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.
Files changed (746) hide show
  1. openpkpd-0.2.1/.gitignore +597 -0
  2. openpkpd-0.2.1/.gitlab-ci.yml +229 -0
  3. openpkpd-0.2.1/.pre-commit-config.yaml +7 -0
  4. openpkpd-0.2.1/.python-version +1 -0
  5. openpkpd-0.2.1/.readthedocs.yaml +10 -0
  6. openpkpd-0.2.1/LICENSE +661 -0
  7. openpkpd-0.2.1/PKG-INFO +578 -0
  8. openpkpd-0.2.1/README.md +502 -0
  9. openpkpd-0.2.1/docs/Makefile +19 -0
  10. openpkpd-0.2.1/docs/OpenPKPD_icon.ico +0 -0
  11. openpkpd-0.2.1/docs/OpenPKPD_logo.png +0 -0
  12. openpkpd-0.2.1/docs/OpenPKPD_logo.svg +161 -0
  13. openpkpd-0.2.1/docs/_static/custom.css +16 -0
  14. openpkpd-0.2.1/docs/_static/examples/01_conc_time.png +0 -0
  15. openpkpd-0.2.1/docs/_static/examples/01_output.txt +26 -0
  16. openpkpd-0.2.1/docs/_static/examples/01_spaghetti.png +0 -0
  17. openpkpd-0.2.1/docs/_static/examples/02_eta_hist.png +0 -0
  18. openpkpd-0.2.1/docs/_static/examples/02_gof_panel.png +0 -0
  19. openpkpd-0.2.1/docs/_static/examples/02_output.txt +22 -0
  20. openpkpd-0.2.1/docs/_static/examples/03_log_conc_time.png +0 -0
  21. openpkpd-0.2.1/docs/_static/examples/03_output.txt +18 -0
  22. openpkpd-0.2.1/docs/_static/examples/03_spaghetti_log.png +0 -0
  23. openpkpd-0.2.1/docs/_static/examples/04_effect_time.png +0 -0
  24. openpkpd-0.2.1/docs/_static/examples/04_emax_curve.png +0 -0
  25. openpkpd-0.2.1/docs/_static/examples/04_gof_panel.png +0 -0
  26. openpkpd-0.2.1/docs/_static/examples/04_output.txt +21 -0
  27. openpkpd-0.2.1/docs/_static/examples/05_effect_time.png +0 -0
  28. openpkpd-0.2.1/docs/_static/examples/05_hysteresis.png +0 -0
  29. openpkpd-0.2.1/docs/_static/examples/05_output.txt +20 -0
  30. openpkpd-0.2.1/docs/_static/examples/06_output.txt +26 -0
  31. openpkpd-0.2.1/docs/_static/examples/07_abs_iwres.png +0 -0
  32. openpkpd-0.2.1/docs/_static/examples/07_conc_time.png +0 -0
  33. openpkpd-0.2.1/docs/_static/examples/07_cwres_pred.png +0 -0
  34. openpkpd-0.2.1/docs/_static/examples/07_cwres_qq.png +0 -0
  35. openpkpd-0.2.1/docs/_static/examples/07_cwres_time.png +0 -0
  36. openpkpd-0.2.1/docs/_static/examples/07_dv_vs_ipred.png +0 -0
  37. openpkpd-0.2.1/docs/_static/examples/07_dv_vs_pred.png +0 -0
  38. openpkpd-0.2.1/docs/_static/examples/07_eta1_vs_wt.png +0 -0
  39. openpkpd-0.2.1/docs/_static/examples/07_eta_hist.png +0 -0
  40. openpkpd-0.2.1/docs/_static/examples/07_eta_pairs.png +0 -0
  41. openpkpd-0.2.1/docs/_static/examples/07_gof_panel.png +0 -0
  42. openpkpd-0.2.1/docs/_static/examples/07_mean_profile.png +0 -0
  43. openpkpd-0.2.1/docs/_static/examples/07_ofv_history.png +0 -0
  44. openpkpd-0.2.1/docs/_static/examples/07_output.txt +24 -0
  45. openpkpd-0.2.1/docs/_static/examples/07_spaghetti.png +0 -0
  46. openpkpd-0.2.1/docs/_static/examples/08_output.txt +36 -0
  47. openpkpd-0.2.1/docs/_static/examples/09_output.txt +62 -0
  48. openpkpd-0.2.1/docs/_static/examples/09_three_cmt_profile.png +0 -0
  49. openpkpd-0.2.1/docs/_static/examples/10_output.txt +94 -0
  50. openpkpd-0.2.1/docs/_static/examples/11_output.txt +44 -0
  51. openpkpd-0.2.1/docs/_static/examples/11_tte_survival.png +0 -0
  52. openpkpd-0.2.1/docs/_static/examples/12_output.txt +78 -0
  53. openpkpd-0.2.1/docs/_static/examples/13_output.txt +125 -0
  54. openpkpd-0.2.1/docs/_static/examples/14_output.txt +55 -0
  55. openpkpd-0.2.1/docs/_static/examples/14_simulation_panel.png +0 -0
  56. openpkpd-0.2.1/docs/_static/examples/14_spaghetti.png +0 -0
  57. openpkpd-0.2.1/docs/_static/examples/14_vpc_engine.png +0 -0
  58. openpkpd-0.2.1/docs/_static/examples/14_vpc_model_perf.png +0 -0
  59. openpkpd-0.2.1/docs/_static/examples/14_vpc_prediction_interval.png +0 -0
  60. openpkpd-0.2.1/docs/_static/examples/15_output.txt +76 -0
  61. openpkpd-0.2.1/docs/_static/examples/16_dde_model.png +0 -0
  62. openpkpd-0.2.1/docs/_static/examples/16_output.txt +22 -0
  63. openpkpd-0.2.1/docs/_static/examples/17_output.txt +37 -0
  64. openpkpd-0.2.1/docs/_static/examples/18_output.txt +21 -0
  65. openpkpd-0.2.1/docs/_static/examples/19_output.txt +60 -0
  66. openpkpd-0.2.1/docs/_static/examples/20_output.txt +44 -0
  67. openpkpd-0.2.1/docs/_static/examples/20_saem_convergence.png +0 -0
  68. openpkpd-0.2.1/docs/_static/examples/21_output.txt +43 -0
  69. openpkpd-0.2.1/docs/_static/examples/21_prior_shrinkage.png +0 -0
  70. openpkpd-0.2.1/docs/_static/examples/22_output.txt +41 -0
  71. openpkpd-0.2.1/docs/_static/examples/22_pbpk.png +0 -0
  72. openpkpd-0.2.1/docs/_static/examples/23_iov_etas.png +0 -0
  73. openpkpd-0.2.1/docs/_static/examples/23_output.txt +37 -0
  74. openpkpd-0.2.1/docs/_static/examples/24_output.txt +0 -0
  75. openpkpd-0.2.1/docs/api/control_stream.md +7 -0
  76. openpkpd-0.2.1/docs/api/estimation.md +13 -0
  77. openpkpd-0.2.1/docs/api/index.md +13 -0
  78. openpkpd-0.2.1/docs/api/model_builder.md +14 -0
  79. openpkpd-0.2.1/docs/api/parameters.md +25 -0
  80. openpkpd-0.2.1/docs/api/plots.md +51 -0
  81. openpkpd-0.2.1/docs/building_installers.md +120 -0
  82. openpkpd-0.2.1/docs/changelog.md +147 -0
  83. openpkpd-0.2.1/docs/conf.py +121 -0
  84. openpkpd-0.2.1/docs/contributing.md +143 -0
  85. openpkpd-0.2.1/docs/developer_performance.md +161 -0
  86. openpkpd-0.2.1/docs/examples/01_theophylline_fo.md +53 -0
  87. openpkpd-0.2.1/docs/examples/02_warfarin_foce.md +48 -0
  88. openpkpd-0.2.1/docs/examples/03_two_compartment_iv.md +61 -0
  89. openpkpd-0.2.1/docs/examples/04_emax_pd_model.md +83 -0
  90. openpkpd-0.2.1/docs/examples/05_indirect_response.md +59 -0
  91. openpkpd-0.2.1/docs/examples/06_from_control_stream.md +85 -0
  92. openpkpd-0.2.1/docs/examples/07_diagnostic_plots.md +59 -0
  93. openpkpd-0.2.1/docs/examples/16_dde_model.md +71 -0
  94. openpkpd-0.2.1/docs/examples/index.md +77 -0
  95. openpkpd-0.2.1/docs/getting_started/index.md +9 -0
  96. openpkpd-0.2.1/docs/getting_started/installation.md +86 -0
  97. openpkpd-0.2.1/docs/getting_started/migrating_from_nonmem.md +99 -0
  98. openpkpd-0.2.1/docs/getting_started/quickstart.md +127 -0
  99. openpkpd-0.2.1/docs/index.md +64 -0
  100. openpkpd-0.2.1/docs/make.bat +28 -0
  101. openpkpd-0.2.1/docs/roadmap.md +204 -0
  102. openpkpd-0.2.1/docs/user_guide/advanced_pk.md +365 -0
  103. openpkpd-0.2.1/docs/user_guide/analysis_tools.md +108 -0
  104. openpkpd-0.2.1/docs/user_guide/analysis_validation_gaps.md +186 -0
  105. openpkpd-0.2.1/docs/user_guide/citations.md +471 -0
  106. openpkpd-0.2.1/docs/user_guide/comparison.md +239 -0
  107. openpkpd-0.2.1/docs/user_guide/control_stream.md +167 -0
  108. openpkpd-0.2.1/docs/user_guide/covariance_step.md +85 -0
  109. openpkpd-0.2.1/docs/user_guide/data_format.md +113 -0
  110. openpkpd-0.2.1/docs/user_guide/estimation_methods.md +212 -0
  111. openpkpd-0.2.1/docs/user_guide/external_validation_benchmarks.md +302 -0
  112. openpkpd-0.2.1/docs/user_guide/gui.md +648 -0
  113. openpkpd-0.2.1/docs/user_guide/index.md +42 -0
  114. openpkpd-0.2.1/docs/user_guide/model_builder.md +253 -0
  115. openpkpd-0.2.1/docs/user_guide/nca.md +229 -0
  116. openpkpd-0.2.1/docs/user_guide/output_files.md +154 -0
  117. openpkpd-0.2.1/docs/user_guide/performance_analysis_simulation_report.md +153 -0
  118. openpkpd-0.2.1/docs/user_guide/performance_profiling_report.md +165 -0
  119. openpkpd-0.2.1/docs/user_guide/pk_subroutines.md +111 -0
  120. openpkpd-0.2.1/docs/user_guide/plots.md +220 -0
  121. openpkpd-0.2.1/docs/user_guide/testing.md +305 -0
  122. openpkpd-0.2.1/docs/user_guide/validation.md +150 -0
  123. openpkpd-0.2.1/examples/01_theophylline_fo.py +124 -0
  124. openpkpd-0.2.1/examples/02_warfarin_foce.py +108 -0
  125. openpkpd-0.2.1/examples/03_two_compartment_iv.py +97 -0
  126. openpkpd-0.2.1/examples/04_emax_pd_model.py +132 -0
  127. openpkpd-0.2.1/examples/05_indirect_response.py +163 -0
  128. openpkpd-0.2.1/examples/06_from_control_stream.py +120 -0
  129. openpkpd-0.2.1/examples/07_diagnostic_plots.py +147 -0
  130. openpkpd-0.2.1/examples/08_ode_transit_absorption.py +235 -0
  131. openpkpd-0.2.1/examples/09_three_compartment.py +289 -0
  132. openpkpd-0.2.1/examples/10_blq_handling.py +365 -0
  133. openpkpd-0.2.1/examples/11_tte_model.py +392 -0
  134. openpkpd-0.2.1/examples/12_nca.py +293 -0
  135. openpkpd-0.2.1/examples/13_covariate_search.py +379 -0
  136. openpkpd-0.2.1/examples/14_simulation_vpc.py +458 -0
  137. openpkpd-0.2.1/examples/15_bayes_laplace.py +227 -0
  138. openpkpd-0.2.1/examples/16_dde_model.py +163 -0
  139. openpkpd-0.2.1/examples/17_sbml_import.py +280 -0
  140. openpkpd-0.2.1/examples/18_parallel_bootstrap.py +220 -0
  141. openpkpd-0.2.1/examples/19_count_categorical_models.py +325 -0
  142. openpkpd-0.2.1/examples/20_saem_estimation.py +170 -0
  143. openpkpd-0.2.1/examples/21_laplacian_prior.py +205 -0
  144. openpkpd-0.2.1/examples/22_pbpk_model.py +206 -0
  145. openpkpd-0.2.1/examples/23_iov_model.py +278 -0
  146. openpkpd-0.2.1/examples/24_advanced_pd_models.py +232 -0
  147. openpkpd-0.2.1/examples/catalog/diagnostics/syntax/same_omega_showcase/manifest.yaml +21 -0
  148. openpkpd-0.2.1/examples/catalog/diagnostics/syntax/same_omega_showcase/model.ctl +28 -0
  149. openpkpd-0.2.1/examples/catalog/nca/basic_nca/manifest.yaml +21 -0
  150. openpkpd-0.2.1/examples/catalog/pk/infusion/covariates_one_cmt_focei/manifest.yaml +22 -0
  151. openpkpd-0.2.1/examples/catalog/pk/infusion/covariates_one_cmt_focei/model.ctl +74 -0
  152. openpkpd-0.2.1/examples/catalog/pk/iv/phenobarbital_fo/manifest.yaml +22 -0
  153. openpkpd-0.2.1/examples/catalog/pk/iv/phenobarbital_fo/model.ctl +70 -0
  154. openpkpd-0.2.1/examples/catalog/pk/iv/three_compartment_iv_advan11_focei/manifest.yaml +22 -0
  155. openpkpd-0.2.1/examples/catalog/pk/iv/three_compartment_iv_advan11_focei/model.ctl +38 -0
  156. openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv/manifest.yaml +22 -0
  157. openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv/model.ctl +32 -0
  158. openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv_focei/manifest.yaml +22 -0
  159. openpkpd-0.2.1/examples/catalog/pk/iv/two_compartment_iv_focei/model.ctl +77 -0
  160. openpkpd-0.2.1/examples/catalog/pk/oral/minimal_theophylline_focei/manifest.yaml +22 -0
  161. openpkpd-0.2.1/examples/catalog/pk/oral/minimal_theophylline_focei/model.ctl +23 -0
  162. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/README.md +17 -0
  163. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/manifest.yaml +24 -0
  164. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_input_drop_and_body_weight_scaling/model.ctl +58 -0
  165. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/README.md +17 -0
  166. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/manifest.yaml +24 -0
  167. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_multiple_table_output_formats/model.ctl +63 -0
  168. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/README.md +17 -0
  169. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/manifest.yaml +24 -0
  170. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate/model.ctl +78 -0
  171. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/README.md +17 -0
  172. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/manifest.yaml +24 -0
  173. openpkpd-0.2.1/examples/catalog/pk/oral/nmdata_saem_age_covariate_block_omega/model.ctl +80 -0
  174. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/README.md +17 -0
  175. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/manifest.yaml +24 -0
  176. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_advan13_one_compartment_des/model.ctl +81 -0
  177. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/README.md +17 -0
  178. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/manifest.yaml +24 -0
  179. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_saem_multi_covariate_age_weight_sex/model.ctl +82 -0
  180. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/README.md +17 -0
  181. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/manifest.yaml +24 -0
  182. openpkpd-0.2.1/examples/catalog/pk/oral/nmsim_two_compartment_block_omega_fo/model.ctl +56 -0
  183. openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_fo/manifest.yaml +22 -0
  184. openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_fo/model.ctl +28 -0
  185. openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_saem/manifest.yaml +22 -0
  186. openpkpd-0.2.1/examples/catalog/pk/oral/theophylline_oral_saem/model.ctl +28 -0
  187. openpkpd-0.2.1/examples/catalog/pk/oral/transit_absorption_advan6_fo/manifest.yaml +22 -0
  188. openpkpd-0.2.1/examples/catalog/pk/oral/transit_absorption_advan6_fo/model.ctl +37 -0
  189. openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_oral_focei/manifest.yaml +22 -0
  190. openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_oral_focei/model.ctl +28 -0
  191. openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_pk_focei/manifest.yaml +22 -0
  192. openpkpd-0.2.1/examples/catalog/pk/oral/warfarin_pk_focei/model.ctl +64 -0
  193. openpkpd-0.2.1/examples/control_streams/00_theophylline_fixture_diagnostics.ctl +38 -0
  194. openpkpd-0.2.1/examples/control_streams/01_theophylline_oral_fo.ctl +28 -0
  195. openpkpd-0.2.1/examples/control_streams/02_warfarin_oral_focei.ctl +28 -0
  196. openpkpd-0.2.1/examples/control_streams/03_two_compartment_iv_fo.ctl +32 -0
  197. openpkpd-0.2.1/examples/control_streams/06_minimal_theophylline_focei.ctl +23 -0
  198. openpkpd-0.2.1/examples/control_streams/08_transit_absorption_advan6_fo.ctl +37 -0
  199. openpkpd-0.2.1/examples/control_streams/09_three_compartment_iv_advan11_focei.ctl +38 -0
  200. openpkpd-0.2.1/examples/control_streams/10_warfarin_pk_focei.ctl +64 -0
  201. openpkpd-0.2.1/examples/control_streams/11_two_compartment_iv_focei.ctl +77 -0
  202. openpkpd-0.2.1/examples/control_streams/12_phenobarbital_fo.ctl +70 -0
  203. openpkpd-0.2.1/examples/control_streams/13_covariates_one_cmt_focei.ctl +74 -0
  204. openpkpd-0.2.1/examples/control_streams/20_theophylline_oral_saem.ctl +28 -0
  205. openpkpd-0.2.1/examples/control_streams/23_same_omega_showcase.ctl +28 -0
  206. openpkpd-0.2.1/examples/control_streams/30_nmdata_input_drop_and_body_weight_scaling.ctl +58 -0
  207. openpkpd-0.2.1/examples/control_streams/31_nmdata_multiple_table_output_formats.ctl +63 -0
  208. openpkpd-0.2.1/examples/control_streams/32_nmdata_saem_age_covariate.ctl +78 -0
  209. openpkpd-0.2.1/examples/control_streams/33_nmdata_saem_age_covariate_block_omega.ctl +80 -0
  210. openpkpd-0.2.1/examples/control_streams/34_nmsim_two_compartment_block_omega_fo.ctl +56 -0
  211. openpkpd-0.2.1/examples/control_streams/35_nmsim_advan13_one_compartment_des.ctl +81 -0
  212. openpkpd-0.2.1/examples/control_streams/36_nmsim_saem_multi_covariate_age_weight_sex.ctl +82 -0
  213. openpkpd-0.2.1/examples/control_streams/README.md +64 -0
  214. openpkpd-0.2.1/examples/control_streams/same_omega.csv +145 -0
  215. openpkpd-0.2.1/examples/control_streams/theo.csv +145 -0
  216. openpkpd-0.2.1/examples/control_streams/theophylline.csv +145 -0
  217. openpkpd-0.2.1/examples/control_streams/theophylline_saem.csv +145 -0
  218. openpkpd-0.2.1/examples/control_streams/three_compartment_iv.csv +65 -0
  219. openpkpd-0.2.1/examples/control_streams/transit_absorption.csv +145 -0
  220. openpkpd-0.2.1/examples/control_streams/two_compartment_iv.csv +65 -0
  221. openpkpd-0.2.1/examples/control_streams/warfarin.csv +29 -0
  222. openpkpd-0.2.1/examples/data/README.md +33 -0
  223. openpkpd-0.2.1/examples/data/xgxr1.csv +120 -0
  224. openpkpd-0.2.1/examples/data/xgxr12.csv +120 -0
  225. openpkpd-0.2.1/examples/data/xgxr2.csv +120 -0
  226. openpkpd-0.2.1/examples/data/xgxr2covs.csv +120 -0
  227. openpkpd-0.2.1/examples/data/xgxr4.csv +120 -0
  228. openpkpd-0.2.1/examples/output/16_dde_model.png +0 -0
  229. openpkpd-0.2.1/examples/output/17_sbml_import.png +0 -0
  230. openpkpd-0.2.1/examples/shared_data/internal/same_omega.csv +145 -0
  231. openpkpd-0.2.1/examples/shared_data/internal/transit_absorption.csv +145 -0
  232. openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr1.csv +120 -0
  233. openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr12.csv +120 -0
  234. openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr2.csv +120 -0
  235. openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr2covs.csv +120 -0
  236. openpkpd-0.2.1/examples/shared_data/nmautoverse/xgxr4.csv +120 -0
  237. openpkpd-0.2.1/examples/shared_data/phenobarbital/phenobarbital_simulated.csv +349 -0
  238. openpkpd-0.2.1/examples/shared_data/pk_iv/three_compartment_iv.csv +65 -0
  239. openpkpd-0.2.1/examples/shared_data/pk_iv/two_compartment_iv.csv +65 -0
  240. openpkpd-0.2.1/examples/shared_data/theophylline/theo.csv +145 -0
  241. openpkpd-0.2.1/examples/shared_data/theophylline/theophylline.csv +145 -0
  242. openpkpd-0.2.1/examples/shared_data/theophylline/theophylline_saem.csv +145 -0
  243. openpkpd-0.2.1/examples/shared_data/warfarin/warfarin.csv +29 -0
  244. openpkpd-0.2.1/justfile +276 -0
  245. openpkpd-0.2.1/notebooks/00_index.py +97 -0
  246. openpkpd-0.2.1/notebooks/01_quickstart.py +363 -0
  247. openpkpd-0.2.1/notebooks/02_data_handling.py +339 -0
  248. openpkpd-0.2.1/notebooks/03_estimation_methods.py +433 -0
  249. openpkpd-0.2.1/notebooks/04_simulation_vpc_npde.py +410 -0
  250. openpkpd-0.2.1/notebooks/05_nca.py +446 -0
  251. openpkpd-0.2.1/notebooks/06_pk_subroutines.py +386 -0
  252. openpkpd-0.2.1/notebooks/07_pkpd_models.py +395 -0
  253. openpkpd-0.2.1/notebooks/08_diagnostics_plots.py +464 -0
  254. openpkpd-0.2.1/notebooks/09_covariate_modeling.py +424 -0
  255. openpkpd-0.2.1/notebooks/10_inference_bootstrap.py +341 -0
  256. openpkpd-0.2.1/notebooks/11_advanced.py +449 -0
  257. openpkpd-0.2.1/pyproject.toml +173 -0
  258. openpkpd-0.2.1/scripts/build_installer.py +300 -0
  259. openpkpd-0.2.1/scripts/bump_version.py +134 -0
  260. openpkpd-0.2.1/scripts/git-hooks/pre-commit +149 -0
  261. openpkpd-0.2.1/scripts/installer.spec +241 -0
  262. openpkpd-0.2.1/scripts/just/docs.py +35 -0
  263. openpkpd-0.2.1/scripts/just/examples.py +116 -0
  264. openpkpd-0.2.1/scripts/just/system.py +97 -0
  265. openpkpd-0.2.1/scripts/packaging/linux/AppDir/AppRun +23 -0
  266. openpkpd-0.2.1/scripts/packaging/linux/AppDir/openpkpd-gui.desktop +11 -0
  267. openpkpd-0.2.1/scripts/packaging/macos/dmgbuild_settings.py +32 -0
  268. openpkpd-0.2.1/scripts/packaging/macos/entitlements.plist +22 -0
  269. openpkpd-0.2.1/scripts/packaging/macos/make_icns.sh +31 -0
  270. openpkpd-0.2.1/scripts/packaging/windows/installer.nsi +76 -0
  271. openpkpd-0.2.1/scripts/prewarm_symbolic_cache.py +26 -0
  272. openpkpd-0.2.1/scripts/profile_analysis.py +284 -0
  273. openpkpd-0.2.1/scripts/profile_pipelines.py +549 -0
  274. openpkpd-0.2.1/src/openpkpd/__init__.py +83 -0
  275. openpkpd-0.2.1/src/openpkpd/api/__init__.py +0 -0
  276. openpkpd-0.2.1/src/openpkpd/api/model_builder.py +487 -0
  277. openpkpd-0.2.1/src/openpkpd/cli/__init__.py +0 -0
  278. openpkpd-0.2.1/src/openpkpd/cli/runner.py +414 -0
  279. openpkpd-0.2.1/src/openpkpd/covariance/__init__.py +0 -0
  280. openpkpd-0.2.1/src/openpkpd/covariance/result.py +7 -0
  281. openpkpd-0.2.1/src/openpkpd/covariance/sandwich.py +228 -0
  282. openpkpd-0.2.1/src/openpkpd/covariate/__init__.py +57 -0
  283. openpkpd-0.2.1/src/openpkpd/covariate/effects.py +232 -0
  284. openpkpd-0.2.1/src/openpkpd/covariate/scm.py +543 -0
  285. openpkpd-0.2.1/src/openpkpd/data/__init__.py +0 -0
  286. openpkpd-0.2.1/src/openpkpd/data/blq.py +245 -0
  287. openpkpd-0.2.1/src/openpkpd/data/columns.py +64 -0
  288. openpkpd-0.2.1/src/openpkpd/data/dataset.py +313 -0
  289. openpkpd-0.2.1/src/openpkpd/data/event_processor.py +324 -0
  290. openpkpd-0.2.1/src/openpkpd/data/impute.py +91 -0
  291. openpkpd-0.2.1/src/openpkpd/data/preprocessor.py +41 -0
  292. openpkpd-0.2.1/src/openpkpd/design/__init__.py +5 -0
  293. openpkpd-0.2.1/src/openpkpd/design/pfim.py +653 -0
  294. openpkpd-0.2.1/src/openpkpd/estimation/__init__.py +81 -0
  295. openpkpd-0.2.1/src/openpkpd/estimation/base.py +324 -0
  296. openpkpd-0.2.1/src/openpkpd/estimation/bayes.py +751 -0
  297. openpkpd-0.2.1/src/openpkpd/estimation/fo.py +233 -0
  298. openpkpd-0.2.1/src/openpkpd/estimation/foce.py +630 -0
  299. openpkpd-0.2.1/src/openpkpd/estimation/imp.py +281 -0
  300. openpkpd-0.2.1/src/openpkpd/estimation/jax_foce.py +251 -0
  301. openpkpd-0.2.1/src/openpkpd/estimation/laplacian.py +136 -0
  302. openpkpd-0.2.1/src/openpkpd/estimation/nonparametric.py +668 -0
  303. openpkpd-0.2.1/src/openpkpd/estimation/nuts.py +470 -0
  304. openpkpd-0.2.1/src/openpkpd/estimation/saem.py +450 -0
  305. openpkpd-0.2.1/src/openpkpd/examples/__init__.py +33 -0
  306. openpkpd-0.2.1/src/openpkpd/examples/catalog_loader.py +447 -0
  307. openpkpd-0.2.1/src/openpkpd/examples/catalog_models.py +106 -0
  308. openpkpd-0.2.1/src/openpkpd/examples/catalog_service.py +44 -0
  309. openpkpd-0.2.1/src/openpkpd/inference/__init__.py +17 -0
  310. openpkpd-0.2.1/src/openpkpd/inference/bootstrap.py +603 -0
  311. openpkpd-0.2.1/src/openpkpd/inference/model_comparison.py +207 -0
  312. openpkpd-0.2.1/src/openpkpd/io/__init__.py +19 -0
  313. openpkpd-0.2.1/src/openpkpd/io/sbml.py +411 -0
  314. openpkpd-0.2.1/src/openpkpd/library/__init__.py +52 -0
  315. openpkpd-0.2.1/src/openpkpd/library/models.py +828 -0
  316. openpkpd-0.2.1/src/openpkpd/math/__init__.py +0 -0
  317. openpkpd-0.2.1/src/openpkpd/math/autodiff.py +136 -0
  318. openpkpd-0.2.1/src/openpkpd/math/matrix.py +171 -0
  319. openpkpd-0.2.1/src/openpkpd/math/ode_solver.py +200 -0
  320. openpkpd-0.2.1/src/openpkpd/mixture/__init__.py +19 -0
  321. openpkpd-0.2.1/src/openpkpd/mixture/mixture.py +520 -0
  322. openpkpd-0.2.1/src/openpkpd/model/__init__.py +0 -0
  323. openpkpd-0.2.1/src/openpkpd/model/derivative_kernels.py +106 -0
  324. openpkpd-0.2.1/src/openpkpd/model/individual.py +1079 -0
  325. openpkpd-0.2.1/src/openpkpd/model/parameters.py +547 -0
  326. openpkpd-0.2.1/src/openpkpd/model/population.py +160 -0
  327. openpkpd-0.2.1/src/openpkpd/model/problem.py +207 -0
  328. openpkpd-0.2.1/src/openpkpd/model/residual_models.py +219 -0
  329. openpkpd-0.2.1/src/openpkpd/model/residuals.py +124 -0
  330. openpkpd-0.2.1/src/openpkpd/model/symbolic_eta.py +2267 -0
  331. openpkpd-0.2.1/src/openpkpd/models/__init__.py +120 -0
  332. openpkpd-0.2.1/src/openpkpd/models/categorical.py +612 -0
  333. openpkpd-0.2.1/src/openpkpd/models/count.py +589 -0
  334. openpkpd-0.2.1/src/openpkpd/models/ddi.py +274 -0
  335. openpkpd-0.2.1/src/openpkpd/models/markov.py +372 -0
  336. openpkpd-0.2.1/src/openpkpd/models/pkpd.py +800 -0
  337. openpkpd-0.2.1/src/openpkpd/models/population_pd.py +283 -0
  338. openpkpd-0.2.1/src/openpkpd/models/tmdd.py +309 -0
  339. openpkpd-0.2.1/src/openpkpd/models/tte.py +775 -0
  340. openpkpd-0.2.1/src/openpkpd/nca/__init__.py +26 -0
  341. openpkpd-0.2.1/src/openpkpd/nca/bioequivalence.py +408 -0
  342. openpkpd-0.2.1/src/openpkpd/nca/cdisc_pp.py +85 -0
  343. openpkpd-0.2.1/src/openpkpd/nca/crossover.py +380 -0
  344. openpkpd-0.2.1/src/openpkpd/nca/nca.py +1003 -0
  345. openpkpd-0.2.1/src/openpkpd/nca/sparse.py +209 -0
  346. openpkpd-0.2.1/src/openpkpd/nca/urine.py +160 -0
  347. openpkpd-0.2.1/src/openpkpd/output/__init__.py +25 -0
  348. openpkpd-0.2.1/src/openpkpd/output/cdisc_writer.py +244 -0
  349. openpkpd-0.2.1/src/openpkpd/output/cov_writer.py +64 -0
  350. openpkpd-0.2.1/src/openpkpd/output/ext_writer.py +112 -0
  351. openpkpd-0.2.1/src/openpkpd/output/lst_writer.py +145 -0
  352. openpkpd-0.2.1/src/openpkpd/output/mixture_writer.py +52 -0
  353. openpkpd-0.2.1/src/openpkpd/output/nonmem_reader.py +458 -0
  354. openpkpd-0.2.1/src/openpkpd/output/phi_writer.py +66 -0
  355. openpkpd-0.2.1/src/openpkpd/output/report.py +525 -0
  356. openpkpd-0.2.1/src/openpkpd/output/table_writer.py +117 -0
  357. openpkpd-0.2.1/src/openpkpd/parallel/__init__.py +417 -0
  358. openpkpd-0.2.1/src/openpkpd/parser/__init__.py +0 -0
  359. openpkpd-0.2.1/src/openpkpd/parser/code_compiler.py +629 -0
  360. openpkpd-0.2.1/src/openpkpd/parser/control_stream.py +281 -0
  361. openpkpd-0.2.1/src/openpkpd/parser/lexer.py +233 -0
  362. openpkpd-0.2.1/src/openpkpd/parser/records/__init__.py +0 -0
  363. openpkpd-0.2.1/src/openpkpd/parser/records/abbreviated.py +36 -0
  364. openpkpd-0.2.1/src/openpkpd/parser/records/base.py +32 -0
  365. openpkpd-0.2.1/src/openpkpd/parser/records/contr.py +14 -0
  366. openpkpd-0.2.1/src/openpkpd/parser/records/covariance.py +42 -0
  367. openpkpd-0.2.1/src/openpkpd/parser/records/data.py +72 -0
  368. openpkpd-0.2.1/src/openpkpd/parser/records/des.py +19 -0
  369. openpkpd-0.2.1/src/openpkpd/parser/records/design.py +19 -0
  370. openpkpd-0.2.1/src/openpkpd/parser/records/error.py +19 -0
  371. openpkpd-0.2.1/src/openpkpd/parser/records/estimation.py +153 -0
  372. openpkpd-0.2.1/src/openpkpd/parser/records/input.py +66 -0
  373. openpkpd-0.2.1/src/openpkpd/parser/records/mixture.py +31 -0
  374. openpkpd-0.2.1/src/openpkpd/parser/records/nonparametric.py +28 -0
  375. openpkpd-0.2.1/src/openpkpd/parser/records/omega.py +122 -0
  376. openpkpd-0.2.1/src/openpkpd/parser/records/pk.py +19 -0
  377. openpkpd-0.2.1/src/openpkpd/parser/records/pred.py +19 -0
  378. openpkpd-0.2.1/src/openpkpd/parser/records/prior.py +93 -0
  379. openpkpd-0.2.1/src/openpkpd/parser/records/problem.py +21 -0
  380. openpkpd-0.2.1/src/openpkpd/parser/records/sigma.py +46 -0
  381. openpkpd-0.2.1/src/openpkpd/parser/records/simulation.py +50 -0
  382. openpkpd-0.2.1/src/openpkpd/parser/records/sizes.py +29 -0
  383. openpkpd-0.2.1/src/openpkpd/parser/records/subroutines.py +60 -0
  384. openpkpd-0.2.1/src/openpkpd/parser/records/table.py +83 -0
  385. openpkpd-0.2.1/src/openpkpd/parser/records/theta.py +169 -0
  386. openpkpd-0.2.1/src/openpkpd/pk/__init__.py +92 -0
  387. openpkpd-0.2.1/src/openpkpd/pk/absorption/__init__.py +7 -0
  388. openpkpd-0.2.1/src/openpkpd/pk/absorption/ehc.py +210 -0
  389. openpkpd-0.2.1/src/openpkpd/pk/absorption/parallel.py +118 -0
  390. openpkpd-0.2.1/src/openpkpd/pk/absorption/transit.py +173 -0
  391. openpkpd-0.2.1/src/openpkpd/pk/analytical/__init__.py +12 -0
  392. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan1.py +81 -0
  393. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan11.py +355 -0
  394. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan12.py +390 -0
  395. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan2.py +254 -0
  396. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan3.py +229 -0
  397. openpkpd-0.2.1/src/openpkpd/pk/analytical/advan4.py +197 -0
  398. openpkpd-0.2.1/src/openpkpd/pk/base.py +99 -0
  399. openpkpd-0.2.1/src/openpkpd/pk/delay/__init__.py +0 -0
  400. openpkpd-0.2.1/src/openpkpd/pk/linear/__init__.py +0 -0
  401. openpkpd-0.2.1/src/openpkpd/pk/ode/__init__.py +11 -0
  402. openpkpd-0.2.1/src/openpkpd/pk/ode/advan10.py +275 -0
  403. openpkpd-0.2.1/src/openpkpd/pk/ode/advan13.py +388 -0
  404. openpkpd-0.2.1/src/openpkpd/pk/ode/advan6.py +437 -0
  405. openpkpd-0.2.1/src/openpkpd/pk/ode/advan8.py +55 -0
  406. openpkpd-0.2.1/src/openpkpd/pk/ode/dde.py +345 -0
  407. openpkpd-0.2.1/src/openpkpd/pk/pbpk/__init__.py +150 -0
  408. openpkpd-0.2.1/src/openpkpd/pk/trans/__init__.py +45 -0
  409. openpkpd-0.2.1/src/openpkpd/pk/trans/trans1.py +18 -0
  410. openpkpd-0.2.1/src/openpkpd/pk/trans/trans2.py +29 -0
  411. openpkpd-0.2.1/src/openpkpd/pk/trans/trans3.py +56 -0
  412. openpkpd-0.2.1/src/openpkpd/pk/trans/trans4.py +71 -0
  413. openpkpd-0.2.1/src/openpkpd/pk/trans/trans5.py +13 -0
  414. openpkpd-0.2.1/src/openpkpd/pk/trans/trans6.py +38 -0
  415. openpkpd-0.2.1/src/openpkpd/plots/__init__.py +146 -0
  416. openpkpd-0.2.1/src/openpkpd/plots/_core.py +92 -0
  417. openpkpd-0.2.1/src/openpkpd/plots/bayesian.py +232 -0
  418. openpkpd-0.2.1/src/openpkpd/plots/bootstrap.py +192 -0
  419. openpkpd-0.2.1/src/openpkpd/plots/categorical.py +280 -0
  420. openpkpd-0.2.1/src/openpkpd/plots/covariate.py +142 -0
  421. openpkpd-0.2.1/src/openpkpd/plots/diagnostics.py +309 -0
  422. openpkpd-0.2.1/src/openpkpd/plots/eta.py +375 -0
  423. openpkpd-0.2.1/src/openpkpd/plots/gof.py +231 -0
  424. openpkpd-0.2.1/src/openpkpd/plots/model_perf.py +739 -0
  425. openpkpd-0.2.1/src/openpkpd/plots/nca.py +380 -0
  426. openpkpd-0.2.1/src/openpkpd/plots/pd.py +377 -0
  427. openpkpd-0.2.1/src/openpkpd/plots/pk.py +260 -0
  428. openpkpd-0.2.1/src/openpkpd/plots/simulation.py +819 -0
  429. openpkpd-0.2.1/src/openpkpd/prior/__init__.py +27 -0
  430. openpkpd-0.2.1/src/openpkpd/prior/prior.py +507 -0
  431. openpkpd-0.2.1/src/openpkpd/r_bridge/__init__.py +322 -0
  432. openpkpd-0.2.1/src/openpkpd/simulation/__init__.py +22 -0
  433. openpkpd-0.2.1/src/openpkpd/simulation/engine.py +664 -0
  434. openpkpd-0.2.1/src/openpkpd/simulation/npc.py +224 -0
  435. openpkpd-0.2.1/src/openpkpd/simulation/npde.py +387 -0
  436. openpkpd-0.2.1/src/openpkpd/simulation/sse.py +273 -0
  437. openpkpd-0.2.1/src/openpkpd/simulation/vpc.py +536 -0
  438. openpkpd-0.2.1/src/openpkpd/utils/__init__.py +0 -0
  439. openpkpd-0.2.1/src/openpkpd/utils/constants.py +133 -0
  440. openpkpd-0.2.1/src/openpkpd/utils/errors.py +65 -0
  441. openpkpd-0.2.1/src/openpkpd/utils/logging.py +42 -0
  442. openpkpd-0.2.1/src/openpkpd_gui/__init__.py +1 -0
  443. openpkpd-0.2.1/src/openpkpd_gui/app/__init__.py +1 -0
  444. openpkpd-0.2.1/src/openpkpd_gui/app/runtime.py +37 -0
  445. openpkpd-0.2.1/src/openpkpd_gui/app/settings.py +564 -0
  446. openpkpd-0.2.1/src/openpkpd_gui/app/theme.py +443 -0
  447. openpkpd-0.2.1/src/openpkpd_gui/domain/__init__.py +20 -0
  448. openpkpd-0.2.1/src/openpkpd_gui/domain/artifact.py +48 -0
  449. openpkpd-0.2.1/src/openpkpd_gui/domain/dataset_asset.py +66 -0
  450. openpkpd-0.2.1/src/openpkpd_gui/domain/model_spec.py +140 -0
  451. openpkpd-0.2.1/src/openpkpd_gui/domain/run_record.py +98 -0
  452. openpkpd-0.2.1/src/openpkpd_gui/domain/workspace.py +377 -0
  453. openpkpd-0.2.1/src/openpkpd_gui/help/__init__.py +1 -0
  454. openpkpd-0.2.1/src/openpkpd_gui/help/gui.md +562 -0
  455. openpkpd-0.2.1/src/openpkpd_gui/jobs/__init__.py +1 -0
  456. openpkpd-0.2.1/src/openpkpd_gui/jobs/base.py +89 -0
  457. openpkpd-0.2.1/src/openpkpd_gui/jobs/runner.py +86 -0
  458. openpkpd-0.2.1/src/openpkpd_gui/resources/__init__.py +0 -0
  459. openpkpd-0.2.1/src/openpkpd_gui/resources/icon.icns +0 -0
  460. openpkpd-0.2.1/src/openpkpd_gui/resources/icon.ico +0 -0
  461. openpkpd-0.2.1/src/openpkpd_gui/resources/icon.png +0 -0
  462. openpkpd-0.2.1/src/openpkpd_gui/services/__init__.py +17 -0
  463. openpkpd-0.2.1/src/openpkpd_gui/services/artifact_service.py +26 -0
  464. openpkpd-0.2.1/src/openpkpd_gui/services/bootstrap_service.py +275 -0
  465. openpkpd-0.2.1/src/openpkpd_gui/services/data_service.py +297 -0
  466. openpkpd-0.2.1/src/openpkpd_gui/services/design_service.py +375 -0
  467. openpkpd-0.2.1/src/openpkpd_gui/services/fit_service.py +1279 -0
  468. openpkpd-0.2.1/src/openpkpd_gui/services/model_translation_service.py +302 -0
  469. openpkpd-0.2.1/src/openpkpd_gui/services/nca_service.py +288 -0
  470. openpkpd-0.2.1/src/openpkpd_gui/services/npde_service.py +203 -0
  471. openpkpd-0.2.1/src/openpkpd_gui/services/project_service.py +570 -0
  472. openpkpd-0.2.1/src/openpkpd_gui/services/report_export_service.py +95 -0
  473. openpkpd-0.2.1/src/openpkpd_gui/services/scm_service.py +235 -0
  474. openpkpd-0.2.1/src/openpkpd_gui/services/serialization_service.py +758 -0
  475. openpkpd-0.2.1/src/openpkpd_gui/services/validation_service.py +71 -0
  476. openpkpd-0.2.1/src/openpkpd_gui/services/vpc_service.py +286 -0
  477. openpkpd-0.2.1/src/openpkpd_gui/services/workflow_state_service.py +506 -0
  478. openpkpd-0.2.1/src/openpkpd_gui/shell/__init__.py +1 -0
  479. openpkpd-0.2.1/src/openpkpd_gui/shell/help_browser.py +311 -0
  480. openpkpd-0.2.1/src/openpkpd_gui/shell/main_window.py +3153 -0
  481. openpkpd-0.2.1/src/openpkpd_gui/widgets/__init__.py +1 -0
  482. openpkpd-0.2.1/src/openpkpd_gui/widgets/collapsible_section.py +62 -0
  483. openpkpd-0.2.1/src/openpkpd_gui/widgets/combined_header.py +76 -0
  484. openpkpd-0.2.1/src/openpkpd_gui/widgets/context_header.py +81 -0
  485. openpkpd-0.2.1/src/openpkpd_gui/widgets/dismissible_hint.py +53 -0
  486. openpkpd-0.2.1/src/openpkpd_gui/widgets/link_formatting.py +64 -0
  487. openpkpd-0.2.1/src/openpkpd_gui/widgets/output_browser.py +282 -0
  488. openpkpd-0.2.1/src/openpkpd_gui/widgets/overview_readiness_card.py +67 -0
  489. openpkpd-0.2.1/src/openpkpd_gui/widgets/responsive_layout.py +78 -0
  490. openpkpd-0.2.1/src/openpkpd_gui/widgets/scrollable_page.py +26 -0
  491. openpkpd-0.2.1/src/openpkpd_gui/widgets/semantic_state.py +133 -0
  492. openpkpd-0.2.1/src/openpkpd_gui/widgets/table_headers.py +14 -0
  493. openpkpd-0.2.1/src/openpkpd_gui/widgets/workflow_shortcut_section.py +161 -0
  494. openpkpd-0.2.1/src/openpkpd_gui/widgets/workflow_status_strip.py +48 -0
  495. openpkpd-0.2.1/src/openpkpd_gui/workflows/__init__.py +1 -0
  496. openpkpd-0.2.1/src/openpkpd_gui/workflows/advanced_workflow.py +1598 -0
  497. openpkpd-0.2.1/src/openpkpd_gui/workflows/covariate_workflow.py +627 -0
  498. openpkpd-0.2.1/src/openpkpd_gui/workflows/dashboard_workflow.py +135 -0
  499. openpkpd-0.2.1/src/openpkpd_gui/workflows/data_workflow.py +753 -0
  500. openpkpd-0.2.1/src/openpkpd_gui/workflows/diagnostics_workflow.py +797 -0
  501. openpkpd-0.2.1/src/openpkpd_gui/workflows/fit_workflow.py +573 -0
  502. openpkpd-0.2.1/src/openpkpd_gui/workflows/home_workflow.py +193 -0
  503. openpkpd-0.2.1/src/openpkpd_gui/workflows/model_workflow.py +1537 -0
  504. openpkpd-0.2.1/src/openpkpd_gui/workflows/nca_workflow.py +527 -0
  505. openpkpd-0.2.1/src/openpkpd_gui/workflows/overview_workflow.py +617 -0
  506. openpkpd-0.2.1/src/openpkpd_gui/workflows/plots_workflow.py +494 -0
  507. openpkpd-0.2.1/src/openpkpd_gui/workflows/registry.py +49 -0
  508. openpkpd-0.2.1/src/openpkpd_gui/workflows/results_workflow.py +1238 -0
  509. openpkpd-0.2.1/tests/__init__.py +0 -0
  510. openpkpd-0.2.1/tests/conftest.py +120 -0
  511. openpkpd-0.2.1/tests/external_validation/data/indometh.csv +67 -0
  512. openpkpd-0.2.1/tests/external_validation/data/phenobarbital_simulated.csv +349 -0
  513. openpkpd-0.2.1/tests/external_validation/data/theophylline_boeckmann.csv +145 -0
  514. openpkpd-0.2.1/tests/external_validation/data/warfarin_pk.csv +284 -0
  515. openpkpd-0.2.1/tests/external_validation/data/warfarin_pkpd.csv +516 -0
  516. openpkpd-0.2.1/tests/external_validation/data/warfarin_pkpd_4.csv +72 -0
  517. openpkpd-0.2.1/tests/external_validation/data/warfarin_pkpd_6.csv +108 -0
  518. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/theophylline_fo.json +29 -0
  519. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/theophylline_foce.json +29 -0
  520. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pk_fo.json +29 -0
  521. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pk_foce.json +29 -0
  522. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pkpd_4_fo.json +34 -0
  523. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pkpd_6_fo.json +34 -0
  524. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pkpd_fo.json +43 -0
  525. openpkpd-0.2.1/tests/external_validation/nlmixr2/reference/warfarin_pkpd_foce.json +43 -0
  526. openpkpd-0.2.1/tests/external_validation/nlmixr2/run_theophylline.R +171 -0
  527. openpkpd-0.2.1/tests/external_validation/nlmixr2/run_warfarin.R +120 -0
  528. openpkpd-0.2.1/tests/external_validation/nlmixr2/run_warfarin_pkpd.R +244 -0
  529. openpkpd-0.2.1/tests/external_validation/reference/grasela1985_phenobarbital_fo.json +47 -0
  530. openpkpd-0.2.1/tests/external_validation/reference/monolix_theophylline_saem.json +28 -0
  531. openpkpd-0.2.1/tests/external_validation/reference/nonmem_402_focei.json +76 -0
  532. openpkpd-0.2.1/tests/external_validation/reference/nonmem_504_focei.json +86 -0
  533. openpkpd-0.2.1/tests/external_validation/reference/nonmem_504f_focei.json +46 -0
  534. openpkpd-0.2.1/tests/external_validation/reference/pknca_theophylline_summary.json +46 -0
  535. openpkpd-0.2.1/tests/external_validation/reference/winnonlin_indometh_nca.json +695 -0
  536. openpkpd-0.2.1/tests/external_validation/test_advanced_estimators_reference.py +119 -0
  537. openpkpd-0.2.1/tests/external_validation/test_bioequivalence_reference.py +497 -0
  538. openpkpd-0.2.1/tests/external_validation/test_covariance_reference.py +276 -0
  539. openpkpd-0.2.1/tests/external_validation/test_covariate_effects_reference.py +460 -0
  540. openpkpd-0.2.1/tests/external_validation/test_cross_method_consistency.py +186 -0
  541. openpkpd-0.2.1/tests/external_validation/test_diagnostics_reference.py +238 -0
  542. openpkpd-0.2.1/tests/external_validation/test_estimation_reference.py +366 -0
  543. openpkpd-0.2.1/tests/external_validation/test_extended_models_reference.py +495 -0
  544. openpkpd-0.2.1/tests/external_validation/test_inference_reference.py +392 -0
  545. openpkpd-0.2.1/tests/external_validation/test_nca_reference.py +328 -0
  546. openpkpd-0.2.1/tests/external_validation/test_phenobarbital.py +154 -0
  547. openpkpd-0.2.1/tests/external_validation/test_pk_subroutines_reference.py +345 -0
  548. openpkpd-0.2.1/tests/external_validation/test_saem_reference.py +211 -0
  549. openpkpd-0.2.1/tests/external_validation/test_vs_monolix.py +86 -0
  550. openpkpd-0.2.1/tests/external_validation/test_vs_nlmixr2.py +935 -0
  551. openpkpd-0.2.1/tests/external_validation/test_vs_nonmem.py +249 -0
  552. openpkpd-0.2.1/tests/external_validation/test_vs_pharmpy.py +418 -0
  553. openpkpd-0.2.1/tests/external_validation/test_vs_pknca.py +105 -0
  554. openpkpd-0.2.1/tests/external_validation/test_vs_winnonlin_indometh.py +134 -0
  555. openpkpd-0.2.1/tests/fixtures/control_streams/theophylline.ctl +36 -0
  556. openpkpd-0.2.1/tests/integration/__init__.py +0 -0
  557. openpkpd-0.2.1/tests/integration/test_blq_pipeline.py +221 -0
  558. openpkpd-0.2.1/tests/integration/test_control_stream_mixture.py +200 -0
  559. openpkpd-0.2.1/tests/integration/test_control_stream_simulation.py +217 -0
  560. openpkpd-0.2.1/tests/integration/test_emax_pd.py +308 -0
  561. openpkpd-0.2.1/tests/integration/test_multi_endpoint_routing.py +145 -0
  562. openpkpd-0.2.1/tests/integration/test_new_design_simulation.py +312 -0
  563. openpkpd-0.2.1/tests/integration/test_notebooks.py +139 -0
  564. openpkpd-0.2.1/tests/integration/test_pk_integration.py +162 -0
  565. openpkpd-0.2.1/tests/integration/test_theophylline.py +151 -0
  566. openpkpd-0.2.1/tests/integration/test_two_compartment.py +287 -0
  567. openpkpd-0.2.1/tests/integration/test_vpc_pipeline.py +285 -0
  568. openpkpd-0.2.1/tests/integration/test_warfarin.py +211 -0
  569. openpkpd-0.2.1/tests/regression/__init__.py +0 -0
  570. openpkpd-0.2.1/tests/regression/diagnostic_helpers.py +191 -0
  571. openpkpd-0.2.1/tests/regression/generate_reference.py +734 -0
  572. openpkpd-0.2.1/tests/regression/pd_model_helpers.py +606 -0
  573. openpkpd-0.2.1/tests/regression/reference_runs/README.md +20 -0
  574. openpkpd-0.2.1/tests/regression/reference_runs/diagnostic_nca.json +27 -0
  575. openpkpd-0.2.1/tests/regression/reference_runs/diagnostic_npc.json +49 -0
  576. openpkpd-0.2.1/tests/regression/reference_runs/diagnostic_npde.json +26 -0
  577. openpkpd-0.2.1/tests/regression/reference_runs/diagnostic_sse.json +60 -0
  578. openpkpd-0.2.1/tests/regression/reference_runs/diagnostic_vpc.json +50 -0
  579. openpkpd-0.2.1/tests/regression/reference_runs/effect_compartment_pd.json +85 -0
  580. openpkpd-0.2.1/tests/regression/reference_runs/emax_direct_pd.json +57 -0
  581. openpkpd-0.2.1/tests/regression/reference_runs/hill_direct_pd.json +60 -0
  582. openpkpd-0.2.1/tests/regression/reference_runs/indirect_response_pd.json +85 -0
  583. openpkpd-0.2.1/tests/regression/reference_runs/joint_emax_pkpd.json +201 -0
  584. openpkpd-0.2.1/tests/regression/reference_runs/placebo_response_pd.json +56 -0
  585. openpkpd-0.2.1/tests/regression/reference_runs/population_emax_pd.json +48 -0
  586. openpkpd-0.2.1/tests/regression/reference_runs/sequential_emax_from_pk_pd.json +40 -0
  587. openpkpd-0.2.1/tests/regression/reference_runs/sequential_emax_pd.json +57 -0
  588. openpkpd-0.2.1/tests/regression/reference_runs/sequential_multi_subject_from_pk_pd.json +93 -0
  589. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_bayes_laplace.json +35 -0
  590. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_foce.json +24 -0
  591. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_imp.json +24 -0
  592. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_laplacian.json +24 -0
  593. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_nonparametric.json +44 -0
  594. openpkpd-0.2.1/tests/regression/reference_runs/theophylline_saem.json +24 -0
  595. openpkpd-0.2.1/tests/regression/reference_runs/tumor_growth_inhibition_pd.json +51 -0
  596. openpkpd-0.2.1/tests/regression/reference_runs/turnover_pd.json +91 -0
  597. openpkpd-0.2.1/tests/regression/test_cross_method_validation.py +259 -0
  598. openpkpd-0.2.1/tests/regression/test_diagnostics_regression.py +184 -0
  599. openpkpd-0.2.1/tests/regression/test_pd_models_regression.py +468 -0
  600. openpkpd-0.2.1/tests/regression/test_pkpd_models_regression.py +108 -0
  601. openpkpd-0.2.1/tests/regression/test_regression.py +530 -0
  602. openpkpd-0.2.1/tests/unit/__init__.py +0 -0
  603. openpkpd-0.2.1/tests/unit/covariance/__init__.py +1 -0
  604. openpkpd-0.2.1/tests/unit/covariance/test_sandwich.py +175 -0
  605. openpkpd-0.2.1/tests/unit/covariate/__init__.py +0 -0
  606. openpkpd-0.2.1/tests/unit/covariate/test_scm.py +620 -0
  607. openpkpd-0.2.1/tests/unit/data/__init__.py +0 -0
  608. openpkpd-0.2.1/tests/unit/data/test_blq.py +319 -0
  609. openpkpd-0.2.1/tests/unit/data/test_dataset.py +97 -0
  610. openpkpd-0.2.1/tests/unit/data/test_event_processor.py +134 -0
  611. openpkpd-0.2.1/tests/unit/data/test_impute.py +243 -0
  612. openpkpd-0.2.1/tests/unit/data/test_preprocessor.py +68 -0
  613. openpkpd-0.2.1/tests/unit/data/test_time_varying_covariates.py +246 -0
  614. openpkpd-0.2.1/tests/unit/design/__init__.py +0 -0
  615. openpkpd-0.2.1/tests/unit/design/test_pfim.py +485 -0
  616. openpkpd-0.2.1/tests/unit/design/test_pfim_wiring.py +132 -0
  617. openpkpd-0.2.1/tests/unit/estimation/__init__.py +0 -0
  618. openpkpd-0.2.1/tests/unit/estimation/test_bayes.py +303 -0
  619. openpkpd-0.2.1/tests/unit/estimation/test_estimation_base.py +418 -0
  620. openpkpd-0.2.1/tests/unit/estimation/test_fo.py +173 -0
  621. openpkpd-0.2.1/tests/unit/estimation/test_foce.py +449 -0
  622. openpkpd-0.2.1/tests/unit/estimation/test_imp.py +179 -0
  623. openpkpd-0.2.1/tests/unit/estimation/test_jax_foce.py +173 -0
  624. openpkpd-0.2.1/tests/unit/estimation/test_laplacian.py +252 -0
  625. openpkpd-0.2.1/tests/unit/estimation/test_laplacian_prior.py +215 -0
  626. openpkpd-0.2.1/tests/unit/estimation/test_n_parallel.py +420 -0
  627. openpkpd-0.2.1/tests/unit/estimation/test_nonparametric.py +369 -0
  628. openpkpd-0.2.1/tests/unit/estimation/test_npem.py +204 -0
  629. openpkpd-0.2.1/tests/unit/estimation/test_nuts.py +207 -0
  630. openpkpd-0.2.1/tests/unit/estimation/test_parameters.py +249 -0
  631. openpkpd-0.2.1/tests/unit/estimation/test_saem.py +461 -0
  632. openpkpd-0.2.1/tests/unit/estimation/test_shrinkage.py +92 -0
  633. openpkpd-0.2.1/tests/unit/examples/__init__.py +1 -0
  634. openpkpd-0.2.1/tests/unit/examples/test_catalog_loader.py +292 -0
  635. openpkpd-0.2.1/tests/unit/gui/test_advanced_workflow.py +815 -0
  636. openpkpd-0.2.1/tests/unit/gui/test_app_settings.py +967 -0
  637. openpkpd-0.2.1/tests/unit/gui/test_bootstrap_service.py +169 -0
  638. openpkpd-0.2.1/tests/unit/gui/test_covariate_workflow.py +577 -0
  639. openpkpd-0.2.1/tests/unit/gui/test_data_service.py +217 -0
  640. openpkpd-0.2.1/tests/unit/gui/test_data_workflow.py +515 -0
  641. openpkpd-0.2.1/tests/unit/gui/test_design_service.py +173 -0
  642. openpkpd-0.2.1/tests/unit/gui/test_diagnostics_workflow.py +443 -0
  643. openpkpd-0.2.1/tests/unit/gui/test_domain_models.py +487 -0
  644. openpkpd-0.2.1/tests/unit/gui/test_fit_service.py +447 -0
  645. openpkpd-0.2.1/tests/unit/gui/test_fit_workflow.py +417 -0
  646. openpkpd-0.2.1/tests/unit/gui/test_help_browser.py +339 -0
  647. openpkpd-0.2.1/tests/unit/gui/test_home_workflow.py +116 -0
  648. openpkpd-0.2.1/tests/unit/gui/test_jobs.py +97 -0
  649. openpkpd-0.2.1/tests/unit/gui/test_link_formatting.py +33 -0
  650. openpkpd-0.2.1/tests/unit/gui/test_model_translation_service.py +120 -0
  651. openpkpd-0.2.1/tests/unit/gui/test_model_workflow.py +753 -0
  652. openpkpd-0.2.1/tests/unit/gui/test_nca_service.py +95 -0
  653. openpkpd-0.2.1/tests/unit/gui/test_nca_workflow.py +229 -0
  654. openpkpd-0.2.1/tests/unit/gui/test_npde_service.py +108 -0
  655. openpkpd-0.2.1/tests/unit/gui/test_report_export_service.py +88 -0
  656. openpkpd-0.2.1/tests/unit/gui/test_results_workflow.py +326 -0
  657. openpkpd-0.2.1/tests/unit/gui/test_runtime.py +15 -0
  658. openpkpd-0.2.1/tests/unit/gui/test_serialization_service.py +665 -0
  659. openpkpd-0.2.1/tests/unit/gui/test_settings.py +365 -0
  660. openpkpd-0.2.1/tests/unit/gui/test_shell_smoke.py +4732 -0
  661. openpkpd-0.2.1/tests/unit/gui/test_vpc_service.py +147 -0
  662. openpkpd-0.2.1/tests/unit/inference/__init__.py +0 -0
  663. openpkpd-0.2.1/tests/unit/inference/test_bootstrap.py +411 -0
  664. openpkpd-0.2.1/tests/unit/inference/test_bootstrap_bca.py +247 -0
  665. openpkpd-0.2.1/tests/unit/inference/test_model_comparison.py +305 -0
  666. openpkpd-0.2.1/tests/unit/io/__init__.py +0 -0
  667. openpkpd-0.2.1/tests/unit/io/test_sbml.py +467 -0
  668. openpkpd-0.2.1/tests/unit/library/__init__.py +1 -0
  669. openpkpd-0.2.1/tests/unit/library/test_models.py +297 -0
  670. openpkpd-0.2.1/tests/unit/math/__init__.py +0 -0
  671. openpkpd-0.2.1/tests/unit/math/test_autodiff.py +60 -0
  672. openpkpd-0.2.1/tests/unit/math/test_matrix.py +101 -0
  673. openpkpd-0.2.1/tests/unit/math/test_ode_solver.py +88 -0
  674. openpkpd-0.2.1/tests/unit/mixture/__init__.py +0 -0
  675. openpkpd-0.2.1/tests/unit/mixture/test_mixture.py +446 -0
  676. openpkpd-0.2.1/tests/unit/model/__init__.py +0 -0
  677. openpkpd-0.2.1/tests/unit/model/test_individual_population.py +1664 -0
  678. openpkpd-0.2.1/tests/unit/model/test_model_builder_fit.py +62 -0
  679. openpkpd-0.2.1/tests/unit/model/test_residual_models.py +131 -0
  680. openpkpd-0.2.1/tests/unit/model/test_residuals.py +120 -0
  681. openpkpd-0.2.1/tests/unit/model/test_symbolic_eta.py +456 -0
  682. openpkpd-0.2.1/tests/unit/models/__init__.py +0 -0
  683. openpkpd-0.2.1/tests/unit/models/test_categorical.py +461 -0
  684. openpkpd-0.2.1/tests/unit/models/test_count.py +534 -0
  685. openpkpd-0.2.1/tests/unit/models/test_ddi.py +206 -0
  686. openpkpd-0.2.1/tests/unit/models/test_markov.py +385 -0
  687. openpkpd-0.2.1/tests/unit/models/test_pkpd.py +339 -0
  688. openpkpd-0.2.1/tests/unit/models/test_population_pd.py +182 -0
  689. openpkpd-0.2.1/tests/unit/models/test_sequential.py +262 -0
  690. openpkpd-0.2.1/tests/unit/models/test_tmdd.py +202 -0
  691. openpkpd-0.2.1/tests/unit/models/test_tte.py +734 -0
  692. openpkpd-0.2.1/tests/unit/nca/__init__.py +0 -0
  693. openpkpd-0.2.1/tests/unit/nca/test_cdisc_pp.py +113 -0
  694. openpkpd-0.2.1/tests/unit/nca/test_crossover.py +177 -0
  695. openpkpd-0.2.1/tests/unit/nca/test_multidose_nca.py +164 -0
  696. openpkpd-0.2.1/tests/unit/nca/test_nca.py +724 -0
  697. openpkpd-0.2.1/tests/unit/nca/test_rsabe.py +121 -0
  698. openpkpd-0.2.1/tests/unit/nca/test_sparse_nca.py +140 -0
  699. openpkpd-0.2.1/tests/unit/nca/test_urine_nca.py +136 -0
  700. openpkpd-0.2.1/tests/unit/output/__init__.py +0 -0
  701. openpkpd-0.2.1/tests/unit/output/test_cdisc_writer.py +288 -0
  702. openpkpd-0.2.1/tests/unit/output/test_nonmem_reader.py +294 -0
  703. openpkpd-0.2.1/tests/unit/output/test_output_writers.py +1002 -0
  704. openpkpd-0.2.1/tests/unit/output/test_report.py +106 -0
  705. openpkpd-0.2.1/tests/unit/parallel/__init__.py +0 -0
  706. openpkpd-0.2.1/tests/unit/parallel/test_parallel.py +242 -0
  707. openpkpd-0.2.1/tests/unit/parser/__init__.py +0 -0
  708. openpkpd-0.2.1/tests/unit/parser/test_code_compiler.py +195 -0
  709. openpkpd-0.2.1/tests/unit/parser/test_complex_records.py +171 -0
  710. openpkpd-0.2.1/tests/unit/parser/test_control_stream.py +172 -0
  711. openpkpd-0.2.1/tests/unit/parser/test_example_control_stream_library.py +90 -0
  712. openpkpd-0.2.1/tests/unit/parser/test_lexer.py +84 -0
  713. openpkpd-0.2.1/tests/unit/parser/test_records.py +145 -0
  714. openpkpd-0.2.1/tests/unit/pk/__init__.py +0 -0
  715. openpkpd-0.2.1/tests/unit/pk/test_absorption.py +411 -0
  716. openpkpd-0.2.1/tests/unit/pk/test_advan.py +211 -0
  717. openpkpd-0.2.1/tests/unit/pk/test_advan11.py +376 -0
  718. openpkpd-0.2.1/tests/unit/pk/test_advan12.py +338 -0
  719. openpkpd-0.2.1/tests/unit/pk/test_advan13_sensitivity.py +390 -0
  720. openpkpd-0.2.1/tests/unit/pk/test_advan3.py +145 -0
  721. openpkpd-0.2.1/tests/unit/pk/test_advan4.py +134 -0
  722. openpkpd-0.2.1/tests/unit/pk/test_dde.py +259 -0
  723. openpkpd-0.2.1/tests/unit/pk/test_ode_advan6.py +582 -0
  724. openpkpd-0.2.1/tests/unit/pk/test_ode_vs_analytical.py +120 -0
  725. openpkpd-0.2.1/tests/unit/pk/test_pbpk.py +126 -0
  726. openpkpd-0.2.1/tests/unit/pk/test_transforms.py +182 -0
  727. openpkpd-0.2.1/tests/unit/plots/__init__.py +0 -0
  728. openpkpd-0.2.1/tests/unit/plots/conftest.py +14 -0
  729. openpkpd-0.2.1/tests/unit/plots/test_diagnostics.py +263 -0
  730. openpkpd-0.2.1/tests/unit/plots/test_nca_plots.py +57 -0
  731. openpkpd-0.2.1/tests/unit/plots/test_plots.py +1150 -0
  732. openpkpd-0.2.1/tests/unit/plots/test_simulation_plots.py +684 -0
  733. openpkpd-0.2.1/tests/unit/prior/__init__.py +0 -0
  734. openpkpd-0.2.1/tests/unit/prior/test_control_stream_prior.py +88 -0
  735. openpkpd-0.2.1/tests/unit/prior/test_prior.py +429 -0
  736. openpkpd-0.2.1/tests/unit/r_bridge/__init__.py +0 -0
  737. openpkpd-0.2.1/tests/unit/r_bridge/test_r_bridge.py +150 -0
  738. openpkpd-0.2.1/tests/unit/simulation/__init__.py +0 -0
  739. openpkpd-0.2.1/tests/unit/simulation/test_engine.py +1028 -0
  740. openpkpd-0.2.1/tests/unit/simulation/test_npc.py +188 -0
  741. openpkpd-0.2.1/tests/unit/simulation/test_npde.py +439 -0
  742. openpkpd-0.2.1/tests/unit/simulation/test_pcvpc.py +218 -0
  743. openpkpd-0.2.1/tests/unit/simulation/test_sse.py +250 -0
  744. openpkpd-0.2.1/tests/unit/test_profile_analysis.py +115 -0
  745. openpkpd-0.2.1/tests/unit/validation/__init__.py +0 -0
  746. openpkpd-0.2.1/tests/unit/validation/test_numerical_accuracy.py +1348 -0
@@ -0,0 +1,597 @@
1
+ ### Project-specific generated files ###
2
+ .history/
3
+ temp/
4
+ manuscript/
5
+
6
+ ### env ###
7
+ .envrc
8
+
9
+ ### C ###
10
+ # Prerequisites
11
+ *.d
12
+
13
+ # Object files
14
+ *.o
15
+ *.ko
16
+ *.obj
17
+ *.elf
18
+
19
+ # Linker output
20
+ *.ilk
21
+ *.map
22
+ *.exp
23
+
24
+ # Precompiled Headers
25
+ *.gch
26
+ *.pch
27
+
28
+ # Libraries
29
+ *.lib
30
+ *.a
31
+ *.la
32
+ *.lo
33
+
34
+ # Shared objects (inc. Windows DLLs)
35
+ *.dll
36
+ *.so
37
+ *.so.*
38
+ *.dylib
39
+
40
+ # Executables
41
+ *.exe
42
+ *.out
43
+ !examples/**/*.out
44
+ *.app
45
+ *.i*86
46
+ *.x86_64
47
+ *.hex
48
+
49
+ # Debug files
50
+ *.dSYM/
51
+ *.su
52
+ *.idb
53
+ *.pdb
54
+
55
+ # Kernel Module Compile Results
56
+ *.mod*
57
+ !*.model
58
+ *.cmd
59
+ .tmp_versions/
60
+ modules.order
61
+ Module.symvers
62
+ Mkfile.old
63
+ dkms.conf
64
+
65
+ ### Linux ###
66
+ *~
67
+
68
+ # temporary files which can be created if a process still has a handle open of a deleted file
69
+ .fuse_hidden*
70
+
71
+ # KDE directory preferences
72
+ .directory
73
+
74
+ # Linux trash folder which might appear on any partition or disk
75
+ .Trash-*
76
+
77
+ # .nfs files are created when an open file is removed but is still being accessed
78
+ .nfs*
79
+
80
+ ### macOS ###
81
+ # General
82
+ .DS_Store
83
+ .AppleDouble
84
+ .LSOverride
85
+
86
+ # Icon must end with two \r
87
+ Icon
88
+
89
+
90
+ # Thumbnails
91
+ ._*
92
+
93
+ # Files that might appear in the root of a volume
94
+ .DocumentRevisions-V100
95
+ .fseventsd
96
+ .Spotlight-V100
97
+ .TemporaryItems
98
+ .Trashes
99
+ .VolumeIcon.icns
100
+ .com.apple.timemachine.donotpresent
101
+
102
+ # Directories potentially created on remote AFP share
103
+ .AppleDB
104
+ .AppleDesktop
105
+ Network Trash Folder
106
+ Temporary Items
107
+ .apdisk
108
+
109
+ ### macOS Patch ###
110
+ # iCloud generated files
111
+ *.icloud
112
+
113
+ ### Python ###
114
+ # Byte-compiled / optimized / DLL files
115
+ __pycache__/
116
+ *.py[cod]
117
+ *$py.class
118
+
119
+ # C extensions
120
+
121
+ # Distribution / packaging
122
+ .Python
123
+ build/
124
+ develop-eggs/
125
+ dist/
126
+ downloads/
127
+ eggs/
128
+ .eggs/
129
+ lib/
130
+ lib64/
131
+ parts/
132
+ sdist/
133
+ var/
134
+ wheels/
135
+ share/python-wheels/
136
+ *.egg-info/
137
+ .installed.cfg
138
+ *.egg
139
+ MANIFEST
140
+
141
+ # PyInstaller
142
+ # Usually these files are written by a python script from a template
143
+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
144
+ *.manifest
145
+ *.spec
146
+ # Exception: our hand-authored installer spec is a committed source file.
147
+ !scripts/installer.spec
148
+
149
+ # Installer logs
150
+ pip-log.txt
151
+ pip-delete-this-directory.txt
152
+
153
+ # Unit test / coverage reports
154
+ htmlcov/
155
+ .tox/
156
+ .nox/
157
+ .coverage
158
+ .coverage.*
159
+ .cache
160
+ nosetests.xml
161
+ coverage.xml
162
+ *.cover
163
+ *.py,cover
164
+ .hypothesis/
165
+ .pytest_cache/
166
+ cover/
167
+
168
+ # Translations
169
+ *.mo
170
+ *.pot
171
+
172
+ # Django stuff:
173
+ *.log
174
+ local_settings.py
175
+ db.sqlite3
176
+ db.sqlite3-journal
177
+
178
+ # Flask stuff:
179
+ instance/
180
+ .webassets-cache
181
+
182
+ # Scrapy stuff:
183
+ .scrapy
184
+
185
+ # Sphinx documentation
186
+ docs/_build/
187
+
188
+ # PyBuilder
189
+ .pybuilder/
190
+ target/
191
+
192
+ # Jupyter Notebook
193
+ .ipynb_checkpoints
194
+
195
+ # IPython
196
+ profile_default/
197
+ ipython_config.py
198
+
199
+ # pyenv
200
+ # For a library or package, you might want to ignore these files since the code is
201
+ # intended to run in multiple environments; otherwise, check them in:
202
+ # .python-version
203
+
204
+ # pipenv
205
+ # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
206
+ # However, in case of collaboration, if having platform-specific dependencies or dependencies
207
+ # having no cross-platform support, pipenv may install dependencies that don't work, or not
208
+ # install all needed dependencies.
209
+ #Pipfile.lock
210
+
211
+ # poetry
212
+ # 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
+ # commonly ignored for libraries.
215
+ # https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
216
+ #poetry.lock
217
+
218
+ # pdm
219
+ # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
220
+ #pdm.lock
221
+ # pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
222
+ # in version control.
223
+ # https://pdm.fming.dev/#use-with-ide
224
+ .pdm.toml
225
+
226
+ # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
227
+ __pypackages__/
228
+
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/
240
+ venv/
241
+ ENV/
242
+ env.bak/
243
+ 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
261
+ .pyre/
262
+
263
+ # pytype static type analyzer
264
+ .pytype/
265
+
266
+ # Cython debug symbols
267
+ cython_debug/
268
+
269
+ # PyCharm
270
+ # JetBrains specific template is maintained in a separate JetBrains.gitignore that can
271
+ # 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
273
+ # option (not recommended) you can uncomment the following to ignore the entire idea folder.
274
+ #.idea/
275
+
276
+ ### Python Patch ###
277
+ # Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
278
+ poetry.toml
279
+
280
+ ### Local tool caches and scratch directories ###
281
+ .r-lib/
282
+ .uv-cache/
283
+ .claude/
284
+ .local/
285
+ .xdg-data/
286
+ artifacts/
287
+ main.py
288
+
289
+ # ruff
290
+ .ruff_cache/
291
+
292
+ # LSP config files
293
+ pyrightconfig.json
294
+
295
+ # project-specific generated files
296
+ uv.lock
297
+ 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
311
+ *.cb
312
+ *.cb2
313
+ .*.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
+