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`](https://github.com/mdtanker/invert4geom/commit/1476e2a5233f38c4a36d3f3c7f9ba4889bf8db2e))

• 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 parameterregional_column. ([a4f24ec`](https://github.com/mdtanker/invert4geom/commit/a4f24ecd3c84a9c545d13e54ad4cebf0e70794d1))

• refactor: deprecate cross_validation.grav_optimal_parameter in favor of new Optuna-based function optimization.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 function optimization.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_dfto plotting functions (64147bf)

• feat: add plotting func for non-grid search 2 parameter CV (b86ebf9)

• feat: add constraints_df arg to plot_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 for create_topography and starting_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 to method in regional_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 within create_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 from random_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' in regional_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 and zref_density_cv_trials in run_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 to plot_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)

v0.7.0 (2024-06-26)

Breaking

• fix: remove density_contrast parameter from run_inversion and extract contrast instead

BREAKING CHANGE: the run_inversion function now doesn't take density_contrast parameter, please remove these parameters from your code! (2883c25)

Build

• build(deps): bump codecov/codecov-action from 4.3.1 to 4.5.0

Bumps codecov/codecov-action from 4.3.1 to 4.5.0.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
  ...

Signed-off-by: dependabot[bot] <[email protected]> (f248498)

Chore

• chore: automatically updating changelog [skip ci] (7f916a5)

• chore: automatically updating changelog [skip ci] (9525318)

• chore: automatically updating changelog [skip ci] (a6b0911)

• chore: add codecov token (9d27f1b)

• chore: automatically updating changelog [skip ci] (1a163ef)

• chore: automatically updating changelog [skip ci] (c4ee971)

• chore: pre-commit autoupdate to monthly (00189aa)

• chore: automatically updating changelog [skip ci] (2736914)

• chore: automatically updating changelog [skip ci] (50a3a40)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.4.4 → v0.4.7
• github.com/codespell-project/codespell: v2.2.6 → v2.3.0 (3f3fdd3)

Documentation

• docs: rerun the docs (322bcc8)

• docs: add variable density example to user guide (bdce402)

• docs: rerun docs (4635876)

• docs: add documentation to density contrast implementation (ca96f76)

• docs: fix error in readme (18b67c8)

• docs: update binder env to v0.6 (19551d7)

Fix

• fix: add warnings for run_inversion_workflow (54fc6b9)

• fix: remove zref and density_contrastparameters, extract from prism layer instead

BREAKING_CHANGE: make sure to remove all zref and density_contrast parameters from the following functions: run_inversion, grav_cv_score, constraints_cv_score. (f995f00)

Style

• style: typo in docstring (d05861a)

Unknown

• Fix Small Bug with non-constant density contrast

Update update_prisms_ds for dealing with non-constant density contrast (117490c)

v0.6.0 (2024-05-29)

Breaking

• refactor: make gravity CV return inversion results

BREAKING CHANGE: first return value of grav_optimal_parameter is ow a tuple of the inversion results. (1048295)

• refactor: regional separation methods only take gravity df not grid.

BREAKING CHANGE: use grav_df and grav_data_column arguments instead of passing a grav_grid to the various regional separation methods. (33fc5ba)

• refactor: switch keyword argument name

BREAKING CHANGE: make sure to switch all mentions of regional_col_name to regional_column in your code! (a71cba1)

• refactor: switch keyword argument for constraint points to constraints_df

BREAKING CHANGE: all use of constraint points need to be supplied via argument constraints_df now! (bf6cd34)

• refactor: switch keyword argument name

BREAKING CHANGE: make sure to switch run_inversion argument weights_after_solver to apply_weighting_grid and supply a xr.DataArray via parameter weighting_grid. (444c43d)

• refactor: switch keyword argument name from input_grav_column to grav_data_column

BREAKING CHANGE: make sure to switch all mentions of 'input_grav_columntograv_data_column in your code! ([f864c1f`](https://github.com/mdtanker/invert4geom/commit/f864c1f0fede206b2c65f0b9ac60814e8e8011f9))

• refactor: switch keyword argument name from input_grav to grav_df

BREAKING CHANGE: make sure to switch all mentions of input_grav to grav_df in your code! (b7656ee)

Build

• build: add plotly as optional dep (0745e2a)

Chore

• chore: automatically updating changelog [skip ci] (6140401)

• chore: add warning if using constraints for regional separation within zref/density CV (0e298aa)

• chore: allow cyclic imports (0c8942b)

• chore: add optuna and plotly as optional imports (3545f71)

• chore: update regional tests (9994cd5)

• chore: update tests to use easting and northing conventions (74eed3e)

• chore: check for valid registration type (6fb491a)

• chore: raise error for wrong grid fill method (c7bc568)

• chore: codespell ignore word (1a8b169)

• chore: pylint ignore changelog (b8a7030)

• chore: git ignore pickle and log files (de4c738)

• chore: add make clean command (55fe0fa)

• chore: fix ruff linting compatibility issue (f82448c)

• chore: remove comprehensive ignore of specific md files in pre-commit (eb9b405)

• chore: ignore md files in pre-commit prettier, ruff, blacken (0fade3b)

• chore: automatically updating changelog [skip ci] (bde09b7)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4 (d00419e)

• chore: automatically updating changelog [skip ci] (ad579ee)

Documentation

• docs: update docstrings (ac9753c)

• docs: add section on conventions for Invert4Geom (650e4e0)

• docs: re-run all notebooks (a68431f)

• docs: clarify intended use of invert4geom in README (0817954)

• docs: fix spacing on md files (727c268)

• docs: update binder env (a6d9690)

Feature

• feat: add warning for global min of optimizing eq source parameters (bbd5f10)

• feat: add optuna optimization plotting function (8e64289)

• feat: add function for performing constraint CV (96f74a0)

• feat: updating logging in CV (45f1f77)

• feat: save and reload best inversion results during grav CV (f390b7c)

• feat: add function to run entire inversion workflow at once (a7b87c7)

• feat: add option to save inversion results (db9ef36)

• feat: add regional_separation function (3a8a626)

• feat: add equivalent sources options to regional_constraints (264c9f5)

• feat: add grav obs height option to regional_constraints (41f1a67)

• feat: add function for creating starting topography (32bb475)

• feat: add option to calculate CV scores as root median or mean square (818eed4)

Fix

• fix: remove numba jit decorator from jacobian_prism (b6166f5)

• fix: add missing imports (bbc4825)

• fix: update imports (362d79d)

• fix: use median not RMSE for constraint point minimization (6d1c686)

• fix: fix warning for best_spline_cv (abb5976)

Refactor

• refactor: update plot 2 parameter CV function (365f5cf)

• refactor: update plot convergence function (7efe1e7)

• refactor: update plot inversion results function (ad2efa8)

• refactor: change default filename for optimize_eq_source_params (c7e4acd)

• refactor: change names for saved inversion parameters (eaa7e55)

• refactor: remove inversion_region from run_inversion (73c1c7c)

• refactor: misc changes to regional functions (446260e)

• refactor: use easting and northing as coordinate names (172b736)

• refactor: change default regional_constraints grid method to verde (ac1320b)

• refactor: update inversion progressbar (d791fcb)

• refactor: update progressbar for grav CV (1ebe1d8)

• refactor: use list of l2 norms for end_inversion (f25e739)

• refactor: change default perc_increase_limit (c456be8)

• refactor: explicitly create density grid (7555f18)

• refactor: use topo variable for getting final topography grid (5596082)

• refactor: enable CV progressbars by default (dc6646e)

Style

• style: automatic style fixes (4a83bdd)

v0.5.0 (2024-05-07)

Build

• build: make semantic release GHA need changelog success (7b7d1c4)

• build: add make command for binder env (3b5d44e)

• build: add optuna-integration package (fa648d5)

Chore

• chore: automatically updating changelog [skip ci] (ee17a58)

• chore: ignore dtype in test utils sampling (f18e356)

• chore: more specific dtypes in tests (1c587fd)

• chore: fix test dtype issue (f16f955)

• chore: use head commit for skip tests on docs (7f4c863)

• chore: don't run test on docs commits [skip ci] (fedf871)

• chore: try stopping tests only for docs (not style) (f1cf974)

• chore: stop tests on docs/style [skip ci] (49de955)

• chore: still trying to stop GHA running on docs / style [skip ci] (7306b35)

• chore: add missing ")" [skip-ci] (49918e9)

• chore: fixing skip test on certain commits [skip ci] (4dfe4cf)

• chore: stop tests running on doc / style commits (1a9e308)

• chore: unpin binder env (e865ddc)

• chore: cleanup Make commands (482d95a)

• chore: don't run tests on docs or style commits (30abcdf)

• chore: remove pre-commit updates from changelog (f7ea9c8)

• chore(deps): bump codecov/codecov-action from 4.3.0 to 4.3.1

Bumps codecov/codecov-action from 4.3.0 to 4.3.1.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
  ...

Signed-off-by: dependabot[bot] <[email protected]> (84215b4)

• chore: automatically updating changelog [skip ci] (84dccb5)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3 (3d243bf)

• chore: automatically updating changelog [skip ci] (2fdb978)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.2
• github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0 (2504dfe)

• chore: automatically updating changelog [skip ci] (b3c68c7)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.3.7 → v0.4.1 (398e222)

• chore: automatically updating changelog [skip ci] (340e460)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.3.0 → v0.3.7
• github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0
• github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0
• github.com/shellcheck-py/shellcheck-py: v0.9.0.6 → v0.10.0.1 (3623095)

• chore(deps): bump codecov/codecov-action from 4.1.0 to 4.3.0

Bumps codecov/codecov-action from 4.1.0 to 4.3.0.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
  ...

Signed-off-by: dependabot[bot] <[email protected]> (0098ab4)

• chore: automatically updating changelog [skip ci] (43a67b1)

• chore: automatically updating changelog [skip ci] (60af250)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.0 (cb7409b)

• chore: automatically updating changelog [skip ci] (651ba91)

• chore(deps): bump codecov/codecov-action from 4.0.1 to 4.1.0

Bumps codecov/codecov-action from 4.0.1 to 4.1.0.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
  ...

Signed-off-by: dependabot[bot] <[email protected]> (8df246c)

Documentation

• docs: remove duplicate thumbnail [skip ci] (507bd06)

• docs: specify thumbnails (18fcac1)

• docs: remove linkcode for API (2d2eeff)

• docs: add links to github code for API (883c706)

• docs: fix error in conf.py (2a7824d)

• docs: fix links to code in API docs (7d1fa5f)

• docs: update notebooks (a74dbee)

• docs: add bishop gallery example (7e55c7e)

• docs: update contrib guide (36baf37)

• docs: update and rerun user guide notebooks (b1c572a)

• docs: update contributing guide (761814c)

• docs: clarify code comment (ef34f57)

• docs: improve inversion docstrings (471a76f)

• docs: fix pinning issue (a8f0ea1)

• docs: pin python-semantic-release in GHA (c5b18da)

Feature

• feat: add termination reason to inversion progress bar (0274d7b)

• feat: add region arg to plot_inversion_topo_results (694b778)

• feat: add DC-shift regional estimation method (2e91771)

• feat: add scale and yoffset args to synthetic topography function (4801f33)

• feat: add iteration progress bar to inversion (25a4e92)

• feat: limit misfit rmse to within optional inversion region (b66d3c4)

• feat: add dynamic convergence plot to inversion (7a5d5b2)

• feat: add inversion_region to plot convergence (52eebdd)

• feat: add plot_title kwarg for plot_cv_scores (3cda4e0)

• feat: fix colorscales for inversion grav results (9218e68)

Fix

• fix: set optuna logging level to warning (0796fef)

• fix: make ipython optional import (ce88f1a)

• fix: allow wiggle room for enforcing confining surfaces (7e4e0b0)

• fix: add warning message to annulus derivative calculation (99a7ade)

• fix: add noise to test regional eq sources (350baca)

• fix: replace pygmt gridding with simple set_index for plotting (ebf6732)

Style

• style: pre-commit fixes (116a612)

• style: pre-commit fixes (b110f23)

• style: pre-commit fixes (9fe3777)

v0.4.0 (2024-02-22)

Breaking

• build: drop python 3.8 support

BREAKING CHANGE: (77cc15d)

Build

• build: add support for Python 3.12 (b0b058a)

• build: add binder env (60f15b7)

• build: update pyproj specs (e70c4bc)

• build: add/remove dev dependencies (ec831f3)

• build: add doc dependencies (d62d855)

Chore

• chore: automatically updating changelog [skip ci] (50898ac)

• chore: fixing semantic release action (cfcfdf1)

• chore: trying to fix semantic-release action (75cadc3)

• chore: manually update GH action and pre-commit versions (46d9357)

• chore: update changelog template (d20c603)

• chore: delete tmp optuna file in test (9b266aa)

• chore: gitignore vscode settings (ad5ab8e)

• chore: remove unnecessary files (74b63ae)

• chore: list packages after install in test GHA (35f05e5)

• chore: include all optimization deps in testing env (cb2f091)

• chore: add optuna to test deps (89e2447)

• chore: update GHA test env (70fcbf7)

• chore: revert to mamba for GHA test env (45c9b7b)

• chore: add make command for GHA test env (9f598bd)

• chore: upgrade pip for GHA test env (e89ba32)

• chore: include setuptools in GHA test env (aa9e569)

• chore: fix typo in pre-commit (b05bab5)

• chore: ignore bib in pre-commit (ecd6d93)

• chore: ignore changelog template in pre-commit (23ed7d4)

• chore: update changelog template (f3a3c9c)

• chore: remove old push GHA (9e2088d)

• chore: replace mamba with pip for GHA test env install (421cffe)

• chore: rename release GHA (32b6c3a)

• chore: add semantic release GHA (204c7a7)

• chore: update pre-commit config (e2dbcdd)

• chore: add make commands (98d6069)

• chore: update RTD env and add make command (83d4199)

• chore: change dependa-bot updates to monthly (3284324)

• chore: update from antarctic-plots to polartoolkit (16bf313)

Documentation

• docs: rerun all user guide notebooks (d8688f2)

• docs: fix incorrect reference styles (93b6cfc)

• docs: fix bibliography references (606c936)

• docs: fix rtd.yml (36376d7)

• docs: use pip to install RTD env (27c063a)

• docs: switch from autodoc to autoapi (e182bac)

• docs: add binder link to docs (ddb80d3)

• docs: add reference .bib and md file (048933e)

• docs: update install instructions (5c051a4)

• docs: add a discretization user guide (8562c06)

• docs: move contributing guide (8d30cda)

• docs: enable nbgallery for user guide (2bcc0aa)

• docs: enable binder links (e134b4a)

Feature

• feat: add plotting options to show_prism_layers (8c1874e)

Fix

• fix: resolve permission denied windows error in optuna test (1084b56)

Style

• style: pre-commit fixes (ed6fed9)

• style: remove unused type ignore (6313e7b)

• style: fix styling (15d96c7)

• style: formatting (ccb890c)

v0.3.1 (2023-12-06)

Build

• build: only install doc optional deps for nox (da69dcb)

Chore

• chore: adds license file to pyproject.toml (ed882d8)

• chore: adds github issue templates amd comments (721b391)

• chore(deps): bump conda-incubator/setup-miniconda from 2 to 3

Bumps conda-incubator/setup-miniconda from 2 to 3.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: conda-incubator/setup-miniconda
  dependency-type: direct:production
  update-type: version-update:semver-major
  ...

Signed-off-by: dependabot[bot] <[email protected]> (93e8abc)

Documentation

• docs: remove optimization deps from RTD env (dad0330)

• docs: fix docstring for jacobian_annular (7b7be72)

• docs: fix intersphinx mapping links (1ca89af)

• docs: add docs link to contributing file (9d7f830)

• docs: fixes minor issues in docs (0bca578)

• docs: add cover figure (5c0d029)

Fix

• fix: adds encoding to open calls (110ff36)

Style

• style: formatting (3ab7fb3)

v0.3.0 (2023-11-30)

Build

• build: restrict xrft version

Seems to be cause issues in conda-forge feedstock, harmonica requires >= 1.0, match this (f9a17ff)

• build: combine optional dependencies into all (d5f038b)

• build: add optimization optional deps (871a870)

• build: alter dependency versions (82695f5)

• build: add new dependencies (8d9982c)

Chore

• chore: add Make changelog command (d433a9d)

• chore: numba-progress install from pip to conda (59099bf)

• chore: move changelog template location (2bdeccb)

• chore: fix env.yml files (2735f09)

• chore: seperate RTD env and testing env (0d1621d)

• chore: remove build api docs to ci.yml (0bf7f87)

• chore: add sphinx-apidoc call to ci.yml (9d0ff3a)

• chore: update pre-commit hooks (#28)

updates:

• github.com/astral-sh/ruff-pre-commit: v0.1.3 → v0.1.6
• github.com/pre-commit/mirrors-prettier: v3.0.3 → v3.1.0
• github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.1

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (161cc9d)

Documentation

• docs: replace Unknown with Other in changelog (e7f274a)

• docs: customize jinja changelog template (203c1c8)

• docs: add rst files for new modules (b9010e5)

• docs: add estimating regional field user guide (7e5b69b)

• docs: add testing instructions to contrib guide (9c2732d)

• docs: add module descriptions to overview (ae7469d)

• docs: fix some docstrings (920e129)

• docs: add cross_validation to pre-commit ignore (b8e8e86)

Feature

• feat: add test files for all modules (2c11f56)

• feat: add regional module (2d52c19)

• feat: add optimization module (a398e12)

• feat: add synthetic regional field function (aeb81b2)

• feat: add eq_sources_score function (6c132d8)

• feat: add best_spline_cv function (3965dcb)

Fix

• fix: optional optuna Journal import (e0a159f)

• fix: make optimization dep imports optional (e7ed8a1)

• fix: use lock_obj to fix file store for windows (f835c74)

• fix: replace psutil cpu affinity with new function

used a function from a stack overlow answer which is able to get cpu core numbers for many operating systems since psutil doesn't seem to work for MacOS or Windows. (f3bf61e)

• fix: typos and formatting (9ce69c2)

Unknown

• Revert "Adding regional and optimization modules (#30)" (#31)

This reverts commit daf3c9ccb32c5dbee137d20b61e959247399b0dc. (99bcfac)

• Adding regional and optimization modules (#30)

• docs: fix some docstrings

• feat: add best_spline_cv function

• feat: add eq_sources_score function

• feat: add synthetic regional field function

• feat: add optimization module

• feat: add regional module

• docs: add module descriptions to overview

• docs: add testing instructions to contrib guide

• build: add new dependencies

• feat: add test files for all modules

• docs: add estimating regional field user guide

• fix: typos and formatting

• fix: replace psutil cpu affinity with new function

used a function from a stack overlow answer which is able to get cpu core numbers for many operating systems since psutil doesn't seem to work for MacOS or Windows.

• build: alter dependency versions

• fix: use lock_obj to fix file store for windows

• chore: add sphinx-apidoc call to ci.yml

• docs: add rst files for new modules

• chore: remove build api docs to ci.yml

• chore: seperate RTD env and testing env

• chore: fix env.yml files

• chore: move changelog template location

• docs: customize jinja changelog template

• build: add optimization optional deps

• build: combine optional dependencies into all

• build: restrict xrft version

Seems to be cause issues in conda-forge feedstock, harmonica requires >= 1.0, match this

• chore: numba-progress install from pip to conda

• docs: replace Unknown with Other in changelog

• chore: add Make changelog command

• fix: make optimization dep imports optional

• fix: optional optuna Journal import (daf3c9c)

• Fixing the docs and add semantic release check workflow (#29)

• build: restrict antarctic_plots version

• build: move changelog template

• build: use conda for readthedocs env

• build: add local install for RTD

• style: pre-commit fixes

• build: add doc deps to RTD env

• build: update RTD env

• build: update RTD dnv

• build: force update

• build: force update

• chore: add non-main branches to semantic release

• chore: add semantic_release_check.yml

• style: formatting

• style: pre-commit fixes

• chore: add autocomment to release check action

• chore: fix release check action

• chore: add ref to release check action

• chore: fixing release check action

• chore: add PAT to release check action

• chore: PAT supplied in wrong location

• chore: switch back to GH token

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cade158)

v0.2.0 (2023-11-27)

Chore

• chore(deps): bump actions/checkout from 3 to 4 (#27)

Bumps actions/checkout from 3 to 4.

• Release notes
• Changelog
• Commits

updated-dependencies:

• dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
  ...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (3f46f5b)

• chore: add ignore option for codespell (bc4f597)

• chore: add semantic-release changelog template (bc93159)

• chore: add semantic release check to makefile (d3bb077)

Documentation

• docs: minor changes (c29c742)

• docs: new user guide notebook

adds notebook which combines damping, density, and zref cross validations, as well as using a starting model and weighting grid. (1ad026a)

• docs: update user guide notebooks

To run faster, this lowers the resolution of the user guide notebooks. It also adds synthetic noise to all the examples. (d63c410)

• docs: update some docstrings (0bf4d7b)

• docs: add references to docstrings (d0357a8)

• docs: add emojis to homepage (eda2938)

• docs: set nb execute to never for docs (ef58202)

• docs: edit the user guide notebooks (aec1fe6)

• docs: add cross validation api docs (03c38d6)

• docs: remove tqdm mapping (088409e)

Feature

• feat: add 2 parameter cross validation plotting (2d1269e)

• feat: add contaminate function for synthetic noise (3a1cf8d)

Fix

• fix: add reference level to iteration plots (960eb44)

Style

• style: formatting (66b0a56)

Unknown

• Merge branch 'main' of https://github.com/mdtanker/invert4geom (86c611b)

v0.1.20 (2023-11-24)

Fix

• fix: forcing a new patch (9a73194)

Unknown

• Hyperparameter cross validation (#25)

• fix: add zref and density args to inversion

• fix: removes references to density and zref

• fix: remove python 3.12 support, add test for 3.10

• chore: specify semantic release options

• chore: remove pypy from testing versions

• feat: add cross validation module

• feat: add cross validation plot function

• build: add tqdm and seaborn deps

• docs: update simple_inversion.ipynb

Lower the grid resolution to run faster, add more detailed comments, use same zref as true topography, change choosen damping value

• docs: add damping_cross_validation.ipynb

new notebook to demonstrate how to perform a CV to find the optimal damping value.

• docs: add damping_cross_validation.ipynb to guide

• style: formatting cross_validation.py

• fix: allow matplotlib and seaborn to be optional

• chore: update deps in .yml and mapping

• chore: add github action workflow

run a python-semantic-release in no operation mode to see what will be done. Runs one all commits to PR's

• style: pre-commit fixes

• style: format fix

• chore: update release check

• chore: updating release check

• chore: remove semantic release check action

• fix: restructure damping cross validation

associated functions are termed "gravity" cross validation since they use the observed and predicted gravity data to determine the score.

• feat: add constraints cv functions

termed "constraints" since they use the difference between constraint point elevations and inverted topography to determine the score. Used for zref and density cross validations

• docs: reorganized damping CV notebook

• docs: restructured simple inversion notebook

• docs: restructured starting model notebook

• docs: add density and zref CV notebooks

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (2546ee4)

v0.1.19 (2023-11-24)

Chore

• chore: remove scm version files (1f99c55)

Fix

• fix: add zref and density args to inversion (#24)

• fix: add zref and density args to inversion

• fix: removes references to density and zref

• fix: remove python 3.12 support, add test for 3.10

• chore: specify semantic release options

• chore: remove pypy from testing versions (c62f189)

Unknown

• Working on the docs (#23)

• docs: update install instructions

• chore: add test env make commands

• chore: fixes issues pointed out in repo-review

• docs: add codecov badge to readme (fb5f7b2)

v0.1.18 (2023-11-23)

Fix

• fix: use PAT instead of GH tocken (f2cb0d1)

This is the first release of invert4geom. We will follow semantic versioning, so this version, v0.1.0, is there not production ready and will likely change significantly before v1.0.0.