstSegment`).
+It inverts all segments between the original first segment and the new first segment.
+```python3
+kinematic_chain_modifier = ModifyKinematicChainTool(original_model)
+kinematic_chain_modifier.add(ChangeFirstSegment(first_segment_name="FOOT"))
+modified_model = kinematic_chain_modifier.modify()
+```
+
+![kinematic_chain_modifier](docs/images/kinematic_chain_modifier.png)
+
+# Note
+Understandably, not all modeling formats have the same functionalities, so some features may not be available for all 
+formats. We will try to keep here a list up to date of the features that are available in BioBuddy that are not 
+available for each format: 
+ - biorbd (.bioMod):
+   - `PathPointCondition` is not implemented yet in biorbd. So if your BioBuddy model has this component, we recommend running `BiomechanicalModelReal.fix_via_points(q)` before `BiomechanicalModelReal.to_biomod(path)`. This will evaluate the via point conditions at the desired posture (which should be close to the range of motion during the movement studied). If the condition is not meet, the via point is inactive, so it is removed from the model. Please note that this is a destructive operation, once the conditions are evaluated, they are removed from the model and the remaining via points are fixed on the segments. 
+   - `PathPointMovement` are not implemented yet in biorbd. So if your BioBuddy model has this components, we recommend running `BiomechanicalModelReal.fix_via_points(q)` before `BiomechanicalModelReal.to_biomod(path)`. This will fix the position of the moving via points, muscle origin, and muscle insertion by evaluating the position function at the desired posture (which should be close to the range of motion during the movement studied). Please note that this is a destructive operation, once the movements are evaluated, they are removed from the model and the remaining via points are fixed on the segments.  
+
+# How to cite
+```
+@software{biobuddy_2025,
+  author       = {Eve Charbonneau, Pierre Puchaud, Teddy Caderby, Mickael Begon, Amedeo Ceglia, Benjamin Michaud},
+  title        = {Bringing the musculoskeletal modeling community together with BioBuddy},
+  month        = april,
+  year         = 2025,
+  publisher    = {submitted to Congrès de la Société de biomécanique},
+  url          = {https://github.com/pyomeca/biobuddy}
+}
+```
+
+# How to contribute
+Our goal is to support as many musculoskeletal model formats as possible, so do not hesitate to contact us if you'd like to see your favorite format supported by BioBuddy. 
+If you are using BioBuddy and encounter any problem, please open an issue on this GitHub repository. 
+We are also open to suggestions for new features or improvements to existing functionality.
+All contributions are welcome!

biobuddy-0.1.0/README.md

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+
+![biobuddy](https://github.com/user-attachments/assets/c8689155-0b26-4e13-835c-cdb6696e1acb)
+
+`BioBuddy` is an open-source tool for [translating](#model-translation), [creating](#model-creation) and [personalizing](#model-personalization) musculoskeletal models across different formats (e.g., .osim, .bioMod). By enabling reliable interoperability between modeling environments, BioBuddy allows researchers to focus on scientific questions rather than technical constraints.
+
+<!---
+[![Actions Status](https://github.com/pyomeca/biobuddy/workflows/CI/badge.svg)](https://github.com/pyomeca/biobuddy/actions)
+[![PyPI](https://anaconda.org/conda-forge/biobuddy/badges/latest_release_date.svg)](https://pypi.org/project/biobuddy/)
+--->
+
+[![codecov](https://codecov.io/gh/pyomeca/biobuddy/branch/main/graph/badge.svg)](https://codecov.io/gh/pyomeca/biobuddy)
+[![Discord](https://img.shields.io/discord/1340640457327247460.svg?label=chat&logo=discord&color=7289DA)](https://discord.gg/Ux7BkdjQFW)
+
+# How to install 
+Currently, the only way to install `BioBuddy` is from source. But it will be available on conda-forge and pip in the near future.
+
+If you are a user, you can set up your environment with minimal dependencies.
+```bash
+conda install -c conda-forge python=3.11.11 pip
+pip install scipy==1.15.1 numpy==1.25.2 lxml ezc3d
+```
+Note: On mac, you might need to add `conda install conda-forge::libcxx`
+
+However, if you are a developer and want to contribute, you will need to set up your environment using the following command:
+Due to the OpenSim dependency used only in BioBuddy's tests, we recommend using python=3.11.
+```bash
+pip install pytest pytest-cov codecov
+conda install -c opensim-org opensim=4.5.1
+conda install -c conda-forge biorbd=1.11.2 deepdiff
+```
+
+# Model translation
+You can load the original model using one of the `BiomechanicalModelReal().from_[format]` methods, and then export it 
+into another format using the `BiomechanicalModelReal.to_[format]` method (see [example](examples/read_and_write_models.py)).
+```python3
+from biobuddy import BiomechanicalModelReal
+
+# Read an .osim file
+model = BiomechanicalModelReal().from_osim(
+    filepath=osim_filepath,
+    # Other optional parameters here
+)
+
+# Translate it into a .bioMod file
+model.to_biomod(biomod_filepath)
+```
+
+# Model creation
+A model can also be created from scratch using the `BiomechanicalModel`. In this generic model, everything can be defined 
+through functions (i.e., without numerical values). The subject specific model (a `BiomechanicalModelReal`) can then be 
+generated by evaluating the generic model with a motion capture trial. This feature is especially useful for kinematic 
+models where the joint centers are defined based on anatomical marker placement (like in the plug in gait, see full 
+[example](examples/create_model_from_c3d.py)). 
+
+Here is a simple example of how to add components to such a model:
+```python3
+
+# Create the model
+model = BiomechanicalModel()
+de_leva = DeLevaTable(total_mass=60, sex=Sex.FEMALE)
+
+# Add components to build the kinematic chain
+model.add_segment(
+    Segment(
+        name="HEAD",
+        parent_name="TRUNK",
+        segment_coordinate_system=SegmentCoordinateSystem(
+            "BOTTOM_HEAD",
+            first_axis=Axis(name=Axis.Name.Z, start="BOTTOM_HEAD", end="HEAD_Z"),
+            second_axis=Axis(name=Axis.Name.X, start="BOTTOM_HEAD", end="HEAD_XZ"),
+            axis_to_keep=Axis.Name.Z,
+        ),
+        mesh=Mesh(("BOTTOM_HEAD", "TOP_HEAD", "HEAD_Z", "HEAD_XZ", "BOTTOM_HEAD")),
+        inertia_parameters=de_leva[SegmentName.HEAD],
+    )
+)
+model.segments["HEAD"].add_marker(Marker("BOTTOM_HEAD"))
+model.segments["HEAD"].add_marker(Marker("TOP_HEAD"))
+model.segments["HEAD"].add_marker(Marker("HEAD_Z"))
+model.segments["HEAD"].add_marker(Marker("HEAD_XZ"))
+
+# Evaluate the model with a motion capture trial
+model_real = model.to_real(C3dData(c3d_filepath))
+```
+
+There are many different components available to build a model (see this [example](examples/create_model.py) to see how to add those components to your model).
+
+![Build_segment](docs/images/Build_segment.png)
+
+# Model personalization/modification
+The current version of BioBuddy allows you to modify your `BiomechanicalModelReal` to personalize it to your subjects by:
+- [Scaling](###scaling)
+- [Identifying joint centers](###joint-center-identification)
+- [Merging segments](#merging-segments)
+- [Modifying the kinematic chain](#modifying-the-kinematic-chain)
+
+### Scaling:
+The scaling is performed by the `ScaleTool` which can be initialized from scratch like this:
+```python3
+original_model = BiomechanicalModelReal()
+
+# Create the scaling configuration
+scaling_configuration = ScaleTool(original_model)
+
+# Add a scaling segment for the pelvis
+scaling_configuration.add_scaling_segment(
+    SegmentScaling(
+        name="pelvis",
+        scaling_type= SegmentWiseScaling(
+            axis=Translations.XYZ,
+            marker_pairs=[
+                ["RASIS", "LASIS"],
+                ["RPSIS", "LPSIS"],
+            ]
+        )
+    )
+)
+
+# Add marker weights for the pelvis segment
+scaling_configuration.add_marker_weight(MarkerWeight(name="RASIS", weight=1.0))
+scaling_configuration.add_marker_weight(MarkerWeight(name="LASIS", weight=1.0))
+scaling_configuration.add_marker_weight(MarkerWeight(name="RPSIS", weight=0.5))
+scaling_configuration.add_marker_weight(MarkerWeight(name="LPSIS", weight=0.5))
+```
+or by reading from an existing file (e.g., `.xml` or `.biomod`) using the appropriate `ScaleTool.from_[format]` method.
+Once the scaling configuration is set up, you can scale your model based on a static trial (`.c3d` file) and the total 
+mass of your participant using the `ScaleTool.scale` like this:
+```python3
+# Performing the scaling based on a static trial
+scale_tool = ScaleTool.from_biomod(biomod_filepath)
+scaled_model = scale_tool.scale(static_c3d=C3dData(filepath), mass=mass)
+```
+
+For now, there are three scaling methods available:
+- `BodyWiseScaling`: scales the entire body based on the total height of the participant.
+- `SegmentWiseScaling`: scales the segment based on the distance between marker pairs.
+- `AxisWiseScaling`: scales each axis of the segment independently based on the distance between marker pairs.
+![scaling_types](docs/images/Scaling_with_names.png)
+
+### Joint center identification:
+The `JointCenterTool` allows you to identify the joint centers of your model based on the movement of segments during 
+functional trials.
+First, you need to define the joint center configuration using `JointCenterTool.add()` method to define the joint 
+you want to modify.
+Then, you can use the `JointCenterTool.replace_joint_centers()` method to modify each joint.
+```python3
+from biobuddy import JointCenterTool
+
+# Set up the joint center identification tool
+joint_center_tool = JointCenterTool(scaled_model)
+# Example for the right hip
+joint_center_tool.add(
+    Score(
+        functional_c3d=C3dData(c3d_filepath, first_frame=100, last_frame=900),
+        parent_name="pelvis",
+        child_name="femur_r",
+        parent_marker_names=["RASIS", "LASIS", "LPSIS", "RPSIS"],
+        child_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg", "RMFE", "RLFE"],
+    )
+)
+# Example for the right knee
+joint_center_tool.add(
+    Sara(
+        functional_c3d=C3dData(c3d_filepath),
+        parent_name="femur_r",
+        child_name="tibia_r",
+        parent_marker_names=["RGT", "RUB_Leg", "RUF_Leg", "FBF_Leg"],
+        child_marker_names=["RATT", "RUB_Tib", "RDF_Tib", "RDB_Tib", "RSPH", "RLM"],
+    )
+)
+
+# Perform the joint center identification
+modified_model = joint_center_tool.replace_joint_centers()
+```
+For now, two algorithms were implemented `SCoRE` to locate the position of the joint center and `SARA` 
+to identify the joint axis of rotation. Please note that in both cases, all segment components stay the same, only the 
+joint position and axis are modified.
+
+![SCoRE_SARA](docs/images/SCoRE_SARA.png)
+
+### Merging segments:
+The `MergeSegmentTool` allows you to merge two segments into one (including inertial parameters and all the components on the segment).
+You can define which segments you want to merge using `SegmentMerge`, which requires the names of the segments to merge and the name of the new segment.
+```python3
+merge_tool = MergeSegmentsTool(original_model)
+# By default, segments merge together setting the new segment coordinate as the mean of the old coordinates
+merge_tool.add(
+   SegmentMerge(
+      name="LOWER_ARMS", 
+      first_segment_name="L_LOWER_ARM", 
+      second_segment_name="R_LOWER_ARM",
+   )
+)
+# But you can also merge one segment on top of another one by specifying the segment coordinate system to keep
+merge_tool.add(
+   SegmentMerge(
+      name="R_LOWER_ARM_AND_HAND", 
+      first_segment_name="R_LOWER_ARM", 
+      second_segment_name="R_HAND", 
+      merged_origin_name="R_LOWER_ARM",
+   )
+)
+modified_model = merge_tool.merge()
+```
+
+![merge_segments](docs/images/merge_segments.png)
+
+### Modifying the kinematic chain:
+The `ModifyKinematicChainTool` allows you to modify the kinematic chain of your model.
+For now, the only modification available is to change which segment is the first segment of the kinematic chain (`ChangeFirstSegment`).
+It inverts all segments between the original first segment and the new first segment.
+```python3
+kinematic_chain_modifier = ModifyKinematicChainTool(original_model)
+kinematic_chain_modifier.add(ChangeFirstSegment(first_segment_name="FOOT"))
+modified_model = kinematic_chain_modifier.modify()
+```
+
+![kinematic_chain_modifier](docs/images/kinematic_chain_modifier.png)
+
+# Note
+Understandably, not all modeling formats have the same functionalities, so some features may not be available for all 
+formats. We will try to keep here a list up to date of the features that are available in BioBuddy that are not 
+available for each format: 
+ - biorbd (.bioMod):
+   - `PathPointCondition` is not implemented yet in biorbd. So if your BioBuddy model has this component, we recommend running `BiomechanicalModelReal.fix_via_points(q)` before `BiomechanicalModelReal.to_biomod(path)`. This will evaluate the via point conditions at the desired posture (which should be close to the range of motion during the movement studied). If the condition is not meet, the via point is inactive, so it is removed from the model. Please note that this is a destructive operation, once the conditions are evaluated, they are removed from the model and the remaining via points are fixed on the segments. 
+   - `PathPointMovement` are not implemented yet in biorbd. So if your BioBuddy model has this components, we recommend running `BiomechanicalModelReal.fix_via_points(q)` before `BiomechanicalModelReal.to_biomod(path)`. This will fix the position of the moving via points, muscle origin, and muscle insertion by evaluating the position function at the desired posture (which should be close to the range of motion during the movement studied). Please note that this is a destructive operation, once the movements are evaluated, they are removed from the model and the remaining via points are fixed on the segments.  
+
+# How to cite
+```
+@software{biobuddy_2025,
+  author       = {Eve Charbonneau, Pierre Puchaud, Teddy Caderby, Mickael Begon, Amedeo Ceglia, Benjamin Michaud},
+  title        = {Bringing the musculoskeletal modeling community together with BioBuddy},
+  month        = april,
+  year         = 2025,
+  publisher    = {submitted to Congrès de la Société de biomécanique},
+  url          = {https://github.com/pyomeca/biobuddy}
+}
+```
+
+# How to contribute
+Our goal is to support as many musculoskeletal model formats as possible, so do not hesitate to contact us if you'd like to see your favorite format supported by BioBuddy. 
+If you are using BioBuddy and encounter any problem, please open an issue on this GitHub repository. 
+We are also open to suggestions for new features or improvements to existing functionality.
+All contributions are welcome!

biobuddy-0.1.0/biobuddy/__init__.py

@@ -0,0 +1,31 @@
+# Version
+from .version import __version__
+
+# Some classes to define the BiomechanicalModel
+from .components import *
+
+# Some utilities
+from .utils import *
+
+# Segment predefined characteristics
+from .characteristics import *
+
+# Mesh modifications
+from .mesh_parser import *
+
+# Model parsers
+from .model_parser import *
+
+# Model modifiers
+from .model_modifiers import *
+
+
+__all__ = (
+    components.__all__
+    + utils.__all__
+    + characteristics.__all__
+    + mesh_parser.__all__
+    + model_parser.__all__
+    + model_modifiers.__all__
+    + ["__version__"]
+)

biobuddy-0.1.0/biobuddy/characteristics/__init__.py

@@ -0,0 +1,8 @@
+from .de_leva import DeLevaTable, Sex, SegmentName
+
+
+__all__ = [
+    DeLevaTable.__name__,
+    Sex.__name__,
+    SegmentName.__name__,
+]