openpkpd 0.2.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- openpkpd-0.2.1/.gitignore +597 -0
- openpkpd-0.2.1/.gitlab-ci.yml +229 -0
- openpkpd-0.2.1/.pre-commit-config.yaml +7 -0
- openpkpd-0.2.1/.python-version +1 -0
- openpkpd-0.2.1/.readthedocs.yaml +10 -0
- openpkpd-0.2.1/LICENSE +661 -0
- openpkpd-0.2.1/PKG-INFO +578 -0
- openpkpd-0.2.1/README.md +502 -0
- openpkpd-0.2.1/docs/Makefile +19 -0
- openpkpd-0.2.1/docs/OpenPKPD_icon.ico +0 -0
- openpkpd-0.2.1/docs/OpenPKPD_logo.png +0 -0
- openpkpd-0.2.1/docs/OpenPKPD_logo.svg +161 -0
- openpkpd-0.2.1/docs/_static/custom.css +16 -0
- openpkpd-0.2.1/docs/_static/examples/01_conc_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/01_output.txt +26 -0
- openpkpd-0.2.1/docs/_static/examples/01_spaghetti.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/02_eta_hist.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/02_gof_panel.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/02_output.txt +22 -0
- openpkpd-0.2.1/docs/_static/examples/03_log_conc_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/03_output.txt +18 -0
- openpkpd-0.2.1/docs/_static/examples/03_spaghetti_log.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/04_effect_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/04_emax_curve.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/04_gof_panel.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/04_output.txt +21 -0
- openpkpd-0.2.1/docs/_static/examples/05_effect_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/05_hysteresis.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/05_output.txt +20 -0
- openpkpd-0.2.1/docs/_static/examples/06_output.txt +26 -0
- openpkpd-0.2.1/docs/_static/examples/07_abs_iwres.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_conc_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_cwres_pred.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_cwres_qq.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_cwres_time.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_dv_vs_ipred.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_dv_vs_pred.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_eta1_vs_wt.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_eta_hist.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_eta_pairs.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_gof_panel.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_mean_profile.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_ofv_history.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/07_output.txt +24 -0
- openpkpd-0.2.1/docs/_static/examples/07_spaghetti.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/08_output.txt +36 -0
- openpkpd-0.2.1/docs/_static/examples/09_output.txt +62 -0
- openpkpd-0.2.1/docs/_static/examples/09_three_cmt_profile.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/10_output.txt +94 -0
- openpkpd-0.2.1/docs/_static/examples/11_output.txt +44 -0
- openpkpd-0.2.1/docs/_static/examples/11_tte_survival.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/12_output.txt +78 -0
- openpkpd-0.2.1/docs/_static/examples/13_output.txt +125 -0
- openpkpd-0.2.1/docs/_static/examples/14_output.txt +55 -0
- openpkpd-0.2.1/docs/_static/examples/14_simulation_panel.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/14_spaghetti.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/14_vpc_engine.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/14_vpc_model_perf.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/14_vpc_prediction_interval.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/15_output.txt +76 -0
- openpkpd-0.2.1/docs/_static/examples/16_dde_model.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/16_output.txt +22 -0
- openpkpd-0.2.1/docs/_static/examples/17_output.txt +37 -0
- openpkpd-0.2.1/docs/_static/examples/18_output.txt +21 -0
- openpkpd-0.2.1/docs/_static/examples/19_output.txt +60 -0
- openpkpd-0.2.1/docs/_static/examples/20_output.txt +44 -0
- openpkpd-0.2.1/docs/_static/examples/20_saem_convergence.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/21_output.txt +43 -0
- openpkpd-0.2.1/docs/_static/examples/21_prior_shrinkage.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/22_output.txt +41 -0
- openpkpd-0.2.1/docs/_static/examples/22_pbpk.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/23_iov_etas.png +0 -0
- openpkpd-0.2.1/docs/_static/examples/23_output.txt +37 -0
- openpkpd-0.2.1/docs/_static/examples/24_output.txt +0 -0
- openpkpd-0.2.1/docs/api/control_stream.md +7 -0
- openpkpd-0.2.1/docs/api/estimation.md +13 -0
- openpkpd-0.2.1/docs/api/index.md +13 -0
- openpkpd-0.2.1/docs/api/model_builder.md +14 -0
- openpkpd-0.2.1/docs/api/parameters.md +25 -0
- openpkpd-0.2.1/docs/api/plots.md +51 -0
- openpkpd-0.2.1/docs/building_installers.md +120 -0
- openpkpd-0.2.1/docs/changelog.md +147 -0
- openpkpd-0.2.1/docs/conf.py +121 -0
- openpkpd-0.2.1/docs/contributing.md +143 -0
- openpkpd-0.2.1/docs/developer_performance.md +161 -0
- openpkpd-0.2.1/docs/examples/01_theophylline_fo.md +53 -0
- openpkpd-0.2.1/docs/examples/02_warfarin_foce.md +48 -0
- openpkpd-0.2.1/docs/examples/03_two_compartment_iv.md +61 -0
- openpkpd-0.2.1/docs/examples/04_emax_pd_model.md +83 -0
- openpkpd-0.2.1/docs/examples/05_indirect_response.md +59 -0
- openpkpd-0.2.1/docs/examples/06_from_control_stream.md +85 -0
- openpkpd-0.2.1/docs/examples/07_diagnostic_plots.md +59 -0
- openpkpd-0.2.1/docs/examples/16_dde_model.md +71 -0
- openpkpd-0.2.1/docs/examples/index.md +77 -0
- openpkpd-0.2.1/docs/getting_started/index.md +9 -0
- openpkpd-0.2.1/docs/getting_started/installation.md +86 -0
- openpkpd-0.2.1/docs/getting_started/migrating_from_nonmem.md +99 -0
- openpkpd-0.2.1/docs/getting_started/quickstart.md +127 -0
- openpkpd-0.2.1/docs/index.md +64 -0
- openpkpd-0.2.1/docs/make.bat +28 -0
- openpkpd-0.2.1/docs/roadmap.md +204 -0
- openpkpd-0.2.1/docs/user_guide/advanced_pk.md +365 -0
- openpkpd-0.2.1/docs/user_guide/analysis_tools.md +108 -0
- openpkpd-0.2.1/docs/user_guide/analysis_validation_gaps.md +186 -0
- openpkpd-0.2.1/docs/user_guide/citations.md +471 -0
- openpkpd-0.2.1/docs/user_guide/comparison.md +239 -0
- openpkpd-0.2.1/docs/user_guide/control_stream.md +167 -0
- openpkpd-0.2.1/docs/user_guide/covariance_step.md +85 -0
- openpkpd-0.2.1/docs/user_guide/data_format.md +113 -0
- openpkpd-0.2.1/docs/user_guide/estimation_methods.md +212 -0
- openpkpd-0.2.1/docs/user_guide/external_validation_benchmarks.md +302 -0
- openpkpd-0.2.1/docs/user_guide/gui.md +648 -0
- openpkpd-0.2.1/docs/user_guide/index.md +42 -0
- openpkpd-0.2.1/docs/user_guide/model_builder.md +253 -0
- openpkpd-0.2.1/docs/user_guide/nca.md +229 -0
- openpkpd-0.2.1/docs/user_guide/output_files.md +154 -0
- openpkpd-0.2.1/docs/user_guide/performance_analysis_simulation_report.md +153 -0
- openpkpd-0.2.1/docs/user_guide/performance_profiling_report.md +165 -0
- openpkpd-0.2.1/docs/user_guide/pk_subroutines.md +111 -0
- openpkpd-0.2.1/docs/user_guide/plots.md +220 -0
- openpkpd-0.2.1/docs/user_guide/testing.md +305 -0
- openpkpd-0.2.1/docs/user_guide/validation.md +150 -0
- openpkpd-0.2.1/examples/01_theophylline_fo.py +124 -0
- openpkpd-0.2.1/examples/02_warfarin_foce.py +108 -0
- openpkpd-0.2.1/examples/03_two_compartment_iv.py +97 -0
- openpkpd-0.2.1/examples/04_emax_pd_model.py +132 -0
- openpkpd-0.2.1/examples/05_indirect_response.py +163 -0
- openpkpd-0.2.1/examples/06_from_control_stream.py +120 -0
- openpkpd-0.2.1/examples/07_diagnostic_plots.py +147 -0
- openpkpd-0.2.1/examples/08_ode_transit_absorption.py +235 -0
- openpkpd-0.2.1/examples/09_three_compartment.py +289 -0
- openpkpd-0.2.1/examples/10_blq_handling.py +365 -0
- openpkpd-0.2.1/examples/11_tte_model.py +392 -0
- openpkpd-0.2.1/examples/12_nca.py +293 -0
- openpkpd-0.2.1/examples/13_covariate_search.py +379 -0
- openpkpd-0.2.1/examples/14_simulation_vpc.py +458 -0
- openpkpd-0.2.1/examples/15_bayes_laplace.py +227 -0
- openpkpd-0.2.1/examples/16_dde_model.py +163 -0
- openpkpd-0.2.1/examples/17_sbml_import.py +280 -0
- openpkpd-0.2.1/examples/18_parallel_bootstrap.py +220 -0
- openpkpd-0.2.1/examples/19_count_categorical_models.py +325 -0
- openpkpd-0.2.1/examples/20_saem_estimation.py +170 -0
- openpkpd-0.2.1/examples/21_laplacian_prior.py +205 -0
- openpkpd-0.2.1/examples/22_pbpk_model.py +206 -0
- openpkpd-0.2.1/examples/23_iov_model.py +278 -0
- openpkpd-0.2.1/examples/24_advanced_pd_models.py +232 -0
- openpkpd-0.2.1/examples/catalog/diagnostics/syntax/same_omega_showcase/manifest.yaml +21 -0
- openpkpd-0.2.1/examples/catalog/diagnostics/syntax/same_omega_showcase/model.ctl +28 -0
- openpkpd-0.2.1/examples/catalog/nca/basic_nca/manifest.yaml +21 -0
- openpkpd-0.2.1/examples/catalog/pk/infusion/covariates_one_cmt_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/infusion/covariates_one_cmt_focei/model.ctl +74 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/phenobarbital_fo/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/phenobarbital_fo/model.ctl +70 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/three_compartment_iv_advan11_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/three_compartment_iv_advan11_focei/model.ctl +38 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv/model.ctl +32 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv_focei/model.ctl +77 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/minimal_theophylline_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/minimal_theophylline_focei/model.ctl +23 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/model.ctl +58 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/model.ctl +63 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/model.ctl +78 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/model.ctl +80 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/model.ctl +81 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/model.ctl +82 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/README.md +17 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/manifest.yaml +24 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/model.ctl +56 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_fo/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_fo/model.ctl +28 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_saem/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_saem/model.ctl +28 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/transit_absorption_advan6_fo/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/transit_absorption_advan6_fo/model.ctl +37 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_oral_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_oral_focei/model.ctl +28 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_pk_focei/manifest.yaml +22 -0
- openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_pk_focei/model.ctl +64 -0
- openpkpd-0.2.1/examples/control_streams/00_theophylline_fixture_diagnostics.ctl +38 -0
- openpkpd-0.2.1/examples/control_streams/01_theophylline_oral_fo.ctl +28 -0
- openpkpd-0.2.1/examples/control_streams/02_warfarin_oral_focei.ctl +28 -0
- openpkpd-0.2.1/examples/control_streams/03_two_compartment_iv_fo.ctl +32 -0
- openpkpd-0.2.1/examples/control_streams/06_minimal_theophylline_focei.ctl +23 -0
- openpkpd-0.2.1/examples/control_streams/08_transit_absorption_advan6_fo.ctl +37 -0
- openpkpd-0.2.1/examples/control_streams/09_three_compartment_iv_advan11_focei.ctl +38 -0
- openpkpd-0.2.1/examples/control_streams/10_warfarin_pk_focei.ctl +64 -0
- openpkpd-0.2.1/examples/control_streams/11_two_compartment_iv_focei.ctl +77 -0
- openpkpd-0.2.1/examples/control_streams/12_phenobarbital_fo.ctl +70 -0
- openpkpd-0.2.1/examples/control_streams/13_covariates_one_cmt_focei.ctl +74 -0
- openpkpd-0.2.1/examples/control_streams/20_theophylline_oral_saem.ctl +28 -0
- openpkpd-0.2.1/examples/control_streams/23_same_omega_showcase.ctl +28 -0
- openpkpd-0.2.1/examples/control_streams/30_nmdata_input_drop_and_body_weight_scaling.ctl +58 -0
- openpkpd-0.2.1/examples/control_streams/31_nmdata_multiple_table_output_formats.ctl +63 -0
- openpkpd-0.2.1/examples/control_streams/32_nmdata_saem_age_covariate.ctl +78 -0
- openpkpd-0.2.1/examples/control_streams/33_nmdata_saem_age_covariate_block_omega.ctl +80 -0
- openpkpd-0.2.1/examples/control_streams/34_nmsim_two_compartment_block_omega_fo.ctl +56 -0
- openpkpd-0.2.1/examples/control_streams/35_nmsim_advan13_one_compartment_des.ctl +81 -0
- openpkpd-0.2.1/examples/control_streams/36_nmsim_saem_multi_covariate_age_weight_sex.ctl +82 -0
- openpkpd-0.2.1/examples/control_streams/README.md +64 -0
- openpkpd-0.2.1/examples/control_streams/same_omega.csv +145 -0
- openpkpd-0.2.1/examples/control_streams/theo.csv +145 -0
- openpkpd-0.2.1/examples/control_streams/theophylline.csv +145 -0
- openpkpd-0.2.1/examples/control_streams/theophylline_saem.csv +145 -0
- openpkpd-0.2.1/examples/control_streams/three_compartment_iv.csv +65 -0
- openpkpd-0.2.1/examples/control_streams/transit_absorption.csv +145 -0
- openpkpd-0.2.1/examples/control_streams/two_compartment_iv.csv +65 -0
- openpkpd-0.2.1/examples/control_streams/warfarin.csv +29 -0
- openpkpd-0.2.1/examples/data/README.md +33 -0
- openpkpd-0.2.1/examples/data/xgxr1.csv +120 -0
- openpkpd-0.2.1/examples/data/xgxr12.csv +120 -0
- openpkpd-0.2.1/examples/data/xgxr2.csv +120 -0
- openpkpd-0.2.1/examples/data/xgxr2covs.csv +120 -0
- openpkpd-0.2.1/examples/data/xgxr4.csv +120 -0
- openpkpd-0.2.1/examples/output/16_dde_model.png +0 -0
- openpkpd-0.2.1/examples/output/17_sbml_import.png +0 -0
- openpkpd-0.2.1/examples/shared_data/internal/same_omega.csv +145 -0
- openpkpd-0.2.1/examples/shared_data/internal/transit_absorption.csv +145 -0
- openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr1.csv +120 -0
- openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr12.csv +120 -0
- openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr2.csv +120 -0
- openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr2covs.csv +120 -0
- openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr4.csv +120 -0
- openpkpd-0.2.1/examples/shared_data/phenobarbital/phenobarbital_simulated.csv +349 -0
- openpkpd-0.2.1/examples/shared_data/pk_iv/three_compartment_iv.csv +65 -0
- openpkpd-0.2.1/examples/shared_data/pk_iv/two_compartment_iv.csv +65 -0
- openpkpd-0.2.1/examples/shared_data/theophylline/theo.csv +145 -0
- openpkpd-0.2.1/examples/shared_data/theophylline/theophylline.csv +145 -0
- openpkpd-0.2.1/examples/shared_data/theophylline/theophylline_saem.csv +145 -0
- openpkpd-0.2.1/examples/shared_data/warfarin/warfarin.csv +29 -0
- openpkpd-0.2.1/justfile +276 -0
- openpkpd-0.2.1/notebooks/00_index.py +97 -0
- openpkpd-0.2.1/notebooks/01_quickstart.py +363 -0
- openpkpd-0.2.1/notebooks/02_data_handling.py +339 -0
- openpkpd-0.2.1/notebooks/03_estimation_methods.py +433 -0
- openpkpd-0.2.1/notebooks/04_simulation_vpc_npde.py +410 -0
- openpkpd-0.2.1/notebooks/05_nca.py +446 -0
- openpkpd-0.2.1/notebooks/06_pk_subroutines.py +386 -0
- openpkpd-0.2.1/notebooks/07_pkpd_models.py +395 -0
- openpkpd-0.2.1/notebooks/08_diagnostics_plots.py +464 -0
- openpkpd-0.2.1/notebooks/09_covariate_modeling.py +424 -0
- openpkpd-0.2.1/notebooks/10_inference_bootstrap.py +341 -0
- openpkpd-0.2.1/notebooks/11_advanced.py +449 -0
- openpkpd-0.2.1/pyproject.toml +173 -0
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dkms.conf
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### Linux ###
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# temporary files which can be created if a process still has a handle open of a deleted file
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# KDE directory preferences
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.directory
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# Linux trash folder which might appear on any partition or disk
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# .nfs files are created when an open file is removed but is still being accessed
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.nfs*
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### macOS ###
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# General
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.AppleDouble
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.LSOverride
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# Icon must end with two \r
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Icon
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# Thumbnails
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._*
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# Files that might appear in the root of a volume
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.VolumeIcon.icns
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# Directories potentially created on remote AFP share
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.AppleDB
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.AppleDesktop
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Temporary Items
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.apdisk
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### macOS Patch ###
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# iCloud generated files
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*.icloud
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### Python ###
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# Byte-compiled / optimized / DLL files
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*.py[cod]
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*$py.class
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# C extensions
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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parts/
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var/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Exception: our hand-authored installer spec is a committed source file.
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!scripts/installer.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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+
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# Translations
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169
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+
*.mo
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170
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*.pot
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+
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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+
|
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# Scrapy stuff:
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.scrapy
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185
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# Sphinx documentation
|
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+
docs/_build/
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+
|
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# PyBuilder
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.pybuilder/
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target/
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|
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# Jupyter Notebook
|
|
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.ipynb_checkpoints
|
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+
|
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195
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+
# IPython
|
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196
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+
profile_default/
|
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ipython_config.py
|
|
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|
+
|
|
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
|
|
201
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# intended to run in multiple environments; otherwise, check them in:
|
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# .python-version
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+
|
|
204
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# pipenv
|
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
|
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206
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
|
|
207
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+
# having no cross-platform support, pipenv may install dependencies that don't work, or not
|
|
208
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+
# install all needed dependencies.
|
|
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#Pipfile.lock
|
|
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|
+
|
|
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# poetry
|
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212
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
|
|
213
|
+
# This is especially recommended for binary packages to ensure reproducibility, and is more
|
|
214
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+
# commonly ignored for libraries.
|
|
215
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
|
|
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|
+
#poetry.lock
|
|
217
|
+
|
|
218
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# pdm
|
|
219
|
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
|
|
220
|
+
#pdm.lock
|
|
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|
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
|
|
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|
+
# in version control.
|
|
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# https://pdm.fming.dev/#use-with-ide
|
|
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|
+
.pdm.toml
|
|
225
|
+
|
|
226
|
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
|
|
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|
+
__pypackages__/
|
|
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|
+
|
|
229
|
+
# Celery stuff
|
|
230
|
+
celerybeat-schedule
|
|
231
|
+
celerybeat.pid
|
|
232
|
+
|
|
233
|
+
# SageMath parsed files
|
|
234
|
+
*.sage.py
|
|
235
|
+
|
|
236
|
+
# Environments
|
|
237
|
+
.env
|
|
238
|
+
.venv
|
|
239
|
+
env/
|
|
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+
venv/
|
|
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|
+
ENV/
|
|
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|
+
env.bak/
|
|
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|
+
venv.bak/
|
|
244
|
+
|
|
245
|
+
# Spyder project settings
|
|
246
|
+
.spyderproject
|
|
247
|
+
.spyproject
|
|
248
|
+
|
|
249
|
+
# Rope project settings
|
|
250
|
+
.ropeproject
|
|
251
|
+
|
|
252
|
+
# mkdocs documentation
|
|
253
|
+
/site
|
|
254
|
+
|
|
255
|
+
# mypy
|
|
256
|
+
.mypy_cache/
|
|
257
|
+
.dmypy.json
|
|
258
|
+
dmypy.json
|
|
259
|
+
|
|
260
|
+
# Pyre type checker
|
|
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|
+
.pyre/
|
|
262
|
+
|
|
263
|
+
# pytype static type analyzer
|
|
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|
+
.pytype/
|
|
265
|
+
|
|
266
|
+
# Cython debug symbols
|
|
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|
+
cython_debug/
|
|
268
|
+
|
|
269
|
+
# PyCharm
|
|
270
|
+
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
|
|
271
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+
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
|
|
272
|
+
# and can be added to the global gitignore or merged into this file. For a more nuclear
|
|
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|
+
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
|
|
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|
+
#.idea/
|
|
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|
+
|
|
276
|
+
### Python Patch ###
|
|
277
|
+
# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
|
|
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|
+
poetry.toml
|
|
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|
+
|
|
280
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+
### Local tool caches and scratch directories ###
|
|
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|
+
.r-lib/
|
|
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|
+
.uv-cache/
|
|
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|
+
.claude/
|
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.local/
|
|
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|
+
.xdg-data/
|
|
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|
+
artifacts/
|
|
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|
+
main.py
|
|
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|
+
|
|
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|
+
# ruff
|
|
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|
+
.ruff_cache/
|
|
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|
+
|
|
292
|
+
# LSP config files
|
|
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|
+
pyrightconfig.json
|
|
294
|
+
|
|
295
|
+
# project-specific generated files
|
|
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|
+
uv.lock
|
|
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|
+
todo/
|
|
298
|
+
.openpkpd_gui_artifacts/
|
|
299
|
+
|
|
300
|
+
### LaTeX ###
|
|
301
|
+
## Core latex/pdflatex auxiliary files:
|
|
302
|
+
*.aux
|
|
303
|
+
*.lof
|
|
304
|
+
*.log
|
|
305
|
+
*.lot
|
|
306
|
+
*.fls
|
|
307
|
+
*.out
|
|
308
|
+
*.toc
|
|
309
|
+
*.fmt
|
|
310
|
+
*.fot
|
|
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|
+
*.cb
|
|
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|
+
*.cb2
|
|
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|
+
.*.lb
|
|
314
|
+
|
|
315
|
+
## Intermediate documents:
|
|
316
|
+
*.dvi
|
|
317
|
+
*.xdv
|
|
318
|
+
*-converted-to.*
|
|
319
|
+
# these rules might exclude image files for figures etc.
|
|
320
|
+
# *.ps
|
|
321
|
+
# *.eps
|
|
322
|
+
# *.pdf
|
|
323
|
+
|
|
324
|
+
## Generated if empty string is given at "Please type another file name for output:"
|
|
325
|
+
.pdf
|
|
326
|
+
|
|
327
|
+
## Bibliography auxiliary files (bibtex/biblatex/biber):
|
|
328
|
+
*.bbl
|
|
329
|
+
*.bcf
|
|
330
|
+
*.blg
|
|
331
|
+
*-blx.aux
|
|
332
|
+
*-blx.bib
|
|
333
|
+
*.run.xml
|
|
334
|
+
|
|
335
|
+
## Build tool auxiliary files:
|
|
336
|
+
*.fdb_latexmk
|
|
337
|
+
*.synctex
|
|
338
|
+
*.synctex(busy)
|
|
339
|
+
*.synctex.gz
|
|
340
|
+
*.synctex.gz(busy)
|
|
341
|
+
*.pdfsync
|
|
342
|
+
|
|
343
|
+
## Build tool directories for auxiliary files
|
|
344
|
+
# latexrun
|
|
345
|
+
latex.out/
|
|
346
|
+
|
|
347
|
+
## Auxiliary and intermediate files from other packages:
|
|
348
|
+
# algorithms
|
|
349
|
+
*.alg
|
|
350
|
+
*.loa
|
|
351
|
+
|
|
352
|
+
# achemso
|
|
353
|
+
acs-*.bib
|
|
354
|
+
|
|
355
|
+
# amsthm
|
|
356
|
+
*.thm
|
|
357
|
+
|
|
358
|
+
# beamer
|
|
359
|
+
*.nav
|
|
360
|
+
*.pre
|
|
361
|
+
*.snm
|
|
362
|
+
*.vrb
|
|
363
|
+
|
|
364
|
+
# changes
|
|
365
|
+
*.soc
|
|
366
|
+
|
|
367
|
+
# comment
|
|
368
|
+
*.cut
|
|
369
|
+
|
|
370
|
+
# cprotect
|
|
371
|
+
*.cpt
|
|
372
|
+
|
|
373
|
+
# elsarticle (documentclass of Elsevier journals)
|
|
374
|
+
*.spl
|
|
375
|
+
|
|
376
|
+
# endnotes
|
|
377
|
+
*.ent
|
|
378
|
+
|
|
379
|
+
# fixme
|
|
380
|
+
*.lox
|
|
381
|
+
|
|
382
|
+
# feynmf/feynmp
|
|
383
|
+
*.mf
|
|
384
|
+
*.mp
|
|
385
|
+
*.t[1-9]
|
|
386
|
+
*.t[1-9][0-9]
|
|
387
|
+
*.tfm
|
|
388
|
+
|
|
389
|
+
#(r)(e)ledmac/(r)(e)ledpar
|
|
390
|
+
*.end
|
|
391
|
+
*.?end
|
|
392
|
+
*.[1-9]
|
|
393
|
+
*.[1-9][0-9]
|
|
394
|
+
*.[1-9][0-9][0-9]
|
|
395
|
+
*.[1-9]R
|
|
396
|
+
*.[1-9][0-9]R
|
|
397
|
+
*.[1-9][0-9][0-9]R
|
|
398
|
+
*.eledsec[1-9]
|
|
399
|
+
*.eledsec[1-9]R
|
|
400
|
+
*.eledsec[1-9][0-9]
|
|
401
|
+
*.eledsec[1-9][0-9]R
|
|
402
|
+
*.eledsec[1-9][0-9][0-9]
|
|
403
|
+
*.eledsec[1-9][0-9][0-9]R
|
|
404
|
+
|
|
405
|
+
# glossaries
|
|
406
|
+
*.acn
|
|
407
|
+
*.acr
|
|
408
|
+
*.glg
|
|
409
|
+
*.glo
|
|
410
|
+
*.gls
|
|
411
|
+
*.glsdefs
|
|
412
|
+
*.lzo
|
|
413
|
+
*.lzs
|
|
414
|
+
*.slg
|
|
415
|
+
*.slo
|
|
416
|
+
*.sls
|
|
417
|
+
|
|
418
|
+
# uncomment this for glossaries-extra (will ignore makeindex's style files!)
|
|
419
|
+
# *.ist
|
|
420
|
+
|
|
421
|
+
# gnuplot
|
|
422
|
+
*.gnuplot
|
|
423
|
+
*.table
|
|
424
|
+
|
|
425
|
+
# gnuplottex
|
|
426
|
+
*-gnuplottex-*
|
|
427
|
+
|
|
428
|
+
# gregoriotex
|
|
429
|
+
*.gaux
|
|
430
|
+
*.glog
|
|
431
|
+
*.gtex
|
|
432
|
+
|
|
433
|
+
# htlatex
|
|
434
|
+
*.4ct
|
|
435
|
+
*.4tc
|
|
436
|
+
*.idv
|
|
437
|
+
*.lg
|
|
438
|
+
*.trc
|
|
439
|
+
*.xref
|
|
440
|
+
|
|
441
|
+
# hyperref
|
|
442
|
+
*.brf
|
|
443
|
+
|
|
444
|
+
# knitr
|
|
445
|
+
*-concordance.tex
|
|
446
|
+
# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
|
|
447
|
+
# *.tikz
|
|
448
|
+
*-tikzDictionary
|
|
449
|
+
|
|
450
|
+
# listings
|
|
451
|
+
*.lol
|
|
452
|
+
|
|
453
|
+
# luatexja-ruby
|
|
454
|
+
*.ltjruby
|
|
455
|
+
|
|
456
|
+
# makeidx
|
|
457
|
+
*.idx
|
|
458
|
+
*.ilg
|
|
459
|
+
*.ind
|
|
460
|
+
|
|
461
|
+
# minitoc
|
|
462
|
+
*.maf
|
|
463
|
+
*.mlf
|
|
464
|
+
*.mlt
|
|
465
|
+
*.mtc[0-9]*
|
|
466
|
+
*.slf[0-9]*
|
|
467
|
+
*.slt[0-9]*
|
|
468
|
+
*.stc[0-9]*
|
|
469
|
+
|
|
470
|
+
# minted
|
|
471
|
+
_minted*
|
|
472
|
+
*.pyg
|
|
473
|
+
|
|
474
|
+
# morewrites
|
|
475
|
+
*.mw
|
|
476
|
+
|
|
477
|
+
# newpax
|
|
478
|
+
*.newpax
|
|
479
|
+
|
|
480
|
+
# nomencl
|
|
481
|
+
*.nlg
|
|
482
|
+
*.nlo
|
|
483
|
+
*.nls
|
|
484
|
+
|
|
485
|
+
# pax
|
|
486
|
+
*.pax
|
|
487
|
+
|
|
488
|
+
# pdfpcnotes
|
|
489
|
+
*.pdfpc
|
|
490
|
+
|
|
491
|
+
# sagetex
|
|
492
|
+
*.sagetex.sage
|
|
493
|
+
*.sagetex.py
|
|
494
|
+
*.sagetex.scmd
|
|
495
|
+
|
|
496
|
+
# scrwfile
|
|
497
|
+
*.wrt
|
|
498
|
+
|
|
499
|
+
# svg
|
|
500
|
+
svg-inkscape/
|
|
501
|
+
|
|
502
|
+
# sympy
|
|
503
|
+
*.sout
|
|
504
|
+
*.sympy
|
|
505
|
+
sympy-plots-for-*.tex/
|
|
506
|
+
|
|
507
|
+
# pdfcomment
|
|
508
|
+
*.upa
|
|
509
|
+
*.upb
|
|
510
|
+
|
|
511
|
+
# pythontex
|
|
512
|
+
*.pytxcode
|
|
513
|
+
pythontex-files-*/
|
|
514
|
+
|
|
515
|
+
# tcolorbox
|
|
516
|
+
*.listing
|
|
517
|
+
|
|
518
|
+
# thmtools
|
|
519
|
+
*.loe
|
|
520
|
+
|
|
521
|
+
# TikZ & PGF
|
|
522
|
+
*.dpth
|
|
523
|
+
*.md5
|
|
524
|
+
*.auxlock
|
|
525
|
+
|
|
526
|
+
# titletoc
|
|
527
|
+
*.ptc
|
|
528
|
+
|
|
529
|
+
# todonotes
|
|
530
|
+
*.tdo
|
|
531
|
+
|
|
532
|
+
# vhistory
|
|
533
|
+
*.hst
|
|
534
|
+
*.ver
|
|
535
|
+
|
|
536
|
+
# easy-todo
|
|
537
|
+
*.lod
|
|
538
|
+
|
|
539
|
+
# xcolor
|
|
540
|
+
*.xcp
|
|
541
|
+
|
|
542
|
+
# xmpincl
|
|
543
|
+
*.xmpi
|
|
544
|
+
|
|
545
|
+
# xindy
|
|
546
|
+
*.xdy
|
|
547
|
+
|
|
548
|
+
# xypic precompiled matrices and outlines
|
|
549
|
+
*.xyc
|
|
550
|
+
*.xyd
|
|
551
|
+
|
|
552
|
+
# endfloat
|
|
553
|
+
*.ttt
|
|
554
|
+
*.fff
|
|
555
|
+
|
|
556
|
+
# Latexian
|
|
557
|
+
TSWLatexianTemp*
|
|
558
|
+
|
|
559
|
+
## Editors:
|
|
560
|
+
# WinEdt
|
|
561
|
+
*.bak
|
|
562
|
+
*.sav
|
|
563
|
+
|
|
564
|
+
# Texpad
|
|
565
|
+
.texpadtmp
|
|
566
|
+
|
|
567
|
+
# LyX
|
|
568
|
+
*.lyx~
|
|
569
|
+
|
|
570
|
+
# Kile
|
|
571
|
+
*.backup
|
|
572
|
+
|
|
573
|
+
# gummi
|
|
574
|
+
.*.swp
|
|
575
|
+
|
|
576
|
+
# KBibTeX
|
|
577
|
+
*~[0-9]*
|
|
578
|
+
|
|
579
|
+
# TeXnicCenter
|
|
580
|
+
*.tps
|
|
581
|
+
|
|
582
|
+
# auto folder when using emacs and auctex
|
|
583
|
+
./auto/*
|
|
584
|
+
*.el
|
|
585
|
+
|
|
586
|
+
# expex forward references with \gathertags
|
|
587
|
+
*-tags.tex
|
|
588
|
+
|
|
589
|
+
# standalone packages
|
|
590
|
+
*.sta
|
|
591
|
+
|
|
592
|
+
# Makeindex log files
|
|
593
|
+
*.lpz
|
|
594
|
+
|
|
595
|
+
# xwatermark package
|
|
596
|
+
*.xwm
|
|
597
|
+
|