aurelian 0.3.2__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 (254) hide show
  1. aurelian/__init__.py +9 -0
  2. aurelian/agents/__init__.py +0 -0
  3. aurelian/agents/amigo/__init__.py +3 -0
  4. aurelian/agents/amigo/amigo_agent.py +77 -0
  5. aurelian/agents/amigo/amigo_config.py +85 -0
  6. aurelian/agents/amigo/amigo_evals.py +73 -0
  7. aurelian/agents/amigo/amigo_gradio.py +52 -0
  8. aurelian/agents/amigo/amigo_mcp.py +152 -0
  9. aurelian/agents/amigo/amigo_tools.py +152 -0
  10. aurelian/agents/biblio/__init__.py +42 -0
  11. aurelian/agents/biblio/biblio_agent.py +94 -0
  12. aurelian/agents/biblio/biblio_config.py +40 -0
  13. aurelian/agents/biblio/biblio_gradio.py +67 -0
  14. aurelian/agents/biblio/biblio_mcp.py +115 -0
  15. aurelian/agents/biblio/biblio_tools.py +164 -0
  16. aurelian/agents/biblio_agent.py +46 -0
  17. aurelian/agents/checklist/__init__.py +44 -0
  18. aurelian/agents/checklist/checklist_agent.py +85 -0
  19. aurelian/agents/checklist/checklist_config.py +28 -0
  20. aurelian/agents/checklist/checklist_gradio.py +70 -0
  21. aurelian/agents/checklist/checklist_mcp.py +86 -0
  22. aurelian/agents/checklist/checklist_tools.py +141 -0
  23. aurelian/agents/checklist/content/checklists.yaml +7 -0
  24. aurelian/agents/checklist/content/streams.csv +136 -0
  25. aurelian/agents/checklist_agent.py +40 -0
  26. aurelian/agents/chemistry/__init__.py +3 -0
  27. aurelian/agents/chemistry/chemistry_agent.py +46 -0
  28. aurelian/agents/chemistry/chemistry_config.py +71 -0
  29. aurelian/agents/chemistry/chemistry_evals.py +79 -0
  30. aurelian/agents/chemistry/chemistry_gradio.py +50 -0
  31. aurelian/agents/chemistry/chemistry_mcp.py +120 -0
  32. aurelian/agents/chemistry/chemistry_tools.py +121 -0
  33. aurelian/agents/chemistry/image_agent.py +15 -0
  34. aurelian/agents/d4d/__init__.py +30 -0
  35. aurelian/agents/d4d/d4d_agent.py +72 -0
  36. aurelian/agents/d4d/d4d_config.py +46 -0
  37. aurelian/agents/d4d/d4d_gradio.py +58 -0
  38. aurelian/agents/d4d/d4d_mcp.py +71 -0
  39. aurelian/agents/d4d/d4d_tools.py +157 -0
  40. aurelian/agents/d4d_agent.py +64 -0
  41. aurelian/agents/diagnosis/__init__.py +33 -0
  42. aurelian/agents/diagnosis/diagnosis_agent.py +53 -0
  43. aurelian/agents/diagnosis/diagnosis_config.py +48 -0
  44. aurelian/agents/diagnosis/diagnosis_evals.py +76 -0
  45. aurelian/agents/diagnosis/diagnosis_gradio.py +52 -0
  46. aurelian/agents/diagnosis/diagnosis_mcp.py +141 -0
  47. aurelian/agents/diagnosis/diagnosis_tools.py +204 -0
  48. aurelian/agents/diagnosis_agent.py +28 -0
  49. aurelian/agents/draw/__init__.py +3 -0
  50. aurelian/agents/draw/draw_agent.py +39 -0
  51. aurelian/agents/draw/draw_config.py +26 -0
  52. aurelian/agents/draw/draw_gradio.py +50 -0
  53. aurelian/agents/draw/draw_mcp.py +94 -0
  54. aurelian/agents/draw/draw_tools.py +100 -0
  55. aurelian/agents/draw/judge_agent.py +18 -0
  56. aurelian/agents/filesystem/__init__.py +0 -0
  57. aurelian/agents/filesystem/filesystem_config.py +27 -0
  58. aurelian/agents/filesystem/filesystem_gradio.py +49 -0
  59. aurelian/agents/filesystem/filesystem_mcp.py +89 -0
  60. aurelian/agents/filesystem/filesystem_tools.py +95 -0
  61. aurelian/agents/filesystem/py.typed +0 -0
  62. aurelian/agents/github/__init__.py +0 -0
  63. aurelian/agents/github/github_agent.py +83 -0
  64. aurelian/agents/github/github_cli.py +248 -0
  65. aurelian/agents/github/github_config.py +22 -0
  66. aurelian/agents/github/github_gradio.py +152 -0
  67. aurelian/agents/github/github_mcp.py +252 -0
  68. aurelian/agents/github/github_tools.py +408 -0
  69. aurelian/agents/github/github_tools.py.tmp +413 -0
  70. aurelian/agents/goann/__init__.py +13 -0
  71. aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.md +1000 -0
  72. aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.pdf +0 -0
  73. aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.md +693 -0
  74. aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.pdf +0 -0
  75. aurelian/agents/goann/goann_agent.py +90 -0
  76. aurelian/agents/goann/goann_config.py +90 -0
  77. aurelian/agents/goann/goann_evals.py +104 -0
  78. aurelian/agents/goann/goann_gradio.py +62 -0
  79. aurelian/agents/goann/goann_mcp.py +0 -0
  80. aurelian/agents/goann/goann_tools.py +65 -0
  81. aurelian/agents/gocam/__init__.py +43 -0
  82. aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.docx +0 -0
  83. aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.pdf +0 -0
  84. aurelian/agents/gocam/documents/DNA-binding_transcription_factor_activity_annotation_guidelines.md +100 -0
  85. aurelian/agents/gocam/documents/E3 ubiquitin ligases.docx +0 -0
  86. aurelian/agents/gocam/documents/E3 ubiquitin ligases.pdf +0 -0
  87. aurelian/agents/gocam/documents/E3_ubiquitin_ligases.md +134 -0
  88. aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.docx +0 -0
  89. aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.pdf +0 -0
  90. aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.docx +0 -0
  91. aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.pdf +0 -0
  92. aurelian/agents/gocam/documents/GO-CAM_annotation_guidelines_README.md +1 -0
  93. aurelian/agents/gocam/documents/GO-CAM_modelling_guidelines_TO_DO.md +3 -0
  94. aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.docx +0 -0
  95. aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.pdf +0 -0
  96. aurelian/agents/gocam/documents/How to annotate molecular adaptors.docx +0 -0
  97. aurelian/agents/gocam/documents/How to annotate molecular adaptors.pdf +0 -0
  98. aurelian/agents/gocam/documents/How to annotate sequestering proteins.docx +0 -0
  99. aurelian/agents/gocam/documents/How to annotate sequestering proteins.pdf +0 -0
  100. aurelian/agents/gocam/documents/How_to_annotate_complexes_in_GO-CAM.md +29 -0
  101. aurelian/agents/gocam/documents/How_to_annotate_molecular_adaptors.md +31 -0
  102. aurelian/agents/gocam/documents/How_to_annotate_sequestering_proteins.md +42 -0
  103. aurelian/agents/gocam/documents/Molecular adaptor activity.docx +0 -0
  104. aurelian/agents/gocam/documents/Molecular adaptor activity.pdf +0 -0
  105. aurelian/agents/gocam/documents/Molecular carrier activity.docx +0 -0
  106. aurelian/agents/gocam/documents/Molecular carrier activity.pdf +0 -0
  107. aurelian/agents/gocam/documents/Molecular_adaptor_activity.md +51 -0
  108. aurelian/agents/gocam/documents/Molecular_carrier_activity.md +41 -0
  109. aurelian/agents/gocam/documents/Protein sequestering activity.docx +0 -0
  110. aurelian/agents/gocam/documents/Protein sequestering activity.pdf +0 -0
  111. aurelian/agents/gocam/documents/Protein_sequestering_activity.md +50 -0
  112. aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.docx +0 -0
  113. aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.pdf +0 -0
  114. aurelian/agents/gocam/documents/Signaling_receptor_activity_annotation_guidelines.md +187 -0
  115. aurelian/agents/gocam/documents/Transcription coregulator activity.docx +0 -0
  116. aurelian/agents/gocam/documents/Transcription coregulator activity.pdf +0 -0
  117. aurelian/agents/gocam/documents/Transcription_coregulator_activity.md +36 -0
  118. aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.docx +0 -0
  119. aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.pdf +0 -0
  120. aurelian/agents/gocam/documents/Transporter_activity_annotation_annotation_guidelines.md +43 -0
  121. Regulatory Processes in GO-CAM.docx +0 -0
  122. Regulatory Processes in GO-CAM.pdf +0 -0
  123. aurelian/agents/gocam/documents/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md +31 -0
  124. aurelian/agents/gocam/documents/md/DNA-binding_transcription_factor_activity_annotation_guidelines.md +131 -0
  125. aurelian/agents/gocam/documents/md/E3_ubiquitin_ligases.md +166 -0
  126. aurelian/agents/gocam/documents/md/GO-CAM_annotation_guidelines_README.md +1 -0
  127. aurelian/agents/gocam/documents/md/GO-CAM_modelling_guidelines_TO_DO.md +5 -0
  128. aurelian/agents/gocam/documents/md/How_to_annotate_complexes_in_GO-CAM.md +28 -0
  129. aurelian/agents/gocam/documents/md/How_to_annotate_molecular_adaptors.md +19 -0
  130. aurelian/agents/gocam/documents/md/How_to_annotate_sequestering_proteins.md +38 -0
  131. aurelian/agents/gocam/documents/md/Molecular_adaptor_activity.md +52 -0
  132. aurelian/agents/gocam/documents/md/Molecular_carrier_activity.md +59 -0
  133. aurelian/agents/gocam/documents/md/Protein_sequestering_activity.md +52 -0
  134. aurelian/agents/gocam/documents/md/Signaling_receptor_activity_annotation_guidelines.md +271 -0
  135. aurelian/agents/gocam/documents/md/Transcription_coregulator_activity.md +54 -0
  136. aurelian/agents/gocam/documents/md/Transporter_activity_annotation_annotation_guidelines.md +38 -0
  137. aurelian/agents/gocam/documents/md/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md +39 -0
  138. aurelian/agents/gocam/documents/pandoc_md/Signaling_receptor_activity_annotation_guidelines.md +334 -0
  139. aurelian/agents/gocam/gocam_agent.py +240 -0
  140. aurelian/agents/gocam/gocam_config.py +85 -0
  141. aurelian/agents/gocam/gocam_curator_agent.py +46 -0
  142. aurelian/agents/gocam/gocam_evals.py +67 -0
  143. aurelian/agents/gocam/gocam_gradio.py +89 -0
  144. aurelian/agents/gocam/gocam_mcp.py +224 -0
  145. aurelian/agents/gocam/gocam_tools.py +294 -0
  146. aurelian/agents/linkml/__init__.py +0 -0
  147. aurelian/agents/linkml/linkml_agent.py +62 -0
  148. aurelian/agents/linkml/linkml_config.py +48 -0
  149. aurelian/agents/linkml/linkml_evals.py +66 -0
  150. aurelian/agents/linkml/linkml_gradio.py +45 -0
  151. aurelian/agents/linkml/linkml_mcp.py +186 -0
  152. aurelian/agents/linkml/linkml_tools.py +102 -0
  153. aurelian/agents/literature/__init__.py +3 -0
  154. aurelian/agents/literature/literature_agent.py +55 -0
  155. aurelian/agents/literature/literature_config.py +35 -0
  156. aurelian/agents/literature/literature_gradio.py +52 -0
  157. aurelian/agents/literature/literature_mcp.py +174 -0
  158. aurelian/agents/literature/literature_tools.py +182 -0
  159. aurelian/agents/monarch/__init__.py +25 -0
  160. aurelian/agents/monarch/monarch_agent.py +44 -0
  161. aurelian/agents/monarch/monarch_config.py +45 -0
  162. aurelian/agents/monarch/monarch_gradio.py +51 -0
  163. aurelian/agents/monarch/monarch_mcp.py +65 -0
  164. aurelian/agents/monarch/monarch_tools.py +113 -0
  165. aurelian/agents/oak/__init__.py +0 -0
  166. aurelian/agents/oak/oak_config.py +27 -0
  167. aurelian/agents/oak/oak_gradio.py +57 -0
  168. aurelian/agents/ontology_mapper/__init__.py +31 -0
  169. aurelian/agents/ontology_mapper/ontology_mapper_agent.py +56 -0
  170. aurelian/agents/ontology_mapper/ontology_mapper_config.py +50 -0
  171. aurelian/agents/ontology_mapper/ontology_mapper_evals.py +108 -0
  172. aurelian/agents/ontology_mapper/ontology_mapper_gradio.py +58 -0
  173. aurelian/agents/ontology_mapper/ontology_mapper_mcp.py +81 -0
  174. aurelian/agents/ontology_mapper/ontology_mapper_tools.py +147 -0
  175. aurelian/agents/phenopackets/__init__.py +3 -0
  176. aurelian/agents/phenopackets/phenopackets_agent.py +58 -0
  177. aurelian/agents/phenopackets/phenopackets_config.py +72 -0
  178. aurelian/agents/phenopackets/phenopackets_evals.py +99 -0
  179. aurelian/agents/phenopackets/phenopackets_gradio.py +55 -0
  180. aurelian/agents/phenopackets/phenopackets_mcp.py +178 -0
  181. aurelian/agents/phenopackets/phenopackets_tools.py +127 -0
  182. aurelian/agents/rag/__init__.py +40 -0
  183. aurelian/agents/rag/rag_agent.py +83 -0
  184. aurelian/agents/rag/rag_config.py +80 -0
  185. aurelian/agents/rag/rag_gradio.py +67 -0
  186. aurelian/agents/rag/rag_mcp.py +107 -0
  187. aurelian/agents/rag/rag_tools.py +189 -0
  188. aurelian/agents/rag_agent.py +54 -0
  189. aurelian/agents/robot/__init__.py +0 -0
  190. aurelian/agents/robot/assets/__init__.py +3 -0
  191. aurelian/agents/robot/assets/template.md +384 -0
  192. aurelian/agents/robot/robot_config.py +25 -0
  193. aurelian/agents/robot/robot_gradio.py +46 -0
  194. aurelian/agents/robot/robot_mcp.py +100 -0
  195. aurelian/agents/robot/robot_ontology_agent.py +139 -0
  196. aurelian/agents/robot/robot_tools.py +50 -0
  197. aurelian/agents/talisman/__init__.py +3 -0
  198. aurelian/agents/talisman/talisman_agent.py +126 -0
  199. aurelian/agents/talisman/talisman_config.py +66 -0
  200. aurelian/agents/talisman/talisman_gradio.py +50 -0
  201. aurelian/agents/talisman/talisman_mcp.py +168 -0
  202. aurelian/agents/talisman/talisman_tools.py +720 -0
  203. aurelian/agents/ubergraph/__init__.py +40 -0
  204. aurelian/agents/ubergraph/ubergraph_agent.py +71 -0
  205. aurelian/agents/ubergraph/ubergraph_config.py +79 -0
  206. aurelian/agents/ubergraph/ubergraph_gradio.py +48 -0
  207. aurelian/agents/ubergraph/ubergraph_mcp.py +69 -0
  208. aurelian/agents/ubergraph/ubergraph_tools.py +118 -0
  209. aurelian/agents/uniprot/__init__.py +37 -0
  210. aurelian/agents/uniprot/uniprot_agent.py +43 -0
  211. aurelian/agents/uniprot/uniprot_config.py +43 -0
  212. aurelian/agents/uniprot/uniprot_evals.py +99 -0
  213. aurelian/agents/uniprot/uniprot_gradio.py +48 -0
  214. aurelian/agents/uniprot/uniprot_mcp.py +168 -0
  215. aurelian/agents/uniprot/uniprot_tools.py +136 -0
  216. aurelian/agents/web/__init__.py +0 -0
  217. aurelian/agents/web/web_config.py +27 -0
  218. aurelian/agents/web/web_gradio.py +48 -0
  219. aurelian/agents/web/web_mcp.py +50 -0
  220. aurelian/agents/web/web_tools.py +108 -0
  221. aurelian/chat.py +23 -0
  222. aurelian/cli.py +800 -0
  223. aurelian/dependencies/__init__.py +0 -0
  224. aurelian/dependencies/workdir.py +78 -0
  225. aurelian/mcp/__init__.py +0 -0
  226. aurelian/mcp/amigo_mcp_test.py +86 -0
  227. aurelian/mcp/config_generator.py +123 -0
  228. aurelian/mcp/example_config.json +43 -0
  229. aurelian/mcp/generate_sample_config.py +37 -0
  230. aurelian/mcp/gocam_mcp_test.py +126 -0
  231. aurelian/mcp/linkml_mcp_tools.py +190 -0
  232. aurelian/mcp/mcp_discovery.py +87 -0
  233. aurelian/mcp/mcp_test.py +31 -0
  234. aurelian/mcp/phenopackets_mcp_test.py +103 -0
  235. aurelian/tools/__init__.py +0 -0
  236. aurelian/tools/web/__init__.py +0 -0
  237. aurelian/tools/web/url_download.py +51 -0
  238. aurelian/utils/__init__.py +0 -0
  239. aurelian/utils/async_utils.py +15 -0
  240. aurelian/utils/data_utils.py +32 -0
  241. aurelian/utils/documentation_manager.py +59 -0
  242. aurelian/utils/doi_fetcher.py +238 -0
  243. aurelian/utils/ontology_utils.py +68 -0
  244. aurelian/utils/pdf_fetcher.py +23 -0
  245. aurelian/utils/process_logs.py +100 -0
  246. aurelian/utils/pubmed_utils.py +238 -0
  247. aurelian/utils/pytest_report_to_markdown.py +67 -0
  248. aurelian/utils/robot_ontology_utils.py +112 -0
  249. aurelian/utils/search_utils.py +95 -0
  250. aurelian-0.3.2.dist-info/LICENSE +22 -0
  251. aurelian-0.3.2.dist-info/METADATA +105 -0
  252. aurelian-0.3.2.dist-info/RECORD +254 -0
  253. aurelian-0.3.2.dist-info/WHEEL +4 -0
  254. aurelian-0.3.2.dist-info/entry_points.txt +3 -0