v0.8.0
v0.8.0 (2024-08-02)
Breaking
- 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
(10e47ef
)
- refactor: update
utils.best_spline_cv
to pass all kwargs directly to 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
) (1546d06
)
- 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 ([
1476e2a`](1476e2a))
- 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
. (a72c8a4
)
- refactor: internally calculate misfit and residual in regional estimation 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. (a501f54
)
- refactor: use standardized column names instead of setting with variables.
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,
reginstead and parameter
regional_column. ([
a4f24ec`](a4f24ec))
- refactor: deprecate
cross_validation.grav_optimal_parameter
in favor of new Optuna-based functionoptimization.optimize_inversion_damping
.
BREAKING CHANGE: please switch to the new function (3062ce3
)
- refactor: deprecate
cross_validation.zref_density_optimal_parameter
in favor of new Optuna-based functionoptimization.optimize_inversion_zref_density_contrast
.
BREAKING CHANGE: please switch to the new function (5059cd0
)
- 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
. (7cbdbb3
)
- 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
. (3496d5f
)
Build
-
build: remove unused optuna parallel functions and dependencies: joblib, psutil, and tqdm_joblib (
56c3887
) -
build: remove
viz
optional deps and add to core deps (b152f1b
) -
build: remove
opti
deps and include as part of core deps (a396318
) -
build: add deprecation to deps (
dec0ec8
)
Chore
-
chore: automatically updating changelog [skip ci] (
491d8c8
) -
chore: remove broken test and decrease timeout (
3639b9c
) -
chore: remove pre-commit GHA in favor for pre-commit.ci (
865c514
) -
chore: delete unused release file (
8118b97
) -
chore: remove check-manifest from pre-commit (
71accc4
) -
chore: updates from learn-scientific-python (
65b1815
) -
chore: gitignore tmp folders (
c228cb2
) -
chore: misc small changes (
b4d247d
) -
chore: make some functions private to declutter API documentation (
e19c6f2
) -
chore: remove test optuna parallel (
a1b2477
) -
chore: ignore optuna experimental warnings (
e1fcb78
) -
chore: remove check import for psutil, joblib and tqdm_joblib (
0a3a925
) -
chore: add debug logging throughout (
70da273
) -
chore: ignore some ruff issues in notebooks (
d18e866
) -
chore: update make commands (
50f1881
) -
chore: fix failing tests (
7edfed2
) -
chore: add pickle and sqlite files to make clean (
71e897f
) -
chore: update pre-commit hooks
updates:
- github.com/adamchainz/blacken-docs: 1.16.0 → 1.18.0
- github.com/astral-sh/ruff-pre-commit: v0.4.7 → v0.5.0
- github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1 (
58782b5
)
-
chore: automatically updating changelog [skip ci] (
882e7ad
) -
chore: add nodefaults to testing env (
9a06f62
) -
chore: update invert4geom version in environment.yml (
7762e06
) -
chore: updates to ci.yml (
b3bb4d4
) -
chore: use micromamba for GHA test env and cache it (
481a296
) -
chore: dont run test on docs or style commits (
8b1065f
) -
chore: set min pylint version (
f36ef0f
) -
chore: update make commands (
e5bc907
) -
chore: precommit ignore doc md files (
78461c3
) -
chore: automatically updating changelog [skip ci] (
0bd49ed
)
Documentation
-
docs: update all doc notebooks (
4cc0b69
) -
docs: update some docstrings (
ff932dd
) -
docs: update overview and conventions (
a225f45
) -
docs: typo in contrib guide (
32a8bdf
) -
docs: add accidentally missing api files (
b0b73d9
) -
docs: update the docs (
afab24d
) -
docs: move contrib guide into docs folder (
3009e90
)
Feature
-
feat: add
uncertainty
module (3d624c7
) -
feat: add upward continuation option to eq_sources regional method (
10e4c3e
) -
feat: add back optuna parallel functions (
4d53fde
) -
feat: add non-optuna function for find best eq source damping (
3f9c6d1
) -
feat: add class for filtering duplicate log messages (
b8df17d
) -
feat: add damping value as dataarray attribute in
create_topography
(6e96f72
) -
feat: add contextmanager function to temporarily set an env variable (
b66bb59
) -
feat: update fname for inversions and CV pickle files to be simpler (
a8c3a1a
) -
feat: add buffer arg to
load_synthetic_model
(8ac6fb1
) -
feat: add checks for regional extent of gravity and constraints (
997b416
) -
feat: add fig_height kwarg to inversion plots (
40cb035
) -
feat: allow separate or combined metrics for regional hyperparameter optimizations (
973d93d
) -
feat: add function
regional_constraints_cv
to automatically perform a K-Folds cv for finding optimal parameter values for constraint point minimization (06ebe79
) -
feat: allow internal CVs for eq sources and splines for
regional_constraints
(4982cc3
) -
feat: allow internal CV in
regional_eq_sources
(24fed1a
) -
feat: add data weights to
regional_eq_sources
(e63e49d
) -
feat: add
grav_obs_height
parameter to regional_eq_sources (ed344ae
) -
feat: add function for loading all synthetic topography and gravity (
d4c8b07
) -
feat: add function for contaminating data with long-wavelength noise (
5d087a2
) -
feat: new function
optimize_inversion_zref_density_contrast_kfolds
for use constraints within the CV via an inner kfolds-CV (f596f37
) -
feat: remove default args for
optimize_eq_source_params
(df1fb14
) -
feat: add progressbar and callbacks to
optimize_eq_source_params
(7156c05
) -
feat: all passing kfolds of constraints to
optimize_inversion_zref_density_constrast
(dc17ed3
) -
feat: add plotting function for fixing hoverdata on plotly-optuna plots (
da2af82
) -
feat: add plotting function for stochastic uncertainty (
88288a9
) -
feat: new function
random_split_test_train
to randomly split data for cross validations. (3b797ab
) -
feat: add optimization for eq source params (
9a31851
) -
feat: add function to give score for regional estimations (
276da98
) -
feat: add function to convert format of test train folds dataframe (
eec2a93
) -
feat: add function for splitting data into test and train sets with several methods (
5e252f1
) -
feat: add optimization functions for all regional estimation techniques. (
7db27cc
) -
feat: add functions for optuna logback to warn about best parameter values being at limits. (
53fafc7
) -
feat: include multi-objective studies in custom optuna logback func (
89d4403
) -
feat: add
constraints_df
to plotting functions (64147bf
) -
feat: add plotting func for non-grid search 2 parameter CV (
b86ebf9
) -
feat: add
constraints_df
arg toplot_inversion_results
(57aefcc
) -
feat: allow already separated train/test sets for gravity data in run_inversion_workflow (
9fa7f27
) -
feat: add fname option to run_inversion_workflow to save results (
d393d7d
) -
feat: add option to turn off inversion progressbar (
17c6b32
) -
feat: add load_bishop_model function (
8006cf5
) -
feat: add weights option to create_topography (
17827b4
)
Fix
-
fix: ensure all dictionary
pop
calls are made on copies (1c80404
) -
fix: enable upward continuation option for CPM with equivalent source gridding (
0c23eca
) -
fix: separate cmaps for starting and ending gravity residual plots (
d6feb0e
) -
fix: explicitly save inversion results in
run_inversion_workflow
(5db892e
) -
fix: bug in eq_sources_score with too many folds (
c78354e
) -
fix: raise error if trying to get regional score from method
constraints_cv
(d35b703
) -
fix: make
dampings
required forcreate_topography
andstarting_topography_kwargs
(c3d407b
) -
fix: only plot optuna importances if >1 parameter (
ba17ed1
) -
fix: update
regional_eq_sources
to work with new param names (68f85f2
) -
fix: bug in
optimize_eq_source_params
(eb0ebbe
) -
fix: add warnings about constraints and regional separation (
c6bc503
) -
fix: add warning in run_inversion_workflow for using constraints with zref/density CV (
88e9a86
) -
fix: add assert thay run_inversion_workflow uses correct zref and density values (
5692da4
) -
fix: minor changes (
dbe8ca5
) -
fix: bug in run_inversion_workflow (
bf875f8
) -
fix: bug in
optimize_inversion_zref_density_contrast_kfolds
(8886438
) -
fix: suppress info logs for run inversionwith kfolds CV (
3bb59d2
) -
fix: suppress info logs for regional separations (
e15d3de
) -
fix: change
regional_method
tomethod
inregional_grav_kwargs
(d52f01d
) -
fix: raise error for bug in
plot_2_param_cv_scores_uneven
(7ec08e7
) -
fix: add check for regional separation scores not being nans (
e98bbfd
) -
fix: bug in regional test (
c618097
) -
fix: bug in CPM kfolds optimization (
30e6763
) -
fix: updating plotting of optuna results in
optimization
(af78985
) -
fix: add regional scores to trial user attrs in regional hyperparameter optimizations (
9ac1bdf
) -
fix: update
best_spline_cv
and use withincreate_topography
(5c3d6c5
) -
fix: raise error if index column already exists in
sample_grids
(7ca6c83
) -
fix: update optuna plotting funcs (
d3b1552
) -
fix: update
plot_2_parameter_cv_scores_unven
function (8b73d43
) -
fix: enqueue trials for value limits in
optimize_eq_source_params
(af519e0
) -
fix: add default value to source_depth in
OptimalEqSourceParams
(03b828e
) -
fix: use more startup trials in optimizing on both zref and density (
789167b
) -
fix: remove warning about using constraints for finding constant regional value in CV as it doesn't seem to affect it. (
14efcfc
) -
fix: add warning if no supplied constraints in run_inversion_workflow if doing density/zref CV (
2783ab4
) -
fix: allow no starting_prisms in
run_inversion_workflow
if doing a density/zref CV (da1674c
) -
fix: remove
data_column
fromrandom_split_test_train
and keep all non-coord columns in dataframe. (3584286
) -
fix: bug in
resample_with_test_points
, drop nans (feda68f
) -
fix: bug fixed to explicitly remove prism_layer in zref/density CV (
b70a893
) -
fix: update plotting for optuna optimization results (
f2c60c4
) -
fix: log warning if using constraints points for finding constant regional value within a zref/density CV. (
f7a135d
) -
fix: bug in
plot_2_parameter_cv_scores_uneven
(b8ca0f4
) -
fix: bug in run_inversion_workflow (
604729b
) -
fix: minor fixes to logging (
4481f5d
) -
fix: add crs parameter for
utils.nearest_grid_fill
(b2eec98
) -
fix: turn off dynamic convergence plotting during CV (
a09ad32
) -
fix: remove unnecessary
depth_type
arg for eq sources (4998705
) -
fix: add warning to run_inversion about unused weighting grid (
e2676fa
)
Refactor
-
refactor: clean up CPM optimization and cv. (
f873490
) -
refactor: clean up zref/density CV functions (
4ecf9ec
) -
refactor: log info instead of warning for params at limits (
24819a5
) -
refactor: redo regional separation with optimal parameters instead of storing results as attributes (
ff369d8
) -
refactor: use
run_optuna
for all optimizations to all for running in parallel. (c59f2c7
) -
refactor: use
split_kwargs
in run_inversion_workflow and minor fixes (849bb39
) -
refactor: move creation of regional sep studies to new function (
be30d53
) -
refactor: default to separate metrics (multi-objective) for regional separation (
91b2e4b
) -
refactor: update
optimize_eq_source_params
to work with recent changes (0e3ce7b
) -
refactor: clean up
regional_constraints
and change default grid_method to "eq_sources" (7170ebd
) -
refactor:
cross_validation.eq_sources_score
now passes all kwargs directly to hm.EquivalentSources class (5f9f7c6
) -
refactor: consolidate optuna logging of results (
68b8dc8
) -
refactor: consolidate optuna warning for best parameter values at their limits (
5a3a7d1
) -
refactor: use context manager to temporarily change logging level (
c14aaca
) -
refactor: minor changes to
optimization
(18f2058
) -
refactor: set default of
source_depth
to 'default' inregional_eq_sources
(ee7575f
) -
refactor: use pygmt instead of xarray for plotting some inversion results (
cf377b3
) -
refactor: use a logger specifically for invert4geom and update all logging calls (
fa111cc
) -
refactor: remove default value for
damping_cv_trials
andzref_density_cv_trials
inrun_inversion_workflow
(7dce943
) -
refactor: cv score functions to return inversion results as well as scores (
15e4369
) -
refactor: remove buffer from delta l2 norm line in convergence plots (
cd85659
) -
refactor: rename function
plot_optuna_inversion_figures
toplot_optuna_figures
(4823cab
) -
refactor: temporarily disable info-level logging in CV score functions (
f5c329d
) -
refactor: use easier to understand names in
update_l2_norms
(1516795
) -
refactor: change point color to gray for
plot_2_parameter_cv_scores
(ccbd4ba
) -
refactor: move eq_sources_score to cross_validation module (
4def683
) -
refactor: explicitly set parameters instead of kwargs for
eq_sources_score
(2a8c133
)
Style
-
style: auto style fixes (
f49df6d
) -
style: minor fixes (
c8283be
) -
style: minor fixes (
bb4ef6f
) -
style: auto style fix (
3eb9a4d
) -
style: pre-commit fixes (
ff4cd99
) -
style: minor fixes (
dc23d05
) -
style: minor fixes to files (
62e623a
) -
style: pre-commit fixes (
e596e12
) -
style: misc style fixes and missing imports (
7ff25a4
) -
style: pre-commit fixes (
ea59410
)