Merge pull request #1032 from pariterre/master

Added example to setup

Author: pariterre

.github/workflows/run_tests_linux.yml

@@ -19,6 +19,10 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
+      - name: Checkout submodules
+        if: matrix.shard == 1
+        run: git submodule update --init --recursive
+        
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -105,4 +109,4 @@ jobs:
           files: ./coverage.xml
           flags: unittests
           fail_ci_if_error: true
-          verbose: true
+          verbose: true

.github/workflows/run_tests_osx_win.yml

@@ -33,6 +33,10 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
+      - name: Checkout submodules
+        if: matrix.shard == 1
+        run: git submodule update --init --recursive
+
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v3
         with:

bioptim/examples/__main__.py

@@ -40,6 +40,7 @@
             "getting_started",
             OrderedDict(
                 [
+                    ("Basic OCP", "basic_ocp.py"),
                     ("Custom objectives", "custom_objectives.py"),
                     ("Custom parameters", "custom_parameters.py"),
                     ("Custom phase transitions", "custom_phase_transitions.py"),
@@ -49,7 +50,6 @@
                     ("Example multiphase", "example_multiphase.py"),
                     ("Example simulation", "example_simulation.py"),
                     ("Example cyclic movement", "example_cyclic_movement.py"),
-                    ("Basic OCP", "basic_ocp.py"),
                     ("Example constraint weight", "custom_constraint_weights.py"),
                     ("How to plot", "how_to_plot.py"),
                 ]

setup.py

@@ -18,16 +18,39 @@
         "bioptim/dynamics",
         "bioptim/dynamics/fatigue",
         "bioptim/dynamics/state_space_dynamics",
+        "bioptim/examples",
+        "bioptim/examples/getting_started",
+        "bioptim/examples/models",
+        "bioptim/examples/models/mesh",
+        "bioptim/examples/toy_examples",
+        "bioptim/examples/toy_examples/acados",
+        "bioptim/examples/toy_examples/custom_model",
+        "bioptim/examples/toy_examples/custom_model/custom_package",
+        "bioptim/examples/toy_examples/discrete_mechanics_and_optimal_control",
+        "bioptim/examples/toy_examples/fatigue",
+        "bioptim/examples/toy_examples/feature_examples",
+        "bioptim/examples/toy_examples/holonomic_constraints",
+        "bioptim/examples/toy_examples/inverse_optimal_control",
+        "bioptim/examples/toy_examples/moving_horizon_estimation",
+        "bioptim/examples/toy_examples/muscle_driven_ocp",
+        "bioptim/examples/toy_examples/muscle_driven_with_contact",
+        "bioptim/examples/toy_examples/optimal_time_ocp",
+        "bioptim/examples/toy_examples/sqp_method",
+        "bioptim/examples/toy_examples/stochastic_optimal_control",
+        "bioptim/examples/toy_examples/symmetrical_torque_driven_ocp",
+        "bioptim/examples/toy_examples/torque_driven_ocp",
+        "bioptim/examples/toy_examples/tracking",
         "bioptim/gui",
         "bioptim/interfaces",
         "bioptim/limits",
         "bioptim/misc",
-        "bioptim/optimization",
-        "bioptim/optimization/solution",
-        "bioptim/models/",
+        "bioptim/models",
         "bioptim/models/biorbd",
         "bioptim/models/protocols",
+        "bioptim/optimization",
+        "bioptim/optimization/solution",
         "examples",
+        "external/biomechanics_models/Geometry_triangle",
     ],
     license="LICENSE",
     keywords=["biorbd", "Ipopt", "CasADi", "Optimal control", "biomechanics"],