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Michaelgemmell/bayes workflow #262

Merged
merged 166 commits into from
Aug 17, 2023
Merged

Michaelgemmell/bayes workflow #262

merged 166 commits into from
Aug 17, 2023

Commits on Mar 28, 2023

  1. initial commit

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  2. magnetic recon tests

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Commits on Mar 30, 2023

  1. use error attribute if it is given

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  2. Added poisson noise and adjusted calibration factor

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  3. changed name magnetic_recon -> equilibrium_reconstruction

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  4. diagnostic data with channel dim are treated as individual measurements

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Commits on Mar 31, 2023

  1. added function of example LOS

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  2. refactoring

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  3. refactoring

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  4. refactoring

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  5. initial commit

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  6. removed obsolete attributes

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  7. Setting up testflow

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  8. more tests

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  9. more test stubs

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Commits on Apr 12, 2023

  1. small fix

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Commits on Apr 25, 2023

  1. Merge branch 'michaelgemmell/magnetic_recon_diagnostic' into michaelg… 

    …emmell/bayes_dev
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  2. cosmetic changes

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  3. changed marker style

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  4. merged with st40

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Commits on Apr 27, 2023

  1. Merge branch 'st40' into michaelgemmell/bayes_dev

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  2. small fix

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  3. adjusting alpha

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Commits on May 3, 2023

  1. Merge branch 'st40' into michaelgemmell/bayes_dev

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  2. black reformatting

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  3. fixing formatting

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  4. flake8 fix

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  5. flake8 fix

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  6. fixing merge conflicts

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  7. boolean indexing -> xarray.where in call

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  8. fixing tests

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  9. removing import

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  10. precommit fixes

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Commits on May 12, 2023

  1. stashing for quick result

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Commits on May 22, 2023

  1. added calc_impurity for generating profiles from concentrations to up… 

    …date profiles method
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  2. added conditional handling of diagnostics in data pipeline

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  3. moved calc_impurity to plasma method

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  4. tweaking calibration factor

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  5. tweaking calibration factor

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  6. tweaking calibration factor

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Commits on May 23, 2023

  1. changed burn_in to burn_in_fraction

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  2. added violinplots

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  3. removed comment

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  4. included dictionary logic for fitting impurities scaled by concentrat… 

    …ions and electron density
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  5. changed name cxff_pi.ti_0d to cxff_pi.ti0

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Commits on May 24, 2023

  1. new option for initialising at maximum-likelihood estimate

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  2. added xlim for violin plot

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Commits on May 31, 2023

  1. tweaking calibration

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  2. fixed neutral density units

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  3. added set plot functions

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  4. added center mass sampling and Ti/Te y0_ref options

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  5. plot formatting changed

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  6. black formatting

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  7. deleted example bayes_opt

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  8. moved sample with autocorr function to bayes_dev_workflow

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  9. renamed bayesworkflow

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Commits on Jun 13, 2023

  1. stashing

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Commits on Jun 22, 2023

  1. multiplot formatting

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Commits on Jun 27, 2023

  1. generalised writing kinetic profiles to blobs

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  2. function autocorr plot added

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  3. ion density added to kinetic profiles saved

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  4. inital commit of abstract workflow and example of usage

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  5. doc strings

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  6. renaming workflow

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Commits on Jun 30, 2023

  1. Ti_ref as default

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  2. abstract methods added

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Commits on Jul 4, 2023

  1. Changed to new MDSPlus structure

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  2. Adding default methods

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  3. moved sampling to it's own function in abstract class

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  4. moved sampling to it's own function in abstract class

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  5. renamed abstract class to AbstractBayesWorkflow

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  6. comments

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  7. added high density sampling as method

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  8. added attributes to __init__

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  9. error handling __init__

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  10. error handling __init__

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  11. moved read data to abstract class

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Commits on Jul 7, 2023

  1. initial commit

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  2. kwargs added

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  3. xrcs wavelength units corrected

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  4. background to int

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Commits on Jul 11, 2023

  1. stash

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  2. renamed impurities

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Commits on Jul 12, 2023

  1. stashing

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Commits on Jul 13, 2023

  1. stashing

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Commits on Jul 14, 2023

  1. stashing

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  2. fixing key names

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  3. updating and testing example

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  4. added background as attribute of helike model

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  5. fixed phantom methods

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  6. rearranged methods

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Commits on Aug 2, 2023

  1. moved background to call kwarg

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  2. params and kwargs now are given as model_{var} and model prefix is re… 

    …moved before model call
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  3. adding _phantom_data and _exp_data abstract methods

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  4. renaming to BayesWorkflowExample

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  5. initial commit

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  6. renamed phantom_params to profile_params

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  7. renamed bayesopt -> bayesmodel

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  8. renamed bayesopt -> bayesmodel

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  9. moved start point sampling to its own method _sample_start_points

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  10. fixed variable name

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  11. fixed bug with start_points being overwritten

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Commits on Aug 8, 2023

  1. removed workflow_dev

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  2. moving equilibrium to workflow object

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  3. when reading raw data save transforms to their own attribute

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  4. transforms saved to workflow class

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  5. fixed name

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  6. renamed example transform

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  7. made example los function

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  8. minor name fix

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  9. made read_test_data function

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  10. made example los function

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  11. minor type

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  12. added reader to read_test_data method

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  13. fixed copying workflow object states

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  14. updated example to work with assign_profiles

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  15. can now run with pulse = None and synthetic transforms/equilibrium

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  16. formatting

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  17. refactoring names

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  18. deleted old bayes_models tests

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  19. reformatted _build_bckc for readability

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  20. moved percentage error to class attribute

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  21. fixing init percent error

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  22. black formatting

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Commits on Aug 10, 2023

  1. renamed kin_prof -> plasma_profiles

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  2. refactored window handling

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  3. replaced doppler_broaden with physics.ev_doppler

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  4. removed methods from __init__

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Commits on Aug 11, 2023

  1. stashing

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Commits on Aug 15, 2023

  1. setup_plasma now takes kwargs

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  2. adding plasma to models now happens in setup_opt_data

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  3. workflow broken up into methods

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  4. Merge branch 'st40' into michaelgemmell/bayes_workflow

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  5. removed redundant kwargs

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  6. fixed non_plasma call option

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  7. fixed plasma_initialisation

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  8. fixing violin plotting

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  9. units for xrcs.spectra.wavelength fixed

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Commits on Aug 17, 2023

  1. nchannels added to example_los

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  2. adding print message for fake data reading

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  3. adjusting example los

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  4. bckc method not printing spectra/fit not available everytime

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  5. adjusting priors

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  6. moved kwargs to sample function

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  7. nsamples kwarg added to sample_from_high_density_region

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  8. mocked bda_tree module

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  9. fixed import

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  10. fixed import

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  11. black formatting

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  12. black formatting

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  13. fixed where mocked module is imported

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  14. black formatting

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  15. mocking bda_tree import

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  16. precommit

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  17. precommit

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  18. moving read_data tvector to kwargs

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  19. precommit formatting

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  20. precommit formatting

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  21. precommit types

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  22. precommit types

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  23. precommit types

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  24. precommit types

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  25. precommit types

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  26. precommit types

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  27. precommit types

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  28. moving kwargs/args around

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