0.3.0

Version 0.3.0

HIGHLIGHTS

• New API
• New User Guide
• More examples

Changes

New API for variable importance methods with .fit(), .importance(), fdr_selection(), fwer_selection()

• LOC0, CFI, CPI #372
• Desparsified Lasso: #381
• CluDL, EnCluDL #533 and #388
• ModelXKnockoffs #367
• d0CRT #220

Contributors

• https://github.com/bthirion
• https://github.com/AngelReyero
• https://github.com/jpaillard
• https://github.com/lionelkusch
• https://github.com/tbng
• https://github.com/Remi-Gau
• https://github.com/jeromedockes
• https://github.com/glemaitre
• https://github.com/antoinebaker
• https://github.com/man-shu
• https://github.com/alexblnn

What's Changed

• Fix build by @bthirion in #15
• REL 0.2.0b by @bthirion in #16
• Refactor CPI by @jpaillard in #14
• Add CPI, LOCO and PermutationImportance to api.rst by @jpaillard in #22
• 25 add support for pd.DataFrame in CPI LOCO and PrmutationImportance by @jpaillard in #27
• 26 Variable importance: support 'decision_fn' 'transform' methods by @jpaillard in #29
• 30 accelerate cpi by using batch prediction and numpy array operations instead of for loop by @jpaillard in #31
• Change README.md to a more precise installation guidance by @tbng in #23
• [MAINT] use scm for version by @Remi-Gau in #55
• Remove all the warning and error from sphinx by @lionelkusch in #82
• Source and test layout by @lionelkusch in #98
• Fix documentation by @lionelkusch in #99
• ADA-SVR (1/4) Unused of parameter full_rank by @lionelkusch in #58
• fix dependencies by @jpaillard in #110
• Fix .gitignore by @lionelkusch in #108
• Fix bug for the version of library in configuration file for the documentation by @lionelkusch in #74
• 120 use hinge loss for svm example by @jpaillard in #124
• Improve the coverage of the tests and fix some minor bugs by @lionelkusch in #64
• ADA-SVR (2/4) add comments and documentation of the functions and test by @lionelkusch in #73
• Small update of the documentation by @lionelkusch in #147
• Add tests, homogenise and document functions of utils for inference model by @lionelkusch in #132
• Permutation_test (1/4): add comments and docstring of the functions by @lionelkusch in #111
• Rename file file of ada_svr by @lionelkusch in #154
• Estimation threshold(1/4): add comments and docstring of the functions by @lionelkusch in #122
• switch to 3-clause BSD license by @jpaillard in #159
• Remove the option y_fit of group_reid by @lionelkusch in #163
• Add support for categorical & binary variables in CPI by @jpaillard in #152
• Fix CI failure by formatting examples. by @jpaillard in #165
• Fix a bug in coverage report by @lionelkusch in #168
• Remove estimators by @lionelkusch in #166
• 85 update documentation theme by @jpaillard in #169
• Fix broken links in API doc by @jpaillard in #184
• Update the dependency by @lionelkusch in #176
• Desparsified lasso(1/4): add comments and docstring of the functions by @lionelkusch in #127
• Add a dependabot for pyhton and github-action by @lionelkusch in #197
• Dependabot by @lionelkusch in #199
• Register missing class attributes by @jpaillard in #200
• Knockoffs(1/4): add comments and docstring of the functions by @lionelkusch in #128
• dcrt0(1/4): add comments and docstring of the functions by @lionelkusch in #133
• WIP add circleci by @jeromedockes in #208
• continue circleci setup by @jeromedockes in #210
• Rename score to importance in CPI, LOCO and PFI by @jpaillard in #221
• Fix bug by storing group ids in list instead of array by @jpaillard in #228
• Fix bibliography by @jpaillard in #224
• Add example on the California housing dataset illustrating pitfalls of PFI by @jpaillard in #213
• Ignore warning in the tests by @lionelkusch in #203
• Improve the coverage of the tests for BasePerturbation and ConditionalSampling by @lionelkusch in #204
• DOC fix docstring in deparsified_lasso_pvalue by @glemaitre in #206
• Move annexe files in folder utils and statistical tools by @lionelkusch in #173
• Fix warning when creating the bibliography by @lionelkusch in #235
• Conditional vs marginal importance on the XOR dataset by @jpaillard in #218
• Improve docstring of knockoff by @lionelkusch in #234
• Improvement of the check_fit for base_perturbation by @lionelkusch in #202
• Update the option for the documentation for failing with warning by @lionelkusch in #237
• Example motivating model agnostic variable selection on circles dataset by @jpaillard in #223
• Remove a warning of duplicate reid in api.rst by @lionelkusch in #238
• Add classification example on the iris dataset by @jpaillard in #229
• Bump codecov/codecov-action from 5.4.0 to 5.4.2 in the actions group by @dependabot[bot] in #245
• Remane PermutationImportance to PermutationFeatureImportance by @lionelkusch in #243
• Add tests for checking the error message of the chek_fit by @lionelkusch in #241
• circleci by @jeromedockes in #214
• Remove example based on complex simulated data by @jpaillard in #233
• Knockoffs example - follow-up by @jpaillard in #236
• Delete the documentation by @lionelkusch in #251
• fix circleci by @lionelkusch in #255
• Fix circleci by @lionelkusch in #256
• EnCluDL(1/4): add comments and docstring of the functions by @lionelkusch in #156
• Remove Perturbation Test, Adaptive Permutation Threshold Support Vector Regression and Empirical Thresholding by @lionelkusch in #242
• Parallelize the example generation and increase the speed of knockoff example by @lionelkusch in #215
• fix warning in the creation of the documentation by @lionelkusch in #239
• Add badge for CircleCI by @lionelkusch in #262
• Bump codecov/codecov-action from 5.4.2 to 5.4.3 in the actions group by @dependabot[bot] in #263
• Improvement of circle ci by @lionelkusch in #261
• Tools for develloper by @lionelkusch in #240
• Update the workflow for the tests by @lionelkusch in #193
• Fix token authorization for CIRCLE_CI by @lionelkusch in #269
• Fix token by @lionelkusch in #270
• Fix token by @lionelkusch in #271
• Fix token by @lionelkusch in #272
• Fix token by @lionelkusch in #273
• Fix token by @lionelkusch in #274
• Fix coverage by @lionelkusch in #276
• Fix codeop and condition by @lionelkusch in #277
• Fix token by @lionelkusch in #278
• Bump actions/checkout from 2 to 4 in the actions group by @dependabot[bot] in #280
• Fix circleci by @lionelkusch in #285
• Fix circle ci action by @lionelkusch in #286
• Fix circle ci action by @lionelkusch in #287
• Fix error of concurency by @lionelkusch in #288
• Update url for pushing data from tests by @lionelkusch in #289
• fix url for sending data to circleci by @lionelkusch in #290
• Fix url cirlceci and fix concurency issue by @lionelkusch in #291
• fix url by @lionelkusch in #292
• Fix curl command by @lionelkusch in #293
• fix url and response by @lionelkusch in #294
• Fix action of circleCI by @lionelkusch in #295
• fix tests workflow by @lionelkusch in #296
• fix compatibility with the nilearn 0.12 by @lionelkusch in #302
• remove figures from example by @lionelkusch in #305
• Fix the condition fo skip the tests by @lionelkusch in #308
• Update the Readme by @lionelkusch in #301
• fix get message of head commit by @lionelkusch in #309
• Reorganization of the documentation folder by @lionelkusch in #304
• fix path for tests results by @lionelkusch in #310
• Bump actions/download-artifact from 4 to 5 in the actions group by @dependabot[bot] in #319
• fix new version for donwload artifact by @lionelkusch in #320
• Minimal version of dependence and associate tests by @lionelkusch in #321
• fix CI installation packages by @lionelkusch in #324
• Bump actions/checkout from 4 to 5 in the actions group by @dependabot[bot] in #323
• dcrt0(1/4): API2: add comments and docstring of the functions by @lionelkusch in #220
• Rename some file by @lionelkusch in #338
• plot_dcrt_example: make plot more readable and reduce computation time by @jpaillard in #341
• Update maximal version for scikitlearn by @lionelkusch in #343
• Bump codecov/codecov-action from 5.4.3 to 5.5.0 in the actions group by @dependabot[bot] in #346
• Rename CPI to Conditional Feature Importance by @lionelkusch in #339
• Add tools for testing and make an example with CPI by @lionelkusch in #265
• Fix link in the API by @lionelkusch in #352
• Forget an initialisation of the parent class. by @lionelkusch in #354
• Fix the docstring of _check_importance by @lionelkusch in #371
• Remove transform for check by @lionelkusch in #380
• Bump codecov/codecov-action from 5.5.0 to 5.5.1 in the actions group by @dependabot[bot] in #382
• Improve a bit the index of the API by @lionelkusch in #355
• Remove not necessary link to library by @lionelkusch in #390
• D0CRT Accept Scikit-learn models directly instead of parameter dictionaries by @jpaillard in #370
• Bump the python-packages group with 2 updates by @dependabot[bot] in #397
• Fix plot_fmri_data_example errors on computers with few possibilities by @lionelkusch in #396
• add base for user guide by @jpaillard in #399
• gitignore update by @antoinebaker in #410
• Minor fixes on the homepage/dev guidelines by @man-shu in #403
• [MAINT] Apply codespell on documentation by @man-shu in #412
• Revert "[MAINT] Apply codespell on documentation" by @lionelkusch in #431
• [DOC] use consistent divider and header length by @Remi-Gau in #416
• [DOC] change pygments for code by @Remi-Gau in #418
• [DOC] remove redundant comment about imports in examples by @Remi-Gau in #415
• [DOC] move subfunction closer to where they are used by @Remi-Gau in #413
• Write the changes found by codespell by @man-shu in #430
• [CI] mention how to style code by @Remi-Gau in #404
• Add isort in the CI by @lionelkusch in #429
• Revert "Add isort in the CI" by @lionelkusch in #435
• Add isort in the CI by @lionelkusch in #436
• fix isort by ignoring specific files by @lionelkusch in #437
• [MAINT] add a link checker by @Remi-Gau in #411
• [DOC] shorten lines in the examples by @Remi-Gau in #421
• fix link in change file for examples in circleci by @lionelkusch in #438
• update style guide line by @lionelkusch in #434
• [DOC] clean up examples by @Remi-Gau in #427
• Bump actions/setup-python from 5 to 6 in the actions group by @dependabot[bot] in #447
• Remove some randomization in the example and in the code base. by @lionelkusch in #344
• Fix some warning in documentation by @lionelkusch in #453
• add a tool for getting the reference generated during the documentation by @lionelkusch in #409
• [DOC] remove duplicated code in diabetes example by @jpaillard in #458
• Change the verbosity of EnCluDL by @lionelkusch in #452
• [DOC] add minimal developer guidelines in developer documentation by @jpaillard in #461
• Control of random generator by @jpaillard in #368
• [DOC] add minimal example for CFI by @jpaillard in #439
• Add a workflow for testing modification of the CI by @lionelkusch in #322
• Fix warning in tests by @lionelkusch in #466
• Drop support for verion 3.9 and upgrade version for pytest-xdist by @lionelkusch in #465
• [DOC] add minimal example for LOCO by @jpaillard in #441
• Fix issue with windows and matplolib by @lionelkusch in #470
• Remove depreciation warning in test minimal by @lionelkusch in #471
• [DOC] remove URLs from the bibliography by @jpaillard in #477
• [DOC] User guide section 3. model-agnostic methods: CFI by @antoinebaker in #402
• Create a base for managing groups of features. by @lionelkusch in #357
• [Tests] fix unstable tests for desparsified Lasso and knockoffs by @jpaillard in #474
• Add selection with fdr and associate test by @lionelkusch in #361
• Bump astral-sh/setup-uv from 6 to 7 in the actions group by @dependabot[bot] in #486
• fix problem of memory issue by @lionelkusch in #487
• Reformat the gaussian conditional sampler by @lionelkusch in #366
• [DOC] fix rendering of sampling classes by @jpaillard in #491
• fix instability of tests by @lionelkusch in #493
• Remove warning: invalid escape sequence '\S' by @lionelkusch in #494
• Add NB-ttest by @lionelkusch in #460
• remove unecesseary import in gaussian knockoff by @lionelkusch in #498
• [DOC] add a glossary and notations page by @jpaillard in #419
• Add new workflow for maintenance by @lionelkusch in #501
• Pr ci maint by @lionelkusch in #502
• Remove parallel generation of example by @lionelkusch in #497
• Bump the actions group with 2 updates by @dependabot[bot] in #514
• add d0CRT logit by @jpaillard in #443
• [API 2]: Model X knockoff by @lionelkusch in #367
• [BUG] fix n_samples, n_features by @jpaillard in #523
• [API 2] add PDP by @jpaillard in #517
• [API 2]: Desparsified Lasso by @lionelkusch in #381
• [API 2]: CFI, PFI, LOCO by @lionelkusch in #372
• Update pytest requirement from <9,>=8.0 to >=8.0,<10 in the python-packages group by @dependabot[bot] in #526
• [MNT] clean-up source imports by @jpaillard in #525
• [API 2] Add Cross validation for perturbation based methods by @jpaillard in #530
• Remove the parameter group_key of _joblib_predict_one_group by @lionelkusch in #475
• Update pytest-reportlog requirement from <1,>=0.2.1 to >=0.2.1,<2 in the python-packages group by @dependabot[bot] in #539
• Bump actions/checkout from 5 to 6 in the actions group by @dependabot[bot] in #538
• [API 2] CluDL and EnCluDL by @jpaillard in #533
• [CORE] remove one_minus_pval attribute, add fwer_selection by @jpaillard in #541
• [CORE] change fdp_power by @jpaillard in #542
• remove eps by @jpaillard in #544
• Element for the first release by @lionelkusch in #258
• [DOC] Section 1 of user guide/definition of concepts by @man-shu in #408
• Release 0.3.0 by @lionelkusch in #551

New Contributors

• @bthirion made their first contribution in #15
• @jpaillard made their first contribution in #14
• @tbng made their first contribution in #23
• @Remi-Gau made their first contribution in #55
• @jeromedockes made their first contribution in #208
• @glemaitre made their first contribution in #206
• @dependabot[bot] made their first contribution in #245
• @antoinebaker made their first contribution in #410
• @man-shu made their first contribution in #403

Full Changelog: 0.2.0...0.3.0