v0.11.1

v0.11.1 (2024-11-20)

Bug Fixes

• Make xesmf optional dependency (664072a)

Chores

• Automatically updating changelog [skip ci] (f579f3a)

• Automatically updating changelog [skip ci] (941ee09)

v0.11.0

v0.11.0 (2024-11-19)

Bug Fixes

• Use duplicate filter on optimize for zref/density (cc825e0)

• Exception for trail worsening warning (313f847)

• Raise warnings for invalid number of splits in test train data splitting (bcef273)

• Raise warnings and use fallback for nan scores in eq source fitting (ad14dc0)

• Re-create starting topography for each fold of training constraint points in density/zref optimization. (91ffb71)

• Re-write long-wavelength contamination function, adding dependency xesmf. (335e11e)

Chores

• Automatically updating changelog [skip ci] (f4af5d4)

• Remove ruff commands and use pre-commit (7495204)

• Bump the actions group with 2 updates (45e0b4a)

Bumps the actions group with 2 updates: mamba-org/setup-micromamba and codecov/codecov-action.

Updates mamba-org/setup-micromamba from 1 to 2 - Release notes - Commits

Updates codecov/codecov-action from 4.5.0 to 4.6.0 - Release notes - Changelog - Commits

--- updated-dependencies: - dependency-name: mamba-org/setup-micromamba dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ...

Signed-off-by: dependabot[bot] [email protected]

• Automatically updating changelog [skip ci] (a2c4523)

• Bump binder env to v.0.10 (0604561)

• Update release checklist and make commands (8943bd0)

• Automatically updating changelog [skip ci] (993f053)

Documentation

• Minor updates (82210b2)

• Rerun docs (9f7348f)

• Fix docstring (b0ec481)

• Add TLDR and conventional comments to contribute guide (1371096)

• Saving progress (bdd6907)

• Restructure to Divio system (865983a)

• Update some docs notebooks (6fe1488)

Features

• Return fig for plot_cv_scores (70e4a0d)

• Add fname kwarg to some plotting functions (155f645)

• Add plotting functions for latin hypercube sampling (2607284)

• Add region parameter for regional_misfit_uncertainty (ef5239e)

• Add uncertainty estimate for equivalent source interpolation (0cb4a21)

• Allow normalizing of sampled values in latin hypercube (b01c210)

• Include discrete uniform distribution for LHS sampling (7bd98e9)

• Allow choice of criterion in sampling of latin hyper cube (f7e94a1)

• Allow weight_by=None in merged_stats (d96e5c2)

• Add normalizing functions (bebaa67)

Refactoring

• Make "default" the default depth for eq sources (6b68c2b)

• Print more decimals for inversion info (05cbda9)

v0.10.0

v0.10.0 (2024-10-09)

Build System

• build: make xesmf optional dependency (8f3494c)

Chores

• chore: automatically updating changelog [skip ci] (63c9c22)

• chore: set ruff rule (7cdb2b0)

• chore: automatically updating changelog [skip ci] (2692a22)

• chore: update pre-commit hooks

updates:

• github.com/astral-sh/ruff-pre-commit: v0.5.0 → v0.6.9
• github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0
• github.com/pre-commit/mirrors-mypy: v1.10.1 → v1.11.2
• github.com/abravalheri/validate-pyproject: v0.18 → v0.20.2
• github.com/python-jsonschema/check-jsonschema: 0.29.0 → 0.29.3 (5c0cfdf)

• chore: automatically updating changelog [skip ci] (5f9b60f)

Code Style

• style: pre-commit fixes (7802143)

• style: pre-commit fixes (28687c5)

Documentation

• docs: update and rerun doc notebooks (7285281)

Features

• feat: allow passing column name for weights in create_topography (1815139)

• feat: add fname option to optimize functions (1bb69b6)

Fixes

• fix: minor changes (338306d)

• fix: re-write long-wavelength contamination function, adding dependency xesmf (6e96870)

• fix: add debug for eq source fitting (43e2855)

• fix: if too few points, reduce K folds until it works for fitting Splines (5d40917)

• fix: re-create starting topography for each fold of training constraint points in density/zref optimization (5da58fb)

• fix: bug for checking gravity inside topo region with density/zref cv (e96099a)

v0.9.1

v0.9.1 (2024-10-03)

Build

• build: add pooch and scikit-learn as dependencies (8bebf45)

Chore

• chore: automatically updating changelog [skip ci] (bfb951a)

• chore: automatically updating changelog [skip ci] (8e28e4e)

• chore: update binder env to v0.9 (0307bd9)

• chore: automatically updating changelog [skip ci] (2267066)

Documentation

• docs: update and rerun docs (1d39529)

Fix

• fix: fixes error of using 1x not 4.5x default depth for eq sources (5746851)

• fix: enable default eq source depth for regional constraints (d9301a3)

v0.9.0

v0.9.0 (2024-08-10)

Build

• build: increase min supported botorch version to include logie_candidates_func (1491b24)

• build: restrict scipy to below v1.14 until UQpy import issue is fixed (474e5b5)

Chore

• chore: automatically updating changelog [skip ci] (f51b519)

• chore: automatically updating changelog [skip ci] (4643891)

• chore: fix binder env (1066cc6)

• chore: automatically updating changelog [skip ci] (b6e1319)

• chore: update binder env (bf45857)

• chore: automatically updating changelog [skip ci] (668c199)

Documentation

• docs: fix notebook error (f7783e2)

• docs: unindent docstring (e0715d6)

Feature

• feat: add constraint_style to plotting inversion grav resutls (c062b43)

Fix

• fix: raise error for NaNs in gravity dataframe (3ca5cca)

• fix: drop nans in constraints_df in regional_constraints (6ee2b6b)

• fix: add warning for missing split_kwargs argument (ef96fd9)

• fix: use copy.deepcopy() for all dictionaries inside functions (10df82f)

• fix: warn instead of raise error for constraints outside of gravity data (08a60b4)

Refactor

• refactor: manually calculate default eq source depth until harmonica v0.7 is released. (aeb675a)

• refactor: simplify UQpy import (783d3dc)

v0.8.1

v0.8.1 (2024-08-05)

Chore

• chore: automatically updating changelog [skip ci] (a6660e2)

• chore: automatically updating changelog [skip ci] (3489538)

• chore: automatically updating changelog [skip ci] (5266862)

• chore: add test deps to conda_install for testing conda releases (c44d59b)

• chore: update binder env to v0.8 (8d9d294)

• chore: automatically updating changelog [skip ci] (6202ae6)

Documentation

• docs: add missing docstring (50591e3)

• docs: fix issues with autoapi and typehints. (af93c02)

Fix

• fix: remove nptyping as dependency (d2534d0)

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 parameterregional_column. ([a4f24ec`](a4f24ec))

• 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)...

v0.7.0

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

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`](f864c1f))

• 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](https://github.com/mdtanker/inv...

v0.5.0

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 ([...