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Dev #81

Merged
merged 161 commits into from
Aug 2, 2024
Merged

Dev #81

merged 161 commits into from
Aug 2, 2024

Commits on Jul 11, 2024

  1. chore: add pickle and sqlite files to make clean

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  2. feat: add weights option to create_topography

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Commits on Jul 12, 2024

  1. refactor: explicitly set parameters instead of kwargs for `eq_sources… 

    …_score`
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  2. refactor: move eq_sources_score to cross_validation module

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  3. feat: add load_bishop_model function

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  4. feat: add option to turn off inversion progressbar

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  5. fix: add warning to run_inversion about unused weighting grid

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  6. feat: add fname option to run_inversion_workflow to save results

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  7. feat: allow already separated train/test sets for gravity data in run… 

    …_inversion_workflow
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Commits on Jul 18, 2024

  1. style: pre-commit fixes

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  2. build: add deprecation to deps

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  3. build: remove opti deps and include as part of core deps

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  4. Merge remote-tracking branch 'origin/dev' into dev

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  5. fix: remove unnecessary depth_type arg for eq sources

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  6. refactor: update regional_constraints func. 

    BREAKING CHANGE: parameter `constraint_block_size` changed to `constraints_block_size`. Instead of supplying a lists of damping values to `dampings` for the `verde` method, now provide a single value with parameter `spline_damping`. For `eq_sources` method, instead of providing limits and trial numbers, just provide single parameter values with parameters `source_depth`, and `eq_damping`, `block_size`.
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  7. feat: add constraints_df arg to plot_inversion_results

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  8. refactor: change point color to gray for plot_2_parameter_cv_scores

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  9. feat: add plotting func for non-grid search 2 parameter CV

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  10. feat: add delta L2 norms to convergence plots. 

    BREAKING CHANGE: `plot_convergence` now takes parameter `params` (output dict from run_inversion) and doesn't plot iteration times. `plot_dynamic_convergence` now takes parameters `l2_norms` and `delta_l2_norms` instead of `results`.
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  11. feat: add constraints_dfto plotting functions

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  12. refactor: use easier to understand names in update_l2_norms

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  13. refactor: deprecate cross_validation.zref_density_optimal_parameter… 

    … in favor of new Optuna-based function `optimization.optimize_inversion_zref_density_contrast`.

BREAKING CHANGE: please switch to the new function
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  14. refactor: deprecate cross_validation.grav_optimal_parameter in favo… 

    …r of new Optuna-based function `optimization.optimize_inversion_damping`.

BREAKING CHANGE: please switch to the new function
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  15. refactor: temporarily disable info-level logging in CV score functions

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  16. fix: turn off dynamic convergence plotting during CV

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  17. feat: include multi-objective studies in custom optuna logback func

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  18. feat: add functions for optuna logback to warn about best parameter v… 

    …alues being at limits.
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  19. feat: add optimization functions for all regional estimation techniques.

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  20. feat: add function for splitting data into test and train sets with s… 

    …everal methods
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  21. feat: add function to convert format of test train folds dataframe

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  22. feat: add function to give score for regional estimations

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  23. feat: add optimization for eq source params

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  24. refactor: rename function plot_optuna_inversion_figures to `plot_op… 

    …tuna_figures`
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  25. style: misc style fixes and missing imports

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  26. style: pre-commit fixes

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  27. docs: add accidentally missing api files

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  28. refactor: remove buffer from delta l2 norm line in convergence plots

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  29. chore: fix failing tests

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Commits on Jul 22, 2024

  1. chore: update make commands

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  2. docs: typo in contrib guide

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  3. refactor: cv score functions to return inversion results as well as s… 

    …cores
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  4. fix: add crs parameter for utils.nearest_grid_fill

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Commits on Jul 23, 2024

  1. refactor: use standardized column names instead of setting with varia… 

    …bles.

BREAKING CHANGE: To simplify the code, all instances of passing the column name for the various data type have been replace with preset names. Please update your code to use column names: `gravity_anomaly` instead of parameter grav_data_column`, `reg` instead and parameter `regional_column`.
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  2. refactor: internally calculate misfit and residual in regional estima… 

    …tion functions and use standardized names.

BREAKING CHANGE: The function `regional_dc_shift` has been removed, please use function `regional_constant` instead. Inputs to all regional functions have changed use to standardized column names. All functions will now automatically calculate the misfit and and residual, as well as the regional.
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  3. fix: minor fixes to logging

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  4. feat: new function random_split_test_train to randomly split data f… 

    …or cross validations.
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  5. refactor: remove default value for damping_cv_trials and `zref_dens… 

    …ity_cv_trials` in `run_inversion_workflow`
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  6. fix: bug in run_inversion_workflow

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  7. feat: add plotting function for stochastic uncertainty

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  8. feat: add plotting function for fixing hoverdata on plotly-optuna plots

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  9. fix: bug in plot_2_parameter_cv_scores_uneven

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  10. fix: log warning if using constraints points for finding constant reg… 

    …ional value within a zref/density CV.
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  11. fix: update plotting for optuna optimization results

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  12. fix: bug fixed to explicitly remove prism_layer in zref/density CV

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Commits on Jul 26, 2024

  1. refactor: use a logger specifically for invert4geom and update all lo… 

    …gging calls
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  2. fix: bug in resample_with_test_points, drop nans

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  3. fix: remove data_column from random_split_test_train and keep all… 

    … non-coord columns in dataframe.
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  4. fix: allow no starting_prisms in run_inversion_workflow if doing a … 

    …density/zref CV
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  5. fix: add warning if no supplied constraints in run_inversion_workflow… 

    … if doing density/zref CV
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  6. feat: all passing kfolds of constraints to `optimize_inversion_zref_d… 

    …ensity_constrast`
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  7. fix: remove warning about using constraints for finding constant regi… 

    …onal value in CV as it doesn't seem to affect it.
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  8. fix: use more startup trials in optimizing on both zref and density

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  9. fix: add default value to source_depth in OptimalEqSourceParams

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  10. feat: add progressbar and callbacks to optimize_eq_source_params

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  11. feat: remove default args for optimize_eq_source_params

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  12. fix: enqueue trials for value limits in optimize_eq_source_params

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  13. feat: new function optimize_inversion_zref_density_contrast_kfolds … 

    …for use constraints within the CV via an inner kfolds-CV
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  14. fix: update plot_2_parameter_cv_scores_unven function

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  15. refactor: use pygmt instead of xarray for plotting some inversion res… 

    …ults
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  16. fix: update optuna plotting funcs

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  17. fix: raise error if index column already exists in sample_grids

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  18. fix: update best_spline_cv and use within create_topography

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  19. feat: add function for contaminating data with long-wavelength noise

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  20. feat: add function for loading all synthetic topography and gravity

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  21. feat: add grav_obs_height parameter to regional_eq_sources

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  22. feat: add data weights to regional_eq_sources

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  23. feat: allow internal CV in regional_eq_sources

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  24. refactor: set default of source_depth to 'default' in `regional_eq_… 

    …sources`
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  25. feat: allow internal CVs for eq sources and splines for `regional_con… 

    …straints`
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  26. feat: add function regional_constraints_cv to automatically perform… 

    … a K-Folds cv for finding optimal parameter values for constraint point minimization
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  27. fix: add regional scores to trial user attrs in regional hyperparamet… 

    …er optimizations
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  28. fix: updating plotting of optuna results in optimization

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  29. fix: bug in CPM kfolds optimization

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  30. feat: allow separate or combined metrics for regional hyperparameter … 

    …optimizations
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  31. refactor: minor changes to optimization

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  32. chore: ignore some ruff issues in notebooks

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  33. style: minor fixes to files

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  34. fix: bug in regional test

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  35. docs: update overview and conventions

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  36. feat: add fig_height kwarg to inversion plots

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  37. build: remove viz optional deps and add to core deps

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  38. refactor: use context manager to temporarily change logging level

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  39. fix: add check for regional separation scores not being nans

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  40. feat: add checks for regional extent of gravity and constraints

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  41. feat: add buffer arg to load_synthetic_model

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  42. chore: add debug logging throughout

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  43. chore: remove check import for psutil, joblib and tqdm_joblib

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  44. fix: raise error for bug in plot_2_param_cv_scores_uneven

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  45. fix: change regional_method to method in regional_grav_kwargs

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  46. feat: update fname for inversions and CV pickle files to be simpler

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  47. fix: suppress info logs for regional separations

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  48. fix: suppress info logs for run inversionwith kfolds CV

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Commits on Jul 27, 2024

  1. refactor: overhaul run_inversion_workflow function to emit warnings… 

    … at beginning, and enable kfolds CV for using constraints in regional separation with density/zref CV, and use better file names.

BREAKING CHANGE: removed `starting_prisms_kwargs`, put `density_contrast` and `zef` into standard kwargs now. All `regional_grav_kwargs` are now directly passed to the relavent functions, same for `starting_topography_kwargs`.
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  2. fix: bug in optimize_inversion_zref_density_contrast_kfolds

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  3. fix: bug in run_inversion_workflow

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  4. fix: minor changes

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  5. chore: ignore optuna experimental warnings

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  6. refactor: consolidate optuna warning for best parameter values at the… 

    …ir limits
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  7. refactor: consolidate optuna logging of results

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  8. build: remove unused optuna parallel functions and dependencies: jobl… 

    …ib, psutil, and tqdm_joblib
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  9. fix: add assert thay run_inversion_workflow uses correct zref and den… 

    …sity values
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  10. style: minor fixes

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  11. fix: add warning in run_inversion_workflow for using constraints with… 

    … zref/density CV
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  12. refactor: cross_validation.eq_sources_score now passes all kwargs d… 

    …irectly to hm.EquivalentSources class
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  13. refactor: change all equivalent source parameter variable names. 

    BREAKING CHANGE: please update all variables names as follows: `eq_damping`-> `damping`, `source_depth`->`depth`, `eq_damping_limits`->`damping_limits, `source_depth_limits`->`depth_limits`
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  14. refactor: update utils.best_spline_cv to pass all kwargs directly t… 

    …o verde.SplineCV.

BREAKING CHANGE: update parameter `spline_damping` to `spline_dampings` in function `regional.regional_constraints` and all functions which feed into it (i.e. `regional.regional_separation`)
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  15. refactor: change equivalent source param names 

    BREAKING CHANGE: update parameter `eq_cv`->`cv` in `regional_eq_sources` and `regional_constraints`, and use parameter `cv_kwargs` to pass args to `optimize_eq_source_params`
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  16. fix: add warnings about constraints and regional separation

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  17. fix: bug in optimize_eq_source_params

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  18. fix: update regional_eq_sources to work with new param names

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  19. refactor: clean up regional_constraints and change default grid_met… 

    …hod to "eq_sources"
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  20. refactor: update optimize_eq_source_params to work with recent changes

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  21. chore: remove test optuna parallel

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  22. docs: update some docstrings

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Commits on Jul 28, 2024

  1. refactor: default to separate metrics (multi-objective) for regional … 

    …separation
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  2. refactor: move creation of regional sep studies to new function

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  3. fix: only plot optuna importances if >1 parameter

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  4. fix: make dampings required for create_topography and `starting_t… 

    …opography_kwargs`
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  5. fix: raise error if trying to get regional score from method `constra… 

    …ints_cv`
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  6. chore: make some functions private to declutter API documentation

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Commits on Jul 30, 2024

  1. refactor: use split_kwargs in run_inversion_workflow and minor fixes

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  2. style: pre-commit fixes

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    pre-commit-ci[bot] committed Jul 30, 2024
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Commits on Aug 1, 2024

  1. style: auto style fix

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    mdtanker committed Aug 1, 2024
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  2. fix: bug in eq_sources_score with too many folds

    @mdtanker
    mdtanker committed Aug 1, 2024
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  3. fix: explicitly save inversion results in run_inversion_workflow

    @mdtanker
    mdtanker committed Aug 1, 2024
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  4. fix: separate cmaps for starting and ending gravity residual plots

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    mdtanker committed Aug 1, 2024
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  5. fix: enable upward continuation option for CPM with equivalent source… 

    … gridding
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    mdtanker committed Aug 1, 2024
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  6. feat: add contextmanager function to temporarily set an env variable

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    mdtanker committed Aug 1, 2024
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  7. feat: add damping value as dataarray attribute in create_topography

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    mdtanker committed Aug 1, 2024
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  8. feat: add class for filtering duplicate log messages

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    mdtanker committed Aug 1, 2024
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  9. feat: add non-optuna function for find best eq source damping

    @mdtanker
    mdtanker committed Aug 1, 2024
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  10. feat: add back optuna parallel functions

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    mdtanker committed Aug 1, 2024
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  11. refactor: use run_optuna for all optimizations to all for running i… 

    …n parallel.
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  12. refactor: redo regional separation with optimal parameters instead of… 

    … storing results as attributes
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  13. refactor: log info instead of warning for params at limits

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  14. refactor: clean up zref/density CV functions

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    mdtanker committed Aug 1, 2024
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  15. refactor: clean up CPM optimization and cv.

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  16. feat: add upward continuation option to eq_sources regional method

    @mdtanker
    mdtanker committed Aug 1, 2024
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  17. chore: misc small changes

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    mdtanker committed Aug 1, 2024
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  18. chore: gitignore tmp folders

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    mdtanker committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. fix: ensure all dictionary pop calls are made on copies

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  2. style: minor fixes

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    mdtanker committed Aug 2, 2024
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  3. feat: add uncertainty module

    @mdtanker
    mdtanker committed Aug 2, 2024
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  4. docs: update all doc notebooks

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    mdtanker committed Aug 2, 2024
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  5. chore: updates from learn-scientific-python

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  6. style: minor fixes

    @mdtanker
    mdtanker committed Aug 2, 2024
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  7. style: auto style fixes

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  8. chore: remove check-manifest from pre-commit

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  9. chore: delete unused release file

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  10. chore: remove pre-commit GHA in favor for pre-commit.ci

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  11. chore: remove broken test and decrease timeout

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