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Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
* intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging
* loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local>
* adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu>
…e minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size
* create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu>
* preparing for paper release (#77) * updating the tmp/readme * updating precommit * fixing cmd line interface in __main__ * updating typing on sigmoid fit * adding logging re how CV is performed * initial topn modeling implementation. This will store the results in a separate output directory to differentiate from all data modeling * initial attempt of stage 3 of modeling. This seems to run without issues based on limited testing. * stepwise modelling * this separates the sigmoid step 3 into its own function; reoganizes cmd line input into reusable groups; sets the evaluate_interactor_significance estimator to LinearRegression by default * removing windows 2019 from CI * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * only running tests on ubuntu * trying to configure codecov * debugging codecov * debugging codecov * removing codecov badge and updating the pytest badge * adding the codecov badge back in -- secret corrected in the repo * debugging codecov * still debugging codecov * Add cubic ptf and standardization (#29) * init * After installing pre-commit * add center and scaling * changing the names for center scaling * Update tfbpmodeling/__main__.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * debugging the names for scale and center * editing annotatioins --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * Add function to exclude all model variables (#33) * adding function to exclude all predictors. this can be used to exclude all and then use args.add_model_variables to customize the formula * casting predictor_variables to list * fixing centering and scaling (#36) * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * setting evaluate_interactor_significance ci_level to the parse args argument * Tommy new stage3 (#41) * WIP * fixing imported but not used * adding argument to include stage4_lasso * changing formatting problems * adding logger infomation for stage 4 method * changing location of logger info for stage 4 method * modifying logger.info to evaluate_interactor_significance * adding f string to Writing the final interactor significance results to {output_significance_file} * fixing logging --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: chasem <chasem@wustl.edu> * fixing error in stratification_classification that reversed the bin_by_binding_only param (#44) * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Add row max in interactor significance (#48) * setting row max depending on model variables * setting row max depending on model variables * adding testing on log for evaluate_interactor_significance * removing ptf from all data formula by default (#51) * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing scale_center from interface (#60) --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * claude developed docs * removing a old comment * updating documentation to reflect that the centering option is removed * removing a old comment * updating documentation to reflect that the centering option is removed --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
* intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging
* loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local>
* adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu>
…e minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size
* create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu>
* stepwise modelling * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing a rebase error * renaming exclude_interaction_variable to exclude_model_variable * clarifying cmd line instructions * updating macos github actions version * Update README.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing plural on exclude_model_variables * Update tfbpmodeling/interface.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpmodeling/interface.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fixing some documentation issues with plural/singular and names around exclude and include variables * Update docs/cli/linear-perturbation-binding-modeling.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* stepwise modelling * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * Fix estimator comment in interface (#83) * preparing for paper release (#77) * updating the tmp/readme * updating precommit * fixing cmd line interface in __main__ * updating typing on sigmoid fit * adding logging re how CV is performed * initial topn modeling implementation. This will store the results in a separate output directory to differentiate from all data modeling * initial attempt of stage 3 of modeling. This seems to run without issues based on limited testing. * stepwise modelling * this separates the sigmoid step 3 into its own function; reoganizes cmd line input into reusable groups; sets the evaluate_interactor_significance estimator to LinearRegression by default * removing windows 2019 from CI * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * only running tests on ubuntu * trying to configure codecov * debugging codecov * debugging codecov * removing codecov badge and updating the pytest badge * adding the codecov badge back in -- secret corrected in the repo * debugging codecov * still debugging codecov * Add cubic ptf and standardization (#29) * init * After installing pre-commit * add center and scaling * changing the names for center scaling * Update tfbpmodeling/__main__.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * debugging the names for scale and center * editing annotatioins --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * Add function to exclude all model variables (#33) * adding function to exclude all predictors. this can be used to exclude all and then use args.add_model_variables to customize the formula * casting predictor_variables to list * fixing centering and scaling (#36) * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * setting evaluate_interactor_significance ci_level to the parse args argument * Tommy new stage3 (#41) * WIP * fixing imported but not used * adding argument to include stage4_lasso * changing formatting problems * adding logger infomation for stage 4 method * changing location of logger info for stage 4 method * modifying logger.info to evaluate_interactor_significance * adding f string to Writing the final interactor significance results to {output_significance_file} * fixing logging --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: chasem <chasem@wustl.edu> * fixing error in stratification_classification that reversed the bin_by_binding_only param (#44) * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Add row max in interactor significance (#48) * setting row max depending on model variables * setting row max depending on model variables * adding testing on log for evaluate_interactor_significance * removing ptf from all data formula by default (#51) * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing scale_center from interface (#60) --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * claude developed docs * removing a old comment * updating documentation to reflect that the centering option is removed * removing a old comment * updating documentation to reflect that the centering option is removed --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * removing a rebase error * stepwise modelling * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing a rebase error * trying to fix logger issue --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: ejiawustl <e.jia@wustl.edu>
* stepwise modelling * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * Fix estimator comment in interface (#83) * preparing for paper release (#77) * updating the tmp/readme * updating precommit * fixing cmd line interface in __main__ * updating typing on sigmoid fit * adding logging re how CV is performed * initial topn modeling implementation. This will store the results in a separate output directory to differentiate from all data modeling * initial attempt of stage 3 of modeling. This seems to run without issues based on limited testing. * stepwise modelling * this separates the sigmoid step 3 into its own function; reoganizes cmd line input into reusable groups; sets the evaluate_interactor_significance estimator to LinearRegression by default * removing windows 2019 from CI * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * only running tests on ubuntu * trying to configure codecov * debugging codecov * debugging codecov * removing codecov badge and updating the pytest badge * adding the codecov badge back in -- secret corrected in the repo * debugging codecov * still debugging codecov * Add cubic ptf and standardization (#29) * init * After installing pre-commit * add center and scaling * changing the names for center scaling * Update tfbpmodeling/__main__.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/tests/test_lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/lasso_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * debugging the names for scale and center * editing annotatioins --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * Add function to exclude all model variables (#33) * adding function to exclude all predictors. this can be used to exclude all and then use args.add_model_variables to customize the formula * casting predictor_variables to list * fixing centering and scaling (#36) * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * setting evaluate_interactor_significance ci_level to the parse args argument * Tommy new stage3 (#41) * WIP * fixing imported but not used * adding argument to include stage4_lasso * changing formatting problems * adding logger infomation for stage 4 method * changing location of logger info for stage 4 method * modifying logger.info to evaluate_interactor_significance * adding f string to Writing the final interactor significance results to {output_significance_file} * fixing logging --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: chasem <chasem@wustl.edu> * fixing error in stratification_classification that reversed the bin_by_binding_only param (#44) * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Add row max in interactor significance (#48) * setting row max depending on model variables * setting row max depending on model variables * adding testing on log for evaluate_interactor_significance * removing ptf from all data formula by default (#51) * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing scale_center from interface (#60) --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * claude developed docs * removing a old comment * updating documentation to reflect that the centering option is removed * removing a old comment * updating documentation to reflect that the centering option is removed --------- Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * removing a rebase error * stepwise modelling * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpmodeling/loop_modeling.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * with pre-commit * removing islice from bootstrap loop * removing fixtures to conftest; fixing spacing in loop module; adding pytest to CI * Set random state on bootstraps; Remove unweighted bootstrap option (#31) * intermediate * propogating bootstrappedmodelinginputdata changes to __main__ * removed unweighted bootstrap options * removing top_n as argparse option from step3 sigmoid parser * adding center_scale to argparse * setting drop_intercept to True permanently for sigmoid worker * the sigmoid parameters must have args.drop_intercept still * handling intercepts * fixing typo in center_scale logging * changing the way the formula is logged * removing truncation from formula logging * adding logging on random_state in bootstrappedmodelinput * removing sample weight cv log * removing sample weight cv logging * loop exits if no variable selected within the loop, fixes issue 34 (#37) * loop exits if no variable selected within the loop, fixes issue 34 * fixing linter issues * linter issues --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> * adding feature stage4_topn (#43) * adding feature stage4_topn * modifying argument parser * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * Align response_df with predictors from get_modeling_data to ensure consistency when top_n_masked is enabled * aligning stratified_cv_r2 * restoring changes to evaluate_interactor_significance_linear * commit after fixing error in stratification_classification * attempt to fixing inconsistent numbers of samples * fixing pr --------- Co-authored-by: chasem <chasem@wustl.edu> * Remove bin by binding and Add check on number of features and increase minimal test case size (#54) * saving changes for remove_bin_by_binding * Add check on number of features and increase minimal test case size * Separate the functions and objects in lasso_modeling.py (#58) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface * separate the functions and objects in lasso_modeling.py * Refactor main by adding interface.py (#56) * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * create interface.py to separate main * add tests to verify important logging statements * move the logging configuration back into main * fixing interface * removing bin_by_binding_only from test arguments to interface * adding name == main to main script * create interface.py to separate main * move the logging configuration back into main * removing bin_by_binding_only from test arguments to interface * rebasing refactor onto dev * adding calling to main * adding a feature column in test_interface --------- Co-authored-by: chasem <chasem@wustl.edu> * create interface.py to separate main move the logging configuration back into main fixing interface create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface rebasing refactor onto dev create interface.py to separate main move the logging configuration back into main removing bin_by_binding_only from test arguments to interface adding name == main to main script separate the functions and objects in lasso_modeling.py * renaming loop_modeling * separate the tests out into files * separate the tests out into files * fixing evaluate_interactor_significance_lassocv --------- Co-authored-by: chasem <chasem@wustl.edu> * removing a rebase error * Added logic for the following: (1) stage3_2b, (2) skip_1st_stage, (3) stage2_set_zero * refactoring * refactoring documentation * versioning to v1.0.0 * addressing scipy future warning on n_alphas to alphas * removing trailing whitespace * Potential fix for pull request finding The top-n bootstrap random_state calculation treats 0 as falsy: args.random_state + 10 if args.random_state else .... If a user passes --random_state 0, Stage 2 will incorrectly reuse the Stage 1 seed instead of offsetting it. Use an explicit is not None check so that 0 is handled as a valid seed. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * addressing copilot suggestions * revising given copilot review * clarifying stage3 order * addressing copilot logger and sorted order of stage3_lassocv terms * adding documentation for sample_weight_normalization in modelinputdata class * changing logging level for no coefficients logs * doing some output name refactoring * refactoring docs * updating output_dir help text --------- Co-authored-by: Zolboo Erdenebaatar <e.zolboo@n039.adm> Co-authored-by: ezolbooe <e.zolboo@wustl.edu> Co-authored-by: zolboo e <admin@zolboos-macbook-pro.local.dhcp.wustl.edu> Co-authored-by: Zolboo Erdenebaatar <e.zolboo@login.adm> Co-authored-by: zolboo e <admin@zolboos-MacBook-Pro.local> Co-authored-by: 17TML <liuchenxing9@gmail.com> Co-authored-by: ejiawustl <e.jia@wustl.edu> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
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- Coverage 72.19% 67.29% -4.91%
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Files 13 14 +1
Lines 838 954 +116
Branches 116 132 +16
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+ Hits 605 642 +37
- Misses 174 247 +73
- Partials 59 65 +6 ☔ View full report in Codecov by Sentry. |
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