SpringCleaning

Over the time, dust accumulate to the point you don't see the floor anymore... electronic code does not make exception! Therefore Bioptimn needed a huge dedusting from years of development

SpringCleaning is a rewrite of the core dynamics of bioptim, not so much of the API except for few breaking changes. All in all, this is a very welcome breath of fresh air for Bioptim!

What's Changed

• [RTR] fix on live optimization by @Ipuch in #702
• [RTM] Bug and BoundsList by @20chupin in #703
• [RTM] Ipopt options were problematic by @Ipuch in #709
• [RTM] IntegralApproximation -> QuadratureRule by @20chupin in #704
• [RTM] restoring the right types for protocols and markervelocities by @Ipuch in #708
• BiorrbdModelHolonomic and VariationalBiorbdModel in core by @20chupin in #699
• [RTR] some little test on preparing the data for animation of tracked markers. by @Ipuch in #714
• [RTR] StochastiOCP merge by @EveCharbie in #715
• [RTR] solver options ipopt test by @Ipuch in #723
• [RTM] Restoring bounds on graphs by @EveCharbie in #724
• [RTM] show bounds test in ocp by @Ipuch in #728
• [RTM if tests pass] implicit formulation of the SOCP by @EveCharbie in #721
• [RTM] added multi-node penalties to objective plots by @EveCharbie in #726
• Made expand modifiable from API by @pariterre in #727
• [RTM when answered] Add min power (joint and muscle) - typo in Readme - new strategy of CI by @mickaelbegon in #733
• [RTM if tests pass] Cholesky decomposition of the covariance matrix by @EveCharbie in #731
• [RTM when #733 is merged] controls piecewise constant with last node by @EveCharbie in #737
• change way to report coverage by @mickaelbegon in #740
• [RTR] s_scaling good version by @EveCharbie in #734
• [RTM] add trapezoidal integrator by @EveCharbie in #738
• [RTM] Not compute the defects if not in implicit by @EveCharbie in #742
• DMOCC now working entirely with honomic constraints. by @Ipuch in #736
• [RTR] Refactor new_variable by @Ipuch in #730
• [RTM] collocations for SOCP by @EveCharbie in #744
• [RTM when tests pass] changed reshape_to_vector/matrix for good (test breaking) by @EveCharbie in #750
• [RTM when tests pass] Including custom functions as built-ins for stochastic problems by @EveCharbie in #743
• [RTR] Multi-threading in SOCP_COLLOCATION by @EveCharbie in #753
• [RTR] extra models for futher computations by @Ipuch in #757
• [To be deleted] Running tests on all platforms by @pariterre in #758
• [WIP] Unique dynamic function for time dependent problem by @Kev1CO in #718
• [RTR] tiny commit to help everyone debugging by @Ipuch in #760
• [RTR] Multimodel, I need animation and displaced the file for more convinience by @Ipuch in #761
• [RTM] Wild refactor trying to understand what's going on in compute_values for graphics by @Ipuch in #762
• Fixed custom_plot by @pariterre in #767
• [RTR] Unit test on helper function. by @Ipuch in #764
• Migrating to biorbd 1.10.0 by @pariterre in #768
• [RTM when tests pass] Time dependent test correction by @Kev1CO in #759
• FIxed a bug of time in plot for multiphase programs by @pariterre in #769
• Update README.md with PhaseDynamics instead of assume_phase_dynamics by @Ipuch in #774
• get_u isolated as a helper+ unit test by @Ipuch in #775
• [RTM when ping] SOCP_COLLOCATION corrections to make it right :) by @EveCharbie in #771
• [RTR] removing assume_phase from readme by @Kev1CO in #777
• [RTM when tests pass] external forces moved out of ocp too by @Ipuch in #779
• [RTM when tests pass] Using integrate_extra_dynamics instead of duplicating code by @EveCharbie in #780
• [RTR] Stochastic variables should not be inputs of OCP by @Ipuch in #765
• [RTM when tested] Added a multi-node constraint for the total duration of the movement by @EveCharbie in #782
• [RTM] Added more complex example of optimal estimation by @EveCharbie in #784
• Minibug patch by @Ipuch in #786
• some unit test in integration for stability purpose. by @Ipuch in #785
• [RTR] Solving a critical issue of codeclimate by @Ipuch in #788
• [RTR] Try to refactor a bit the initialisation of Solution by @Ipuch in #787
• [RTM when tests pass] Refactor solution with classmethods by @Ipuch in #789
• [RTM when tests pass] Breaking up solution in multiple scripts by @Ipuch in #790
• [RTR] Udpate min max + test by @Ipuch in #798
• [RTR] duplicate_collocation_starting_point by @Ipuch in #796
• [RTR] Refactoring solver interface utils for the better by @Ipuch in #793
• [RTR] Mayer_TRACK_CONTACT_FORCES by @Alpha2Shahiri in #797
• [RTM when tests pass] Reorganize files by @Ipuch in #792
• [RTM] Added the commit ID + version to sol by @EveCharbie in #806
• Major refactor towards 3.2.0 by @pariterre in #814
• [RTM] Commit for mickael by @Ipuch in #811
• [RTM] yml code climate by @Ipuch in #800
• Final stretch of the reformating! by @pariterre in #816

New Contributors

• @Alpha2Shahiri made their first contribution in #797

Full Changelog: Release_3.1.0...Release_3.2.0