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* MODIFY Internals initial * new api examples * MODIFY Internals initial * Make JuTransformer work * Hyper Tuning + new API working Co-authored-by: Sami Hamdan <[email protected]> * fix for deslib import * Estimators test OK + no more binary/multiclass * model selection tests ok * scoring tests OK * merge conflict * transformers + utils test ok * Fix CI * codespell * small clean up * fix do_scoring tests * Stacked classifiers * For Sami to fix * Fix rebase * Fix pipeline tests * Improve SetColumnTypes * Improve some Tests on X_types * Make Stacking work with filtering * example ready * Make stares shine as regexes * Adjust warnings and errors +testing for pipeline.py * Make models use apply_to and needed_types * fixed print * remove old returned features from julearn * rename and clean julearn.estimators to julearn.models * remove default apply_to from available transformers * Modify prepare clean up a bit * Adjust confound removal, get rid of pick_columns, modify JuModel, JuTransformer, JuBaseEstiamtor * refactor juestimators DataFrameConfoundRemover add ColumnTypes * Modify examples * Modify/Add important Docstrings * Correct: check consitency imports * Example/stratifiedkfoldcv (#181) * Adjust example stratifiedkfoldcv * Integrade ColumnTypes in pipeline * Oops left print * Refactor Structure to have a base module for ColumnTypes and JuBaseClasses * Move JuColumnTransformer and make setting default of apply to in PipelienCreator possible * Fix tests for old versions * Add preprocess inspection tool * Modify inspect * Modify inspect * get the right dependency for CI * Fix lint * Fix codespell * Fix test api, but Sami broke it :( * Trigger CI * Fix coverage * Trigger CI * Adjust dataclass for python=3.11 * Bring back return train scores * updated example to inspect preprocessing steps (#182) * Add docstrings to column_types * Fix for X_types checks in pipeline * add/update docstrings to DataFrameConfoundRemover (#184) * add/update docstrings to DataFrameConfoundRemover * Make some test green again * Adjust preprocess to remove column_types per default and improve import * Fix tests * Bringing back the prepare testing * Sk pandas examples (#185) * updated multiclass classification example * updated inspect SVM example Co-authored-by: More, Shammi <[email protected]> Co-authored-by: Sami Hamdan <[email protected]> Co-authored-by: Fede Raimondo <[email protected]> * Adjust target transforming * Fix building doc * disable examples * fix stacked classifier example * Fix linter * update: add default apply_to to pipeline creator * LINTEEER * update: combine pandas examples running * Fix codespell * Basic regress example (#188) * fixed regression example * formatted with black * One more example * One more example * Random forest example * Stratified kfold for regression example * Make Scoring with classification work (#191) * Make Scoring with classificication work * flake * Refactor column types * Flake8 * Fix PipelineCreator and problem type issues * Linter * chore: update `pyproject.toml` (#189) * fix: use text instead of file for license to make PyPI happy * fix: correct format for authors and maintainers in pyproject.toml * chore: use lowercase for keywords in pyproject.toml * chore: make package classifier development status to 5 in pyproject.toml Co-authored-by: Fede Raimondo <[email protected]> * Add example transforming the target variable with zscore (#197) * Add example transforming the target variable with zscore * Correcting script with flake8 * Correct white space in title * Adding = to title * fix syntax * Removing white lines to new syntax * Removing white line for title * Remove useless plot Co-authored-by: Paas Oliveros, Lya Katarina <[email protected]> Co-authored-by: Fede Raimondo <[email protected]> * update confound removal example (#196) * update confound removal example * change name of file * change name of file * Fix confound removal * Spelling Co-authored-by: Fede <[email protected]> * Sk pandas examples (#190) * added pipeline creator * updated multiclass classification example * updated inspect SVM example * updated multiclass classification example * formatted dis_plot_groupcv_inspect_svm.py * formatted plot_cm_acc_multiclass.py Co-authored-by: More, Shammi <[email protected]> Co-authored-by: Fede Raimondo <[email protected]> * Fix hyperparameter tuning and remove "wrapping" from model and transformer name (#200) * Fix Hyperparameter tuning * Remove Wrapper naming convention Co-authored-by: Sami Hamdan <[email protected]> * Example pca featsets (#198) * [not working] example for two PCAs * Fix double PCA issue * [working] multiple PCA steps * Fix remainder in name * Add a name in PipelineCreator.add * [working] multiple PCA steps with preprocess showcase * rename * rename * Codespell * Fix doc * Fix scoring Co-authored-by: Fede <[email protected]> * Adjust scoring to work with registered once (#203) * Adjust scoring to work with registered once * Revert back the problem type to not be overwritable * Revert back the problem type to not be overwritable * Grouped cv example (#205) * Added new file for grouped CV. * Created example of Grouped CV. * deleted the old file of Grouped CV and created the new file for that. * Target transformer (#215) * WIP: Target transfomers + pipeline * WIP * damn git ignore * The example works * A todo for @samihamdan * Type hints + docstrings in progress * Base module ready * Typing + docstrings of conftest * Tests for inspect preprocessing + more types * Fix linting * model selection with types and docstrings * Fix linter * More tests with docstrings and typing hints * linter * Models sub-package done * Some more tests + typing + docstrings for the pipeline module * tests + docstrings + types for TargetPipelineCreator * Almost done with tranformers.target, but got tired... * Test for target confound remover done * Some WIP... go sick and I don't remember where I was * Finished testing confounds * JuColumnTransformer tested * More fixes * Updated prepare and tests * Updates to the docstings * Basic API test * I think the API is tested for the moment * All test pass, no warnings * Updated examples * fix linting * Codespell * codespell doesn't like the new verb we invented * ENH: allow to set X_types using regexp * some symmetry in the log * Fix tests * Fix for leo * WIP: model comparison * add corrected t_test * Add dependencies + fix other tets * fix test for user-specified splits * fix test * chore: improve ci-docs.yml * chore: improve ci.yml * chore: improve docs-preview.yml * chore: improve docs.yml * chore: improve pypi.yml * chore: isort * chore: black * chore: flake8 fixes * Retry * fix coverage * Add deslib for testing in tox * increase coverage * test api with apply_to * Cbpm sum (#221) * Minimal version of CPM without weighting but sum as default, only old test adjusted * Flake8 * lint * Resolve set_output bug in cbpm * Fix lint * Julearn sk pandas row select (#220) * Add row_select_col * Add test row_select simple * Adjust some logic * Lint * Adjust row selection to be accessible from PipelineCreator * Adjust row selection via column type not type. * Test and fix change_column_types transformer * fix #213 and #141 * add return confound example * fix groups * fix for [ENH] Validate run_cross_validate parameters #178 * fix for #214 * Inspection (#223) * ADD inspection tools * Add get_fitted_params to PipelineInspector * Add bugfix #219 * Fix preprocess import * adjust pipe * adjust pipe * CV Inpsection WIP * [WIP] Inspection tool (needs testing) * sort the index * Fix tests and ling * Add some test and func for _cv * Add inspection and test, fix predict_log_proba remove unnecessary todo notes * Add tests inspector * Add tests * New docs (#228) * Update docs theme to furo * Add content to index * Add new chapter * modify requirements * Add copybutton extension * Add installation related info to get started * Installation was replaced by getting started * setup structure for chapter 4 * Add messy chapter 3 to push uptodate * Number files based on chapter order * Add basic index for chapter 4 and reference * Change numbering to display in real time * Add chapter 4 to toctree * Comment data.rst to make build possible * Work in progress push for Leo * initial cbpm * some formatting * add introductory paragraph for confound removal and some references * add docs on confound removal * fix typo * capitalise titles * Work in progress push Leo * Work in progress push for Leo * Clean up made changes * data section preliminary version done * available pipeline steps * clean the docs * correct layout error * structure and add references * modify indices * Update docs theme to furo * Add content to index * Add new chapter * modify requirements * Add copybutton extension * Add installation related info to get started * Installation was replaced by getting started * setup structure for chapter 4 * Add messy chapter 3 to push uptodate * Number files based on chapter order * Add basic index for chapter 4 and reference * Change numbering to display in real time * Add chapter 4 to toctree * Comment data.rst to make build possible * Work in progress push for Leo * initial cbpm * some formatting * add introductory paragraph for confound removal and some references * add docs on confound removal * fix typo * capitalise titles * Work in progress push Leo * Work in progress push for Leo * Clean up made changes * data section preliminary version done * available pipeline steps * clean the docs * correct layout error * structure and add references * modify indices * WIP: Docs fixing, rearanging API * restructure * Add description of pipeline * Update examples structure + API reference * work in progress * Some refactoring of the what really need know section * fix CI * remove comments --------- Co-authored-by: Vera Komeyer <[email protected]> Co-authored-by: LeSasse <[email protected]> * refactor index * Add general CV information * Add target preprocessing and refactor * add reference * Add model evaluation illustration pictures * Add further needed scikitlearn links * Correct typo * Add cross-reference link * Add cv-splitter as potential further selcted topic * Add model evaluation content * Fix doc sectioning and order * Fix TOCTREE * One less numbered element in the TOC * Add/viz (#227) * VIZ WIP * add viz to the dependencies for docs * add viz dependencies to tox * fix linter * delete old files * add example back * delete this file * More doc on VIZ * Add stats to viz * Finish with VIZ docs * Fix linter * Fix tests * Adaptations for proper toctree * Rearrange content to solve toctree * Minor clean-ups * Add visualization information * Fix building * added initial version of stacking documentation for julearn * fix markup in cbpm * some slight improvements to stacked model documentation * Adjust tests and fix bugs for dataframe transformers * fix bug no hyperparameters * fix bug hyperparams with target * fix bug hyperparams with target * ADD tests not fitted error target transformer * ADD test returning inspection tool with differen return_estimator settings * ADD test rais errors pipeline * MODIFY insect to allow for gridsearch * initial start with model inspection * initial version of model_inspect.rst * a few small typo fixes * fix bug in which estimators were not picklable due to local function definition inside a function in base/column_types.py * whitespaces * apparently codespell does not like .sav as a file extension and thinks it should be save. Calling it .joblib instead * [CI]: Use towncrier for news (#222) * update: add towncrier configuration in pyproject.toml * docs: refactor whats_new.rst for towncrier integration * docs: improve contributing.rst and add towncrier instructions * docs: improve maintaining.rst and add towncrier instructions * update: add docs/changes/newsfragments * chore: add 151.bugfix changelog * chore: add 170.enh changelog * update: improve docs/Makefile and add towncrier integration * chore: delete Makefile * update: add towncrier to pyproject.toml * [ENH] Allow list of hyperparameter options for tunning (#47) * [WIP] Multiple hyperparam grids * fix linter * increase coverage * add more tests * More tests for merger * add news fragemtn * Add specific gallery section for doc pages that need to be run. * Docs on hyperparameter tuning * some more updates * FIX predict proba * Update dependencies * Fix CV + update first chapter of docs * Fix tests * codespell * fix test for 3.8 maybe * Fix inspector * fix inpsecto * Fix issues with doc building * Improving some titles * Update intesphinx links * Fix inspection + docs * Docs (almost) ready * Fix codespell * Update example of stratification for regression * Update dependencies * Fix the run_cross_validation docstring * Fix test for stats * MODIFY Target Transformation * MODIFY K-fold for regression * Fix for scikit-learn 1.3.0 * Fix whats'new * Maybe ready for release? * Lint * codespell * Add pearson's R scorer * ADD: folds inspector prediction returns target value + avoid regexp when no patterns in X * Set column types even if input is an array * WIP: Config module * Add tests for new config flags * Update X Warns to 5k * linter * update doc * Typo in DOC --------- Co-authored-by: Sami Hamdan <[email protected]> Co-authored-by: Leonard Sasse <[email protected]> Co-authored-by: Shammi270787 <[email protected]> Co-authored-by: More, Shammi <[email protected]> Co-authored-by: antogeo <[email protected]> Co-authored-by: Synchon Mandal <[email protected]> Co-authored-by: Lya K. Paas <[email protected]> Co-authored-by: Paas Oliveros, Lya Katarina <[email protected]> Co-authored-by: Vera Komeyer <[email protected]> Co-authored-by: kaurao <[email protected]> Co-authored-by: Kimia Nazarzadeh <[email protected]> Co-authored-by: Vera Komeyer <[email protected]>
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