know-do-graph 0.1.0__tar.gz

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  1. know_do_graph-0.1.0/.gitignore +12 -0
  2. know_do_graph-0.1.0/PKG-INFO +765 -0
  3. know_do_graph-0.1.0/README.md +741 -0
  4. know_do_graph-0.1.0/agents/__init__.py +0 -0
  5. know_do_graph-0.1.0/agents/extraction_agent/__init__.py +0 -0
  6. know_do_graph-0.1.0/agents/extraction_agent/agent.py +170 -0
  7. know_do_graph-0.1.0/agents/graph_agent/__init__.py +5 -0
  8. know_do_graph-0.1.0/agents/graph_agent/agent.py +373 -0
  9. know_do_graph-0.1.0/agents/graph_agent/tools.py +2106 -0
  10. know_do_graph-0.1.0/agents/maintenance_agent/__init__.py +0 -0
  11. know_do_graph-0.1.0/agents/maintenance_agent/agent.py +283 -0
  12. know_do_graph-0.1.0/agents/orchestrator/__init__.py +0 -0
  13. know_do_graph-0.1.0/agents/orchestrator/agent.py +217 -0
  14. know_do_graph-0.1.0/agents/review_agent/__init__.py +0 -0
  15. know_do_graph-0.1.0/agents/review_agent/agent.py +188 -0
  16. know_do_graph-0.1.0/agents/review_agent/tools.py +472 -0
  17. know_do_graph-0.1.0/api/__init__.py +0 -0
  18. know_do_graph-0.1.0/api/main.py +136 -0
  19. know_do_graph-0.1.0/api/routes/__init__.py +0 -0
  20. know_do_graph-0.1.0/api/routes/agent.py +81 -0
  21. know_do_graph-0.1.0/api/routes/entries.py +411 -0
  22. know_do_graph-0.1.0/api/routes/graph.py +132 -0
  23. know_do_graph-0.1.0/api/routes/mem.py +179 -0
  24. know_do_graph-0.1.0/api/routes/remote.py +815 -0
  25. know_do_graph-0.1.0/api/routes/remote_sync.py +230 -0
  26. know_do_graph-0.1.0/api/routes/retrieve.py +88 -0
  27. know_do_graph-0.1.0/assets/starter.db +0 -0
  28. know_do_graph-0.1.0/core/__init__.py +0 -0
  29. know_do_graph-0.1.0/core/app_state.py +9 -0
  30. know_do_graph-0.1.0/core/events.py +84 -0
  31. know_do_graph-0.1.0/core/extraction/__init__.py +0 -0
  32. know_do_graph-0.1.0/core/extraction/wikilink_parser.py +48 -0
  33. know_do_graph-0.1.0/core/graph/__init__.py +0 -0
  34. know_do_graph-0.1.0/core/graph/graph.py +204 -0
  35. know_do_graph-0.1.0/core/memory/__init__.py +0 -0
  36. know_do_graph-0.1.0/core/memory/memgraph.py +458 -0
  37. know_do_graph-0.1.0/core/retrieval/__init__.py +0 -0
  38. know_do_graph-0.1.0/core/retrieval/embedder.py +122 -0
  39. know_do_graph-0.1.0/core/retrieval/fusion.py +52 -0
  40. know_do_graph-0.1.0/core/retrieval/progressive.py +399 -0
  41. know_do_graph-0.1.0/core/retrieval/retrieval.py +346 -0
  42. know_do_graph-0.1.0/core/retrieval/vector_store.py +91 -0
  43. know_do_graph-0.1.0/core/schemas/__init__.py +0 -0
  44. know_do_graph-0.1.0/core/schemas/edge.py +46 -0
  45. know_do_graph-0.1.0/core/schemas/entry.py +388 -0
  46. know_do_graph-0.1.0/core/storage/__init__.py +0 -0
  47. know_do_graph-0.1.0/core/storage/database.py +104 -0
  48. know_do_graph-0.1.0/core/storage/models.py +66 -0
  49. know_do_graph-0.1.0/core/storage/repository.py +243 -0
  50. know_do_graph-0.1.0/core/sync/__init__.py +20 -0
  51. know_do_graph-0.1.0/core/sync/autolink.py +301 -0
  52. know_do_graph-0.1.0/core/sync/db_merge.py +297 -0
  53. know_do_graph-0.1.0/core/sync/db_watcher.py +84 -0
  54. know_do_graph-0.1.0/core/sync/remote_sync.py +345 -0
  55. know_do_graph-0.1.0/data/edges/.gitkeep +1 -0
  56. know_do_graph-0.1.0/data/memory/matcreator-hsa-docking-20250518.json +22 -0
  57. know_do_graph-0.1.0/data/memory/test-flex.json +29 -0
  58. know_do_graph-0.1.0/data/metadata/.gitkeep +1 -0
  59. know_do_graph-0.1.0/data/nodes/.gitkeep +1 -0
  60. know_do_graph-0.1.0/entries.txt +0 -0
  61. know_do_graph-0.1.0/examples/__init__.py +0 -0
  62. know_do_graph-0.1.0/examples/example_entries.py +206 -0
  63. know_do_graph-0.1.0/examples/pymatgen_interface_examples.py +811 -0
  64. know_do_graph-0.1.0/frontend/.gitignore +4 -0
  65. know_do_graph-0.1.0/frontend/README.md +63 -0
  66. know_do_graph-0.1.0/frontend/dist/assets/index-BLfo7ZZu.css +1 -0
  67. know_do_graph-0.1.0/frontend/dist/assets/index-G-mYbZ9R.js +83 -0
  68. know_do_graph-0.1.0/frontend/dist/assets/index-G-mYbZ9R.js.map +1 -0
  69. know_do_graph-0.1.0/frontend/dist/index.html +92 -0
  70. know_do_graph-0.1.0/frontend/index.html +95 -0
  71. know_do_graph-0.1.0/frontend/node_modules/.bin/csv2json +1 -0
  72. know_do_graph-0.1.0/frontend/node_modules/.bin/csv2tsv +1 -0
  73. know_do_graph-0.1.0/frontend/node_modules/.bin/dsv2dsv +1 -0
  74. know_do_graph-0.1.0/frontend/node_modules/.bin/dsv2json +1 -0
  75. know_do_graph-0.1.0/frontend/node_modules/.bin/esbuild +1 -0
  76. know_do_graph-0.1.0/frontend/node_modules/.bin/json2csv +1 -0
  77. know_do_graph-0.1.0/frontend/node_modules/.bin/json2dsv +1 -0
  78. know_do_graph-0.1.0/frontend/node_modules/.bin/json2tsv +1 -0
  79. know_do_graph-0.1.0/frontend/node_modules/.bin/nanoid +1 -0
  80. know_do_graph-0.1.0/frontend/node_modules/.bin/rollup +1 -0
  81. know_do_graph-0.1.0/frontend/node_modules/.bin/tsv2csv +1 -0
  82. know_do_graph-0.1.0/frontend/node_modules/.bin/tsv2json +1 -0
  83. know_do_graph-0.1.0/frontend/node_modules/.bin/vite +1 -0
  84. know_do_graph-0.1.0/frontend/node_modules/.package-lock.json +727 -0
  85. know_do_graph-0.1.0/frontend/node_modules/.vite/deps/_metadata.json +15 -0
  86. know_do_graph-0.1.0/frontend/node_modules/.vite/deps/d3.js +17106 -0
  87. know_do_graph-0.1.0/frontend/node_modules/.vite/deps/d3.js.map +7 -0
  88. know_do_graph-0.1.0/frontend/node_modules/.vite/deps/package.json +3 -0
  89. know_do_graph-0.1.0/frontend/node_modules/@esbuild/linux-x64/README.md +3 -0
  90. know_do_graph-0.1.0/frontend/node_modules/@esbuild/linux-x64/bin/esbuild +0 -0
  91. know_do_graph-0.1.0/frontend/node_modules/@esbuild/linux-x64/package.json +20 -0
  92. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-gnu/README.md +3 -0
  93. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-gnu/package.json +25 -0
  94. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-gnu/rollup.linux-x64-gnu.node +0 -0
  95. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-musl/README.md +3 -0
  96. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-musl/package.json +25 -0
  97. know_do_graph-0.1.0/frontend/node_modules/@rollup/rollup-linux-x64-musl/rollup.linux-x64-musl.node +0 -0
  98. know_do_graph-0.1.0/frontend/node_modules/@types/estree/LICENSE +21 -0
  99. know_do_graph-0.1.0/frontend/node_modules/@types/estree/README.md +15 -0
  100. know_do_graph-0.1.0/frontend/node_modules/@types/estree/flow.d.ts +167 -0
  101. know_do_graph-0.1.0/frontend/node_modules/@types/estree/index.d.ts +694 -0
  102. know_do_graph-0.1.0/frontend/node_modules/@types/estree/package.json +27 -0
  103. know_do_graph-0.1.0/frontend/node_modules/commander/CHANGELOG.md +440 -0
  104. know_do_graph-0.1.0/frontend/node_modules/commander/LICENSE +22 -0
  105. know_do_graph-0.1.0/frontend/node_modules/commander/Readme.md +917 -0
  106. know_do_graph-0.1.0/frontend/node_modules/commander/esm.mjs +4 -0
  107. know_do_graph-0.1.0/frontend/node_modules/commander/index.js +2217 -0
  108. know_do_graph-0.1.0/frontend/node_modules/commander/package-support.json +16 -0
  109. know_do_graph-0.1.0/frontend/node_modules/commander/package.json +68 -0
  110. know_do_graph-0.1.0/frontend/node_modules/commander/typings/index.d.ts +627 -0
  111. know_do_graph-0.1.0/frontend/node_modules/d3/LICENSE +13 -0
  112. know_do_graph-0.1.0/frontend/node_modules/d3/README.md +12 -0
  113. know_do_graph-0.1.0/frontend/node_modules/d3/package.json +92 -0
  114. know_do_graph-0.1.0/frontend/node_modules/d3/src/index.js +30 -0
  115. know_do_graph-0.1.0/frontend/node_modules/d3-array/LICENSE +13 -0
  116. know_do_graph-0.1.0/frontend/node_modules/d3-array/README.md +954 -0
  117. know_do_graph-0.1.0/frontend/node_modules/d3-array/package.json +61 -0
  118. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/array.js +4 -0
  119. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/ascending.js +3 -0
  120. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/bin.js +125 -0
  121. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/bisect.js +9 -0
  122. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/bisector.js +56 -0
  123. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/blur.js +115 -0
  124. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/constant.js +3 -0
  125. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/count.js +18 -0
  126. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/cross.js +33 -0
  127. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/cumsum.js +6 -0
  128. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/descending.js +7 -0
  129. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/deviation.js +6 -0
  130. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/difference.js +11 -0
  131. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/disjoint.js +15 -0
  132. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/every.js +10 -0
  133. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/extent.js +29 -0
  134. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/filter.js +11 -0
  135. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/fsum.js +69 -0
  136. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/greatest.js +29 -0
  137. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/greatestIndex.js +19 -0
  138. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/group.js +65 -0
  139. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/groupSort.js +10 -0
  140. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/identity.js +3 -0
  141. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/index.js +57 -0
  142. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/intersection.js +19 -0
  143. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/least.js +29 -0
  144. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/leastIndex.js +19 -0
  145. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/map.js +5 -0
  146. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/max.js +20 -0
  147. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/maxIndex.js +22 -0
  148. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/mean.js +19 -0
  149. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/median.js +9 -0
  150. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/merge.js +9 -0
  151. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/min.js +20 -0
  152. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/minIndex.js +22 -0
  153. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/mode.js +28 -0
  154. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/nice.js +18 -0
  155. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/number.js +20 -0
  156. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/pairs.js +15 -0
  157. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/permute.js +3 -0
  158. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/quantile.js +47 -0
  159. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/quickselect.js +53 -0
  160. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/range.js +13 -0
  161. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/rank.js +24 -0
  162. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/reduce.js +14 -0
  163. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/reverse.js +4 -0
  164. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/scan.js +6 -0
  165. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/shuffle.js +13 -0
  166. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/some.js +10 -0
  167. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/sort.js +39 -0
  168. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/subset.js +5 -0
  169. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/sum.js +18 -0
  170. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/superset.js +19 -0
  171. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/threshold/freedmanDiaconis.js +7 -0
  172. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/threshold/scott.js +7 -0
  173. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/threshold/sturges.js +5 -0
  174. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/ticks.js +55 -0
  175. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/transpose.js +15 -0
  176. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/union.js +11 -0
  177. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/variance.js +25 -0
  178. know_do_graph-0.1.0/frontend/node_modules/d3-array/src/zip.js +5 -0
  179. know_do_graph-0.1.0/frontend/node_modules/d3-axis/LICENSE +13 -0
  180. know_do_graph-0.1.0/frontend/node_modules/d3-axis/README.md +210 -0
  181. know_do_graph-0.1.0/frontend/node_modules/d3-axis/package.json +54 -0
  182. know_do_graph-0.1.0/frontend/node_modules/d3-axis/src/axis.js +174 -0
  183. know_do_graph-0.1.0/frontend/node_modules/d3-axis/src/identity.js +3 -0
  184. know_do_graph-0.1.0/frontend/node_modules/d3-axis/src/index.js +6 -0
  185. know_do_graph-0.1.0/frontend/node_modules/d3-brush/LICENSE +13 -0
  186. know_do_graph-0.1.0/frontend/node_modules/d3-brush/README.md +185 -0
  187. know_do_graph-0.1.0/frontend/node_modules/d3-brush/package.json +55 -0
  188. know_do_graph-0.1.0/frontend/node_modules/d3-brush/src/brush.js +621 -0
  189. know_do_graph-0.1.0/frontend/node_modules/d3-brush/src/constant.js +1 -0
  190. know_do_graph-0.1.0/frontend/node_modules/d3-brush/src/event.js +16 -0
  191. know_do_graph-0.1.0/frontend/node_modules/d3-brush/src/index.js +6 -0
  192. know_do_graph-0.1.0/frontend/node_modules/d3-brush/src/noevent.js +8 -0
  193. know_do_graph-0.1.0/frontend/node_modules/d3-chord/LICENSE +13 -0
  194. know_do_graph-0.1.0/frontend/node_modules/d3-chord/README.md +234 -0
  195. know_do_graph-0.1.0/frontend/node_modules/d3-chord/package.json +54 -0
  196. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/array.js +1 -0
  197. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/chord.js +122 -0
  198. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/constant.js +5 -0
  199. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/index.js +2 -0
  200. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/math.js +8 -0
  201. know_do_graph-0.1.0/frontend/node_modules/d3-chord/src/ribbon.js +134 -0
  202. know_do_graph-0.1.0/frontend/node_modules/d3-color/LICENSE +13 -0
  203. know_do_graph-0.1.0/frontend/node_modules/d3-color/README.md +203 -0
  204. know_do_graph-0.1.0/frontend/node_modules/d3-color/package.json +54 -0
  205. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/color.js +396 -0
  206. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/cubehelix.js +61 -0
  207. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/define.js +10 -0
  208. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/index.js +3 -0
  209. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/lab.js +123 -0
  210. know_do_graph-0.1.0/frontend/node_modules/d3-color/src/math.js +2 -0
  211. know_do_graph-0.1.0/frontend/node_modules/d3-contour/LICENSE +13 -0
  212. know_do_graph-0.1.0/frontend/node_modules/d3-contour/README.md +187 -0
  213. know_do_graph-0.1.0/frontend/node_modules/d3-contour/package.json +66 -0
  214. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/area.js +5 -0
  215. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/array.js +3 -0
  216. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/ascending.js +3 -0
  217. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/constant.js +1 -0
  218. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/contains.js +27 -0
  219. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/contours.js +225 -0
  220. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/density.js +149 -0
  221. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/index.js +2 -0
  222. know_do_graph-0.1.0/frontend/node_modules/d3-contour/src/noop.js +1 -0
  223. know_do_graph-0.1.0/frontend/node_modules/d3-delaunay/LICENSE +14 -0
  224. know_do_graph-0.1.0/frontend/node_modules/d3-delaunay/README.md +216 -0
  225. know_do_graph-0.1.0/frontend/node_modules/d3-delaunay/package.json +62 -0
  226. know_do_graph-0.1.0/frontend/node_modules/d3-delaunay/src/delaunay.js +248 -0
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