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Optimal Control extension #247

Merged
merged 284 commits into from
Dec 22, 2023
Merged

Optimal Control extension #247

merged 284 commits into from
Dec 22, 2023
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Commits on Jul 28, 2022

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  2. example folder

    lenasal committed Jul 28, 2022
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Commits on Jul 29, 2022

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  2. start readme

    lenasal committed Jul 29, 2022
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  3. Update README.md

    lenasal committed Jul 29, 2022
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  4. added contributing file

    lenasal committed Jul 29, 2022
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  5. Update README.md

    lenasal committed Jul 29, 2022
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  6. Update README.md

    lenasal committed Jul 29, 2022
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  7. Update CONTRIBUTING.md

    lenasal committed Jul 29, 2022
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  8. Update CONTRIBUTING.md

    lenasal committed Jul 29, 2022
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  9. Update CONTRIBUTING.md

    lenasal committed Jul 29, 2022
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  10. Update CONTRIBUTING.md

    lenasal committed Jul 29, 2022
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  11. Update README.md

    lenasal committed Jul 29, 2022
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  12. Update README.md

    lenasal committed Jul 29, 2022
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  13. update with code formatter

    lenasal committed Jul 29, 2022
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Commits on Aug 2, 2022

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Commits on Aug 4, 2022

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  2. revised code

    lenasal committed Aug 4, 2022
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Commits on Aug 5, 2022

  1. - docstrings according to Sphinx docstring format

    - updated test cases according to changed default parameters
    - applied automated code formatting to all changed files and test-files
    martinptm committed Aug 5, 2022
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Commits on Aug 9, 2022

  1. Update CONTRIBUTING.md

    lenasal committed Aug 9, 2022
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  2. Merge branch 'documentation' into OCdev

    # Conflicts:
    #	neurolib/optimal_control/cost_functions.py
    #	neurolib/optimal_control/oc_fhn/oc_fhn.py
    #	neurolib/optimal_control/oc_fhn/oc_fhn_jit.py
    #	neurolib/optimal_control/tests/test_fhn_noisy.py
    martinptm committed Aug 9, 2022
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Commits on Aug 10, 2022

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Commits on Aug 11, 2022

  1. starting testing

    lenasal committed Aug 11, 2022
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Commits on Aug 12, 2022

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  2. cleaned up

    lenasal committed Aug 12, 2022
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  3. stochastic method

    lenasal committed Aug 12, 2022
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Commits on Aug 16, 2022

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Commits on Aug 17, 2022

  1. - noisy network example

    martinptm committed Aug 17, 2022
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  2. check cmat diagonal entries

    lenasal committed Aug 17, 2022
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  3. - added some description for noisy network example and made the setti…

    …ng fully equivalent to deterministic model example (prec_mat & control_mat)
    martinptm committed Aug 17, 2022
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Commits on Aug 18, 2022

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  2. speed up solve_adjoint method

    lenasal committed Aug 18, 2022
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Commits on Aug 19, 2022

  1. - removed unused matplotlib import in test_fhn.py

    - Cmat entries set to interval [0,1] in test_fhn.py and deterministic example
    martinptm committed Aug 19, 2022
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Commits on Aug 22, 2022

  1. adjust parameters in test_fhn

    lenasal committed Aug 22, 2022
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Commits on Aug 24, 2022

  1. - baseclass for OC

    - inherit from OC-baseclass for OC of fhn, passes all tests for fhn-OC
    - updated docstrings
    - use "isinstance(x, type(None))" for None-checks
    martinptm committed Aug 24, 2022
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  2. - skeleton for OC for Hopf model

    - Jacobian for Hopf model
    - code formatting
    martinptm committed Aug 24, 2022
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Commits on Aug 26, 2022

  1. - optimal control for Hopf model with quick visual evaluation of the …

    …performance in the example files
    martinptm committed Aug 26, 2022
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Commits on Sep 2, 2022

  1. - fix overwriting attributes of the neurolib-model that is passed to …

    …OC -> 'self.model' is deepcopy of the passed 'model'
    
    - restructured: jit-functions into the file of derived OC class definition
    - updated comments & documentation
    - identified "compute_gradient" as model dependent in its current implementation
    - Dxdot is currently unused for Hopf & FHN
    - single test case for Hopf, rely on tests for FHN for shared methods for the moment
    - updated dt in example to avoid numerical inaccuracies
    martinptm committed Sep 2, 2022
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Commits on Sep 13, 2022

  1. - add check for passed model in model specific OC

    - place plotting functions of examples in oc-utility-folder
    - provide a single example (using the FHN), since completely analogous for Hopf
    martinptm committed Sep 13, 2022
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Commits on Sep 14, 2022

  1. refactoring stochastic OC

    lenasal committed Sep 14, 2022
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Commits on Sep 15, 2022

  1. refactored stochastic control

    lenasal committed Sep 15, 2022
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  2. fixed bugs

    lenasal committed Sep 15, 2022
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Commits on Sep 19, 2022

  1. implemented wc model

    lenasal committed Sep 19, 2022
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Commits on Sep 29, 2022

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Commits on Oct 15, 2022

  1. - improved performance of cost functions and derivatives (derivative_…

    …precision_cost x7, precision_cost x2 with better readability), all tests passed
    martinptm committed Oct 15, 2022
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Commits on Oct 18, 2022

  1. merged OCdev

    lenasal committed Oct 18, 2022
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  4. remove file

    lenasal committed Oct 18, 2022
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Commits on Oct 19, 2022

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Commits on Oct 20, 2022

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  3. - added function 'update_control_with_limit' to limit the absolute va…

    …lue of the control strength at all points in time. Passes tests.
    
    - added new attribute 'maximum_control_strength' to the 'OC' class to set the absolute maximum value for the control strength
    - test cases for the new function 'update_control_with_limit'
    martinptm committed Oct 20, 2022
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Commits on Oct 21, 2022

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  2. - fix: added scaling by time step of precision- and energy cost, adde…

    …d parameter in function calls
    
    - adjusted corresponding test cases
    martinptm committed Oct 21, 2022
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Commits on Oct 25, 2022

  1. corrected background missing

    lenasal committed Oct 25, 2022
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  2. - interval in which precision cost is now positional argument to avoi…

    …d repeated checks of specification and allow notation with "negative indices" in Oc-object initialization
    
    - added 'convert_interval' to allow for the different ways of interval specification
    - updated function calls accordingly
    - changed test structure: separate tests for the interval-specification
    martinptm committed Oct 25, 2022
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Commits on Oct 26, 2022

  1. - added: apply maximal-absolute-control-strength constraint even befo…

    …re first optimization
    
    - added: new test cases; passes all tests
    - minor fixes
    martinptm committed Oct 26, 2022
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Commits on Oct 28, 2022

  1. - additional assertions for interval specification

    - checks for repeated calls of ".optimize()"
    - new test cases
    - removed unused variable and old comments
    martinptm committed Oct 28, 2022
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Commits on Nov 3, 2022

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  2. - adjusted to naming 'Duh' for Jacobian

    - jit the compute_gradient-functions
    - added documentation & docstrings
    martinptm committed Nov 3, 2022
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Commits on Nov 7, 2022

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  3. merged OCdev

    lenasal committed Nov 7, 2022
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Commits on Nov 11, 2022

  1. remove background from oc.py

    lenasal committed Nov 11, 2022
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Commits on Dec 3, 2022

  1. - adaptive step size computation:

         * adaptive step-size reduction or -increment, reduces relevance of hyperparameter for initial step size
         * memorize last step, heavily increases efficiency in many cases
    - added very generic test case for step-size computation based on derived OcWc-class
    - "convert_interval" not further numba-compiled
    - improved documentation, added type-description in model specific OC classes
    - added todo-hints for automated control-adjustments
    - set default of "precision_cost_interval" in OcWc to same values as for the the other models
    martinptm committed Dec 3, 2022
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Commits on Dec 7, 2022

  1. - add counter=0 in case of zero gradient

    - remove distinction (not-)noisy step within the noise-free step size computation, that is not required at this point
    - add test case for zero-step
    martinptm committed Dec 7, 2022
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  2. - combine the step-size combination for the noisy and the noise free …

    …setting in the adaptive step-size algorithm
    martinptm committed Dec 7, 2022
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Commits on Dec 8, 2022

  1. - shared "factor_down" for noisy and deterministic case

    - "factor_down**2" in loop for finding numerically stable regime for faster exit of loop
    - call the new step-size function for noisy case and delete unused method
    -> passes all tests in test-oc and test-fhn-noisy
    - adjust parameters in test case to range [0,1] in Cmat
    martinptm committed Dec 8, 2022
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Commits on Dec 16, 2022

  1. - revision of documentation

    - changed variable names for clarity
    martinptm committed Dec 16, 2022
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Commits on Dec 19, 2022

  1. - revision of docstrings for clean documentation build

    - fix typos and add comments
    - rename variables and functions for clarity
    martinptm committed Dec 19, 2022
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Commits on Dec 22, 2022

  1. - fix mistake in equation

    martinptm committed Dec 22, 2022
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Commits on Jan 12, 2023

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  3. removed commented debug code

    lenasal committed Jan 12, 2023
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Commits on Feb 1, 2023

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Commits on Feb 2, 2023

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Commits on Feb 3, 2023

  1. - add comments

    - variable naming for clarity
    - remove unused code and comments
    - use fixed seed in test-cases for reproducibility in all cases
    martinptm committed Feb 3, 2023
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Commits on Feb 6, 2023

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  3. delay test cases

    lenasal committed Feb 6, 2023
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Commits on Feb 7, 2023

  1. - restructure project

    martinptm committed Feb 7, 2023
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  2. - move example file

    martinptm committed Feb 7, 2023
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  4. corrected failing test

    lenasal committed Feb 7, 2023
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  5. corrected failing test

    lenasal authored and martinptm committed Feb 7, 2023
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  6. - move the calculation of Jacobian matrices to neurolib core modules …

    …and adjust imports in the OC submodule
    martinptm committed Feb 7, 2023
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Commits on Feb 8, 2023

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Commits on Feb 13, 2023

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Commits on Feb 22, 2023

  1. - restore documentation-updates:

       + improved docstrings and comments
       + better aligned to PEP
       + clear variable naming
    martinptm committed Feb 22, 2023
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Commits on Mar 10, 2023

  1. fixed bug in time delay

    lenasal committed Mar 10, 2023
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  2. delete check zero in cmat/ run model once at initilaization/ revise e…

    …xample notebooks/ fix bugs in step_size and delay
    lenasal committed Mar 10, 2023
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Commits on Mar 13, 2023

  1. revise test files

    lenasal committed Mar 13, 2023
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  2. correct typo in jacobian

    lenasal committed Mar 13, 2023
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  3. correct typo in jacobian

    lenasal committed Mar 13, 2023
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Commits on Mar 14, 2023

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Commits on Mar 15, 2023

  1. Merge branch 'proj_restructure_bugfixes' into OCdev

    # Conflicts:
    #	neurolib/control/optimal_control/oc.py
    #	neurolib/control/optimal_control/oc_wc/oc_wc.py
    martinptm committed Mar 15, 2023
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Commits on Mar 17, 2023

  1. Merge branch 'restore_improved_docs' into OCdev

    # Conflicts:
    #	neurolib/control/optimal_control/oc.py
    #	neurolib/control/optimal_control/oc_hopf/oc_hopf.py
    #	neurolib/models/wc/timeIntegration.py
    martinptm committed Mar 17, 2023
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Commits on Apr 13, 2023

  1. cost functional restructure

    lenasal committed Apr 13, 2023
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Commits on Apr 17, 2023

  1. update test wc

    lenasal committed Apr 17, 2023
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  2. update test wc

    lenasal committed Apr 17, 2023
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  3. update test wc

    lenasal committed Apr 17, 2023
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  4. update test wc

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  1. revision

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  3. Merge remote-tracking branch 'origin/cost_functionals_as_dict' into O…

    …Cdev
    
    # Conflicts:
    #	examples/example-5-optimal-control/example-5.3-oc-wc-model-deterministic.ipynb
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  1. Update README.md

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Commits on Apr 24, 2023

  1. start implementation oc aln

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  7. time dependent variables

    lenasal committed Apr 24, 2023
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  8. fixed mistake

    lenasal committed Apr 24, 2023
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  13. notebook description

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  15. Merge branch 'OCdev' into aln

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  16. implementation

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  17. aln implementation

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  20. aln imp

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  22. merge

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  3. refactoring

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  6. merge neurolib updates

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  1. network implementation

    lenasal committed May 3, 2023
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  1. finalize(?) aln

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  2. finalize tests

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  2. finish test cases

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  1. finalize aln implmentation

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  2. added Dxdoth in hopf and fhn

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  4. pass N, V, T for iterations

    lenasal committed May 12, 2023
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  6. update comments

    lenasal committed May 12, 2023
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  7. fix bug in network input aln

    lenasal committed May 12, 2023
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  8. revise example notebooks

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  1. merge aln into OCdev

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  3. cleaned up repository

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  4. clean up

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  5. Delete workflow.txt

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Commits on Aug 28, 2023

  1. checkout files from master

    lenasal committed Aug 28, 2023
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Commits on Aug 30, 2023

  1. fixed solve_adjoint

    lenasal committed Aug 30, 2023
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  3. update example

    lenasal committed Aug 30, 2023
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  4. revert example change

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  6. mergw wc time integration

    lenasal committed Aug 30, 2023
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  1. revise test wc

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  3. revised cost functional tests

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  4. revised remaining test files

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  1. refactoring tests

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  1. state vars as dict

    lenasal committed Sep 5, 2023
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  4. merging

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  5. merging

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  6. finish test revision

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  2. remove comments

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  5. refactor aln oc test

    lenasal committed Sep 7, 2023
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  6. refactor etst cases

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  7. remove unnecessary parameter

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  3. Update timeIntegration.py

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  4. Update plot_oc.py

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  5. Merge pull request #2 from lenasal/lenasal-patch-1

    Update plot_oc.py
    lenasal committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. shorten example runtime

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  2. Update cost_functions.py

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  3. added test for solve_adjoint

    lenasal committed Sep 20, 2023
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  1. Update test_oc.py

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Commits on Sep 25, 2023

  1. Update oc.py

    lenasal committed Sep 25, 2023
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  1. Update oc.py

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Commits on Dec 11, 2023

  1. fix bug in WC jacobian

    lenasal committed Dec 11, 2023
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Commits on Dec 15, 2023

  1. Rename example-5.3-oc-wc-model-deterministic.ipynb to example-5.2-oc-…

    …wc-model-deterministic.ipynb
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  3. Rename example-5.5-oc-aln-model-deterministic.ipynb to example-5.4-oc…

    …-aln-model-deterministic.ipynb
    lenasal committed Dec 15, 2023
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  4. Update README.md

    lenasal committed Dec 15, 2023
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  5. Update README.md

    lenasal committed Dec 15, 2023
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  6. Update README.md

    lenasal committed Dec 15, 2023
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Commits on Dec 20, 2023

  1. Update README.md

    Co-authored-by: Caglar Cakan <caglorithm@gmail.com>
    lenasal and caglorithm committed Dec 20, 2023
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Commits on Dec 21, 2023

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