Merge pull request #55 from Ipuch/ground_joints

ground joints and github action

.github/workflows/run_tests.yml

@@ -0,0 +1,55 @@
+name: Run the tests
+
+on: [pull_request]
+jobs:
+  build:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-20.04
+            label: linux-64
+            prefix: /usr/share/miniconda3/envs/bionc
+          - os: macos-latest
+            label: osx-64
+            prefix: /Users/runner/miniconda3/envs/bionc
+          - os: windows-latest
+            label: win-64
+            prefix: C:\Miniconda3\envs\bionc
+    name: ${{ matrix.label }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+          activate-environment: bionc
+          environment-file: environment.yml
+
+      - name: Print mamba info
+        run: | 
+          mamba config --show
+          mamba info
+          mamba list
+          
+      - name: Install extra dependencies
+        run: mamba install pytest-cov pytest pytest-cov codecov -cconda-forge
+
+      - name: Run the actual tests
+        run: pytest -v --color=yes --cov-report term-missing --cov=bionc tests
+
+      - name: Test installed version of bionc
+        run: | 
+          python setup.py install
+          cd
+          python -c "import bionc"
+        
+      - name: Upload coverage to Codecov
+        run: codecov
+        if: matrix.label == 'linux-64'

bionc/__init__.py

@@ -28,11 +28,11 @@
 from .protocols.natural_accelerations import SegmentNaturalAccelerations, NaturalAccelerations
 from .protocols.homogenous_transform import HomogeneousTransform
 
+from .utils.enums import NaturalAxis, CartesianAxis
+
 from casadi.casadi import MX as MX_type
 from numpy import ndarray
 
 # global variable to store the type of the math interface
 casadi_type = MX_type
 numpy_type = ndarray
-
-from .utils.enums import NaturalAxis

bionc/bionc_casadi/__init__.py

@@ -12,5 +12,5 @@
 from .natural_marker import NaturalMarker, Marker
 from .natural_segment import NaturalSegment
 from .inertia_parameters import InertiaParameters
-from .joint import Joint
+from .joint import Joint, GroundJoint
 from .natural_vector import NaturalVector

bionc/bionc_casadi/biomechanical_model.py

@@ -106,7 +106,9 @@ def joint_constraints(self, Q: NaturalCoordinates) -> MX:
         for joint_name, joint in self.joints.items():
             idx = slice(nb_constraints, nb_constraints + joint.nb_constraints)
 
-            Q_parent = Q.vector(self.segments[joint.parent.name].index)
+            Q_parent = (
+                None if joint.parent is None else Q.vector(self.segments[joint.parent.name].index)
+            )  # if the joint is a joint with the ground, the parent is None
             Q_child = Q.vector(self.segments[joint.child.name].index)
             Phi_k[idx] = joint.constraint(Q_parent, Q_child)
 
@@ -129,16 +131,21 @@ def joint_constraints_jacobian(self, Q: NaturalCoordinates) -> np.ndarray:
         nb_constraints = 0
         for joint_name, joint in self.joints.items():
             idx_row = slice(nb_constraints, nb_constraints + joint.nb_constraints)
-            idx_col_parent = slice(
-                12 * self.segments[joint.parent.name].index, 12 * (self.segments[joint.parent.name].index + 1)
-            )
+
+            if joint.parent is not None:  # If the joint is not a ground joint
+                idx_col_parent = slice(
+                    12 * self.segments[joint.parent.name].index, 12 * (self.segments[joint.parent.name].index + 1)
+                )
+                Q_child = Q.vector(self.segments[joint.child.name].index)
+                K_k[idx_row, idx_col_parent] = joint.parent_constraint_jacobian(Q_child)
+
             idx_col_child = slice(
                 12 * self.segments[joint.child.name].index, 12 * (self.segments[joint.child.name].index + 1)
             )
-
-            Q_parent = Q.vector(self.segments[joint.parent.name].index)
-            Q_child = Q.vector(self.segments[joint.child.name].index)
-            K_k[idx_row, idx_col_parent], K_k[idx_row, idx_col_child] = joint.constraint_jacobian(Q_parent, Q_child)
+            Q_parent = (
+                None if joint.parent is None else Q.vector(self.segments[joint.parent.name].index)
+            )  # if the joint is a joint with the ground, the parent is None
+            K_k[idx_row, idx_col_child] = joint.child_constraint_jacobian(Q_parent)
 
             nb_constraints += self.joints[joint_name].nb_constraints
 

bionc/bionc_casadi/cartesian_vector.py

@@ -0,0 +1,43 @@
+from casadi import MX
+import numpy as np
+from ..utils.enums import CartesianAxis
+
+
+class CartesianVector(MX):
+    """
+    Class used to create a natural vector, a vector that is expressed in the natural coordinate system of a segment
+    """
+
+    def __new__(cls, input_array: MX | np.ndarray | list | tuple):
+        """
+        Create a new instance of the class.
+        """
+
+        if not isinstance(input_array, (MX, np.ndarray)):
+            input_array = np.array(input_array)
+
+        obj = MX.__new__(cls)
+
+        if isinstance(input_array, MX):
+            size1 = input_array.shape[0]
+            size2 = input_array.shape[1]
+        else:
+            size1 = input_array.shape[0]
+            size2 = input_array.shape[1] if input_array.shape.__len__() == 2 else 1
+
+        if size1 != 3:
+            raise ValueError("The input array must have 3 elements")
+
+        if size2 != 1:
+            raise ValueError("The position must be a 3d vector with only one column")
+
+        return obj
+
+    @classmethod
+    def axis(cls, axis: CartesianAxis):
+        if axis == CartesianAxis.X:
+            return cls(np.array([1, 0, 0]))
+        elif axis == CartesianAxis.Y:
+            return cls(np.array([0, 1, 0]))
+        elif axis == CartesianAxis.Z:
+            return cls(np.array([0, 0, 1]))