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Updates to likelihoods, bug fix GaussianLogLikelihood class #338

Merged
merged 93 commits into from
Jul 5, 2024
Merged

Updates to likelihoods, bug fix GaussianLogLikelihood class #338

merged 93 commits into from
Jul 5, 2024

Commits on Jun 2, 2024

  1. fix: Enables GaussLogLikelihood with optimisers, adds testing, defaul… 

    …t values, updt non-bounded parameter logic, bugfix pints.CMAES construction
    @BradyPlanden
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Commits on Jun 3, 2024

  1. Add changelog entry, add arg for bounds std, align sigma->sigma0 acro… 

    …ss likelihoods, move MAP
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Commits on Jun 5, 2024

  1. tests: updates incorrect sigma0 values

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  2. Merge branch 'develop' into gauss-log-like-fixes

    @BradyPlanden
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  3. adds x0 / bounds within BaseCost and BaseOptimiser for GaussLogLikeli… 

    …hood, aligns tests
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Commits on Jun 6, 2024

  1. tests: Add skip for Adam + GaussLogLikelihood SPM integration test

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  2. Merge branch 'develop', tune spm_param tests

    @BradyPlanden
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  3. tests: up coverage

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  4. Merge branch 'develop' into gauss-log-like-fixes

    @BradyPlanden
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  5. refactor: change sigma0 attr logic on GaussLogLikelihoodKnownSigma, a… 

    …dd default and arg for parameter boundary multiplier, adds tests
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Commits on Jun 7, 2024

  1. Suggestions from review

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  2. Apply remainder suggestions from code review

    @BradyPlanden
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  3. fix: imports List for type-hints

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  4. tests: up coverage, add sigma0 to BaseLikelihood

    @BradyPlanden
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  5. Add fit_keys and sigma as a Parameter

    @NicolaCourtier
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  6. Update CMAES x0 check

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  7. Add plot2d warning if not 2 parameters

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  8. Fix integration tests' get_data

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  9. Update exp_UKF example

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  10. Fix case with sigma length 1

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  11. Reset parameters not None checks

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  12. Fix sigma2 in GLLKnownSigma

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  13. Update dsigma_scale

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  14. style: pre-commit fixes

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Commits on Jun 10, 2024

  1. Merge branch 'develop' into gauss-log-like-fixes

    @BradyPlanden
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  2. Fix GaussianLogLikelihoodKnownSigma

    @NicolaCourtier
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  3. Update plot2d for wrong number of parameters

    @NicolaCourtier
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  4. Fix classify_and_update_parameters

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  5. Add get_initial_value

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  6. Update sigma setting and tests

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  7. style: pre-commit fixes

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  8. Merge branch 'gauss-log-like-fixes' into 338b-gauss-loglikelihood

    @NicolaCourtier
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  9. Update optim trace for >2 parameters

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  10. Add test_scipy_minimize_invalid_x0

    @NicolaCourtier
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  11. Add log prior gradient

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Commits on Jun 11, 2024

  1. Add optimiser.parameters, remove problem.x0

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  2. Update integration tests

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  3. Pass inputs instead of x

    @NicolaCourtier
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Commits on Jun 12, 2024

  1. Specify inputs as Inputs

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  2. Update notebooks

    @NicolaCourtier
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  3. Add initial and true options to as_dict

    @NicolaCourtier
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  4. Reset notebook versions

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  5. Update parameter_values to inputs

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  6. Update notebooks

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Commits on Jun 13, 2024

  1. Add parameters tests

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  2. Add quick_plot test

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  3. Add test_no_optimisation_parameters

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  4. Add test_error_in_cost_calculation

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  5. Add parameters.verify

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  6. Fix change to base_model

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  7. Add more base_model tests

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  8. Merge branch 'develop' into gauss-log-like-fixes

    @NicolaCourtier
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  9. Merge branch '358-passing-inputs' into 338b-gauss-loglikelihood

    @NicolaCourtier
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  10. Update base_cost.py

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  11. Merge branch 'gauss-log-like-fixes' into 338b-gauss-loglikelihood

    @NicolaCourtier
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  12. Remove fit_keys

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  13. Update base_model.py

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Commits on Jun 14, 2024

  1. Replace store_optimised_parameters with update

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  2. Update value() output to ndarray

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  3. Update likelihood inputs

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Commits on Jun 18, 2024

  1. Merge branch 'develop' into gauss-log-like-fixes

    @BradyPlanden
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Commits on Jun 19, 2024

  1. Merge branch 'gauss-log-like-fixes' into 338b-gauss-loglikelihood

    @NicolaCourtier
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  2. style: pre-commit fixes

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  3. Re-implement get item check

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Commits on Jun 28, 2024

  1. Merge pull request #352 from pybop-team/338b-gauss-loglikelihood 

    Suggesting changes to #338
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  2. Merge branch 'develop' into 358-passing-inputs

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  3. fix: restore ValueError on incorrect parameter __getitem__

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  4. Merge branch '358-passing-inputs' into gauss-log-like-fixes

    @BradyPlanden
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  5. fix: likelihood powers as floats, bugfix outdated Adam logic conditio… 

    …n in test_spm_parameterisation
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  6. refactor: default dsigma_scale update, changes to GaussLogLikelihood … 

    …__init__
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  7. feat: improve robustness of MAP prior grad approximate

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  8. refactor: MAP finite difference gradient

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Commits on Jun 29, 2024

  1. tests: refactor optimiser construction, add asserts for sigma identif… 

    …ication
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Commits on Jul 1, 2024

  1. test: add test for sampling parameter initial value

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  2. refactor: GaussLogLikelihood __init__, revert temporary test workaround

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Commits on Jul 3, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
    @NicolaCourtier @BradyPlanden
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  2. style: pre-commit fixes

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  3. Merge branch 'develop' into 358-passing-inputs

    @NicolaCourtier
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  4. Import Union and Inputs

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  5. Move Inputs definition to parameter.py

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  6. Retrieve x0 from SciPyDE

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  7. Add test for evaluate(List)

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  8. Refactor as suggested 

    Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
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  9. style: pre-commit fixes

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  10. Remove duplicate line

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  11. Change quick_plot inputs to problem_inputs

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Commits on Jul 4, 2024

  1. Merge branch 'develop' into 358-passing-inputs

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  2. Remove duplicate lines

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  3. Merge branch '358-passing-inputs' into gauss-log-like-fixes

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  4. fix: incorrect dimensions self._dl, tweak settings integration tests

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  5. Merge branch 'develop' into gauss-log-like-fixes

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  6. tests: updt to GaussLogLikelihood sigma0 values

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Commits on Jul 5, 2024

  1. fixes from code review, user output for boundaries

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