Move package up, make repo itself the package

ratschlab · Sep 29, 2023 · ed434e1 · ed434e1
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diff --git a/README.md b/README.md
@@ -45,7 +45,7 @@ The `famews` package contains the relevant code components
 for the pipeline. Install the package into your environment
 with:
 ```
-pip install -e ./famews
+pip install -e ./
 ```
 
 ### Configurations

diff --git a/famews/README.md b/famews/README.md
diff --git a/famews/famews/__init__.py → famews/__init__.py b/famews/famews/__init__.py → famews/__init__.py
diff --git a/famews/famews/data/__init__.py → famews/data/__init__.py b/famews/famews/data/__init__.py → famews/data/__init__.py
diff --git a/famews/famews/data/datasets.py → famews/data/datasets.py b/famews/famews/data/datasets.py → famews/data/datasets.py
diff --git a/famews/famews/data/hirid/__init__.py → famews/data/hirid/__init__.py b/famews/famews/data/hirid/__init__.py → famews/data/hirid/__init__.py
diff --git a/famews/famews/data/hirid/constants.py → famews/data/hirid/constants.py b/famews/famews/data/hirid/constants.py → famews/data/hirid/constants.py
diff --git a/famews/famews/data/hirid/reading.py → famews/data/hirid/reading.py b/famews/famews/data/hirid/reading.py → famews/data/hirid/reading.py
diff --git a/famews/famews/data/utils.py → famews/data/utils.py b/famews/famews/data/utils.py → famews/data/utils.py
diff --git a/famews/famews/fairness_check/__init__.py → famews/fairness_check/__init__.py b/famews/famews/fairness_check/__init__.py → famews/fairness_check/__init__.py
diff --git a/...amews/fairness_check/analysis_pipeline.py → famews/fairness_check/analysis_pipeline.py b/...amews/fairness_check/analysis_pipeline.py → famews/fairness_check/analysis_pipeline.py
diff --git a/..._importance/analyse_feature_importance.py → ..._importance/analyse_feature_importance.py b/..._importance/analyse_feature_importance.py → ..._importance/analyse_feature_importance.py
diff --git a/...ss_check/feature_importance/helper_rbo.py → ...ss_check/feature_importance/helper_rbo.py b/...ss_check/feature_importance/helper_rbo.py → ...ss_check/feature_importance/helper_rbo.py
diff --git a/.../feature_importance/helper_shap_values.py → .../feature_importance/helper_shap_values.py b/.../feature_importance/helper_shap_values.py → .../feature_importance/helper_shap_values.py
diff --git a/...eck/medical_variables/analyse_med_vars.py → ...eck/medical_variables/analyse_med_vars.py b/...eck/medical_variables/analyse_med_vars.py → ...eck/medical_variables/analyse_med_vars.py
diff --git a/...ss_check/medical_variables/build_table.py → ...ss_check/medical_variables/build_table.py b/...ss_check/medical_variables/build_table.py → ...ss_check/medical_variables/build_table.py
diff --git a/...ess_check/medical_variables/draw_graph.py → ...ess_check/medical_variables/draw_graph.py b/...ess_check/medical_variables/draw_graph.py → ...ess_check/medical_variables/draw_graph.py
diff --git a/famews/famews/fairness_check/metrics.py → famews/fairness_check/metrics.py b/famews/famews/fairness_check/metrics.py → famews/fairness_check/metrics.py
diff --git a/.../famews/fairness_check/metrics_wrapper.py → famews/fairness_check/metrics_wrapper.py b/.../famews/fairness_check/metrics_wrapper.py → famews/fairness_check/metrics_wrapper.py
diff --git a/..._check/missingness/analyse_missingness.py → ..._check/missingness/analyse_missingness.py b/..._check/missingness/analyse_missingness.py → ..._check/missingness/analyse_missingness.py
diff --git a/...fairness_check/missingness/build_table.py → ...fairness_check/missingness/build_table.py b/...fairness_check/missingness/build_table.py → ...fairness_check/missingness/build_table.py
diff --git a/.../fairness_check/missingness/draw_graph.py → .../fairness_check/missingness/draw_graph.py b/.../fairness_check/missingness/draw_graph.py → .../fairness_check/missingness/draw_graph.py
diff --git a/...missingness/helper_analyse_missingness.py → ...missingness/helper_analyse_missingness.py b/...missingness/helper_analyse_missingness.py → ...missingness/helper_analyse_missingness.py
diff --git a/.../model_performance/analyse_performance.py → .../model_performance/analyse_performance.py b/.../model_performance/analyse_performance.py → .../model_performance/analyse_performance.py
diff --git a/...ss_check/model_performance/build_table.py → ...ss_check/model_performance/build_table.py b/...ss_check/model_performance/build_table.py → ...ss_check/model_performance/build_table.py
diff --git a/...ness_check/model_performance/constants.py → ...ness_check/model_performance/constants.py b/...ness_check/model_performance/constants.py → ...ness_check/model_performance/constants.py
diff --git a/...ess_check/model_performance/draw_graph.py → ...ess_check/model_performance/draw_graph.py b/...ess_check/model_performance/draw_graph.py → ...ess_check/model_performance/draw_graph.py
diff --git a/...performance/helper_analyse_performance.py → ...performance/helper_analyse_performance.py b/...performance/helper_analyse_performance.py → ...performance/helper_analyse_performance.py
diff --git a/...ess_check/report_generation/create_pdf.py → ...ess_check/report_generation/create_pdf.py b/...ess_check/report_generation/create_pdf.py → ...ess_check/report_generation/create_pdf.py
diff --git a/...port_generation/helper_feat_importance.py → ...port_generation/helper_feat_importance.py b/...port_generation/helper_feat_importance.py → ...port_generation/helper_feat_importance.py
diff --git a/...heck/report_generation/helper_glossary.py → ...heck/report_generation/helper_glossary.py b/...heck/report_generation/helper_glossary.py → ...heck/report_generation/helper_glossary.py
diff --git a/...check/report_generation/helper_medvars.py → ...check/report_generation/helper_medvars.py b/...check/report_generation/helper_medvars.py → ...check/report_generation/helper_medvars.py
diff --git a/...k/report_generation/helper_missingness.py → ...k/report_generation/helper_missingness.py b/...k/report_generation/helper_missingness.py → ...k/report_generation/helper_missingness.py
diff --git a/...rt_generation/helper_model_performance.py → ...rt_generation/helper_model_performance.py b/...rt_generation/helper_model_performance.py → ...rt_generation/helper_model_performance.py
diff --git a/...check/report_generation/helper_timegap.py → ...check/report_generation/helper_timegap.py b/...check/report_generation/helper_timegap.py → ...check/report_generation/helper_timegap.py
diff --git a/...fairness_check/report_generation/utils.py → ...fairness_check/report_generation/utils.py b/...fairness_check/report_generation/utils.py → ...fairness_check/report_generation/utils.py
diff --git a/...ck/timegap_alarm_event/analyse_timegap.py → ...ck/timegap_alarm_event/analyse_timegap.py b/...ck/timegap_alarm_event/analyse_timegap.py → ...ck/timegap_alarm_event/analyse_timegap.py
diff --git a/..._check/timegap_alarm_event/build_table.py → ..._check/timegap_alarm_event/build_table.py b/..._check/timegap_alarm_event/build_table.py → ..._check/timegap_alarm_event/build_table.py
diff --git a/...s_check/timegap_alarm_event/draw_graph.py → ...s_check/timegap_alarm_event/draw_graph.py b/...s_check/timegap_alarm_event/draw_graph.py → ...s_check/timegap_alarm_event/draw_graph.py
diff --git a/...ss_check/utils/compute_threshold_score.py → ...ss_check/utils/compute_threshold_score.py b/...ss_check/utils/compute_threshold_score.py → ...ss_check/utils/compute_threshold_score.py
diff --git a/...mews/fairness_check/utils/get_pop_info.py → famews/fairness_check/utils/get_pop_info.py b/...mews/fairness_check/utils/get_pop_info.py → famews/fairness_check/utils/get_pop_info.py
diff --git a/.../fairness_check/utils/helper_bootstrap.py → .../fairness_check/utils/helper_bootstrap.py b/.../fairness_check/utils/helper_bootstrap.py → .../fairness_check/utils/helper_bootstrap.py
diff --git a/.../fairness_check/utils/helper_endpoints.py → .../fairness_check/utils/helper_endpoints.py b/.../fairness_check/utils/helper_endpoints.py → .../fairness_check/utils/helper_endpoints.py
diff --git a/...ews/fairness_check/utils/helper_format.py → famews/fairness_check/utils/helper_format.py b/...ews/fairness_check/utils/helper_format.py → famews/fairness_check/utils/helper_format.py
diff --git a/...ews/fairness_check/utils/helper_groups.py → famews/fairness_check/utils/helper_groups.py b/...ews/fairness_check/utils/helper_groups.py → famews/fairness_check/utils/helper_groups.py
diff --git a/...heck/utils/hirid/extract_info_patients.py → ...heck/utils/hirid/extract_info_patients.py b/...heck/utils/hirid/extract_info_patients.py → ...heck/utils/hirid/extract_info_patients.py
diff --git a/...ness_check/utils/hirid/map_apache_code.py → ...ness_check/utils/hirid/map_apache_code.py b/...ness_check/utils/hirid/map_apache_code.py → ...ness_check/utils/hirid/map_apache_code.py
diff --git a/...heck/utils/mimic/extract_info_patients.py → ...heck/utils/mimic/extract_info_patients.py b/...heck/utils/mimic/extract_info_patients.py → ...heck/utils/mimic/extract_info_patients.py
diff --git a/...famews/fairness_check/utils/stat_tests.py → famews/fairness_check/utils/stat_tests.py b/...famews/fairness_check/utils/stat_tests.py → famews/fairness_check/utils/stat_tests.py
diff --git a/famews/famews/models/__init__.py → famews/models/__init__.py b/famews/famews/models/__init__.py → famews/models/__init__.py
diff --git a/famews/famews/models/encoders.py → famews/models/encoders.py b/famews/famews/models/encoders.py → famews/models/encoders.py
diff --git a/famews/famews/models/utility_layers.py → famews/models/utility_layers.py b/famews/famews/models/utility_layers.py → famews/models/utility_layers.py
diff --git a/famews/famews/pipeline.py → famews/pipeline.py b/famews/famews/pipeline.py → famews/pipeline.py
diff --git a/famews/famews/scripts/__init__.py → famews/scripts/__init__.py b/famews/famews/scripts/__init__.py → famews/scripts/__init__.py
diff --git a/...s/famews/scripts/run_fairness_analysis.py → famews/scripts/run_fairness_analysis.py b/...s/famews/scripts/run_fairness_analysis.py → famews/scripts/run_fairness_analysis.py
diff --git a/famews/famews/scripts/submit_wrapper.py → famews/scripts/submit_wrapper.py b/famews/famews/scripts/submit_wrapper.py → famews/scripts/submit_wrapper.py
diff --git a/...ews/scripts/submit_wrapper_pred_models.py → famews/scripts/submit_wrapper_pred_models.py b/...ews/scripts/submit_wrapper_pred_models.py → famews/scripts/submit_wrapper_pred_models.py
diff --git a/famews/famews/scripts/synthetic/__init__.py → famews/scripts/synthetic/__init__.py b/famews/famews/scripts/synthetic/__init__.py → famews/scripts/synthetic/__init__.py
diff --git a/...ipts/synthetic/generate_hirid_syn_data.py → ...ipts/synthetic/generate_hirid_syn_data.py b/...ipts/synthetic/generate_hirid_syn_data.py → ...ipts/synthetic/generate_hirid_syn_data.py
diff --git a/...ws/famews/scripts/train_sequence_model.py → famews/scripts/train_sequence_model.py b/...ws/famews/scripts/train_sequence_model.py → famews/scripts/train_sequence_model.py
diff --git a/famews/famews/scripts/train_tabular_model.py → famews/scripts/train_tabular_model.py b/famews/famews/scripts/train_tabular_model.py → famews/scripts/train_tabular_model.py
diff --git a/famews/famews/train/__init__.py → famews/train/__init__.py b/famews/famews/train/__init__.py → famews/train/__init__.py
diff --git a/famews/famews/train/pipeline.py → famews/train/pipeline.py b/famews/famews/train/pipeline.py → famews/train/pipeline.py
diff --git a/famews/famews/train/sequence.py → famews/train/sequence.py b/famews/famews/train/sequence.py → famews/train/sequence.py
diff --git a/famews/famews/train/utils.py → famews/train/utils.py b/famews/famews/train/utils.py → famews/train/utils.py
diff --git a/famews/famews/utils/__init__.py → famews/utils/__init__.py b/famews/famews/utils/__init__.py → famews/utils/__init__.py
diff --git a/famews/famews/utils/handle_predictions.py → famews/utils/handle_predictions.py b/famews/famews/utils/handle_predictions.py → famews/utils/handle_predictions.py
diff --git a/famews/pyproject.toml → pyproject.toml b/famews/pyproject.toml → pyproject.toml
diff --git a/famews/setup.py → setup.py b/famews/setup.py → setup.py