pyorerun

.github/workflows/run_tests.yml

@@ -26,19 +26,18 @@ jobs:
       - 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
+      - name: Print conda info
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda list
 
       - name: Install extra dependencies
-        run: mamba install pytest-cov pytest codecov coverage -cconda-forge
+        run: conda install pytest-cov pytest codecov coverage -cconda-forge
 
       - name: Run the actual tests on LINUX
         run: |

bionc/__init__.py

@@ -34,4 +34,5 @@
 from .utils.enums import NaturalAxis, CartesianAxis, EulerSequence, TransformationMatrixType
 from .utils.ode_solver import RK4, forward_integration
 from .utils.transformation_matrix import TransformationMatrixUtil
-from .vizualization import Viz
+
+# from .vizualization import Viz

bionc/bionc_numpy/biomechanical_model_markers.py

@@ -45,11 +45,14 @@ def markers(self, Q: NaturalCoordinates) -> np.ndarray:
             The position of the markers [3, nbMarkers, nbFrames]
             in the global coordinate system/ inertial coordinate system
         """
-        markers = np.zeros((3, self.nb_markers, Q.shape[1]))
+
+        markers = np.zeros((3, self.nb_markers, Q.shape[1] if len(Q.shape) == 2 else 1))
 
         for segment in self.segments.segments_no_ground.values():
             idx = self.indexes(segment.index, only_technical=False)
-            markers[:, idx] = segment.markers(Q.vector(segment.index))
+            markers[:, idx] = segment.markers(
+                Q.vector(segment.index) if len(Q.shape) == 2 else Q[segment.coordinates_slice]
+            )
 
         return markers
 

bionc/vizualization/__init__.py

@@ -1 +1 @@
-from .animations import Viz
+