aiagents4pharma 1.46.1__tar.gz → 1.46.3__tar.gz

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  1. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/dependabot.yml +1 -18
  2. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/docker_build.yml +6 -6
  3. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/docker_compose_release.yml +36 -9
  4. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/mkdocs_deploy.yml +2 -2
  5. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/package_build.yml +4 -4
  6. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/pr-automation.yml +1 -1
  7. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/release.yml +3 -3
  8. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/security_audit.yml +7 -7
  9. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/sonarcloud.yml +3 -3
  10. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2aiagents4pharma.yml +5 -5
  11. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2biomodels.yml +5 -5
  12. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2cells.yml +5 -5
  13. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2knowledgegraphs.yml +5 -5
  14. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2scholars.yml +5 -5
  15. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/PKG-INFO +31 -30
  16. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/README.md +1 -0
  17. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/docs/index.md +1 -0
  18. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/package-lock.json +2 -2
  19. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/package.json +1 -1
  20. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/pyproject.toml +32 -32
  21. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/uv.lock +493 -309
  22. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.coveragerc +0 -0
  23. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/CODEOWNERS +0 -0
  24. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
  25. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  26. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/ISSUE_TEMPLATE/documentation.md +0 -0
  27. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
  28. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/ISSUE_TEMPLATE/question.md +0 -0
  29. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  30. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.github/labeler.yml +0 -0
  31. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.gitignore +0 -0
  32. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/.pre-commit-config.yaml +0 -0
  33. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/CHANGELOG.md +0 -0
  34. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/CODE_OF_CONDUCT.md +0 -0
  35. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/CONTRIBUTING.md +0 -0
  36. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/LICENSE +0 -0
  37. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/SECURITY.md +0 -0
  38. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/__init__.py +0 -0
  39. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/.dockerignore +0 -0
  40. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/Dockerfile +0 -0
  41. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/README.md +0 -0
  42. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/__init__.py +0 -0
  43. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/agents/__init__.py +0 -0
  44. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py +0 -0
  45. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/__init__.py +0 -0
  46. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py +0 -0
  47. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml +0 -0
  48. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/app/__init__.py +0 -0
  49. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/__init__.py +0 -0
  50. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/default.yaml +0 -0
  51. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/configs/config.yaml +0 -0
  52. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example +0 -0
  53. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml +0 -0
  54. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example +0 -0
  55. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/docker-compose.yml +0 -0
  56. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/install.md +0 -0
  57. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/states/__init__.py +0 -0
  58. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py +0 -0
  59. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/tests/__init__.py +0 -0
  60. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +0 -0
  61. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/.dockerignore +0 -0
  62. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/Dockerfile +0 -0
  63. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/README.md +0 -0
  64. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/__init__.py +0 -0
  65. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/agents/__init__.py +0 -0
  66. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py +0 -0
  67. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/api/__init__.py +0 -0
  68. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/api/ols.py +0 -0
  69. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/api/uniprot.py +0 -0
  70. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/__init__.py +0 -0
  71. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/agents/__init__.py +0 -0
  72. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py +0 -0
  73. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml +0 -0
  74. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/app/__init__.py +0 -0
  75. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/app/frontend/__init__.py +0 -0
  76. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/app/frontend/default.yaml +0 -0
  77. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/config.yaml +0 -0
  78. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/__init__.py +0 -0
  79. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py +0 -0
  80. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml +0 -0
  81. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/__init__.py +0 -0
  82. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml +0 -0
  83. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py +0 -0
  84. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml +0 -0
  85. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/install.md +0 -0
  86. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/models/__init__.py +0 -0
  87. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/models/basico_model.py +0 -0
  88. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/models/sys_bio_model.py +0 -0
  89. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/states/__init__.py +0 -0
  90. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py +0 -0
  91. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml +0 -0
  92. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/__init__.py +0 -0
  93. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf +0 -0
  94. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_api.py +0 -0
  95. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_ask_question.py +0 -0
  96. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_basico_model.py +0 -0
  97. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py +0 -0
  98. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py +0 -0
  99. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_integration.py +0 -0
  100. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py +0 -0
  101. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_param_scan.py +0 -0
  102. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_query_article.py +0 -0
  103. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_search_models.py +0 -0
  104. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_simulate_model.py +0 -0
  105. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_steady_state.py +0 -0
  106. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py +0 -0
  107. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/__init__.py +0 -0
  108. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/ask_question.py +0 -0
  109. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/custom_plotter.py +0 -0
  110. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/get_annotation.py +0 -0
  111. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/get_modelinfo.py +0 -0
  112. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/load_arguments.py +0 -0
  113. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/load_biomodel.py +0 -0
  114. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/parameter_scan.py +0 -0
  115. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/query_article.py +0 -0
  116. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/search_models.py +0 -0
  117. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/simulate_model.py +0 -0
  118. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/steady_state.py +0 -0
  119. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2biomodels/tools/utils.py +0 -0
  120. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/README.md +0 -0
  121. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/__init__.py +0 -0
  122. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/agents/__init__.py +0 -0
  123. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/agents/scp_agent.py +0 -0
  124. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/states/__init__.py +0 -0
  125. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/states/state_talk2cells.py +0 -0
  126. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/tests/scp_agent/test_scp_agent.py +0 -0
  127. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/tools/__init__.py +0 -0
  128. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/tools/scp_agent/__init__.py +0 -0
  129. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py +0 -0
  130. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py +0 -0
  131. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/.dockerignore +0 -0
  132. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/Dockerfile +0 -0
  133. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/README.md +0 -0
  134. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/__init__.py +0 -0
  135. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/agents/__init__.py +0 -0
  136. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +0 -0
  137. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/__init__.py +0 -0
  138. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py +0 -0
  139. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml +0 -0
  140. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py +0 -0
  141. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py +0 -0
  142. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +0 -0
  143. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +0 -0
  144. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py +0 -0
  145. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py +0 -0
  146. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml +0 -0
  147. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py +0 -0
  148. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +0 -0
  149. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py +0 -0
  150. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml +0 -0
  151. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py +0 -0
  152. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml +0 -0
  153. {aiagents4pharma-1.46.1 → aiagents4pharma-1.46.3}/aiagents4pharma/talk2knowledgegraphs/configs/utils/database/milvus/__init__.py +0 -0
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  # Disabled for now: repo has no Dockerfiles or Kubernetes manifests
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+ RELEASE_BODY=$(gh release view "$VERSION" --json body --jq .body 2>/dev/null || echo "")
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+
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+ # If no release found or empty, create basic release info from git
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+ else
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+ RELEASE_NOTES="$RELEASE_BODY"
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+ fi
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+ fi
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+ ---
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  ## 🚀 Ready-to-Deploy Docker Configurations
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  **One-click deployment** for all AIAgents4Pharma applications with the latest updates from ${{ needs.detect-changes.outputs.version }}.
344
377
 
345
- ### 📦 What's New in This Release
346
- - **Updated Docker images** with latest application code
347
- - **Production-ready** compose configurations for CPU & GPU
348
- - **Complete setup** with Milvus, Minio, and all dependencies
349
- - **Environment templates** for easy configuration
350
-
351
378
  ### ⚡ Quick Deploy
352
379
  ```bash
353
380
  # Download and extract
@@ -15,7 +15,7 @@ jobs:
15
15
  deploy:
16
16
  runs-on: ubuntu-latest
17
17
  steps:
18
- - uses: actions/checkout@v4
18
+ - uses: actions/checkout@v5
19
19
 
20
20
  - name: Configure Git Credentials
21
21
  run: |
@@ -23,7 +23,7 @@ jobs:
23
23
  git config user.email 41898282+github-actions[bot]@users.noreply.github.com
24
24
 
25
25
  - name: Install uv
26
- uses: astral-sh/setup-uv@v4
26
+ uses: astral-sh/setup-uv@v6
27
27
 
28
28
  - name: Set up Python
29
29
  run: uv python install 3.12
@@ -19,12 +19,12 @@ jobs:
19
19
  version: ${{ steps.version.outputs.version }}
20
20
 
21
21
  steps:
22
- - uses: actions/checkout@v4
22
+ - uses: actions/checkout@v5
23
23
  with:
24
24
  fetch-depth: 0
25
25
 
26
26
  - name: Install uv
27
- uses: astral-sh/setup-uv@v4
27
+ uses: astral-sh/setup-uv@v6
28
28
 
29
29
  - name: Set up Python
30
30
  run: uv python install 3.12
@@ -75,13 +75,13 @@ jobs:
75
75
 
76
76
  steps:
77
77
  - name: Download build artifacts
78
- uses: actions/download-artifact@v4
78
+ uses: actions/download-artifact@v5
79
79
  with:
80
80
  name: dist-artifacts
81
81
  path: dist/
82
82
 
83
83
  - name: Install uv
84
- uses: astral-sh/setup-uv@v4
84
+ uses: astral-sh/setup-uv@v6
85
85
 
86
86
  - name: Set up Python ${{ matrix.python-version }}
87
87
  run: uv python install ${{ matrix.python-version }}
@@ -34,7 +34,7 @@ jobs:
34
34
 
35
35
  # Auto-label based on files changed
36
36
  - name: Checkout Repository
37
- uses: actions/checkout@v4
37
+ uses: actions/checkout@v5
38
38
 
39
39
  - name: Label PR based on files changed
40
40
  uses: actions/labeler@v5
@@ -20,12 +20,12 @@ jobs:
20
20
  runs-on: ubuntu-latest
21
21
 
22
22
  steps:
23
- - uses: actions/checkout@v4
23
+ - uses: actions/checkout@v5
24
24
  with:
25
25
  fetch-depth: 0
26
26
 
27
27
  - name: Install uv
28
- uses: astral-sh/setup-uv@v4
28
+ uses: astral-sh/setup-uv@v6
29
29
 
30
30
  - name: Set up Python
31
31
  run: uv python install 3.12
@@ -82,7 +82,7 @@ jobs:
82
82
  skip-existing: true
83
83
 
84
84
  - name: Create GitHub Release
85
- uses: softprops/action-gh-release@v1
85
+ uses: softprops/action-gh-release@v2
86
86
  with:
87
87
  files: dist/*
88
88
  tag_name: ${{ env.RELEASE_VERSION }}
@@ -24,10 +24,10 @@ jobs:
24
24
  runs-on: ubuntu-latest
25
25
 
26
26
  steps:
27
- - uses: actions/checkout@v4
27
+ - uses: actions/checkout@v5
28
28
 
29
29
  - name: Install uv
30
- uses: astral-sh/setup-uv@v4
30
+ uses: astral-sh/setup-uv@v6
31
31
 
32
32
  - name: Set up Python
33
33
  run: uv python install 3.12
@@ -71,16 +71,16 @@ jobs:
71
71
  if: always()
72
72
 
73
73
  steps:
74
- - uses: actions/checkout@v4
74
+ - uses: actions/checkout@v5
75
75
 
76
76
  - name: Download reports
77
- uses: actions/download-artifact@v4
77
+ uses: actions/download-artifact@v5
78
78
  with:
79
79
  pattern: "*-report*"
80
80
  merge-multiple: true
81
81
 
82
82
  - name: Install uv
83
- uses: astral-sh/setup-uv@v4
83
+ uses: astral-sh/setup-uv@v6
84
84
 
85
85
  - name: Set up Python
86
86
  run: uv python install 3.12
@@ -111,10 +111,10 @@ jobs:
111
111
  if: always()
112
112
 
113
113
  steps:
114
- - uses: actions/checkout@v4
114
+ - uses: actions/checkout@v5
115
115
 
116
116
  - name: Download all reports
117
- uses: actions/download-artifact@v4
117
+ uses: actions/download-artifact@v5
118
118
  with:
119
119
  pattern: "*-report*"
120
120
  merge-multiple: true
@@ -21,13 +21,13 @@ jobs:
21
21
 
22
22
  steps:
23
23
  - name: Checkout code
24
- uses: actions/checkout@v4
24
+ uses: actions/checkout@v5
25
25
  with:
26
26
  fetch-depth: 0 # Shallow clones should be disabled for better analysis
27
27
  ref: ${{ github.event.workflow_run.head_branch }}
28
28
 
29
29
  - name: Download test artifacts
30
- uses: actions/download-artifact@v4
30
+ uses: actions/download-artifact@v5
31
31
  with:
32
32
  github-token: ${{ secrets.GITHUB_TOKEN }}
33
33
  run-id: ${{ github.event.workflow_run.id }}
@@ -43,7 +43,7 @@ jobs:
43
43
  fi
44
44
 
45
45
  - name: SonarCloud Scan
46
- uses: SonarSource/sonarqube-scan-action@v5.0.0
46
+ uses: SonarSource/sonarqube-scan-action@v5.3.1
47
47
  env:
48
48
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
49
49
  SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -22,12 +22,12 @@ jobs:
22
22
  name: Code Quality
23
23
  runs-on: ubuntu-latest
24
24
  steps:
25
- - uses: actions/checkout@v4
25
+ - uses: actions/checkout@v5
26
26
  with:
27
27
  fetch-depth: 0
28
28
 
29
29
  - name: Install uv
30
- uses: astral-sh/setup-uv@v4
30
+ uses: astral-sh/setup-uv@v6
31
31
 
32
32
  - name: Set up Python
33
33
  run: uv python install 3.12
@@ -76,12 +76,12 @@ jobs:
76
76
  runs-on: ${{ matrix.os }}
77
77
 
78
78
  steps:
79
- - uses: actions/checkout@v4
79
+ - uses: actions/checkout@v5
80
80
  with:
81
81
  fetch-depth: 0
82
82
 
83
83
  - name: Install uv
84
- uses: astral-sh/setup-uv@v4
84
+ uses: astral-sh/setup-uv@v6
85
85
 
86
86
  - name: Set up Python ${{ matrix.python-version }}
87
87
  run: uv python install ${{ matrix.python-version }}
@@ -169,7 +169,7 @@ jobs:
169
169
 
170
170
  - name: Upload coverage to Codecov
171
171
  if: matrix.os == 'ubuntu-latest'
172
- uses: codecov/codecov-action@v4
172
+ uses: codecov/codecov-action@v5
173
173
  with:
174
174
  file: ./coverage.xml
175
175
  flags: talk2aiagents4pharma
@@ -19,12 +19,12 @@ jobs:
19
19
  name: Code Quality
20
20
  runs-on: ubuntu-latest
21
21
  steps:
22
- - uses: actions/checkout@v4
22
+ - uses: actions/checkout@v5
23
23
  with:
24
24
  fetch-depth: 0
25
25
 
26
26
  - name: Install uv
27
- uses: astral-sh/setup-uv@v4
27
+ uses: astral-sh/setup-uv@v6
28
28
 
29
29
  - name: Set up Python
30
30
  run: uv python install 3.12
@@ -73,12 +73,12 @@ jobs:
73
73
  runs-on: ${{ matrix.os }}
74
74
 
75
75
  steps:
76
- - uses: actions/checkout@v4
76
+ - uses: actions/checkout@v5
77
77
  with:
78
78
  fetch-depth: 0
79
79
 
80
80
  - name: Install uv
81
- uses: astral-sh/setup-uv@v4
81
+ uses: astral-sh/setup-uv@v6
82
82
 
83
83
  - name: Set up Python ${{ matrix.python-version }}
84
84
  run: uv python install ${{ matrix.python-version }}
@@ -106,7 +106,7 @@ jobs:
106
106
 
107
107
  - name: Upload coverage to Codecov
108
108
  if: matrix.os == 'ubuntu-latest'
109
- uses: codecov/codecov-action@v4
109
+ uses: codecov/codecov-action@v5
110
110
  with:
111
111
  file: ./coverage.xml
112
112
  flags: talk2biomodels
@@ -19,12 +19,12 @@ jobs:
19
19
  name: Code Quality
20
20
  runs-on: ubuntu-latest
21
21
  steps:
22
- - uses: actions/checkout@v4
22
+ - uses: actions/checkout@v5
23
23
  with:
24
24
  fetch-depth: 0
25
25
 
26
26
  - name: Install uv
27
- uses: astral-sh/setup-uv@v4
27
+ uses: astral-sh/setup-uv@v6
28
28
 
29
29
  - name: Set up Python
30
30
  run: uv python install 3.12
@@ -73,12 +73,12 @@ jobs:
73
73
  runs-on: ${{ matrix.os }}
74
74
 
75
75
  steps:
76
- - uses: actions/checkout@v4
76
+ - uses: actions/checkout@v5
77
77
  with:
78
78
  fetch-depth: 0
79
79
 
80
80
  - name: Install uv
81
- uses: astral-sh/setup-uv@v4
81
+ uses: astral-sh/setup-uv@v6
82
82
 
83
83
  - name: Set up Python ${{ matrix.python-version }}
84
84
  run: uv python install ${{ matrix.python-version }}
@@ -106,7 +106,7 @@ jobs:
106
106
 
107
107
  - name: Upload coverage to Codecov
108
108
  if: matrix.os == 'ubuntu-latest'
109
- uses: codecov/codecov-action@v4
109
+ uses: codecov/codecov-action@v5
110
110
  with:
111
111
  file: ./coverage.xml
112
112
  flags: talk2cells
@@ -20,12 +20,12 @@ jobs:
20
20
  name: Code Quality
21
21
  runs-on: ubuntu-latest
22
22
  steps:
23
- - uses: actions/checkout@v4
23
+ - uses: actions/checkout@v5
24
24
  with:
25
25
  fetch-depth: 0
26
26
 
27
27
  - name: Install uv
28
- uses: astral-sh/setup-uv@v4
28
+ uses: astral-sh/setup-uv@v6
29
29
 
30
30
  - name: Set up Python
31
31
  run: uv python install 3.12
@@ -74,12 +74,12 @@ jobs:
74
74
  runs-on: ${{ matrix.os }}
75
75
 
76
76
  steps:
77
- - uses: actions/checkout@v4
77
+ - uses: actions/checkout@v5
78
78
  with:
79
79
  fetch-depth: 0
80
80
 
81
81
  - name: Install uv
82
- uses: astral-sh/setup-uv@v4
82
+ uses: astral-sh/setup-uv@v6
83
83
 
84
84
  - name: Set up Python ${{ matrix.python-version }}
85
85
  run: uv python install ${{ matrix.python-version }}
@@ -167,7 +167,7 @@ jobs:
167
167
 
168
168
  - name: Upload coverage to Codecov
169
169
  if: matrix.os == 'ubuntu-latest'
170
- uses: codecov/codecov-action@v4
170
+ uses: codecov/codecov-action@v5
171
171
  with:
172
172
  file: ./coverage.xml
173
173
  flags: talk2knowledgegraphs
@@ -21,12 +21,12 @@ jobs:
21
21
  name: Code Quality
22
22
  runs-on: ubuntu-latest
23
23
  steps:
24
- - uses: actions/checkout@v4
24
+ - uses: actions/checkout@v5
25
25
  with:
26
26
  fetch-depth: 0
27
27
 
28
28
  - name: Install uv
29
- uses: astral-sh/setup-uv@v4
29
+ uses: astral-sh/setup-uv@v6
30
30
 
31
31
  - name: Set up Python
32
32
  run: uv python install 3.12
@@ -75,12 +75,12 @@ jobs:
75
75
  runs-on: ${{ matrix.os }}
76
76
 
77
77
  steps:
78
- - uses: actions/checkout@v4
78
+ - uses: actions/checkout@v5
79
79
  with:
80
80
  fetch-depth: 0
81
81
 
82
82
  - name: Install uv
83
- uses: astral-sh/setup-uv@v4
83
+ uses: astral-sh/setup-uv@v6
84
84
 
85
85
  - name: Set up Python ${{ matrix.python-version }}
86
86
  run: uv python install ${{ matrix.python-version }}
@@ -108,7 +108,7 @@ jobs:
108
108
 
109
109
  - name: Upload coverage to Codecov
110
110
  if: matrix.os == 'ubuntu-latest'
111
- uses: codecov/codecov-action@v4
111
+ uses: codecov/codecov-action@v5
112
112
  with:
113
113
  file: ./coverage.xml
114
114
  flags: talk2scholars
@@ -1,89 +1,89 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: aiagents4pharma
3
- Version: 1.46.1
3
+ Version: 1.46.3
4
4
  Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
5
5
  License-File: LICENSE
6
6
  Classifier: License :: OSI Approved :: MIT License
7
7
  Classifier: Operating System :: OS Independent
8
8
  Classifier: Programming Language :: Python :: 3
9
9
  Requires-Python: >=3.12
10
- Requires-Dist: anndata==0.11.3
10
+ Requires-Dist: anndata==0.12.2
11
11
  Requires-Dist: azure-identity==1.24.0
12
- Requires-Dist: beautifulsoup4==4.13.4
12
+ Requires-Dist: beautifulsoup4==4.13.5
13
13
  Requires-Dist: cell2sentence==1.1.0
14
14
  Requires-Dist: cloudscraper==1.2.71
15
15
  Requires-Dist: copasi-basico==0.84
16
- Requires-Dist: coverage==7.6.4
16
+ Requires-Dist: coverage==7.10.6
17
17
  Requires-Dist: datasets==4.0.0
18
- Requires-Dist: einops==0.8.0
18
+ Requires-Dist: einops==0.8.1
19
19
  Requires-Dist: gdown==5.2.0
20
20
  Requires-Dist: gravis==0.1.0
21
- Requires-Dist: gseapy==1.1.8
22
- Requires-Dist: h5py==3.13.0
21
+ Requires-Dist: gseapy==1.1.9
22
+ Requires-Dist: h5py==3.14.0
23
23
  Requires-Dist: huggingface-hub==0.34.4
24
24
  Requires-Dist: hydra-core==1.3.2
25
- Requires-Dist: igraph==0.11.8
26
- Requires-Dist: ipykernel==6.29.5
25
+ Requires-Dist: igraph==0.11.9
26
+ Requires-Dist: ipykernel==6.30.1
27
27
  Requires-Dist: ipython==8.32.0
28
- Requires-Dist: joblib==1.4.2
28
+ Requires-Dist: joblib==1.5.2
29
29
  Requires-Dist: langchain-community==0.3.5
30
30
  Requires-Dist: langchain-core==0.3.40
31
- Requires-Dist: langchain-experimental==0.3.3
32
- Requires-Dist: langchain-milvus==0.2.0
31
+ Requires-Dist: langchain-experimental==0.3.4
32
+ Requires-Dist: langchain-milvus==0.2.1
33
33
  Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
34
34
  Requires-Dist: langchain-ollama==0.2.3
35
35
  Requires-Dist: langchain-openai==0.3.0
36
36
  Requires-Dist: langchain==0.3.7
37
37
  Requires-Dist: langgraph-supervisor==0.0.9
38
38
  Requires-Dist: langgraph==0.3.34
39
- Requires-Dist: matplotlib==3.9.2
40
- Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
39
+ Requires-Dist: matplotlib==3.10.6
40
+ Requires-Dist: mkdocs-include-markdown-plugin==7.1.7
41
41
  Requires-Dist: mkdocs-jupyter==0.25.1
42
- Requires-Dist: mkdocs-material==9.5.47
42
+ Requires-Dist: mkdocs-material==9.6.18
43
43
  Requires-Dist: mkdocs==1.6.1
44
- Requires-Dist: mkdocstrings-python==1.12.2
45
- Requires-Dist: mkdocstrings==0.27.0
44
+ Requires-Dist: mkdocstrings-python==1.18.2
45
+ Requires-Dist: mkdocstrings==0.30.0
46
46
  Requires-Dist: nbformat==5.10.4
47
47
  Requires-Dist: numpy==1.26.4
48
48
  Requires-Dist: ollama==0.4.7
49
49
  Requires-Dist: openai==1.59.6
50
50
  Requires-Dist: openpyxl==3.1.5
51
- Requires-Dist: pandas==2.2.3
51
+ Requires-Dist: pandas==2.3.2
52
52
  Requires-Dist: pcst-fast==1.0.10
53
53
  Requires-Dist: plotly-express==0.4.1
54
- Requires-Dist: plotly==5.24.1
54
+ Requires-Dist: plotly==6.3.0
55
55
  Requires-Dist: pubchempy==1.0.4
56
56
  Requires-Dist: pyarrow==21.0.0
57
- Requires-Dist: pydantic==2.10.5
57
+ Requires-Dist: pydantic==2.11.7
58
58
  Requires-Dist: pygeneconverter==0.3
59
- Requires-Dist: pylint==3.3.1
60
- Requires-Dist: pymilvus==2.5.11
59
+ Requires-Dist: pylint==3.3.8
60
+ Requires-Dist: pymilvus==2.6.1
61
61
  Requires-Dist: pypdf==6.0.0
62
62
  Requires-Dist: pytest-asyncio==0.25.2
63
- Requires-Dist: pytest==8.3.3
63
+ Requires-Dist: pytest==8.4.1
64
64
  Requires-Dist: python-magic==0.4.27
65
- Requires-Dist: pyzotero==1.6.9
66
- Requires-Dist: requests==2.32.4
67
- Requires-Dist: scanpy==1.11.0
68
- Requires-Dist: scipy==1.15.2
65
+ Requires-Dist: pyzotero==1.6.11
66
+ Requires-Dist: requests==2.32.5
67
+ Requires-Dist: scanpy==1.11.4
68
+ Requires-Dist: scipy==1.16.1
69
69
  Requires-Dist: seaborn==0.13.2
70
70
  Requires-Dist: sentence-transformers==3.3.1
71
71
  Requires-Dist: setuptools==80.9.0
72
72
  Requires-Dist: streamlit-feedback==0.1.4
73
- Requires-Dist: streamlit==1.41.1
73
+ Requires-Dist: streamlit==1.49.1
74
74
  Requires-Dist: tabulate==0.9.0
75
75
  Requires-Dist: torch-geometric==2.6.1
76
76
  Requires-Dist: torch==2.8.0
77
77
  Requires-Dist: tqdm==4.67.1
78
78
  Requires-Dist: transformers==4.55.2
79
- Requires-Dist: umap-learn==0.5.7
79
+ Requires-Dist: umap-learn==0.5.9.post2
80
80
  Requires-Dist: xlsxwriter==3.2.5
81
81
  Provides-Extra: dev
82
82
  Requires-Dist: bandit==1.8.6; extra == 'dev'
83
83
  Requires-Dist: mypy==1.17.1; extra == 'dev'
84
84
  Requires-Dist: pip-audit==2.9.0; extra == 'dev'
85
85
  Requires-Dist: pre-commit==4.3.0; extra == 'dev'
86
- Requires-Dist: ruff==0.12.8; extra == 'dev'
86
+ Requires-Dist: ruff==0.12.11; extra == 'dev'
87
87
  Requires-Dist: safety==3.2.9; extra == 'dev'
88
88
  Requires-Dist: twine==6.1.0; extra == 'dev'
89
89
  Description-Content-Type: text/markdown
@@ -275,6 +275,7 @@ For contributors and developers, we have comprehensive documentation:
275
275
  - **[SonarCloud Integration](docs/developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
276
276
  - **[GitHub Workflows](docs/developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
277
277
  - **[Streamlit Security](docs/developer/STREAMLIT_SECURITY.md)** - File upload security implementation
278
+ - **[Azure Deployment](developer/AZURE_DEPLOYMENT.md)** - Understanding our Azure deployment setup
278
279
 
279
280
  #### How to contribute
280
281
 
@@ -185,6 +185,7 @@ For contributors and developers, we have comprehensive documentation:
185
185
  - **[SonarCloud Integration](docs/developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
186
186
  - **[GitHub Workflows](docs/developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
187
187
  - **[Streamlit Security](docs/developer/STREAMLIT_SECURITY.md)** - File upload security implementation
188
+ - **[Azure Deployment](developer/AZURE_DEPLOYMENT.md)** - Understanding our Azure deployment setup
188
189
 
189
190
  #### How to contribute
190
191
 
@@ -183,6 +183,7 @@ For contributors and developers, we have comprehensive documentation:
183
183
  - **[SonarCloud Integration](developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
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184
  - **[GitHub Workflows](developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
185
185
  - **[Streamlit Security](developer/STREAMLIT_SECURITY.md)** - File upload security implementation
186
+ - **[Azure Deployment](developer/AZURE_DEPLOYMENT.md)** - Understanding our Azure deployment setup
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187
 
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  #### How to contribute
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189
 
@@ -10,7 +10,7 @@
10
10
  "@semantic-release/github": "^11.0.1",
11
11
  "semantic-release": "^24.0.0"
12
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  },
13
- "version": "1.46.1"
13
+ "version": "1.46.3"
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  },
15
15
  "node_modules/@babel/code-frame": {
16
16
  "version": "7.26.2",
@@ -11110,5 +11110,5 @@
11110
11110
  "dev": true
11111
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  }
11112
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  },
11113
- "version": "1.46.1"
11113
+ "version": "1.46.3"
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  }