@pikaa-ai/pikaa 0.2.5 → 0.3.1

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 (2430) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +153 -104
  3. package/assets/frames/blocks/frame_1.txt +17 -0
  4. package/assets/frames/blocks/frame_10.txt +17 -0
  5. package/assets/frames/blocks/frame_11.txt +17 -0
  6. package/assets/frames/blocks/frame_12.txt +17 -0
  7. package/assets/frames/blocks/frame_13.txt +17 -0
  8. package/assets/frames/blocks/frame_14.txt +17 -0
  9. package/assets/frames/blocks/frame_15.txt +17 -0
  10. package/assets/frames/blocks/frame_16.txt +17 -0
  11. package/assets/frames/blocks/frame_17.txt +17 -0
  12. package/assets/frames/blocks/frame_18.txt +17 -0
  13. package/assets/frames/blocks/frame_19.txt +17 -0
  14. package/assets/frames/blocks/frame_2.txt +17 -0
  15. package/assets/frames/blocks/frame_20.txt +17 -0
  16. package/assets/frames/blocks/frame_21.txt +17 -0
  17. package/assets/frames/blocks/frame_22.txt +17 -0
  18. package/assets/frames/blocks/frame_23.txt +17 -0
  19. package/assets/frames/blocks/frame_24.txt +17 -0
  20. package/assets/frames/blocks/frame_25.txt +17 -0
  21. package/assets/frames/blocks/frame_26.txt +17 -0
  22. package/assets/frames/blocks/frame_27.txt +17 -0
  23. package/assets/frames/blocks/frame_28.txt +17 -0
  24. package/assets/frames/blocks/frame_29.txt +17 -0
  25. package/assets/frames/blocks/frame_3.txt +17 -0
  26. package/assets/frames/blocks/frame_30.txt +17 -0
  27. package/assets/frames/blocks/frame_31.txt +17 -0
  28. package/assets/frames/blocks/frame_32.txt +17 -0
  29. package/assets/frames/blocks/frame_33.txt +17 -0
  30. package/assets/frames/blocks/frame_34.txt +17 -0
  31. package/assets/frames/blocks/frame_35.txt +17 -0
  32. package/assets/frames/blocks/frame_36.txt +17 -0
  33. package/assets/frames/blocks/frame_4.txt +17 -0
  34. package/assets/frames/blocks/frame_5.txt +17 -0
  35. package/assets/frames/blocks/frame_6.txt +17 -0
  36. package/assets/frames/blocks/frame_7.txt +17 -0
  37. package/assets/frames/blocks/frame_8.txt +17 -0
  38. package/assets/frames/blocks/frame_9.txt +17 -0
  39. package/assets/frames/default/frame_1.txt +17 -0
  40. package/assets/frames/default/frame_10.txt +17 -0
  41. package/assets/frames/default/frame_11.txt +17 -0
  42. package/assets/frames/default/frame_12.txt +17 -0
  43. package/assets/frames/default/frame_13.txt +17 -0
  44. package/assets/frames/default/frame_14.txt +17 -0
  45. package/assets/frames/default/frame_15.txt +17 -0
  46. package/assets/frames/default/frame_16.txt +17 -0
  47. package/assets/frames/default/frame_17.txt +17 -0
  48. package/assets/frames/default/frame_18.txt +17 -0
  49. package/assets/frames/default/frame_19.txt +17 -0
  50. package/assets/frames/default/frame_2.txt +17 -0
  51. package/assets/frames/default/frame_20.txt +17 -0
  52. package/assets/frames/default/frame_21.txt +17 -0
  53. package/assets/frames/default/frame_22.txt +17 -0
  54. package/assets/frames/default/frame_23.txt +17 -0
  55. package/assets/frames/default/frame_24.txt +17 -0
  56. package/assets/frames/default/frame_25.txt +17 -0
  57. package/assets/frames/default/frame_26.txt +17 -0
  58. package/assets/frames/default/frame_27.txt +17 -0
  59. package/assets/frames/default/frame_28.txt +17 -0
  60. package/assets/frames/default/frame_29.txt +17 -0
  61. package/assets/frames/default/frame_3.txt +17 -0
  62. package/assets/frames/default/frame_30.txt +17 -0
  63. package/assets/frames/default/frame_31.txt +17 -0
  64. package/assets/frames/default/frame_32.txt +17 -0
  65. package/assets/frames/default/frame_33.txt +17 -0
  66. package/assets/frames/default/frame_34.txt +17 -0
  67. package/assets/frames/default/frame_35.txt +17 -0
  68. package/assets/frames/default/frame_36.txt +17 -0
  69. package/assets/frames/default/frame_4.txt +17 -0
  70. package/assets/frames/default/frame_5.txt +17 -0
  71. package/assets/frames/default/frame_6.txt +17 -0
  72. package/assets/frames/default/frame_7.txt +17 -0
  73. package/assets/frames/default/frame_8.txt +17 -0
  74. package/assets/frames/default/frame_9.txt +17 -0
  75. package/assets/frames/dots/frame_1.txt +17 -0
  76. package/assets/frames/dots/frame_10.txt +17 -0
  77. package/assets/frames/dots/frame_11.txt +17 -0
  78. package/assets/frames/dots/frame_12.txt +17 -0
  79. package/assets/frames/dots/frame_13.txt +17 -0
  80. package/assets/frames/dots/frame_14.txt +17 -0
  81. package/assets/frames/dots/frame_15.txt +17 -0
  82. package/assets/frames/dots/frame_16.txt +17 -0
  83. package/assets/frames/dots/frame_17.txt +17 -0
  84. package/assets/frames/dots/frame_18.txt +17 -0
  85. package/assets/frames/dots/frame_19.txt +17 -0
  86. package/assets/frames/dots/frame_2.txt +17 -0
  87. package/assets/frames/dots/frame_20.txt +17 -0
  88. package/assets/frames/dots/frame_21.txt +17 -0
  89. package/assets/frames/dots/frame_22.txt +17 -0
  90. package/assets/frames/dots/frame_23.txt +17 -0
  91. package/assets/frames/dots/frame_24.txt +17 -0
  92. package/assets/frames/dots/frame_25.txt +17 -0
  93. package/assets/frames/dots/frame_26.txt +17 -0
  94. package/assets/frames/dots/frame_27.txt +17 -0
  95. package/assets/frames/dots/frame_28.txt +17 -0
  96. package/assets/frames/dots/frame_29.txt +17 -0
  97. package/assets/frames/dots/frame_3.txt +17 -0
  98. package/assets/frames/dots/frame_30.txt +17 -0
  99. package/assets/frames/dots/frame_31.txt +17 -0
  100. package/assets/frames/dots/frame_32.txt +17 -0
  101. package/assets/frames/dots/frame_33.txt +17 -0
  102. package/assets/frames/dots/frame_34.txt +17 -0
  103. package/assets/frames/dots/frame_35.txt +17 -0
  104. package/assets/frames/dots/frame_36.txt +17 -0
  105. package/assets/frames/dots/frame_4.txt +17 -0
  106. package/assets/frames/dots/frame_5.txt +17 -0
  107. package/assets/frames/dots/frame_6.txt +17 -0
  108. package/assets/frames/dots/frame_7.txt +17 -0
  109. package/assets/frames/dots/frame_8.txt +17 -0
  110. package/assets/frames/dots/frame_9.txt +17 -0
  111. package/assets/frames/groupy/frame_1.txt +17 -0
  112. package/assets/frames/groupy/frame_10.txt +17 -0
  113. package/assets/frames/groupy/frame_11.txt +17 -0
  114. package/assets/frames/groupy/frame_12.txt +17 -0
  115. package/assets/frames/groupy/frame_13.txt +17 -0
  116. package/assets/frames/groupy/frame_14.txt +17 -0
  117. package/assets/frames/groupy/frame_15.txt +17 -0
  118. package/assets/frames/groupy/frame_16.txt +17 -0
  119. package/assets/frames/groupy/frame_17.txt +17 -0
  120. package/assets/frames/groupy/frame_18.txt +17 -0
  121. package/assets/frames/groupy/frame_19.txt +17 -0
  122. package/assets/frames/groupy/frame_2.txt +17 -0
  123. package/assets/frames/groupy/frame_20.txt +17 -0
  124. package/assets/frames/groupy/frame_21.txt +17 -0
  125. package/assets/frames/groupy/frame_22.txt +17 -0
  126. package/assets/frames/groupy/frame_23.txt +17 -0
  127. package/assets/frames/groupy/frame_24.txt +17 -0
  128. package/assets/frames/groupy/frame_25.txt +17 -0
  129. package/assets/frames/groupy/frame_26.txt +17 -0
  130. package/assets/frames/groupy/frame_27.txt +17 -0
  131. package/assets/frames/groupy/frame_28.txt +17 -0
  132. package/assets/frames/groupy/frame_29.txt +17 -0
  133. package/assets/frames/groupy/frame_3.txt +17 -0
  134. package/assets/frames/groupy/frame_30.txt +17 -0
  135. package/assets/frames/groupy/frame_31.txt +17 -0
  136. package/assets/frames/groupy/frame_32.txt +17 -0
  137. package/assets/frames/groupy/frame_33.txt +17 -0
  138. package/assets/frames/groupy/frame_34.txt +17 -0
  139. package/assets/frames/groupy/frame_35.txt +17 -0
  140. package/assets/frames/groupy/frame_36.txt +17 -0
  141. package/assets/frames/groupy/frame_4.txt +17 -0
  142. package/assets/frames/groupy/frame_5.txt +17 -0
  143. package/assets/frames/groupy/frame_6.txt +17 -0
  144. package/assets/frames/groupy/frame_7.txt +17 -0
  145. package/assets/frames/groupy/frame_8.txt +17 -0
  146. package/assets/frames/groupy/frame_9.txt +17 -0
  147. package/assets/frames/hash/frame_1.txt +17 -0
  148. package/assets/frames/hash/frame_10.txt +17 -0
  149. package/assets/frames/hash/frame_11.txt +17 -0
  150. package/assets/frames/hash/frame_12.txt +17 -0
  151. package/assets/frames/hash/frame_13.txt +17 -0
  152. package/assets/frames/hash/frame_14.txt +17 -0
  153. package/assets/frames/hash/frame_15.txt +17 -0
  154. package/assets/frames/hash/frame_16.txt +17 -0
  155. package/assets/frames/hash/frame_17.txt +17 -0
  156. package/assets/frames/hash/frame_18.txt +17 -0
  157. package/assets/frames/hash/frame_19.txt +17 -0
  158. package/assets/frames/hash/frame_2.txt +17 -0
  159. package/assets/frames/hash/frame_20.txt +17 -0
  160. package/assets/frames/hash/frame_21.txt +17 -0
  161. package/assets/frames/hash/frame_22.txt +17 -0
  162. package/assets/frames/hash/frame_23.txt +17 -0
  163. package/assets/frames/hash/frame_24.txt +17 -0
  164. package/assets/frames/hash/frame_25.txt +17 -0
  165. package/assets/frames/hash/frame_26.txt +17 -0
  166. package/assets/frames/hash/frame_27.txt +17 -0
  167. package/assets/frames/hash/frame_28.txt +17 -0
  168. package/assets/frames/hash/frame_29.txt +17 -0
  169. package/assets/frames/hash/frame_3.txt +17 -0
  170. package/assets/frames/hash/frame_30.txt +17 -0
  171. package/assets/frames/hash/frame_31.txt +17 -0
  172. package/assets/frames/hash/frame_32.txt +17 -0
  173. package/assets/frames/hash/frame_33.txt +17 -0
  174. package/assets/frames/hash/frame_34.txt +17 -0
  175. package/assets/frames/hash/frame_35.txt +17 -0
  176. package/assets/frames/hash/frame_36.txt +17 -0
  177. package/assets/frames/hash/frame_4.txt +17 -0
  178. package/assets/frames/hash/frame_5.txt +17 -0
  179. package/assets/frames/hash/frame_6.txt +17 -0
  180. package/assets/frames/hash/frame_7.txt +17 -0
  181. package/assets/frames/hash/frame_8.txt +17 -0
  182. package/assets/frames/hash/frame_9.txt +17 -0
  183. package/assets/frames/hbars/frame_1.txt +17 -0
  184. package/assets/frames/hbars/frame_10.txt +17 -0
  185. package/assets/frames/hbars/frame_11.txt +17 -0
  186. package/assets/frames/hbars/frame_12.txt +17 -0
  187. package/assets/frames/hbars/frame_13.txt +17 -0
  188. package/assets/frames/hbars/frame_14.txt +17 -0
  189. package/assets/frames/hbars/frame_15.txt +17 -0
  190. package/assets/frames/hbars/frame_16.txt +17 -0
  191. package/assets/frames/hbars/frame_17.txt +17 -0
  192. package/assets/frames/hbars/frame_18.txt +17 -0
  193. package/assets/frames/hbars/frame_19.txt +17 -0
  194. package/assets/frames/hbars/frame_2.txt +17 -0
  195. package/assets/frames/hbars/frame_20.txt +17 -0
  196. package/assets/frames/hbars/frame_21.txt +17 -0
  197. package/assets/frames/hbars/frame_22.txt +17 -0
  198. package/assets/frames/hbars/frame_23.txt +17 -0
  199. package/assets/frames/hbars/frame_24.txt +17 -0
  200. package/assets/frames/hbars/frame_25.txt +17 -0
  201. package/assets/frames/hbars/frame_26.txt +17 -0
  202. package/assets/frames/hbars/frame_27.txt +17 -0
  203. package/assets/frames/hbars/frame_28.txt +17 -0
  204. package/assets/frames/hbars/frame_29.txt +17 -0
  205. package/assets/frames/hbars/frame_3.txt +17 -0
  206. package/assets/frames/hbars/frame_30.txt +17 -0
  207. package/assets/frames/hbars/frame_31.txt +17 -0
  208. package/assets/frames/hbars/frame_32.txt +17 -0
  209. package/assets/frames/hbars/frame_33.txt +17 -0
  210. package/assets/frames/hbars/frame_34.txt +17 -0
  211. package/assets/frames/hbars/frame_35.txt +17 -0
  212. package/assets/frames/hbars/frame_36.txt +17 -0
  213. package/assets/frames/hbars/frame_4.txt +17 -0
  214. package/assets/frames/hbars/frame_5.txt +17 -0
  215. package/assets/frames/hbars/frame_6.txt +17 -0
  216. package/assets/frames/hbars/frame_7.txt +17 -0
  217. package/assets/frames/hbars/frame_8.txt +17 -0
  218. package/assets/frames/hbars/frame_9.txt +17 -0
  219. package/assets/frames/mesosfer/frame_1.txt +17 -0
  220. package/assets/frames/mesosfer/frame_10.txt +17 -0
  221. package/assets/frames/mesosfer/frame_11.txt +17 -0
  222. package/assets/frames/mesosfer/frame_12.txt +17 -0
  223. package/assets/frames/mesosfer/frame_13.txt +17 -0
  224. package/assets/frames/mesosfer/frame_14.txt +17 -0
  225. package/assets/frames/mesosfer/frame_15.txt +17 -0
  226. package/assets/frames/mesosfer/frame_16.txt +17 -0
  227. package/assets/frames/mesosfer/frame_17.txt +17 -0
  228. package/assets/frames/mesosfer/frame_18.txt +17 -0
  229. package/assets/frames/mesosfer/frame_19.txt +17 -0
  230. package/assets/frames/mesosfer/frame_2.txt +17 -0
  231. package/assets/frames/mesosfer/frame_20.txt +17 -0
  232. package/assets/frames/mesosfer/frame_21.txt +17 -0
  233. package/assets/frames/mesosfer/frame_22.txt +17 -0
  234. package/assets/frames/mesosfer/frame_23.txt +17 -0
  235. package/assets/frames/mesosfer/frame_24.txt +17 -0
  236. package/assets/frames/mesosfer/frame_25.txt +17 -0
  237. package/assets/frames/mesosfer/frame_26.txt +17 -0
  238. package/assets/frames/mesosfer/frame_27.txt +17 -0
  239. package/assets/frames/mesosfer/frame_28.txt +17 -0
  240. package/assets/frames/mesosfer/frame_29.txt +17 -0
  241. package/assets/frames/mesosfer/frame_3.txt +17 -0
  242. package/assets/frames/mesosfer/frame_30.txt +17 -0
  243. package/assets/frames/mesosfer/frame_31.txt +17 -0
  244. package/assets/frames/mesosfer/frame_32.txt +17 -0
  245. package/assets/frames/mesosfer/frame_33.txt +17 -0
  246. package/assets/frames/mesosfer/frame_34.txt +17 -0
  247. package/assets/frames/mesosfer/frame_35.txt +17 -0
  248. package/assets/frames/mesosfer/frame_36.txt +17 -0
  249. package/assets/frames/mesosfer/frame_4.txt +17 -0
  250. package/assets/frames/mesosfer/frame_5.txt +17 -0
  251. package/assets/frames/mesosfer/frame_6.txt +17 -0
  252. package/assets/frames/mesosfer/frame_7.txt +17 -0
  253. package/assets/frames/mesosfer/frame_8.txt +17 -0
  254. package/assets/frames/mesosfer/frame_9.txt +17 -0
  255. package/assets/frames/shapes/frame_1.txt +17 -0
  256. package/assets/frames/shapes/frame_10.txt +17 -0
  257. package/assets/frames/shapes/frame_11.txt +17 -0
  258. package/assets/frames/shapes/frame_12.txt +17 -0
  259. package/assets/frames/shapes/frame_13.txt +17 -0
  260. package/assets/frames/shapes/frame_14.txt +17 -0
  261. package/assets/frames/shapes/frame_15.txt +17 -0
  262. package/assets/frames/shapes/frame_16.txt +17 -0
  263. package/assets/frames/shapes/frame_17.txt +17 -0
  264. package/assets/frames/shapes/frame_18.txt +17 -0
  265. package/assets/frames/shapes/frame_19.txt +17 -0
  266. package/assets/frames/shapes/frame_2.txt +17 -0
  267. package/assets/frames/shapes/frame_20.txt +17 -0
  268. package/assets/frames/shapes/frame_21.txt +17 -0
  269. package/assets/frames/shapes/frame_22.txt +17 -0
  270. package/assets/frames/shapes/frame_23.txt +17 -0
  271. package/assets/frames/shapes/frame_24.txt +17 -0
  272. package/assets/frames/shapes/frame_25.txt +17 -0
  273. package/assets/frames/shapes/frame_26.txt +17 -0
  274. package/assets/frames/shapes/frame_27.txt +17 -0
  275. package/assets/frames/shapes/frame_28.txt +17 -0
  276. package/assets/frames/shapes/frame_29.txt +17 -0
  277. package/assets/frames/shapes/frame_3.txt +17 -0
  278. package/assets/frames/shapes/frame_30.txt +17 -0
  279. package/assets/frames/shapes/frame_31.txt +17 -0
  280. package/assets/frames/shapes/frame_32.txt +17 -0
  281. package/assets/frames/shapes/frame_33.txt +17 -0
  282. package/assets/frames/shapes/frame_34.txt +17 -0
  283. package/assets/frames/shapes/frame_35.txt +17 -0
  284. package/assets/frames/shapes/frame_36.txt +17 -0
  285. package/assets/frames/shapes/frame_4.txt +17 -0
  286. package/assets/frames/shapes/frame_5.txt +17 -0
  287. package/assets/frames/shapes/frame_6.txt +17 -0
  288. package/assets/frames/shapes/frame_7.txt +17 -0
  289. package/assets/frames/shapes/frame_8.txt +17 -0
  290. package/assets/frames/shapes/frame_9.txt +17 -0
  291. package/assets/frames/slug/frame_1.txt +17 -0
  292. package/assets/frames/slug/frame_10.txt +17 -0
  293. package/assets/frames/slug/frame_11.txt +17 -0
  294. package/assets/frames/slug/frame_12.txt +17 -0
  295. package/assets/frames/slug/frame_13.txt +17 -0
  296. package/assets/frames/slug/frame_14.txt +17 -0
  297. package/assets/frames/slug/frame_15.txt +17 -0
  298. package/assets/frames/slug/frame_16.txt +17 -0
  299. package/assets/frames/slug/frame_17.txt +17 -0
  300. package/assets/frames/slug/frame_18.txt +17 -0
  301. package/assets/frames/slug/frame_19.txt +17 -0
  302. package/assets/frames/slug/frame_2.txt +17 -0
  303. package/assets/frames/slug/frame_20.txt +17 -0
  304. package/assets/frames/slug/frame_21.txt +17 -0
  305. package/assets/frames/slug/frame_22.txt +17 -0
  306. package/assets/frames/slug/frame_23.txt +17 -0
  307. package/assets/frames/slug/frame_24.txt +17 -0
  308. package/assets/frames/slug/frame_25.txt +17 -0
  309. package/assets/frames/slug/frame_26.txt +17 -0
  310. package/assets/frames/slug/frame_27.txt +17 -0
  311. package/assets/frames/slug/frame_28.txt +17 -0
  312. package/assets/frames/slug/frame_29.txt +17 -0
  313. package/assets/frames/slug/frame_3.txt +17 -0
  314. package/assets/frames/slug/frame_30.txt +17 -0
  315. package/assets/frames/slug/frame_31.txt +17 -0
  316. package/assets/frames/slug/frame_32.txt +17 -0
  317. package/assets/frames/slug/frame_33.txt +17 -0
  318. package/assets/frames/slug/frame_34.txt +17 -0
  319. package/assets/frames/slug/frame_35.txt +17 -0
  320. package/assets/frames/slug/frame_36.txt +17 -0
  321. package/assets/frames/slug/frame_4.txt +17 -0
  322. package/assets/frames/slug/frame_5.txt +17 -0
  323. package/assets/frames/slug/frame_6.txt +17 -0
  324. package/assets/frames/slug/frame_7.txt +17 -0
  325. package/assets/frames/slug/frame_8.txt +17 -0
  326. package/assets/frames/slug/frame_9.txt +17 -0
  327. package/assets/frames/vbars/frame_1.txt +17 -0
  328. package/assets/frames/vbars/frame_10.txt +17 -0
  329. package/assets/frames/vbars/frame_11.txt +17 -0
  330. package/assets/frames/vbars/frame_12.txt +17 -0
  331. package/assets/frames/vbars/frame_13.txt +17 -0
  332. package/assets/frames/vbars/frame_14.txt +17 -0
  333. package/assets/frames/vbars/frame_15.txt +17 -0
  334. package/assets/frames/vbars/frame_16.txt +17 -0
  335. package/assets/frames/vbars/frame_17.txt +17 -0
  336. package/assets/frames/vbars/frame_18.txt +17 -0
  337. package/assets/frames/vbars/frame_19.txt +17 -0
  338. package/assets/frames/vbars/frame_2.txt +17 -0
  339. package/assets/frames/vbars/frame_20.txt +17 -0
  340. package/assets/frames/vbars/frame_21.txt +17 -0
  341. package/assets/frames/vbars/frame_22.txt +17 -0
  342. package/assets/frames/vbars/frame_23.txt +17 -0
  343. package/assets/frames/vbars/frame_24.txt +17 -0
  344. package/assets/frames/vbars/frame_25.txt +17 -0
  345. package/assets/frames/vbars/frame_26.txt +17 -0
  346. package/assets/frames/vbars/frame_27.txt +17 -0
  347. package/assets/frames/vbars/frame_28.txt +17 -0
  348. package/assets/frames/vbars/frame_29.txt +17 -0
  349. package/assets/frames/vbars/frame_3.txt +17 -0
  350. package/assets/frames/vbars/frame_30.txt +17 -0
  351. package/assets/frames/vbars/frame_31.txt +17 -0
  352. package/assets/frames/vbars/frame_32.txt +17 -0
  353. package/assets/frames/vbars/frame_33.txt +17 -0
  354. package/assets/frames/vbars/frame_34.txt +17 -0
  355. package/assets/frames/vbars/frame_35.txt +17 -0
  356. package/assets/frames/vbars/frame_36.txt +17 -0
  357. package/assets/frames/vbars/frame_4.txt +17 -0
  358. package/assets/frames/vbars/frame_5.txt +17 -0
  359. package/assets/frames/vbars/frame_6.txt +17 -0
  360. package/assets/frames/vbars/frame_7.txt +17 -0
  361. package/assets/frames/vbars/frame_8.txt +17 -0
  362. package/assets/frames/vbars/frame_9.txt +17 -0
  363. package/bin/pikaa.js +1 -0
  364. package/dist/cli.js +3484 -879
  365. package/dist/index.js +6835 -437
  366. package/package.json +6 -1
  367. package/skills/adaptyv/SKILL.md +240 -0
  368. package/skills/adaptyv/references/api-endpoints.md +690 -0
  369. package/skills/aeon/SKILL.md +402 -0
  370. package/skills/aeon/references/anomaly_detection.md +154 -0
  371. package/skills/aeon/references/classification.md +144 -0
  372. package/skills/aeon/references/clustering.md +123 -0
  373. package/skills/aeon/references/datasets_benchmarking.md +392 -0
  374. package/skills/aeon/references/distances.md +256 -0
  375. package/skills/aeon/references/forecasting.md +109 -0
  376. package/skills/aeon/references/networks.md +289 -0
  377. package/skills/aeon/references/regression.md +118 -0
  378. package/skills/aeon/references/segmentation.md +163 -0
  379. package/skills/aeon/references/similarity_search.md +187 -0
  380. package/skills/aeon/references/transformations.md +246 -0
  381. package/skills/analytical-method-validation/SKILL.md +299 -0
  382. package/skills/analytical-method-validation/assets/validation-protocol-template.md +106 -0
  383. package/skills/analytical-method-validation/assets/validation-report-template.md +116 -0
  384. package/skills/analytical-method-validation/references/compendial-and-clsi.md +96 -0
  385. package/skills/analytical-method-validation/references/framework-selection.md +87 -0
  386. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +123 -0
  387. package/skills/analytical-method-validation/references/ich-q2r2.md +229 -0
  388. package/skills/analytical-method-validation/references/source-ledger.md +125 -0
  389. package/skills/analytical-method-validation/references/statistics.md +209 -0
  390. package/skills/analytical-method-validation/scripts/_catalog.py +499 -0
  391. package/skills/analytical-method-validation/scripts/_common.py +955 -0
  392. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +328 -0
  393. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +293 -0
  394. package/skills/analytical-method-validation/scripts/check_detection_limits.py +310 -0
  395. package/skills/analytical-method-validation/scripts/check_response.py +243 -0
  396. package/skills/analytical-method-validation/scripts/compare_methods.py +215 -0
  397. package/skills/analytical-method-validation/scripts/plan_validation.py +381 -0
  398. package/skills/anndata/SKILL.md +431 -0
  399. package/skills/anndata/references/best_practices.md +532 -0
  400. package/skills/anndata/references/concatenation.md +399 -0
  401. package/skills/anndata/references/data_structure.md +314 -0
  402. package/skills/anndata/references/io_operations.md +466 -0
  403. package/skills/anndata/references/manipulation.md +516 -0
  404. package/skills/arbor/SKILL.md +152 -0
  405. package/skills/arbor/references/arbor-upstream.md +91 -0
  406. package/skills/arbor/references/executor-brief.md +68 -0
  407. package/skills/arbor/references/htr-methodology.md +177 -0
  408. package/skills/arbor/references/report-template.md +39 -0
  409. package/skills/arbor/scripts/tree.py +564 -0
  410. package/skills/arboreto/SKILL.md +267 -0
  411. package/skills/arboreto/references/algorithms.md +152 -0
  412. package/skills/arboreto/references/basic_inference.md +181 -0
  413. package/skills/arboreto/references/distributed_computing.md +242 -0
  414. package/skills/arboreto/scripts/basic_grn_inference.py +107 -0
  415. package/skills/astropy/SKILL.md +353 -0
  416. package/skills/astropy/references/coordinates.md +280 -0
  417. package/skills/astropy/references/cosmology.md +309 -0
  418. package/skills/astropy/references/fits.md +398 -0
  419. package/skills/astropy/references/tables.md +495 -0
  420. package/skills/astropy/references/time.md +412 -0
  421. package/skills/astropy/references/units.md +178 -0
  422. package/skills/astropy/references/wcs_and_other_modules.md +377 -0
  423. package/skills/autoskill/SKILL.md +233 -0
  424. package/skills/autoskill/config.yaml +53 -0
  425. package/skills/autoskill/references/https-proxy.md +62 -0
  426. package/skills/autoskill/references/screenpipe-config.yaml +61 -0
  427. package/skills/autoskill/scripts/autoskill.py +35 -0
  428. package/skills/autoskill/scripts/backends.py +116 -0
  429. package/skills/autoskill/scripts/cluster.py +54 -0
  430. package/skills/autoskill/scripts/doctor.py +108 -0
  431. package/skills/autoskill/scripts/fetch_window.py +33 -0
  432. package/skills/autoskill/scripts/match_skills.py +46 -0
  433. package/skills/autoskill/scripts/promote.py +58 -0
  434. package/skills/autoskill/scripts/redact.py +40 -0
  435. package/skills/autoskill/scripts/run.py +194 -0
  436. package/skills/autoskill/scripts/synthesize.py +72 -0
  437. package/skills/benchling-integration/SKILL.md +229 -0
  438. package/skills/benchling-integration/references/api_endpoints.md +883 -0
  439. package/skills/benchling-integration/references/authentication.md +390 -0
  440. package/skills/benchling-integration/references/core_capabilities.md +355 -0
  441. package/skills/benchling-integration/references/eventbridge.md +255 -0
  442. package/skills/benchling-integration/references/sdk_reference.md +772 -0
  443. package/skills/bgpt-paper-search/SKILL.md +75 -0
  444. package/skills/bids/SKILL.md +237 -0
  445. package/skills/bids/references/beps.yml +637 -0
  446. package/skills/bids/references/bids_schema.json +21015 -0
  447. package/skills/bids/references/bids_specification.md +165 -0
  448. package/skills/bids/references/conversion_tools.md +475 -0
  449. package/skills/bids/references/core_workflows.md +552 -0
  450. package/skills/bids/references/metadata_fields.md +365 -0
  451. package/skills/bids/scripts/update_schema.py +89 -0
  452. package/skills/biopython/SKILL.md +472 -0
  453. package/skills/biopython/references/advanced.md +580 -0
  454. package/skills/biopython/references/alignment.md +377 -0
  455. package/skills/biopython/references/blast.md +463 -0
  456. package/skills/biopython/references/databases.md +492 -0
  457. package/skills/biopython/references/phylogenetics.md +566 -0
  458. package/skills/biopython/references/sequence_io.md +289 -0
  459. package/skills/biopython/references/structure.md +564 -0
  460. package/skills/bioservices/SKILL.md +399 -0
  461. package/skills/bioservices/references/identifier_mapping.md +685 -0
  462. package/skills/bioservices/references/services_reference.md +638 -0
  463. package/skills/bioservices/references/workflow_patterns.md +813 -0
  464. package/skills/bioservices/scripts/batch_id_converter.py +347 -0
  465. package/skills/bioservices/scripts/compound_cross_reference.py +387 -0
  466. package/skills/bioservices/scripts/pathway_analysis.py +309 -0
  467. package/skills/bioservices/scripts/protein_analysis_workflow.py +441 -0
  468. package/skills/bulk-rnaseq/SKILL.md +198 -0
  469. package/skills/bulk-rnaseq/references/counts-and-handoff.md +91 -0
  470. package/skills/bulk-rnaseq/references/design-and-qc.md +68 -0
  471. package/skills/bulk-rnaseq/references/upstream-manual.md +128 -0
  472. package/skills/bulk-rnaseq/references/upstream-nfcore.md +108 -0
  473. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +203 -0
  474. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +206 -0
  475. package/skills/cellxgene-census/SKILL.md +283 -0
  476. package/skills/cellxgene-census/references/census_schema.md +218 -0
  477. package/skills/cellxgene-census/references/common_patterns.md +368 -0
  478. package/skills/cellxgene-census/references/core_workflow_patterns.md +297 -0
  479. package/skills/cirq/SKILL.md +370 -0
  480. package/skills/cirq/references/building.md +307 -0
  481. package/skills/cirq/references/experiments.md +572 -0
  482. package/skills/cirq/references/hardware.md +527 -0
  483. package/skills/cirq/references/noise.md +514 -0
  484. package/skills/cirq/references/simulation.md +353 -0
  485. package/skills/cirq/references/transformation.md +416 -0
  486. package/skills/citation-management/SKILL.md +329 -0
  487. package/skills/citation-management/assets/bibtex_template.bib +264 -0
  488. package/skills/citation-management/assets/citation_checklist.md +386 -0
  489. package/skills/citation-management/references/best_practices.md +91 -0
  490. package/skills/citation-management/references/bibtex_formatting.md +908 -0
  491. package/skills/citation-management/references/citation_validation.md +835 -0
  492. package/skills/citation-management/references/core_workflow.md +569 -0
  493. package/skills/citation-management/references/example_workflows.md +126 -0
  494. package/skills/citation-management/references/google_scholar_search.md +732 -0
  495. package/skills/citation-management/references/metadata_extraction.md +870 -0
  496. package/skills/citation-management/references/pubmed_search.md +839 -0
  497. package/skills/citation-management/references/script_reference.md +250 -0
  498. package/skills/citation-management/references/search_strategies.md +110 -0
  499. package/skills/citation-management/scripts/_common.py +331 -0
  500. package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  501. package/skills/citation-management/scripts/extract_metadata.py +690 -0
  502. package/skills/citation-management/scripts/format_bibtex.py +356 -0
  503. package/skills/citation-management/scripts/search_google_scholar.py +268 -0
  504. package/skills/citation-management/scripts/search_openalex.py +297 -0
  505. package/skills/citation-management/scripts/search_pubmed.py +419 -0
  506. package/skills/citation-management/scripts/validate_citations.py +688 -0
  507. package/skills/clinical-decision-support/SKILL.md +238 -0
  508. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +114 -0
  509. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +115 -0
  510. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +81 -0
  511. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +108 -0
  512. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +176 -0
  513. package/skills/clinical-decision-support/assets/evidence_profile_template.json +139 -0
  514. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +134 -0
  515. package/skills/clinical-decision-support/references/README.md +62 -0
  516. package/skills/clinical-decision-support/references/cohort_evaluation.md +142 -0
  517. package/skills/clinical-decision-support/references/decision_logic_traceability.md +146 -0
  518. package/skills/clinical-decision-support/references/evidence_profiles.md +153 -0
  519. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +152 -0
  520. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +144 -0
  521. package/skills/clinical-decision-support/references/regulatory_and_governance.md +104 -0
  522. package/skills/clinical-decision-support/references/safety_and_scope.md +103 -0
  523. package/skills/clinical-decision-support/references/security_validation.md +60 -0
  524. package/skills/clinical-decision-support/references/sources.md +119 -0
  525. package/skills/clinical-decision-support/references/study_reporting.md +134 -0
  526. package/skills/clinical-decision-support/references/survival_analysis.md +156 -0
  527. package/skills/clinical-decision-support/scripts/_common.py +223 -0
  528. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +288 -0
  529. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +313 -0
  530. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +260 -0
  531. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +259 -0
  532. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +345 -0
  533. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +294 -0
  534. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +269 -0
  535. package/skills/clinical-reports/SKILL.md +248 -0
  536. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +1 -0
  537. package/skills/clinical-reports/assets/case_report_template.json +43 -0
  538. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +51 -0
  539. package/skills/clinical-reports/assets/clinical_trial_results_template.json +66 -0
  540. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +49 -0
  541. package/skills/clinical-reports/assets/consistency_manifest_template.json +15 -0
  542. package/skills/clinical-reports/assets/deidentification_process_checklist.json +56 -0
  543. package/skills/clinical-reports/assets/lab_report_template.json +36 -0
  544. package/skills/clinical-reports/assets/pathology_report_template.json +36 -0
  545. package/skills/clinical-reports/assets/provenance_manifest_template.json +17 -0
  546. package/skills/clinical-reports/assets/quality_review_checklist.json +34 -0
  547. package/skills/clinical-reports/assets/radiology_report_template.json +34 -0
  548. package/skills/clinical-reports/assets/research_summary_template.json +36 -0
  549. package/skills/clinical-reports/assets/terminology_manifest_template.json +11 -0
  550. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +70 -0
  551. package/skills/clinical-reports/references/README.md +34 -0
  552. package/skills/clinical-reports/references/case_report_guidelines.md +72 -0
  553. package/skills/clinical-reports/references/clinical_trial_reporting.md +97 -0
  554. package/skills/clinical-reports/references/data_presentation.md +92 -0
  555. package/skills/clinical-reports/references/diagnostic_reports_standards.md +76 -0
  556. package/skills/clinical-reports/references/medical_terminology.md +84 -0
  557. package/skills/clinical-reports/references/privacy_and_deidentification.md +84 -0
  558. package/skills/clinical-reports/references/professional_review.md +78 -0
  559. package/skills/clinical-reports/references/report_type_routing.md +57 -0
  560. package/skills/clinical-reports/references/safety_reporting.md +109 -0
  561. package/skills/clinical-reports/references/sources.md +75 -0
  562. package/skills/clinical-reports/scripts/_common.py +263 -0
  563. package/skills/clinical-reports/scripts/check_deidentification.py +298 -0
  564. package/skills/clinical-reports/scripts/consistency_checker.py +390 -0
  565. package/skills/clinical-reports/scripts/format_adverse_events.py +455 -0
  566. package/skills/clinical-reports/scripts/generate_report_template.py +115 -0
  567. package/skills/clinical-reports/scripts/provenance_validator.py +263 -0
  568. package/skills/clinical-reports/scripts/terminology_validator.py +277 -0
  569. package/skills/clinical-reports/scripts/validate_case_report.py +278 -0
  570. package/skills/clinical-reports/scripts/validate_trial_report.py +534 -0
  571. package/skills/cobrapy/SKILL.md +496 -0
  572. package/skills/cobrapy/references/api_quick_reference.md +665 -0
  573. package/skills/cobrapy/references/workflows.md +600 -0
  574. package/skills/consciousness-council/SKILL.md +151 -0
  575. package/skills/consciousness-council/references/advanced-configurations.md +96 -0
  576. package/skills/dask/SKILL.md +482 -0
  577. package/skills/dask/references/arrays.md +495 -0
  578. package/skills/dask/references/bags.md +468 -0
  579. package/skills/dask/references/best-practices.md +277 -0
  580. package/skills/dask/references/dataframes.md +370 -0
  581. package/skills/dask/references/futures.md +541 -0
  582. package/skills/dask/references/schedulers.md +517 -0
  583. package/skills/database-lookup/SKILL.md +386 -0
  584. package/skills/database-lookup/references/addgene.md +38 -0
  585. package/skills/database-lookup/references/alphafold.md +52 -0
  586. package/skills/database-lookup/references/alphavantage.md +261 -0
  587. package/skills/database-lookup/references/bea.md +409 -0
  588. package/skills/database-lookup/references/bindingdb.md +85 -0
  589. package/skills/database-lookup/references/biogrid.md +110 -0
  590. package/skills/database-lookup/references/bls.md +235 -0
  591. package/skills/database-lookup/references/brenda.md +71 -0
  592. package/skills/database-lookup/references/cbioportal.md +206 -0
  593. package/skills/database-lookup/references/census.md +251 -0
  594. package/skills/database-lookup/references/chebi.md +103 -0
  595. package/skills/database-lookup/references/chembl.md +80 -0
  596. package/skills/database-lookup/references/clinicaltrials.md +86 -0
  597. package/skills/database-lookup/references/clinpgx.md +64 -0
  598. package/skills/database-lookup/references/clinvar.md +91 -0
  599. package/skills/database-lookup/references/cod.md +121 -0
  600. package/skills/database-lookup/references/cosmic.md +59 -0
  601. package/skills/database-lookup/references/dailymed.md +65 -0
  602. package/skills/database-lookup/references/database_selection_guide.md +166 -0
  603. package/skills/database-lookup/references/datacommons.md +237 -0
  604. package/skills/database-lookup/references/dbsnp.md +143 -0
  605. package/skills/database-lookup/references/disgenet.md +52 -0
  606. package/skills/database-lookup/references/drugbank.md +54 -0
  607. package/skills/database-lookup/references/ecb.md +191 -0
  608. package/skills/database-lookup/references/emdb.md +37 -0
  609. package/skills/database-lookup/references/ena.md +372 -0
  610. package/skills/database-lookup/references/encode.md +47 -0
  611. package/skills/database-lookup/references/ensembl.md +539 -0
  612. package/skills/database-lookup/references/epa.md +232 -0
  613. package/skills/database-lookup/references/eurostat.md +237 -0
  614. package/skills/database-lookup/references/fda.md +64 -0
  615. package/skills/database-lookup/references/federal-reserve.md +216 -0
  616. package/skills/database-lookup/references/fred.md +297 -0
  617. package/skills/database-lookup/references/gene-ontology.md +147 -0
  618. package/skills/database-lookup/references/geo.md +130 -0
  619. package/skills/database-lookup/references/gnomad.md +93 -0
  620. package/skills/database-lookup/references/gtex.md +136 -0
  621. package/skills/database-lookup/references/gwas-catalog.md +46 -0
  622. package/skills/database-lookup/references/hca.md +35 -0
  623. package/skills/database-lookup/references/hpo.md +48 -0
  624. package/skills/database-lookup/references/human-protein-atlas.md +57 -0
  625. package/skills/database-lookup/references/interpro.md +120 -0
  626. package/skills/database-lookup/references/jaspar.md +50 -0
  627. package/skills/database-lookup/references/kegg.md +78 -0
  628. package/skills/database-lookup/references/lincs-l1000.md +68 -0
  629. package/skills/database-lookup/references/materials-project.md +123 -0
  630. package/skills/database-lookup/references/metabolomics-workbench.md +98 -0
  631. package/skills/database-lookup/references/monarch.md +46 -0
  632. package/skills/database-lookup/references/mousemine.md +40 -0
  633. package/skills/database-lookup/references/nasa-exoplanet-archive.md +112 -0
  634. package/skills/database-lookup/references/nasa.md +121 -0
  635. package/skills/database-lookup/references/ncbi-gene.md +64 -0
  636. package/skills/database-lookup/references/ncbi-protein.md +104 -0
  637. package/skills/database-lookup/references/ncbi-taxonomy.md +121 -0
  638. package/skills/database-lookup/references/nist.md +105 -0
  639. package/skills/database-lookup/references/noaa.md +199 -0
  640. package/skills/database-lookup/references/omim.md +114 -0
  641. package/skills/database-lookup/references/opentargets.md +459 -0
  642. package/skills/database-lookup/references/openweathermap.md +255 -0
  643. package/skills/database-lookup/references/pdb.md +121 -0
  644. package/skills/database-lookup/references/pride.md +74 -0
  645. package/skills/database-lookup/references/pubchem.md +145 -0
  646. package/skills/database-lookup/references/quickgo.md +45 -0
  647. package/skills/database-lookup/references/reactome.md +140 -0
  648. package/skills/database-lookup/references/retrieval-contract.md +123 -0
  649. package/skills/database-lookup/references/rummageo.md +32 -0
  650. package/skills/database-lookup/references/sdss.md +130 -0
  651. package/skills/database-lookup/references/sec-edgar.md +315 -0
  652. package/skills/database-lookup/references/simbad.md +405 -0
  653. package/skills/database-lookup/references/sra.md +149 -0
  654. package/skills/database-lookup/references/string.md +283 -0
  655. package/skills/database-lookup/references/tcga-gdc.md +58 -0
  656. package/skills/database-lookup/references/treasury.md +215 -0
  657. package/skills/database-lookup/references/ucsc-genome.md +135 -0
  658. package/skills/database-lookup/references/uniprot.md +283 -0
  659. package/skills/database-lookup/references/usgs.md +260 -0
  660. package/skills/database-lookup/references/uspto.md +130 -0
  661. package/skills/database-lookup/references/who.md +283 -0
  662. package/skills/database-lookup/references/worldbank.md +239 -0
  663. package/skills/database-lookup/references/zinc.md +202 -0
  664. package/skills/datamol/SKILL.md +200 -0
  665. package/skills/datamol/references/conformers_module.md +131 -0
  666. package/skills/datamol/references/core_api.md +136 -0
  667. package/skills/datamol/references/core_workflows.md +451 -0
  668. package/skills/datamol/references/descriptors_viz.md +195 -0
  669. package/skills/datamol/references/fragments_scaffolds.md +174 -0
  670. package/skills/datamol/references/io_module.md +112 -0
  671. package/skills/datamol/references/reactions_data.md +218 -0
  672. package/skills/datamol/references/workflow_patterns.md +104 -0
  673. package/skills/deepchem/SKILL.md +244 -0
  674. package/skills/deepchem/references/api_reference.md +305 -0
  675. package/skills/deepchem/references/core_capabilities.md +276 -0
  676. package/skills/deepchem/references/typical_workflows.md +109 -0
  677. package/skills/deepchem/references/workflows.md +491 -0
  678. package/skills/deepchem/scripts/graph_neural_network.py +350 -0
  679. package/skills/deepchem/scripts/predict_solubility.py +223 -0
  680. package/skills/deepchem/scripts/transfer_learning.py +443 -0
  681. package/skills/deepspot-m/SKILL.md +175 -0
  682. package/skills/deepspot-m/references/api.md +186 -0
  683. package/skills/deepspot-m/references/whole_slide.md +174 -0
  684. package/skills/deeptools/SKILL.md +412 -0
  685. package/skills/deeptools/assets/quick_reference.md +65 -0
  686. package/skills/deeptools/references/core_workflows.md +134 -0
  687. package/skills/deeptools/references/effective_genome_sizes.md +118 -0
  688. package/skills/deeptools/references/normalization_methods.md +424 -0
  689. package/skills/deeptools/references/tools_reference.md +569 -0
  690. package/skills/deeptools/references/workflows.md +476 -0
  691. package/skills/deeptools/scripts/validate_files.py +195 -0
  692. package/skills/deeptools/scripts/workflow_generator.py +520 -0
  693. package/skills/depmap/SKILL.md +301 -0
  694. package/skills/depmap/references/dependency_analysis.md +178 -0
  695. package/skills/dhdna-profiler/SKILL.md +184 -0
  696. package/skills/dhdna-profiler/references/advanced-profiling.md +72 -0
  697. package/skills/diffdock/SKILL.md +488 -0
  698. package/skills/diffdock/assets/batch_template.csv +4 -0
  699. package/skills/diffdock/assets/custom_inference_config.yaml +94 -0
  700. package/skills/diffdock/references/confidence_and_limitations.md +182 -0
  701. package/skills/diffdock/references/parameters_reference.md +173 -0
  702. package/skills/diffdock/references/workflows_examples.md +401 -0
  703. package/skills/diffdock/scripts/analyze_results.py +346 -0
  704. package/skills/diffdock/scripts/prepare_batch_csv.py +257 -0
  705. package/skills/diffdock/scripts/setup_check.py +283 -0
  706. package/skills/dnanexus-integration/SKILL.md +325 -0
  707. package/skills/dnanexus-integration/references/app-development.md +371 -0
  708. package/skills/dnanexus-integration/references/authentication.md +226 -0
  709. package/skills/dnanexus-integration/references/configuration.md +444 -0
  710. package/skills/dnanexus-integration/references/data-operations.md +474 -0
  711. package/skills/dnanexus-integration/references/job-execution.md +482 -0
  712. package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +506 -0
  713. package/skills/dnanexus-integration/references/python-sdk.md +548 -0
  714. package/skills/dnanexus-integration/references/sources.md +168 -0
  715. package/skills/dnanexus-integration/references/workflow-languages.md +292 -0
  716. package/skills/dnanexus-integration/scripts/inspect_dxpy.py +366 -0
  717. package/skills/dnanexus-integration/scripts/validate_dxapp.py +796 -0
  718. package/skills/docx/LICENSE.txt +30 -0
  719. package/skills/docx/SKILL.md +99 -0
  720. package/skills/docx/scripts/__init__.py +1 -0
  721. package/skills/docx/scripts/accept_changes.py +135 -0
  722. package/skills/docx/scripts/comment.py +368 -0
  723. package/skills/docx/scripts/merge_runs.py +310 -0
  724. package/skills/docx/scripts/office/helpers/__init__.py +111 -0
  725. package/skills/docx/scripts/office/helpers/pptx_chart.py +170 -0
  726. package/skills/docx/scripts/office/helpers/pptx_slide.py +60 -0
  727. package/skills/docx/scripts/office/helpers/pptx_theme.py +114 -0
  728. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  729. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  730. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  731. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  732. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  733. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  734. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  735. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  736. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  737. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  738. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  739. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  740. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  741. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  742. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  743. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  744. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  745. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  746. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  747. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  748. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  749. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  750. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  751. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  752. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  753. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  754. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  755. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  756. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  757. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  758. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  759. package/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
  760. package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  761. package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  762. package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  763. package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  764. package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  765. package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  766. package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  767. package/skills/docx/scripts/office/soffice.py +232 -0
  768. package/skills/docx/scripts/office/validate.py +173 -0
  769. package/skills/docx/scripts/office/validators/__init__.py +15 -0
  770. package/skills/docx/scripts/office/validators/base.py +875 -0
  771. package/skills/docx/scripts/office/validators/docx.py +466 -0
  772. package/skills/docx/scripts/office/validators/pptx.py +441 -0
  773. package/skills/docx/scripts/office/validators/redlining.py +299 -0
  774. package/skills/docx/scripts/templates/comments.xml +3 -0
  775. package/skills/docx/scripts/templates/commentsExtended.xml +3 -0
  776. package/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  777. package/skills/docx/scripts/templates/commentsIds.xml +3 -0
  778. package/skills/docx/scripts/templates/people.xml +3 -0
  779. package/skills/esm/SKILL.md +334 -0
  780. package/skills/esm/references/biohub-platform.md +111 -0
  781. package/skills/esm/references/esm-c-api.md +609 -0
  782. package/skills/esm/references/esm3-api.md +462 -0
  783. package/skills/esm/references/forge-api.md +675 -0
  784. package/skills/esm/references/workflows.md +685 -0
  785. package/skills/etetoolkit/SKILL.md +327 -0
  786. package/skills/etetoolkit/references/api_reference.md +546 -0
  787. package/skills/etetoolkit/references/migration-ete3-to-ete4.md +579 -0
  788. package/skills/etetoolkit/references/taxonomy.md +362 -0
  789. package/skills/etetoolkit/references/visualization.md +516 -0
  790. package/skills/etetoolkit/references/workflows.md +537 -0
  791. package/skills/etetoolkit/scripts/quick_visualize.py +455 -0
  792. package/skills/etetoolkit/scripts/tree_operations.py +446 -0
  793. package/skills/exa-search/SKILL.md +102 -0
  794. package/skills/exa-search/references/web-extract.md +53 -0
  795. package/skills/exa-search/references/web-search.md +119 -0
  796. package/skills/exa-search/scripts/exa_extract.py +117 -0
  797. package/skills/exa-search/scripts/exa_search.py +179 -0
  798. package/skills/executing-plans/SKILL.md +14 -0
  799. package/skills/experimental-design/SKILL.md +234 -0
  800. package/skills/experimental-design/references/design_types.md +129 -0
  801. package/skills/experimental-design/references/factorial_and_doe.md +130 -0
  802. package/skills/experimental-design/references/randomization_and_blocking.md +116 -0
  803. package/skills/experimental-design/references/sequential_and_adaptive.md +97 -0
  804. package/skills/experimental-design/scripts/doe_designs.py +183 -0
  805. package/skills/experimental-design/scripts/randomization.py +171 -0
  806. package/skills/exploratory-data-analysis/SKILL.md +280 -0
  807. package/skills/exploratory-data-analysis/assets/report_template.md +202 -0
  808. package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +192 -0
  809. package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +183 -0
  810. package/skills/exploratory-data-analysis/references/general_scientific_formats.md +259 -0
  811. package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +189 -0
  812. package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +217 -0
  813. package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +191 -0
  814. package/skills/exploratory-data-analysis/scripts/__init__.py +1 -0
  815. package/skills/exploratory-data-analysis/scripts/_capabilities.py +576 -0
  816. package/skills/exploratory-data-analysis/scripts/_common.py +460 -0
  817. package/skills/exploratory-data-analysis/scripts/_structured.py +391 -0
  818. package/skills/exploratory-data-analysis/scripts/_tabular.py +905 -0
  819. package/skills/exploratory-data-analysis/scripts/capability_manifest.py +184 -0
  820. package/skills/exploratory-data-analysis/scripts/distribution_sensitivity.py +117 -0
  821. package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +345 -0
  822. package/skills/exploratory-data-analysis/scripts/image_inspector.py +214 -0
  823. package/skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py +130 -0
  824. package/skills/exploratory-data-analysis/scripts/report_scaffold.py +143 -0
  825. package/skills/exploratory-data-analysis/scripts/sequence_inspector.py +255 -0
  826. package/skills/exploratory-data-analysis/scripts/tabular_profile.py +109 -0
  827. package/skills/flowio/SKILL.md +310 -0
  828. package/skills/flowio/references/api_reference.md +355 -0
  829. package/skills/flowio/references/fcs_semantics.md +315 -0
  830. package/skills/flowio/references/sources.md +89 -0
  831. package/skills/flowio/references/troubleshooting.md +399 -0
  832. package/skills/flowio/references/workflows.md +368 -0
  833. package/skills/flowio/scripts/inspect_fcs.py +439 -0
  834. package/skills/fluidsim/SKILL.md +279 -0
  835. package/skills/fluidsim/references/advanced_features.md +347 -0
  836. package/skills/fluidsim/references/installation.md +263 -0
  837. package/skills/fluidsim/references/output_analysis.md +314 -0
  838. package/skills/fluidsim/references/parameters.md +322 -0
  839. package/skills/fluidsim/references/simulation_workflow.md +329 -0
  840. package/skills/fluidsim/references/solvers.md +191 -0
  841. package/skills/fluidsim/scripts/__init__.py +1 -0
  842. package/skills/fluidsim/scripts/_common.py +491 -0
  843. package/skills/fluidsim/scripts/_schema.py +872 -0
  844. package/skills/fluidsim/scripts/budget_summary.py +396 -0
  845. package/skills/fluidsim/scripts/grid_resource_estimator.py +286 -0
  846. package/skills/fluidsim/scripts/output_inventory.py +353 -0
  847. package/skills/fluidsim/scripts/restart_compatibility.py +424 -0
  848. package/skills/fluidsim/scripts/simulation_dry_run.py +246 -0
  849. package/skills/fluidsim/scripts/solver_config_validator.py +70 -0
  850. package/skills/frontend-design/SKILL.md +99 -0
  851. package/skills/generate-image/SKILL.md +304 -0
  852. package/skills/generate-image/references/models.md +173 -0
  853. package/skills/generate-image/scripts/generate_image.py +752 -0
  854. package/skills/geniml/SKILL.md +310 -0
  855. package/skills/geniml/references/bedspace.md +267 -0
  856. package/skills/geniml/references/consensus_peaks.md +334 -0
  857. package/skills/geniml/references/region2vec.md +289 -0
  858. package/skills/geniml/references/scembed.md +307 -0
  859. package/skills/geniml/references/utilities.md +385 -0
  860. package/skills/geniml/scripts/__init__.py +1 -0
  861. package/skills/geniml/scripts/_common.py +399 -0
  862. package/skills/geniml/scripts/bed_validator.py +363 -0
  863. package/skills/geniml/scripts/consensus_plan.py +416 -0
  864. package/skills/geniml/scripts/corpus_auditor.py +304 -0
  865. package/skills/geniml/scripts/embedding_plan.py +476 -0
  866. package/skills/geniml/scripts/model_artifact_inspector.py +358 -0
  867. package/skills/geniml/scripts/tokenizer_compatibility.py +321 -0
  868. package/skills/genomic-coordinates/SKILL.md +189 -0
  869. package/skills/genomic-coordinates/references/format-conventions.md +205 -0
  870. package/skills/genomic-coordinates/references/reference-builds.md +154 -0
  871. package/skills/genomic-coordinates/references/transcript-coordinates.md +141 -0
  872. package/skills/genomic-coordinates/references/variant-representation.md +155 -0
  873. package/skills/genomic-coordinates/scripts/_common.py +335 -0
  874. package/skills/genomic-coordinates/scripts/audit_intervals.py +511 -0
  875. package/skills/genomic-coordinates/scripts/check_contigs.py +382 -0
  876. package/skills/genomic-coordinates/scripts/convert_coords.py +180 -0
  877. package/skills/genomic-coordinates/scripts/normalize_variant.py +290 -0
  878. package/skills/genomic-intelligence/SKILL.md +243 -0
  879. package/skills/genomic-intelligence/references/api-and-auth.md +45 -0
  880. package/skills/genomic-intelligence/references/mcp.md +94 -0
  881. package/skills/genomic-intelligence/references/sequence-acquisition.md +52 -0
  882. package/skills/genomic-intelligence/references/tasks.md +75 -0
  883. package/skills/geomaster/README.md +105 -0
  884. package/skills/geomaster/SKILL.md +366 -0
  885. package/skills/geomaster/references/advanced-gis.md +376 -0
  886. package/skills/geomaster/references/big-data.md +363 -0
  887. package/skills/geomaster/references/code-examples.md +531 -0
  888. package/skills/geomaster/references/coordinate-systems.md +364 -0
  889. package/skills/geomaster/references/core-libraries.md +273 -0
  890. package/skills/geomaster/references/data-sources.md +330 -0
  891. package/skills/geomaster/references/gis-software.md +369 -0
  892. package/skills/geomaster/references/industry-applications.md +420 -0
  893. package/skills/geomaster/references/machine-learning.md +462 -0
  894. package/skills/geomaster/references/programming-languages.md +456 -0
  895. package/skills/geomaster/references/remote-sensing.md +370 -0
  896. package/skills/geomaster/references/scientific-domains.md +416 -0
  897. package/skills/geomaster/references/specialized-topics.md +428 -0
  898. package/skills/geomaster/references/troubleshooting.md +439 -0
  899. package/skills/geopandas/SKILL.md +250 -0
  900. package/skills/geopandas/references/crs-management.md +231 -0
  901. package/skills/geopandas/references/data-io.md +323 -0
  902. package/skills/geopandas/references/data-structures.md +207 -0
  903. package/skills/geopandas/references/geometric-operations.md +262 -0
  904. package/skills/geopandas/references/spatial-analysis.md +294 -0
  905. package/skills/geopandas/references/visualization.md +230 -0
  906. package/skills/geopandas/scripts/_common.py +605 -0
  907. package/skills/geopandas/scripts/crs_reprojection_plan.py +210 -0
  908. package/skills/geopandas/scripts/export_plan.py +305 -0
  909. package/skills/geopandas/scripts/geometry_validity_report.py +227 -0
  910. package/skills/geopandas/scripts/sensitive_coordinates_checklist.py +230 -0
  911. package/skills/geopandas/scripts/spatial_join_audit.py +368 -0
  912. package/skills/geopandas/scripts/vector_inventory.py +140 -0
  913. package/skills/get-available-resources/SKILL.md +260 -0
  914. package/skills/get-available-resources/references/resource_semantics.md +206 -0
  915. package/skills/get-available-resources/references/snapshot_schema.md +172 -0
  916. package/skills/get-available-resources/references/sources.md +124 -0
  917. package/skills/get-available-resources/scripts/_common.py +190 -0
  918. package/skills/get-available-resources/scripts/accelerator_diagnostics.py +151 -0
  919. package/skills/get-available-resources/scripts/detect_resources.py +1767 -0
  920. package/skills/get-available-resources/scripts/plan_workload.py +311 -0
  921. package/skills/get-available-resources/scripts/snapshot_tools.py +486 -0
  922. package/skills/gget/SKILL.md +153 -0
  923. package/skills/gget/references/common_workflows.md +120 -0
  924. package/skills/gget/references/database_info.md +336 -0
  925. package/skills/gget/references/module_catalog.md +733 -0
  926. package/skills/gget/references/module_reference.md +526 -0
  927. package/skills/gget/references/workflows.md +815 -0
  928. package/skills/gget/scripts/batch_sequence_analysis.py +192 -0
  929. package/skills/gget/scripts/enrichment_pipeline.py +235 -0
  930. package/skills/gget/scripts/gene_analysis.py +175 -0
  931. package/skills/ginkgo-cloud-lab/SKILL.md +106 -0
  932. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md +53 -0
  933. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +85 -0
  934. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +71 -0
  935. package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md +60 -0
  936. package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md +63 -0
  937. package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md +55 -0
  938. package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md +49 -0
  939. package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md +56 -0
  940. package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md +49 -0
  941. package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md +62 -0
  942. package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md +44 -0
  943. package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md +47 -0
  944. package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +73 -0
  945. package/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md +67 -0
  946. package/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md +58 -0
  947. package/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md +43 -0
  948. package/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md +58 -0
  949. package/skills/glycoengineering/SKILL.md +339 -0
  950. package/skills/glycoengineering/references/glycan_databases.md +165 -0
  951. package/skills/gtars/SKILL.md +282 -0
  952. package/skills/gtars/references/cli.md +334 -0
  953. package/skills/gtars/references/coverage.md +224 -0
  954. package/skills/gtars/references/overlap.md +220 -0
  955. package/skills/gtars/references/python-api.md +280 -0
  956. package/skills/gtars/references/refget.md +318 -0
  957. package/skills/gtars/references/tokenizers.md +256 -0
  958. package/skills/gtars/scripts/__init__.py +1 -0
  959. package/skills/gtars/scripts/_common.py +461 -0
  960. package/skills/gtars/scripts/artifact_inspector.py +328 -0
  961. package/skills/gtars/scripts/bed_validator.py +183 -0
  962. package/skills/gtars/scripts/coverage_preflight.py +256 -0
  963. package/skills/gtars/scripts/execution_plan.py +365 -0
  964. package/skills/gtars/scripts/refget_digest_plan.py +311 -0
  965. package/skills/gtars/scripts/tokenizer_manifest.py +238 -0
  966. package/skills/histolab/SKILL.md +243 -0
  967. package/skills/histolab/references/core_capabilities.md +305 -0
  968. package/skills/histolab/references/filters_preprocessing.md +537 -0
  969. package/skills/histolab/references/slide_management.md +184 -0
  970. package/skills/histolab/references/tile_extraction.md +421 -0
  971. package/skills/histolab/references/tissue_masks.md +251 -0
  972. package/skills/histolab/references/typical_workflows.md +196 -0
  973. package/skills/histolab/references/visualization.md +548 -0
  974. package/skills/hugging-science/SKILL.md +132 -0
  975. package/skills/hugging-science/references/flagship-resources.md +81 -0
  976. package/skills/hugging-science/references/topics-and-slugs.md +82 -0
  977. package/skills/hugging-science/references/using-datasets.md +107 -0
  978. package/skills/hugging-science/references/using-models.md +122 -0
  979. package/skills/hugging-science/references/using-spaces.md +119 -0
  980. package/skills/hugging-science/scripts/fetch_catalog.py +358 -0
  981. package/skills/hypogenic/SKILL.md +290 -0
  982. package/skills/hypogenic/assets/dataset_manifest.example.json +30 -0
  983. package/skills/hypogenic/assets/result.example.json +18 -0
  984. package/skills/hypogenic/assets/run_config.example.json +46 -0
  985. package/skills/hypogenic/assets/task_config.example.yaml +38 -0
  986. package/skills/hypogenic/references/configuration.md +136 -0
  987. package/skills/hypogenic/references/datasets.md +146 -0
  988. package/skills/hypogenic/references/evaluation.md +155 -0
  989. package/skills/hypogenic/references/security.md +167 -0
  990. package/skills/hypogenic/references/sources.md +113 -0
  991. package/skills/hypogenic/references/upstream.md +188 -0
  992. package/skills/hypogenic/scripts/__init__.py +1 -0
  993. package/skills/hypogenic/scripts/_common.py +1312 -0
  994. package/skills/hypogenic/scripts/audit_dataset.py +410 -0
  995. package/skills/hypogenic/scripts/evaluate_local.py +250 -0
  996. package/skills/hypogenic/scripts/inspect_outputs.py +166 -0
  997. package/skills/hypogenic/scripts/plan_run.py +247 -0
  998. package/skills/hypogenic/scripts/validate_config.py +192 -0
  999. package/skills/hypothesis-generation/SKILL.md +264 -0
  1000. package/skills/hypothesis-generation/assets/evidence_ledger_template.csv +2 -0
  1001. package/skills/hypothesis-generation/assets/falsification_controls_template.json +116 -0
  1002. package/skills/hypothesis-generation/assets/hypothesis_record_template.json +331 -0
  1003. package/skills/hypothesis-generation/assets/operationalization_template.json +56 -0
  1004. package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv +3 -0
  1005. package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md +137 -0
  1006. package/skills/hypothesis-generation/assets/search_boundary_template.json +23 -0
  1007. package/skills/hypothesis-generation/assets/source_ledger.csv +37 -0
  1008. package/skills/hypothesis-generation/references/causal_inference_and_claims.md +190 -0
  1009. package/skills/hypothesis-generation/references/concepts_and_workflow.md +173 -0
  1010. package/skills/hypothesis-generation/references/ethics_safety_and_ai.md +216 -0
  1011. package/skills/hypothesis-generation/references/experimental_design_patterns.md +301 -0
  1012. package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +203 -0
  1013. package/skills/hypothesis-generation/references/literature_search_strategies.md +208 -0
  1014. package/skills/hypothesis-generation/references/preregistration_and_open_science.md +205 -0
  1015. package/skills/hypothesis-generation/references/security_validation.md +74 -0
  1016. package/skills/hypothesis-generation/references/source_ledger.md +116 -0
  1017. package/skills/hypothesis-generation/references/tool_reference.md +246 -0
  1018. package/skills/hypothesis-generation/scripts/_common.py +412 -0
  1019. package/skills/hypothesis-generation/scripts/audit_evidence_ledger.py +337 -0
  1020. package/skills/hypothesis-generation/scripts/check_falsification_controls.py +455 -0
  1021. package/skills/hypothesis-generation/scripts/check_operationalization.py +237 -0
  1022. package/skills/hypothesis-generation/scripts/generate_preregistration_scaffold.py +384 -0
  1023. package/skills/hypothesis-generation/scripts/lint_causal_claims.py +189 -0
  1024. package/skills/hypothesis-generation/scripts/validate_hypothesis_schema.py +1078 -0
  1025. package/skills/hypothesis-generation/scripts/validate_prediction_matrix.py +286 -0
  1026. package/skills/imaging-data-commons/SKILL.md +496 -0
  1027. package/skills/imaging-data-commons/references/bigquery_guide.md +858 -0
  1028. package/skills/imaging-data-commons/references/cli_guide.md +287 -0
  1029. package/skills/imaging-data-commons/references/clinical_data_guide.md +328 -0
  1030. package/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
  1031. package/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
  1032. package/skills/imaging-data-commons/references/digital_pathology_guide.md +403 -0
  1033. package/skills/imaging-data-commons/references/index_tables_guide.md +203 -0
  1034. package/skills/imaging-data-commons/references/licensing_and_citation.md +230 -0
  1035. package/skills/imaging-data-commons/references/mcp_guide.md +181 -0
  1036. package/skills/imaging-data-commons/references/parquet_access_guide.md +200 -0
  1037. package/skills/imaging-data-commons/references/rest_api_guide.md +612 -0
  1038. package/skills/imaging-data-commons/references/sql_patterns.md +462 -0
  1039. package/skills/imaging-data-commons/references/use_cases.md +277 -0
  1040. package/skills/imaging-data-commons/scripts/check_version.py +132 -0
  1041. package/skills/infographics/SKILL.md +315 -0
  1042. package/skills/infographics/references/color_palettes.md +496 -0
  1043. package/skills/infographics/references/design_principles.md +636 -0
  1044. package/skills/infographics/references/infographic_type_catalog.md +158 -0
  1045. package/skills/infographics/references/infographic_types.md +907 -0
  1046. package/skills/infographics/references/iterative_refinement.md +119 -0
  1047. package/skills/infographics/scripts/generate_infographic.py +291 -0
  1048. package/skills/infographics/scripts/generate_infographic_ai.py +1446 -0
  1049. package/skills/iso-standards-readiness/SKILL.md +352 -0
  1050. package/skills/iso-standards-readiness/assets/templates/capa-record-template.json +99 -0
  1051. package/skills/iso-standards-readiness/assets/templates/document-register-template.json +75 -0
  1052. package/skills/iso-standards-readiness/assets/templates/evidence-manifest-template.json +65 -0
  1053. package/skills/iso-standards-readiness/assets/templates/laboratory-scope-intake-template.json +111 -0
  1054. package/skills/iso-standards-readiness/assets/templates/medical-laboratory-scope-intake-template.json +111 -0
  1055. package/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md +148 -0
  1056. package/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md +132 -0
  1057. package/skills/iso-standards-readiness/assets/templates/qmsr-transition-template.json +181 -0
  1058. package/skills/iso-standards-readiness/assets/templates/quality-manual-template.md +182 -0
  1059. package/skills/iso-standards-readiness/assets/templates/scope-intake-template.json +109 -0
  1060. package/skills/iso-standards-readiness/assets/templates/supplier-controls-template.json +119 -0
  1061. package/skills/iso-standards-readiness/assets/templates/traceability-matrix-template.json +154 -0
  1062. package/skills/iso-standards-readiness/references/assurance-lanes.md +116 -0
  1063. package/skills/iso-standards-readiness/references/evidence-architecture.md +282 -0
  1064. package/skills/iso-standards-readiness/references/gap-analysis-checklist.md +346 -0
  1065. package/skills/iso-standards-readiness/references/iso-13485.md +236 -0
  1066. package/skills/iso-standards-readiness/references/iso-14971.md +172 -0
  1067. package/skills/iso-standards-readiness/references/iso-15189.md +219 -0
  1068. package/skills/iso-standards-readiness/references/iso-17025.md +208 -0
  1069. package/skills/iso-standards-readiness/references/quality-manual-guide.md +282 -0
  1070. package/skills/iso-standards-readiness/references/source-ledger.md +357 -0
  1071. package/skills/iso-standards-readiness/scripts/_catalog.py +248 -0
  1072. package/skills/iso-standards-readiness/scripts/_common.py +558 -0
  1073. package/skills/iso-standards-readiness/scripts/audit_document_records.py +148 -0
  1074. package/skills/iso-standards-readiness/scripts/check_capa.py +240 -0
  1075. package/skills/iso-standards-readiness/scripts/check_qmsr_transition.py +164 -0
  1076. package/skills/iso-standards-readiness/scripts/check_supplier_controls.py +166 -0
  1077. package/skills/iso-standards-readiness/scripts/check_traceability.py +171 -0
  1078. package/skills/iso-standards-readiness/scripts/gap_analyzer.py +167 -0
  1079. package/skills/iso-standards-readiness/scripts/validate_evidence_manifest.py +246 -0
  1080. package/skills/iso-standards-readiness/scripts/validate_scope_intake.py +209 -0
  1081. package/skills/lab-hardware-cad/SKILL.md +372 -0
  1082. package/skills/lab-hardware-cad/assets/standards.json +198 -0
  1083. package/skills/lab-hardware-cad/references/behavior-rigs.md +136 -0
  1084. package/skills/lab-hardware-cad/references/build123d-patterns.md +363 -0
  1085. package/skills/lab-hardware-cad/references/fabrication-limits.md +156 -0
  1086. package/skills/lab-hardware-cad/references/labware-adapters.md +190 -0
  1087. package/skills/lab-hardware-cad/references/microfluidics.md +157 -0
  1088. package/skills/lab-hardware-cad/references/optomechanics.md +148 -0
  1089. package/skills/lab-hardware-cad/references/validation.md +132 -0
  1090. package/skills/lab-hardware-cad/scripts/_common.py +650 -0
  1091. package/skills/lab-hardware-cad/scripts/check.py +645 -0
  1092. package/skills/lab-hardware-cad/scripts/gen.py +264 -0
  1093. package/skills/lab-hardware-cad/scripts/snapshot.py +278 -0
  1094. package/skills/labarchive-integration/SKILL.md +216 -0
  1095. package/skills/labarchive-integration/references/api_reference.md +250 -0
  1096. package/skills/labarchive-integration/references/authentication_guide.md +191 -0
  1097. package/skills/labarchive-integration/references/integrations.md +162 -0
  1098. package/skills/labarchive-integration/references/sources.md +213 -0
  1099. package/skills/labarchive-integration/scripts/entry_operations.py +381 -0
  1100. package/skills/labarchive-integration/scripts/notebook_operations.py +451 -0
  1101. package/skills/labarchive-integration/scripts/setup_config.py +258 -0
  1102. package/skills/lamindb/SKILL.md +408 -0
  1103. package/skills/lamindb/references/annotation-validation.md +510 -0
  1104. package/skills/lamindb/references/core-concepts.md +383 -0
  1105. package/skills/lamindb/references/data-management.md +432 -0
  1106. package/skills/lamindb/references/integrations.md +663 -0
  1107. package/skills/lamindb/references/ontologies.md +498 -0
  1108. package/skills/lamindb/references/setup-deployment.md +755 -0
  1109. package/skills/latchbio-integration/SKILL.md +227 -0
  1110. package/skills/latchbio-integration/references/data-management.md +257 -0
  1111. package/skills/latchbio-integration/references/latch-mcp.md +158 -0
  1112. package/skills/latchbio-integration/references/nextflow-snakemake.md +258 -0
  1113. package/skills/latchbio-integration/references/operations-and-debugging.md +320 -0
  1114. package/skills/latchbio-integration/references/registry.md +275 -0
  1115. package/skills/latchbio-integration/references/resource-configuration.md +274 -0
  1116. package/skills/latchbio-integration/references/ui-and-automation.md +355 -0
  1117. package/skills/latchbio-integration/references/verified-workflows.md +226 -0
  1118. package/skills/latchbio-integration/references/workflow-creation.md +275 -0
  1119. package/skills/latchbio-integration/scripts/inspect_latch_sdk.py +290 -0
  1120. package/skills/latex-posters/SKILL.md +369 -0
  1121. package/skills/latex-posters/assets/baposter_template.tex +257 -0
  1122. package/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  1123. package/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  1124. package/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  1125. package/skills/latex-posters/references/README.md +439 -0
  1126. package/skills/latex-posters/references/ai_graphics_for_posters.md +524 -0
  1127. package/skills/latex-posters/references/compilation_and_quality_control.md +467 -0
  1128. package/skills/latex-posters/references/latex_poster_packages.md +745 -0
  1129. package/skills/latex-posters/references/latex_poster_reference.md +241 -0
  1130. package/skills/latex-posters/references/poster_content_guide.md +748 -0
  1131. package/skills/latex-posters/references/poster_design_principles.md +806 -0
  1132. package/skills/latex-posters/references/poster_layout_design.md +900 -0
  1133. package/skills/latex-posters/references/poster_patterns_and_presentation.md +81 -0
  1134. package/skills/latex-posters/scripts/generate_schematic.py +198 -0
  1135. package/skills/latex-posters/scripts/generate_schematic_ai.py +950 -0
  1136. package/skills/latex-posters/scripts/review_poster.sh +214 -0
  1137. package/skills/liteparse/SKILL.md +295 -0
  1138. package/skills/liteparse/references/api_reference.md +169 -0
  1139. package/skills/liteparse/references/choosing_a_parser.md +70 -0
  1140. package/skills/liteparse/references/cli_reference.md +118 -0
  1141. package/skills/liteparse/references/ocr_and_formats.md +143 -0
  1142. package/skills/liteparse/references/output_formats.md +146 -0
  1143. package/skills/liteparse/scripts/batch_parse_dir.py +163 -0
  1144. package/skills/literature-review/SKILL.md +263 -0
  1145. package/skills/literature-review/assets/review_template.md +412 -0
  1146. package/skills/literature-review/references/citation_styles.md +166 -0
  1147. package/skills/literature-review/references/core_workflow.md +260 -0
  1148. package/skills/literature-review/references/database_strategies.md +455 -0
  1149. package/skills/literature-review/references/example_workflow.md +68 -0
  1150. package/skills/literature-review/references/search_and_citation.md +157 -0
  1151. package/skills/literature-review/scripts/generate_pdf.py +176 -0
  1152. package/skills/literature-review/scripts/generate_schematic.py +198 -0
  1153. package/skills/literature-review/scripts/generate_schematic_ai.py +950 -0
  1154. package/skills/literature-review/scripts/search_databases.py +303 -0
  1155. package/skills/literature-review/scripts/verify_citations.py +222 -0
  1156. package/skills/markdown-mermaid-writing/SKILL.md +322 -0
  1157. package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +221 -0
  1158. package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +108 -0
  1159. package/skills/markdown-mermaid-writing/references/diagrams/block.md +177 -0
  1160. package/skills/markdown-mermaid-writing/references/diagrams/c4.md +136 -0
  1161. package/skills/markdown-mermaid-writing/references/diagrams/class.md +246 -0
  1162. package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +384 -0
  1163. package/skills/markdown-mermaid-writing/references/diagrams/er.md +222 -0
  1164. package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +177 -0
  1165. package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +138 -0
  1166. package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +74 -0
  1167. package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +107 -0
  1168. package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +74 -0
  1169. package/skills/markdown-mermaid-writing/references/diagrams/packet.md +55 -0
  1170. package/skills/markdown-mermaid-writing/references/diagrams/pie.md +52 -0
  1171. package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +66 -0
  1172. package/skills/markdown-mermaid-writing/references/diagrams/radar.md +59 -0
  1173. package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +88 -0
  1174. package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +71 -0
  1175. package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +174 -0
  1176. package/skills/markdown-mermaid-writing/references/diagrams/state.md +150 -0
  1177. package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +96 -0
  1178. package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +66 -0
  1179. package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +108 -0
  1180. package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +53 -0
  1181. package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +71 -0
  1182. package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +733 -0
  1183. package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +458 -0
  1184. package/skills/markdown-mermaid-writing/templates/decision_record.md +211 -0
  1185. package/skills/markdown-mermaid-writing/templates/how_to_guide.md +275 -0
  1186. package/skills/markdown-mermaid-writing/templates/issue.md +303 -0
  1187. package/skills/markdown-mermaid-writing/templates/kanban.md +223 -0
  1188. package/skills/markdown-mermaid-writing/templates/presentation.md +312 -0
  1189. package/skills/markdown-mermaid-writing/templates/project_documentation.md +412 -0
  1190. package/skills/markdown-mermaid-writing/templates/pull_request.md +319 -0
  1191. package/skills/markdown-mermaid-writing/templates/research_paper.md +304 -0
  1192. package/skills/markdown-mermaid-writing/templates/status_report.md +185 -0
  1193. package/skills/market-research-reports/SKILL.md +337 -0
  1194. package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +149 -0
  1195. package/skills/market-research-reports/assets/claims_ledger_template.csv +4 -0
  1196. package/skills/market-research-reports/assets/competitor_feature_matrix_template.csv +5 -0
  1197. package/skills/market-research-reports/assets/consistency_check_template.csv +3 -0
  1198. package/skills/market-research-reports/assets/forecast_sensitivity_template.json +90 -0
  1199. package/skills/market-research-reports/assets/market_report_template.tex +279 -0
  1200. package/skills/market-research-reports/assets/market_research.sty +241 -0
  1201. package/skills/market-research-reports/assets/market_sizing_scenarios_template.json +129 -0
  1202. package/skills/market-research-reports/assets/report_manifest_template.json +27 -0
  1203. package/skills/market-research-reports/assets/source_ledger_template.csv +4 -0
  1204. package/skills/market-research-reports/references/data_analysis_patterns.md +290 -0
  1205. package/skills/market-research-reports/references/evidence_model.md +148 -0
  1206. package/skills/market-research-reports/references/methods_and_ethics.md +162 -0
  1207. package/skills/market-research-reports/references/official_data_sources.md +196 -0
  1208. package/skills/market-research-reports/references/report_structure_guide.md +283 -0
  1209. package/skills/market-research-reports/references/sources.md +73 -0
  1210. package/skills/market-research-reports/references/visual_generation_guide.md +158 -0
  1211. package/skills/market-research-reports/scripts/_common.py +312 -0
  1212. package/skills/market-research-reports/scripts/audit_claim_citations.py +326 -0
  1213. package/skills/market-research-reports/scripts/calculate_market_sizing.py +389 -0
  1214. package/skills/market-research-reports/scripts/check_unit_consistency.py +217 -0
  1215. package/skills/market-research-reports/scripts/forecast_sensitivity.py +326 -0
  1216. package/skills/market-research-reports/scripts/generate_report_scaffold.py +444 -0
  1217. package/skills/market-research-reports/scripts/validate_competitor_matrix.py +223 -0
  1218. package/skills/market-research-reports/scripts/validate_evidence_ledger.py +291 -0
  1219. package/skills/markitdown/SKILL.md +264 -0
  1220. package/skills/markitdown/references/api_reference.md +418 -0
  1221. package/skills/markitdown/references/cloud_and_ocr.md +320 -0
  1222. package/skills/markitdown/references/file_formats.md +281 -0
  1223. package/skills/markitdown/references/mcp_and_plugins.md +243 -0
  1224. package/skills/markitdown/references/migration.md +356 -0
  1225. package/skills/markitdown/references/security.md +246 -0
  1226. package/skills/markitdown/references/workflows.md +309 -0
  1227. package/skills/markitdown/scripts/batch_convert.py +354 -0
  1228. package/skills/markitdown/scripts/convert_literature.py +405 -0
  1229. package/skills/markitdown/scripts/inspect_installation.py +162 -0
  1230. package/skills/matchms/SKILL.md +276 -0
  1231. package/skills/matchms/references/filtering.md +299 -0
  1232. package/skills/matchms/references/importing_exporting.md +323 -0
  1233. package/skills/matchms/references/migration.md +387 -0
  1234. package/skills/matchms/references/similarity.md +413 -0
  1235. package/skills/matchms/references/sources.md +113 -0
  1236. package/skills/matchms/references/workflows.md +451 -0
  1237. package/skills/matchms/scripts/library_search.py +593 -0
  1238. package/skills/matlab/SKILL.md +274 -0
  1239. package/skills/matlab/assets/project_manifest_template.json +33 -0
  1240. package/skills/matlab/assets/python_compatibility_r2026a.json +27 -0
  1241. package/skills/matlab/assets/reproducibility_manifest_template.json +32 -0
  1242. package/skills/matlab/references/data-import-export.md +221 -0
  1243. package/skills/matlab/references/executing-scripts.md +213 -0
  1244. package/skills/matlab/references/graphics-visualization.md +181 -0
  1245. package/skills/matlab/references/mathematics.md +208 -0
  1246. package/skills/matlab/references/matrices-arrays.md +228 -0
  1247. package/skills/matlab/references/octave-compatibility.md +212 -0
  1248. package/skills/matlab/references/programming.md +225 -0
  1249. package/skills/matlab/references/python-integration.md +248 -0
  1250. package/skills/matlab/scripts/_common.py +263 -0
  1251. package/skills/matlab/scripts/generate_function_scaffold.py +165 -0
  1252. package/skills/matlab/scripts/inventory_mat_file.py +351 -0
  1253. package/skills/matlab/scripts/plan_batch_command.py +257 -0
  1254. package/skills/matlab/scripts/plan_python_compatibility.py +176 -0
  1255. package/skills/matlab/scripts/reproducibility_report.py +233 -0
  1256. package/skills/matlab/scripts/scan_m_code.py +433 -0
  1257. package/skills/matlab/scripts/validate_project_manifest.py +348 -0
  1258. package/skills/matplotlib/SKILL.md +378 -0
  1259. package/skills/matplotlib/references/api_reference.md +409 -0
  1260. package/skills/matplotlib/references/common_issues.md +562 -0
  1261. package/skills/matplotlib/references/plot_types.md +469 -0
  1262. package/skills/matplotlib/references/styling_guide.md +600 -0
  1263. package/skills/matplotlib/scripts/plot_template.py +406 -0
  1264. package/skills/matplotlib/scripts/style_configurator.py +412 -0
  1265. package/skills/medchem/SKILL.md +321 -0
  1266. package/skills/medchem/references/api_guide.md +331 -0
  1267. package/skills/medchem/references/rules_catalog.md +328 -0
  1268. package/skills/medchem/scripts/filter_molecules.py +302 -0
  1269. package/skills/modal/SKILL.md +468 -0
  1270. package/skills/modal/references/api_reference.md +225 -0
  1271. package/skills/modal/references/examples.md +276 -0
  1272. package/skills/modal/references/functions.md +260 -0
  1273. package/skills/modal/references/getting-started.md +171 -0
  1274. package/skills/modal/references/gpu.md +177 -0
  1275. package/skills/modal/references/images.md +266 -0
  1276. package/skills/modal/references/resources.md +117 -0
  1277. package/skills/modal/references/scaling.md +173 -0
  1278. package/skills/modal/references/scheduled-jobs.md +147 -0
  1279. package/skills/modal/references/secrets.md +119 -0
  1280. package/skills/modal/references/volumes.md +247 -0
  1281. package/skills/modal/references/web-endpoints.md +259 -0
  1282. package/skills/molecular-dynamics/SKILL.md +458 -0
  1283. package/skills/molecular-dynamics/references/mdanalysis_analysis.md +208 -0
  1284. package/skills/molfeat/SKILL.md +348 -0
  1285. package/skills/molfeat/references/api_reference.md +429 -0
  1286. package/skills/molfeat/references/available_featurizers.md +335 -0
  1287. package/skills/molfeat/references/choosing_a_featurizer.md +192 -0
  1288. package/skills/molfeat/references/examples.md +720 -0
  1289. package/skills/ncats-arax/SKILL.md +178 -0
  1290. package/skills/ncats-arax/references/output-schema.md +186 -0
  1291. package/skills/ncats-arax/references/query-contract.md +140 -0
  1292. package/skills/ncats-arax/scripts/arax_client.py +2087 -0
  1293. package/skills/networkx/SKILL.md +440 -0
  1294. package/skills/networkx/references/algorithms.md +384 -0
  1295. package/skills/networkx/references/generators.md +385 -0
  1296. package/skills/networkx/references/graph-basics.md +284 -0
  1297. package/skills/networkx/references/io.md +457 -0
  1298. package/skills/networkx/references/visualization.md +531 -0
  1299. package/skills/neurokit2/SKILL.md +323 -0
  1300. package/skills/neurokit2/references/bio_module.md +244 -0
  1301. package/skills/neurokit2/references/complexity.md +212 -0
  1302. package/skills/neurokit2/references/ecg_cardiac.md +193 -0
  1303. package/skills/neurokit2/references/eda.md +185 -0
  1304. package/skills/neurokit2/references/eeg.md +204 -0
  1305. package/skills/neurokit2/references/emg.md +157 -0
  1306. package/skills/neurokit2/references/eog.md +154 -0
  1307. package/skills/neurokit2/references/epochs_events.md +199 -0
  1308. package/skills/neurokit2/references/hrv.md +205 -0
  1309. package/skills/neurokit2/references/ppg.md +191 -0
  1310. package/skills/neurokit2/references/rsp.md +212 -0
  1311. package/skills/neurokit2/references/signal_processing.md +160 -0
  1312. package/skills/neurokit2/scripts/_common.py +567 -0
  1313. package/skills/neurokit2/scripts/ecg_hrv_pipeline.py +303 -0
  1314. package/skills/neurokit2/scripts/eda_pipeline.py +288 -0
  1315. package/skills/neurokit2/scripts/generate_synthetic.py +221 -0
  1316. package/skills/neurokit2/scripts/inspect_signal.py +362 -0
  1317. package/skills/neurokit2/scripts/plan_epochs.py +281 -0
  1318. package/skills/neurokit2/scripts/validate_multimodal.py +350 -0
  1319. package/skills/neuropixels-analysis/SKILL.md +412 -0
  1320. package/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
  1321. package/skills/neuropixels-analysis/references/AI_CURATION.md +164 -0
  1322. package/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
  1323. package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +435 -0
  1324. package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
  1325. package/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
  1326. package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
  1327. package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
  1328. package/skills/neuropixels-analysis/references/api_reference.md +229 -0
  1329. package/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
  1330. package/skills/neuropixels-analysis/references/standard_workflow.md +305 -0
  1331. package/skills/neuropixels-analysis/scripts/compute_metrics.py +182 -0
  1332. package/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
  1333. package/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
  1334. package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +442 -0
  1335. package/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
  1336. package/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
  1337. package/skills/nextflow/SKILL.md +195 -0
  1338. package/skills/nextflow/references/configuration.md +276 -0
  1339. package/skills/nextflow/references/containers.md +92 -0
  1340. package/skills/nextflow/references/developing.md +301 -0
  1341. package/skills/nextflow/references/language.md +327 -0
  1342. package/skills/nextflow/references/nf-core-tools.md +130 -0
  1343. package/skills/nextflow/references/running-pipelines.md +131 -0
  1344. package/skills/nextflow/references/testing.md +189 -0
  1345. package/skills/omero-integration/SKILL.md +222 -0
  1346. package/skills/omero-integration/references/advanced.md +273 -0
  1347. package/skills/omero-integration/references/connection.md +293 -0
  1348. package/skills/omero-integration/references/data_access.md +359 -0
  1349. package/skills/omero-integration/references/image_processing.md +286 -0
  1350. package/skills/omero-integration/references/metadata.md +313 -0
  1351. package/skills/omero-integration/references/rois.md +291 -0
  1352. package/skills/omero-integration/references/scripts.md +304 -0
  1353. package/skills/omero-integration/references/sources.md +194 -0
  1354. package/skills/omero-integration/references/tables.md +269 -0
  1355. package/skills/omero-integration/scripts/export_image_metadata.py +560 -0
  1356. package/skills/omero-integration/scripts/inventory.py +302 -0
  1357. package/skills/omero-integration/scripts/omero_common.py +490 -0
  1358. package/skills/omero-integration/scripts/plan_transfer.py +393 -0
  1359. package/skills/omero-integration/scripts/validate_config.py +140 -0
  1360. package/skills/onekgpd/SKILL.md +371 -0
  1361. package/skills/onekgpd/assets/kgpe.json +48032 -0
  1362. package/skills/onekgpd/references/annotation_vocabularies.md +187 -0
  1363. package/skills/onekgpd/references/onekgpd_commands.md +296 -0
  1364. package/skills/onekgpd/scripts/onekgpd_api.py +794 -0
  1365. package/skills/onekgpd/scripts/onekgpd_meta.py +485 -0
  1366. package/skills/ontology-term-resolution/SKILL.md +147 -0
  1367. package/skills/ontology-term-resolution/references/curation-rules.md +110 -0
  1368. package/skills/ontology-term-resolution/references/ols4-api.md +135 -0
  1369. package/skills/ontology-term-resolution/references/ontology-registry.md +110 -0
  1370. package/skills/ontology-term-resolution/scripts/ols_client.py +341 -0
  1371. package/skills/ontology-term-resolution/scripts/resolve_terms.py +255 -0
  1372. package/skills/ontology-term-resolution/scripts/validate_terms.py +297 -0
  1373. package/skills/open-notebook/SKILL.md +297 -0
  1374. package/skills/open-notebook/references/api_reference.md +715 -0
  1375. package/skills/open-notebook/references/architecture.md +163 -0
  1376. package/skills/open-notebook/references/configuration.md +226 -0
  1377. package/skills/open-notebook/references/examples.md +290 -0
  1378. package/skills/open-notebook/scripts/chat_interaction.py +190 -0
  1379. package/skills/open-notebook/scripts/notebook_management.py +142 -0
  1380. package/skills/open-notebook/scripts/source_ingestion.py +160 -0
  1381. package/skills/openpiv/SKILL.md +469 -0
  1382. package/skills/openpiv/references/advanced_algorithms.md +233 -0
  1383. package/skills/openpiv/scripts/__init__.py +1 -0
  1384. package/skills/openpiv/scripts/analyze.py +143 -0
  1385. package/skills/openpiv/scripts/run_example.py +78 -0
  1386. package/skills/openpiv/scripts/runner.py +214 -0
  1387. package/skills/opentrons-integration/SKILL.md +322 -0
  1388. package/skills/opentrons-integration/references/api_reference.md +382 -0
  1389. package/skills/opentrons-integration/references/liquid_handling.md +387 -0
  1390. package/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md +328 -0
  1391. package/skills/opentrons-integration/references/modules_and_deck.md +409 -0
  1392. package/skills/opentrons-integration/references/protocol_authoring.md +352 -0
  1393. package/skills/opentrons-integration/references/sources.md +151 -0
  1394. package/skills/opentrons-integration/references/validation_and_operations.md +314 -0
  1395. package/skills/opentrons-integration/requirements-flex.txt +1 -0
  1396. package/skills/opentrons-integration/requirements-ot2.txt +1 -0
  1397. package/skills/opentrons-integration/scripts/absorbance_reader_template.py +82 -0
  1398. package/skills/opentrons-integration/scripts/basic_protocol_template.py +68 -0
  1399. package/skills/opentrons-integration/scripts/ot2_basic_protocol_template.py +63 -0
  1400. package/skills/opentrons-integration/scripts/pcr_setup_template.py +146 -0
  1401. package/skills/opentrons-integration/scripts/runtime_parameters_template.py +110 -0
  1402. package/skills/opentrons-integration/scripts/serial_dilution_template.py +113 -0
  1403. package/skills/optimize-for-gpu/SKILL.md +176 -0
  1404. package/skills/optimize-for-gpu/references/code_transformation_patterns.md +301 -0
  1405. package/skills/optimize-for-gpu/references/cucim.md +679 -0
  1406. package/skills/optimize-for-gpu/references/cudf.md +762 -0
  1407. package/skills/optimize-for-gpu/references/cugraph.md +733 -0
  1408. package/skills/optimize-for-gpu/references/cuml.md +710 -0
  1409. package/skills/optimize-for-gpu/references/cupy.md +668 -0
  1410. package/skills/optimize-for-gpu/references/cuspatial.md +420 -0
  1411. package/skills/optimize-for-gpu/references/cuvs.md +671 -0
  1412. package/skills/optimize-for-gpu/references/cuxfilter.md +600 -0
  1413. package/skills/optimize-for-gpu/references/decision_framework.md +234 -0
  1414. package/skills/optimize-for-gpu/references/installation.md +121 -0
  1415. package/skills/optimize-for-gpu/references/kvikio.md +612 -0
  1416. package/skills/optimize-for-gpu/references/numba.md +808 -0
  1417. package/skills/optimize-for-gpu/references/raft.md +312 -0
  1418. package/skills/optimize-for-gpu/references/warp.md +623 -0
  1419. package/skills/owasp-top10/SKILL.md +48 -0
  1420. package/skills/pacsomatic/LICENSE +21 -0
  1421. package/skills/pacsomatic/SKILL.md +150 -0
  1422. package/skills/pacsomatic/config.yaml +42 -0
  1423. package/skills/pacsomatic/references/agent-playbook.md +73 -0
  1424. package/skills/pacsomatic/references/config-and-output.md +100 -0
  1425. package/skills/pacsomatic/references/pacsomatic_guide.md +254 -0
  1426. package/skills/pacsomatic/scripts/run_pacsomatic.py +794 -0
  1427. package/skills/paper-lookup/SKILL.md +263 -0
  1428. package/skills/paper-lookup/references/arxiv.md +275 -0
  1429. package/skills/paper-lookup/references/biorxiv.md +163 -0
  1430. package/skills/paper-lookup/references/core.md +150 -0
  1431. package/skills/paper-lookup/references/crossref.md +181 -0
  1432. package/skills/paper-lookup/references/europepmc.md +226 -0
  1433. package/skills/paper-lookup/references/medrxiv.md +126 -0
  1434. package/skills/paper-lookup/references/openalex.md +174 -0
  1435. package/skills/paper-lookup/references/pmc.md +228 -0
  1436. package/skills/paper-lookup/references/pubmed.md +124 -0
  1437. package/skills/paper-lookup/references/semantic-scholar.md +203 -0
  1438. package/skills/paper-lookup/references/unpaywall.md +127 -0
  1439. package/skills/paper-lookup/scripts/_common.py +227 -0
  1440. package/skills/paper-lookup/scripts/arxiv_atom.py +200 -0
  1441. package/skills/paper-lookup/scripts/jats_to_text.py +324 -0
  1442. package/skills/paper-lookup/scripts/openalex_abstract.py +163 -0
  1443. package/skills/paper-lookup/scripts/paginate.py +490 -0
  1444. package/skills/paperclip/SKILL.md +413 -0
  1445. package/skills/paperclip/references/cli-reference.md +389 -0
  1446. package/skills/paperclip/references/installation.md +341 -0
  1447. package/skills/paperclip/references/map-reduce.md +252 -0
  1448. package/skills/paperclip/references/python-sdk.md +323 -0
  1449. package/skills/paperclip/references/repos-and-workspace.md +271 -0
  1450. package/skills/paperclip/references/search-and-retrieval.md +281 -0
  1451. package/skills/paperzilla/SKILL.md +159 -0
  1452. package/skills/parallel-web/SKILL.md +128 -0
  1453. package/skills/parallel-web/references/data-enrichment.md +104 -0
  1454. package/skills/parallel-web/references/deep-research.md +91 -0
  1455. package/skills/parallel-web/references/findall.md +81 -0
  1456. package/skills/parallel-web/references/monitor.md +83 -0
  1457. package/skills/parallel-web/references/web-extract.md +59 -0
  1458. package/skills/parallel-web/references/web-search.md +100 -0
  1459. package/skills/pathml/SKILL.md +222 -0
  1460. package/skills/pathml/references/data_management.md +357 -0
  1461. package/skills/pathml/references/graphs.md +335 -0
  1462. package/skills/pathml/references/image_loading.md +301 -0
  1463. package/skills/pathml/references/machine_learning.md +408 -0
  1464. package/skills/pathml/references/multiparametric.md +352 -0
  1465. package/skills/pathml/references/preprocessing.md +371 -0
  1466. package/skills/pathml/scripts/_common.py +385 -0
  1467. package/skills/pathml/scripts/image_qc.py +325 -0
  1468. package/skills/pathml/scripts/plan_inference.py +282 -0
  1469. package/skills/pathml/scripts/plan_pipeline.py +239 -0
  1470. package/skills/pathml/scripts/slide_manifest.py +405 -0
  1471. package/skills/pathml/scripts/validate_spatial_schema.py +420 -0
  1472. package/skills/pathogen-variant-surveillance/SKILL.md +208 -0
  1473. package/skills/pathogen-variant-surveillance/references/lapis-api.md +209 -0
  1474. package/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md +126 -0
  1475. package/skills/pathogen-variant-surveillance/references/surveillance-caveats.md +149 -0
  1476. package/skills/pathogen-variant-surveillance/scripts/lapis_client.py +776 -0
  1477. package/skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py +310 -0
  1478. package/skills/pathogen-variant-surveillance/scripts/mutation_profile.py +215 -0
  1479. package/skills/pathogen-variant-surveillance/scripts/reporting_lag.py +217 -0
  1480. package/skills/pathogen-variant-surveillance/scripts/resolve_lineage.py +198 -0
  1481. package/skills/pathway-enrichment/SKILL.md +194 -0
  1482. package/skills/pathway-enrichment/references/databases-and-gene-sets.md +140 -0
  1483. package/skills/pathway-enrichment/references/gseapy.md +189 -0
  1484. package/skills/pathway-enrichment/references/interpretation.md +118 -0
  1485. package/skills/pathway-enrichment/scripts/run_enrichment.py +231 -0
  1486. package/skills/pdf/LICENSE.txt +30 -0
  1487. package/skills/pdf/SKILL.md +322 -0
  1488. package/skills/pdf/forms.md +294 -0
  1489. package/skills/pdf/reference.md +612 -0
  1490. package/skills/pdf/scripts/check_bounding_boxes.py +65 -0
  1491. package/skills/pdf/scripts/check_fillable_fields.py +11 -0
  1492. package/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
  1493. package/skills/pdf/scripts/create_validation_image.py +37 -0
  1494. package/skills/pdf/scripts/extract_form_field_info.py +122 -0
  1495. package/skills/pdf/scripts/extract_form_structure.py +115 -0
  1496. package/skills/pdf/scripts/fill_fillable_fields.py +98 -0
  1497. package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
  1498. package/skills/peer-review/SKILL.md +288 -0
  1499. package/skills/peer-review/assets/citation_references_template.csv +2 -0
  1500. package/skills/peer-review/assets/claim_evidence_matrix_template.csv +4 -0
  1501. package/skills/peer-review/assets/reporting_checklist_template.csv +31 -0
  1502. package/skills/peer-review/assets/reporting_guidelines.json +466 -0
  1503. package/skills/peer-review/assets/review_intake_template.json +52 -0
  1504. package/skills/peer-review/assets/review_scaffold_template.md +68 -0
  1505. package/skills/peer-review/assets/source_ledger.csv +32 -0
  1506. package/skills/peer-review/assets/statistical_reproducibility_template.json +210 -0
  1507. package/skills/peer-review/assets/study_profile_template.json +12 -0
  1508. package/skills/peer-review/references/common_issues.md +257 -0
  1509. package/skills/peer-review/references/ethical_review_practice.md +233 -0
  1510. package/skills/peer-review/references/reporting_standards.md +249 -0
  1511. package/skills/peer-review/references/security_validation.md +75 -0
  1512. package/skills/peer-review/references/statistical_reproducibility.md +329 -0
  1513. package/skills/peer-review/references/tool_reference.md +253 -0
  1514. package/skills/peer-review/scripts/_common.py +398 -0
  1515. package/skills/peer-review/scripts/audit_citations.py +207 -0
  1516. package/skills/peer-review/scripts/audit_statistics_reproducibility.py +305 -0
  1517. package/skills/peer-review/scripts/generate_review_scaffold.py +81 -0
  1518. package/skills/peer-review/scripts/lint_review.py +254 -0
  1519. package/skills/peer-review/scripts/select_reporting_guidelines.py +383 -0
  1520. package/skills/peer-review/scripts/validate_claim_evidence.py +221 -0
  1521. package/skills/peer-review/scripts/validate_review_intake.py +452 -0
  1522. package/skills/penetration-testing/SKILL.md +31 -0
  1523. package/skills/pennylane/SKILL.md +240 -0
  1524. package/skills/pennylane/references/advanced_features.md +667 -0
  1525. package/skills/pennylane/references/devices_backends.md +562 -0
  1526. package/skills/pennylane/references/getting_started.md +232 -0
  1527. package/skills/pennylane/references/optimization.md +670 -0
  1528. package/skills/pennylane/references/quantum_chemistry.md +576 -0
  1529. package/skills/pennylane/references/quantum_circuits.md +443 -0
  1530. package/skills/pennylane/references/quantum_ml.md +555 -0
  1531. package/skills/phylogenetics/SKILL.md +409 -0
  1532. package/skills/phylogenetics/references/iqtree_inference.md +181 -0
  1533. package/skills/phylogenetics/scripts/phylogenetic_analysis.py +272 -0
  1534. package/skills/pi-agent/SKILL.md +83 -0
  1535. package/skills/pi-agent/references/compaction.md +76 -0
  1536. package/skills/pi-agent/references/containerization.md +80 -0
  1537. package/skills/pi-agent/references/custom-provider.md +131 -0
  1538. package/skills/pi-agent/references/development.md +61 -0
  1539. package/skills/pi-agent/references/environment-variables.md +57 -0
  1540. package/skills/pi-agent/references/extensions.md +185 -0
  1541. package/skills/pi-agent/references/json.md +69 -0
  1542. package/skills/pi-agent/references/keybindings.md +58 -0
  1543. package/skills/pi-agent/references/llama-cpp.md +69 -0
  1544. package/skills/pi-agent/references/models.md +114 -0
  1545. package/skills/pi-agent/references/overview.md +37 -0
  1546. package/skills/pi-agent/references/packages.md +103 -0
  1547. package/skills/pi-agent/references/pi-interview.md +123 -0
  1548. package/skills/pi-agent/references/pi-mcp-adapter.md +191 -0
  1549. package/skills/pi-agent/references/pi-subagents.md +371 -0
  1550. package/skills/pi-agent/references/pi-web-access.md +243 -0
  1551. package/skills/pi-agent/references/prompt-templates.md +48 -0
  1552. package/skills/pi-agent/references/providers.md +122 -0
  1553. package/skills/pi-agent/references/quickstart.md +73 -0
  1554. package/skills/pi-agent/references/rpc.md +95 -0
  1555. package/skills/pi-agent/references/sdk.md +151 -0
  1556. package/skills/pi-agent/references/security.md +52 -0
  1557. package/skills/pi-agent/references/session-format.md +90 -0
  1558. package/skills/pi-agent/references/sessions.md +56 -0
  1559. package/skills/pi-agent/references/settings.md +102 -0
  1560. package/skills/pi-agent/references/shell-aliases.md +15 -0
  1561. package/skills/pi-agent/references/skills.md +83 -0
  1562. package/skills/pi-agent/references/terminal-setup.md +87 -0
  1563. package/skills/pi-agent/references/termux.md +31 -0
  1564. package/skills/pi-agent/references/themes.md +69 -0
  1565. package/skills/pi-agent/references/tmux.md +44 -0
  1566. package/skills/pi-agent/references/tui.md +97 -0
  1567. package/skills/pi-agent/references/usage.md +129 -0
  1568. package/skills/pi-agent/references/windows.md +23 -0
  1569. package/skills/pkpd-modeling/SKILL.md +381 -0
  1570. package/skills/pkpd-modeling/assets/nca-reporting-checklist.md +72 -0
  1571. package/skills/pkpd-modeling/assets/popk-analysis-plan.md +136 -0
  1572. package/skills/pkpd-modeling/references/antimicrobial-and-tdm.md +110 -0
  1573. package/skills/pkpd-modeling/references/bioequivalence.md +132 -0
  1574. package/skills/pkpd-modeling/references/dataset-standards.md +103 -0
  1575. package/skills/pkpd-modeling/references/ddi-and-qt.md +132 -0
  1576. package/skills/pkpd-modeling/references/nca-conventions.md +128 -0
  1577. package/skills/pkpd-modeling/references/pbpk.md +103 -0
  1578. package/skills/pkpd-modeling/references/pd-and-exposure-response.md +149 -0
  1579. package/skills/pkpd-modeling/references/population-pk.md +133 -0
  1580. package/skills/pkpd-modeling/references/regulatory-guidance.md +82 -0
  1581. package/skills/pkpd-modeling/references/software-ecosystem.md +123 -0
  1582. package/skills/pkpd-modeling/references/source-ledger.md +89 -0
  1583. package/skills/pkpd-modeling/references/special-populations.md +126 -0
  1584. package/skills/pkpd-modeling/references/structural-models.md +140 -0
  1585. package/skills/pkpd-modeling/references/tmdd-and-biologics.md +115 -0
  1586. package/skills/pkpd-modeling/scripts/_common.py +327 -0
  1587. package/skills/pkpd-modeling/scripts/_models.py +673 -0
  1588. package/skills/pkpd-modeling/scripts/allometry_and_fih.py +346 -0
  1589. package/skills/pkpd-modeling/scripts/bioequivalence.py +480 -0
  1590. package/skills/pkpd-modeling/scripts/check_popk_dataset.py +400 -0
  1591. package/skills/pkpd-modeling/scripts/ddi_static.py +346 -0
  1592. package/skills/pkpd-modeling/scripts/exposure_response.py +328 -0
  1593. package/skills/pkpd-modeling/scripts/fit_compartmental.py +558 -0
  1594. package/skills/pkpd-modeling/scripts/nca.py +587 -0
  1595. package/skills/pkpd-modeling/scripts/simulate_regimen.py +323 -0
  1596. package/skills/pkpd-modeling/scripts/tdm_bayes.py +312 -0
  1597. package/skills/polars/SKILL.md +393 -0
  1598. package/skills/polars/references/best_practices.md +651 -0
  1599. package/skills/polars/references/core_concepts.md +380 -0
  1600. package/skills/polars/references/io_guide.md +564 -0
  1601. package/skills/polars/references/operations.md +602 -0
  1602. package/skills/polars/references/pandas_migration.md +417 -0
  1603. package/skills/polars/references/transformations.md +549 -0
  1604. package/skills/polars-bio/SKILL.md +379 -0
  1605. package/skills/polars-bio/references/bioframe_migration.md +250 -0
  1606. package/skills/polars-bio/references/configuration.md +187 -0
  1607. package/skills/polars-bio/references/file_io.md +469 -0
  1608. package/skills/polars-bio/references/interval_operations.md +370 -0
  1609. package/skills/polars-bio/references/pileup_operations.md +176 -0
  1610. package/skills/polars-bio/references/sql_processing.md +224 -0
  1611. package/skills/ponytail/SKILL.md +31 -0
  1612. package/skills/ponytail-audit/SKILL.md +18 -0
  1613. package/skills/pptx/LICENSE.txt +30 -0
  1614. package/skills/pptx/SKILL.md +246 -0
  1615. package/skills/pptx/scripts/__init__.py +0 -0
  1616. package/skills/pptx/scripts/add_slide.py +367 -0
  1617. package/skills/pptx/scripts/clean.py +309 -0
  1618. package/skills/pptx/scripts/office/helpers/__init__.py +111 -0
  1619. package/skills/pptx/scripts/office/helpers/pptx_chart.py +170 -0
  1620. package/skills/pptx/scripts/office/helpers/pptx_slide.py +60 -0
  1621. package/skills/pptx/scripts/office/helpers/pptx_theme.py +114 -0
  1622. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  1623. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  1624. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  1625. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  1626. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  1627. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  1628. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  1629. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  1630. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  1631. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  1632. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  1633. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  1634. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  1635. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  1636. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  1637. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  1638. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  1639. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  1640. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  1641. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  1642. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  1643. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  1644. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  1645. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  1646. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  1647. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  1648. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  1649. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  1650. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  1651. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  1652. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  1653. package/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
  1654. package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  1655. package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  1656. package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  1657. package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  1658. package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  1659. package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  1660. package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  1661. package/skills/pptx/scripts/office/soffice.py +232 -0
  1662. package/skills/pptx/scripts/office/validate.py +173 -0
  1663. package/skills/pptx/scripts/office/validators/__init__.py +15 -0
  1664. package/skills/pptx/scripts/office/validators/base.py +875 -0
  1665. package/skills/pptx/scripts/office/validators/docx.py +466 -0
  1666. package/skills/pptx/scripts/office/validators/pptx.py +441 -0
  1667. package/skills/pptx/scripts/office/validators/redlining.py +299 -0
  1668. package/skills/pptx/scripts/thumbnail.py +311 -0
  1669. package/skills/pptx-posters/SKILL.md +258 -0
  1670. package/skills/pptx-posters/assets/generation_dependencies.json +5 -0
  1671. package/skills/pptx-posters/assets/poster_manifest_template.json +154 -0
  1672. package/skills/pptx-posters/assets/poster_quality_checklist.md +192 -0
  1673. package/skills/pptx-posters/references/manifest_spec.md +297 -0
  1674. package/skills/pptx-posters/references/poster_content_guide.md +176 -0
  1675. package/skills/pptx-posters/references/poster_design_principles.md +226 -0
  1676. package/skills/pptx-posters/references/poster_layout_design.md +189 -0
  1677. package/skills/pptx-posters/references/pptx_security.md +202 -0
  1678. package/skills/pptx-posters/references/security_validation.md +90 -0
  1679. package/skills/pptx-posters/references/source_ledger.md +256 -0
  1680. package/skills/pptx-posters/scripts/_common.py +396 -0
  1681. package/skills/pptx-posters/scripts/_manifest.py +1318 -0
  1682. package/skills/pptx-posters/scripts/_pptx.py +1484 -0
  1683. package/skills/pptx-posters/scripts/check_layout.py +179 -0
  1684. package/skills/pptx-posters/scripts/check_palette.py +142 -0
  1685. package/skills/pptx-posters/scripts/generate_poster.py +427 -0
  1686. package/skills/pptx-posters/scripts/inspect_pptx.py +40 -0
  1687. package/skills/pptx-posters/scripts/inventory_images.py +252 -0
  1688. package/skills/pptx-posters/scripts/plan_export.py +201 -0
  1689. package/skills/pptx-posters/scripts/validate_manifest.py +55 -0
  1690. package/skills/primekg/SKILL.md +99 -0
  1691. package/skills/primekg/scripts/query_primekg.py +128 -0
  1692. package/skills/protocolsio-integration/SKILL.md +236 -0
  1693. package/skills/protocolsio-integration/assets/protocol-snapshot.schema.json +179 -0
  1694. package/skills/protocolsio-integration/references/additional_features.md +202 -0
  1695. package/skills/protocolsio-integration/references/authentication.md +135 -0
  1696. package/skills/protocolsio-integration/references/discussions.md +192 -0
  1697. package/skills/protocolsio-integration/references/file_manager.md +256 -0
  1698. package/skills/protocolsio-integration/references/protocols_api.md +256 -0
  1699. package/skills/protocolsio-integration/references/workspaces.md +192 -0
  1700. package/skills/protocolsio-integration/scripts/__init__.py +1 -0
  1701. package/skills/protocolsio-integration/scripts/_common.py +613 -0
  1702. package/skills/protocolsio-integration/scripts/pagination_helper.py +248 -0
  1703. package/skills/protocolsio-integration/scripts/plan_write_request.py +657 -0
  1704. package/skills/protocolsio-integration/scripts/protocols_read.py +493 -0
  1705. package/skills/protocolsio-integration/scripts/validate_auth_config.py +128 -0
  1706. package/skills/protocolsio-integration/scripts/validate_protocol_json.py +358 -0
  1707. package/skills/pufferlib/SKILL.md +328 -0
  1708. package/skills/pufferlib/references/environments.md +260 -0
  1709. package/skills/pufferlib/references/integration.md +192 -0
  1710. package/skills/pufferlib/references/policies.md +181 -0
  1711. package/skills/pufferlib/references/training.md +287 -0
  1712. package/skills/pufferlib/references/vectorization.md +210 -0
  1713. package/skills/pufferlib/scripts/__init__.py +1 -0
  1714. package/skills/pufferlib/scripts/_common.py +199 -0
  1715. package/skills/pufferlib/scripts/benchmark_vectorization.py +244 -0
  1716. package/skills/pufferlib/scripts/env_contract_validator.py +198 -0
  1717. package/skills/pufferlib/scripts/env_template.py +210 -0
  1718. package/skills/pufferlib/scripts/inspect_checkpoint.py +225 -0
  1719. package/skills/pufferlib/scripts/repro_plan.py +177 -0
  1720. package/skills/pufferlib/scripts/train_template.py +282 -0
  1721. package/skills/pufferlib/scripts/validate_plan.py +570 -0
  1722. package/skills/pydeseq2/SKILL.md +369 -0
  1723. package/skills/pydeseq2/references/analysis_patterns.md +70 -0
  1724. package/skills/pydeseq2/references/api_reference.md +256 -0
  1725. package/skills/pydeseq2/references/core_workflow_steps.md +162 -0
  1726. package/skills/pydeseq2/references/workflow_guide.md +603 -0
  1727. package/skills/pydeseq2/scripts/run_deseq2_analysis.py +388 -0
  1728. package/skills/pydicom/SKILL.md +381 -0
  1729. package/skills/pydicom/references/common_tags.md +277 -0
  1730. package/skills/pydicom/references/transfer_syntaxes.md +348 -0
  1731. package/skills/pydicom/scripts/__init__.py +1 -0
  1732. package/skills/pydicom/scripts/_common.py +916 -0
  1733. package/skills/pydicom/scripts/anonymize_dicom.py +713 -0
  1734. package/skills/pydicom/scripts/deidentification_audit.py +380 -0
  1735. package/skills/pydicom/scripts/dicom_inventory.py +402 -0
  1736. package/skills/pydicom/scripts/dicom_to_image.py +459 -0
  1737. package/skills/pydicom/scripts/extract_metadata.py +330 -0
  1738. package/skills/pydicom/scripts/pixel_frame_planner.py +303 -0
  1739. package/skills/pydicom/scripts/transfer_syntax_inspector.py +245 -0
  1740. package/skills/pydicom/scripts/uid_mapping_validator.py +240 -0
  1741. package/skills/pyhealth/SKILL.md +124 -0
  1742. package/skills/pyhealth/assets/starter_pipeline.py +58 -0
  1743. package/skills/pyhealth/references/datasets.md +126 -0
  1744. package/skills/pyhealth/references/examples.md +237 -0
  1745. package/skills/pyhealth/references/installation.md +112 -0
  1746. package/skills/pyhealth/references/medcode.md +94 -0
  1747. package/skills/pyhealth/references/models.md +114 -0
  1748. package/skills/pyhealth/references/tasks.md +143 -0
  1749. package/skills/pylabrobot/SKILL.md +216 -0
  1750. package/skills/pylabrobot/assets/protocol-manifest.schema.json +367 -0
  1751. package/skills/pylabrobot/references/analytical-equipment.md +200 -0
  1752. package/skills/pylabrobot/references/hardware-backends.md +215 -0
  1753. package/skills/pylabrobot/references/liquid-handling.md +223 -0
  1754. package/skills/pylabrobot/references/material-handling.md +229 -0
  1755. package/skills/pylabrobot/references/resources.md +238 -0
  1756. package/skills/pylabrobot/references/visualization.md +187 -0
  1757. package/skills/pylabrobot/scripts/__init__.py +1 -0
  1758. package/skills/pylabrobot/scripts/_common.py +718 -0
  1759. package/skills/pylabrobot/scripts/check_deck_geometry.py +52 -0
  1760. package/skills/pylabrobot/scripts/generate_simulation_plan.py +140 -0
  1761. package/skills/pylabrobot/scripts/inspect_backends.py +216 -0
  1762. package/skills/pylabrobot/scripts/plan_transfers.py +59 -0
  1763. package/skills/pylabrobot/scripts/validate_manifest.py +47 -0
  1764. package/skills/pymatgen/SKILL.md +404 -0
  1765. package/skills/pymatgen/references/analysis_modules.md +352 -0
  1766. package/skills/pymatgen/references/core_classes.md +290 -0
  1767. package/skills/pymatgen/references/io_formats.md +323 -0
  1768. package/skills/pymatgen/references/materials_project_api.md +406 -0
  1769. package/skills/pymatgen/references/transformations_workflows.md +385 -0
  1770. package/skills/pymatgen/scripts/_common.py +316 -0
  1771. package/skills/pymatgen/scripts/artifact_manifest.py +172 -0
  1772. package/skills/pymatgen/scripts/composition_structure_validator.py +300 -0
  1773. package/skills/pymatgen/scripts/io_conversion_plan.py +204 -0
  1774. package/skills/pymatgen/scripts/mp_query.py +416 -0
  1775. package/skills/pymatgen/scripts/phase_diagram_generator.py +415 -0
  1776. package/skills/pymatgen/scripts/structure_analyzer.py +293 -0
  1777. package/skills/pymatgen/scripts/structure_converter.py +219 -0
  1778. package/skills/pymatgen/scripts/symmetry_sensitivity_report.py +212 -0
  1779. package/skills/pymc/SKILL.md +310 -0
  1780. package/skills/pymc/assets/hierarchical_model_template.py +332 -0
  1781. package/skills/pymc/assets/linear_regression_template.py +244 -0
  1782. package/skills/pymc/references/distributions.md +345 -0
  1783. package/skills/pymc/references/model_patterns.md +130 -0
  1784. package/skills/pymc/references/sampling_inference.md +432 -0
  1785. package/skills/pymc/references/standard_workflow.md +176 -0
  1786. package/skills/pymc/references/workflows.md +530 -0
  1787. package/skills/pymc/scripts/model_comparison.py +409 -0
  1788. package/skills/pymc/scripts/model_diagnostics.py +328 -0
  1789. package/skills/pymoo/SKILL.md +276 -0
  1790. package/skills/pymoo/references/algorithms.md +232 -0
  1791. package/skills/pymoo/references/constraints_mcdm.md +417 -0
  1792. package/skills/pymoo/references/operators.md +345 -0
  1793. package/skills/pymoo/references/parallelization.md +80 -0
  1794. package/skills/pymoo/references/problems.md +265 -0
  1795. package/skills/pymoo/references/quick_start_workflows.md +404 -0
  1796. package/skills/pymoo/references/visualization.md +353 -0
  1797. package/skills/pymoo/scripts/custom_problem_example.py +181 -0
  1798. package/skills/pymoo/scripts/decision_making_example.py +161 -0
  1799. package/skills/pymoo/scripts/many_objective_example.py +74 -0
  1800. package/skills/pymoo/scripts/multi_objective_example.py +63 -0
  1801. package/skills/pymoo/scripts/single_objective_example.py +59 -0
  1802. package/skills/pyopenms/SKILL.md +179 -0
  1803. package/skills/pyopenms/references/data_structures.md +498 -0
  1804. package/skills/pyopenms/references/feature_detection.md +495 -0
  1805. package/skills/pyopenms/references/file_io.md +359 -0
  1806. package/skills/pyopenms/references/identification.md +431 -0
  1807. package/skills/pyopenms/references/metabolomics.md +548 -0
  1808. package/skills/pyopenms/references/signal_processing.md +444 -0
  1809. package/skills/pyopenms/scripts/accurate_mass_search.py +111 -0
  1810. package/skills/pyopenms/scripts/align_link_quantify.py +140 -0
  1811. package/skills/pyopenms/scripts/consensus_to_matrix.py +70 -0
  1812. package/skills/pyopenms/scripts/convert_format.py +95 -0
  1813. package/skills/pyopenms/scripts/detect_adducts.py +90 -0
  1814. package/skills/pyopenms/scripts/detect_features_centroided.py +80 -0
  1815. package/skills/pyopenms/scripts/detect_features_metabo.py +110 -0
  1816. package/skills/pyopenms/scripts/digest_protein.py +102 -0
  1817. package/skills/pyopenms/scripts/export_gnps_sirius.py +90 -0
  1818. package/skills/pyopenms/scripts/extract_chromatograms.py +105 -0
  1819. package/skills/pyopenms/scripts/inspect_ms_data.py +167 -0
  1820. package/skills/pyopenms/scripts/mass_calculator.py +92 -0
  1821. package/skills/pyopenms/scripts/plot_ms_data.py +129 -0
  1822. package/skills/pyopenms/scripts/process_identifications.py +111 -0
  1823. package/skills/pyopenms/scripts/process_spectra.py +124 -0
  1824. package/skills/pyopenms/scripts/theoretical_spectrum.py +75 -0
  1825. package/skills/pysam/SKILL.md +330 -0
  1826. package/skills/pysam/references/alignment_files.md +374 -0
  1827. package/skills/pysam/references/api_reference.md +421 -0
  1828. package/skills/pysam/references/common_workflows.md +442 -0
  1829. package/skills/pysam/references/coordinates_and_indexing.md +318 -0
  1830. package/skills/pysam/references/cram_and_performance.md +314 -0
  1831. package/skills/pysam/references/migration_to_0_24.md +177 -0
  1832. package/skills/pysam/references/sequence_files.md +316 -0
  1833. package/skills/pysam/references/sources.md +132 -0
  1834. package/skills/pysam/references/variant_files.md +396 -0
  1835. package/skills/pysam/scripts/alignment_qc.py +326 -0
  1836. package/skills/pysam/scripts/filter_alignments.py +359 -0
  1837. package/skills/pysam/scripts/inspect_hts.py +485 -0
  1838. package/skills/pysam/scripts/variant_summary.py +362 -0
  1839. package/skills/pytdc/SKILL.md +297 -0
  1840. package/skills/pytdc/references/datasets.md +242 -0
  1841. package/skills/pytdc/references/oracles.md +273 -0
  1842. package/skills/pytdc/references/sources.md +165 -0
  1843. package/skills/pytdc/references/utilities.md +364 -0
  1844. package/skills/pytdc/scripts/_common.py +205 -0
  1845. package/skills/pytdc/scripts/benchmark_evaluation.py +367 -0
  1846. package/skills/pytdc/scripts/cache_audit.py +146 -0
  1847. package/skills/pytdc/scripts/discover_metadata.py +174 -0
  1848. package/skills/pytdc/scripts/load_and_split_data.py +374 -0
  1849. package/skills/pytdc/scripts/molecular_generation.py +417 -0
  1850. package/skills/pytorch-lightning/SKILL.md +191 -0
  1851. package/skills/pytorch-lightning/references/best_practices.md +724 -0
  1852. package/skills/pytorch-lightning/references/callbacks.md +564 -0
  1853. package/skills/pytorch-lightning/references/data_module.md +565 -0
  1854. package/skills/pytorch-lightning/references/distributed_training.md +644 -0
  1855. package/skills/pytorch-lightning/references/lightning_module.md +487 -0
  1856. package/skills/pytorch-lightning/references/logging.md +636 -0
  1857. package/skills/pytorch-lightning/references/trainer.md +641 -0
  1858. package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +473 -0
  1859. package/skills/pytorch-lightning/scripts/template_datamodule.py +328 -0
  1860. package/skills/pytorch-lightning/scripts/template_lightning_module.py +220 -0
  1861. package/skills/pyzotero/SKILL.md +137 -0
  1862. package/skills/pyzotero/references/authentication.md +105 -0
  1863. package/skills/pyzotero/references/cli.md +102 -0
  1864. package/skills/pyzotero/references/collections.md +113 -0
  1865. package/skills/pyzotero/references/error-handling.md +108 -0
  1866. package/skills/pyzotero/references/exports.md +102 -0
  1867. package/skills/pyzotero/references/files-attachments.md +97 -0
  1868. package/skills/pyzotero/references/full-text.md +68 -0
  1869. package/skills/pyzotero/references/mcp.md +90 -0
  1870. package/skills/pyzotero/references/pagination.md +79 -0
  1871. package/skills/pyzotero/references/read-api.md +137 -0
  1872. package/skills/pyzotero/references/saved-searches.md +77 -0
  1873. package/skills/pyzotero/references/search-params.md +90 -0
  1874. package/skills/pyzotero/references/tags.md +87 -0
  1875. package/skills/pyzotero/references/write-api.md +123 -0
  1876. package/skills/qiskit/SKILL.md +259 -0
  1877. package/skills/qiskit/references/algorithms.md +311 -0
  1878. package/skills/qiskit/references/backends.md +382 -0
  1879. package/skills/qiskit/references/circuits.md +319 -0
  1880. package/skills/qiskit/references/migration.md +338 -0
  1881. package/skills/qiskit/references/patterns.md +386 -0
  1882. package/skills/qiskit/references/primitives.md +400 -0
  1883. package/skills/qiskit/references/setup.md +253 -0
  1884. package/skills/qiskit/references/sources.md +156 -0
  1885. package/skills/qiskit/references/testing.md +428 -0
  1886. package/skills/qiskit/references/transpilation.md +333 -0
  1887. package/skills/qiskit/references/visualization.md +361 -0
  1888. package/skills/qiskit/scripts/check_environment.py +260 -0
  1889. package/skills/qiskit/scripts/inspect_runtime.py +224 -0
  1890. package/skills/qiskit/scripts/run_local_primitives.py +200 -0
  1891. package/skills/qutip/SKILL.md +317 -0
  1892. package/skills/qutip/references/advanced.md +413 -0
  1893. package/skills/qutip/references/analysis.md +319 -0
  1894. package/skills/qutip/references/core_concepts.md +300 -0
  1895. package/skills/qutip/references/time_evolution.md +373 -0
  1896. package/skills/qutip/references/visualization.md +334 -0
  1897. package/skills/qutip/scripts/_common.py +370 -0
  1898. package/skills/qutip/scripts/convergence_sweep.py +358 -0
  1899. package/skills/qutip/scripts/qobj_model_validator.py +327 -0
  1900. package/skills/qutip/scripts/result_audit.py +395 -0
  1901. package/skills/qutip/scripts/solver_config_planner.py +297 -0
  1902. package/skills/qutip/scripts/steady_state_spectrum_planner.py +245 -0
  1903. package/skills/qutip/scripts/two_level_simulation.py +394 -0
  1904. package/skills/rdkit/SKILL.md +94 -0
  1905. package/skills/rdkit/references/api_reference.md +443 -0
  1906. package/skills/rdkit/references/core_capabilities.md +604 -0
  1907. package/skills/rdkit/references/descriptors_reference.md +595 -0
  1908. package/skills/rdkit/references/smarts_patterns.md +668 -0
  1909. package/skills/rdkit/references/workflows_and_best_practices.md +169 -0
  1910. package/skills/rdkit/scripts/molecular_properties.py +243 -0
  1911. package/skills/rdkit/scripts/similarity_search.py +297 -0
  1912. package/skills/rdkit/scripts/substructure_filter.py +386 -0
  1913. package/skills/relsa-severity-assessment/SKILL.md +354 -0
  1914. package/skills/relsa-severity-assessment/assets/example_cohort.csv +55 -0
  1915. package/skills/relsa-severity-assessment/references/forecasting.md +155 -0
  1916. package/skills/relsa-severity-assessment/references/relsa-method.md +175 -0
  1917. package/skills/relsa-severity-assessment/references/thresholds-and-zones.md +154 -0
  1918. package/skills/relsa-severity-assessment/scripts/_common.py +287 -0
  1919. package/skills/relsa-severity-assessment/scripts/forecast_relsa.py +757 -0
  1920. package/skills/relsa-severity-assessment/scripts/kde_thresholds.py +369 -0
  1921. package/skills/relsa-severity-assessment/scripts/relsa_score.py +488 -0
  1922. package/skills/research-grants/SKILL.md +296 -0
  1923. package/skills/research-grants/assets/budget_justification_template.md +453 -0
  1924. package/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  1925. package/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  1926. package/skills/research-grants/references/README.md +287 -0
  1927. package/skills/research-grants/references/broader_impacts.md +392 -0
  1928. package/skills/research-grants/references/core_components.md +397 -0
  1929. package/skills/research-grants/references/darpa_guidelines.md +636 -0
  1930. package/skills/research-grants/references/doe_guidelines.md +586 -0
  1931. package/skills/research-grants/references/nih_guidelines.md +853 -0
  1932. package/skills/research-grants/references/nsf_guidelines.md +570 -0
  1933. package/skills/research-grants/references/nstc_guidelines.md +733 -0
  1934. package/skills/research-grants/references/proposal_types_and_resubmission.md +81 -0
  1935. package/skills/research-grants/references/review_criteria.md +93 -0
  1936. package/skills/research-grants/references/specific_aims_guide.md +458 -0
  1937. package/skills/research-grants/references/writing_principles.md +94 -0
  1938. package/skills/research-lookup/README.md +106 -0
  1939. package/skills/research-lookup/SKILL.md +338 -0
  1940. package/skills/research-lookup/scripts/manuscript_packet.py +754 -0
  1941. package/skills/research-lookup/scripts/research_lookup.py +1204 -0
  1942. package/skills/rowan/SKILL.md +398 -0
  1943. package/skills/rowan/references/access_and_pricing.md +37 -0
  1944. package/skills/rowan/references/batch_and_webhooks.md +255 -0
  1945. package/skills/rowan/references/end_to_end_example.md +119 -0
  1946. package/skills/rowan/references/troubleshooting.md +106 -0
  1947. package/skills/rowan/references/workflow_catalog.md +308 -0
  1948. package/skills/scanpy/SKILL.md +303 -0
  1949. package/skills/scanpy/assets/analysis_template.py +301 -0
  1950. package/skills/scanpy/assets/celltype_mapping.json +10 -0
  1951. package/skills/scanpy/assets/gene_signatures.json +9 -0
  1952. package/skills/scanpy/assets/pipeline_config.json +19 -0
  1953. package/skills/scanpy/references/analysis_workflow.md +236 -0
  1954. package/skills/scanpy/references/api_reference.md +267 -0
  1955. package/skills/scanpy/references/plotting_guide.md +365 -0
  1956. package/skills/scanpy/references/r_interop.md +292 -0
  1957. package/skills/scanpy/references/standard_workflow.md +223 -0
  1958. package/skills/scanpy/scripts/_common.py +127 -0
  1959. package/skills/scanpy/scripts/annotate.py +84 -0
  1960. package/skills/scanpy/scripts/batch_correct.py +65 -0
  1961. package/skills/scanpy/scripts/cluster.py +63 -0
  1962. package/skills/scanpy/scripts/convert.py +43 -0
  1963. package/skills/scanpy/scripts/find_markers.py +75 -0
  1964. package/skills/scanpy/scripts/inspect_data.py +81 -0
  1965. package/skills/scanpy/scripts/plot.py +78 -0
  1966. package/skills/scanpy/scripts/preprocess.py +88 -0
  1967. package/skills/scanpy/scripts/pseudobulk.py +74 -0
  1968. package/skills/scanpy/scripts/qc_analysis.py +104 -0
  1969. package/skills/scanpy/scripts/reduce_dimensions.py +64 -0
  1970. package/skills/scanpy/scripts/run_pipeline.py +182 -0
  1971. package/skills/scanpy/scripts/score_genes.py +82 -0
  1972. package/skills/scanpy/scripts/subset.py +64 -0
  1973. package/skills/scholar-evaluation/SKILL.md +296 -0
  1974. package/skills/scholar-evaluation/assets/evaluation_template.json +50 -0
  1975. package/skills/scholar-evaluation/assets/evidence_manifest_template.json +63 -0
  1976. package/skills/scholar-evaluation/assets/process_checklist_template.json +70 -0
  1977. package/skills/scholar-evaluation/assets/ratings_template.csv +21 -0
  1978. package/skills/scholar-evaluation/assets/rubric_template.json +301 -0
  1979. package/skills/scholar-evaluation/references/evaluation_framework.md +264 -0
  1980. package/skills/scholar-evaluation/references/local_tooling.md +232 -0
  1981. package/skills/scholar-evaluation/references/responsible_assessment.md +196 -0
  1982. package/skills/scholar-evaluation/references/security_validation.md +95 -0
  1983. package/skills/scholar-evaluation/references/source_ledger.md +222 -0
  1984. package/skills/scholar-evaluation/scripts/_common.py +986 -0
  1985. package/skills/scholar-evaluation/scripts/calculate_scores.py +57 -0
  1986. package/skills/scholar-evaluation/scripts/check_process.py +231 -0
  1987. package/skills/scholar-evaluation/scripts/check_traceability.py +233 -0
  1988. package/skills/scholar-evaluation/scripts/generate_report_scaffold.py +231 -0
  1989. package/skills/scholar-evaluation/scripts/summarize_agreement.py +235 -0
  1990. package/skills/scholar-evaluation/scripts/validate_rubric.py +54 -0
  1991. package/skills/scholar-evaluation/scripts/weight_sensitivity.py +251 -0
  1992. package/skills/scientific-brainstorming/SKILL.md +282 -0
  1993. package/skills/scientific-brainstorming/references/brainstorming_methods.md +292 -0
  1994. package/skills/scientific-brainstorming/references/facilitation_workflows.md +284 -0
  1995. package/skills/scientific-brainstorming/references/idea_evaluation.md +268 -0
  1996. package/skills/scientific-brainstorming/references/responsible_ai.md +220 -0
  1997. package/skills/scientific-brainstorming/references/sources.md +364 -0
  1998. package/skills/scientific-brainstorming/scripts/_common.py +307 -0
  1999. package/skills/scientific-brainstorming/scripts/evaluate_matrix.py +518 -0
  2000. package/skills/scientific-brainstorming/scripts/session_scaffold.py +248 -0
  2001. package/skills/scientific-brainstorming/scripts/validate_register.py +654 -0
  2002. package/skills/scientific-critical-thinking/SKILL.md +180 -0
  2003. package/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  2004. package/skills/scientific-critical-thinking/references/core_capabilities.md +407 -0
  2005. package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +485 -0
  2006. package/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  2007. package/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  2008. package/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  2009. package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  2010. package/skills/scientific-schematics/SKILL.md +370 -0
  2011. package/skills/scientific-schematics/references/best_practices.md +574 -0
  2012. package/skills/scientific-schematics/references/iterative_refinement.md +315 -0
  2013. package/skills/scientific-schematics/scripts/example_usage.sh +92 -0
  2014. package/skills/scientific-schematics/scripts/generate_schematic.py +198 -0
  2015. package/skills/scientific-schematics/scripts/generate_schematic_ai.py +950 -0
  2016. package/skills/scientific-slides/SKILL.md +379 -0
  2017. package/skills/scientific-slides/assets/beamer_template_conference.tex +407 -0
  2018. package/skills/scientific-slides/assets/beamer_template_defense.tex +906 -0
  2019. package/skills/scientific-slides/assets/beamer_template_seminar.tex +870 -0
  2020. package/skills/scientific-slides/assets/powerpoint_design_guide.md +662 -0
  2021. package/skills/scientific-slides/assets/timing_guidelines.md +597 -0
  2022. package/skills/scientific-slides/references/beamer_guide.md +1019 -0
  2023. package/skills/scientific-slides/references/common_pitfalls.md +85 -0
  2024. package/skills/scientific-slides/references/data_visualization_slides.md +708 -0
  2025. package/skills/scientific-slides/references/presentation_structure.md +642 -0
  2026. package/skills/scientific-slides/references/presentation_workflow.md +196 -0
  2027. package/skills/scientific-slides/references/prompt_writing.md +42 -0
  2028. package/skills/scientific-slides/references/script_reference.md +143 -0
  2029. package/skills/scientific-slides/references/slide_capabilities.md +360 -0
  2030. package/skills/scientific-slides/references/slide_design_principles.md +849 -0
  2031. package/skills/scientific-slides/references/talk_types_guide.md +687 -0
  2032. package/skills/scientific-slides/references/visual_review_workflow.md +775 -0
  2033. package/skills/scientific-slides/scripts/generate_schematic.py +198 -0
  2034. package/skills/scientific-slides/scripts/generate_schematic_ai.py +950 -0
  2035. package/skills/scientific-slides/scripts/generate_slide_image.py +197 -0
  2036. package/skills/scientific-slides/scripts/generate_slide_image_ai.py +877 -0
  2037. package/skills/scientific-slides/scripts/pdf_to_images.py +221 -0
  2038. package/skills/scientific-slides/scripts/slides_to_pdf.py +235 -0
  2039. package/skills/scientific-slides/scripts/validate_presentation.py +408 -0
  2040. package/skills/scientific-visualization/SKILL.md +285 -0
  2041. package/skills/scientific-visualization/assets/color_palettes.py +263 -0
  2042. package/skills/scientific-visualization/assets/nature.mplstyle +68 -0
  2043. package/skills/scientific-visualization/assets/presentation.mplstyle +68 -0
  2044. package/skills/scientific-visualization/assets/publication.mplstyle +77 -0
  2045. package/skills/scientific-visualization/assets/publisher_profiles.json +269 -0
  2046. package/skills/scientific-visualization/references/color_palettes.md +227 -0
  2047. package/skills/scientific-visualization/references/journal_requirements.md +169 -0
  2048. package/skills/scientific-visualization/references/matplotlib_examples.md +336 -0
  2049. package/skills/scientific-visualization/references/publication_guidelines.md +196 -0
  2050. package/skills/scientific-visualization/references/sources.md +76 -0
  2051. package/skills/scientific-visualization/scripts/_common.py +136 -0
  2052. package/skills/scientific-visualization/scripts/export_plan.py +493 -0
  2053. package/skills/scientific-visualization/scripts/figure_export.py +642 -0
  2054. package/skills/scientific-visualization/scripts/image_metadata.py +731 -0
  2055. package/skills/scientific-visualization/scripts/palette_audit.py +327 -0
  2056. package/skills/scientific-visualization/scripts/style_presets.py +501 -0
  2057. package/skills/scientific-visualization/scripts/style_preview.py +232 -0
  2058. package/skills/scientific-writing/SKILL.md +356 -0
  2059. package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +60 -0
  2060. package/skills/scientific-writing/assets/authorship_template.json +56 -0
  2061. package/skills/scientific-writing/assets/claim_evidence_template.csv +2 -0
  2062. package/skills/scientific-writing/assets/consistency_manifest_template.json +43 -0
  2063. package/skills/scientific-writing/assets/manuscript_manifest_template.json +37 -0
  2064. package/skills/scientific-writing/assets/manuscript_scaffold.md +65 -0
  2065. package/skills/scientific-writing/assets/reporting_coverage_template.json +6 -0
  2066. package/skills/scientific-writing/assets/reporting_guidelines.json +529 -0
  2067. package/skills/scientific-writing/assets/source_manifest_template.json +27 -0
  2068. package/skills/scientific-writing/references/authorship_ai_confidentiality.md +111 -0
  2069. package/skills/scientific-writing/references/citation_styles.md +92 -0
  2070. package/skills/scientific-writing/references/cli_reference.md +113 -0
  2071. package/skills/scientific-writing/references/evidence_workflow.md +94 -0
  2072. package/skills/scientific-writing/references/figures_tables.md +94 -0
  2073. package/skills/scientific-writing/references/imrad_structure.md +114 -0
  2074. package/skills/scientific-writing/references/journal_policies.md +56 -0
  2075. package/skills/scientific-writing/references/professional_report_formatting.md +82 -0
  2076. package/skills/scientific-writing/references/reporting_guidelines.md +107 -0
  2077. package/skills/scientific-writing/references/research_integrity_open_science.md +97 -0
  2078. package/skills/scientific-writing/references/source_ledger.md +268 -0
  2079. package/skills/scientific-writing/references/writing_principles.md +97 -0
  2080. package/skills/scientific-writing/scripts/_common.py +240 -0
  2081. package/skills/scientific-writing/scripts/audit_claims.py +241 -0
  2082. package/skills/scientific-writing/scripts/check_consistency.py +408 -0
  2083. package/skills/scientific-writing/scripts/check_references.py +219 -0
  2084. package/skills/scientific-writing/scripts/lint_manuscript.py +171 -0
  2085. package/skills/scientific-writing/scripts/scaffold_manuscript.py +143 -0
  2086. package/skills/scientific-writing/scripts/select_reporting_guidelines.py +214 -0
  2087. package/skills/scientific-writing/scripts/validate_authorship.py +322 -0
  2088. package/skills/scientific-writing/scripts/validate_manifest.py +460 -0
  2089. package/skills/scikit-bio/SKILL.md +470 -0
  2090. package/skills/scikit-bio/references/api_reference.md +766 -0
  2091. package/skills/scikit-learn/SKILL.md +324 -0
  2092. package/skills/scikit-learn/references/common_workflows.md +107 -0
  2093. package/skills/scikit-learn/references/core_capabilities.md +133 -0
  2094. package/skills/scikit-learn/references/model_evaluation.md +592 -0
  2095. package/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
  2096. package/skills/scikit-learn/references/preprocessing.md +606 -0
  2097. package/skills/scikit-learn/references/quick_reference.md +436 -0
  2098. package/skills/scikit-learn/references/supervised_learning.md +379 -0
  2099. package/skills/scikit-learn/references/unsupervised_learning.md +517 -0
  2100. package/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
  2101. package/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
  2102. package/skills/scikit-survival/SKILL.md +313 -0
  2103. package/skills/scikit-survival/references/competing-risks.md +302 -0
  2104. package/skills/scikit-survival/references/cox-models.md +252 -0
  2105. package/skills/scikit-survival/references/data-handling.md +278 -0
  2106. package/skills/scikit-survival/references/ensemble-models.md +287 -0
  2107. package/skills/scikit-survival/references/evaluation-metrics.md +391 -0
  2108. package/skills/scikit-survival/references/svm-models.md +277 -0
  2109. package/skills/scikit-survival/scripts/_common.py +456 -0
  2110. package/skills/scikit-survival/scripts/competing_risk_cif.py +286 -0
  2111. package/skills/scikit-survival/scripts/evaluate_survival_metrics.py +296 -0
  2112. package/skills/scikit-survival/scripts/model_report.py +297 -0
  2113. package/skills/scikit-survival/scripts/train_survival_model.py +583 -0
  2114. package/skills/scikit-survival/scripts/validate_survival_csv.py +172 -0
  2115. package/skills/scvelo/SKILL.md +328 -0
  2116. package/skills/scvelo/references/velocity_models.md +168 -0
  2117. package/skills/scvelo/scripts/rna_velocity_workflow.py +240 -0
  2118. package/skills/scvi-tools/SKILL.md +201 -0
  2119. package/skills/scvi-tools/references/differential-expression.md +597 -0
  2120. package/skills/scvi-tools/references/models-atac-seq.md +329 -0
  2121. package/skills/scvi-tools/references/models-multimodal.md +400 -0
  2122. package/skills/scvi-tools/references/models-scrna-seq.md +333 -0
  2123. package/skills/scvi-tools/references/models-spatial.md +432 -0
  2124. package/skills/scvi-tools/references/models-specialized.md +376 -0
  2125. package/skills/scvi-tools/references/theoretical-foundations.md +438 -0
  2126. package/skills/scvi-tools/references/workflows.md +559 -0
  2127. package/skills/seaborn/SKILL.md +254 -0
  2128. package/skills/seaborn/references/examples.md +824 -0
  2129. package/skills/seaborn/references/function_reference.md +772 -0
  2130. package/skills/seaborn/references/grids_and_levels.md +85 -0
  2131. package/skills/seaborn/references/objects_interface.md +963 -0
  2132. package/skills/seaborn/references/palettes_and_theming.md +110 -0
  2133. package/skills/seaborn/references/patterns_and_troubleshooting.md +114 -0
  2134. package/skills/seaborn/references/plotting_functions.md +178 -0
  2135. package/skills/security-auditor/SKILL.md +37 -0
  2136. package/skills/shap/SKILL.md +282 -0
  2137. package/skills/shap/references/data-maskers.md +287 -0
  2138. package/skills/shap/references/explainers.md +376 -0
  2139. package/skills/shap/references/migration.md +415 -0
  2140. package/skills/shap/references/modalities.md +353 -0
  2141. package/skills/shap/references/plots.md +406 -0
  2142. package/skills/shap/references/theory.md +352 -0
  2143. package/skills/shap/references/troubleshooting.md +442 -0
  2144. package/skills/shap/references/workflows.md +565 -0
  2145. package/skills/shap/scripts/tabular_report.py +326 -0
  2146. package/skills/simpy/SKILL.md +283 -0
  2147. package/skills/simpy/references/cli-guide.md +266 -0
  2148. package/skills/simpy/references/events.md +225 -0
  2149. package/skills/simpy/references/monitoring.md +260 -0
  2150. package/skills/simpy/references/process-interaction.md +269 -0
  2151. package/skills/simpy/references/real-time.md +174 -0
  2152. package/skills/simpy/references/resources.md +274 -0
  2153. package/skills/simpy/references/simulation-methodology.md +293 -0
  2154. package/skills/simpy/references/sources.md +167 -0
  2155. package/skills/simpy/scripts/_common.py +473 -0
  2156. package/skills/simpy/scripts/basic_simulation_template.py +415 -0
  2157. package/skills/simpy/scripts/bounded_queue_scenario.py +126 -0
  2158. package/skills/simpy/scripts/event_trace_summary.py +296 -0
  2159. package/skills/simpy/scripts/replication_runner.py +194 -0
  2160. package/skills/simpy/scripts/resource_monitor.py +474 -0
  2161. package/skills/simpy/scripts/validate_simulation_config.py +111 -0
  2162. package/skills/stable-baselines3/SKILL.md +325 -0
  2163. package/skills/stable-baselines3/references/algorithms.md +348 -0
  2164. package/skills/stable-baselines3/references/callbacks.md +571 -0
  2165. package/skills/stable-baselines3/references/custom_environments.md +528 -0
  2166. package/skills/stable-baselines3/references/vectorized_envs.md +580 -0
  2167. package/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
  2168. package/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
  2169. package/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
  2170. package/skills/statistical-analysis/SKILL.md +446 -0
  2171. package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +379 -0
  2172. package/skills/statistical-analysis/references/bayesian_statistics.md +686 -0
  2173. package/skills/statistical-analysis/references/effect_sizes_and_power.md +649 -0
  2174. package/skills/statistical-analysis/references/reporting_standards.md +482 -0
  2175. package/skills/statistical-analysis/references/test_selection_guide.md +129 -0
  2176. package/skills/statistical-analysis/scripts/assumption_checks.py +652 -0
  2177. package/skills/statistical-power/SKILL.md +200 -0
  2178. package/skills/statistical-power/references/closed_form_recipes.md +174 -0
  2179. package/skills/statistical-power/references/effect_sizes.md +121 -0
  2180. package/skills/statistical-power/references/simulation_based_power.md +101 -0
  2181. package/skills/statistical-power/scripts/power.py +320 -0
  2182. package/skills/statistical-power/scripts/simulate_power.py +217 -0
  2183. package/skills/statsmodels/SKILL.md +238 -0
  2184. package/skills/statsmodels/references/discrete_choice.md +669 -0
  2185. package/skills/statsmodels/references/glm.md +619 -0
  2186. package/skills/statsmodels/references/linear_models.md +447 -0
  2187. package/skills/statsmodels/references/model_selection.md +99 -0
  2188. package/skills/statsmodels/references/modeling_capabilities.md +168 -0
  2189. package/skills/statsmodels/references/quick_start_guide.md +154 -0
  2190. package/skills/statsmodels/references/stats_diagnostics.md +859 -0
  2191. package/skills/statsmodels/references/time_series.md +723 -0
  2192. package/skills/sympy/SKILL.md +354 -0
  2193. package/skills/sympy/references/advanced-topics.md +635 -0
  2194. package/skills/sympy/references/code-generation-printing.md +628 -0
  2195. package/skills/sympy/references/core-capabilities.md +348 -0
  2196. package/skills/sympy/references/core_capabilities.md +190 -0
  2197. package/skills/sympy/references/matrices-linear-algebra.md +526 -0
  2198. package/skills/sympy/references/physics-mechanics.md +592 -0
  2199. package/skills/systematic-debugging/SKILL.md +35 -0
  2200. package/skills/tamarind/SKILL.md +285 -0
  2201. package/skills/tamarind/references/api_reference.md +165 -0
  2202. package/skills/tamarind/references/examples.md +132 -0
  2203. package/skills/tamarind/references/tool_catalog.md +66 -0
  2204. package/skills/tamarind/references/workflows.md +263 -0
  2205. package/skills/tdd/SKILL.md +26 -0
  2206. package/skills/tiledbvcf/SKILL.md +456 -0
  2207. package/skills/timesfm-forecasting/SKILL.md +408 -0
  2208. package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +524 -0
  2209. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +448 -0
  2210. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
  2211. package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +568 -0
  2212. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
  2213. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +59 -0
  2214. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +109 -0
  2215. package/skills/timesfm-forecasting/examples/global-temperature/README.md +178 -0
  2216. package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +147 -0
  2217. package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +248 -0
  2218. package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +544 -0
  2219. package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +5441 -0
  2220. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
  2221. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +13 -0
  2222. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +188 -0
  2223. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
  2224. package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +5939 -0
  2225. package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +53 -0
  2226. package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +167 -0
  2227. package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +37 -0
  2228. package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +123 -0
  2229. package/skills/timesfm-forecasting/references/api_reference.md +231 -0
  2230. package/skills/timesfm-forecasting/references/data_preparation.md +272 -0
  2231. package/skills/timesfm-forecasting/references/examples_and_validation.md +103 -0
  2232. package/skills/timesfm-forecasting/references/output_and_config.md +93 -0
  2233. package/skills/timesfm-forecasting/references/performance_tuning.md +80 -0
  2234. package/skills/timesfm-forecasting/references/system_requirements.md +201 -0
  2235. package/skills/timesfm-forecasting/references/workflows.md +126 -0
  2236. package/skills/timesfm-forecasting/scripts/check_system.py +521 -0
  2237. package/skills/timesfm-forecasting/scripts/forecast_csv.py +269 -0
  2238. package/skills/torch-geometric/SKILL.md +458 -0
  2239. package/skills/torch-geometric/references/custom_datasets.md +239 -0
  2240. package/skills/torch-geometric/references/explainability.md +208 -0
  2241. package/skills/torch-geometric/references/heterogeneous.md +241 -0
  2242. package/skills/torch-geometric/references/link_prediction.md +226 -0
  2243. package/skills/torch-geometric/references/message_passing.md +121 -0
  2244. package/skills/torch-geometric/references/scaling.md +269 -0
  2245. package/skills/torchdrug/SKILL.md +241 -0
  2246. package/skills/torchdrug/references/core_concepts.md +241 -0
  2247. package/skills/torchdrug/references/datasets.md +179 -0
  2248. package/skills/torchdrug/references/knowledge_graphs.md +226 -0
  2249. package/skills/torchdrug/references/models_architectures.md +223 -0
  2250. package/skills/torchdrug/references/molecular_generation.md +246 -0
  2251. package/skills/torchdrug/references/molecular_property_prediction.md +239 -0
  2252. package/skills/torchdrug/references/protein_modeling.md +221 -0
  2253. package/skills/torchdrug/references/retrosynthesis.md +247 -0
  2254. package/skills/transformers/SKILL.md +195 -0
  2255. package/skills/transformers/references/generation.md +473 -0
  2256. package/skills/transformers/references/models.md +371 -0
  2257. package/skills/transformers/references/pipelines.md +334 -0
  2258. package/skills/transformers/references/tokenizers.md +449 -0
  2259. package/skills/transformers/references/training.md +504 -0
  2260. package/skills/treatment-plans/SKILL.md +174 -0
  2261. package/skills/treatment-plans/assets/clinician_authored_intervention_template.json +11 -0
  2262. package/skills/treatment-plans/assets/goals_monitoring_checkpoint_template.json +13 -0
  2263. package/skills/treatment-plans/assets/informed_preference_shared_decision_template.json +11 -0
  2264. package/skills/treatment-plans/assets/intended_use_handoff_template.json +83 -0
  2265. package/skills/treatment-plans/assets/source_fact_manifest_template.json +11 -0
  2266. package/skills/treatment-plans/assets/transition_reconciliation_template.json +27 -0
  2267. package/skills/treatment-plans/references/README.md +19 -0
  2268. package/skills/treatment-plans/references/documentation_workflow.md +165 -0
  2269. package/skills/treatment-plans/references/privacy_governance.md +119 -0
  2270. package/skills/treatment-plans/references/safety_scope.md +101 -0
  2271. package/skills/treatment-plans/references/security_validation.md +68 -0
  2272. package/skills/treatment-plans/references/shared_decision_handoff.md +138 -0
  2273. package/skills/treatment-plans/references/source_boundaries.md +127 -0
  2274. package/skills/treatment-plans/references/source_ledger.md +131 -0
  2275. package/skills/treatment-plans/scripts/_common.py +1160 -0
  2276. package/skills/treatment-plans/scripts/check_completeness.py +572 -0
  2277. package/skills/treatment-plans/scripts/check_consistency.py +386 -0
  2278. package/skills/treatment-plans/scripts/generate_template.py +133 -0
  2279. package/skills/treatment-plans/scripts/privacy_process_check.py +213 -0
  2280. package/skills/treatment-plans/scripts/timeline_generator.py +260 -0
  2281. package/skills/treatment-plans/scripts/validate_traceability.py +147 -0
  2282. package/skills/treatment-plans/scripts/validate_treatment_plan.py +95 -0
  2283. package/skills/umap-learn/SKILL.md +488 -0
  2284. package/skills/umap-learn/references/api_reference.md +574 -0
  2285. package/skills/uncertainty-and-units/SKILL.md +384 -0
  2286. package/skills/uncertainty-and-units/references/domain-conversions.md +188 -0
  2287. package/skills/uncertainty-and-units/references/gum-methodology.md +219 -0
  2288. package/skills/uncertainty-and-units/references/pint-recipes.md +228 -0
  2289. package/skills/uncertainty-and-units/references/plausibility-scales.md +168 -0
  2290. package/skills/uncertainty-and-units/references/reporting-rules.md +133 -0
  2291. package/skills/uncertainty-and-units/references/uncertainties-recipes.md +167 -0
  2292. package/skills/uncertainty-and-units/scripts/_common.py +666 -0
  2293. package/skills/uncertainty-and-units/scripts/audit_units.py +575 -0
  2294. package/skills/uncertainty-and-units/scripts/check_plausibility.py +894 -0
  2295. package/skills/uncertainty-and-units/scripts/convert_units.py +280 -0
  2296. package/skills/uncertainty-and-units/scripts/format_result.py +326 -0
  2297. package/skills/uncertainty-and-units/scripts/propagate_uncertainty.py +662 -0
  2298. package/skills/uncertainty-and-units/scripts/uncertainty_budget.py +363 -0
  2299. package/skills/usfiscaldata/SKILL.md +171 -0
  2300. package/skills/usfiscaldata/references/api-basics.md +105 -0
  2301. package/skills/usfiscaldata/references/datasets-debt.md +166 -0
  2302. package/skills/usfiscaldata/references/datasets-fiscal.md +212 -0
  2303. package/skills/usfiscaldata/references/datasets-interest-rates.md +188 -0
  2304. package/skills/usfiscaldata/references/datasets-securities.md +238 -0
  2305. package/skills/usfiscaldata/references/examples.md +258 -0
  2306. package/skills/usfiscaldata/references/parameters.md +182 -0
  2307. package/skills/usfiscaldata/references/response-format.md +178 -0
  2308. package/skills/vaex/SKILL.md +204 -0
  2309. package/skills/vaex/references/core_dataframes.md +373 -0
  2310. package/skills/vaex/references/data_processing.md +555 -0
  2311. package/skills/vaex/references/io_operations.md +718 -0
  2312. package/skills/vaex/references/machine_learning.md +728 -0
  2313. package/skills/vaex/references/performance.md +571 -0
  2314. package/skills/vaex/references/visualization.md +644 -0
  2315. package/skills/venue-templates/SKILL.md +269 -0
  2316. package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
  2317. package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
  2318. package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
  2319. package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
  2320. package/skills/venue-templates/assets/grants/nih_specific_aims.tex +237 -0
  2321. package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +384 -0
  2322. package/skills/venue-templates/assets/journals/elsarticle-harv.bst +1598 -0
  2323. package/skills/venue-templates/assets/journals/elsarticle-num-names.bst +1535 -0
  2324. package/skills/venue-templates/assets/journals/elsarticle-num.bst +1509 -0
  2325. package/skills/venue-templates/assets/journals/elsarticle-template-harv.tex +286 -0
  2326. package/skills/venue-templates/assets/journals/elsarticle-template-num-names.tex +284 -0
  2327. package/skills/venue-templates/assets/journals/elsarticle-template-num.tex +286 -0
  2328. package/skills/venue-templates/assets/journals/nature_article.tex +174 -0
  2329. package/skills/venue-templates/assets/journals/neurips_article.tex +292 -0
  2330. package/skills/venue-templates/assets/journals/plos_one.tex +320 -0
  2331. package/skills/venue-templates/assets/posters/beamerposter_academic.tex +312 -0
  2332. package/skills/venue-templates/references/cell_press_style.md +486 -0
  2333. package/skills/venue-templates/references/conferences_formatting.md +175 -0
  2334. package/skills/venue-templates/references/cs_conference_style.md +465 -0
  2335. package/skills/venue-templates/references/grants_requirements.md +267 -0
  2336. package/skills/venue-templates/references/journals_formatting.md +200 -0
  2337. package/skills/venue-templates/references/medical_journal_styles.md +536 -0
  2338. package/skills/venue-templates/references/ml_conference_style.md +562 -0
  2339. package/skills/venue-templates/references/nature_science_style.md +407 -0
  2340. package/skills/venue-templates/references/posters_guidelines.md +630 -0
  2341. package/skills/venue-templates/references/reviewer_expectations.md +422 -0
  2342. package/skills/venue-templates/references/venue_writing_styles.md +323 -0
  2343. package/skills/venue-templates/scripts/customize_template.py +206 -0
  2344. package/skills/venue-templates/scripts/query_template.py +202 -0
  2345. package/skills/venue-templates/scripts/validate_format.py +321 -0
  2346. package/skills/verification-before-completion/SKILL.md +21 -0
  2347. package/skills/waypoint-bio/SKILL.md +273 -0
  2348. package/skills/waypoint-bio/references/cli-reference.md +210 -0
  2349. package/skills/waypoint-bio/references/compass-benchmark.md +124 -0
  2350. package/skills/waypoint-bio/references/data-preparation.md +200 -0
  2351. package/skills/waypoint-bio/references/python-api.md +219 -0
  2352. package/skills/waypoint-bio/scripts/profiler_to_waypoint.py +481 -0
  2353. package/skills/waypoint-bio/scripts/vocab_coverage.py +235 -0
  2354. package/skills/what-if-oracle/SKILL.md +184 -0
  2355. package/skills/what-if-oracle/references/scenario-templates.md +137 -0
  2356. package/skills/writing-plans/SKILL.md +15 -0
  2357. package/skills/xlsx/LICENSE.txt +30 -0
  2358. package/skills/xlsx/SKILL.md +110 -0
  2359. package/skills/xlsx/scripts/office/helpers/__init__.py +111 -0
  2360. package/skills/xlsx/scripts/office/helpers/pptx_chart.py +170 -0
  2361. package/skills/xlsx/scripts/office/helpers/pptx_slide.py +60 -0
  2362. package/skills/xlsx/scripts/office/helpers/pptx_theme.py +114 -0
  2363. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  2364. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  2365. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  2366. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  2367. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  2368. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  2369. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  2370. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  2371. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  2372. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  2373. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  2374. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  2375. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  2376. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  2377. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  2378. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  2379. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  2380. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  2381. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  2382. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  2383. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  2384. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  2385. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  2386. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  2387. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  2388. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  2389. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  2390. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  2391. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  2392. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  2393. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  2394. package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
  2395. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  2396. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  2397. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  2398. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  2399. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  2400. package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  2401. package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  2402. package/skills/xlsx/scripts/office/soffice.py +232 -0
  2403. package/skills/xlsx/scripts/office/validate.py +173 -0
  2404. package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
  2405. package/skills/xlsx/scripts/office/validators/base.py +875 -0
  2406. package/skills/xlsx/scripts/office/validators/docx.py +466 -0
  2407. package/skills/xlsx/scripts/office/validators/pptx.py +441 -0
  2408. package/skills/xlsx/scripts/office/validators/redlining.py +299 -0
  2409. package/skills/xlsx/scripts/recalc.py +308 -0
  2410. package/skills/zarr-python/SKILL.md +241 -0
  2411. package/skills/zarr-python/references/api_reference.md +162 -0
  2412. package/skills/zarr-python/references/chunking_and_compression.md +138 -0
  2413. package/skills/zarr-python/references/integration.md +147 -0
  2414. package/skills/zarr-python/references/performance_and_patterns.md +198 -0
  2415. package/skills/zarr-python/references/storage_backends.md +91 -0
  2416. package/skills/zarr-python/references/v3_migration.md +127 -0
  2417. package/templates/agents/orchestrator.md +37 -0
  2418. package/templates/base/groupy_prompt.md +92 -0
  2419. package/templates/compact/prompt.md +9 -0
  2420. package/templates/compact/summary_prefix.md +1 -0
  2421. package/templates/modes/default.md +19 -0
  2422. package/templates/modes/plan.md +128 -0
  2423. package/templates/modes/review.md +60 -0
  2424. package/templates/permissions/approval_policy/never.md +1 -0
  2425. package/templates/permissions/approval_policy/on_request.md +23 -0
  2426. package/templates/permissions/sandbox_mode/danger_full_access.md +1 -0
  2427. package/templates/permissions/sandbox_mode/read_only.md +1 -0
  2428. package/templates/permissions/sandbox_mode/workspace_write.md +1 -0
  2429. package/templates/personalities/friendly.md +19 -0
  2430. package/templates/personalities/pragmatic.md +17 -0
@@ -0,0 +1,61 @@
1
+ # Development
2
+
3
+ Source: https://pi.dev/docs/latest/development
4
+
5
+ Use this when working on Pi itself.
6
+
7
+ ## Setup
8
+
9
+ ```bash
10
+ git clone https://github.com/earendil-works/pi-mono
11
+ cd pi-mono
12
+ npm install
13
+ npm run build
14
+ ```
15
+
16
+ Run from source:
17
+
18
+ ```bash
19
+ /path/to/pi-mono/pi-test.sh
20
+ ```
21
+
22
+ The script can be run from any directory and preserves the caller's cwd.
23
+
24
+ ## Forking and Rebranding
25
+
26
+ Configure `package.json`:
27
+
28
+ ```json
29
+ {
30
+ "piConfig": {
31
+ "name": "pi",
32
+ "configDir": ".pi"
33
+ }
34
+ }
35
+ ```
36
+
37
+ Change `name`, `configDir`, and `bin` for a fork. This affects CLI banner, config paths, and environment variable names.
38
+
39
+ ## Path Resolution
40
+
41
+ Pi has npm install, standalone binary, and tsx-from-source execution modes. Always use `src/config.ts` helpers such as `getPackageDir` and `getThemeDir` for package assets. Do not use `__dirname` directly for assets.
42
+
43
+ ## Debugging and Tests
44
+
45
+ `/debug` writes rendered TUI lines and last LLM messages to `~/.pi/agent/pi-debug.log`.
46
+
47
+ ```bash
48
+ ./test.sh
49
+ npm test
50
+ npm test -- test/specific.test.ts
51
+ ```
52
+
53
+ ## Project Structure
54
+
55
+ ```text
56
+ packages/
57
+ ai/ # LLM provider abstraction
58
+ agent/ # Agent loop and message types
59
+ tui/ # Terminal UI components
60
+ coding-agent/ # CLI and interactive mode
61
+ ```
@@ -0,0 +1,57 @@
1
+ # Environment Variables
2
+
3
+ Source: https://pi.dev/docs/latest/environment-variables
4
+
5
+ Pi uses environment variables three ways: variables that configure the Pi process, markers Pi sets so child processes know they run inside Pi, and session metadata injected into commands run by the LLM-callable bash tool. Provider API-key variables live in `references/providers.md`.
6
+
7
+ ## Process Markers
8
+
9
+ The CLI and RPC entry points set two markers:
10
+
11
+ - `AI_AGENT=pi` — generic marker letting tooling identify Pi as the launching agent.
12
+ - `PI_CODING_AGENT=true` — Pi-specific marker for detecting that a process runs inside Pi.
13
+
14
+ Child processes inherit both. Neither is session-specific, and neither is set automatically when Pi is embedded through the SDK.
15
+
16
+ ## Bash Tool Session Environment
17
+
18
+ Commands run by the LLM-callable bash tool receive:
19
+
20
+ | Variable | Description |
21
+ |---|---|
22
+ | `PI_SESSION_ID` | Current session ID |
23
+ | `PI_SESSION_FILE` | Absolute path to the session JSONL file; unset for ephemeral sessions |
24
+ | `PI_PROVIDER` | Currently selected model provider |
25
+ | `PI_MODEL` | Currently selected model ID |
26
+ | `PI_REASONING_LEVEL` | Effective reasoning level: `off`, `minimal`, `low`, `medium`, `high`, `xhigh`, `max` |
27
+
28
+ Values resolve when each command starts, so switching models affects the next bash command without restarting. `PI_PROVIDER`/`PI_MODEL` identify the selected Pi model, not an upstream model a router picks internally. When asked which model is running, inspect these variables instead of inferring from the system prompt:
29
+
30
+ ```bash
31
+ printf '%s/%s\n' "$PI_PROVIDER" "$PI_MODEL"
32
+ ```
33
+
34
+ These are injected into the LLM-callable bash tool only — not into user-entered `!` or `!!` commands.
35
+
36
+ Custom bash tools built with `createBashTool()` expose the same variables by default, injected **before** `spawnHook` so hooks see them in `ctx.env`. Disable with `exposeSessionEnvironment: false`; Pi then also clears inherited values so nested Pi processes do not leak stale parent-session metadata.
37
+
38
+ ## Pi Process Configuration
39
+
40
+ | Variable | Description |
41
+ |---|---|
42
+ | `PI_CODING_AGENT_DIR` | Override the config directory; default `~/.pi/agent` |
43
+ | `PI_CODING_AGENT_SESSION_DIR` | Override session storage; overridden by `--session-dir` |
44
+ | `PI_PACKAGE_DIR` | Override the package directory (useful for Nix/Guix store paths) |
45
+ | `PI_OFFLINE` | Disable startup network operations: update checks, package updates, install/update telemetry |
46
+ | `PI_SKIP_VERSION_CHECK` | Disable the `pi.dev` latest-version request |
47
+ | `PI_TELEMETRY` | Override install/update telemetry and provider attribution headers: `1`/`true`/`yes` or `0`/`false`/`no` |
48
+ | `PI_CACHE_RETENTION` | Set to `long` for extended provider prompt caching where supported |
49
+ | `PI_SHARE_VIEWER_URL` | Override the base URL used by `/share` |
50
+ | `PI_HARDWARE_CURSOR` | Set to `1` to show the hardware cursor (IME positioning) |
51
+ | `PI_TUI_ESC_TIMEOUT` | Milliseconds to wait after a lone ESC before treating it as Escape; defaults to `100` over SSH and `10` otherwise. Increase when Alt-key input is misread as Escape |
52
+ | `VISUAL`, `EDITOR` | External editor fallback when the `externalEditor` setting is unset |
53
+ | `HTTP_PROXY`, `HTTPS_PROXY` | Proxy outbound HTTP requests |
54
+
55
+ Names are derived from the rebrandable app name (`package.json` `piConfig.name`), so a fork uses a different prefix — see `references/development.md`.
56
+
57
+ Other variables documented elsewhere: `PI_EXPERIMENTAL` (experimental first-time setup, `references/settings.md`), `PI_TUI_WRITE_LOG` (raw ANSI capture, `references/tui.md`), `AWS_BEDROCK_FORCE_CACHE` and other cloud variables (`references/providers.md`), `LLAMA_BASE_URL`/`LLAMA_API_KEY` (`references/llama-cpp.md`).
@@ -0,0 +1,185 @@
1
+ # Extensions
2
+
3
+ Source: https://pi.dev/docs/latest/extensions
4
+
5
+ Extensions are TypeScript modules that extend Pi. They register tools, commands, shortcuts, CLI flags, providers, renderers, UI, event handlers, and persistent session entries. They run with the full permissions of the Pi process — only install extensions you trust.
6
+
7
+ ## Locations
8
+
9
+ - `~/.pi/agent/extensions/*.ts` and `~/.pi/agent/extensions/*/index.ts` (global)
10
+ - `.pi/extensions/*.ts` and `.pi/extensions/*/index.ts` (project-local, loaded only after project trust)
11
+ - Paths from `settings.json` `extensions` / `packages`
12
+
13
+ Use `pi -e ./my-extension.ts` for quick tests only; auto-discovered extensions can be hot-reloaded with `/reload`. Extensions load via [jiti](https://github.com/unjs/jiti), so TypeScript needs no compilation.
14
+
15
+ ## Quick Extension
16
+
17
+ ```ts
18
+ import type { ExtensionAPI } from "@earendil-works/pi-coding-agent";
19
+ import { Type } from "typebox";
20
+
21
+ export default function (pi: ExtensionAPI) {
22
+ pi.on("session_start", async (_event, ctx) => {
23
+ ctx.ui.notify("Extension loaded", "info");
24
+ });
25
+
26
+ pi.on("tool_call", async (event, ctx) => {
27
+ if (event.toolName === "bash" && event.input.command?.includes("rm -rf")) {
28
+ const ok = await ctx.ui.confirm("Dangerous", "Allow rm -rf?");
29
+ if (!ok) return { block: true, reason: "Blocked by user" };
30
+ }
31
+ });
32
+
33
+ pi.registerTool({
34
+ name: "greet",
35
+ label: "Greet",
36
+ description: "Greet someone by name",
37
+ parameters: Type.Object({ name: Type.String() }),
38
+ async execute(_toolCallId, params) {
39
+ return { content: [{ type: "text", text: `Hello, ${params.name}!` }], details: {} };
40
+ },
41
+ });
42
+
43
+ pi.registerCommand("hello", {
44
+ description: "Say hello",
45
+ handler: async (args, ctx) => ctx.ui.notify(`Hello ${args || "world"}`, "info"),
46
+ });
47
+ }
48
+ ```
49
+
50
+ ## Imports
51
+
52
+ `@earendil-works/pi-coding-agent` (extension types and APIs), `typebox` (tool parameter schemas), `@earendil-works/pi-ai` (`StringEnum` for Google-compatible enums), `@earendil-works/pi-tui` (TUI components), plus Node built-ins. Add a `package.json` next to the extension and run `npm install` for npm dependencies. Distributed packages must put runtime deps in `dependencies` — package installs use `npm install --omit=dev`.
53
+
54
+ ## Factory Semantics
55
+
56
+ The default export receives `ExtensionAPI` and may be async; Pi awaits it before `session_start`, `resources_discover`, and flushing queued `pi.registerProvider()` calls. Use async factories for one-time startup work such as dynamic model discovery. Do **not** start background resources (processes, sockets, watchers, timers) in the factory — factories can run in invocations that never start a session. Start them in `session_start` or on demand, and close them in an idempotent `session_shutdown` handler.
57
+
58
+ ## Event Lifecycle
59
+
60
+ Startup: `project_trust` (user/global and CLI `-e` extensions only) → `session_start { reason: "startup" }` → `resources_discover { reason: "startup" }`.
61
+
62
+ Prompt: extension commands checked first (they bypass `input`) → `input` → skill/template expansion → `before_agent_start` → `agent_start` → message events → per turn: `turn_start`, `context`, `before_provider_headers`, `before_provider_request`, `after_provider_response`, then `tool_execution_start`, `tool_call`, `tool_execution_update`, `tool_result`, `tool_execution_end` → `turn_end` → `agent_end` → `agent_settled`.
63
+
64
+ Session replacement (`/new`, `/resume`): `session_before_switch` (cancellable) → `session_shutdown` → `session_start { reason: "new" | "resume", previousSessionFile }` → `resources_discover`. `/fork` and `/clone` use `session_before_fork` (with `position: "before" | "at"`) then `reason: "fork"`. `/name` emits `session_info_changed`. Compaction: `session_before_compact` → `session_compact`. `/tree`: `session_before_tree` → `session_tree`. Model changes: `thinking_level_select` then `model_select`. Exit: `session_shutdown`.
65
+
66
+ ## High-Value Hooks
67
+
68
+ - `project_trust` — must return `{ trusted: "yes" | "no" | "undecided", remember?: boolean }`. First yes/no decision wins and suppresses the built-in prompt. `ctx` is a limited trust context (cwd, mode, hasUI, select/confirm/input/notify).
69
+ - `resources_discover` — return `{ skillPaths, promptPaths, themePaths }`.
70
+ - `before_agent_start` — return `{ message }` to inject a persistent custom message and/or `{ systemPrompt }` to replace it for this turn (chained across handlers). `event.systemPromptOptions` exposes the structured inputs Pi used: `customPrompt`, `selectedTools`, `toolSnippets`, `promptGuidelines`, `appendSystemPrompt`, `cwd`, `contextFiles`, `skills`.
71
+ - `context` — `event.messages` is a deep copy; return `{ messages }` to modify what the LLM sees.
72
+ - `before_provider_headers` — mutate `event.headers` in place; a string adds/overrides, `null` deletes. Fires once per request; retries reuse the headers.
73
+ - `before_provider_request` — inspect or replace `event.payload`; handlers run in load order and `undefined` keeps it unchanged. Payload-level system-instruction rewrites are not reflected by `ctx.getSystemPrompt()`.
74
+ - `after_provider_response` — `event.status` and normalized `event.headers` before the stream body is consumed.
75
+ - `tool_call` — `event.input` is mutable and mutations affect execution (no re-validation); return `{ block: true, reason?, terminate? }` to block. `terminate` applies only to a blocked call, and the agent stops early only when every finalized result in the batch is terminating. Narrow with `isToolCallEventType("bash", event)`, or `isToolCallEventType<"my_tool", MyToolInput>(...)` for custom tools.
76
+ - `tool_result` — middleware-style chain; return partial patches (`content`, `details`, `isError`, `usage`). Use `isBashToolResult(event)` for typed bash details and `ctx.signal` for nested async work.
77
+ - `message_end` — return `{ message }` to replace the finalized message; the replacement must keep the same `role`.
78
+ - `user_bash` — intercept `!`/`!!`: return `{ operations }` (optionally wrapping `createLocalBashOperations()`) or `{ result }`.
79
+ - `input` — sees raw text before skill/template expansion. Return `{ action: "continue" | "transform" | "handled" }`; `event.source` is `"interactive" | "rpc" | "extension"` and `event.streamingBehavior` is `"steer" | "followUp" | undefined`.
80
+
81
+ In parallel tool mode, sibling tool calls are preflighted sequentially then executed concurrently, so `tool_call` is not guaranteed to see sibling tool results; `tool_result`/`tool_execution_end` may interleave in completion order while final `toolResult` message events stay in assistant source order.
82
+
83
+ ## ExtensionContext
84
+
85
+ `ctx.ui` (see Custom UI), `ctx.mode` (`"tui" | "rpc" | "json" | "print"`), `ctx.hasUI` (true in TUI and RPC), `ctx.cwd`, `ctx.signal` (agent abort signal; usually `undefined` outside active turns), `ctx.isProjectTrusted()`, `ctx.sessionManager` (read-only: `getEntries`, `getBranch`, `buildContextEntries`, `getLeafId`, …), `ctx.modelRegistry` (`getProvider(id)`, `getProviderAuth(id)`, `find(...)`), `ctx.model`, `ctx.thinkingLevel`, `ctx.scopedModels`, `ctx.isIdle()`, `ctx.abort()`, `ctx.hasPendingMessages()`, `ctx.shutdown()`, `ctx.getContextUsage()`, `ctx.compact({ customInstructions, onComplete, onError })`, `ctx.getSystemPrompt()`.
86
+
87
+ `ctx.scopedModels` is the read-only list of models scoped to the session — the same set `/scoped-models` shows, resolved at session start from `--models` and the `enabledModels` setting (minimatch against `provider/modelId` or a bare `modelId`). It is empty when no scoping is configured, meaning every available model is usable. Entries are `{ model, thinkingLevel? }`, with `thinkingLevel` set only when a pattern pinned it (e.g. `anthropic/*:high`). Use it for a model picker that mirrors the built-in one instead of enumerating `ctx.modelRegistry.getAvailable()`.
88
+
89
+ Use the exported `CONFIG_DIR_NAME` instead of hardcoding `.pi` — rebranded distributions use a different name.
90
+
91
+ ## ExtensionCommandContext
92
+
93
+ Command handlers additionally get session-control methods that would deadlock from event handlers: `getSystemPromptOptions()`, `waitForIdle()`, `newSession({ parentSession, setup, withSession })`, `fork(entryId, { position: "before" | "at", withSession })`, `navigateTree(targetId, { summarize, customInstructions, replaceInstructions, label })`, `switchSession(path, { withSession })`, `reload()`.
94
+
95
+ `withSession` receives a fresh `ReplacedSessionContext` with async `sendMessage()`/`sendUserMessage()`. It runs only after the old session emitted `session_shutdown` and the new instance already received `session_start`, but still executes in the original closure — so captured old `pi`/`ctx`/`sessionManager` objects are stale and throw. Capture only plain data (strings, ids) across the boundary. Treat `await ctx.reload()` as terminal for that handler (`await ctx.reload(); return;`); tools cannot call it, so expose a command and have the tool queue it with `pi.sendUserMessage("/my-reload", { deliverAs: "followUp" })`.
96
+
97
+ ## ExtensionAPI
98
+
99
+ Tools: `registerTool(definition)` (works during load and at runtime — new tools are callable without `/reload`), `getActiveTools()`, `getAllTools()` (returns `name`, `description`, `parameters`, `promptGuidelines`, `sourceInfo`), `setActiveTools(names)`.
100
+
101
+ Messages and session: `sendMessage(message, { deliverAs: "steer" | "followUp" | "nextTurn", triggerTurn })`, `sendUserMessage(content, { deliverAs, expandPromptTemplates })` (`deliverAs` required while streaming; `expandPromptTemplates` defaults to `false` and opts into extension-command dispatch plus skill/prompt-template expansion), `appendEntry(customType, data)`, `setSessionName`, `getSessionName`, `setLabel(entryId, label)`.
102
+
103
+ Commands and input: `registerCommand(name, { description, handler, getArgumentCompletions })` (duplicate names get `:1`/`:2` suffixes in load order), `getCommands()` (extension → prompt → skill order, each with `sourceInfo.scope`/`origin`), `registerShortcut(key, options)`, `registerFlag(name, options)` + `getFlag(name)`.
104
+
105
+ Rendering: `registerMessageRenderer(customType, renderer)` (custom messages, in LLM context), `registerEntryRenderer(customType, renderer)` (custom entries, TUI only), `registerMarkdownTransformer(transformer)`.
106
+
107
+ `registerMarkdownTransformer` transforms the Markdown of normal user text, assistant text, and thinking blocks before Pi's built-in renderer runs. Transformers run in extension load order, each receiving the previous transformer's output plus a context of `messageType` (`"user" | "assistant" | "assistant-thinking"`), `isStreaming` (true only for partial assistant updates), and `availableWidth` (exact terminal columns):
108
+
109
+ ```typescript
110
+ pi.registerMarkdownTransformer((markdown, { messageType, isStreaming }) => {
111
+ if (isStreaming || messageType === "assistant-thinking") return markdown;
112
+ return markdown.replaceAll("-->", "→");
113
+ });
114
+ ```
115
+
116
+ A throwing transformer keeps the Markdown produced so far and continues with the next one. The hook is display-only — the session and model context keep the original message. It fires for new user messages, assistant streaming updates, restored session messages, and terminal width changes, so keep transformers synchronous and cheap.
117
+
118
+ Model and provider: `setModel(model)` (returns `false` without an API key), `getThinkingLevel()`, `setThinkingLevel(level)`, `registerProvider(nameOrProvider, config?)`, `unregisterProvider(name)`. Calls after the load phase take effect immediately. Dynamic providers can implement `refreshModels`, and a complete pi-ai `Provider` from `createProvider(...)` can be registered as the composition base with `models.json` overrides layered above.
119
+
120
+ `refreshModels` receives the canonical credential/stored-catalog/network/signal context: `context.stored` is the persisted provider snapshot, and persistence goes through generation-checked `context.publish({ persist: entry })` (`persist: null` deletes the snapshot). Live servers such as llama.cpp can return models without persisting. `context.signal` is always a concrete signal and provider callbacks must pass it to blocking I/O; public `ModelRuntime.refresh()` / `ModelRegistry.refresh()` accept an optional signal and are unbounded when it is omitted, so extensions choose their own deadlines. Cancellation stops the caller waiting even if a provider ignores the signal. OAuth `refreshToken(credentials, signal)` now takes the signal as a second argument.
121
+
122
+ Other: `exec(command, args, { signal, timeout })` → `{ stdout, stderr, code, killed }`, `on(event, handler)`, `events` (inter-extension bus).
123
+
124
+ ## Custom Tools
125
+
126
+ ```ts
127
+ pi.registerTool({
128
+ name: "my_tool",
129
+ label: "My Tool",
130
+ description: "What this tool does (shown to the LLM)",
131
+ promptSnippet: "One-line entry in the system prompt's Available tools section",
132
+ promptGuidelines: ["Use my_tool when the user asks to summarize generated text."],
133
+ parameters: Type.Object({ action: StringEnum(["list", "add"] as const), text: Type.Optional(Type.String()) }),
134
+ prepareArguments(args) { return args; },
135
+ async execute(toolCallId, params, signal, onUpdate, ctx) {
136
+ onUpdate?.({ content: [{ type: "text", text: "Working..." }], details: { progress: 50 } });
137
+ return { content: [{ type: "text", text: "Done" }], details: {}, terminate: true };
138
+ },
139
+ renderShell: "self",
140
+ renderCall(args, theme, context) { /* Component */ },
141
+ renderResult(result, options, theme, context) { /* Component */ },
142
+ });
143
+ ```
144
+
145
+ - Use `StringEnum` from `@earendil-works/pi-ai` for string enums; `Type.Union`/`Type.Literal` breaks Google's API.
146
+ - `promptGuidelines` bullets are appended flat with no tool-name prefix — always name the tool ("Use my_tool when…"), never "this tool".
147
+ - `prepareArguments` runs before schema validation; use it to fold legacy argument shapes from resumed sessions instead of loosening `parameters`.
148
+ - Signal errors by **throwing** — returning a value never sets `isError`.
149
+ - `terminate: true` hints that the follow-up LLM call should be skipped, and only applies when every finalized result in the batch terminates.
150
+ - Return `usage` for nested LLM calls; Pi persists it and includes it in footer, `/session`, and RPC totals.
151
+ - Strip a leading `@` from path arguments (some models add it), and wrap read-modify-write windows in `withFileMutationQueue(absolutePath, fn)` so the tool shares the per-file queue with built-in `edit`/`write` — tools run in parallel by default. Resolve to an absolute path first; the helper canonicalizes existing files through `realpath()`.
152
+ - Truncate output. The built-in limit is 50 KB / 2000 lines, whichever hits first. Use `truncateHead` (beginning matters), `truncateTail` (end matters), `truncateLine`, `formatSize`, `DEFAULT_MAX_BYTES`, `DEFAULT_MAX_LINES`, and tell the LLM where the full output was saved.
153
+
154
+ Overriding built-ins (`read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`) works by registering the same name; interactive mode warns. Renderer inheritance is per slot, so omitting `renderCall`/`renderResult` keeps the built-in UI. `promptSnippet`/`promptGuidelines` are **not** inherited. The result shape, including `details`, must match exactly.
155
+
156
+ Remote execution: built-in tool factories accept pluggable `operations` (`ReadOperations`, `WriteOperations`, `EditOperations`, `BashOperations`, `LsOperations`, `GrepOperations`, `FindOperations`). `createBashTool(cwd, { spawnHook, exposeSessionEnvironment })` can rewrite command/cwd/env; session variables are injected before `spawnHook` (`references/environment-variables.md`).
157
+
158
+ ### Dynamic Tool Loading
159
+
160
+ Register every tool, keep only loader tools active, then call `pi.setActiveTools([...current, ...matched])` during loader execution. The change must be purely additive. Pi records the added names on the loader's tool result and exposes the definitions before the next model request — natively via `defer_loading`/`tool_reference` on Anthropic Sonnet/Opus/Fable 4.5+ and via `tool_search_call`/`tool_search_output` on OpenAI `gpt-5.4`+, otherwise by sending the normal active tool list. Verified custom endpoints can opt in with `compat.supportsToolReferences` (anthropic-messages) or `compat.supportsToolSearch` (openai-responses / openai-codex-responses). Non-additive changes fall back to the full list. Lazily loaded tools should rely on `description` and omit `promptSnippet`/`promptGuidelines`, which rebuild the system prompt and can invalidate the cached prefix.
161
+
162
+ ## State Management
163
+
164
+ Store state in tool result `details` so branching works, and rebuild it in `session_start` by walking `ctx.sessionManager.getBranch()`. `pi.appendEntry(customType, data)` persists extension state that does not enter LLM context.
165
+
166
+ ## Custom UI
167
+
168
+ Dialogs: `ctx.ui.select(title, options)`, `confirm(title, message)`, `input(prompt, placeholder)`, `editor(title, prefill)`, `notify(message, "info" | "warning" | "error")`. Dialogs accept `{ timeout }` (live countdown; `select`/`input` return `undefined`, `confirm` returns `false`) or `{ signal }` when you need to distinguish timeout from user cancel.
169
+
170
+ Chrome: `setStatus(key, text)`, `setWidget(key, lines | factory, { placement: "aboveEditor" | "belowEditor" })`, `setFooter(factory)`, `setHeader(...)`, `setTitle(text)`, `setEditorText` / `getEditorText` / `pasteToEditor`, `setWorkingMessage`, `setWorkingVisible`, `setWorkingIndicator({ frames, intervalMs })`, `setToolsExpanded` / `getToolsExpanded`, `setEditorComponent(factory)` / `getEditorComponent()`, `addAutocompleteProvider(current => provider)`, `getAllThemes` / `getTheme` / `setTheme` / `theme`, and `custom(factory, { overlay, overlayOptions, onHandle })`.
171
+
172
+ Custom-component details, overlays, built-in components, and copy-paste patterns are in `references/tui.md`. Syntax highlighting helpers: `highlightCode(code, lang, theme)`, `getLanguageFromPath(path)`. Keybinding hints: `keyHint(id, description)`, `keyText(id)`, `rawKeyHint(key, description)` with namespaced ids (`app.*` for the coding agent, `tui.*` for shared TUI).
173
+
174
+ ## Error Handling and Mode Behavior
175
+
176
+ Extension errors are logged and the agent continues; `tool_call` errors block the tool (fail-safe); tool `execute` errors must be thrown and are reported to the LLM with `isError: true`.
177
+
178
+ | Mode | `ctx.mode` | `ctx.hasUI` | Notes |
179
+ |---|---|---|---|
180
+ | Interactive | `"tui"` | `true` | Full TUI |
181
+ | RPC | `"rpc"` | `true` | Dialogs/notifications over the JSON protocol; `custom()` returns `undefined` |
182
+ | JSON | `"json"` | `false` | UI methods are no-ops |
183
+ | Print (`-p`) | `"print"` | `false` | Extensions run but cannot prompt |
184
+
185
+ Guard TUI-only features with `ctx.mode === "tui"`; guard dialogs and notifications with `ctx.hasUI`.
@@ -0,0 +1,69 @@
1
+ # JSON Event Stream Mode
2
+
3
+ Source: https://pi.dev/docs/latest/json
4
+
5
+ Use JSON mode for one-shot prompts that output all session events as JSON lines to stdout.
6
+
7
+ ```bash
8
+ pi --mode json "Your prompt"
9
+ ```
10
+
11
+ ## Event Types
12
+
13
+ Wire events use `JsonAgentSessionEvent`, which matches `AgentSessionEvent` except that streaming message updates omit cumulative snapshots:
14
+
15
+ ```typescript
16
+ type WithoutPartial<T> = T extends { partial: unknown } ? Omit<T, "partial"> : T;
17
+
18
+ type JsonAgentSessionEvent =
19
+ | Exclude<AgentSessionEvent, { type: "message_update" }>
20
+ | { type: "message_update"; usage: Usage; assistantMessageEvent: WithoutPartial<AssistantMessageEvent> };
21
+ ```
22
+
23
+ `AgentSessionEvent` is `AgentEvent` plus session-level events:
24
+
25
+ - `queue_update` — `{ steering: readonly string[], followUp: readonly string[] }`, emitted whenever either queue changes
26
+ - `compaction_start` — `{ reason: "manual" | "threshold" | "overflow" }`
27
+ - `compaction_end` — `{ reason, result: CompactionResult | undefined, aborted, willRetry, errorMessage? }`
28
+ - `auto_retry_start` — `{ attempt, maxAttempts, delayMs, errorMessage }`
29
+ - `auto_retry_end` — `{ success, attempt, finalError? }`
30
+ - `summarization_retry_scheduled` — `{ attempt, maxAttempts, delayMs, errorMessage }`
31
+ - `summarization_retry_attempt_start` — `{ source: "branchSummary" }` or `{ source: "compaction", reason }`
32
+ - `summarization_retry_finished`
33
+
34
+ Base `AgentEvent` types:
35
+
36
+ - `agent_start`, `agent_end` (`messages`)
37
+ - `turn_start`, `turn_end` (`message`, `toolResults`)
38
+ - `message_start` (`message`), `message_update` (`usage`, `assistantMessageEvent`), `message_end` (`message`)
39
+ - `tool_execution_start` (`toolCallId`, `toolName`, `args`), `tool_execution_update` (+ `partialResult`), `tool_execution_end` (`result`, `isError`)
40
+
41
+ ## Output Format
42
+
43
+ First line is the session header:
44
+
45
+ ```json
46
+ {"type":"session","version":3,"id":"uuid","timestamp":"...","cwd":"/path"}
47
+ ```
48
+
49
+ Then events as they occur:
50
+
51
+ ```json
52
+ {"type":"agent_start"}
53
+ {"type":"turn_start"}
54
+ {"type":"message_start","message":{"role":"assistant","content":[]}}
55
+ {"type":"message_update","usage":{},"assistantMessageEvent":{"type":"text_delta","contentIndex":0,"delta":"Hello"}}
56
+ {"type":"message_end","message":{}}
57
+ {"type":"turn_end","message":{},"toolResults":[]}
58
+ {"type":"agent_end","messages":[]}
59
+ ```
60
+
61
+ `message_update` records are delta-only: they omit both the cumulative `message` field and `assistantMessageEvent.partial` to keep stream size linear. The top-level `usage` field carries the latest cumulative provider-reported usage and may stay zero when a provider only reports usage at completion. Assemble live text, thinking, or tool-call arguments from `contentIndex` and `delta`; `message_end` holds the final authoritative message.
62
+
63
+ ## Example
64
+
65
+ ```bash
66
+ pi --mode json "List files" 2>/dev/null | jq -c 'select(.type == "message_end")'
67
+ ```
68
+
69
+ For bidirectional control, use RPC instead of JSON mode.
@@ -0,0 +1,58 @@
1
+ # Keybindings
2
+
3
+ Source: https://pi.dev/docs/latest/keybindings
4
+
5
+ All shortcuts are customizable in `~/.pi/agent/keybindings.json`, which uses the same namespaced ids Pi uses internally and that extension authors pass to `keyHint()` and the injected `keybindings` manager. Pre-namespaced ids from older configs (`cursorUp`, `expandTools`, …) migrate automatically on startup. Run `/reload` after editing.
6
+
7
+ ## Key Format
8
+
9
+ `modifier+key` where modifiers are `ctrl`, `shift`, `alt`, `super` (combinable, e.g. `ctrl+shift+x`, `alt+ctrl+1`, `super+k`, `ctrl+super+k`). `super` bindings need a terminal that reports the modifier separately, typically via the Kitty keyboard protocol. Keys:
10
+
11
+ - Letters `a-z`, digits `0-9`
12
+ - Special: `escape`/`esc`, `enter`/`return`, `tab`, `space`, `backspace`, `delete`, `insert`, `clear`, `home`, `end`, `pageUp`, `pageDown`, `up`, `down`, `left`, `right`
13
+ - Function: `f1`–`f12`
14
+ - Symbols: `` ` ``, `-`, `=`, `[`, `]`, `\`, `;`, `'`, `,`, `.`, `/`, `!`, `@`, `#`, `$`, `%`, `^`, `&`, `*`, `(`, `)`, `_`, `+`, `|`, `~`, `{`, `}`, `:`, `<`, `>`, `?`
15
+
16
+ ## Actions
17
+
18
+ **`tui.editor.*` cursor** — `cursorUp` (up; browses older history at the top), `cursorDown` (down; browses newer history at the bottom), `historyPrevious` / `historyNext` (no defaults), `cursorLeft` (left, ctrl+b), `cursorRight` (right, ctrl+f), `cursorWordLeft` (alt+left, ctrl+left, alt+b), `cursorWordRight` (alt+right, ctrl+right, alt+f), `cursorLineStart` (home, ctrl+home, ctrl+a), `cursorLineEnd` (end, ctrl+end, ctrl+e), `jumpForward` (ctrl+]), `jumpBackward` (ctrl+alt+]), `pageUp` (pageUp, ctrl+pageUp), `pageDown` (pageDown, ctrl+pageDown).
19
+
20
+ The dedicated `historyPrevious`/`historyNext` actions always change history entries regardless of cursor position in a multiline prompt, and explicit history bindings take precedence over application actions while the main editor is focused — binding `tui.editor.historyPrevious` to `ctrl+p` overrides model cycling in that context without changing `Ctrl+P` in selectors.
21
+
22
+ **`tui.editor.*` deletion** — `deleteCharBackward` (backspace), `deleteCharForward` (delete, ctrl+d), `deleteWordBackward` (ctrl+w, alt+backspace), `deleteWordForward` (alt+d, alt+delete), `deleteToLineStart` (ctrl+u), `deleteToLineEnd` (ctrl+k).
23
+
24
+ **`tui.editor.*` kill ring** — `yank` (ctrl+y), `yankPop` (alt+y), `undo` (ctrl+-).
25
+
26
+ **`tui.input.*`** — `newLine` (shift+enter, ctrl+j), `submit` (enter), `tab` (tab), `copy` (ctrl+c).
27
+
28
+ **`tui.select.*`** — `up`, `down`, `pageUp`, `pageDown`, `confirm` (enter), `cancel` (escape, ctrl+c).
29
+
30
+ **`tui.altScreen.*` fullscreen viewport** (only in `--tui-mode fullscreen`) — `pageUp` (pageUp), `pageDown` (pageDown), `halfPageUp` / `halfPageDown` / `lineUp` / `lineDown` (no defaults), `previousPrompt` (ctrl+shift+up), `nextPrompt` (ctrl+shift+down), `search` (ctrl+shift+f), `searchNext` (enter, ctrl+g), `searchPrevious` (shift+enter, ctrl+shift+g), `searchClose` (escape), `top` (home), `bottom` (end).
31
+
32
+ These target the primary transcript scroll region and take precedence over editor bindings, so in fullscreen mode unmodified `home`/`end`/`pageUp`/`pageDown` drive the transcript while their `ctrl` variants still drive the editor; outside fullscreen both variants drive the editor. Rebind normally to change the routing (`"tui.altScreen.pageUp": "ctrl+pageUp"`), or set `[]` to disable a transcript shortcut. Mouse-wheel and two-finger input scroll the region under the pointer, OSC 8 hyperlinks open on click, and primary-button drag selects text and copies it (holding at an edge auto-scrolls).
33
+
34
+ **`app.*` application** — `interrupt` (escape), `clear` (ctrl+c; clears the editor first, exits on a second press), `exit` (ctrl+d when editor empty), `suspend` (ctrl+z; none on Windows), `editor.external` (ctrl+g), `clipboard.pasteImage` (ctrl+v; alt+v on Windows — pastes images or text).
35
+
36
+ **`app.session.*`** — `new`, `tree`, `fork`, `resume` (no defaults), `togglePath` (ctrl+p), `toggleSort` (ctrl+s), `toggleNamedFilter` (ctrl+n), `rename` (ctrl+r), `delete` (ctrl+d), `deleteNoninvasive` (ctrl+backspace).
37
+
38
+ **`app.model.*` / `app.thinking.*`** — `model.select` (ctrl+l), `model.cycleForward` (ctrl+p), `model.cycleBackward` (shift+ctrl+p), `thinking.cycle` (shift+tab), `thinking.toggle` (ctrl+t).
39
+
40
+ **`app.tools.*` / `app.message.*`** — `tools.expand` (ctrl+o), `message.copy` (ctrl+x), `message.followUp` (alt+enter), `message.dequeue` (alt+up).
41
+
42
+ **`app.tree.*`** — `foldOrUp` (ctrl+left, alt+left), `unfoldOrDown` (ctrl+right, alt+right), `editLabel` (shift+l), `toggleLabelTimestamp` (shift+t), `filter.default` (ctrl+d), `filter.noTools` (ctrl+t), `filter.userOnly` (ctrl+u), `filter.labeledOnly` (ctrl+l), `filter.all` (ctrl+a), `filter.cycleForward` (ctrl+o), `filter.cycleBackward` (shift+ctrl+o).
43
+
44
+ **`app.models.*`** (inside the `/scoped-models` selector) — `save` (ctrl+s), `enableAll` (ctrl+a), `clearAll` (ctrl+x), `toggleProvider` (ctrl+p), `reorderUp` (alt+up), `reorderDown` (alt+down).
45
+
46
+ ## Custom Config
47
+
48
+ ```json
49
+ {
50
+ "tui.editor.historyPrevious": "ctrl+p",
51
+ "tui.editor.historyNext": "ctrl+n",
52
+ "tui.editor.deleteWordBackward": ["ctrl+w", "alt+backspace"]
53
+ }
54
+ ```
55
+
56
+ Each action takes a single key or an array; user config overrides defaults. The docs include full Emacs and Vim example configs.
57
+
58
+ On native Windows, `app.suspend` has no default because Windows terminals lack Unix job control — bound manually, Pi shows a status message instead of suspending. WSL keeps normal `ctrl+z`/`fg` behavior.
@@ -0,0 +1,69 @@
1
+ # llama.cpp
2
+
3
+ Source: https://pi.dev/docs/latest/llama-cpp
4
+
5
+ Pi supports the llama.cpp **router** server, which discovers multiple GGUF models and loads or unloads them on demand. Use a current llama.cpp build with router support.
6
+
7
+ ## Start the Router
8
+
9
+ Start `llama-server` **without** `--model`, `-m`, or `-hf`. Passing a model starts single-model mode instead of router mode.
10
+
11
+ ```bash
12
+ llama-server \
13
+ --models-dir ~/models \
14
+ --no-models-autoload \
15
+ --jinja \
16
+ --host 127.0.0.1 \
17
+ --port 8080 \
18
+ -ngl 999 \
19
+ -c 32768
20
+ ```
21
+
22
+ - `--models-dir` discovers local GGUF files.
23
+ - `--no-models-autoload` keeps loading explicit through `/llama`.
24
+ - `--jinja` enables compatible chat templates and tool calling.
25
+ - `-ngl 999` offloads as many layers as possible to the GPU.
26
+ - `-c 32768` sets the context window per loaded model; omit to use the model's native context (may need much more memory).
27
+
28
+ Single-file models sit directly in the models directory. Multimodal and multi-shard models go in their own subdirectories with all components included. Restart the router after manually adding files; use llama.cpp model presets for per-model context sizes.
29
+
30
+ ## Configure Pi
31
+
32
+ ```text
33
+ /login llama.cpp
34
+ ```
35
+
36
+ Enter the router URL (default `http://127.0.0.1:8080`) and optional API key. Environment variables configure the same values without `/login`:
37
+
38
+ ```bash
39
+ export LLAMA_BASE_URL=http://127.0.0.1:8080
40
+ export LLAMA_API_KEY=optional-secret
41
+ pi
42
+ ```
43
+
44
+ If the server uses an API key, start `llama-server` with the matching `--api-key`. Keep `--host 127.0.0.1` for local-only access.
45
+
46
+ ## Manage Models with `/llama`
47
+
48
+ - Select an unloaded model to load it; select a loaded model to unload it.
49
+ - Select **Download model…** to search Hugging Face, then choose a repository and quantization. Exact `owner/repository[:quant]` values also work.
50
+ - Escape during a load or download prompts to confirm cancellation.
51
+ - If the router disconnects, `/llama` offers **Retry** and **Close**; Retry reconnects and refreshes state without replaying the interrupted operation.
52
+
53
+ Hugging Face search uses `HF_TOKEN` when set, then `$HF_TOKEN_PATH`, `$HF_HOME/token`, `$XDG_CACHE_HOME/huggingface/token`, and `~/.cache/huggingface/token`. Search works unauthenticated with lower rate limits. Pi warns before downloading gated repositories. The llama.cpp server performs the download, so its process also needs `HF_TOKEN` for gated repositories.
54
+
55
+ Pi never silently unloads models and never deletes model files; it asks whether to unload others first. The router may be shared with other clients, so `/llama` always displays the router's current state.
56
+
57
+ Only loaded models appear in `/model`. Load with `/llama`, then select the model with `/model`.
58
+
59
+ ## Troubleshooting
60
+
61
+ ```bash
62
+ curl http://127.0.0.1:8080/health
63
+ curl http://127.0.0.1:8080/models
64
+ ```
65
+
66
+ - No models in `/llama`: check `--models-dir`, the directory layout, and restart the router.
67
+ - Model missing from `/model`: load it with `/llama` first.
68
+ - Load fails or uses too much memory: lower `-c` or unload another model.
69
+ - Server not in router mode: start it without `--model`, `-m`, or `-hf`.
@@ -0,0 +1,114 @@
1
+ # Custom Models
2
+
3
+ Source: https://pi.dev/docs/latest/models
4
+
5
+ Add custom providers and models through `~/.pi/agent/models.json` for Ollama, LM Studio, vLLM, SGLang, proxies, and custom endpoints.
6
+
7
+ ## Minimal Local Example
8
+
9
+ ```json
10
+ {
11
+ "providers": {
12
+ "ollama": {
13
+ "baseUrl": "http://localhost:11434/v1",
14
+ "api": "openai-completions",
15
+ "apiKey": "ollama",
16
+ "compat": {
17
+ "supportsDeveloperRole": false,
18
+ "supportsReasoningEffort": false
19
+ },
20
+ "models": [
21
+ { "id": "llama3.1:8b" },
22
+ { "id": "qwen2.5-coder:7b" }
23
+ ]
24
+ }
25
+ }
26
+ }
27
+ ```
28
+
29
+ Only `id` is required per model. The `apiKey` placeholder matters because Pi treats models as requiring auth before they appear in `/model`; keyless local servers should keep a dummy value, store a key via `/login`, or pass `--api-key`. Set `compat.supportsDeveloperRole: false` for OpenAI-compatible servers that reject the `developer` role, and `compat.supportsReasoningEffort: false` when `reasoning_effort` is unsupported. `compat` can be set at provider level (all models) or model level (override). The file reloads each time `/model` opens — no restart needed.
30
+
31
+ For `google-generative-ai` custom models, `baseUrl` is required (for example `https://generativelanguage.googleapis.com/v1beta`).
32
+
33
+ ## Supported APIs
34
+
35
+ `openai-completions` (most compatible), `openai-responses`, `anthropic-messages`, `google-generative-ai`. Set `api` at provider level as the default, or per model to override.
36
+
37
+ ## Provider Fields
38
+
39
+ `baseUrl`, `api`, `apiKey`, `oauth`, `headers`, `authHeader`, `models`, `modelOverrides`.
40
+
41
+ - `oauth`: dynamic OAuth provider type; currently `"radius"`, which requires the gateway `baseUrl`.
42
+ - `authHeader: true` adds `Authorization: Bearer <apiKey>`.
43
+ - `apiKey` is optional — omit it when auth comes from `/login`/`auth.json`/`--api-key`. Non-built-in providers with `models` need `baseUrl` and an `api` value at provider or model level. Without any auth, models load but stay unavailable in `/model` and `--list-models`.
44
+
45
+ `apiKey` and `headers` support command execution (`!command`, whole value), env interpolation (`$ENV` / `${ENV}`, works inside larger literals), escapes (`$$`, `$!`), and literals (plain uppercase strings are literals). Shell commands in `models.json` resolve at request time with no built-in TTL, stale reuse, or recovery — wrap slow or flaky secret commands yourself. `/model` availability checks use configured auth presence and do not execute shell commands.
46
+
47
+ ## Model Fields
48
+
49
+ Required: `id`. Optional: `name` (defaults to `id`), `api`, `reasoning` (`false`), `thinkingLevelMap`, `input` (`["text"]` or `["text","image"]`), `contextWindow` (`128000`), `maxTokens` (`16384`), `samplingParams`, `cost` (zeros), `compat` (merged with provider `compat`).
50
+
51
+ `/model`, `--list-models`, and the footer display entries by model `id`; `name` is used for `--model` pattern matching and secondary detail text.
52
+
53
+ `cost` is per million tokens and supports request-wide input pricing tiers. A tier supplies a complete alternate rate set and applies to the whole request when `input + cacheRead + cacheWrite` exceeds `inputTokensAbove`; the highest matching threshold wins.
54
+
55
+ ```json
56
+ {
57
+ "cost": {
58
+ "input": 5, "output": 30, "cacheRead": 0.5, "cacheWrite": 6.25,
59
+ "tiers": [{ "inputTokensAbove": 272000, "input": 10, "output": 45, "cacheRead": 1, "cacheWrite": 12.5 }]
60
+ }
61
+ }
62
+ ```
63
+
64
+ ## Sampling Parameters
65
+
66
+ `samplingParams` is a free-form object merged verbatim into every request body for that model, after the fields Pi sets itself — so its keys win, including over Pi's own `temperature`. Use it for sampling controls Pi does not model, such as llama.cpp `min_p` or vLLM `top_k`:
67
+
68
+ ```json
69
+ { "id": "deepseek-v4-flash",
70
+ "samplingParams": { "temperature": 1.0, "top_p": 0.95, "top_k": 0, "min_p": 0.0 } }
71
+ ```
72
+
73
+ Only OpenAI-compatible APIs apply it (`openai-completions`, `openai-responses`, `azure-openai-responses`); other APIs ignore it. Treat it as the single source of sampling truth for a model. In `modelOverrides`, `samplingParams` merges per key with the base model's value.
74
+
75
+ ## Thinking Level Map
76
+
77
+ Keys are Pi levels: `off`, `minimal`, `low`, `medium`, `high`, `xhigh`, `max`. Maps may have holes. Values are tristate: omitted means standard levels through `high` use the provider default mapping while `xhigh`/`max` are unsupported; a string is sent to the provider; `null` marks the level unsupported so it is hidden/skipped/clamped away.
78
+
79
+ ```json
80
+ { "id": "deepseek-v4-pro", "reasoning": true,
81
+ "thinkingLevelMap": { "minimal": null, "low": null, "medium": null, "high": "high", "xhigh": null, "max": "max" } }
82
+ ```
83
+
84
+ Use `{ "off": null }` for models where thinking cannot be disabled. Older `compat.reasoningEffortMap` configs should move to model-level `thinkingLevelMap`.
85
+
86
+ ## Overriding Built-in Providers
87
+
88
+ Base-URL-only overrides keep all built-in models and existing auth:
89
+
90
+ ```json
91
+ { "providers": { "anthropic": { "baseUrl": "https://my-proxy.example.com/v1" } } }
92
+ ```
93
+
94
+ If `models` is included, built-in models are kept and custom models are upserted by `id` — a matching `id` replaces the built-in, a new `id` is added.
95
+
96
+ `modelOverrides` customizes built-in and matching extension-registered models without replacing the provider list. Supported per-model fields: `name`, `reasoning`, `thinkingLevelMap`, `input`, `cost` (partial), `contextWindow`, `maxTokens`, `samplingParams` (merged per key), `headers`, `compat`. Unknown model IDs are ignored; provider-level `baseUrl`/`headers` can be combined with it. If `models` is also defined, custom models merge after built-in overrides.
97
+
98
+ Example — opt a direct OpenAI GPT-5.6 model into the 1.05M context window (they default to `272000` to stay in the short-context pricing tier):
99
+
100
+ ```json
101
+ { "providers": { "openai": { "modelOverrides": { "gpt-5.6-sol": { "contextWindow": 1050000 } } } } }
102
+ ```
103
+
104
+ ## Anthropic Messages Compatibility Flags
105
+
106
+ `supportsEagerToolInputStreaming` (default `true`; `false` omits `tools[].eager_input_streaming` and sends the legacy fine-grained-tool-streaming beta header), `supportsLongCacheRetention` (default `true`, `cache_control.ttl: "1h"`), `sendSessionAffinityHeaders` (auto-detected), `supportsCacheControlOnTools` (default `true`), `forceAdaptiveThinking` (`thinking.type: "adaptive"` plus `output_config.effort`; built-in adaptive models set it automatically), `allowEmptySignature` (replay empty thinking signatures as `signature: ""`), `supportsStrictTools` (default `false`; built-in Anthropic models enable it).
107
+
108
+ ## OpenAI Compatibility Flags
109
+
110
+ `supportsStore`, `supportsDeveloperRole`, `supportsReasoningEffort`, `supportsUsageInStreaming` (default `true`), `supportsFinishReason` (default `true`; `false` makes Pi infer `stop`/`toolUse` when the stream ends without one), `maxTokensField` (`max_completion_tokens` | `max_tokens`), `requiresToolResultName`, `requiresAssistantAfterToolResult`, `requiresThinkingAsText`, `requiresReasoningContentOnAssistantMessages`, `thinkingFormat` (`reasoning_effort`, `openrouter`, `deepseek`, `together`, `baseten`, `zai`, `qwen`, `chat-template`, `qwen-chat-template`), `chatTemplateKwargs`, `chatTemplateArgs` (`chat_template_args` values for `thinkingFormat: "baseten"`), `cacheControlFormat` (`anthropic`), `sendSessionAffinityHeaders` (default `false`), `sessionAffinityFormat` (`openai`, `openai-nosession`, `openrouter`), `supportsStrictMode`, `supportsOpenAIGrammarTools` (default `false`; the built-in catalog enables it for GPT-5+ on OpenAI, OpenAI Codex, Azure OpenAI, GitHub Copilot, opencode, Cloudflare AI Gateway), `deferredToolsMode` (`"kimi"`), `supportsLongCacheRetention` (default `true`; `prompt_cache_retention: "24h"`), `openRouterRouting`, `vercelGatewayRouting`.
111
+
112
+ Thinking-format notes: `openrouter` uses `reasoning: { effort }`; `together` uses `reasoning: { enabled }` plus `reasoning_effort` when `supportsReasoningEffort`; `qwen` uses top-level `enable_thinking`; `qwen-chat-template` targets local Qwen servers needing `chat_template_kwargs.enable_thinking` and `preserve_thinking`; `chat-template` plus `chatTemplateKwargs` targets vLLM/Hugging Face templates, e.g. `chatTemplateKwargs: { "thinking": { "$var": "thinking.enabled" } }` for DeepSeek V3.x. `baseten` plus `chatTemplateArgs` targets providers exposing toggle controls through `chat_template_args`, optionally with top-level `reasoning_effort`. `$var` accepts `thinking.enabled` or `thinking.effort`.
113
+
114
+ `openRouterRouting` is sent as-is in the OpenRouter `provider` field (`only`, `order`, `ignore`, `sort`, `max_price`, `quantizations`, `zdr`, …). `vercelGatewayRouting` takes `only`/`order`.