Merge pull request #21 from MyoHub/development

Merge development to main

.github/workflows/python-app.yml

@@ -6,7 +6,7 @@ on:
       - "**/README.md"
 
   pull_request:
-    branches: ["main", "feature/**"]
+    branches: ["main", "dev/*"]
     paths-ignore:
       - "doc/**"
       - "**/README.md"
@@ -27,7 +27,7 @@ jobs:
       matrix:
         os: ["ubuntu-22.04"]
 #        os: ["ubuntu-22.04", "ubuntu-latest", "windows-latest"]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         include:
           - os: ubuntu-22.04
             use-mamba: false

conda_env.yml

@@ -5,17 +5,17 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9.16
-  - mujoco-python=2.3.3
-  - loguru=0.5.3
-  - lxml=4.9.1
-  - numpy=1.21.5
-  - scipy=1.10.0
-  - scikit-learn=1.2.0
-  - opensim=4.4
-  - matplotlib=3.6.2
-  - trimesh=3.22.2
-  - pyvista=0.39.1
-  - networkx=2.8.4
-  - fpdf2=2.7.4
+  - python=3.10
+  - 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
+  - opensim=4.4.1
+  - matplotlib=3.7.2
+  - trimesh=3.23.5
+  - pyvista=0.41.1
+  - networkx=3.1
+  - fpdf2=2.7.5
   - seaborn=0.12.2

examples/cli.py

@@ -0,0 +1,18 @@
+import argparse
+from myoconverter.O2MPipeline import O2MPipeline
+
+parser = argparse.ArgumentParser(description='Convert OpenSim model to Mujoco', prog='O2M')
+parser.add_argument('--osim_file', type=str, help='OpenSim model file')
+parser.add_argument('--geometry_folder', type=str, help='Folder containing geometry files')
+parser.add_argument('--output_folder', type=str, help='Folder to store the converted model')
+parser.add_argument('--convert_steps', type=list, default=[1,2,3], help='List of steps to convert')
+parser.add_argument('--muscle_list', type=list, default=None, help='List of muscles to convert')
+parser.add_argument('--osim_data_overwrite', type=bool, default=True, help='Overwrite the Osim model state files')
+parser.add_argument('--conversion', type=bool, default=True, help='Perform "Cvt#" process')
+parser.add_argument('--validation', type=bool, default=True, help='Perform "Vlt#" process')
+parser.add_argument('--speedy', type=bool, default=False, help='Do not reduce the checking notes to increase speed')
+parser.add_argument('--generate_pdf', type=bool, default=True, help='Generate validation pdf report')
+parser.add_argument('--add_ground_geom', type=bool, default=True, help='Add ground to the model')
+parser.add_argument('--treat_as_normal_path_point', type=bool, default=False, help='Using constraints to represent moving and conditional path points')
+args = parser.parse_args()
+O2MPipeline(**vars(args))

pyproject.toml

@@ -6,11 +6,10 @@ authors = ["Your Name <you@example.com>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.13"
-mujoco = "^2.3.6"
+python = ">=3.9,<3.11"
 loguru = "^0.7.0"
 lxml = "^4.9.2"
-numpy = "^1.25.0"
+numpy = "1.21.6"
 scipy = "^1.11.1"
 scikit-learn = "^1.3.0"
 matplotlib = "^3.7.1"
@@ -19,6 +18,7 @@ pyvista = "^0.40.0"
 networkx = "^3.1"
 fpdf2 = "^2.7.4"
 seaborn = "^0.12.2"
+mujoco = "^2.3.6"
 
 
 [build-system]