aiagents4pharma 1.8.0__py3-none-any.whl → 1.15.0__py3-none-any.whl

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 (85) hide show
  1. aiagents4pharma/__init__.py +9 -5
  2. aiagents4pharma/configs/__init__.py +5 -0
  3. aiagents4pharma/configs/config.yaml +4 -0
  4. aiagents4pharma/configs/talk2biomodels/__init__.py +6 -0
  5. aiagents4pharma/configs/talk2biomodels/agents/__init__.py +5 -0
  6. aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py +3 -0
  7. aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml +14 -0
  8. aiagents4pharma/configs/talk2biomodels/tools/__init__.py +4 -0
  9. aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py +3 -0
  10. aiagents4pharma/talk2biomodels/__init__.py +3 -0
  11. aiagents4pharma/talk2biomodels/agents/__init__.py +5 -0
  12. aiagents4pharma/talk2biomodels/agents/t2b_agent.py +96 -0
  13. aiagents4pharma/talk2biomodels/api/__init__.py +6 -0
  14. aiagents4pharma/talk2biomodels/api/kegg.py +83 -0
  15. aiagents4pharma/talk2biomodels/api/ols.py +72 -0
  16. aiagents4pharma/talk2biomodels/api/uniprot.py +35 -0
  17. aiagents4pharma/talk2biomodels/models/basico_model.py +29 -32
  18. aiagents4pharma/talk2biomodels/models/sys_bio_model.py +9 -6
  19. aiagents4pharma/talk2biomodels/states/__init__.py +5 -0
  20. aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +41 -0
  21. aiagents4pharma/talk2biomodels/tests/__init__.py +3 -0
  22. aiagents4pharma/talk2biomodels/tests/test_api.py +57 -0
  23. aiagents4pharma/talk2biomodels/tests/test_ask_question.py +44 -0
  24. aiagents4pharma/talk2biomodels/tests/test_basico_model.py +54 -0
  25. aiagents4pharma/talk2biomodels/tests/test_get_annotation.py +171 -0
  26. aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py +26 -0
  27. aiagents4pharma/talk2biomodels/tests/test_integration.py +126 -0
  28. aiagents4pharma/talk2biomodels/tests/test_param_scan.py +68 -0
  29. aiagents4pharma/talk2biomodels/tests/test_query_article.py +76 -0
  30. aiagents4pharma/talk2biomodels/tests/test_search_models.py +28 -0
  31. aiagents4pharma/talk2biomodels/tests/test_simulate_model.py +39 -0
  32. aiagents4pharma/talk2biomodels/tests/test_steady_state.py +90 -0
  33. aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +63 -0
  34. aiagents4pharma/talk2biomodels/tools/__init__.py +5 -0
  35. aiagents4pharma/talk2biomodels/tools/ask_question.py +61 -18
  36. aiagents4pharma/talk2biomodels/tools/custom_plotter.py +20 -14
  37. aiagents4pharma/talk2biomodels/tools/get_annotation.py +304 -0
  38. aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +11 -9
  39. aiagents4pharma/talk2biomodels/tools/load_arguments.py +114 -0
  40. aiagents4pharma/talk2biomodels/tools/load_biomodel.py +0 -1
  41. aiagents4pharma/talk2biomodels/tools/parameter_scan.py +287 -0
  42. aiagents4pharma/talk2biomodels/tools/query_article.py +59 -0
  43. aiagents4pharma/talk2biomodels/tools/simulate_model.py +35 -90
  44. aiagents4pharma/talk2biomodels/tools/steady_state.py +167 -0
  45. aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py +23 -0
  46. aiagents4pharma/talk2cells/tools/scp_agent/__init__.py +6 -0
  47. aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py +25 -0
  48. aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py +79 -0
  49. aiagents4pharma/talk2competitors/__init__.py +5 -0
  50. aiagents4pharma/talk2competitors/agents/__init__.py +6 -0
  51. aiagents4pharma/talk2competitors/agents/main_agent.py +130 -0
  52. aiagents4pharma/talk2competitors/agents/s2_agent.py +75 -0
  53. aiagents4pharma/talk2competitors/config/__init__.py +5 -0
  54. aiagents4pharma/talk2competitors/config/config.py +110 -0
  55. aiagents4pharma/talk2competitors/state/__init__.py +5 -0
  56. aiagents4pharma/talk2competitors/state/state_talk2competitors.py +32 -0
  57. aiagents4pharma/talk2competitors/tests/__init__.py +3 -0
  58. aiagents4pharma/talk2competitors/tests/test_langgraph.py +274 -0
  59. aiagents4pharma/talk2competitors/tools/__init__.py +7 -0
  60. aiagents4pharma/talk2competitors/tools/s2/__init__.py +8 -0
  61. aiagents4pharma/talk2competitors/tools/s2/display_results.py +25 -0
  62. aiagents4pharma/talk2competitors/tools/s2/multi_paper_rec.py +132 -0
  63. aiagents4pharma/talk2competitors/tools/s2/search.py +119 -0
  64. aiagents4pharma/talk2competitors/tools/s2/single_paper_rec.py +141 -0
  65. aiagents4pharma/talk2knowledgegraphs/__init__.py +2 -1
  66. aiagents4pharma/talk2knowledgegraphs/tests/__init__.py +0 -0
  67. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py +242 -0
  68. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py +29 -0
  69. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py +73 -0
  70. aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py +116 -0
  71. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py +47 -0
  72. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py +45 -0
  73. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py +40 -0
  74. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py +39 -0
  75. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py +117 -0
  76. aiagents4pharma/talk2knowledgegraphs/utils/__init__.py +5 -0
  77. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py +5 -0
  78. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py +36 -0
  79. aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py +123 -0
  80. {aiagents4pharma-1.8.0.dist-info → aiagents4pharma-1.15.0.dist-info}/METADATA +44 -25
  81. aiagents4pharma-1.15.0.dist-info/RECORD +102 -0
  82. aiagents4pharma-1.8.0.dist-info/RECORD +0 -35
  83. {aiagents4pharma-1.8.0.dist-info → aiagents4pharma-1.15.0.dist-info}/LICENSE +0 -0
  84. {aiagents4pharma-1.8.0.dist-info → aiagents4pharma-1.15.0.dist-info}/WHEEL +0 -0
  85. {aiagents4pharma-1.8.0.dist-info → aiagents4pharma-1.15.0.dist-info}/top_level.txt +0 -0
aiagents4pharma-1.15.0.dist-info/RECORD ADDED
@@ -0,0 +1,102 @@
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+ aiagents4pharma/__init__.py,sha256=5muWWIg89VHPybfxonO_5xOMJPasKNsGdQRhozDaEmk,177
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+ aiagents4pharma/configs/__init__.py,sha256=hNkSrXw1Ix1HhkGn_aaidr2coBYySfM0Hm_pMeRcX7k,76
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+ aiagents4pharma/configs/config.yaml,sha256=4t7obD0gOSfqnDDZZBB53ZC7zsmk7QDcM7T_1Hf1wIQ,112
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+ aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
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+ aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
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+ aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
7
+ aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=eLrJIezoPJ6_DvrSYsi3eALl03o0hJhntej3ESoeKKg,551
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+ aiagents4pharma/configs/talk2biomodels/tools/__init__.py,sha256=WxK7h5n39l-NSMvjLZyxDqzwWlVA6mQ69gzsbJ17vEk,72
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+ aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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+ aiagents4pharma/talk2biomodels/__init__.py,sha256=2ICwVh1u07SZv31Jd2DKHobauOxWNWY29_Gqq3kOnNQ,159
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+ aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
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+ aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=5h4n7dF13KuT5f9vzfK7EQTu_b0a0hB7ScLFlTKaNko,3449
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+ aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
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+ aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
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+ aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
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+ aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=aPUAVBR7UYXDuuhDpKezAK2aTMzo-NxFYFq6C0W5u6U,1175
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+ aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
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+ aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
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+ aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
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+ aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
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+ aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=d_tDh93ip36hlUpMh-KOkYfBZ2SQwZlaY8p-1ZWKPhY,1355
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+ aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
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+ aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
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+ aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=yRkKK9HLB1bGGWm_WwOckwaUmmRfRAD9z2NFFGLIGTY,1560
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+ aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
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+ aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=mKOacH28OB6xpFPygAlhBUQS93gnI5j-jAfSGu6uQMI,7465
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+ aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=6kChSc_MCnzXlDao_R8pKdhIELlg3MZrUa7hg8piJ4E,883
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+ aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=ZsBXWSFLIcdzrO8obLJx8Ib2f9AAW3BI7H9Eqjdc5to,5057
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+ aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
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+ aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=HhFgU5HzCipecEYlfbpPxN-SCIPKep22gpXCutWXRb8,2820
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+ aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=8ODFubLxWYD3I3KQWuUnJ2GZRzMjFpXInFBLxKxG_ME,929
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+ aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
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+ aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=zt15KQoQku6jyzvpJXwINGTyhEnQl8wX81ueHlxnUCA,3467
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+ aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
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+ aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
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+ aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=hWXg7o0sTMDWH1ZnxtashTALvXpvNoaomfcniEhw-Bw,4684
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+ aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
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+ aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=jCGkidvafuk1YzAH9GFwaVUF35maXTjg6XqBg_zLk44,12475
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+ aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=qA-4FOI-O728Nmn7s8JJ8HKwxvA9MZbst7NkPKTAMV4,5391
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+ aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
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+ aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
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+ aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
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+ aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=1tpYiE69MYcqiNcRaBgNiYzkkNmuTnlxLuBL_FnRuBU,2058
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+ aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
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+ aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
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+ aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
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+ aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
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+ aiagents4pharma/talk2cells/agents/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
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+ aiagents4pharma/talk2cells/agents/scp_agent.py,sha256=gDMfhUNWHa_XWOqm1Ql6yLAdI_7bnIk5sRYn43H2sYk,3090
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+ aiagents4pharma/talk2cells/states/__init__.py,sha256=e4s8pHZaR6UC42DtmsOzCVms5gxp5QEzLE4bG54YYko,135
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+ aiagents4pharma/talk2cells/states/state_talk2cells.py,sha256=en5LikmabPZA6lLVpmYXff0Q3Fno0N2PBSMxk3gLWaE,253
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+ aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py,sha256=f8bsUXvEElvYM5KGvpPzI1xOR5Y_zpm3_Jzk7gCX1CE,732
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+ aiagents4pharma/talk2cells/tools/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
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+ aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=s7g0lyH1lMD9pcWHLPtwRJRvzmTh2II7DrxyLulpjmQ,163
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+ aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQaiOU2rn55A3sIIFKlXi4SK3iKgySvUDrtQ,600
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+ aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
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+ aiagents4pharma/talk2competitors/__init__.py,sha256=haaikzND3c0Euqq86ndA4fl9q42aOop5rYG_8Zh1D-o,119
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+ aiagents4pharma/talk2competitors/agents/__init__.py,sha256=ykszlVGxz3egLHZAttlNoTPxIrnQJZYva_ssR8fwIFk,117
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+ aiagents4pharma/talk2competitors/agents/main_agent.py,sha256=UoHCpZd-HoeG0B6_gAF1cEP2OqMvrTuGe7MZDwL_u1U,3878
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+ aiagents4pharma/talk2competitors/agents/s2_agent.py,sha256=eTrhc4ZPvWOUWMHNYxK0WltsZedZUnAWNu-TeUa-ruk,2501
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+ aiagents4pharma/talk2competitors/config/__init__.py,sha256=HyM6paOpKZ5_tZnyVheSAFmxjT6Mb3PxvWKfP0rz-dE,113
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+ aiagents4pharma/talk2competitors/config/config.py,sha256=jd4ltMBJyTztm9wT7j3ujOyYxL2SXRgxQJ4OZUBmCG4,5387
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+ aiagents4pharma/talk2competitors/state/__init__.py,sha256=DzFjV3hZNes_pL4bDW2_8RsyK9BJcj6ejfBzU0KWn1k,106
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+ aiagents4pharma/talk2competitors/state/state_talk2competitors.py,sha256=GUl1ZfM77XsjIEu-3xy4dtvaiMTA1pXf6i1ozVcX5Gg,993
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+ aiagents4pharma/talk2competitors/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
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+ aiagents4pharma/talk2competitors/tests/test_langgraph.py,sha256=sEROK1aU3wFqJhZohONVI6Pr7t1d3PSqs-4erVIyiJw,9283
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+ aiagents4pharma/talk2competitors/tools/__init__.py,sha256=YudBDRwaEzDnAcpxGZvEOfyh5-6xd51CTvTKTkywgXw,68
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+ aiagents4pharma/talk2competitors/tools/s2/__init__.py,sha256=9RQH3efTj6qkXk0ICKSc7Mzpkitt4gRGsQ1pGPrrREU,181
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+ aiagents4pharma/talk2competitors/tools/s2/display_results.py,sha256=B8JJGohi1Eyx8C3MhO_SiyQP3R6hPyUKJOAzcHmq3FU,584
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+ aiagents4pharma/talk2competitors/tools/s2/multi_paper_rec.py,sha256=FYLt47DAk6WOKfEk1Gj9zVvJGNyxA283PCp8IKW9U5M,4262
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+ aiagents4pharma/talk2competitors/tools/s2/search.py,sha256=pppjrQv5-8ep4fnqgTSBNgnbSnQsVIcNrRrH0p2TP1o,4025
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+ aiagents4pharma/talk2competitors/tools/s2/single_paper_rec.py,sha256=dAfUQxI7T5eu0eDxK8VAl7-JH0Wnw24CVkOQqwj-hXc,4810
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+ aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=4smVQoSMM6rflVnNkABqlDAAlSn4bYsq7rMVWjRGvis,103
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+ aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py,sha256=L3gPuHskSegmtXskVrLIYr7FXe_ibKgJ2GGr1_Wok6k,173
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+ aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
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+ aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=-LaPLse8BkALqwFetNK7wch2dt9Dz6QKGKZKBKM6bIk,409
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+ aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=KBMhCJ7yjMWqQJJctFYdpjYAlwv48Jl6i1dddXP4f08,7599
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+ aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py,sha256=Y-6-nORsnBJlU6rH0skyfr9S9J4PfTWK-af_p5UuknQ,7483
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+ aiagents4pharma/talk2knowledgegraphs/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py,sha256=crH0eFA3P8P6IYzi1UWNa4YvRVrtlBzoScf9NaE1lDk,9827
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py,sha256=NFUlsZvhfIrkF4YenWfahrLK93Xhm5UYEGG_uYN2LVM,566
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py,sha256=Pvu0r93CpnhjkfMxc-EiVLpAJ04FdW9iTamCnetu654,2272
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py,sha256=TuIsqcN1Mww3DTqGk6ebgJBWzUWdMWEq2yRQuYSFqvA,4416
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py,sha256=uYFoE_6zeU10_1mLLAHUr5c4S2XZMSc0Q_860o-KWEw,1517
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