aiagents4pharma 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

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Files changed (290) hide show
  1. aiagents4pharma/__init__.py +2 -2
  2. aiagents4pharma/talk2aiagents4pharma/.dockerignore +13 -0
  3. aiagents4pharma/talk2aiagents4pharma/Dockerfile +105 -0
  4. aiagents4pharma/talk2aiagents4pharma/README.md +1 -0
  5. aiagents4pharma/talk2aiagents4pharma/__init__.py +4 -5
  6. aiagents4pharma/talk2aiagents4pharma/agents/__init__.py +3 -2
  7. aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py +24 -23
  8. aiagents4pharma/talk2aiagents4pharma/configs/__init__.py +2 -2
  9. aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py +2 -2
  10. aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml +2 -2
  11. aiagents4pharma/talk2aiagents4pharma/configs/config.yaml +1 -1
  12. aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example +23 -0
  13. aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml +93 -0
  14. aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example +23 -0
  15. aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/docker-compose.yml +108 -0
  16. aiagents4pharma/talk2aiagents4pharma/install.md +127 -0
  17. aiagents4pharma/talk2aiagents4pharma/states/__init__.py +3 -2
  18. aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py +5 -3
  19. aiagents4pharma/talk2aiagents4pharma/tests/__init__.py +2 -2
  20. aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +72 -50
  21. aiagents4pharma/talk2biomodels/.dockerignore +13 -0
  22. aiagents4pharma/talk2biomodels/Dockerfile +104 -0
  23. aiagents4pharma/talk2biomodels/README.md +1 -0
  24. aiagents4pharma/talk2biomodels/__init__.py +4 -8
  25. aiagents4pharma/talk2biomodels/agents/__init__.py +3 -2
  26. aiagents4pharma/talk2biomodels/agents/t2b_agent.py +47 -42
  27. aiagents4pharma/talk2biomodels/api/__init__.py +4 -5
  28. aiagents4pharma/talk2biomodels/api/kegg.py +14 -10
  29. aiagents4pharma/talk2biomodels/api/ols.py +13 -10
  30. aiagents4pharma/talk2biomodels/api/uniprot.py +7 -6
  31. aiagents4pharma/talk2biomodels/configs/__init__.py +3 -4
  32. aiagents4pharma/talk2biomodels/configs/agents/__init__.py +2 -2
  33. aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py +2 -2
  34. aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml +1 -1
  35. aiagents4pharma/talk2biomodels/configs/config.yaml +1 -1
  36. aiagents4pharma/talk2biomodels/configs/tools/__init__.py +4 -5
  37. aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py +2 -2
  38. aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml +1 -2
  39. aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py +2 -2
  40. aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml +1 -1
  41. aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py +2 -2
  42. aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml +1 -1
  43. aiagents4pharma/talk2biomodels/install.md +63 -0
  44. aiagents4pharma/talk2biomodels/models/__init__.py +4 -4
  45. aiagents4pharma/talk2biomodels/models/basico_model.py +36 -28
  46. aiagents4pharma/talk2biomodels/models/sys_bio_model.py +13 -10
  47. aiagents4pharma/talk2biomodels/states/__init__.py +3 -2
  48. aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +12 -8
  49. aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml +1585 -0
  50. aiagents4pharma/talk2biomodels/tests/__init__.py +2 -2
  51. aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf +0 -0
  52. aiagents4pharma/talk2biomodels/tests/test_api.py +18 -14
  53. aiagents4pharma/talk2biomodels/tests/test_ask_question.py +8 -9
  54. aiagents4pharma/talk2biomodels/tests/test_basico_model.py +15 -9
  55. aiagents4pharma/talk2biomodels/tests/test_get_annotation.py +54 -55
  56. aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py +28 -27
  57. aiagents4pharma/talk2biomodels/tests/test_integration.py +21 -33
  58. aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py +14 -11
  59. aiagents4pharma/talk2biomodels/tests/test_param_scan.py +21 -20
  60. aiagents4pharma/talk2biomodels/tests/test_query_article.py +129 -29
  61. aiagents4pharma/talk2biomodels/tests/test_search_models.py +9 -13
  62. aiagents4pharma/talk2biomodels/tests/test_simulate_model.py +16 -15
  63. aiagents4pharma/talk2biomodels/tests/test_steady_state.py +12 -22
  64. aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +33 -29
  65. aiagents4pharma/talk2biomodels/tools/__init__.py +15 -12
  66. aiagents4pharma/talk2biomodels/tools/ask_question.py +42 -32
  67. aiagents4pharma/talk2biomodels/tools/custom_plotter.py +51 -43
  68. aiagents4pharma/talk2biomodels/tools/get_annotation.py +99 -75
  69. aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +57 -51
  70. aiagents4pharma/talk2biomodels/tools/load_arguments.py +52 -32
  71. aiagents4pharma/talk2biomodels/tools/load_biomodel.py +8 -2
  72. aiagents4pharma/talk2biomodels/tools/parameter_scan.py +107 -90
  73. aiagents4pharma/talk2biomodels/tools/query_article.py +14 -13
  74. aiagents4pharma/talk2biomodels/tools/search_models.py +37 -26
  75. aiagents4pharma/talk2biomodels/tools/simulate_model.py +47 -37
  76. aiagents4pharma/talk2biomodels/tools/steady_state.py +76 -58
  77. aiagents4pharma/talk2biomodels/tools/utils.py +4 -3
  78. aiagents4pharma/talk2cells/README.md +1 -0
  79. aiagents4pharma/talk2cells/__init__.py +4 -5
  80. aiagents4pharma/talk2cells/agents/__init__.py +3 -2
  81. aiagents4pharma/talk2cells/agents/scp_agent.py +21 -19
  82. aiagents4pharma/talk2cells/states/__init__.py +3 -2
  83. aiagents4pharma/talk2cells/states/state_talk2cells.py +4 -2
  84. aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py +8 -9
  85. aiagents4pharma/talk2cells/tools/__init__.py +3 -2
  86. aiagents4pharma/talk2cells/tools/scp_agent/__init__.py +4 -4
  87. aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py +5 -3
  88. aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py +21 -22
  89. aiagents4pharma/talk2knowledgegraphs/.dockerignore +13 -0
  90. aiagents4pharma/talk2knowledgegraphs/Dockerfile +103 -0
  91. aiagents4pharma/talk2knowledgegraphs/README.md +1 -0
  92. aiagents4pharma/talk2knowledgegraphs/__init__.py +4 -7
  93. aiagents4pharma/talk2knowledgegraphs/agents/__init__.py +3 -2
  94. aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +40 -30
  95. aiagents4pharma/talk2knowledgegraphs/configs/__init__.py +3 -6
  96. aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py +2 -2
  97. aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml +8 -8
  98. aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py +3 -2
  99. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py +2 -2
  100. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +1 -1
  101. aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +1 -1
  102. aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py +4 -5
  103. aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py +2 -2
  104. aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml +1 -1
  105. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +17 -2
  106. aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py +2 -2
  107. aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml +1 -1
  108. aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py +2 -2
  109. aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml +1 -1
  110. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml +1 -1
  111. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml +1 -1
  112. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml +1 -1
  113. aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml +1 -1
  114. aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py +4 -6
  115. aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py +115 -67
  116. aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py +2 -0
  117. aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py +35 -24
  118. aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py +29 -21
  119. aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example +23 -0
  120. aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/docker-compose.yml +93 -0
  121. aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example +23 -0
  122. aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/docker-compose.yml +108 -0
  123. aiagents4pharma/talk2knowledgegraphs/entrypoint.sh +190 -0
  124. aiagents4pharma/talk2knowledgegraphs/install.md +140 -0
  125. aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py +31 -65
  126. aiagents4pharma/talk2knowledgegraphs/states/__init__.py +3 -2
  127. aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py +1 -0
  128. aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py +65 -40
  129. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py +54 -48
  130. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py +4 -0
  131. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py +17 -4
  132. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py +33 -24
  133. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py +116 -69
  134. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_milvus_multimodal_subgraph_extraction.py +736 -413
  135. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py +22 -15
  136. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py +19 -12
  137. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_summarization.py +95 -48
  138. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py +4 -0
  139. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py +5 -0
  140. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_nim_molmim.py +13 -18
  141. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py +10 -3
  142. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py +4 -3
  143. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py +3 -2
  144. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py +1 -0
  145. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py +9 -4
  146. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py +6 -6
  147. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py +4 -0
  148. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_extractions_milvus_multimodal_pcst.py +442 -42
  149. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py +3 -4
  150. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py +10 -6
  151. aiagents4pharma/talk2knowledgegraphs/tools/__init__.py +10 -7
  152. aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py +15 -20
  153. aiagents4pharma/talk2knowledgegraphs/tools/milvus_multimodal_subgraph_extraction.py +245 -205
  154. aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py +92 -90
  155. aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py +25 -37
  156. aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py +10 -13
  157. aiagents4pharma/talk2knowledgegraphs/utils/__init__.py +4 -7
  158. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py +4 -7
  159. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py +4 -0
  160. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py +11 -14
  161. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/nim_molmim.py +7 -7
  162. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/ollama.py +12 -6
  163. aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py +8 -6
  164. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py +9 -6
  165. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py +1 -0
  166. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py +15 -9
  167. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py +23 -20
  168. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py +12 -10
  169. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py +16 -10
  170. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py +26 -18
  171. aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py +4 -5
  172. aiagents4pharma/talk2knowledgegraphs/utils/extractions/milvus_multimodal_pcst.py +218 -81
  173. aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py +53 -47
  174. aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py +18 -14
  175. aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py +22 -23
  176. aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py +11 -10
  177. aiagents4pharma/talk2scholars/.dockerignore +13 -0
  178. aiagents4pharma/talk2scholars/Dockerfile +104 -0
  179. aiagents4pharma/talk2scholars/README.md +1 -0
  180. aiagents4pharma/talk2scholars/agents/__init__.py +1 -5
  181. aiagents4pharma/talk2scholars/agents/main_agent.py +6 -4
  182. aiagents4pharma/talk2scholars/agents/paper_download_agent.py +5 -4
  183. aiagents4pharma/talk2scholars/agents/pdf_agent.py +4 -2
  184. aiagents4pharma/talk2scholars/agents/s2_agent.py +2 -2
  185. aiagents4pharma/talk2scholars/agents/zotero_agent.py +10 -11
  186. aiagents4pharma/talk2scholars/configs/__init__.py +1 -3
  187. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py +1 -4
  188. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml +1 -1
  189. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml +1 -1
  190. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +8 -8
  191. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml +7 -7
  192. aiagents4pharma/talk2scholars/configs/tools/__init__.py +8 -6
  193. aiagents4pharma/talk2scholars/docker-compose/cpu/.env.example +21 -0
  194. aiagents4pharma/talk2scholars/docker-compose/cpu/docker-compose.yml +90 -0
  195. aiagents4pharma/talk2scholars/docker-compose/gpu/.env.example +21 -0
  196. aiagents4pharma/talk2scholars/docker-compose/gpu/docker-compose.yml +105 -0
  197. aiagents4pharma/talk2scholars/install.md +122 -0
  198. aiagents4pharma/talk2scholars/state/state_talk2scholars.py +8 -8
  199. aiagents4pharma/talk2scholars/tests/{test_main_agent.py → test_agents_main_agent.py} +41 -23
  200. aiagents4pharma/talk2scholars/tests/{test_paper_download_agent.py → test_agents_paper_agents_download_agent.py} +10 -16
  201. aiagents4pharma/talk2scholars/tests/{test_pdf_agent.py → test_agents_pdf_agent.py} +6 -10
  202. aiagents4pharma/talk2scholars/tests/{test_s2_agent.py → test_agents_s2_agent.py} +8 -16
  203. aiagents4pharma/talk2scholars/tests/{test_zotero_agent.py → test_agents_zotero_agent.py} +5 -7
  204. aiagents4pharma/talk2scholars/tests/{test_s2_display_dataframe.py → test_s2_tools_display_dataframe.py} +6 -7
  205. aiagents4pharma/talk2scholars/tests/{test_s2_query_dataframe.py → test_s2_tools_query_dataframe.py} +5 -15
  206. aiagents4pharma/talk2scholars/tests/{test_paper_downloader.py → test_tools_paper_downloader.py} +25 -63
  207. aiagents4pharma/talk2scholars/tests/{test_question_and_answer_tool.py → test_tools_question_and_answer_tool.py} +2 -6
  208. aiagents4pharma/talk2scholars/tests/{test_s2_multi.py → test_tools_s2_multi.py} +5 -5
  209. aiagents4pharma/talk2scholars/tests/{test_s2_retrieve.py → test_tools_s2_retrieve.py} +2 -1
  210. aiagents4pharma/talk2scholars/tests/{test_s2_search.py → test_tools_s2_search.py} +5 -5
  211. aiagents4pharma/talk2scholars/tests/{test_s2_single.py → test_tools_s2_single.py} +5 -5
  212. aiagents4pharma/talk2scholars/tests/{test_arxiv_downloader.py → test_utils_arxiv_downloader.py} +16 -25
  213. aiagents4pharma/talk2scholars/tests/{test_base_paper_downloader.py → test_utils_base_paper_downloader.py} +25 -47
  214. aiagents4pharma/talk2scholars/tests/{test_biorxiv_downloader.py → test_utils_biorxiv_downloader.py} +14 -42
  215. aiagents4pharma/talk2scholars/tests/{test_medrxiv_downloader.py → test_utils_medrxiv_downloader.py} +15 -49
  216. aiagents4pharma/talk2scholars/tests/{test_nvidia_nim_reranker.py → test_utils_nvidia_nim_reranker.py} +6 -16
  217. aiagents4pharma/talk2scholars/tests/{test_pdf_answer_formatter.py → test_utils_pdf_answer_formatter.py} +1 -0
  218. aiagents4pharma/talk2scholars/tests/{test_pdf_batch_processor.py → test_utils_pdf_batch_processor.py} +6 -15
  219. aiagents4pharma/talk2scholars/tests/{test_pdf_collection_manager.py → test_utils_pdf_collection_manager.py} +34 -11
  220. aiagents4pharma/talk2scholars/tests/{test_pdf_document_processor.py → test_utils_pdf_document_processor.py} +2 -3
  221. aiagents4pharma/talk2scholars/tests/{test_pdf_generate_answer.py → test_utils_pdf_generate_answer.py} +3 -6
  222. aiagents4pharma/talk2scholars/tests/{test_pdf_gpu_detection.py → test_utils_pdf_gpu_detection.py} +5 -16
  223. aiagents4pharma/talk2scholars/tests/{test_pdf_rag_pipeline.py → test_utils_pdf_rag_pipeline.py} +7 -17
  224. aiagents4pharma/talk2scholars/tests/{test_pdf_retrieve_chunks.py → test_utils_pdf_retrieve_chunks.py} +4 -11
  225. aiagents4pharma/talk2scholars/tests/{test_pdf_singleton_manager.py → test_utils_pdf_singleton_manager.py} +26 -23
  226. aiagents4pharma/talk2scholars/tests/{test_pdf_vector_normalization.py → test_utils_pdf_vector_normalization.py} +1 -1
  227. aiagents4pharma/talk2scholars/tests/{test_pdf_vector_store.py → test_utils_pdf_vector_store.py} +27 -55
  228. aiagents4pharma/talk2scholars/tests/{test_pubmed_downloader.py → test_utils_pubmed_downloader.py} +31 -91
  229. aiagents4pharma/talk2scholars/tests/{test_read_helper_utils.py → test_utils_read_helper_utils.py} +2 -6
  230. aiagents4pharma/talk2scholars/tests/{test_s2_utils_ext_ids.py → test_utils_s2_utils_ext_ids.py} +5 -15
  231. aiagents4pharma/talk2scholars/tests/{test_zotero_human_in_the_loop.py → test_utils_zotero_human_in_the_loop.py} +6 -13
  232. aiagents4pharma/talk2scholars/tests/{test_zotero_path.py → test_utils_zotero_path.py} +53 -45
  233. aiagents4pharma/talk2scholars/tests/{test_zotero_read.py → test_utils_zotero_read.py} +30 -91
  234. aiagents4pharma/talk2scholars/tests/{test_zotero_write.py → test_utils_zotero_write.py} +6 -16
  235. aiagents4pharma/talk2scholars/tools/__init__.py +1 -4
  236. aiagents4pharma/talk2scholars/tools/paper_download/paper_downloader.py +20 -35
  237. aiagents4pharma/talk2scholars/tools/paper_download/utils/__init__.py +7 -5
  238. aiagents4pharma/talk2scholars/tools/paper_download/utils/arxiv_downloader.py +9 -11
  239. aiagents4pharma/talk2scholars/tools/paper_download/utils/base_paper_downloader.py +14 -21
  240. aiagents4pharma/talk2scholars/tools/paper_download/utils/biorxiv_downloader.py +14 -22
  241. aiagents4pharma/talk2scholars/tools/paper_download/utils/medrxiv_downloader.py +11 -13
  242. aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py +14 -28
  243. aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py +4 -8
  244. aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py +16 -14
  245. aiagents4pharma/talk2scholars/tools/pdf/utils/answer_formatter.py +4 -4
  246. aiagents4pharma/talk2scholars/tools/pdf/utils/batch_processor.py +15 -17
  247. aiagents4pharma/talk2scholars/tools/pdf/utils/collection_manager.py +2 -2
  248. aiagents4pharma/talk2scholars/tools/pdf/utils/document_processor.py +5 -5
  249. aiagents4pharma/talk2scholars/tools/pdf/utils/generate_answer.py +4 -4
  250. aiagents4pharma/talk2scholars/tools/pdf/utils/get_vectorstore.py +2 -6
  251. aiagents4pharma/talk2scholars/tools/pdf/utils/gpu_detection.py +5 -9
  252. aiagents4pharma/talk2scholars/tools/pdf/utils/nvidia_nim_reranker.py +4 -4
  253. aiagents4pharma/talk2scholars/tools/pdf/utils/paper_loader.py +2 -2
  254. aiagents4pharma/talk2scholars/tools/pdf/utils/rag_pipeline.py +6 -15
  255. aiagents4pharma/talk2scholars/tools/pdf/utils/retrieve_chunks.py +7 -15
  256. aiagents4pharma/talk2scholars/tools/pdf/utils/singleton_manager.py +2 -2
  257. aiagents4pharma/talk2scholars/tools/pdf/utils/tool_helper.py +3 -4
  258. aiagents4pharma/talk2scholars/tools/pdf/utils/vector_normalization.py +8 -17
  259. aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py +17 -33
  260. aiagents4pharma/talk2scholars/tools/s2/__init__.py +8 -6
  261. aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py +3 -7
  262. aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +7 -6
  263. aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +5 -12
  264. aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +2 -4
  265. aiagents4pharma/talk2scholars/tools/s2/search.py +6 -6
  266. aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +5 -3
  267. aiagents4pharma/talk2scholars/tools/s2/utils/__init__.py +1 -3
  268. aiagents4pharma/talk2scholars/tools/s2/utils/multi_helper.py +12 -18
  269. aiagents4pharma/talk2scholars/tools/s2/utils/search_helper.py +11 -18
  270. aiagents4pharma/talk2scholars/tools/s2/utils/single_helper.py +11 -16
  271. aiagents4pharma/talk2scholars/tools/zotero/__init__.py +1 -4
  272. aiagents4pharma/talk2scholars/tools/zotero/utils/__init__.py +1 -4
  273. aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py +21 -39
  274. aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py +2 -6
  275. aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py +8 -11
  276. aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py +4 -12
  277. aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py +13 -27
  278. aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py +4 -7
  279. aiagents4pharma/talk2scholars/tools/zotero/zotero_review.py +8 -10
  280. aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py +3 -2
  281. {aiagents4pharma-1.43.0.dist-info → aiagents4pharma-1.45.0.dist-info}/METADATA +115 -50
  282. aiagents4pharma-1.45.0.dist-info/RECORD +324 -0
  283. {aiagents4pharma-1.43.0.dist-info → aiagents4pharma-1.45.0.dist-info}/WHEEL +1 -2
  284. aiagents4pharma-1.43.0.dist-info/RECORD +0 -293
  285. aiagents4pharma-1.43.0.dist-info/top_level.txt +0 -1
  286. /aiagents4pharma/talk2scholars/tests/{test_state.py → test_states_state.py} +0 -0
  287. /aiagents4pharma/talk2scholars/tests/{test_pdf_paper_loader.py → test_utils_pdf_paper_loader.py} +0 -0
  288. /aiagents4pharma/talk2scholars/tests/{test_tool_helper_utils.py → test_utils_tool_helper_utils.py} +0 -0
  289. /aiagents4pharma/talk2scholars/tests/{test_zotero_pdf_downloader_utils.py → test_utils_zotero_pdf_downloader_utils.py} +0 -0
  290. {aiagents4pharma-1.43.0.dist-info → aiagents4pharma-1.45.0.dist-info}/licenses/LICENSE +0 -0
aiagents4pharma-1.43.0.dist-info/RECORD DELETED
@@ -1,293 +0,0 @@
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