Merge pull request #32 from MyoHub/feature/update-numpy

Upgrade versions of numpy e.a.

conda_env.yml

@@ -5,17 +5,17 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.10
+  - python=3.11
   - mujoco=2.3.7
-  - loguru=0.7.0
-  - lxml=4.9.3
-  - numpy=1.21.6
-  - scipy=1.11.2
-  - scikit-learn=1.3.0
+  - loguru=0.7.2
+  - lxml=4.9.4
+  - numpy=1.23.5
+  - scipy=1.13.0
+  - scikit-learn=1.4.2
   - opensim=4.4.1
-  - matplotlib=3.7.2
+  - matplotlib=3.8.4
   - trimesh=3.23.5
-  - pyvista=0.41.1
-  - networkx=3.1
-  - fpdf2=2.7.5
+  - pyvista=0.43.5
+  - networkx=3.2.1
+  - fpdf2=2.7.8
   - seaborn=0.12.2

docker/Dockerfile

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
 
-ARG PYTHON_VERSION="3.9"
+ARG PYTHON_VERSION="3.11"
 ARG VARIANT="-slim-bullseye"
 
 FROM python:${PYTHON_VERSION}${VARIANT} as build
@@ -63,7 +63,7 @@ RUN set -ex \
     && pip install --upgrade pip \
     && pip install --no-cache-dir -r requirements.txt \
     # Install Mambaforge
-    && curl --location --silent --output ~/mamba-install.sh https://github.com/conda-forge/miniforge/releases/download/23.1.0-3/Mambaforge-23.1.0-3-$(uname)-$(uname -m).sh \
+    && curl --location --silent --output ~/mamba-install.sh https://github.com/conda-forge/miniforge/releases/download/24.1.2-0/Mambaforge-24.1.2-0-$(uname)-$(uname -m).sh \
     && chmod +x ~/mamba-install.sh \
     && ~/mamba-install.sh -b -p ${MAMBAFORGE_HOME} \
     # Set permissions on cache folder

myoconverter/xml/bodies/utils.py

@@ -48,7 +48,7 @@ def copy_mesh_file(mesh_file, geometry_folder, output_geometry_folder):
 
     # Convert into trimesh (see https://github.com/pyvista/pyvista/discussions/2268)
     pymesh = pymesh.extract_surface().triangulate()
-    faces_as_array = pymesh.faces.reshape((pymesh.n_faces, 4))[:, 1:]
+    faces_as_array = pymesh.faces.reshape((pymesh.n_faces_strict, 4))[:, 1:]
     tmesh = trimesh.Trimesh(pymesh.points, faces_as_array)
 
     # Repair the mesh