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Implement options for pseudo-time stepping #243

Merged
merged 107 commits into from
Aug 3, 2022
Merged

Implement options for pseudo-time stepping #243

merged 107 commits into from
Aug 3, 2022

Commits on Apr 8, 2022

  1. Add PseudoSteppingSchemes options

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  2. Add inverse_normalize! convenience for use in GPR

    @adelinehillier
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  3. Update adaptive_step_parameters arguments

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  4. Merge branch 'glw/pseudotime' of https://github.com/CliMA/ParameterEs… 

    …timocean.jl into ah/adaptive
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Commits on Apr 9, 2022

  1. Merge branch 'glw/pseudotime' of https://github.com/CliMA/ParameterEs… 

    …timocean.jl into ah/adaptive
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  2. Add LineSearches to dependencies

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  3. Use outer constructors instead

    @adelinehillier
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  4. Merge branch 'glw/pseudotime' of https://github.com/CliMA/ParameterEs… 

    …timocean.jl into ah/adaptive
    @adelinehillier
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  5. Refactor function arguments

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  6. Merge branch 'glw/pseudotime' of https://github.com/CliMA/ParameterEs… 

    …timocean.jl into ah/adaptive
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  7. Typo

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  8. Fix cholesky factorization bug

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    adelinehillier committed Apr 9, 2022
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  9. Updates

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Commits on Apr 10, 2022

  1. Typos

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    adelinehillier committed Apr 10, 2022
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  2. Add tests

    @adelinehillier
    adelinehillier committed Apr 10, 2022
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  3. Cleanup

    @adelinehillier
    adelinehillier committed Apr 10, 2022
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  4. Add precomputed_matrices attribute to EnsembleKalmanInversion

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Commits on Apr 11, 2022

  1. Use precomputed matrices

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  2. Return mean and variance information of GP

    @adelinehillier
    adelinehillier committed Apr 11, 2022
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  3. Reduce redundant computations

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    adelinehillier committed Apr 11, 2022
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  4. Standardize GP inputs

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  5. Typo

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  6. Typo

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    adelinehillier committed Apr 11, 2022
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  7. update manifest

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  8. Update Project.toml

    @glwagner
    glwagner committed Apr 11, 2022
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  9. Typo

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  10. Rebuild manifest

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  11. Merge branch 'ah/adaptive' of https://github.com/CliMA/ParameterEstim… 

    …ocean.jl into ah/adaptive
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Commits on Apr 12, 2022

  1. Add inv_sqrt_Γθ and μθ to precomputed_arrays

    @adelinehillier
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  2. Don't precompute inv_sqrt_Γθ in IterationSummary constructor

    @adelinehillier
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  3. Simplify

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  4. Add option tikhonov for regularization

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  5. Add Iglesias2021 stepping scheme

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  6. Merge branch 'main' of https://github.com/CliMA/ParameterEstimocean.jl … 

    …into ah/adaptive
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  7. Demote Manifest.toml to older version of Julia

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Commits on Apr 13, 2022

  1. bugfixes

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Commits on Apr 15, 2022

  1. Add warnings

    @adelinehillier
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  2. Add unconstrained parameters to iteration summary

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  3. Update manifest

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Commits on Apr 16, 2022

  1. Bugfixes

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  2. Add GaussianProcesses to dependencies

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  3. Oceananigans JLD2OutputWriter updates

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  4. More JLD2OutputWriter fixes

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Commits on Apr 18, 2022

  1. Update previously saved pseudo_Δt with used pseudo_Δt

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  2. Add option to compute objectives from augmented matrices

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  3. Add info statements

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Commits on Apr 19, 2022

  1. Fix misaligned pseudo_Δt summary

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  2. Add augmented noise mean to objective calculation

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  3. Testing

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  4. Fix default for covariance_inflation parameter

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  5. Clear accidental code

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  6. Change covariance_inflation default

    @adelinehillier
    adelinehillier committed Apr 19, 2022
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  7. Implement Kovachki2018InitialConvergenceThreshold

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  8. Export Kovachki2018InitialConvergenceThreshold

    @adelinehillier
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  9. Bugfix

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  10. Bugfix

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  11. Add docstrings and speed up transformation matrix computation for Kov… 

    …achki2018 pseudo scheme
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Commits on Apr 20, 2022

  1. Prevent cholesky factorization error

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  2. sqrt(cov -> std

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  3. Add zscore_limit parameter for GP training

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  4. Delete unwanted code

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  5. Bugfix

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Commits on Apr 21, 2022

  1. ΣΔt⁻¹Γy

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  2. Fix info report for zscore_limit

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Commits on Apr 22, 2022

  1. Try a squared exponential kernel

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  2. Transform Normal priors to unit normal

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Commits on Apr 23, 2022

  1. Save forward map output to IterationSummary (for emulation)

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Commits on Apr 27, 2022

  1. Replace Kovachki2018InitialConvergenceThreshold with `Kovachki2018I… 

    …nitialConvergenceRatio`
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  2. Distinguish reference time step from Δt

    @adelinehillier
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  3. Add Kovachki2018InitialConvergenceRatio to tests

    @adelinehillier
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  4. Report the correct time step

    @adelinehillier
    adelinehillier committed Apr 27, 2022
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  5. Rename Constant ConstantPseudoTimeStep

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  6. Cleanup

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  7. Avoid NaNs for Kovachki2018InitialConvergenceRatio

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  8. Bugfix

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  9. Add show statements for debugging

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  10. Make Kovachki2018InitialConvergenceRatio time step calculation more… 

    … robust
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Commits on May 1, 2022

  1. Add option to override kernel in trained_gp_predict_function

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  2. typo

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Commits on Jun 7, 2022

  1. Merge branch 'main' of https://github.com/CliMA/ParameterEstimocean.jl … 

    …into ah/adaptive
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  2. @AutoDoc PseudoSteppingSchemes

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Commits on Jun 9, 2022

  1. Update docs

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Commits on Jun 10, 2022

  1. Merge branch 'main' of https://github.com/CliMA/ParameterEstimocean.jl … 

    …into ah/adaptive
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Commits on Jun 14, 2022

  1. Merge branch 'main' of https://github.com/CliMA/ParameterEstimocean.jl … 

    …into ah/adaptive
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  2. Resolve dependency issues

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Commits on Jun 15, 2022

  1. Remove autodocs

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Commits on Jun 16, 2022

  1. Remove GPLineSearch

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  2. Add Iglesias2021 to tests

    @adelinehillier
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  3. Add pseudo_step! function to replace iterate! for single iterations

    @adelinehillier
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  4. Stop saving forward map output in IterationSummary

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  5. Parametric typing error

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  6. Export pseudo_step!

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  7. Uncomment tests

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Commits on Jun 17, 2022

  1. Default pseudo_Δt to nothing; else Number overrides `pseudo_ste… 

    …pping`
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  2. Replace Default with ThresholdedConvergenceRatio

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  3. Replace Default with ThresholdedConvergenceRatio

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  4. Add test for pseudo_Δt == nothing

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  5. Cleanup

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  6. Default pseudo_stepping to nothing

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  7. Update tests

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    adelinehillier committed Jun 17, 2022
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  8. Fix test

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Commits on Jul 18, 2022

  1. Fix RescaledZScore

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  2. Merge remote-tracking branch 'origin/ah/fix-rescaledzscore' into ah/a… 

    …daptive
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  3. inverse_normalize! -> denormalize!

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  4. parameters_unconstrained -> unconstrained_parameters

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  5. Remove debugging @Assert

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  6. Accidental autoreplace

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