aurelian 0.1.0__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 (266) 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 +95 -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 +86 -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 +47 -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 +73 -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 +54 -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 +52 -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 +243 -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 +64 -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 +181 -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 +75 -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 +0 -0
  160. aurelian/agents/monarch/monarch_agent.py +45 -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 +112 -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 +57 -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/paperqa/__init__.py +27 -0
  176. aurelian/agents/paperqa/paperqa_agent.py +66 -0
  177. aurelian/agents/paperqa/paperqa_cli.py +305 -0
  178. aurelian/agents/paperqa/paperqa_config.py +142 -0
  179. aurelian/agents/paperqa/paperqa_gradio.py +90 -0
  180. aurelian/agents/paperqa/paperqa_mcp.py +155 -0
  181. aurelian/agents/paperqa/paperqa_tools.py +566 -0
  182. aurelian/agents/phenopackets/__init__.py +3 -0
  183. aurelian/agents/phenopackets/phenopackets_agent.py +58 -0
  184. aurelian/agents/phenopackets/phenopackets_config.py +72 -0
  185. aurelian/agents/phenopackets/phenopackets_evals.py +99 -0
  186. aurelian/agents/phenopackets/phenopackets_gradio.py +55 -0
  187. aurelian/agents/phenopackets/phenopackets_mcp.py +178 -0
  188. aurelian/agents/phenopackets/phenopackets_tools.py +127 -0
  189. aurelian/agents/rag/__init__.py +40 -0
  190. aurelian/agents/rag/rag_agent.py +84 -0
  191. aurelian/agents/rag/rag_config.py +80 -0
  192. aurelian/agents/rag/rag_gradio.py +67 -0
  193. aurelian/agents/rag/rag_mcp.py +107 -0
  194. aurelian/agents/rag/rag_tools.py +189 -0
  195. aurelian/agents/rag_agent.py +54 -0
  196. aurelian/agents/robot/__init__.py +0 -0
  197. aurelian/agents/robot/assets/__init__.py +3 -0
  198. aurelian/agents/robot/assets/template.md +384 -0
  199. aurelian/agents/robot/robot_config.py +25 -0
  200. aurelian/agents/robot/robot_gradio.py +46 -0
  201. aurelian/agents/robot/robot_mcp.py +100 -0
  202. aurelian/agents/robot/robot_ontology_agent.py +139 -0
  203. aurelian/agents/robot/robot_tools.py +50 -0
  204. aurelian/agents/talisman/__init__.py +3 -0
  205. aurelian/agents/talisman/__main__.py +17 -0
  206. aurelian/agents/talisman/cli.py +70 -0
  207. aurelian/agents/talisman/run_talisman.py +18 -0
  208. aurelian/agents/talisman/talisman_agent.py +143 -0
  209. aurelian/agents/talisman/talisman_config.py +66 -0
  210. aurelian/agents/talisman/talisman_gradio.py +50 -0
  211. aurelian/agents/talisman/talisman_mcp.py +75 -0
  212. aurelian/agents/talisman/talisman_tools.py +962 -0
  213. aurelian/agents/ubergraph/__init__.py +40 -0
  214. aurelian/agents/ubergraph/ubergraph_agent.py +72 -0
  215. aurelian/agents/ubergraph/ubergraph_config.py +79 -0
  216. aurelian/agents/ubergraph/ubergraph_gradio.py +48 -0
  217. aurelian/agents/ubergraph/ubergraph_mcp.py +69 -0
  218. aurelian/agents/ubergraph/ubergraph_tools.py +118 -0
  219. aurelian/agents/uniprot/__init__.py +0 -0
  220. aurelian/agents/uniprot/uniprot_agent.py +43 -0
  221. aurelian/agents/uniprot/uniprot_config.py +43 -0
  222. aurelian/agents/uniprot/uniprot_evals.py +99 -0
  223. aurelian/agents/uniprot/uniprot_gradio.py +48 -0
  224. aurelian/agents/uniprot/uniprot_mcp.py +168 -0
  225. aurelian/agents/uniprot/uniprot_tools.py +136 -0
  226. aurelian/agents/web/__init__.py +0 -0
  227. aurelian/agents/web/web_config.py +27 -0
  228. aurelian/agents/web/web_gradio.py +48 -0
  229. aurelian/agents/web/web_mcp.py +50 -0
  230. aurelian/agents/web/web_tools.py +121 -0
  231. aurelian/chat.py +23 -0
  232. aurelian/cli.py +1004 -0
  233. aurelian/dependencies/__init__.py +0 -0
  234. aurelian/dependencies/workdir.py +78 -0
  235. aurelian/evaluators/model.py +9 -0
  236. aurelian/evaluators/substring_evaluator.py +30 -0
  237. aurelian/mcp/__init__.py +0 -0
  238. aurelian/mcp/amigo_mcp_test.py +86 -0
  239. aurelian/mcp/config_generator.py +123 -0
  240. aurelian/mcp/example_config.json +43 -0
  241. aurelian/mcp/generate_sample_config.py +37 -0
  242. aurelian/mcp/gocam_mcp_test.py +126 -0
  243. aurelian/mcp/linkml_mcp_tools.py +190 -0
  244. aurelian/mcp/mcp_discovery.py +87 -0
  245. aurelian/mcp/mcp_test.py +31 -0
  246. aurelian/mcp/phenopackets_mcp_test.py +103 -0
  247. aurelian/tools/__init__.py +0 -0
  248. aurelian/tools/web/__init__.py +0 -0
  249. aurelian/tools/web/url_download.py +51 -0
  250. aurelian/utils/__init__.py +0 -0
  251. aurelian/utils/async_utils.py +18 -0
  252. aurelian/utils/data_utils.py +32 -0
  253. aurelian/utils/documentation_manager.py +59 -0
  254. aurelian/utils/doi_fetcher.py +238 -0
  255. aurelian/utils/ontology_utils.py +68 -0
  256. aurelian/utils/pdf_fetcher.py +23 -0
  257. aurelian/utils/process_logs.py +100 -0
  258. aurelian/utils/pubmed_utils.py +238 -0
  259. aurelian/utils/pytest_report_to_markdown.py +67 -0
  260. aurelian/utils/robot_ontology_utils.py +112 -0
  261. aurelian/utils/search_utils.py +95 -0
  262. aurelian-0.1.0.dist-info/LICENSE +22 -0
  263. aurelian-0.1.0.dist-info/METADATA +109 -0
  264. aurelian-0.1.0.dist-info/RECORD +266 -0
  265. aurelian-0.1.0.dist-info/WHEEL +4 -0
  266. aurelian-0.1.0.dist-info/entry_points.txt +4 -0
aurelian-0.1.0.dist-info/RECORD ADDED
@@ -0,0 +1,266 @@
1
+ aurelian/__init__.py,sha256=1Ax7CyE77tBC8DdUVJDGaYjKjSJkJwoZnhpSq3_hx_Y,244
2
+ aurelian/agents/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
+ aurelian/agents/amigo/__init__.py,sha256=h6-P24x926HWTbb5pCQbas6qUcQAXEYevCA-bTVTdII,89
4
+ aurelian/agents/amigo/amigo_agent.py,sha256=nCOlaXR0aLBDmUDt33AmimKaVWN0-bgswCOdILFmquY,2720
5
+ aurelian/agents/amigo/amigo_config.py,sha256=lVewvJ8bGyLUfklsi8-4wegdSE6qRcKASzpaUWFBwgQ,2068
6
+ aurelian/agents/amigo/amigo_evals.py,sha256=uY-Vz3OrjnUJYq598guCJl_dYDubCuYlQrYDQskEsSc,2288
7
+ aurelian/agents/amigo/amigo_gradio.py,sha256=UYJW2ZdDQJz77wZNetxejWEI5tz39lVRWXZwQHJovmg,1634
8
+ aurelian/agents/amigo/amigo_mcp.py,sha256=byLMDguj_osVV5Q4m1Fp_I1megZm28TzV3YVoi5qa1Q,3831
9
+ aurelian/agents/amigo/amigo_tools.py,sha256=upTjjw4rKCFe3qX-633-9mlQZmXGcNsU8IV7Zd9XJvE,5561
10
+ aurelian/agents/biblio/__init__.py,sha256=xBuwjRYjyWRbABMaa7NaMwJUmSDj0AATQ_55Oy_FitA,814
11
+ aurelian/agents/biblio/biblio_agent.py,sha256=7icG6TzCr1vNgkMHju662IceRQOsEt5XLkipnybxHlw,3726
12
+ aurelian/agents/biblio/biblio_config.py,sha256=K2crtuWIsvzLaoD0bINrx7_VPucp4Qwbfwj8DEn_09E,1254
13
+ aurelian/agents/biblio/biblio_gradio.py,sha256=4YTqYn4Jw0MX29udZ4iCJP-YXKl9yQdPAwouPRr_B1I,1911
14
+ aurelian/agents/biblio/biblio_mcp.py,sha256=zZpRHTc7tVAcBL190sDSPcmvous7vjYx0S0OD8-q4IE,3156
15
+ aurelian/agents/biblio/biblio_tools.py,sha256=tTihpzOTjLBwvMm6QNAHsUb9yWdT4DziOt7t3XWe0_o,4936
16
+ aurelian/agents/biblio_agent.py,sha256=0Uvh6N6AQdva-4NgjOlFHXQFPuEwLyAqUVGtRkokn-U,1241
17
+ aurelian/agents/checklist/__init__.py,sha256=ZN70snI4C871K-76oRCMU3XZPYl_4lKH4VzPUx9tvCg,1034
18
+ aurelian/agents/checklist/checklist_agent.py,sha256=G7NpLDSqKvqz3mti1t8SAceFnXHko0knjotqx1YpMQY,2788
19
+ aurelian/agents/checklist/checklist_config.py,sha256=8V_fwWj3dPEyJmcle0nscfvcxdUFiAGsE1T17GnFNIk,828
20
+ aurelian/agents/checklist/checklist_gradio.py,sha256=UOwL7BCjyRsnldP-3RVhzxQsRGLC5QztY8iuAxqjIsY,1981
21
+ aurelian/agents/checklist/checklist_mcp.py,sha256=cQo_VmP_U-A0cQEHBMrgt5gYIr3nkVFTLv-8ucS0D20,2238
22
+ aurelian/agents/checklist/checklist_tools.py,sha256=dgQ2OTBbz3rSPDjQahHOeiDLez47oCtwekVN1rIOncE,3999
23
+ aurelian/agents/checklist/content/checklists.yaml,sha256=QVPp65lnPfRJvHxXgFEFu_W2KxZh878OcUthmEiLZto,1678
24
+ aurelian/agents/checklist/content/streams.csv,sha256=VjqssvA05-tdJC5Egr-ZR6RZVTSfHvucZRQFEOlqGm4,50132
25
+ aurelian/agents/checklist_agent.py,sha256=2K1l2ctb8oIWGOqMuWBfuM0WEZ0pa2BiQUefXWAvnJI,1187
26
+ aurelian/agents/chemistry/__init__.py,sha256=_a0iQB50o5cF-t-SI5EkaP8oCeDWc2QKvJ0m628Typ8,68
27
+ aurelian/agents/chemistry/chemistry_agent.py,sha256=ah8ba8-WLyi-5DIjmRfRURbmienbwyx_h1TXkR16o98,1594
28
+ aurelian/agents/chemistry/chemistry_config.py,sha256=r348qJwBpvp6Q8MbnA3OOOSBjhFj-J_5J68OpKgTijE,1900
29
+ aurelian/agents/chemistry/chemistry_evals.py,sha256=s_elRDsjle8fNrkL4c4Ud2NrFnoCM3goJkcwORhi-4Y,2611
30
+ aurelian/agents/chemistry/chemistry_gradio.py,sha256=2tF6HhRhbJK_3zQfydBn0kwFAJiQQcHzeva8tax4DEM,1545
31
+ aurelian/agents/chemistry/chemistry_mcp.py,sha256=ZS8lXMjCwj60RCv4t6BFxqU0uiiGxLFhWoG9vNb_Ld0,2892
32
+ aurelian/agents/chemistry/chemistry_tools.py,sha256=sJ0FWMqwvf1cOd1XEmdOkViYY7FhWUZ_z0zMD8EyQ30,3387
33
+ aurelian/agents/chemistry/image_agent.py,sha256=Taty5MYbhg7XPzpGgfMeu7Ll6D5f_grClGPF9M3boTE,562
34
+ aurelian/agents/d4d/__init__.py,sha256=h7jmgzmu_zEU-5HpejrDs0Wsigq4kpvdNLC3s-MHXuI,597
35
+ aurelian/agents/d4d/d4d_agent.py,sha256=tmWb3qnHQcS1o5GMyyePN-UaC7231KOGIPUDEK1-Tg0,2119
36
+ aurelian/agents/d4d/d4d_config.py,sha256=vQz1ym2NDim2cQV4gFMXTDcAEeg5RAVBkWvVIdo7CNo,1471
37
+ aurelian/agents/d4d/d4d_gradio.py,sha256=gJXImWqQv9PAPKVlexhdvXqTcDpQWbEi1xLWVGIly9Q,1844
38
+ aurelian/agents/d4d/d4d_mcp.py,sha256=QjRqFd4miAbfFwzos5idHA-wfdN5-djpD2Ot0xogb58,1810
39
+ aurelian/agents/d4d/d4d_tools.py,sha256=ymyWSOOYF6vgv06mpU_GQH7gecIUYluqvT3eXgEhfVA,4803
40
+ aurelian/agents/d4d_agent.py,sha256=hDS5RVisPcKzDX202vYzz54kyGZ1_L8VfBCDfXPlpPk,1896
41
+ aurelian/agents/diagnosis/__init__.py,sha256=HhW4NEjr8Zo6Lqxiq0AW3pzGZu1N8xEkdAd0EG_7fak,668
42
+ aurelian/agents/diagnosis/diagnosis_agent.py,sha256=-nJ7gwZZ6N6I-A6y9SVxrqKV98b-DgrkAE82jpiZ20s,2369
43
+ aurelian/agents/diagnosis/diagnosis_config.py,sha256=TCoJ9tPmXS0gvXgmziSqAMHKXdl48Mg5AFejS_0Wvxo,1565
44
+ aurelian/agents/diagnosis/diagnosis_evals.py,sha256=FL42urNIAsWo9iMRmpynlrvMYLnazsC9tMPdPm86JG8,2582
45
+ aurelian/agents/diagnosis/diagnosis_gradio.py,sha256=We_ZxhxmlvcxcvVmf2NuflmeHVIYmDJ_LvrO4hL1Y9U,1754
46
+ aurelian/agents/diagnosis/diagnosis_mcp.py,sha256=tvkYXNpTRv4qGK-nORu2MOwCn6C-hNu1ddu1rxD9xJM,3621
47
+ aurelian/agents/diagnosis/diagnosis_tools.py,sha256=gE8wzS69ebZSoT_pTAIvaKAPD_SRQK36bRVhQL4gVY8,5956
48
+ aurelian/agents/diagnosis_agent.py,sha256=7CMWybHygBHEYs-pqKL1p2UHel-QTJkOrIkQY26Vxc4,789
49
+ aurelian/agents/draw/__init__.py,sha256=sIqGW86l_jzO5nm9E8kAc7Dkth4JqHFeRyoQ7GTunOU,52
50
+ aurelian/agents/draw/draw_agent.py,sha256=Osx2bWwqLQQcW5m-1OTGk-XeRoA6qrdZIF8LM-43C48,1176
51
+ aurelian/agents/draw/draw_config.py,sha256=Pu4dWRmSSWUfLaC_eL9c-u7nFwCDAhfp_5uVHFLiYCo,579
52
+ aurelian/agents/draw/draw_gradio.py,sha256=WofD0AQMvr8jLJZACWgn-AOq2uDLOz_bj46c8Ooi2-o,1405
53
+ aurelian/agents/draw/draw_mcp.py,sha256=WBjqmR7W8qdGS8jtOfzKMIV2BGiXCBK19HhVWIYLzNo,2332
54
+ aurelian/agents/draw/draw_tools.py,sha256=hVjHPPxNsebNUQDTlsXlVYnsrtI3yfAg22eVQfzzJ2w,3074
55
+ aurelian/agents/draw/judge_agent.py,sha256=SycTT778CK7-L2K5bIqD2DeRFzEq0IGOmh7WBgUHvuY,511
56
+ aurelian/agents/filesystem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
57
+ aurelian/agents/filesystem/filesystem_config.py,sha256=lz7HjCvWypRP-RD9Ypc0OavqJTm_p1ULH7vmxQ9_sng,724
58
+ aurelian/agents/filesystem/filesystem_gradio.py,sha256=eozMRnT44zolzdGH7E0bkBSC6eFbv_6aVLF-PX9lqUM,1479
59
+ aurelian/agents/filesystem/filesystem_mcp.py,sha256=vLjRo-lXgzZvF3XYmantECbpUuIHjqhpix9inab5gIQ,2074
60
+ aurelian/agents/filesystem/filesystem_tools.py,sha256=7yrYo8uFbHLS0RyA5MrZFfpiiy1nbKyz39lfhl8JyDk,2431
61
+ aurelian/agents/filesystem/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
62
+ aurelian/agents/github/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
63
+ aurelian/agents/github/github_agent.py,sha256=1FlKMWQ0qGbB5gFsxhj7MisUbzy-xLu_qRBy7igomQ0,2358
64
+ aurelian/agents/github/github_cli.py,sha256=y0HHbul63c1k7-jqXgxOStA5NG_ve0BvxtHW7mSaH20,9084
65
+ aurelian/agents/github/github_config.py,sha256=gAdmJMdkdqfIO_YFegvlqWAMoJpBW270ecuS0sBjM_k,557
66
+ aurelian/agents/github/github_gradio.py,sha256=CAhS8IgSPuI23SVvgt0n0G-5eFJ4oboUvFlhksXbAT4,5372
67
+ aurelian/agents/github/github_mcp.py,sha256=fWSvzN1UuE2_rcBeofxrQ2IMQWhUUUUnaH7tnBxzwfw,8211
68
+ aurelian/agents/github/github_tools.py,sha256=gRyMA3TEUb7uL0eAEfBw8LOZ1QpApRC4CeL_CU7Bt4o,12276
69
+ aurelian/agents/github/github_tools.py.tmp,sha256=NwQnFr9Y8R7wC3Ki7nriuQQUe1CEPGS8VTmonJHzS7I,12462
70
+ aurelian/agents/goann/__init__.py,sha256=bRUsVm-752ALw5kFYodSiwhUnp0ZR7DkrTctrFcYxCE,246
71
+ aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.md,sha256=A89MT1KOVaZPeKP1Z8pMqBat8tJYJ1hnUTpf1aC2bR4,32570
72
+ aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.pdf,sha256=bkhAE0-Bbpb1eJVqu8k0S5d4NLoKq6AxplVRUzaYCK0,876813
73
+ aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.md,sha256=BZKX-BGS_XBgMVxhQ5-tQYtCfJcbBWUQ07FXDE6Ltkw,38831
74
+ aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.pdf,sha256=KfAYb_5H4_ZouaqujClgGz4HTV0Iifmmcxa56hVqKvc,2238913
75
+ aurelian/agents/goann/goann_agent.py,sha256=20qTduJIaWeC8k9S3svcmz11wQxStxokr3Md-BrDVP4,3450
76
+ aurelian/agents/goann/goann_config.py,sha256=yfgUNjA_7YWMg15PJIRQHLg-pkC0An2ZvyD2FeJHxUM,2542
77
+ aurelian/agents/goann/goann_evals.py,sha256=foDikX0KBYcfBamf0G5UWcJstADbNrRB7q_TY7ToRdc,3724
78
+ aurelian/agents/goann/goann_gradio.py,sha256=s_mx4Qh2_5SgXdR3NuY_Jr1h38vTjz__-Tv0yk8QLU0,2025
79
+ aurelian/agents/goann/goann_mcp.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
80
+ aurelian/agents/goann/goann_tools.py,sha256=m5nM41nbH45IZ8-BXCaWOX970j0spYwjQJhFs23EvAs,2059
81
+ aurelian/agents/gocam/__init__.py,sha256=CuXryR9hlrCSdlDSctqKsorHO7jbrI2eGBwcoBDYEJY,1196
82
+ aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.docx,sha256=aohQYDq-iI6dj4AWpWZO-6dG91i_UhJ9Cvre40hsO5I,946469
83
+ aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.pdf,sha256=ffnp3EwWD-guJtv69IEo2y-Sw-mQn-ZiXPK-V2CvWC8,602114
84
+ aurelian/agents/gocam/documents/DNA-binding_transcription_factor_activity_annotation_guidelines.md,sha256=m2C4wIk0snHbG5BEH2ys_u1bisdK6D-2l5rxbWYiDww,5604
85
+ aurelian/agents/gocam/documents/E3 ubiquitin ligases.docx,sha256=V1hNs7OpJlCoDGB7viSInFCxqyQbl25w2GJKCwIq_JI,1056277
86
+ aurelian/agents/gocam/documents/E3 ubiquitin ligases.pdf,sha256=dW22GkLESJopbf4C4bn9QqRBK7XrXMIx2I71y1Zzbgo,534944
87
+ aurelian/agents/gocam/documents/E3_ubiquitin_ligases.md,sha256=LG9nvMKJWyWBHScZmFa0tfHlDkukDjVo9Ri4ndm-ibQ,10279
88
+ aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.docx,sha256=pJQS3s4QIZcFkm5qPejFcMoTBfDeucB-eNMtiD6KhCg,6386
89
+ aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.pdf,sha256=K6LmoWVrftha87NiLxd4G7oPC-jXIMYY7pJRat1NHkI,6624
90
+ aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.docx,sha256=ERpcemJbV22DcpHYiI3zU7FcOLtsC69MhuZdX085hqE,6503
91
+ aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.pdf,sha256=aQkQQN2b3iI4Xch0KaKsu8I8IV4HDmVtfd-_45tcuzM,27404
92
+ aurelian/agents/gocam/documents/GO-CAM_annotation_guidelines_README.md,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
93
+ aurelian/agents/gocam/documents/GO-CAM_modelling_guidelines_TO_DO.md,sha256=S1dWTltHqCSrAPfIBA8S4QQITcYQjK2PAJelFuEDCVY,99
94
+ aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.docx,sha256=1i1Cy-_1DTeDcOwcxtPVVOIfxYwECG_Kk3vEj2xhfh0,732409
95
+ aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.pdf,sha256=cDqe8SQSGz9uFQW05dLyeRDawcaSZR_3NM9EADog05s,494400
96
+ aurelian/agents/gocam/documents/How to annotate molecular adaptors.docx,sha256=6Y2ISmtruoZJsuj9L3OjKw3uWvhX7CWdCXx1uwpK3oU,1079302
97
+ aurelian/agents/gocam/documents/How to annotate molecular adaptors.pdf,sha256=5JAZL1UvCfBVLLdqHqwf8p5U-gpmof_jcbiKvWy-CBE,572546
98
+ aurelian/agents/gocam/documents/How to annotate sequestering proteins.docx,sha256=xYO1HYBLXnFRSukxIs5wfi2VqlzeGndvF64AI5Y0S_w,960739
99
+ aurelian/agents/gocam/documents/How to annotate sequestering proteins.pdf,sha256=bEP4d-04WelWmG13dAJhsHXMjY5e8JIeXlkpcSiIPq8,574363
100
+ aurelian/agents/gocam/documents/How_to_annotate_complexes_in_GO-CAM.md,sha256=-bJrOIuUKaCUuncgwLTYSN_BCprfyVTkSMIt7pmGWfQ,1419
101
+ aurelian/agents/gocam/documents/How_to_annotate_molecular_adaptors.md,sha256=eXcvTfkvUdATIquU4YNKRm_oYxThEO-DoM41kb0Qnv0,1420
102
+ aurelian/agents/gocam/documents/How_to_annotate_sequestering_proteins.md,sha256=KO1Phcfmsa9tFn8kba6K_GChHs0D8kjCeaGtUlTjok0,1966
103
+ aurelian/agents/gocam/documents/Molecular adaptor activity.docx,sha256=81XvvOsNOXvssHrLpzD2_gzevHkwcu9PcSdgN8vn4Ug,887781
104
+ aurelian/agents/gocam/documents/Molecular adaptor activity.pdf,sha256=YPEZxc7-OxJ3WleksQ178AusG6Cofvq1aA_dJeUcb3M,606499
105
+ aurelian/agents/gocam/documents/Molecular carrier activity.docx,sha256=xyjYIvVQfONjNMI_xm4MKdLR14Gns3a6jQKHCtVHKTs,733353
106
+ aurelian/agents/gocam/documents/Molecular carrier activity.pdf,sha256=AbWiRxwPOftwZsu85OsYtOYxzsaLjTXFjotAkhIu3DM,315598
107
+ aurelian/agents/gocam/documents/Molecular_adaptor_activity.md,sha256=6JU0HEVGgretdMH9-WeR7vReUINL3qaJ_QfgY26YsIU,2541
108
+ aurelian/agents/gocam/documents/Molecular_carrier_activity.md,sha256=vyZCNDQy5H81l5SZ1msSAGRBnmRDquFXH0R9VluZKHw,2113
109
+ aurelian/agents/gocam/documents/Protein sequestering activity.docx,sha256=r1bNYu4FIbNHghIRlP5Rg3E-4VAokdbKasux8QJs82Y,905100
110
+ aurelian/agents/gocam/documents/Protein sequestering activity.pdf,sha256=hx6kj4PKhmlUdj47jZpHFQoGccipbaHCPEwvdI7307c,546621
111
+ aurelian/agents/gocam/documents/Protein_sequestering_activity.md,sha256=39K831hLWWE9PcJihjh6E4rXC11j1wmz158O0xZ_XJs,2693
112
+ aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.docx,sha256=-ekOsLCkb-KFpNgvUha7_UwBd8o_xM4NJXffUJ-YzjI,1717037
113
+ aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.pdf,sha256=_uOuW9oBFX1DF3TurYVh5T0mnS7mB4swy4sFLlMSonQ,1159210
114
+ aurelian/agents/gocam/documents/Signaling_receptor_activity_annotation_guidelines.md,sha256=bAy_oemvDmtsEZXeZUFL9cDsySU75RMNIVMH0AkWmmc,9549
115
+ aurelian/agents/gocam/documents/Transcription coregulator activity.docx,sha256=_flIlkm6npxUuA_kxxDbFe77VzYVTfCDF-ags5p1WlM,702958
116
+ aurelian/agents/gocam/documents/Transcription coregulator activity.pdf,sha256=OoGvXOBMoWL-uXvEUr-QBJdQTSnPCkUna3mT7urnn5A,328581
117
+ aurelian/agents/gocam/documents/Transcription_coregulator_activity.md,sha256=inZjcs1IkQR_qs0hKVHwGIJaX43RDSDgC7mACD81d0I,2083
118
+ aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.docx,sha256=1-p0MrCo_7nV7sUf4QFQ7pr6wM-HvA3ZOWZMFgdxW0Y,560971
119
+ aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.pdf,sha256=qTTUQ6r7u18yu-DceDhfV52gDbpvaKK8DUk0qTdvEl4,273662
120
+ aurelian/agents/gocam/documents/Transporter_activity_annotation_annotation_guidelines.md,sha256=cajW81gsvKKqt_1OSagoJ5pCbauaU_tKk76TlmxjAxk,2340
121
+ aurelian/agents/gocam/documents/WIP - Regulation and Regulatory Processes in GO-CAM.docx,sha256=mNncvB7-oBj_D4NiquHEFOcopCMfJMOz6d8NwK3HO2c,1002108
122
+ aurelian/agents/gocam/documents/WIP - Regulation and Regulatory Processes in GO-CAM.pdf,sha256=W5uyZdv6EorQaRUA00Yh1XTYsA8pCL0RykRRTjGpghw,343694
123
+ aurelian/agents/gocam/documents/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md,sha256=7HWKIJy9X8Z0Jmye-9ak0tnte17c7twWjGRAm3_UqIc,2922
124
+ aurelian/agents/gocam/documents/md/DNA-binding_transcription_factor_activity_annotation_guidelines.md,sha256=RGWDaCw_eIoFsmyqsf5h3GjBNNW88FgYW9lLkzkSEKc,4264
125
+ aurelian/agents/gocam/documents/md/E3_ubiquitin_ligases.md,sha256=8s24FkHDJwMlpV0CvfSquOCmyloCyilizgDxq8gKyMo,7476
126
+ aurelian/agents/gocam/documents/md/GO-CAM_annotation_guidelines_README.md,sha256=72y9IWHq6nlDzoaTuYJNI9F5P_scD8oFtgDTiZtEyXc,1
127
+ aurelian/agents/gocam/documents/md/GO-CAM_modelling_guidelines_TO_DO.md,sha256=9Klg_NyCTSI4W0N_uh5z4SVmLcVoA4hZFja9aD-dCDY,101
128
+ aurelian/agents/gocam/documents/md/How_to_annotate_complexes_in_GO-CAM.md,sha256=1GMSlhg3Snr4cwkpvktc3VzgApzEPXvfcS2P1iWsO7A,1274
129
+ aurelian/agents/gocam/documents/md/How_to_annotate_molecular_adaptors.md,sha256=p8w3-UhUkaWxUDRcxgE9zzO8ClC3EAx6Vt8hIPL7ryU,992
130
+ aurelian/agents/gocam/documents/md/How_to_annotate_sequestering_proteins.md,sha256=jaUHNLS4Iany-KfzgJ762r0vRKYYAVaIuWzyZ13IZOE,1459
131
+ aurelian/agents/gocam/documents/md/Molecular_adaptor_activity.md,sha256=GSHzVQ4dhf1FTFkE4NcbcBTzwxbbGRtDqUjIboSAawI,1983
132
+ aurelian/agents/gocam/documents/md/Molecular_carrier_activity.md,sha256=5xThVA38OYmEPDhXr43CPb8ysanKJySa5x20xmTweso,1792
133
+ aurelian/agents/gocam/documents/md/Protein_sequestering_activity.md,sha256=WpXieshSG4a_Sldfrm1wh9t7dtPQF5KYrF2-QQGzCfA,1961
134
+ aurelian/agents/gocam/documents/md/Signaling_receptor_activity_annotation_guidelines.md,sha256=NvmTqaYgY76-3X0JjaTJPj0fal69CaOzZTmwpCLp-JU,6980
135
+ aurelian/agents/gocam/documents/md/Transcription_coregulator_activity.md,sha256=FQtdZRjPl3n5BIEsouOEzam4TF5yrNtsVnnWFlDyGaw,1277
136
+ aurelian/agents/gocam/documents/md/Transporter_activity_annotation_annotation_guidelines.md,sha256=7wrC8TryecwxXdXN6_XpUP7dHoUZ2-vzCHhLitCm42A,1688
137
+ aurelian/agents/gocam/documents/md/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md,sha256=Ug84Aa640VBwpMom5blksjweKjCutHKUYqBBzwzgG-I,2653
138
+ aurelian/agents/gocam/documents/pandoc_md/Signaling_receptor_activity_annotation_guidelines.md,sha256=TGw39vKs5XE0jF3s0A6XzP4_ovKS3nohqlrGlK7kVFo,11990
139
+ aurelian/agents/gocam/gocam_agent.py,sha256=5em_lS64D2eG_srlGU4B_76FTx3NABPAgmTrYcPr1a0,9497
140
+ aurelian/agents/gocam/gocam_config.py,sha256=MU7jRhrkB05kRT-ruPDoPpHMPFCn2y2Od6B13XIj6R0,2492
141
+ aurelian/agents/gocam/gocam_curator_agent.py,sha256=4OK3PoNCNA3pVLV6yq7Rm0ZN7YQ5todAvjJvYzAPPrY,1452
142
+ aurelian/agents/gocam/gocam_evals.py,sha256=x9K04niguY2BVtPA99ifj3gb7dIlu5Xt_YEpqpPcky4,1934
143
+ aurelian/agents/gocam/gocam_gradio.py,sha256=Ah1VnlGSYVzLPQel5SbZ-RNsI_QRg0PJBt6VGGIOOfo,3098
144
+ aurelian/agents/gocam/gocam_mcp.py,sha256=S-KT5GuQKtzvq33Qemm1Wwg3jhl64GnGbic_tA4-XoQ,5915
145
+ aurelian/agents/gocam/gocam_tools.py,sha256=tmhXLIYHDbXiteChzV6n-RzRhMiX2GSR9D2b47MmyxI,9671
146
+ aurelian/agents/linkml/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
147
+ aurelian/agents/linkml/linkml_agent.py,sha256=JhYfg-xMGhlj2VqaqeqTZEOhTcBkGzTj5aSn948pRtY,2208
148
+ aurelian/agents/linkml/linkml_config.py,sha256=VIPPX7H5eGbw7Rx-YyDorOYVHZz1TQxqFtFKwFtmFwg,1450
149
+ aurelian/agents/linkml/linkml_evals.py,sha256=odQ6unXhobBT6krqYVtdx1Jl91xh4m6avBk7-BlnHvc,2124
150
+ aurelian/agents/linkml/linkml_gradio.py,sha256=XaaBQEZTJdW2HdENbs2LjlHjcfjAr2-setFePJKp6bg,1303
151
+ aurelian/agents/linkml/linkml_mcp.py,sha256=8CttCtfiFrRU4FX4-JjXvDBnpMYnz3oOVvVuP2OlMjE,4711
152
+ aurelian/agents/linkml/linkml_tools.py,sha256=-y53s1MIJdLsqJstZF-8t5ocigHOLtXTDxmRIhY7uyc,3684
153
+ aurelian/agents/literature/__init__.py,sha256=8EY_j4JWf5Mbowv6mzUE6TLpkhwrbNZSKT-NEH65KpU,101
154
+ aurelian/agents/literature/literature_agent.py,sha256=LB9RYOK4bzaQUfs8D6rmLQ-1NCwNAPSFsfu_hCY4f00,2275
155
+ aurelian/agents/literature/literature_config.py,sha256=uDyhonTSdMP5L1dXgIGhgwlaHeyRPxjpVQkmt6kx7cE,947
156
+ aurelian/agents/literature/literature_gradio.py,sha256=5GAef4fB8GgfOokwpL016MIpyIZ20gfb5snZJWGF-k8,1646
157
+ aurelian/agents/literature/literature_mcp.py,sha256=fVBW7Vg8pW2vRq8RPio6Ltk_xe4KJCs_UCQzlsLDrJo,3925
158
+ aurelian/agents/literature/literature_tools.py,sha256=vZMTV-V3xpo4SvkEPnuJAsbv6gGCwQGbcvLW6ec6jX8,5849
159
+ aurelian/agents/monarch/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
160
+ aurelian/agents/monarch/monarch_agent.py,sha256=nve0m3BDj9_QwbUBy4Ht5ltVXElo1H_Hh3lPgc43rE4,1826
161
+ aurelian/agents/monarch/monarch_config.py,sha256=3g5OXmMnuH0by1IZY9YLn4WPR6hr4XKCreq1SBGMzXo,1390
162
+ aurelian/agents/monarch/monarch_gradio.py,sha256=GG5m4m8x4crFwP2a5z8s97nylG6gwuRXHa7RO82PPvY,1528
163
+ aurelian/agents/monarch/monarch_mcp.py,sha256=U-K0XlpRIMPlAm5dKQkqemepz-DemCmFLMJWLASV0AI,1839
164
+ aurelian/agents/monarch/monarch_tools.py,sha256=z6ohe4wzO8vBVSV_23FSPwLzFNhFrk6Hkdy7FCOmhos,3554
165
+ aurelian/agents/oak/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
166
+ aurelian/agents/oak/oak_config.py,sha256=Gc9_edlkZKF-8377xwx2QiIxVHGiHA2xWPgYVyG-tvE,675
167
+ aurelian/agents/oak/oak_gradio.py,sha256=-y99MoEORea2sLIvcvEEbeKDojxm0I7bXzzZkoSHu_s,1669
168
+ aurelian/agents/ontology_mapper/__init__.py,sha256=5SCUej1UyBJSuSwZrNHHO8rrTPElup_ufOClKom6_v8,646
169
+ aurelian/agents/ontology_mapper/ontology_mapper_agent.py,sha256=sE22zXyAru9dc1nlZB-0uAWWmd2RsoUndqoiwvrL_yk,2796
170
+ aurelian/agents/ontology_mapper/ontology_mapper_config.py,sha256=iqJzuZ6M7BSs0qGgeah5u7THOusZ3VjvH8lJ6IiYgSE,1639
171
+ aurelian/agents/ontology_mapper/ontology_mapper_evals.py,sha256=6kympT8LV570rRozgeBIyEdZ3dDfRGH2o3x4x2F__9Q,3591
172
+ aurelian/agents/ontology_mapper/ontology_mapper_gradio.py,sha256=nzkwPvK3k6Sze8oNS2R8z4k2XeXj4LU2wjV4G_Jn-Ec,1819
173
+ aurelian/agents/ontology_mapper/ontology_mapper_mcp.py,sha256=YnXCKU2Yzy_RPqEba8hJPWwtb1H07Wo-zlZY-nnKurw,2208
174
+ aurelian/agents/ontology_mapper/ontology_mapper_tools.py,sha256=S0azD3wR0pTh-9ipjVBUiNRkgsDEb30n1KMZD0qWvyw,4272
175
+ aurelian/agents/paperqa/__init__.py,sha256=Dfff3fyx9PeoeqA4DcvyE_loW-UXegYM281alttwLvI,590
176
+ aurelian/agents/paperqa/paperqa_agent.py,sha256=FAPgHVeW63jT07trjV2HzNqq7OivRDlhp2Kn50Kb5Gs,2643
177
+ aurelian/agents/paperqa/paperqa_cli.py,sha256=A0cwGUUTVcFVO1e_PsXusvBae9N5ElyeCtsZuQh-eGo,10357
178
+ aurelian/agents/paperqa/paperqa_config.py,sha256=CUj3BARcII8AippAYJXAq9MsqrQlkRm36ucHyuCGnII,4554
179
+ aurelian/agents/paperqa/paperqa_gradio.py,sha256=Thz82905TBeUQSiKcT40ZFs9MOqlN3YzYrJ5LNZPjHs,2844
180
+ aurelian/agents/paperqa/paperqa_mcp.py,sha256=ApnH43iZpM4ToPpSpE1KQf2mF4o7HCTXPb_X6tjX0ic,4665
181
+ aurelian/agents/paperqa/paperqa_tools.py,sha256=k0WtWPhkyAndnpPjP7XRF5llkW-Ktkxx2JhChO-SKU4,20238
182
+ aurelian/agents/phenopackets/__init__.py,sha256=TrXNpK2KDUjxok4nCuhepVPGH4RvALOZJoXjD4S-i1g,73
183
+ aurelian/agents/phenopackets/phenopackets_agent.py,sha256=R--xoY558TaVcAG2HoQvj7lWwCr_PrpfG7xl33rCIpk,2229
184
+ aurelian/agents/phenopackets/phenopackets_config.py,sha256=hpc3m2IboYlQoJselVMPf_EK0Z1YJBNp7qbj3TLk7PM,2304
185
+ aurelian/agents/phenopackets/phenopackets_evals.py,sha256=fG1du14j1rIcYJNWMIDGO2yPHc45G4VUtTpZzbwSgco,3503
186
+ aurelian/agents/phenopackets/phenopackets_gradio.py,sha256=KJdu5ZIgyYhAvpQLQ012JKMheAU08CiTK-MXqjGDDXU,1935
187
+ aurelian/agents/phenopackets/phenopackets_mcp.py,sha256=PzhqNW6RC9E5jRG9xBzMGVP3u-tQmTt6Idq_zDAeEsE,4677
188
+ aurelian/agents/phenopackets/phenopackets_tools.py,sha256=3U8mjA_mi3K6Sb5VOSfT3Z-ytTx2cuz8zFLnFxxp-U8,4052
189
+ aurelian/agents/rag/__init__.py,sha256=eqnU5tVCH52qW5KKSAgUzhh7WDYl-HZb84j-V5fs48g,749
190
+ aurelian/agents/rag/rag_agent.py,sha256=vkOsAwDWyt-uexqdUuHQ1QehLiYjk8P8E83QK61f9-0,2554
191
+ aurelian/agents/rag/rag_config.py,sha256=M5q56xOp7ZfK21mi0gOCJP8dXiWjPvbTHmv-36YyVq8,2692
192
+ aurelian/agents/rag/rag_gradio.py,sha256=Vl9GicDP0xlL7126RUHx9f0loQGa_JnFwN0QtOT_58w,1844
193
+ aurelian/agents/rag/rag_mcp.py,sha256=-o0c868DZdqfB38QOHFDqGHrwyWqI7vAK6aNAtDP3XA,2543
194
+ aurelian/agents/rag/rag_tools.py,sha256=VNt-jd3h-hkm-V65dnCwcIKJXFLiuyzuota-y0xqOq0,5574
195
+ aurelian/agents/rag_agent.py,sha256=yoofpPbA_umQzOnEatnOPzLBfebthlwZgDwa2vLhi9I,1455
196
+ aurelian/agents/robot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
197
+ aurelian/agents/robot/assets/__init__.py,sha256=jjfIEiaeYSAbuktyu-5sp_7-RG97ctm40-yLZCpDef0,83
198
+ aurelian/agents/robot/assets/template.md,sha256=FkWFKW4w4YzDL67ZqIBR_0NbxMAFJtdunQqTb3ebWgI,25422
199
+ aurelian/agents/robot/robot_config.py,sha256=KqCqnzW2jSukiHXDeenBz3LdecppGwMVtrPwnK3EpTM,785
200
+ aurelian/agents/robot/robot_gradio.py,sha256=r-QkGvsYc652B0TgJogu1XBFlPLE2c5BG7aGT-zSfwg,1430
201
+ aurelian/agents/robot/robot_mcp.py,sha256=KkYg_l-VfHM0cTAeBrfWuv0zN3U6S7oxGZGd6RQpes0,2439
202
+ aurelian/agents/robot/robot_ontology_agent.py,sha256=DNdo1zlkYEUqByVXY6-vrSTvBRl--R1hmlbdwFbB8gY,5733
203
+ aurelian/agents/robot/robot_tools.py,sha256=6V4jCUb2e6SvK_JndUnVATVBVpiHGj8yUbHhHYh1yDU,1821
204
+ aurelian/agents/talisman/__init__.py,sha256=oeaxm4LKY4-I3h14ecRXJll2S8ywz1eQRyc3sAAK6-E,88
205
+ aurelian/agents/talisman/__main__.py,sha256=iHcq-LxdMI5yWQ92ADFOq7yC-3oCVOF5fN1U3cXbUHQ,499
206
+ aurelian/agents/talisman/cli.py,sha256=iMEnxfgSkm3CaoOtv8aJZIDTd9izlbZJj7hYqO8KFwY,3324
207
+ aurelian/agents/talisman/run_talisman.py,sha256=K_GX9eqA2wrhXIDjtTfpCh7UHRObniSYDq1T9tr4SWw,518
208
+ aurelian/agents/talisman/talisman_agent.py,sha256=KBvCCkzl-j_PObfMBrsyXg3kvCDmCpi2DAOnuaURdMI,6641
209
+ aurelian/agents/talisman/talisman_config.py,sha256=bYjgMecVrKXwwZwv7n7Leseks6DFEfqVEZF9MqgoShQ,2301
210
+ aurelian/agents/talisman/talisman_gradio.py,sha256=ogpFwnxVngvu5UmQ1GKz2JdbpCWlIK7duQDLJGisWs8,1617
211
+ aurelian/agents/talisman/talisman_mcp.py,sha256=yQbLR6ITvl3qsV-p4nnqEDYW_R5qRyQNl56CkEWiY8k,2189
212
+ aurelian/agents/talisman/talisman_tools.py,sha256=ZzvpFxZBXpeZrIFV9aqtwVqa6O3z_5WvUReWOHh-aS4,42256
213
+ aurelian/agents/ubergraph/__init__.py,sha256=Nl81e1H7XKBSQ2nIHoY0UCHgcOW5N-PJ1AugKh_YGOs,767
214
+ aurelian/agents/ubergraph/ubergraph_agent.py,sha256=dW1IG35w7OgNgC5SDgNFB6K2RJCsRrfnTRd2nqrU9Tg,3066
215
+ aurelian/agents/ubergraph/ubergraph_config.py,sha256=Fi2hFVu92v55IinNYFlLjdvt9THXtRFPkSEcXtTrC10,2774
216
+ aurelian/agents/ubergraph/ubergraph_gradio.py,sha256=Gig_3AK0B4AkfvjlNklHkr87z2vcphll2I9DLgfdmdU,1372
217
+ aurelian/agents/ubergraph/ubergraph_mcp.py,sha256=p_YbEkSF4yN0T5OJ8FKIkuOtutOYvFL3TJDtJydSnws,2475
218
+ aurelian/agents/ubergraph/ubergraph_tools.py,sha256=9LLlOWXWu8crXCADpvzEJ0gQVNi9fuFYx8SkrDS175s,3428
219
+ aurelian/agents/uniprot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
220
+ aurelian/agents/uniprot/uniprot_agent.py,sha256=KMTRKGVpRpSchz7YEShh9ZSSGHzmeaGEUaNFKJPDWSI,1648
221
+ aurelian/agents/uniprot/uniprot_config.py,sha256=YhL265Z0GnTeXINHawe5iMcpR2ETLmdY3XhNXcYIc8w,1404
222
+ aurelian/agents/uniprot/uniprot_evals.py,sha256=aZAZAOYFfvywqWuWV1-6p3PpXCxEl_ZkHppl88z5GUw,3178
223
+ aurelian/agents/uniprot/uniprot_gradio.py,sha256=H38UY7g-hIXdMOjp4V5QHJ8aTkV-8aV9X1dvB3s0x6s,1444
224
+ aurelian/agents/uniprot/uniprot_mcp.py,sha256=B2OJB2MFCgYUxkqi9ae_XZOpj3zidqnLb--prDJ2v28,4594
225
+ aurelian/agents/uniprot/uniprot_tools.py,sha256=KyrjKCNDpa8BaJBftv6Rsc01Xica69P6rNnnByC3fGU,4250
226
+ aurelian/agents/web/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
227
+ aurelian/agents/web/web_config.py,sha256=uk-etu-DzYgeuS2zBs0SVfX_BvZ6QGs0X5PFsf1NR-Q,675
228
+ aurelian/agents/web/web_gradio.py,sha256=T7qzuRuBaWCYckWjpLu3L0LzHPLEKkxUYp2rj-Og_ms,1334
229
+ aurelian/agents/web/web_mcp.py,sha256=3mrUlxBqeMSOmtpnD2wWedsOiRJbtveEnbyJqQdfEXQ,1163
230
+ aurelian/agents/web/web_tools.py,sha256=oSS8MFxFqtcPfdEhmEuuiRKW8_NTg3ktLxahlF8h0Ec,4645
231
+ aurelian/chat.py,sha256=hg9eGKiz_NAjwG5jNGwNqoFrhhx029XX3dWdMRrk-EU,563
232
+ aurelian/cli.py,sha256=-6r3w8H43fhoHrkzn3GQmpQ37McsFHjWP5wZIrnk0gQ,34856
233
+ aurelian/dependencies/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
234
+ aurelian/dependencies/workdir.py,sha256=G_eGlxKpHRjO3EL2hHN8lvtticgSZvJe300KkJP4vZQ,2228
235
+ aurelian/evaluators/model.py,sha256=USfoHcYTMTlPJaM9-BPksb3asBoDd7amqSnHIbg9YYs,253
236
+ aurelian/evaluators/substring_evaluator.py,sha256=cx1fF3f5FulEeD9iTkgtwo-zByt5qgdmk1XKWJ1_eqQ,1039
237
+ aurelian/mcp/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
238
+ aurelian/mcp/amigo_mcp_test.py,sha256=TtlYU-5AKcXf2XubFUNpZE2RxFHYi_cVbtte6KJQnzE,2902
239
+ aurelian/mcp/config_generator.py,sha256=QIaLqURiuOPgGfOImItf89d4ZltYonpybzAcO2vjA2Y,4350
240
+ aurelian/mcp/example_config.json,sha256=1kegjmwIdNRcPxvBOy_fCF3WZ2-lt4HO9w3zFDYQvaE,952
241
+ aurelian/mcp/generate_sample_config.py,sha256=k6UlX-KT6Tb11wM6gT4dVYbUNJnbJjpvckMQYQg-Auw,1150
242
+ aurelian/mcp/gocam_mcp_test.py,sha256=a7_6b328Cde28osc3xBCNfyflamiT59Jg9N3kguOUCg,5005
243
+ aurelian/mcp/linkml_mcp_tools.py,sha256=WABtgKAtgXoM3lJ_I4YDZ0oxRxP29EV_b_yqYbPjkcs,4891
244
+ aurelian/mcp/mcp_discovery.py,sha256=scK7U50z5rNirMAQTCFQE_BNSlH6dqgcJv-FH6NiaUY,2551
245
+ aurelian/mcp/mcp_test.py,sha256=oBvPUi43hmHm8rf5YC0FYGZE_3flZMsfP2TjWZlWkgI,593
246
+ aurelian/mcp/phenopackets_mcp_test.py,sha256=1KkAsN1KR6LRRALK3UzFQQCtCHJFoaQF5itS1PWgDUg,3880
247
+ aurelian/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
248
+ aurelian/tools/web/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
249
+ aurelian/tools/web/url_download.py,sha256=Tpg41yx4Sd3dToV-kGBZggwYUq3hmeLwJttSQrnqz4M,1435
250
+ aurelian/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
251
+ aurelian/utils/async_utils.py,sha256=mqjYPr8RlXlIXKYRgQ95ZcGTbdIeOw4PHvr37Clopd0,417
252
+ aurelian/utils/data_utils.py,sha256=LFuSKWtApLJxFGuHLG4-Zhw42cbaQK0juCEXD44b3S4,1047
253
+ aurelian/utils/documentation_manager.py,sha256=uvAnI_N1V1ITQX53ytOSgvDLbV0IIsSkxpKDg0y3E4g,1767
254
+ aurelian/utils/doi_fetcher.py,sha256=BNIsYaS9cb2uOSY0jxdjnZAFI2VSk2odzP4ppz3ToHg,8553
255
+ aurelian/utils/ontology_utils.py,sha256=4r31gmSo_Q3SCFGmydYdHJw1KUHRok1MEes9osnuUSE,2320
256
+ aurelian/utils/pdf_fetcher.py,sha256=odR1PO8yLldr-H0h9dT_zHlNN609SD_CrxihsnYJn_0,762
257
+ aurelian/utils/process_logs.py,sha256=aSg_IzK9eAqxaKN5x0skgOfl1gfpJNue2gLZu_37_rY,3249
258
+ aurelian/utils/pubmed_utils.py,sha256=Gk00lu1Lv0GRSNeF5M4zplp3UMSpe5byCaVKCJimUH0,6862
259
+ aurelian/utils/pytest_report_to_markdown.py,sha256=WH1NlkVYj0UfUqpXjRD1KMpkMgEW3qev3fDdPvZG9Yw,1406
260
+ aurelian/utils/robot_ontology_utils.py,sha256=aaRe9eyLgJCtj1EfV13v4Q7khFTWzUoFFEE_lizGuGg,3591
261
+ aurelian/utils/search_utils.py,sha256=9MloT3SzOE4JsElsYlCznp9N6fv_OQK7YWOU8MIy1WU,2818
262
+ aurelian-0.1.0.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
263
+ aurelian-0.1.0.dist-info/METADATA,sha256=biMhtaEF-lJNseb5Y06wfFPlXoxxnbJSwW6ngm8e_ag,3557
264
+ aurelian-0.1.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
265
+ aurelian-0.1.0.dist-info/entry_points.txt,sha256=EnGehbtRm0YmhdfwfcoGJjVG3Man-zgKvob20fTIBik,102
266
+ aurelian-0.1.0.dist-info/RECORD,,
aurelian-0.1.0.dist-info/WHEEL ADDED
@@ -0,0 +1,4 @@
1
+ Wheel-Version: 1.0
2
+ Generator: poetry-core 2.1.3
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any
aurelian-0.1.0.dist-info/entry_points.txt ADDED
@@ -0,0 +1,4 @@
1
+ [console_scripts]
2
+ aurelian=aurelian.cli:main
3
+ aurelian-mcp-gocam=aurelian.agents.gocam.gocam_mcp:main
4
+