Merge pull request #351 from pariterre/SymbolicPenalty

Major refactor of the whole code

Author: pariterre

.appveyor.yml

@@ -5,7 +5,7 @@
 # Build worker image (VM template)
 image:
   - Ubuntu2004
-  # - Visual Studio 2019
+  - Visual Studio 2019
   - macos
 
 # set clone depth
@@ -16,43 +16,42 @@ build: off
 
 # scripts that run after cloning repository
 install:
-  - if [[ "$CI_LINUX" == true ]]; then 
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-      bash miniconda.sh -b -p $HOME/miniconda;
-    else
-      curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -L -o miniconda.sh;
-      bash miniconda.sh -b -p $HOME/miniconda;
-    fi
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
+  - sh: if [[ $CI_LINUX == true ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda; export PATH="$HOME/miniconda/bin:$PATH"; else curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -L -o miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda; export PATH="$HOME/miniconda/bin:$PATH"; fi
+  - sh: hash -r
+  - sh: source activate
+  - cmd: SET MINICONDA_PATH="C:\\Miniconda38-x64"
+  - cmd: SET PATH=%MINICONDA_PATH%;%MINICONDA_PATH%"\\Scripts";%PATH%
+  - cmd: conda init cmd.exe
   - conda config --set always_yes yes --set changeps1 no
   - conda config --set auto_update_conda no
   - conda update -q conda
-  - source activate
+  
+  # Set environment variables  
+  - sh: BIOPTIM_FOLDER=`pwd`
+  - cmd: SET BIOPTIM_FOLDER=%cd%
+  
+  # Setup the conda environment
   - conda env update -n bioptim -f environment.yml
   - conda activate bioptim
   - conda install pytest-cov black pytest pytest-cov codecov -cconda-forge
-  - conda install xorg-libx11 xorg-libxtst -cconda-forge
+  - sh: if [[ $CI_LINUX == true ]]; then conda install xorg-libx11 xorg-libxtst -cconda-forge; fi
   - conda list
+  
+  # Install ACADOS on LINUX and MAC
   - cd external
-  - if [[ "$CI_LINUX" == true ]]; then 
-      ./acados_install_linux.sh;
-    else
-      ./acados_install_mac.sh;
-    fi
+  - sh: if [[ $CI_LINUX == true ]]; then  ./acados_install_linux.sh; else ./acados_install_mac.sh; fi
   - cd ..
-
+  
 # to run your custom scripts instead of automatic tests
 test_script:
-  - bioptim_folder=`pwd`
-  - if [[ "$CI_LINUX" == true ]]; then 
-      black . -l120 --exclude "external/*" --check;
-    fi
+  - sh: if [[ $CI_LINUX == true ]]; then black . -l120 --exclude "external/*" --check; fi
   - pytest -v --color=yes --cov-report term-missing --cov=bioptim tests
   - python setup.py install
-  - cd
+  - sh: cd
+  - cmd: cd C:/
   - python -c "import bioptim"
-  - cd $bioptim_folder
+  - sh: cd $BIOPTIM_FOLDER
+  - cmd: cd %BIOPTIM_FOLDER%
 
 
 #---------------------------------#
@@ -61,8 +60,5 @@ test_script:
 
 # on successful build
 on_success:
-  - if [[ "$CI_LINUX" == true ]]; then 
-      codecov;
-    fi
-
+  - sh: if [[ $CI_LINUX == true ]]; then codecov; fi
 

README.md

@@ -211,7 +211,7 @@ Please note that this tutorial is designed to recreate the `examples/getting_sta
 ## The import
 We won't spend time explaining the import, since every one of them will be explained in details later, and that it is pretty straightforward anyway.
 ```python
-import biorbd
+import biorbd_casadi as biorbd
 from bioptim import (
     OptimalControlProgram,
     DynamicsFcn,
@@ -339,7 +339,7 @@ You will find that the file is a bit different from the `example/getting_started
 
 ### The pendulum.py file
 ```python
-import biorbd
+import biorbd_casadi as biorbd
 from bioptim import (
     OptimalControlProgram,
     DynamicsFcn,

bioptim/__init__.py

@@ -148,11 +148,12 @@
 from .dynamics.configure_problem import ConfigureProblem, DynamicsFcn, DynamicsList, Dynamics
 from .dynamics.dynamics_functions import DynamicsFunctions
 from .dynamics.ode_solver import OdeSolver
+from .interfaces.biorbd_interface import BiorbdInterface
 from .limits.constraints import ConstraintFcn, ConstraintList, Constraint
 from .limits.phase_transition import PhaseTransitionFcn, PhaseTransitionList
 from .limits.objective_functions import ObjectiveFcn, ObjectiveList, Objective
 from .limits.path_conditions import BoundsList, Bounds, InitialGuessList, InitialGuess, QAndQDotBounds
-from .limits.penalty_node import PenaltyNode
+from .limits.penalty_node import PenaltyNode, PenaltyNodeList
 from .misc.enums import Axis, Node, InterpolationType, PlotType, Solver, ControlType, CostType, Shooting
 from .misc.mapping import BiMappingList, BiMapping, Mapping
 from .optimization.non_linear_program import NonLinearProgram