bioguider 0.2.21__py3-none-any.whl → 0.2.23__py3-none-any.whl

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Files changed (20) hide show
  1. bioguider/agents/consistency_collection_step.py +9 -7
  2. bioguider/agents/consistency_evaluation_task.py +3 -2
  3. bioguider/agents/consistency_evaluation_task_utils.py +2 -1
  4. bioguider/agents/consistency_observe_step.py +15 -13
  5. bioguider/agents/evaluation_task.py +0 -110
  6. bioguider/agents/evaluation_tutorial_task.py +157 -0
  7. bioguider/agents/evaluation_tutorial_task_prompts.py +114 -0
  8. bioguider/agents/evaluation_userguide_task.py +4 -1
  9. bioguider/agents/prompt_utils.py +9 -0
  10. bioguider/database/code_structure_db.py +20 -9
  11. bioguider/database/summarized_file_db.py +6 -3
  12. bioguider/managers/evaluation_manager.py +14 -16
  13. bioguider/rag/data_pipeline.py +1 -1
  14. bioguider/utils/code_structure_builder.py +6 -4
  15. bioguider/utils/notebook_utils.py +117 -0
  16. bioguider/utils/r_file_handler.py +528 -347
  17. {bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/METADATA +1 -1
  18. {bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/RECORD +20 -17
  19. {bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/LICENSE +0 -0
  20. {bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/WHEEL +0 -0
{bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: bioguider
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- Version: 0.2.21
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+ Version: 0.2.23
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  Summary: An AI-Powered package to help biomedical developers to generate clear documentation
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  License: MIT
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  Author: Cankun Wang
{bioguider-0.2.21.dist-info → bioguider-0.2.23.dist-info}/RECORD RENAMED
@@ -12,10 +12,10 @@ bioguider/agents/common_agent.py,sha256=TpfxbYskwuwWrjs1g9RaG7sdA5rOLdiVac7If7uK
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  bioguider/agents/common_agent_2step.py,sha256=rGiDzUkmmUIFnmJJxzXK5M5BfIyINHXLZ0pmPRUVqQg,7911
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  bioguider/agents/common_conversation.py,sha256=_9l6SunRmOZ_3R4Q8CTO9oE_qmP7aYYKFX1EiFBIrm8,2589
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  bioguider/agents/common_step.py,sha256=GdOCbmj1pwh4etg-futVFYVDQuoUG89DnIrw-B6QbzM,2594
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- bioguider/agents/consistency_collection_step.py,sha256=eZg0aso0hEVioO_c9yk0bDFOPzGXCUoY82YSasqSSmg,3487
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- bioguider/agents/consistency_evaluation_task.py,sha256=l4RfC2LwKfSoTQ1V6V2IeJVIy_WaU0k1kXssUpzVwto,1913
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- bioguider/agents/consistency_evaluation_task_utils.py,sha256=zWeYKMAQ3rojVvfvKadjq_1icikF_y9TApP5JnTvHls,443
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- bioguider/agents/consistency_observe_step.py,sha256=g3m8RZJkDGlczHS6dl19c8zDx6P1NZh1WqRC_NBD7GE,4502
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+ bioguider/agents/consistency_collection_step.py,sha256=evgb0W3PD5pXfViuP_0T5LqLnNxQCuvP14oY0KEtwSc,3424
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+ bioguider/agents/consistency_evaluation_task.py,sha256=_nYPEs3xhj1jraQWMRML_Y6vZJD_zydY4BstQYXmXJk,1908
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+ bioguider/agents/consistency_evaluation_task_utils.py,sha256=8PC4KS14ek9NJy3bLuhZNmpOUKFx3_06nKXzuTWb0tE,444
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+ bioguider/agents/consistency_observe_step.py,sha256=0FEtNpkaGcuL30wb2d43uTlSyHJ9Pxttn9r3NzPD0oo,4409
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  bioguider/agents/consistency_query_step.py,sha256=uYE_V_e74kqoDSxmIkMpZpBjoZRKRsJPmiqs1xHhRF8,3674
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  bioguider/agents/dockergeneration_execute_step.py,sha256=F92jDlkc6KjAvTkX7q1FsCYP8J15SCaNgmwh3YPqfDo,6500
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  bioguider/agents/dockergeneration_observe_step.py,sha256=Bo5Td0fzMYLbLki0FvwamzqRFOy4eu3AvIUa8oFApE4,6131
@@ -25,21 +25,23 @@ bioguider/agents/dockergeneration_task_utils.py,sha256=v7emqrJlVW-A5ZdLmPSdiaMSK
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  bioguider/agents/evaluation_installation_task.py,sha256=0RNH5NV7YKwn_we_d3IjnFf_ee9IPCEQ_olebq2y8Ng,12130
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  bioguider/agents/evaluation_readme_task.py,sha256=pi3oAGJgZhJgJG1xLgiobrk3Uy2a_JIarD5QSPBkmHA,30647
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  bioguider/agents/evaluation_submission_requirements_task.py,sha256=J_6C-M2AfYue2C-gWBHl7KqGrTBuFBn9zmMV5vSRk-U,7834
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- bioguider/agents/evaluation_task.py,sha256=c3kvc3xgzGbT0C2KpkE-zHBvaxx9zKdmpLzeKHddrds,12690
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+ bioguider/agents/evaluation_task.py,sha256=uu0BjalctF9hQjGtT53whbeJHv2RVvs8_2woVUmOLRE,8132
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+ bioguider/agents/evaluation_tutorial_task.py,sha256=wRhHqvuOhGEICOhAlZrtshHJ8LkmnAYfjazFe090aeU,8441
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+ bioguider/agents/evaluation_tutorial_task_prompts.py,sha256=WTqIKBI3JErYaiQfLcPNj_hb3D-hSZrae50uJ7526zw,5996
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  bioguider/agents/evaluation_userguide_prompts.py,sha256=eyJUx5nUr8v9k0B5GpKDaX2dBxSLVZGA0fwOWS4Uiow,7154
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- bioguider/agents/evaluation_userguide_task.py,sha256=5Z2abE_yiy1SvZ-KECLBk2N4nyRGVR4OV1uOhCfO3qU,6382
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+ bioguider/agents/evaluation_userguide_task.py,sha256=ONdempCOyn_N-LGV35diKciBbnjDSItXchcLV738XTw,6456
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  bioguider/agents/identification_execute_step.py,sha256=w3IjL8f2WiHCyiLjVSoySnIAXpi1-hK1DLKCnXbAN2Y,5587
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  bioguider/agents/identification_observe_step.py,sha256=Me5mhEM4e7FGnVFcluNtqfhIxzng6guGIu39xi1TrS8,4341
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  bioguider/agents/identification_plan_step.py,sha256=owsTK1NZIuiZL7QPVknJyp9TBRK-mhnuf2RwK4YzaxU,5442
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  bioguider/agents/identification_task.py,sha256=bTbovxxQVpO1TcdcQAxDxwPISuAcXndO7zsvHpJSb64,10147
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  bioguider/agents/identification_task_utils.py,sha256=Lf0Rj0L0KSiyJmPAgeSz0vLUFQr6TSFuzgufimEN4H0,630
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  bioguider/agents/peo_common_step.py,sha256=iw2c1h7X11WJzSE2tSRg0UAoXH0QOlQDxW9CCzSVMOY,2677
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- bioguider/agents/prompt_utils.py,sha256=eDi3UY52aTfjQ-337tvXHe8wyUOLq7bs2B7mYp9FDkw,18383
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+ bioguider/agents/prompt_utils.py,sha256=T7ec7DbdGacIMOE4GAnlzHjuNzbzPDeSVWHvmWt1UGk,19427
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  bioguider/agents/python_ast_repl_tool.py,sha256=o7-4P1h8jS8ikhGSA4CI_OWQ2a0Eg5tEdmuAp_qrO-0,2519
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  bioguider/agents/rag_collection_task.py,sha256=r_jPAMjQcC7dIydKxX77UuMqjJ3MiVKswNZ-yNw7yx8,5199
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  bioguider/conversation.py,sha256=DIvk_d7pz_guuORByK1eaaF09FAK-8shcNTrbSUHz9Y,1779
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- bioguider/database/code_structure_db.py,sha256=drYkoQa7mDexCpulG3885Gwcnu92lnHNRlWT8byjF-A,16630
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- bioguider/database/summarized_file_db.py,sha256=gGubM5vH3SN_1vouKO0LemvE_EfyjinAScRhlvxJsi0,4654
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+ bioguider/database/code_structure_db.py,sha256=q9tGZLWrjPi7a3u1b2iUnMO30lNWKbeMOkpDRffev2M,16973
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+ bioguider/database/summarized_file_db.py,sha256=U60c62e2Bx7PwsTAcCQgljNxD5u5awjpj5qpHEgJbac,4801
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  bioguider/generation/__init__.py,sha256=esV02QgCsY67-HBwSHDbA5AcbKzNRIT3wDwwh6N4OFM,945
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  bioguider/generation/change_planner.py,sha256=1u_1tcVwggVw6QebXvPJVULYnRAIkKMteFxbnf42aAw,6964
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  bioguider/generation/document_renderer.py,sha256=67-XGFGNe8WgHJpqkHLMecgk2OeV8a5cJRAeDTLsXG4,1806
@@ -53,25 +55,26 @@ bioguider/generation/report_loader.py,sha256=KtJ6JHGPDL-PQoucU8hkVzMSz-B0bHbF2WS
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  bioguider/generation/style_analyzer.py,sha256=Vn9FAK1qJBNLolLC1tz362k4UBaPl107BlvkQc8pV2I,983
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  bioguider/generation/suggestion_extractor.py,sha256=tfkyWtdbAo-maLCF_wqwBXyh93yjulvDY17FuvTnTjk,7611
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  bioguider/generation/test_metrics.py,sha256=fG6H1jVikHEx1YvN5Ds4QbVinudJ5OEYkzrV760oLLQ,3766
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- bioguider/managers/evaluation_manager.py,sha256=xzCjbbYLLOZNjvqXh9JtPIKtIfpyHcHfczcSGe3t30A,5852
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+ bioguider/managers/evaluation_manager.py,sha256=EoZ8V4rmx16zk1J3N9cNjeo0aCa7i32fLEQ3b2UolEQ,5917
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  bioguider/managers/generation_manager.py,sha256=EbAJSvUz-SIriVlozuJ6wa5_1aIbbFfpgg3c9Vcz34g,7615
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  bioguider/managers/generation_test_manager.py,sha256=0ty8IibdfN90Oj6M6lkYbxASnQxHYb9I3w9eG7hvEsQ,3270
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  bioguider/rag/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  bioguider/rag/config.py,sha256=5g4IqTzgyfZfax9Af9CTkXShgItPOt4_9TEMSekCPik,4602
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- bioguider/rag/data_pipeline.py,sha256=bkJ2IUCgPx_OL2uZtPd6cIBor2VFZEIfGd5kVlmiPjw,27292
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+ bioguider/rag/data_pipeline.py,sha256=hyBmjOpP1ka_y_4X0lUwlNKEBjmPNOmETEfQf-s86ZY,27316
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  bioguider/rag/embedder.py,sha256=jofR8hOj3Aj2IyBQ9y6FeAc84tgq5agbIfCGyFxYpJ8,650
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  bioguider/rag/rag.py,sha256=JFPwrJlKDSyd3U3Gce_NSxI5343eNUbqPG9Fs5Pfoq0,4696
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  bioguider/settings.py,sha256=BD_iz9aYarxmWUl0XaKl4-D4oTXMhFzljsXLNn2phis,3143
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- bioguider/utils/code_structure_builder.py,sha256=vrTGYu-IpMTKlmioFRz3xVo-vUszQeIaCQ-_R6Cn9HU,1849
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+ bioguider/utils/code_structure_builder.py,sha256=PVeooVKxkiBEkX_VEu8h1ACGs-ynrgk_ce2FKJfeeZc,1947
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  bioguider/utils/constants.py,sha256=NGmqEgxNDL1fe-htJbtHGcU94EVUK28YAupxGYOJO_c,9012
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  bioguider/utils/default.gitignore,sha256=XjPdyO2KV8z8iyuqluaNR_70tBQftMpyKL8HboVNyeI,1605
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  bioguider/utils/file_utils.py,sha256=9VfAHsz1UkFPtzAmvWZvPl1TMaKIYNjNlLgsfB8tNjg,3683
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  bioguider/utils/gitignore_checker.py,sha256=pOYUwsS9D5014LxcZb0cj3s2CAYaD2uF_pYJpaNKcho,6532
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+ bioguider/utils/notebook_utils.py,sha256=SfU1iLuwgbDzNN-TUh_qbnfUSgn-PI6NrK6QfmdpMqQ,4009
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  bioguider/utils/pyphen_utils.py,sha256=cdZc3qphkvMDeL5NiZ8Xou13M_uVNP7ifJ-FwxO-0BE,2680
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  bioguider/utils/python_file_handler.py,sha256=BERiE2RHxpu3gAzv26jr8ZQetkrtnMZOv9SjpQ7WIdg,2650
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- bioguider/utils/r_file_handler.py,sha256=7pUJ0tnKMFDVLLqE3T34YF3vsxN7uT7kBEQnN932aiY,14126
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+ bioguider/utils/r_file_handler.py,sha256=8HpFaYKP8N1nItwr9tOx49m99pcLSt8EUtTNTJ7xNoE,19564
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  bioguider/utils/utils.py,sha256=1N7Wv_i9spTBQ_FbZnlxsjC8mszbBzaegrmvuKGUISg,3531
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- bioguider-0.2.21.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
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- bioguider-0.2.21.dist-info/METADATA,sha256=cZk86BBC_rcGPz_a-Qs8liD9Iun__D9pP5UOONzzAtI,1868
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- bioguider-0.2.21.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- bioguider-0.2.21.dist-info/RECORD,,
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+ bioguider-0.2.23.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
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+ bioguider-0.2.23.dist-info/METADATA,sha256=PL0Y-nFP-6pf2aafsz4zSiJ4UCQZKtCq6pYsp3r_kVg,1868
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+ bioguider-0.2.23.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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+ bioguider-0.2.23.dist-info/RECORD,,