@pikaa-ai/pikaa 0.2.5 → 0.3.0

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 +1,282 @@
1
+ # Quality Manual Development Guide
2
+
3
+ Research basis: **2026-07-23**, extended **2026-07-26** for laboratory lanes. This guide
4
+ explains an evidence-controlled authoring process. It does not reproduce standard text
5
+ or prescribe a universal manual format.
6
+
7
+ The authoring process applies to any management-system documentation this skill covers.
8
+ Where it says "QMS scope," a laboratory's equivalent is the **scope of laboratory
9
+ activities** — per location and per method or examination — and a laboratory manual
10
+ should point to the accredited scope schedule rather than restate it. Read
11
+ `references/iso-17025.md` or `references/iso-15189.md` alongside this guide.
12
+
13
+ ## Boundary and copyright
14
+
15
+ A quality manual template cannot establish an effective QMS, conformity,
16
+ certification, FDA compliance, MDSAP acceptance, EU conformity, or legal
17
+ applicability. It cannot replace authorized management, RA/QA, legal, notified-body,
18
+ regulatory-authority, MDSAP Auditing Organization, or certification-body decisions.
19
+
20
+ ISO publications are copyrighted. Obtain ISO 13485 from
21
+ [ISO](https://www.iso.org/standard/59752.html), a national member, or an authorized
22
+ source. Do not paste standard text into the manual. Summarize the organization's
23
+ actual processes and reference its controlled authorized copy.
24
+
25
+ ## Purpose of a manual
26
+
27
+ A useful manual or equivalent policy architecture:
28
+
29
+ - identifies the approved QMS scope;
30
+ - identifies controlled processes and their interactions;
31
+ - states governance, authorities, and responsibilities;
32
+ - explains the documentation/evidence hierarchy;
33
+ - points to organization-specific controlled procedures and records; and
34
+ - distinguishes the applicable standard, regulatory, audit, and product sources.
35
+
36
+ The manual should be the length and structure needed for the organization. Page count,
37
+ a fixed procedure list, or mirroring standard headings does not prove adequacy.
38
+
39
+ ## Development workflow
40
+
41
+ ### 1. Establish an authorized source baseline
42
+
43
+ Create a controlled source ledger before drafting. At minimum record:
44
+
45
+ - ISO 13485:2016, Edition 3, and authorized location;
46
+ - the applicable EN adoption/amendment/corrigendum if European harmonisation is
47
+ being used;
48
+ - current FDA QMSR/eCFR sources if U.S. operations are in declared scope;
49
+ - current MDSAP Audit Approach if MDSAP is in declared scope;
50
+ - current consolidated MDR or IVDR, OJEU harmonised-standard decisions, and relevant
51
+ MDCG guidance if EU work is in declared scope;
52
+ - ISO 14971/EN A11 and product-specific standards where applicable; and
53
+ - current product/jurisdictional regulations and guidance.
54
+
55
+ For each source, capture publisher, title, edition/version/date, official URL or
56
+ authorized location, access date, owner, currency-review date, impact assessment,
57
+ status, and approval.
58
+
59
+ ### 2. Freeze purpose and scope
60
+
61
+ Record:
62
+
63
+ - legal entities and sites;
64
+ - product types/families and controlled intended-use references;
65
+ - lifecycle activities performed at each site;
66
+ - outsourced processes and interfaces;
67
+ - markets being considered;
68
+ - organizational and physical boundaries;
69
+ - assurance purpose (ISO certification, FDA, MDSAP, EU, internal); and
70
+ - limitations and unresolved applicability decisions.
71
+
72
+ Do not let an agent decide applicability. `Undetermined` remains a blocker until an
73
+ authorized human approves a decision and rationale.
74
+
75
+ ### 3. Map actual process interactions
76
+
77
+ Interview accountable process owners and inspect actual records. Build a process map
78
+ from the organization's work—not from copied standard headings.
79
+
80
+ For each process record:
81
+
82
+ - inputs and outputs;
83
+ - owner, authority, delegate, and escalation;
84
+ - controlled procedure/system;
85
+ - implementation records;
86
+ - interfaces to risk and change control;
87
+ - measures and review method;
88
+ - source/version basis;
89
+ - status and approval.
90
+
91
+ Include management, support, product lifecycle, assurance, feedback, and improvement
92
+ processes. Show how complaints/postmarket data update risk, design, production,
93
+ suppliers, CAPA, and management review.
94
+
95
+ ### 4. Build a controlled cross-reference
96
+
97
+ Create a matrix that links manual statements to:
98
+
99
+ - controlled procedure IDs and revisions;
100
+ - forms and record series;
101
+ - product/device/technical files;
102
+ - risk and traceability evidence;
103
+ - system/software validation;
104
+ - process owners and approvals;
105
+ - source/version criteria; and
106
+ - open gaps/change/CAPA records.
107
+
108
+ Do not describe a referenced document as effective until its approval, effective date,
109
+ training, and availability are evidenced.
110
+
111
+ ### 5. Draft policy-level content
112
+
113
+ Use the fail-closed template in
114
+ `assets/templates/quality-manual-template.md`. Keep statements factual and
115
+ organization-specific:
116
+
117
+ - “The approved process is defined in `<controlled ID/revision>`.”
118
+ - “Evidence is retained in `<controlled record series/location>`.”
119
+ - “`<role>` owns the decision, with approval in `<record ID>`.”
120
+ - “Applicability remains undetermined pending `<authorized review>`.”
121
+
122
+ Avoid:
123
+
124
+ - “The organization is compliant” or “audit ready”;
125
+ - “This template satisfies ISO/FDA/EU requirements”;
126
+ - generic quality policies presented as approved;
127
+ - fixed timelines or retention periods without source/risk basis;
128
+ - unsupported “not applicable” statements;
129
+ - old QSR clause maps presented as current QMSR; and
130
+ - claims that an ISO certificate covers FDA, MDSAP, or EU product conformity.
131
+
132
+ ### 6. Review against evidence
133
+
134
+ Perform independent review in two directions:
135
+
136
+ 1. **Manual to evidence:** every material statement points to a current controlled
137
+ source, procedure, owner, and record set.
138
+ 2. **Evidence to manual:** sampled implementation records match the described scope,
139
+ roles, interactions, and controls.
140
+
141
+ Sample across products, sites, shifts/time periods, suppliers, systems, changes, and
142
+ risk as justified. Record limitations and open gaps.
143
+
144
+ ### 7. Approve, train, release, and maintain
145
+
146
+ Before release:
147
+
148
+ - resolve placeholders;
149
+ - obtain technical, RA/QA, document-control, and authorized management approvals;
150
+ - complete source and applicability reviews;
151
+ - close or formally control open document/process gaps;
152
+ - approve process map and cross-reference;
153
+ - complete affected-person training;
154
+ - verify controlled point-of-use access;
155
+ - assign effective date and obsolete prior revisions; and
156
+ - record maintenance/currency-review triggers.
157
+
158
+ Review when products, sites, roles, processes, suppliers, systems, standards,
159
+ regulations, audit programs, certificates, or postmarket evidence change—not only on
160
+ an arbitrary calendar date.
161
+
162
+ ## Suggested content architecture
163
+
164
+ ### Controlled-document front matter
165
+
166
+ Include document ID, revision, owner, status, effective date, confidentiality,
167
+ controlled location, change record, superseded revision, reviewers, approvers, dates,
168
+ and approval evidence.
169
+
170
+ ### Purpose, limits, and definitions
171
+
172
+ State the intended organizational use and hard boundaries. Use definitions from
173
+ approved organizational and regulatory sources; do not copy protected standard text.
174
+
175
+ ### QMS scope and applicability
176
+
177
+ State entities, sites, products, activities, outsourced processes, and interfaces.
178
+ Reference the approved scope/applicability intake. List unresolved decisions as
179
+ blockers.
180
+
181
+ ### Source/version basis
182
+
183
+ Identify exact ISO, FDA, MDSAP, EU, and product sources separately. Include owner and
184
+ currency-review controls.
185
+
186
+ ### Governance and roles
187
+
188
+ Describe top-management authority, authorized management representative, RA/QA,
189
+ process owners, document/record control, release authorities, audit independence,
190
+ complaint/reportability roles, CAPA/change approval, delegates, and escalation.
191
+
192
+ ### Process architecture
193
+
194
+ At a policy level, describe and cross-reference:
195
+
196
+ - document/record/external-source control;
197
+ - risk management;
198
+ - design/development and transfer/change;
199
+ - suppliers and outsourced processes;
200
+ - production, service, acceptance/release, and traceability;
201
+ - process/equipment/test/software validation;
202
+ - feedback, complaints, postmarket, and vigilance;
203
+ - nonconformity, CAPA, and effectiveness;
204
+ - internal audit and management review;
205
+ - competence/training; and
206
+ - integrated change control.
207
+
208
+ ### Product evidence architecture
209
+
210
+ Explain how product/family files point to requirements, specifications, risk,
211
+ design, validation, production, release, distribution, clinical/performance,
212
+ postmarket, complaint, vigilance, and change evidence. Preserve jurisdiction-specific
213
+ records rather than claiming one file concept replaces another.
214
+
215
+ ### Appendices
216
+
217
+ Use controlled appendices or references for:
218
+
219
+ - procedure/record index;
220
+ - source ledger;
221
+ - scope/product/site register;
222
+ - organization chart/authorities;
223
+ - process interaction map;
224
+ - risk-design-production-postmarket traceability matrix;
225
+ - supplier/outsourced-process register;
226
+ - validation/software inventory;
227
+ - open gap/change/CAPA register; and
228
+ - certificate/audit scope and status register.
229
+
230
+ ## Regime-specific cautions
231
+
232
+ ### FDA QMSR
233
+
234
+ QMSR became effective **2026-02-02**. Describe current Part 820 and relevant FDA
235
+ processes; do not present the former QSR/QSIT structure as current. Link to current
236
+ [21 CFR Part 820](https://www.ecfr.gov/current/title-21/chapter-I/subchapter-H/part-820)
237
+ and [Compliance Program 7382.850](https://www.fda.gov/media/80195/download?attachment).
238
+ An ISO certificate does not exempt a manufacturer from FDA inspection.
239
+
240
+ ### MDSAP
241
+
242
+ Reference current **MDSAP AU P0002.010** (2026-02-02) and declared participating
243
+ jurisdictions. Do not describe an ISO-only audit as MDSAP or an FDA inspection as
244
+ using the MDSAP plan.
245
+
246
+ ### EU MDR/IVDR
247
+
248
+ Reference the current consolidated regulation, applicable conformity-assessment
249
+ route, technical documentation, postmarket/vigilance, economic-operator, and
250
+ notified-body evidence separately. Verify notified-body designation scope in NANDO.
251
+ MDCG guidance is nonbinding and must be version-controlled.
252
+
253
+ ### Certification and accreditation
254
+
255
+ Record the certification body's scope and, if accredited certification is sought, the
256
+ accreditation scope relevant to ISO 13485 technical areas. This does not establish
257
+ notified-body designation or product conformity.
258
+
259
+ For a laboratory, the manual describes a system that an accreditation body assesses —
260
+ the laboratory is accredited, not certified, and the manual must not say otherwise.
261
+ Record the accreditation body, the scope schedule reference, authorized signatories and
262
+ what each may sign, and the rules for using accreditation symbols and endorsement
263
+ wording. Verify current recognition-arrangement phrasing before reproducing it: Global
264
+ Accreditation Cooperation Incorporated replaced ILAC and IAF on 2026-01-01, so legacy
265
+ "ILAC MRA" or "IAF MLA" wording may be transitional rather than current.
266
+
267
+ ## Review questions
268
+
269
+ - Does the scope match actual sites, products, and activities?
270
+ - Are all applicability decisions owned and approved by authorized humans?
271
+ - Does every statement link to current controlled evidence?
272
+ - Are records sampled, not just procedures listed?
273
+ - Are risk, design, production, suppliers, validation/software, and postmarket
274
+ connected?
275
+ - Are complaint/vigilance and CAPA decisions owned by authorized roles?
276
+ - Do changes link to validation, training, source/version, and product impacts?
277
+ - Are ISO, FDA, MDSAP, EU, and product-specific claims clearly separated?
278
+ - Are certificate, notified-body, and accreditation scopes accurately bounded?
279
+ - Does the manual avoid compliance, conformity, certification, and readiness claims?
280
+
281
+ Use `scripts/gap_analyzer.py` and `scripts/validate_evidence_manifest.py` only to
282
+ identify structural gaps before substantive human review.
@@ -0,0 +1,357 @@
1
+ # Official Source Ledger
2
+
3
+ **Baseline research date:** 2026-07-23 — device lanes (ISO 13485, ISO 14971, FDA
4
+ QMSR, MDSAP, EU MDR/IVDR), established with targeted `parallel-cli search` and
5
+ `parallel-cli extract` against official publishers and regulator/program sites.
6
+
7
+ **Extension research date:** 2026-07-26 — laboratory lanes (ISO/IEC 17025,
8
+ ISO 15189), ISO/TR 24971, and accreditation-scheme documents, established with web
9
+ search against official publishers, accreditation bodies, and CMS.
10
+
11
+ **Purpose:** version baseline for this skill; not legal advice, an applicability
12
+ decision, certification or accreditation criteria, or a substitute for controlled
13
+ source copies.
14
+
15
+ **Provenance limitation on the 2026-07-26 additions.** `iso.org` returned HTTP 403
16
+ to automated fetching during that research, so the ISO catalogue metadata below was
17
+ taken from search-result summaries and from accreditation-body and ILAC pages rather
18
+ than read directly off the ISO catalogue page. Entries carrying that limitation are
19
+ marked **[confirm on iso.org]**. Confirm each against the linked official page, or an
20
+ authorized copy, before relying on an edition, date, or stage.
21
+
22
+ Recheck every source before operational use. Web pages and consolidated texts can
23
+ change after the research date.
24
+
25
+ ## ISO standards and copyright
26
+
27
+ ### ISO 13485:2016
28
+
29
+ - Official page:
30
+ [ISO 13485:2016](https://www.iso.org/standard/59752.html)
31
+ - Verified metadata: Edition 3; publication date 2016-03; stage 90.93
32
+ (confirmed); 2025 systematic review closed 2025-06-05 and confirmation recorded
33
+ 2025-10-31.
34
+ - Use: identifies the current international edition and lifecycle status.
35
+ - Limitation: the ISO page is not the complete normative text. Obtain an authorized
36
+ copy.
37
+
38
+ ### EN ISO 13485:2016/A11:2021 distinction
39
+
40
+ - Current Commission index:
41
+ [Harmonised standards](https://health.ec.europa.eu/medical-devices-topics-interest/harmonised-standards_en)
42
+ - Current MDR decision:
43
+ [Consolidated Decision (EU) 2021/1182, 2026-06-17](https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:02021D1182-20260617)
44
+ - IVDR amendment decision:
45
+ [Decision (EU) 2022/729](https://eur-lex.europa.eu/eli/dec_impl/2022/729/oj)
46
+ - Verified fact: current EU lists include EN ISO 13485:2016, AC:2018, and
47
+ A11:2021. A11:2021 is a European EN amendment, not an ISO international
48
+ “Amendment 1:2021.”
49
+ - Limitation: verify the latest OJEU citation and the exact requirements for which
50
+ presumption of conformity is claimed; use of harmonised standards is not a blanket
51
+ product-conformity decision.
52
+
53
+ ### ISO 14971:2019 and European A11
54
+
55
+ - Official page:
56
+ [ISO 14971:2019](https://www.iso.org/standard/72704.html)
57
+ - Verified metadata: Edition 3; publication 2019-12; reviewed and confirmed in 2025.
58
+ - EU source:
59
+ [Decision (EU) 2022/757](https://eur-lex.europa.eu/eli/dec_impl/2022/757/oj/eng)
60
+ - Verified fact: EN ISO 14971:2019/A11:2021 is cited for MDR and, through the
61
+ corresponding IVDR decision, IVDR support. A11 is European; it does not change the
62
+ international ISO 14971 normative part.
63
+ - Limitation: risk-management evidence remains product- and jurisdiction-specific.
64
+
65
+ ### ISO/TR 24971:2020
66
+
67
+ - Official page:
68
+ [ISO/TR 24971:2020](https://www.iso.org/standard/74437.html)
69
+ - Verified metadata: Edition 2; guidance companion to ISO 14971:2019, with the same
70
+ clause structure and numbering. **[confirm on iso.org]**
71
+ - Verified status: a Technical Report. Its guidance is informative, not normative, and
72
+ conformity is claimed to ISO 14971, never to ISO/TR 24971.
73
+ - Limitation: a TR cannot be used to relax or reinterpret a normative requirement.
74
+ Record which guidance the organization adopted and why.
75
+
76
+ ### ISO/IEC 17025:2017
77
+
78
+ - Official page:
79
+ [ISO/IEC 17025:2017](https://www.iso.org/standard/66912.html)
80
+ - Landing page:
81
+ [ISO/IEC 17025 — Testing and calibration laboratories](https://www.iso.org/ISO-IEC-17025-testing-and-calibration-laboratories.html)
82
+ - Verified metadata: Edition 3; published 2017; no successor edition identified at the
83
+ research date. **[confirm on iso.org]**
84
+ - Use: identifies the current edition for laboratory competence work.
85
+ - Limitation: ISO/IEC 17025 is an accreditation standard, not a certification scheme
86
+ and not a product standard. Accreditation is granted by an accreditation body for a
87
+ defined scope of laboratory activities; nothing in this skill grants or predicts it.
88
+
89
+ ### ISO 15189:2022
90
+
91
+ - Official page:
92
+ [ISO 15189:2022](https://www.iso.org/standard/76677.html)
93
+ - ILAC announcement:
94
+ [ISO 15189:2022 for medical labs published](https://ilac.org/latest_ilac_news/iso-151892022-for-medical-labs-published/)
95
+ - Verified metadata: Edition 4; published December 2022; cancels and replaces
96
+ ISO 15189:2012. **[confirm on iso.org]**
97
+ - Verified structural facts: the 2022 edition aligns structurally with
98
+ ISO/IEC 17025:2017 and incorporates point-of-care testing requirements previously
99
+ held in ISO 22870. Do not cite ISO 22870 as a separate current POCT basis without
100
+ confirming its status.
101
+ - Verified transition: the ILAC-agreed transition period for accredited medical
102
+ laboratories ran to **December 2025**. Treat the 2022 edition as implemented, not
103
+ upcoming; a 2012-based quality system is out of date, not "in transition."
104
+ - Limitation: accreditation scope is per laboratory, per location, and per
105
+ examination. It is not organization-wide and not equivalent to licensure.
106
+
107
+ ### ISO copyright
108
+
109
+ - Official page: [ISO copyright](https://www.iso.org/copyright.html)
110
+ - Verified fact: ISO publications are copyright protected; unauthorized copying,
111
+ scanning, or distribution is prohibited, and reproduction requires permission.
112
+ - Operational rule: this skill summarizes processes and bibliographic metadata only.
113
+ Do not paste or generate copyrighted clause text.
114
+
115
+ ## United States: FDA QMSR
116
+
117
+ ### Final rule
118
+
119
+ - Source:
120
+ [Medical Devices; Quality System Regulation Amendments](https://www.federalregister.gov/documents/2024/02/02/2024-01709/medical-devices-quality-system-regulation-amendments)
121
+ - Citation/date: 89 FR 7496; published 2024-02-02.
122
+ - Verified effective date: **2026-02-02**.
123
+ - Verified boundary: ISO certification does not exempt a manufacturer from FDA
124
+ inspection; FDA does not issue ISO 13485 certificates.
125
+ - Correction:
126
+ [2024 correction](https://www.federalregister.gov/documents/2024/10/15/2024-23701/medical-devices-quality-system-regulation-amendments-correction).
127
+ - Later source:
128
+ [2025 QMSR technical amendments](https://www.federalregister.gov/documents/2025/12/04/2025-21955/medical-devices-quality-management-system-regulation-technical-amendments).
129
+ Use the current eCFR rather than reconstructing current requirements from the
130
+ original final rule alone.
131
+
132
+ ### FDA QMSR landing page
133
+
134
+ - Source:
135
+ [Quality Management System Regulation (QMSR)](https://www.fda.gov/medical-devices/postmarket-requirements-devices/quality-management-system-regulation-qmsr)
136
+ - Page update: 2026-02-02.
137
+ - Verified current state: QMSR became effective 2026-02-02; it incorporates
138
+ ISO 13485:2016 and ISO 9000:2015 Clause 3 by reference, with FDA provisions and
139
+ other applicable FDA requirements controlling as stated in the regulation.
140
+ - Verified inspection transition: FDA stopped using QSIT and began the inspection
141
+ process in Compliance Program 7382.850 on 2026-02-02.
142
+
143
+ ### Current eCFR
144
+
145
+ - Source:
146
+ [21 CFR Part 820](https://www.ecfr.gov/current/title-21/chapter-I/subchapter-H/part-820)
147
+ - Verified current title: *Quality Management System Regulation*.
148
+ - Verified current structure: Subpart A contains current general provisions; Subpart B
149
+ contains supplemental provisions; remaining legacy subparts are reserved.
150
+ - Verified incorporation: ISO 13485:2016(E), Third edition, March 1, 2016, and
151
+ ISO 9000:2015 Clause 3.
152
+ - Operational rule: use the current eCFR and linked current regulations. Do not use
153
+ the former QSR section structure as a current requirements map.
154
+ - Limitation: eCFR is continuously updated and authoritative but unofficial; consult
155
+ official CFR/Federal Register publications when legal status matters.
156
+
157
+ ### FDA QMSR FAQ
158
+
159
+ - Source:
160
+ [QMSR Frequently Asked Questions](https://www.fda.gov/medical-devices/quality-management-system-regulation-qmsr/quality-management-system-regulation-frequently-asked-questions)
161
+ - Page update: 2026-02-02.
162
+ - Verified implementation status: FDA began enforcing QMSR on the effective date.
163
+ - Verified records point: FDA investigators may review QMS records created before
164
+ 2026-02-02. The former exemption for management-review, quality-audit, and
165
+ supplier-audit reports was not retained.
166
+ - Verified boundary: FDA QMSR inspections do not follow the MDSAP audit plan; an
167
+ ISO certificate does not replace or prevent FDA inspection.
168
+ - Verified access: FDA points to ANSI read-only IBR access for incorporated standards.
169
+
170
+ ### Current inspection program
171
+
172
+ - Source:
173
+ [Inspection of Medical Device Manufacturers Compliance Program 7382.850](https://www.fda.gov/media/80195/download?attachment)
174
+ - Effective date: 2026-02-02.
175
+ - Verified use: current FDA inspection process aligned to QMSR; QSIT and the
176
+ superseded device inspection programs are no longer used.
177
+ - Supplemental education:
178
+ [April 2026 FDA town hall](https://www.fda.gov/medical-devices/medical-devices-news-and-events/town-hall-fdas-quality-management-system-regulation-qmsr-medical-device-risk-based-inspections).
179
+ - Limitation: prepare evidence for actual applicable FDA requirements; this skill
180
+ does not predict inspection scope, classification, or enforcement outcome.
181
+
182
+ ## MDSAP and IMDRF
183
+
184
+ ### Current MDSAP Audit Approach
185
+
186
+ - Source:
187
+ [MDSAP Audit Approach](https://www.mdsap.global/documents/library/audit-approach)
188
+ - Current document: **MDSAP AU P0002.010**.
189
+ - Version date: **2026-02-02**.
190
+ - Verified high-level model: process-based regulatory audit by recognized Auditing
191
+ Organizations, with four primary process areas, supporting purchasing linkages, a
192
+ risk-management foundation, jurisdiction-specific requirements, and a three-year
193
+ audit cycle.
194
+ - Superseded baseline observed during research: FDA-hosted P0002.009 dated
195
+ 2024-08-06. Use the current MDSAP.global library instead.
196
+
197
+ ### MDSAP program and IMDRF foundation
198
+
199
+ - Current program site:
200
+ [MDSAP.global](https://www.mdsap.global/)
201
+ - IMDRF background:
202
+ [IMDRF MDSAP working group](https://www.imdrf.org/working-groups/medical-device-single-audit-program-mdsap)
203
+ - FDA program page:
204
+ [Medical Device Single Audit Program](https://www.fda.gov/medical-devices/cdrh-international-affairs/medical-device-single-audit-program-mdsap)
205
+ - Verified status: IMDRF development work moved to implementation; current MDSAP
206
+ documents are managed on MDSAP.global.
207
+ - Boundary: an MDSAP audit is not generic ISO certification, an FDA inspection plan,
208
+ or EU notified-body conformity assessment.
209
+
210
+ ## European Union: MDR, IVDR, and MDCG
211
+
212
+ ### MDR
213
+
214
+ - Source:
215
+ [Regulation (EU) 2017/745, consolidated 2026-01-01](https://eur-lex.europa.eu/eli/reg/2017/745/2026-01-01/eng)
216
+ - Verified status as of research: consolidated version dated 2026-01-01.
217
+ - Relevant scope for this skill: manufacturer QMS, technical documentation,
218
+ conformity assessment, notified bodies, postmarket surveillance, vigilance, and
219
+ market surveillance.
220
+ - Limitation: consolidated texts are documentation tools; authentic acts are those
221
+ published in the Official Journal.
222
+
223
+ ### IVDR
224
+
225
+ - Source:
226
+ [Regulation (EU) 2017/746, consolidated 2025-01-10](https://eur-lex.europa.eu/eli/reg/2017/746/2025-01-10/eng)
227
+ - Verified status as of research: 2025-01-10 was the current consolidated version.
228
+ - Relevant scope for this skill: IVD QMS, technical/performance documentation,
229
+ conformity assessment, notified bodies, postmarket surveillance, vigilance, and
230
+ market surveillance.
231
+ - Limitation: transitional provisions and device-specific deadlines require current,
232
+ authorized analysis; this skill does not calculate them.
233
+
234
+ ### MDCG guidance
235
+
236
+ - Source:
237
+ [MDCG endorsed documents and other guidance](https://health.ec.europa.eu/medical-devices-sector/new-regulations/guidance-mdcg-endorsed-documents-and-other-guidance_en)
238
+ - Verified legal status: MDCG guidance is not legally binding; it expresses a common
239
+ implementation understanding and is regularly revised or archived.
240
+ - Relevant current item:
241
+ [MDCG 2025-10, post-market surveillance](https://health.ec.europa.eu/document/download/a9ad86b7-1b8e-4bae-beb4-48b2b3ed2f05_en?filename=mdcg_2025-10_en.pdf),
242
+ published December 2025.
243
+ - Other items must be selected by device, role, transition, and conformity route.
244
+
245
+ ## Notified bodies, certification, and accreditation
246
+
247
+ ### EU notified bodies
248
+
249
+ - Commission overview:
250
+ [Notified bodies for medical devices](https://health.ec.europa.eu/medical-devices-topics-interest/notified-bodies-medical-devices_en)
251
+ - Official list:
252
+ [NANDO](https://webgate.ec.europa.eu/single-market-compliance-space/notified-bodies)
253
+ - Verified boundary: Member States designate and notify bodies for defined
254
+ legislation, conformity-assessment tasks, and product/designation codes. NANDO
255
+ lists the current notified scope.
256
+ - Operational rule: verify legislation, annex/task, and designation-code scope.
257
+ Accreditation or ISO certification alone is not notified-body designation.
258
+
259
+ ### ISO 13485 certification-body accreditation
260
+
261
+ - Current Global ACI documents:
262
+ [Global ACI document library](https://global-aci.org/en/global_aci-documents/)
263
+ - Current cross-reference:
264
+ [Global ACI–IAF/ILAC table, version 1.2, 2026-06-10](https://sys.global-aci.org/uploads/documents/Global_ACI_IAF_and_ILAC_Document_Cross-Reference_Table_10_June_20262.pdf)
265
+ - Carried document:
266
+ [IAF MD 9:2023 Issue 5](https://sys.global-aci.org/uploads/documents/IAF_MD9_Issue_5_20112023.pdf)
267
+ - Verified transition: Global Accreditation Cooperation Incorporated began full
268
+ operations on 2026-01-01, replacing IAF/ILAC operational functions. The
269
+ 2026-06-10 table showed successor Global ACI documents for former MD 8/MD 9 as
270
+ in process while the prior documents remained in the current library.
271
+ - Verified boundary: MD 9 concerns bodies auditing/certifying management systems to
272
+ ISO 13485 under ISO/IEC 17021-1. It does not establish product conformity,
273
+ notified-body designation, regulatory applicability, or market authorization.
274
+
275
+ ### Accreditation: GLOBAC and the recognition arrangement
276
+
277
+ - Launch announcement:
278
+ [Global Accreditation Cooperation Incorporated launch](https://iaf.nu/en/news/global-accreditation-cooperation-incorporated-launch-unifies-international-accreditation-organisations-and-strengthens-worldwide-trust/)
279
+ - Transition guidance:
280
+ [Specifying use of GLOBAC accreditation](https://ilac.org/latest_ilac_news/iaf-and-ilac-release-information-on-specifying-use-of-globac-accreditation/)
281
+ - Verified transition: Global Accreditation Cooperation Incorporated commenced full
282
+ operations on **2026-01-01**, bringing together the former ILAC and IAF and
283
+ launching its own Multilateral Recognition Arrangement. Certificates and accredited
284
+ results issued under the former IAF MLA / ILAC MRA continue to be recognized during
285
+ the transition.
286
+ - Operational rule: check the *current* recognition-arrangement wording, logo rules,
287
+ and document designations before reproducing any accreditation claim in a document.
288
+ Legacy "ILAC MRA" / "IAF MLA" phrasing may be transitional rather than current.
289
+ - Boundary: recognition arrangements concern accreditation bodies. They do not make an
290
+ accredited result a regulatory approval or a product conformity decision.
291
+
292
+ ### Accreditation: traceability and decision-rule policy
293
+
294
+ - Policy series:
295
+ [ILAC policy series (P documents)](https://ilac.org/publications-and-resources/ilac-policy-series/)
296
+ - Metrological traceability: **ILAC P10:07/2020**, implementation date July 2021,
297
+ revised to reflect ISO/IEC 17025:2017.
298
+ - Decision rules and statements of conformity: **ILAC G8:09/2019**; JCGM 106:2012 /
299
+ ISO/IEC Guide 98-4 is the companion metrological basis.
300
+ - Limitation and open item: no GLOBAC renumbering of the P/G series was identified at
301
+ the research date, and the ILAC designations above were still in use. Confirm the
302
+ current designation and issue before citing either document in a controlled
303
+ procedure — this is the most likely item in this ledger to have moved.
304
+ - Boundary: a stated decision rule is a documented rule for declaring conformity
305
+ against a specification. It is not a compliance determination, and this skill does
306
+ not evaluate whether a chosen rule is fit for a customer's purpose.
307
+
308
+ ### United States medical laboratories: CLIA is a separate lane
309
+
310
+ - CMS program page:
311
+ [Clinical Laboratory Improvement Amendments (CLIA)](https://www.cms.gov/medicare/quality/clinical-laboratory-improvement-amendments)
312
+ - Accreditation and exemption page:
313
+ [CLIA accreditation and testing](https://www.cms.gov/medicare/quality/clinical-laboratory-improvement-amendments/accreditation-exemptions)
314
+ - Approved accreditation organizations:
315
+ [Specialty/subspecialty information for approved AOs](https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/Downloads/AOList.pdf)
316
+ - Verified facts: CLIA certification by CMS is mandatory before a US laboratory may
317
+ accept human specimens for testing. CMS approves a limited set of accreditation
318
+ organizations whose standards must meet or exceed CLIA requirements; approval is
319
+ reapplied for every six years or more often. Seven approved AOs were reported at the
320
+ research date — read the current AO list rather than repeating that count.
321
+ - Verified boundary: **ISO 15189 accreditation does not satisfy CLIA and cannot
322
+ replace a CLIA-based accreditation for a US laboratory.** Deemed status flows only
323
+ from a CMS-approved accreditation organization's program, not from ISO 15189 itself.
324
+ - Program note: the CAP 15189 program is layered on top of CAP Laboratory
325
+ Accreditation Program accreditation rather than offered as a standalone substitute.
326
+ See [CAP 15189](https://www.cap.org/laboratory-improvement/accreditation/cap-15189-accreditation-program);
327
+ confirm current program prerequisites with CAP.
328
+ - Operational rule: never present an ISO 15189 readiness output as CLIA compliance,
329
+ deemed status, licensure, or an inspection result. Keep the CLIA decision with the
330
+ authorized laboratory director and compliance owner.
331
+
332
+ ## Research queries used
333
+
334
+ Parallel searches/extracts covered:
335
+
336
+ - ISO 13485 edition, review/confirmation, and amendment metadata;
337
+ - ISO versus EN A11:2021 distinction and current EU citations;
338
+ - FDA final rule, QMSR page/FAQ, eCFR Part 820, and Compliance Program 7382.850;
339
+ - current MDSAP/IMDRF program and Audit Approach version;
340
+ - current MDR/IVDR consolidated versions and MDCG guidance;
341
+ - ISO 14971 and EN A11 status;
342
+ - NANDO/notified-body designation boundaries; and
343
+ - the 2026 Global ACI transition and current MD 8/MD 9 documents.
344
+
345
+ The 2026-07-26 extension searched:
346
+
347
+ - ISO/IEC 17025 revision status and whether a successor edition exists;
348
+ - ISO 15189 edition, POCT consolidation, and the ILAC transition deadline;
349
+ - ISO/TR 24971 edition and its status relative to ISO 14971;
350
+ - the GLOBAC launch date, its MRA, and transitional recognition wording;
351
+ - ILAC P10 and ILAC G8 current issues; and
352
+ - CMS CLIA certification, approved accreditation organizations, and whether
353
+ ISO 15189 confers deemed status.
354
+
355
+ No Parallel research JSON was saved in the repository. Several 2026-07-26 results came
356
+ from secondary summaries of ISO catalogue pages because `iso.org` refused automated
357
+ access; those entries are marked **[confirm on iso.org]** above.