aiagents4pharma 1.39.1__tar.gz → 1.39.2__tar.gz

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  1. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/PKG-INFO +5 -5
  2. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/README.md +4 -4
  3. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml +5 -0
  4. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml +5 -0
  5. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml +4 -0
  6. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml +2 -0
  7. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml +2 -0
  8. aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml +22 -0
  9. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/PKG-INFO +5 -5
  10. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/SOURCES.txt +6 -0
  11. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/pyproject.toml +9 -3
  12. aiagents4pharma-1.39.2/release_version.txt +1 -0
  13. aiagents4pharma-1.39.1/release_version.txt +0 -1
  14. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/LICENSE +0 -0
  15. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/__init__.py +0 -0
  16. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/__init__.py +0 -0
  17. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/agents/__init__.py +0 -0
  18. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py +0 -0
  19. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/configs/__init__.py +0 -0
  20. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py +0 -0
  21. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml +0 -0
  22. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/configs/config.yaml +0 -0
  23. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/states/__init__.py +0 -0
  24. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py +0 -0
  25. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/tests/__init__.py +0 -0
  26. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +0 -0
  27. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/__init__.py +0 -0
  28. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/agents/__init__.py +0 -0
  29. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py +0 -0
  30. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/api/__init__.py +0 -0
  31. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/api/kegg.py +0 -0
  32. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/api/ols.py +0 -0
  33. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/api/uniprot.py +0 -0
  34. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/__init__.py +0 -0
  35. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/agents/__init__.py +0 -0
  36. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py +0 -0
  37. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml +0 -0
  38. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/config.yaml +0 -0
  39. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/__init__.py +0 -0
  40. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py +0 -0
  41. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml +0 -0
  42. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py +0 -0
  43. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml +0 -0
  44. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py +0 -0
  45. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml +0 -0
  46. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/models/__init__.py +0 -0
  47. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/models/basico_model.py +0 -0
  48. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/models/sys_bio_model.py +0 -0
  49. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/states/__init__.py +0 -0
  50. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +0 -0
  51. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/__init__.py +0 -0
  52. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_api.py +0 -0
  53. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_ask_question.py +0 -0
  54. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_basico_model.py +0 -0
  55. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py +0 -0
  56. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py +0 -0
  57. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_integration.py +0 -0
  58. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py +0 -0
  59. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_param_scan.py +0 -0
  60. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_query_article.py +0 -0
  61. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_search_models.py +0 -0
  62. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_simulate_model.py +0 -0
  63. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_steady_state.py +0 -0
  64. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +0 -0
  65. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/__init__.py +0 -0
  66. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/ask_question.py +0 -0
  67. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/custom_plotter.py +0 -0
  68. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/get_annotation.py +0 -0
  69. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +0 -0
  70. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/load_arguments.py +0 -0
  71. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/load_biomodel.py +0 -0
  72. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/parameter_scan.py +0 -0
  73. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/query_article.py +0 -0
  74. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/search_models.py +0 -0
  75. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/simulate_model.py +0 -0
  76. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/steady_state.py +0 -0
  77. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2biomodels/tools/utils.py +0 -0
  78. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/__init__.py +0 -0
  79. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/agents/__init__.py +0 -0
  80. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/agents/scp_agent.py +0 -0
  81. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/states/__init__.py +0 -0
  82. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/states/state_talk2cells.py +0 -0
  83. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py +0 -0
  84. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/tools/__init__.py +0 -0
  85. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/tools/scp_agent/__init__.py +0 -0
  86. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py +0 -0
  87. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py +0 -0
  88. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/__init__.py +0 -0
  89. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/agents/__init__.py +0 -0
  90. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +0 -0
  91. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/__init__.py +0 -0
  92. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py +0 -0
  93. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml +0 -0
  94. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py +0 -0
  95. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py +0 -0
  96. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +0 -0
  97. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +0 -0
  98. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py +0 -0
  99. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py +0 -0
  100. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml +0 -0
  101. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py +0 -0
  102. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py +0 -0
  103. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml +0 -0
  104. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py +0 -0
  105. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml +0 -0
  106. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py +0 -0
  107. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py +0 -0
  108. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py +0 -0
  109. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py +0 -0
  110. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py +0 -0
  111. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/states/__init__.py +0 -0
  112. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py +0 -0
  113. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/__init__.py +0 -0
  114. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py +0 -0
  115. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py +0 -0
  116. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py +0 -0
  117. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py +0 -0
  118. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py +0 -0
  119. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py +0 -0
  120. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py +0 -0
  121. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py +0 -0
  122. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_summarization.py +0 -0
  123. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py +0 -0
  124. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py +0 -0
  125. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_nim_molmim.py +0 -0
  126. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py +0 -0
  127. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py +0 -0
  128. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py +0 -0
  129. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py +0 -0
  130. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py +0 -0
  131. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py +0 -0
  132. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py +0 -0
  133. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py +0 -0
  134. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py +0 -0
  135. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py +0 -0
  136. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/__init__.py +0 -0
  137. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py +0 -0
  138. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py +0 -0
  139. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py +0 -0
  140. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py +0 -0
  141. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py +0 -0
  142. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/__init__.py +0 -0
  143. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py +0 -0
  144. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py +0 -0
  145. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py +0 -0
  146. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/nim_molmim.py +0 -0
  147. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/ollama.py +0 -0
  148. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py +0 -0
  149. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py +0 -0
  150. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py +0 -0
  151. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py +0 -0
  152. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py +0 -0
  153. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py +0 -0
  154. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py +0 -0
  155. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py +0 -0
  156. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py +0 -0
  157. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py +0 -0
  158. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py +0 -0
  159. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py +0 -0
  160. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2knowledgegraphs/utils/pubchem_utils.py +0 -0
  161. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/__init__.py +0 -0
  162. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/__init__.py +0 -0
  163. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/main_agent.py +0 -0
  164. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/paper_download_agent.py +0 -0
  165. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/pdf_agent.py +0 -0
  166. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/s2_agent.py +0 -0
  167. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/agents/zotero_agent.py +0 -0
  168. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/__init__.py +0 -0
  169. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/__init__.py +0 -0
  170. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py +0 -0
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  173. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py +0 -0
  174. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py +0 -0
  175. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py +0 -0
  176. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +0 -0
  177. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py +0 -0
  178. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml +0 -0
  179. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/app/__init__.py +0 -0
  180. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py +0 -0
  181. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml +0 -0
  182. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/config.yaml +0 -0
  183. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/__init__.py +0 -0
  184. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py +0 -0
  185. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py +0 -0
  186. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py +0 -0
  187. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py +0 -0
  188. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml +0 -0
  189. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py +0 -0
  190. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py +0 -0
  191. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml +0 -0
  192. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/search/__init__.py +0 -0
  193. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/search/default.yaml +0 -0
  194. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py +0 -0
  195. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml +0 -0
  196. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py +0 -0
  197. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml +0 -0
  198. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py +0 -0
  199. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/configs/tools/zotero_write/default.yaml +0 -0
  200. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/state/__init__.py +0 -0
  201. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/state/state_talk2scholars.py +0 -0
  202. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/__init__.py +0 -0
  203. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_main_agent.py +0 -0
  204. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker_utils.py +0 -0
  205. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py +0 -0
  206. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_paper_download_biorxiv.py +0 -0
  207. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_paper_download_medrxiv.py +0 -0
  208. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py +0 -0
  209. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_pdf_agent.py +0 -0
  210. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py +0 -0
  211. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_read_helper_utils.py +0 -0
  212. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_agent.py +0 -0
  213. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_display_dataframe.py +0 -0
  214. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_multi.py +0 -0
  215. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_query_dataframe.py +0 -0
  216. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_retrieve.py +0 -0
  217. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_search.py +0 -0
  218. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_single.py +0 -0
  219. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_s2_utils_ext_ids.py +0 -0
  220. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_state.py +0 -0
  221. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_tool_helper_utils.py +0 -0
  222. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_agent.py +0 -0
  223. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_human_in_the_loop.py +0 -0
  224. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_path.py +0 -0
  225. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_pdf_downloader_utils.py +0 -0
  226. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_read.py +0 -0
  227. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tests/test_zotero_write.py +0 -0
  228. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/__init__.py +0 -0
  229. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/paper_download/__init__.py +0 -0
  230. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py +0 -0
  231. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py +0 -0
  232. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py +0 -0
  233. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/__init__.py +0 -0
  234. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py +0 -0
  235. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py +0 -0
  236. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/generate_answer.py +0 -0
  237. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/nvidia_nim_reranker.py +0 -0
  238. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/retrieve_chunks.py +0 -0
  239. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/tool_helper.py +0 -0
  240. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py +0 -0
  241. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/__init__.py +0 -0
  242. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py +0 -0
  243. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +0 -0
  244. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +0 -0
  245. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +0 -0
  246. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/search.py +0 -0
  247. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +0 -0
  248. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/utils/__init__.py +0 -0
  249. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/utils/multi_helper.py +0 -0
  250. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/utils/search_helper.py +0 -0
  251. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/s2/utils/single_helper.py +0 -0
  252. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/__init__.py +0 -0
  253. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/__init__.py +0 -0
  254. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py +0 -0
  255. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py +0 -0
  256. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py +0 -0
  257. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py +0 -0
  258. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py +0 -0
  259. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py +0 -0
  260. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/zotero_review.py +0 -0
  261. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py +0 -0
  262. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/dependency_links.txt +0 -0
  263. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/requires.txt +0 -0
  264. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/top_level.txt +0 -0
  265. {aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/setup.cfg +0 -0
{aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
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  Name: aiagents4pharma
3
- Version: 1.39.1
3
+ Version: 1.39.2
4
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  Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
5
5
  Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
@@ -145,7 +145,7 @@ LANGCHAIN_TRACING_V2=true # Optional for both agents
145
145
  LANGCHAIN_API_KEY=... # Optional for both agents
146
146
  ```
147
147
 
148
- [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
148
+ [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users)
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150
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  ##### **3. Start the application**
151
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@@ -154,7 +154,7 @@ chmod +x startup.sh
154
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  ./startup.sh # Add --cpu flag to force CPU mode if needed
155
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  ```
156
156
 
157
- [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
157
+ [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#about-startupsh)
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159
159
  ##### **To Run Talk2Biomodels / Talk2Scholars**
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@@ -196,11 +196,11 @@ To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key
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197
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  Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
198
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199
- If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma).
199
+ If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users).
200
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  **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
202
202
 
203
- [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
203
+ [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#to-run-multiple-agents-simultaneously)
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205
205
  #### Option 2: git (for developers and contributors)
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{aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/README.md RENAMED
@@ -78,7 +78,7 @@ LANGCHAIN_TRACING_V2=true # Optional for both agents
78
78
  LANGCHAIN_API_KEY=... # Optional for both agents
79
79
  ```
80
80
 
81
- [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
81
+ [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users)
82
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83
83
  ##### **3. Start the application**
84
84
 
@@ -87,7 +87,7 @@ chmod +x startup.sh
87
87
  ./startup.sh # Add --cpu flag to force CPU mode if needed
88
88
  ```
89
89
 
90
- [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
90
+ [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#about-startupsh)
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92
92
  ##### **To Run Talk2Biomodels / Talk2Scholars**
93
93
 
@@ -129,11 +129,11 @@ To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key
129
129
 
130
130
  Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
131
131
 
132
- If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma).
132
+ If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users).
133
133
 
134
134
  **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
135
135
 
136
- [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
136
+ [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#to-run-multiple-agents-simultaneously)
137
137
 
138
138
  #### Option 2: git (for developers and contributors)
139
139
 
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml ADDED
@@ -0,0 +1,5 @@
1
+ _target_: agents.paper_download_agent.get_app
2
+ paper_download_agent: |
3
+ You are the Paper Download Agent.
4
+
5
+ You are responsible for downloading PDFs of papers using their IDs. Use all the provied Ids to download the papers. Only when the user asks a question related to PDFs, please forward the query to the `question_and_answer` tool from the `pdf_agent`
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml ADDED
@@ -0,0 +1,5 @@
1
+ _target_: agents.pdf_agent.get_app
2
+ pdf_agent: |
3
+ You are the PDF Agent.
4
+
5
+ You are responsible for performing question-and-answer tasks on papers, articles, or PDFs
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml ADDED
@@ -0,0 +1,4 @@
1
+ api_url: "http://export.arxiv.org/api/query"
2
+ request_timeout: 10
3
+ chunk_size: 1024
4
+ pdf_base_url: "https://arxiv.org/pdf"
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml ADDED
@@ -0,0 +1,2 @@
1
+ api_url: "https://api.biorxiv.org/details/biorxiv/"
2
+ request_timeout: 20
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml ADDED
@@ -0,0 +1,2 @@
1
+ api_url: "https://api.biorxiv.org/details/medrxiv"
2
+ request_timeout: 20
aiagents4pharma-1.39.2/aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml ADDED
@@ -0,0 +1,22 @@
1
+ # Default configuration for the PDF question_and_answer Tool
2
+ chunk_size: 1200 # Number of characters per text chunk
3
+ chunk_overlap: 200 # Overlap between adjacent chunks
4
+ top_k_papers: 5 # Number of papers to rank and retrieve
5
+ top_k_chunks: 25 # Number of chunks to retrieve
6
+ reranker:
7
+ model: "nvidia/nv-rerankqa-mistral-4b-v3"
8
+ api_key: ${oc.env:NVIDIA_API_KEY}
9
+ prompt_template: |
10
+ You are a scientific research assistant specialized in reading and extracting information from research papers.
11
+ Your role is to answer questions by retrieving relevant information from the provided context.
12
+
13
+ - Provide detailed, structured, and well-argued explanations—not just brief summaries.
14
+ - Cite specific sources using onky the title of the paper.
15
+ - If the context is insufficient, clearly state that more information is needed.
16
+
17
+ Context:
18
+ {context}
19
+
20
+ Question: {question}
21
+
22
+ Your answer should be comprehensive, accurate, and clearly structured for a scientific audience.
{aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: aiagents4pharma
3
- Version: 1.39.1
3
+ Version: 1.39.2
4
4
  Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
5
5
  Classifier: Programming Language :: Python :: 3
6
6
  Classifier: License :: OSI Approved :: MIT License
@@ -145,7 +145,7 @@ LANGCHAIN_TRACING_V2=true # Optional for both agents
145
145
  LANGCHAIN_API_KEY=... # Optional for both agents
146
146
  ```
147
147
 
148
- [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
148
+ [Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users)
149
149
 
150
150
  ##### **3. Start the application**
151
151
 
@@ -154,7 +154,7 @@ chmod +x startup.sh
154
154
  ./startup.sh # Add --cpu flag to force CPU mode if needed
155
155
  ```
156
156
 
157
- [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
157
+ [More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#about-startupsh)
158
158
 
159
159
  ##### **To Run Talk2Biomodels / Talk2Scholars**
160
160
 
@@ -196,11 +196,11 @@ To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key
196
196
 
197
197
  Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
198
198
 
199
- If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma).
199
+ If you are using docker on Windows, please follow these [Windows Setup Notes](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users).
200
200
 
201
201
  **LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
202
202
 
203
- [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/install.md)
203
+ [More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#to-run-multiple-agents-simultaneously)
204
204
 
205
205
  #### Option 2: git (for developers and contributors)
206
206
 
{aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/aiagents4pharma.egg-info/SOURCES.txt RENAMED
@@ -167,7 +167,9 @@ aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py
167
167
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py
168
168
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml
169
169
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py
170
+ aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml
170
171
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py
172
+ aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml
171
173
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py
172
174
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml
173
175
  aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py
@@ -177,11 +179,15 @@ aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py
177
179
  aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml
178
180
  aiagents4pharma/talk2scholars/configs/tools/__init__.py
179
181
  aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py
182
+ aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml
180
183
  aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py
184
+ aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml
181
185
  aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py
186
+ aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml
182
187
  aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py
183
188
  aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml
184
189
  aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py
190
+ aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml
185
191
  aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py
186
192
  aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml
187
193
  aiagents4pharma/talk2scholars/configs/tools/search/__init__.py
{aiagents4pharma-1.39.1 → aiagents4pharma-1.39.2}/pyproject.toml RENAMED
@@ -102,13 +102,19 @@ aiagents4pharma = [
102
102
  "talk2scholars/configs/agents/talk2scholars/main_agent/*",
103
103
  "talk2scholars/configs/agents/talk2scholars/s2_agent/*",
104
104
  "talk2scholars/configs/agents/talk2scholars/zotero_agent/*",
105
+ "talk2scholars/configs/agents/talk2scholars/paper_download_agent/*",
106
+ "talk2scholars/configs/agents/talk2scholars/pdf_agent/*",
105
107
  "talk2scholars/configs/app/frontend/*",
106
- "talk2scholars/configs/tools/multi_paper_recommendation/*",
108
+ "talk2scholars/configs/tools/download_arxiv_paper/*",
109
+ "talk2scholars/configs/tools/download_medrxiv_paper/*",
110
+ "talk2scholars/configs/tools/download_biorxiv_paper/*",
111
+ "talk2scholars/configs/tools/question_and_answer/*",
107
112
  "talk2scholars/configs/tools/search/*",
108
- "talk2scholars/configs/tools/single_paper_recommendation/*",
109
113
  "talk2scholars/configs/tools/zotero_read/*",
110
- "talk2scholars/configs/tools/zotero_write/*",
114
+ "talk2scholars/configs/tools/multi_paper_recommendation/*",
111
115
  "talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/*",
116
+ "talk2scholars/configs/tools/single_paper_recommendation/*",
117
+ "talk2scholars/configs/tools/zotero_write/*",
112
118
 
113
119
  ]
114
120
 
aiagents4pharma-1.39.2/release_version.txt ADDED
@@ -0,0 +1 @@
1
+ v1.39.2
aiagents4pharma-1.39.1/release_version.txt DELETED
@@ -1 +0,0 @@
1
- v1.39.1