@researai/deepscientist 1.5.17 → 1.6.0

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 (894) hide show
  1. package/AGENTS.md +309 -130
  2. package/AISB/catalog/aisb.b1.agentic_coding.yaml +244 -0
  3. package/AISB/catalog/aisb.b10.climate_earth.yaml +235 -0
  4. package/AISB/catalog/aisb.b11.model_efficiency.yaml +231 -0
  5. package/AISB/catalog/aisb.b12.embodied_ai.yaml +238 -0
  6. package/AISB/catalog/aisb.b2.agent_systems.yaml +229 -0
  7. package/AISB/catalog/aisb.b3.self_evolving_rl.yaml +237 -0
  8. package/AISB/catalog/aisb.b4.lm_reasoning.yaml +240 -0
  9. package/AISB/catalog/aisb.b5.math_proof.yaml +235 -0
  10. package/AISB/catalog/aisb.b6.research_process.yaml +243 -0
  11. package/AISB/catalog/aisb.b7.multimodal_fusion.yaml +232 -0
  12. package/AISB/catalog/aisb.b8.lifesci_drug.yaml +275 -0
  13. package/AISB/catalog/aisb.b9.material_science.yaml +237 -0
  14. package/AISB/catalog/aisb.t3.001_savvy.yaml +159 -0
  15. package/AISB/catalog/aisb.t3.001_savvy.zh.yaml +121 -0
  16. package/AISB/catalog/aisb.t3.002_pinet.yaml +189 -0
  17. package/AISB/catalog/aisb.t3.002_pinet.zh.yaml +130 -0
  18. package/AISB/catalog/aisb.t3.004_decentralattn.yaml +184 -0
  19. package/AISB/catalog/aisb.t3.004_decentralattn.zh.yaml +153 -0
  20. package/AISB/catalog/aisb.t3.005_tsae.yaml +193 -0
  21. package/AISB/catalog/aisb.t3.005_tsae.zh.yaml +139 -0
  22. package/AISB/catalog/aisb.t3.006_physense.yaml +194 -0
  23. package/AISB/catalog/aisb.t3.006_physense.zh.yaml +118 -0
  24. package/AISB/catalog/aisb.t3.007_reasoningiqa.yaml +169 -0
  25. package/AISB/catalog/aisb.t3.007_reasoningiqa.zh.yaml +133 -0
  26. package/AISB/catalog/aisb.t3.008_meanflows.yaml +188 -0
  27. package/AISB/catalog/aisb.t3.008_meanflows.zh.yaml +140 -0
  28. package/AISB/catalog/aisb.t3.009_scoremissing.yaml +179 -0
  29. package/AISB/catalog/aisb.t3.009_scoremissing.zh.yaml +119 -0
  30. package/AISB/catalog/aisb.t3.010_suitabilityfilter.yaml +221 -0
  31. package/AISB/catalog/aisb.t3.010_suitabilityfilter.zh.yaml +141 -0
  32. package/AISB/catalog/aisb.t3.011_osd.yaml +206 -0
  33. package/AISB/catalog/aisb.t3.011_osd.zh.yaml +163 -0
  34. package/AISB/catalog/aisb.t3.012_efficientqat.yaml +206 -0
  35. package/AISB/catalog/aisb.t3.012_efficientqat.zh.yaml +159 -0
  36. package/AISB/catalog/aisb.t3.013_appl.yaml +152 -0
  37. package/AISB/catalog/aisb.t3.013_appl.zh.yaml +126 -0
  38. package/AISB/catalog/aisb.t3.014_piguard.yaml +207 -0
  39. package/AISB/catalog/aisb.t3.014_piguard.zh.yaml +164 -0
  40. package/AISB/catalog/aisb.t3.015_frspec.yaml +209 -0
  41. package/AISB/catalog/aisb.t3.015_frspec.zh.yaml +163 -0
  42. package/AISB/catalog/aisb.t3.016_mathfusion.yaml +166 -0
  43. package/AISB/catalog/aisb.t3.016_mathfusion.zh.yaml +145 -0
  44. package/AISB/catalog/aisb.t3.017_multimodalglp.yaml +171 -0
  45. package/AISB/catalog/aisb.t3.017_multimodalglp.zh.yaml +122 -0
  46. package/AISB/catalog/aisb.t3.018_cotsynth.yaml +206 -0
  47. package/AISB/catalog/aisb.t3.018_cotsynth.zh.yaml +162 -0
  48. package/AISB/catalog/aisb.t3.019_dyscaleut.yaml +211 -0
  49. package/AISB/catalog/aisb.t3.019_dyscaleut.zh.yaml +148 -0
  50. package/AISB/catalog/aisb.t3.020_aristotle.yaml +173 -0
  51. package/AISB/catalog/aisb.t3.020_aristotle.zh.yaml +119 -0
  52. package/AISB/catalog/aisb.t3.021_tokenrecycling.yaml +160 -0
  53. package/AISB/catalog/aisb.t3.021_tokenrecycling.zh.yaml +129 -0
  54. package/AISB/catalog/aisb.t3.022_chainofreasoning.yaml +204 -0
  55. package/AISB/catalog/aisb.t3.022_chainofreasoning.zh.yaml +161 -0
  56. package/AISB/catalog/aisb.t3.023_guidedembed.yaml +211 -0
  57. package/AISB/catalog/aisb.t3.023_guidedembed.zh.yaml +189 -0
  58. package/AISB/catalog/aisb.t3.024_outputcentric.yaml +148 -0
  59. package/AISB/catalog/aisb.t3.024_outputcentric.zh.yaml +131 -0
  60. package/AISB/catalog/aisb.t3.025_deeper.yaml +143 -0
  61. package/AISB/catalog/aisb.t3.025_deeper.zh.yaml +116 -0
  62. package/AISB/catalog/aisb.t3.026_gartkg.yaml +195 -0
  63. package/AISB/catalog/aisb.t3.026_gartkg.zh.yaml +127 -0
  64. package/AISB/catalog/aisb.t3.027_citeeval.yaml +182 -0
  65. package/AISB/catalog/aisb.t3.027_citeeval.zh.yaml +135 -0
  66. package/AISB/catalog/aisb.t3.028_sbam.yaml +206 -0
  67. package/AISB/catalog/aisb.t3.028_sbam.zh.yaml +166 -0
  68. package/AISB/catalog/aisb.t3.029_cdqgeoembed.yaml +224 -0
  69. package/AISB/catalog/aisb.t3.029_cdqgeoembed.zh.yaml +142 -0
  70. package/AISB/catalog/aisb.t3.030_processrm.yaml +211 -0
  71. package/AISB/catalog/aisb.t3.030_processrm.zh.yaml +166 -0
  72. package/AISB/catalog/aisb.t3.031_circuitstability.yaml +172 -0
  73. package/AISB/catalog/aisb.t3.031_circuitstability.zh.yaml +134 -0
  74. package/AISB/catalog/aisb.t3.032_ptsolver.yaml +169 -0
  75. package/AISB/catalog/aisb.t3.032_ptsolver.zh.yaml +135 -0
  76. package/AISB/catalog/aisb.t3.033_gcse.yaml +144 -0
  77. package/AISB/catalog/aisb.t3.033_gcse.zh.yaml +126 -0
  78. package/AISB/catalog/aisb.t3.034_ensemblewm.yaml +183 -0
  79. package/AISB/catalog/aisb.t3.034_ensemblewm.zh.yaml +146 -0
  80. package/AISB/catalog/aisb.t3.035_moralvalueswa.yaml +207 -0
  81. package/AISB/catalog/aisb.t3.035_moralvalueswa.zh.yaml +165 -0
  82. package/AISB/catalog/aisb.t3.036_weakstrongpref.yaml +210 -0
  83. package/AISB/catalog/aisb.t3.036_weakstrongpref.zh.yaml +194 -0
  84. package/AISB/catalog/aisb.t3.037_dementiamask.yaml +172 -0
  85. package/AISB/catalog/aisb.t3.037_dementiamask.zh.yaml +132 -0
  86. package/AISB/catalog/aisb.t3.038_tinysam.yaml +284 -0
  87. package/AISB/catalog/aisb.t3.038_tinysam.zh.yaml +240 -0
  88. package/AISB/catalog/aisb.t3.039_calf.yaml +224 -0
  89. package/AISB/catalog/aisb.t3.039_calf.zh.yaml +194 -0
  90. package/AISB/catalog/aisb.t3.040_graniteguardian.yaml +199 -0
  91. package/AISB/catalog/aisb.t3.040_graniteguardian.zh.yaml +174 -0
  92. package/AISB/catalog/aisb.t3.041_amdm.yaml +149 -0
  93. package/AISB/catalog/aisb.t3.041_amdm.zh.yaml +137 -0
  94. package/AISB/catalog/aisb.t3.042_xpatch.yaml +216 -0
  95. package/AISB/catalog/aisb.t3.042_xpatch.zh.yaml +182 -0
  96. package/AISB/catalog/aisb.t3.043_vhm.yaml +268 -0
  97. package/AISB/catalog/aisb.t3.043_vhm.zh.yaml +193 -0
  98. package/AISB/catalog/aisb.t3.044_rgvi.yaml +224 -0
  99. package/AISB/catalog/aisb.t3.044_rgvi.zh.yaml +176 -0
  100. package/AISB/catalog/aisb.t3.045_pslstm.yaml +203 -0
  101. package/AISB/catalog/aisb.t3.045_pslstm.zh.yaml +179 -0
  102. package/AISB/catalog/aisb.t3.046_nonstatts.yaml +208 -0
  103. package/AISB/catalog/aisb.t3.046_nonstatts.zh.yaml +194 -0
  104. package/AISB/catalog/aisb.t3.047_timepfn.yaml +156 -0
  105. package/AISB/catalog/aisb.t3.047_timepfn.zh.yaml +124 -0
  106. package/AISB/catalog/aisb.t3.048_proxyspex.yaml +148 -0
  107. package/AISB/catalog/aisb.t3.048_proxyspex.zh.yaml +125 -0
  108. package/AISB/catalog/aisb.t3.049_hogwildinference.yaml +183 -0
  109. package/AISB/catalog/aisb.t3.049_hogwildinference.zh.yaml +138 -0
  110. package/AISB/catalog/aisb.t3.050_causalpfn.yaml +214 -0
  111. package/AISB/catalog/aisb.t3.050_causalpfn.zh.yaml +190 -0
  112. package/AISB/catalog/aisb.t3.051_flashtp.yaml +169 -0
  113. package/AISB/catalog/aisb.t3.051_flashtp.zh.yaml +124 -0
  114. package/AISB/catalog/aisb.t3.052_nsdiff.yaml +155 -0
  115. package/AISB/catalog/aisb.t3.052_nsdiff.zh.yaml +138 -0
  116. package/AISB/catalog/aisb.t3.053_k2vae.yaml +158 -0
  117. package/AISB/catalog/aisb.t3.053_k2vae.zh.yaml +132 -0
  118. package/AISB/catalog/aisb.t3.054_timebase.yaml +178 -0
  119. package/AISB/catalog/aisb.t3.054_timebase.zh.yaml +158 -0
  120. package/AISB/catalog/aisb.t3.055_csbrain.yaml +238 -0
  121. package/AISB/catalog/aisb.t3.055_csbrain.zh.yaml +184 -0
  122. package/AISB/catalog/aisb.t3.056_infosam.yaml +224 -0
  123. package/AISB/catalog/aisb.t3.056_infosam.zh.yaml +189 -0
  124. package/AISB/catalog/aisb.t3.057_mdreid.yaml +129 -0
  125. package/AISB/catalog/aisb.t3.057_mdreid.zh.yaml +117 -0
  126. package/AISB/catalog/aisb.t3.058_mindglitch.yaml +171 -0
  127. package/AISB/catalog/aisb.t3.058_mindglitch.zh.yaml +145 -0
  128. package/AISB/catalog/aisb.t3.059_selfsupervised.yaml +154 -0
  129. package/AISB/catalog/aisb.t3.059_selfsupervised.zh.yaml +125 -0
  130. package/AISB/catalog/aisb.t3.060_iaggad.yaml +121 -0
  131. package/AISB/catalog/aisb.t3.060_iaggad.zh.yaml +100 -0
  132. package/AISB/catalog/aisb.t3.061_hsgkn.yaml +136 -0
  133. package/AISB/catalog/aisb.t3.061_hsgkn.zh.yaml +113 -0
  134. package/AISB/catalog/aisb.t3.062_visionts.yaml +237 -0
  135. package/AISB/catalog/aisb.t3.062_visionts.zh.yaml +216 -0
  136. package/AISB/catalog/aisb.t3.063_tsrag.yaml +162 -0
  137. package/AISB/catalog/aisb.t3.063_tsrag.zh.yaml +138 -0
  138. package/AISB/catalog/aisb.t3.064_pir.yaml +221 -0
  139. package/AISB/catalog/aisb.t3.064_pir.zh.yaml +197 -0
  140. package/AISB/catalog/aisb.t3.065_proteinbinding.yaml +234 -0
  141. package/AISB/catalog/aisb.t3.065_proteinbinding.zh.yaml +167 -0
  142. package/AISB/catalog/aisb.t3.066_tropicalattention.yaml +267 -0
  143. package/AISB/catalog/aisb.t3.066_tropicalattention.zh.yaml +229 -0
  144. package/AISB/catalog/aisb.t3.067_kanad.yaml +193 -0
  145. package/AISB/catalog/aisb.t3.067_kanad.zh.yaml +167 -0
  146. package/AISB/catalog/aisb.t3.068_sempo.yaml +187 -0
  147. package/AISB/catalog/aisb.t3.068_sempo.zh.yaml +148 -0
  148. package/AISB/catalog/aisb.t3.069_treehfd.yaml +129 -0
  149. package/AISB/catalog/aisb.t3.069_treehfd.zh.yaml +111 -0
  150. package/AISB/catalog/aisb.t3.070_certifiedunlearning.yaml +224 -0
  151. package/AISB/catalog/aisb.t3.070_certifiedunlearning.zh.yaml +171 -0
  152. package/AISB/catalog/aisb.t3.071_neuralmjd.yaml +142 -0
  153. package/AISB/catalog/aisb.t3.071_neuralmjd.zh.yaml +120 -0
  154. package/AISB/catalog/aisb.t3.072_fedgmt.yaml +181 -0
  155. package/AISB/catalog/aisb.t3.072_fedgmt.zh.yaml +158 -0
  156. package/AISB/catalog/aisb.t3.073_rld.yaml +161 -0
  157. package/AISB/catalog/aisb.t3.073_rld.zh.yaml +129 -0
  158. package/AISB/catalog/aisb.t3.074_lsvi.yaml +163 -0
  159. package/AISB/catalog/aisb.t3.074_lsvi.zh.yaml +129 -0
  160. package/AISB/catalog/aisb.t3.075_treeslicedentropy.yaml +201 -0
  161. package/AISB/catalog/aisb.t3.075_treeslicedentropy.zh.yaml +148 -0
  162. package/AISB/catalog/aisb.t3.076_aanet.yaml +169 -0
  163. package/AISB/catalog/aisb.t3.076_aanet.zh.yaml +129 -0
  164. package/AISB/catalog/aisb.t3.077_cmnn.yaml +199 -0
  165. package/AISB/catalog/aisb.t3.077_cmnn.zh.yaml +165 -0
  166. package/AISB/catalog/aisb.t3.078_conformalanomaly.yaml +146 -0
  167. package/AISB/catalog/aisb.t3.078_conformalanomaly.zh.yaml +117 -0
  168. package/AISB/catalog/aisb.t3.079_dpfkmeans.yaml +131 -0
  169. package/AISB/catalog/aisb.t3.079_dpfkmeans.zh.yaml +104 -0
  170. package/AISB/catalog/aisb.t3.080_latentscorereweight.yaml +169 -0
  171. package/AISB/catalog/aisb.t3.080_latentscorereweight.zh.yaml +123 -0
  172. package/AISB/catalog/aisb.t3.081_qmamba.yaml +150 -0
  173. package/AISB/catalog/aisb.t3.081_qmamba.zh.yaml +117 -0
  174. package/AISB/catalog/aisb.t3.082_onlinellmrouting.yaml +160 -0
  175. package/AISB/catalog/aisb.t3.082_onlinellmrouting.zh.yaml +133 -0
  176. package/AISB/catalog/aisb.t3.083_starformer.yaml +178 -0
  177. package/AISB/catalog/aisb.t3.083_starformer.zh.yaml +140 -0
  178. package/AISB/catalog/aisb.t3.084_ift.yaml +139 -0
  179. package/AISB/catalog/aisb.t3.084_ift.zh.yaml +111 -0
  180. package/AISB/catalog/aisb.t3.085_neuralsurv.yaml +183 -0
  181. package/AISB/catalog/aisb.t3.085_neuralsurv.zh.yaml +143 -0
  182. package/AISB/catalog/aisb.t3.086_stella.yaml +197 -0
  183. package/AISB/catalog/aisb.t3.086_stella.zh.yaml +142 -0
  184. package/AISB/catalog/aisb.t3.087_moses.yaml +167 -0
  185. package/AISB/catalog/aisb.t3.087_moses.zh.yaml +132 -0
  186. package/AISB/catalog/aisb.t3.088_channelnorm.yaml +140 -0
  187. package/AISB/catalog/aisb.t3.088_channelnorm.zh.yaml +109 -0
  188. package/AISB/catalog/aisb.t3.089_causalvelocity.yaml +730 -0
  189. package/AISB/catalog/aisb.t3.089_causalvelocity.zh.yaml +668 -0
  190. package/AISB/catalog/aisb.t3.090_rstib.yaml +144 -0
  191. package/AISB/catalog/aisb.t3.090_rstib.zh.yaml +109 -0
  192. package/AISB/catalog/aisb.t3.091_timeawarecausal.yaml +132 -0
  193. package/AISB/catalog/aisb.t3.091_timeawarecausal.zh.yaml +107 -0
  194. package/AISB/catalog/aisb.t3.092_kmeanslocalopt.yaml +138 -0
  195. package/AISB/catalog/aisb.t3.092_kmeanslocalopt.zh.yaml +110 -0
  196. package/AISB/catalog/aisb.t3.093_fedwmsam.yaml +134 -0
  197. package/AISB/catalog/aisb.t3.093_fedwmsam.zh.yaml +106 -0
  198. package/AISB/catalog/aisb.t3.094_boundre.yaml +147 -0
  199. package/AISB/catalog/aisb.t3.094_boundre.zh.yaml +114 -0
  200. package/AISB/catalog/aisb.t3.095_fastfeaturecp.yaml +153 -0
  201. package/AISB/catalog/aisb.t3.095_fastfeaturecp.zh.yaml +118 -0
  202. package/AISB/catalog/aisb.t3.096_m3svm.yaml +189 -0
  203. package/AISB/catalog/aisb.t3.096_m3svm.zh.yaml +149 -0
  204. package/AISB/catalog/aisb.t3.097_wassersteintl.yaml +212 -0
  205. package/AISB/catalog/aisb.t3.097_wassersteintl.zh.yaml +169 -0
  206. package/AISB/catalog/aisb.t3.098_xmahalanobis.yaml +171 -0
  207. package/AISB/catalog/aisb.t3.098_xmahalanobis.zh.yaml +127 -0
  208. package/AISB/catalog/aisb.t3.099_ollalanding.yaml +248 -0
  209. package/AISB/catalog/aisb.t3.099_ollalanding.zh.yaml +182 -0
  210. package/AISB/catalog/aisb.t3.100_invmissingdata.yaml +179 -0
  211. package/AISB/catalog/aisb.t3.100_invmissingdata.zh.yaml +150 -0
  212. package/AISB/catalog/aisb.t3.101_acia.yaml +164 -0
  213. package/AISB/catalog/aisb.t3.101_acia.zh.yaml +109 -0
  214. package/AISB/catalog/aisb.t3.102_stochasticff.yaml +178 -0
  215. package/AISB/catalog/aisb.t3.102_stochasticff.zh.yaml +130 -0
  216. package/AISB/catalog/aisb.t3.103_qdcp.yaml +150 -0
  217. package/AISB/catalog/aisb.t3.103_qdcp.zh.yaml +116 -0
  218. package/AISB/catalog/aisb.t3.104_balancedactiveinf.yaml +137 -0
  219. package/AISB/catalog/aisb.t3.104_balancedactiveinf.zh.yaml +104 -0
  220. package/AISB/catalog/aisb.t3.105_binaryclasseval.yaml +161 -0
  221. package/AISB/catalog/aisb.t3.105_binaryclasseval.zh.yaml +130 -0
  222. package/AISB/image/001_aisb.t3.001_savvy.jpg +0 -0
  223. package/AISB/image/002_aisb.t3.002_pinet.jpg +0 -0
  224. package/AISB/image/003_aisb.t3.003_dmsqd.jpg +0 -0
  225. package/AISB/image/004_aisb.t3.004_decentralattn.jpg +0 -0
  226. package/AISB/image/005_aisb.t3.005_tsae.jpg +0 -0
  227. package/AISB/image/006_aisb.t3.006_physense.jpg +0 -0
  228. package/AISB/image/007_aisb.t3.007_reasoningiqa.jpg +0 -0
  229. package/AISB/image/008_aisb.t3.008_meanflows.jpg +0 -0
  230. package/AISB/image/009_aisb.t3.009_scoremissing.jpg +0 -0
  231. package/AISB/image/010_aisb.t3.010_suitabilityfilter.jpg +0 -0
  232. package/AISB/image/011_aisb.t3.011_osd.jpg +0 -0
  233. package/AISB/image/012_aisb.t3.012_efficientqat.jpg +0 -0
  234. package/AISB/image/013_aisb.t3.013_appl.jpg +0 -0
  235. package/AISB/image/014_aisb.t3.014_piguard.jpg +0 -0
  236. package/AISB/image/015_aisb.t3.015_frspec.jpg +0 -0
  237. package/AISB/image/016_aisb.t3.016_mathfusion.jpg +0 -0
  238. package/AISB/image/017_aisb.t3.017_multimodalglp.jpg +0 -0
  239. package/AISB/image/018_aisb.t3.018_cotsynth.jpg +0 -0
  240. package/AISB/image/019_aisb.t3.019_dyscaleut.jpg +0 -0
  241. package/AISB/image/020_aisb.t3.020_aristotle.jpg +0 -0
  242. package/AISB/image/021_aisb.t3.021_tokenrecycling.jpg +0 -0
  243. package/AISB/image/022_aisb.t3.022_chainofreasoning.jpg +0 -0
  244. package/AISB/image/023_aisb.t3.023_guidedembed.jpg +0 -0
  245. package/AISB/image/024_aisb.t3.024_outputcentric.jpg +0 -0
  246. package/AISB/image/025_aisb.t3.025_deeper.jpg +0 -0
  247. package/AISB/image/026_aisb.t3.026_gartkg.jpg +0 -0
  248. package/AISB/image/027_aisb.t3.027_citeeval.jpg +0 -0
  249. package/AISB/image/028_aisb.t3.028_sbam.jpg +0 -0
  250. package/AISB/image/029_aisb.t3.029_cdqgeoembed.jpg +0 -0
  251. package/AISB/image/030_aisb.t3.030_processrm.jpg +0 -0
  252. package/AISB/image/031_aisb.t3.031_circuitstability.jpg +0 -0
  253. package/AISB/image/032_aisb.t3.032_ptsolver.jpg +0 -0
  254. package/AISB/image/033_aisb.t3.033_gcse.jpg +0 -0
  255. package/AISB/image/034_aisb.t3.034_ensemblewm.jpg +0 -0
  256. package/AISB/image/035_aisb.t3.035_moralvalueswa.jpg +0 -0
  257. package/AISB/image/036_aisb.t3.036_weakstrongpref.jpg +0 -0
  258. package/AISB/image/037_aisb.t3.037_dementiamask.jpg +0 -0
  259. package/AISB/image/038_aisb.t3.038_tinysam.jpg +0 -0
  260. package/AISB/image/039_aisb.t3.039_calf.jpg +0 -0
  261. package/AISB/image/040_aisb.t3.040_graniteguardian.jpg +0 -0
  262. package/AISB/image/041_aisb.t3.041_amdm.jpg +0 -0
  263. package/AISB/image/042_aisb.t3.042_xpatch.jpg +0 -0
  264. package/AISB/image/043_aisb.t3.043_vhm.jpg +0 -0
  265. package/AISB/image/044_aisb.t3.044_rgvi.jpg +0 -0
  266. package/AISB/image/045_aisb.t3.045_pslstm.jpg +0 -0
  267. package/AISB/image/046_aisb.t3.046_nonstatts.jpg +0 -0
  268. package/AISB/image/047_aisb.t3.047_timepfn.jpg +0 -0
  269. package/AISB/image/048_aisb.t3.048_proxyspex.jpg +0 -0
  270. package/AISB/image/049_aisb.t3.049_hogwildinference.jpg +0 -0
  271. package/AISB/image/050_aisb.t3.050_causalpfn.jpg +0 -0
  272. package/AISB/image/051_aisb.t3.051_flashtp.jpg +0 -0
  273. package/AISB/image/052_aisb.t3.052_nsdiff.jpg +0 -0
  274. package/AISB/image/053_aisb.t3.053_k2vae.jpg +0 -0
  275. package/AISB/image/054_aisb.t3.054_timebase.jpg +0 -0
  276. package/AISB/image/055_aisb.t3.055_csbrain.jpg +0 -0
  277. package/AISB/image/056_aisb.t3.056_infosam.jpg +0 -0
  278. package/AISB/image/057_aisb.t3.057_mdreid.jpg +0 -0
  279. package/AISB/image/058_aisb.t3.058_mindglitch.jpg +0 -0
  280. package/AISB/image/059_aisb.t3.059_selfsupervised.jpg +0 -0
  281. package/AISB/image/060_aisb.t3.060_iaggad.jpg +0 -0
  282. package/AISB/image/061_aisb.t3.061_hsgkn.jpg +0 -0
  283. package/AISB/image/062_aisb.t3.062_visionts.jpg +0 -0
  284. package/AISB/image/063_aisb.t3.063_tsrag.jpg +0 -0
  285. package/AISB/image/064_aisb.t3.064_pir.jpg +0 -0
  286. package/AISB/image/065_aisb.t3.065_proteinbinding.jpg +0 -0
  287. package/AISB/image/066_aisb.t3.066_tropicalattention.jpg +0 -0
  288. package/AISB/image/067_aisb.t3.067_kanad.jpg +0 -0
  289. package/AISB/image/068_aisb.t3.068_sempo.jpg +0 -0
  290. package/AISB/image/069_aisb.t3.069_treehfd.jpg +0 -0
  291. package/AISB/image/070_aisb.t3.070_certifiedunlearning.jpg +0 -0
  292. package/AISB/image/071_aisb.t3.071_neuralmjd.jpg +0 -0
  293. package/AISB/image/072_aisb.t3.072_fedgmt.jpg +0 -0
  294. package/AISB/image/073_aisb.t3.073_rld.jpg +0 -0
  295. package/AISB/image/074_aisb.t3.074_lsvi.jpg +0 -0
  296. package/AISB/image/075_aisb.t3.075_treeslicedentropy.jpg +0 -0
  297. package/AISB/image/076_aisb.t3.076_aanet.jpg +0 -0
  298. package/AISB/image/077_aisb.t3.077_cmnn.jpg +0 -0
  299. package/AISB/image/078_aisb.t3.078_conformalanomaly.jpg +0 -0
  300. package/AISB/image/079_aisb.t3.079_dpfkmeans.jpg +0 -0
  301. package/AISB/image/080_aisb.t3.080_latentscorereweight.jpg +0 -0
  302. package/AISB/image/081_aisb.t3.081_qmamba.jpg +0 -0
  303. package/AISB/image/082_aisb.t3.082_onlinellmrouting.jpg +0 -0
  304. package/AISB/image/083_aisb.t3.083_starformer.jpg +0 -0
  305. package/AISB/image/084_aisb.t3.084_ift.jpg +0 -0
  306. package/AISB/image/085_aisb.t3.085_neuralsurv.jpg +0 -0
  307. package/AISB/image/086_aisb.t3.086_stella.jpg +0 -0
  308. package/AISB/image/087_aisb.t3.087_moses.jpg +0 -0
  309. package/AISB/image/088_aisb.t3.088_channelnorm.jpg +0 -0
  310. package/AISB/image/089_aisb.t3.089_causalvelocity.jpg +0 -0
  311. package/AISB/image/090_aisb.t3.090_rstib.jpg +0 -0
  312. package/AISB/image/091_aisb.t3.091_timeawarecausal.jpg +0 -0
  313. package/AISB/image/092_aisb.t3.092_kmeanslocalopt.jpg +0 -0
  314. package/AISB/image/093_aisb.t3.093_fedwmsam.jpg +0 -0
  315. package/AISB/image/094_aisb.t3.094_boundre.jpg +0 -0
  316. package/AISB/image/095_aisb.t3.095_fastfeaturecp.jpg +0 -0
  317. package/AISB/image/096_aisb.t3.096_m3svm.jpg +0 -0
  318. package/AISB/image/097_aisb.t3.097_wassersteintl.jpg +0 -0
  319. package/AISB/image/098_aisb.t3.098_xmahalanobis.jpg +0 -0
  320. package/AISB/image/099_aisb.t3.099_ollalanding.jpg +0 -0
  321. package/AISB/image/100_aisb.t3.100_invmissingdata.jpg +0 -0
  322. package/AISB/image/101_aisb.t3.101_acia.jpg +0 -0
  323. package/AISB/image/102_aisb.t3.102_stochasticff.jpg +0 -0
  324. package/AISB/image/103_aisb.t3.103_qdcp.jpg +0 -0
  325. package/AISB/image/104_aisb.t3.104_balancedactiveinf.jpg +0 -0
  326. package/AISB/image/105_aisb.t3.105_binaryclasseval.jpg +0 -0
  327. package/AISB/image/106_aisb.t1.reasoning_lite.jpg +0 -0
  328. package/AISB/image/107_aisb.t2.paper_audit.jpg +0 -0
  329. package/AISB/image/108_aisb.t3.multi_gpu_search.jpg +0 -0
  330. package/AISB/image/109_aisb.t3.tdc_admet.jpg +0 -0
  331. package/AISB/image/aisb.b1.agentic_coding.svg +16 -0
  332. package/AISB/image/aisb.b10.climate_earth.svg +16 -0
  333. package/AISB/image/aisb.b11.model_efficiency.svg +16 -0
  334. package/AISB/image/aisb.b12.embodied_ai.svg +16 -0
  335. package/AISB/image/aisb.b2.agent_systems.svg +16 -0
  336. package/AISB/image/aisb.b3.self_evolving_rl.svg +16 -0
  337. package/AISB/image/aisb.b4.lm_reasoning.svg +16 -0
  338. package/AISB/image/aisb.b5.math_proof.svg +16 -0
  339. package/AISB/image/aisb.b6.research_process.svg +16 -0
  340. package/AISB/image/aisb.b7.multimodal_fusion.svg +16 -0
  341. package/AISB/image/aisb.b8.lifesci_drug.svg +16 -0
  342. package/AISB/image/aisb.b9.material_science.svg +16 -0
  343. package/README.md +132 -11
  344. package/bin/ds.js +376 -49
  345. package/docs/en/00_QUICK_START.md +135 -18
  346. package/docs/en/01_SETTINGS_REFERENCE.md +468 -96
  347. package/docs/en/02_START_RESEARCH_GUIDE.md +26 -5
  348. package/docs/en/03_QQ_CONNECTOR_GUIDE.md +14 -3
  349. package/docs/en/04_LINGZHU_CONNECTOR_GUIDE.md +2 -0
  350. package/docs/en/05_TUI_GUIDE.md +171 -2
  351. package/docs/en/07_MEMORY_AND_MCP.md +38 -2
  352. package/docs/en/09_DOCTOR.md +64 -4
  353. package/docs/en/10_WEIXIN_CONNECTOR_GUIDE.md +38 -1
  354. package/docs/en/11_LICENSE_AND_RISK.md +4 -0
  355. package/docs/en/12_GUIDED_WORKFLOW_TOUR.md +15 -0
  356. package/docs/en/14_PROMPT_SKILLS_AND_MCP_GUIDE.md +9 -0
  357. package/docs/en/15_CODEX_PROVIDER_SETUP.md +622 -187
  358. package/docs/en/16_TELEGRAM_CONNECTOR_GUIDE.md +14 -0
  359. package/docs/en/17_WHATSAPP_CONNECTOR_GUIDE.md +14 -0
  360. package/docs/en/18_FEISHU_CONNECTOR_GUIDE.md +14 -0
  361. package/docs/en/21_LOCAL_MODEL_BACKENDS_GUIDE.md +105 -2
  362. package/docs/en/22_BENCHSTORE_YAML_REFERENCE.md +469 -0
  363. package/docs/en/23_BENCHSTORE_GITHUB_RELEASES_SPEC.md +316 -0
  364. package/docs/en/24_CLAUDE_CODE_PROVIDER_SETUP.md +469 -0
  365. package/docs/en/25_OPENCODE_PROVIDER_SETUP.md +653 -0
  366. package/docs/en/26_CITATION_AND_ATTRIBUTION.md +119 -0
  367. package/docs/en/27_KIMI_CODE_PROVIDER_SETUP.md +180 -0
  368. package/docs/en/28_DISCORD_CONNECTOR_GUIDE.md +61 -0
  369. package/docs/en/29_SLACK_CONNECTOR_GUIDE.md +60 -0
  370. package/docs/en/30_SETTINGS_CONTROL_CENTER_GUIDE.md +371 -0
  371. package/docs/en/{19_LOCAL_BROWSER_AUTH.md → 31_LOCAL_BROWSER_AUTH.md} +1 -1
  372. package/docs/en/32_WINDOWS_WSL2_DEPLOYMENT_GUIDE.md +273 -0
  373. package/docs/en/33_WORKSPACE_EXPLORER_QA.md +121 -0
  374. package/docs/en/91_DEVELOPMENT.md +29 -0
  375. package/docs/en/99_ACKNOWLEDGEMENTS.md +24 -19
  376. package/docs/en/README.md +44 -7
  377. package/docs/images/admin/admin-connectors-health-en.png +0 -0
  378. package/docs/images/admin/admin-controllers-en.png +0 -0
  379. package/docs/images/admin/admin-diagnostics-en.png +0 -0
  380. package/docs/images/admin/admin-errors-en.png +0 -0
  381. package/docs/images/admin/admin-issues-en.png +0 -0
  382. package/docs/images/admin/admin-logs-en.png +0 -0
  383. package/docs/images/admin/admin-quest-detail-en.png +0 -0
  384. package/docs/images/admin/admin-quests-en.png +0 -0
  385. package/docs/images/admin/admin-repairs-en.png +0 -0
  386. package/docs/images/admin/admin-runtime-en.png +0 -0
  387. package/docs/images/admin/admin-search-en.png +0 -0
  388. package/docs/images/admin/admin-stats-en.png +0 -0
  389. package/docs/images/admin/admin-summary-en.png +0 -0
  390. package/docs/images/connectors/connector-discord-en.png +0 -0
  391. package/docs/images/connectors/connector-feishu-en.png +0 -0
  392. package/docs/images/connectors/connector-lingzhu-en.png +0 -0
  393. package/docs/images/connectors/connector-qq-en.png +0 -0
  394. package/docs/images/connectors/connector-slack-en.png +0 -0
  395. package/docs/images/connectors/connector-telegram-en.png +0 -0
  396. package/docs/images/connectors/connector-weixin-en.png +0 -0
  397. package/docs/images/connectors/connector-whatsapp-en.png +0 -0
  398. package/docs/images/settings/settings-baselines-en.png +0 -0
  399. package/docs/images/settings/settings-config-en.png +0 -0
  400. package/docs/images/settings/settings-connectors-overview-en.png +0 -0
  401. package/docs/images/settings/settings-deepxiv-en.png +0 -0
  402. package/docs/images/settings/settings-mcp-servers-en.png +0 -0
  403. package/docs/images/settings/settings-plugins-en.png +0 -0
  404. package/docs/images/settings/settings-runners-en.png +0 -0
  405. package/docs/zh/00_QUICK_START.md +92 -17
  406. package/docs/zh/01_SETTINGS_REFERENCE.md +219 -98
  407. package/docs/zh/02_START_RESEARCH_GUIDE.md +26 -5
  408. package/docs/zh/05_TUI_GUIDE.md +171 -2
  409. package/docs/zh/07_MEMORY_AND_MCP.md +29 -2
  410. package/docs/zh/09_DOCTOR.md +39 -4
  411. package/docs/zh/10_WEIXIN_CONNECTOR_GUIDE.md +24 -1
  412. package/docs/zh/11_LICENSE_AND_RISK.md +4 -0
  413. package/docs/zh/12_GUIDED_WORKFLOW_TOUR.md +15 -0
  414. package/docs/zh/14_PROMPT_SKILLS_AND_MCP_GUIDE.md +9 -0
  415. package/docs/zh/15_CODEX_PROVIDER_SETUP.md +550 -188
  416. package/docs/zh/21_LOCAL_MODEL_BACKENDS_GUIDE.md +105 -2
  417. package/docs/zh/22_BENCHSTORE_YAML_REFERENCE.md +459 -0
  418. package/docs/zh/23_BENCHSTORE_GITHUB_RELEASES_SPEC.md +287 -0
  419. package/docs/zh/23_CLAUDE_RUNNER_GUIDE.md +103 -0
  420. package/docs/zh/24_CLAUDE_CODE_PROVIDER_SETUP.md +460 -0
  421. package/docs/zh/25_OPENCODE_PROVIDER_SETUP.md +660 -0
  422. package/docs/zh/26_CITATION_AND_ATTRIBUTION.md +102 -0
  423. package/docs/zh/27_KIMI_CODE_PROVIDER_SETUP.md +51 -0
  424. package/docs/zh/{19_LOCAL_BROWSER_AUTH.md → 31_LOCAL_BROWSER_AUTH.md} +1 -1
  425. package/docs/zh/32_WINDOWS_WSL2_DEPLOYMENT_GUIDE.md +264 -0
  426. package/docs/zh/33_WORKSPACE_EXPLORER_QA.md +127 -0
  427. package/docs/zh/99_ACKNOWLEDGEMENTS.md +23 -19
  428. package/docs/zh/README.md +29 -7
  429. package/install.sh +122 -16
  430. package/package.json +4 -1
  431. package/pyproject.toml +2 -1
  432. package/src/deepscientist/__init__.py +1 -1
  433. package/src/deepscientist/acp/envelope.py +13 -0
  434. package/src/deepscientist/admin/__init__.py +3 -0
  435. package/src/deepscientist/admin/charts.py +681 -0
  436. package/src/deepscientist/admin/logs.py +119 -0
  437. package/src/deepscientist/admin/repairs.py +217 -0
  438. package/src/deepscientist/admin/service.py +1310 -0
  439. package/src/deepscientist/admin/system_info.py +700 -0
  440. package/src/deepscientist/admin/tasks.py +465 -0
  441. package/src/deepscientist/admin/tool_metrics.py +600 -0
  442. package/src/deepscientist/artifact/guidance.py +8 -4
  443. package/src/deepscientist/artifact/schemas.py +115 -0
  444. package/src/deepscientist/artifact/service.py +4268 -260
  445. package/src/deepscientist/bash_exec/monitor.py +30 -3
  446. package/src/deepscientist/bash_exec/service.py +134 -1
  447. package/src/deepscientist/benchstore/__init__.py +4 -0
  448. package/src/deepscientist/benchstore/prompt_builder.py +224 -0
  449. package/src/deepscientist/benchstore/service.py +1716 -0
  450. package/src/deepscientist/channels/weixin_ilink.py +8 -1
  451. package/src/deepscientist/cli.py +92 -17
  452. package/src/deepscientist/codex_cli_compat.py +2 -2
  453. package/src/deepscientist/config/models.py +82 -11
  454. package/src/deepscientist/config/service.py +927 -91
  455. package/src/deepscientist/connector/weixin_support.py +48 -17
  456. package/src/deepscientist/daemon/api/handlers.py +697 -210
  457. package/src/deepscientist/daemon/api/router.py +76 -1
  458. package/src/deepscientist/daemon/app.py +1054 -51
  459. package/src/deepscientist/diagnostics/runner_failures.py +147 -0
  460. package/src/deepscientist/doctor.py +212 -65
  461. package/src/deepscientist/evidence_packets.py +590 -0
  462. package/src/deepscientist/home.py +52 -4
  463. package/src/deepscientist/kimi_cli_compat.py +50 -0
  464. package/src/deepscientist/latex_runtime.py +2 -2
  465. package/src/deepscientist/mcp/context.py +2 -0
  466. package/src/deepscientist/mcp/schemas.py +114 -0
  467. package/src/deepscientist/mcp/server.py +1566 -126
  468. package/src/deepscientist/memory/service.py +203 -16
  469. package/src/deepscientist/process_control.py +8 -1
  470. package/src/deepscientist/prompts/builder.py +836 -92
  471. package/src/deepscientist/quest/__init__.py +2 -2
  472. package/src/deepscientist/quest/layout.py +12 -1
  473. package/src/deepscientist/quest/node_traces.py +10 -0
  474. package/src/deepscientist/quest/service.py +1430 -139
  475. package/src/deepscientist/quest/stage_views.py +1 -1
  476. package/src/deepscientist/runners/__init__.py +18 -0
  477. package/src/deepscientist/runners/base.py +89 -1
  478. package/src/deepscientist/runners/builtins.py +13 -1
  479. package/src/deepscientist/runners/claude.py +391 -0
  480. package/src/deepscientist/runners/codex.py +421 -21
  481. package/src/deepscientist/runners/codex_telemetry.py +127 -0
  482. package/src/deepscientist/runners/kimi.py +334 -0
  483. package/src/deepscientist/runners/metadata.py +68 -0
  484. package/src/deepscientist/runners/opencode.py +414 -0
  485. package/src/deepscientist/runners/runtime_overrides.py +100 -0
  486. package/src/deepscientist/runners/simple_cli.py +538 -0
  487. package/src/deepscientist/runtime_storage.py +303 -0
  488. package/src/deepscientist/shared.py +61 -16
  489. package/src/deepscientist/skills/installer.py +37 -0
  490. package/src/deepscientist/skills/registry.py +2 -0
  491. package/src/deepscientist/tinytex.py +2 -2
  492. package/src/deepscientist/tui.py +10 -3
  493. package/src/prompts/benchstore/system.md +77 -0
  494. package/src/prompts/connectors/qq.md +33 -2
  495. package/src/prompts/connectors/weixin.md +208 -23
  496. package/src/prompts/contracts/admin_ops.md +74 -0
  497. package/src/prompts/contracts/admin_ops_knowledge.md +138 -0
  498. package/src/prompts/contracts/shared_interaction.md +5 -11
  499. package/src/prompts/start_setup/system.md +422 -0
  500. package/src/prompts/system.md +409 -315
  501. package/src/prompts/system_copilot.md +88 -12
  502. package/src/skills/analysis-campaign/SKILL.md +239 -578
  503. package/src/skills/analysis-campaign/references/artifact-flow-examples.md +102 -0
  504. package/src/skills/analysis-campaign/references/boundary-cases.md +98 -0
  505. package/src/skills/analysis-campaign/references/campaign-checklist-template.md +39 -24
  506. package/src/skills/analysis-campaign/references/campaign-design.md +26 -10
  507. package/src/skills/analysis-campaign/references/campaign-plan-template.md +53 -54
  508. package/src/skills/analysis-campaign/references/operational-guidance.md +97 -0
  509. package/src/skills/analysis-campaign/references/writing-facing-slice-examples.md +10 -20
  510. package/src/skills/baseline/SKILL.md +183 -461
  511. package/src/skills/baseline/references/artifact-flow-examples.md +106 -0
  512. package/src/skills/baseline/references/artifact-payload-examples.md +1 -1
  513. package/src/skills/baseline/references/baseline-checklist-template.md +27 -35
  514. package/src/skills/baseline/references/baseline-plan-template.md +37 -76
  515. package/src/skills/baseline/references/boundary-cases.md +86 -0
  516. package/src/skills/baseline/references/codebase-audit-checklist.md +2 -6
  517. package/src/skills/baseline/references/comparability-contract.md +7 -12
  518. package/src/skills/baseline/references/operational-guidance.md +56 -0
  519. package/src/skills/baseline/references/route-selection.md +5 -25
  520. package/src/skills/decision/SKILL.md +113 -306
  521. package/src/skills/decision/references/checkpoint-memory-template.md +47 -0
  522. package/src/skills/decision/references/operational-guidance.md +94 -0
  523. package/src/skills/decision/references/research-route-criteria.md +7 -8
  524. package/src/skills/decision/references/strategic-decision-template.md +13 -26
  525. package/src/skills/experiment/SKILL.md +132 -670
  526. package/src/skills/experiment/references/execution-playbook.md +374 -0
  527. package/src/skills/experiment/references/main-experiment-checklist-template.md +26 -2
  528. package/src/skills/experiment/references/main-experiment-plan-template.md +28 -17
  529. package/src/skills/experiment/references/operational-guidance.md +108 -0
  530. package/src/skills/finalize/SKILL.md +62 -0
  531. package/src/skills/finalize/references/checkpoint-memory-template.md +49 -0
  532. package/src/skills/finalize/references/resume-packet-template.md +7 -0
  533. package/src/skills/idea/SKILL.md +228 -15
  534. package/src/skills/idea/references/controlled-brainstorming-playbook.md +78 -0
  535. package/src/skills/idea/references/current-board-packet-template.md +61 -0
  536. package/src/skills/idea/references/high-value-idea-sourcing.md +119 -0
  537. package/src/skills/idea/references/idea-generation-playbook.md +21 -0
  538. package/src/skills/idea/references/idea-thinking-flow.md +6 -0
  539. package/src/skills/idea/references/literature-survey-template.md +3 -0
  540. package/src/skills/idea/references/objective-contract-template.md +54 -0
  541. package/src/skills/idea/references/outline-seeding-example.md +56 -0
  542. package/src/skills/idea/references/pre-idea-draft-template.md +105 -0
  543. package/src/skills/idea/references/related-work-playbook.md +75 -2
  544. package/src/skills/idea/references/research-history-playbook.md +114 -0
  545. package/src/skills/idea/references/selection-gate.md +58 -6
  546. package/src/skills/intake-audit/SKILL.md +43 -2
  547. package/src/skills/intake-audit/references/state-audit-template.md +10 -0
  548. package/src/skills/nature-data/SKILL.md +128 -0
  549. package/src/skills/nature-data/UPSTREAM_LICENSE.txt +21 -0
  550. package/src/skills/nature-data/agents/openai.yaml +4 -0
  551. package/src/skills/nature-data/references/chinese-author-alignment.md +84 -0
  552. package/src/skills/nature-data/references/fair-metadata-checklist.md +105 -0
  553. package/src/skills/nature-data/references/policy-principles.md +103 -0
  554. package/src/skills/nature-data/references/repository-and-identifiers.md +96 -0
  555. package/src/skills/nature-data/references/source-basis.md +54 -0
  556. package/src/skills/nature-data/references/statement-patterns.md +153 -0
  557. package/src/skills/nature-figure/SKILL.md +197 -0
  558. package/src/skills/nature-figure/UPSTREAM_LICENSE.txt +21 -0
  559. package/src/skills/nature-figure/agents/openai.yaml +4 -0
  560. package/src/skills/nature-figure/evals/evals.json +37 -0
  561. package/src/skills/nature-figure/references/api.md +428 -0
  562. package/src/skills/nature-figure/references/backend-selection.md +100 -0
  563. package/src/skills/nature-figure/references/chart-types.md +281 -0
  564. package/src/skills/nature-figure/references/common-patterns.md +349 -0
  565. package/src/skills/nature-figure/references/design-theory.md +436 -0
  566. package/src/skills/nature-figure/references/figure-contract.md +93 -0
  567. package/src/skills/nature-figure/references/nature-2026-observations.md +112 -0
  568. package/src/skills/nature-figure/references/qa-contract.md +119 -0
  569. package/src/skills/nature-figure/references/r-template-index.md +66 -0
  570. package/src/skills/nature-figure/references/r-workflow.md +161 -0
  571. package/src/skills/nature-figure/references/tutorials.md +250 -0
  572. package/src/skills/nature-paper2ppt/SKILL.md +507 -0
  573. package/src/skills/nature-paper2ppt/UPSTREAM_LICENSE.txt +21 -0
  574. package/src/skills/nature-paper2ppt/agents/openai.yaml +4 -0
  575. package/src/skills/nature-polishing/SKILL.md +385 -0
  576. package/src/skills/nature-polishing/UPSTREAM_LICENSE.txt +21 -0
  577. package/src/skills/nature-polishing/agents/openai.yaml +4 -0
  578. package/src/skills/nature-polishing/references/phrasebank-playbook.md +162 -0
  579. package/src/skills/nature-polishing/references/section-moves.md +240 -0
  580. package/src/skills/nature-polishing/references/style-guardrails.md +94 -0
  581. package/src/skills/nature-polishing/references/writing-strategy.md +148 -0
  582. package/src/skills/optimize/SKILL.md +177 -1568
  583. package/src/skills/optimize/references/brief-shaping-playbook.md +95 -0
  584. package/src/skills/optimize/references/candidate-board-template.md +13 -0
  585. package/src/skills/optimize/references/candidate-ranking-template.md +51 -0
  586. package/src/skills/optimize/references/codegen-route-playbook.md +50 -0
  587. package/src/skills/optimize/references/debug-response-template.md +29 -0
  588. package/src/skills/optimize/references/frontier-review-template.md +32 -0
  589. package/src/skills/optimize/references/fusion-playbook.md +36 -0
  590. package/src/skills/optimize/references/method-brief-template.md +73 -0
  591. package/src/skills/optimize/references/operational-guidance.md +621 -0
  592. package/src/skills/optimize/references/optimization-memory-template.md +30 -0
  593. package/src/skills/optimize/references/optimize-checklist-template.md +18 -0
  594. package/src/skills/optimize/references/plateau-response-playbook.md +28 -0
  595. package/src/skills/optimize/references/prompt-patterns.md +49 -0
  596. package/src/skills/paper-outline/SKILL.md +227 -0
  597. package/src/skills/paper-outline/references/outline-patterns.md +87 -0
  598. package/src/skills/paper-plot/SKILL.md +79 -0
  599. package/src/skills/paper-plot/agents/openai.yaml +4 -0
  600. package/src/skills/paper-plot/references/bar_grouped_hatch.md +96 -0
  601. package/src/skills/paper-plot/references/bar_paired_delta.md +72 -0
  602. package/src/skills/paper-plot/references/line_confidence_band.md +75 -0
  603. package/src/skills/paper-plot/references/line_loss_with_inset.md +65 -0
  604. package/src/skills/paper-plot/references/line_training_curve.md +44 -0
  605. package/src/skills/paper-plot/references/radar_dual_series.md +59 -0
  606. package/src/skills/paper-plot/references/scatter_broken_axis.md +59 -0
  607. package/src/skills/paper-plot/references/scatter_tsne_cluster.md +72 -0
  608. package/src/skills/paper-plot/scripts/bar_memevolve.py +109 -0
  609. package/src/skills/paper-plot/scripts/bar_spice.py +166 -0
  610. package/src/skills/paper-plot/scripts/line_aime.py +94 -0
  611. package/src/skills/paper-plot/scripts/line_loss_inset.py +157 -0
  612. package/src/skills/paper-plot/scripts/line_selfdistill.py +168 -0
  613. package/src/skills/paper-plot/scripts/radar_dora.py +151 -0
  614. package/src/skills/paper-plot/scripts/scatter_break.py +169 -0
  615. package/src/skills/paper-plot/scripts/scatter_tsne.py +133 -0
  616. package/src/skills/rebuttal/SKILL.md +9 -0
  617. package/src/skills/references/tool-usage-by-stage.md +438 -0
  618. package/src/skills/review/SKILL.md +105 -7
  619. package/src/skills/science/PROVENANCE.md +44 -0
  620. package/src/skills/science/SKILL.md +137 -0
  621. package/src/skills/science/references/artifact-science-tool.md +110 -0
  622. package/src/skills/science/references/claim-type-discipline.md +56 -0
  623. package/src/skills/science/references/domain-index.md +422 -0
  624. package/src/skills/science/references/hpc-via-bash-exec.md +42 -0
  625. package/src/skills/science/references/package-check-playbook.md +64 -0
  626. package/src/skills/science/references/package-index.min.json +3616 -0
  627. package/src/skills/science/references/packages/abinit.md +80 -0
  628. package/src/skills/science/references/packages/acts.md +73 -0
  629. package/src/skills/science/references/packages/aiida-core.md +80 -0
  630. package/src/skills/science/references/packages/alamode.md +80 -0
  631. package/src/skills/science/references/packages/amuse.md +88 -0
  632. package/src/skills/science/references/packages/anndata.md +88 -0
  633. package/src/skills/science/references/packages/arbor.md +80 -0
  634. package/src/skills/science/references/packages/arc.md +73 -0
  635. package/src/skills/science/references/packages/astropy.md +88 -0
  636. package/src/skills/science/references/packages/astroquery.md +88 -0
  637. package/src/skills/science/references/packages/atomate2.md +80 -0
  638. package/src/skills/science/references/packages/atomsmltr.md +73 -0
  639. package/src/skills/science/references/packages/awkward.md +73 -0
  640. package/src/skills/science/references/packages/batman.md +88 -0
  641. package/src/skills/science/references/packages/biopython.md +88 -0
  642. package/src/skills/science/references/packages/bloqade.md +73 -0
  643. package/src/skills/science/references/packages/brian2.md +73 -0
  644. package/src/skills/science/references/packages/bullet3.md +73 -0
  645. package/src/skills/science/references/packages/calculix.md +80 -0
  646. package/src/skills/science/references/packages/cantera.md +73 -0
  647. package/src/skills/science/references/packages/cavity-md-ipi.md +80 -0
  648. package/src/skills/science/references/packages/ccdproc.md +88 -0
  649. package/src/skills/science/references/packages/celerite2.md +88 -0
  650. package/src/skills/science/references/packages/cellrank.md +73 -0
  651. package/src/skills/science/references/packages/cesm.md +80 -0
  652. package/src/skills/science/references/packages/chemicals.md +73 -0
  653. package/src/skills/science/references/packages/chempy.md +73 -0
  654. package/src/skills/science/references/packages/cirq.md +73 -0
  655. package/src/skills/science/references/packages/coffea.md +73 -0
  656. package/src/skills/science/references/packages/cp2k.md +88 -0
  657. package/src/skills/science/references/packages/custodian.md +80 -0
  658. package/src/skills/science/references/packages/dart.md +73 -0
  659. package/src/skills/science/references/packages/datamol.md +88 -0
  660. package/src/skills/science/references/packages/dd4hep.md +73 -0
  661. package/src/skills/science/references/packages/dealii.md +80 -0
  662. package/src/skills/science/references/packages/deepchem.md +88 -0
  663. package/src/skills/science/references/packages/delphes.md +73 -0
  664. package/src/skills/science/references/packages/devito.md +80 -0
  665. package/src/skills/science/references/packages/dftb.md +88 -0
  666. package/src/skills/science/references/packages/dftd4.md +88 -0
  667. package/src/skills/science/references/packages/dftk-jl.md +80 -0
  668. package/src/skills/science/references/packages/dolfinx.md +80 -0
  669. package/src/skills/science/references/packages/drake.md +73 -0
  670. package/src/skills/science/references/packages/dumux.md +73 -0
  671. package/src/skills/science/references/packages/elk.md +80 -0
  672. package/src/skills/science/references/packages/elmerfem.md +80 -0
  673. package/src/skills/science/references/packages/enzo-e.md +88 -0
  674. package/src/skills/science/references/packages/espresso.md +80 -0
  675. package/src/skills/science/references/packages/exoplanet.md +88 -0
  676. package/src/skills/science/references/packages/fairroot.md +73 -0
  677. package/src/skills/science/references/packages/fbpic.md +80 -0
  678. package/src/skills/science/references/packages/fdtdbath-meep.md +80 -0
  679. package/src/skills/science/references/packages/geant4.md +73 -0
  680. package/src/skills/science/references/packages/geosx.md +80 -0
  681. package/src/skills/science/references/packages/gprmax.md +80 -0
  682. package/src/skills/science/references/packages/gromacs.md +80 -0
  683. package/src/skills/science/references/packages/gwaslab.md +73 -0
  684. package/src/skills/science/references/packages/gz-sim.md +73 -0
  685. package/src/skills/science/references/packages/hail.md +88 -0
  686. package/src/skills/science/references/packages/hiphive.md +80 -0
  687. package/src/skills/science/references/packages/hoomd-blue.md +80 -0
  688. package/src/skills/science/references/packages/itensor.md +73 -0
  689. package/src/skills/science/references/packages/itensors-jl.md +73 -0
  690. package/src/skills/science/references/packages/jdftx.md +73 -0
  691. package/src/skills/science/references/packages/jobflow.md +80 -0
  692. package/src/skills/science/references/packages/kadanoffbaym-jl.md +73 -0
  693. package/src/skills/science/references/packages/kite.md +80 -0
  694. package/src/skills/science/references/packages/kratos.md +80 -0
  695. package/src/skills/science/references/packages/kwant.md +73 -0
  696. package/src/skills/science/references/packages/lammps.md +80 -0
  697. package/src/skills/science/references/packages/lightkurve.md +88 -0
  698. package/src/skills/science/references/packages/limix.md +73 -0
  699. package/src/skills/science/references/packages/maxwelllink.md +80 -0
  700. package/src/skills/science/references/packages/mcdc.md +73 -0
  701. package/src/skills/science/references/packages/meep.md +80 -0
  702. package/src/skills/science/references/packages/mfem.md +80 -0
  703. package/src/skills/science/references/packages/mitgcm.md +73 -0
  704. package/src/skills/science/references/packages/modflow6.md +73 -0
  705. package/src/skills/science/references/packages/molecool.md +73 -0
  706. package/src/skills/science/references/packages/mom6.md +73 -0
  707. package/src/skills/science/references/packages/moose.md +80 -0
  708. package/src/skills/science/references/packages/mpas-model.md +73 -0
  709. package/src/skills/science/references/packages/mujoco.md +73 -0
  710. package/src/skills/science/references/packages/mumax3.md +73 -0
  711. package/src/skills/science/references/packages/nekrs.md +80 -0
  712. package/src/skills/science/references/packages/nessi.md +73 -0
  713. package/src/skills/science/references/packages/nest-simulator.md +73 -0
  714. package/src/skills/science/references/packages/netket.md +73 -0
  715. package/src/skills/science/references/packages/neuron.md +73 -0
  716. package/src/skills/science/references/packages/nextflow.md +88 -0
  717. package/src/skills/science/references/packages/nwchem.md +88 -0
  718. package/src/skills/science/references/packages/openbabel.md +88 -0
  719. package/src/skills/science/references/packages/openems.md +80 -0
  720. package/src/skills/science/references/packages/openff-toolkit.md +88 -0
  721. package/src/skills/science/references/packages/openfoam-dev.md +80 -0
  722. package/src/skills/science/references/packages/openmc.md +73 -0
  723. package/src/skills/science/references/packages/openmm.md +80 -0
  724. package/src/skills/science/references/packages/openmoc.md +73 -0
  725. package/src/skills/science/references/packages/openmx.md +80 -0
  726. package/src/skills/science/references/packages/opensees.md +80 -0
  727. package/src/skills/science/references/packages/opensn.md +80 -0
  728. package/src/skills/science/references/packages/opm-simulators.md +73 -0
  729. package/src/skills/science/references/packages/oqupy.md +73 -0
  730. package/src/skills/science/references/packages/packmol.md +80 -0
  731. package/src/skills/science/references/packages/palabos.md +80 -0
  732. package/src/skills/science/references/packages/parflow.md +80 -0
  733. package/src/skills/science/references/packages/pennylane.md +88 -0
  734. package/src/skills/science/references/packages/perceval.md +73 -0
  735. package/src/skills/science/references/packages/phono3py.md +73 -0
  736. package/src/skills/science/references/packages/phonopy.md +73 -0
  737. package/src/skills/science/references/packages/photutils.md +88 -0
  738. package/src/skills/science/references/packages/picongpu.md +80 -0
  739. package/src/skills/science/references/packages/plink-ng.md +88 -0
  740. package/src/skills/science/references/packages/precice.md +73 -0
  741. package/src/skills/science/references/packages/psc.md +80 -0
  742. package/src/skills/science/references/packages/psi4.md +88 -0
  743. package/src/skills/science/references/packages/pybinding.md +73 -0
  744. package/src/skills/science/references/packages/pyfr.md +80 -0
  745. package/src/skills/science/references/packages/pyhf.md +73 -0
  746. package/src/skills/science/references/packages/pyiron_base.md +80 -0
  747. package/src/skills/science/references/packages/pylcp.md +73 -0
  748. package/src/skills/science/references/packages/pylith.md +80 -0
  749. package/src/skills/science/references/packages/pynbody.md +88 -0
  750. package/src/skills/science/references/packages/pysam.md +88 -0
  751. package/src/skills/science/references/packages/pyscf.md +88 -0
  752. package/src/skills/science/references/packages/q-e.md +73 -0
  753. package/src/skills/science/references/packages/qibo.md +73 -0
  754. package/src/skills/science/references/packages/qiskit.md +73 -0
  755. package/src/skills/science/references/packages/quantica-jl.md +73 -0
  756. package/src/skills/science/references/packages/quantumoptics-jl.md +73 -0
  757. package/src/skills/science/references/packages/quimb.md +73 -0
  758. package/src/skills/science/references/packages/qulacs.md +73 -0
  759. package/src/skills/science/references/packages/qutip.md +73 -0
  760. package/src/skills/science/references/packages/rdkit.md +88 -0
  761. package/src/skills/science/references/packages/rmg-py.md +73 -0
  762. package/src/skills/science/references/packages/root.md +73 -0
  763. package/src/skills/science/references/packages/scanpy.md +88 -0
  764. package/src/skills/science/references/packages/scikit-allel.md +88 -0
  765. package/src/skills/science/references/packages/scikit-bio.md +88 -0
  766. package/src/skills/science/references/packages/scqubits.md +73 -0
  767. package/src/skills/science/references/packages/scuff-em.md +80 -0
  768. package/src/skills/science/references/packages/scvi-tools.md +73 -0
  769. package/src/skills/science/references/packages/seissol.md +73 -0
  770. package/src/skills/science/references/packages/sfepy.md +80 -0
  771. package/src/skills/science/references/packages/sisl.md +73 -0
  772. package/src/skills/science/references/packages/smilei.md +80 -0
  773. package/src/skills/science/references/packages/snakemake.md +88 -0
  774. package/src/skills/science/references/packages/specfem3d-globe.md +80 -0
  775. package/src/skills/science/references/packages/specutils.md +88 -0
  776. package/src/skills/science/references/packages/spglib.md +80 -0
  777. package/src/skills/science/references/packages/squidpy.md +88 -0
  778. package/src/skills/science/references/packages/starry.md +88 -0
  779. package/src/skills/science/references/packages/strawberryfields.md +73 -0
  780. package/src/skills/science/references/packages/su2.md +80 -0
  781. package/src/skills/science/references/packages/sunny-jl.md +73 -0
  782. package/src/skills/science/references/packages/sw4.md +73 -0
  783. package/src/skills/science/references/packages/swift.md +88 -0
  784. package/src/skills/science/references/packages/tdnegf.md +73 -0
  785. package/src/skills/science/references/packages/tenpy.md +73 -0
  786. package/src/skills/science/references/packages/thermo.md +73 -0
  787. package/src/skills/science/references/packages/tkwant.md +73 -0
  788. package/src/skills/science/references/packages/tvb-root.md +73 -0
  789. package/src/skills/science/references/packages/uproot5.md +73 -0
  790. package/src/skills/science/references/packages/vampire.md +80 -0
  791. package/src/skills/science/references/packages/wannier_tools.md +73 -0
  792. package/src/skills/science/references/packages/warpx.md +80 -0
  793. package/src/skills/science/references/packages/wrf.md +73 -0
  794. package/src/skills/science/references/packages/xtb.md +88 -0
  795. package/src/skills/science/references/packages/yt.md +73 -0
  796. package/src/skills/science/references/science-task-brief-template.md +71 -0
  797. package/src/skills/scout/SKILL.md +83 -425
  798. package/src/skills/scout/references/literature-scout-template.md +5 -24
  799. package/src/skills/scout/references/operational-guidance.md +191 -0
  800. package/src/skills/scout/references/paper-triage-playbook.md +11 -35
  801. package/src/skills/write/SKILL.md +744 -1246
  802. package/src/skills/write/references/experiments_analysis_patterns.md +129 -0
  803. package/src/skills/write/references/oral_package_patterns.md +252 -0
  804. package/src/skills/write/references/oral_writing_principles.md +291 -0
  805. package/src/skills/write/references/section_rewrite_checklist.md +234 -0
  806. package/src/tui/dist/app/AppContainer.js +1314 -27
  807. package/src/tui/dist/components/Composer.js +26 -1
  808. package/src/tui/dist/components/ConfigScreen.js +2 -1
  809. package/src/tui/dist/components/InputPrompt.js +25 -9
  810. package/src/tui/dist/components/MainContent.js +18 -3
  811. package/src/tui/dist/components/QuestScreen.js +3 -2
  812. package/src/tui/dist/components/UtilityScreen.js +37 -0
  813. package/src/tui/dist/hooks/useSafeInput.js +10 -0
  814. package/src/tui/dist/index.js +13 -1
  815. package/src/tui/dist/layouts/DefaultAppLayout.js +11 -8
  816. package/src/tui/dist/lib/api.js +89 -1
  817. package/src/tui/package.json +1 -1
  818. package/src/ui/dist/assets/{AnalysisPlugin-BCKAfjba.js → AnalysisPlugin-CA94NGmI.js} +1 -1
  819. package/src/ui/dist/assets/CliPlugin-DHBzphZU.js +79 -0
  820. package/src/ui/dist/assets/CodeEditorPlugin-BOFwD2rn.js +2 -0
  821. package/src/ui/dist/assets/{CodeViewerPlugin-CbaFRrUU.js → CodeViewerPlugin-CqDpgjik.js} +4 -4
  822. package/src/ui/dist/assets/{DocViewerPlugin-DAjLVeQD.js → DocViewerPlugin-UDBgt8-4.js} +3 -3
  823. package/src/ui/dist/assets/GitCommitViewerPlugin-BmHtZ0bZ.js +6 -0
  824. package/src/ui/dist/assets/{GitDiffViewerPlugin-CQACjoAA.js → GitDiffViewerPlugin-CAxjNorQ.js} +2 -2
  825. package/src/ui/dist/assets/{GitSnapshotViewer-0r4nLPke.js → GitSnapshotViewer-CweA6VON.js} +2 -2
  826. package/src/ui/dist/assets/{ImageViewerPlugin-nBOmI2v_.js → ImageViewerPlugin-C8wHGvGN.js} +5 -5
  827. package/src/ui/dist/assets/LabPlugin-COyyLUol.js +32 -0
  828. package/src/ui/dist/assets/{LatexPlugin-ZwtV8pIp.js → LatexPlugin-BQjAaA5J.js} +4 -4
  829. package/src/ui/dist/assets/{MarkdownViewerPlugin-DKqVfKyW.js → MarkdownViewerPlugin-Dy1NE2dI.js} +3 -3
  830. package/src/ui/dist/assets/{MarketplacePlugin-BwxStZ9D.js → MarketplacePlugin-DMIZtEJ2.js} +2 -2
  831. package/src/ui/dist/assets/NotebookEditor-CFHMq_Qt.js +91 -0
  832. package/src/ui/dist/assets/{NotebookEditor-DB9N_T9q.js → NotebookEditor-WFyd8Ybt.js} +3 -3
  833. package/src/ui/dist/assets/{PdfLoader-eWBONbQP.js → PdfLoader-CLE5u5TS.js} +3 -3
  834. package/src/ui/dist/assets/{PdfMarkdownPlugin-D22YOZL3.js → PdfMarkdownPlugin-_iNK_H83.js} +1 -1
  835. package/src/ui/dist/assets/PdfViewerPlugin-DgWsbInT.js +22 -0
  836. package/src/ui/dist/assets/SearchPlugin-DrZmn5iw.js +11 -0
  837. package/src/ui/dist/assets/{TextViewerPlugin-C5xqeeUH.js → TextViewerPlugin-D1-T3aC7.js} +4 -4
  838. package/src/ui/dist/assets/branding/runner-claude.svg +107 -0
  839. package/src/ui/dist/assets/branding/runner-codex.svg +10 -0
  840. package/src/ui/dist/assets/branding/runner-kimi.svg +14 -0
  841. package/src/ui/dist/assets/branding/runner-opencode.svg +7 -0
  842. package/src/ui/dist/assets/cli-store-CoZ-x5Ip.js +1 -0
  843. package/src/ui/dist/assets/{code-WlFHE7z_.js → code-DbsmSd3Y.js} +1 -1
  844. package/src/ui/dist/assets/file-diff-panel-DsvyRz47.js +1 -0
  845. package/src/ui/dist/assets/{wrap-text-BC-Hltpd.js → file-jump-queue-DeQBikaw.js} +3 -3
  846. package/src/ui/dist/assets/{file-socket-CfQPKQKj.js → file-socket-DA5XIx88.js} +1 -1
  847. package/src/ui/dist/assets/fonts/ds-fonts.css +50 -4
  848. package/src/ui/dist/assets/images/deepxiv/register-guide.png +0 -0
  849. package/src/ui/dist/assets/index-39vY9LmZ.js +1 -0
  850. package/src/ui/dist/assets/{index-CwNu1aH4.js → index-BsO46tJA.js} +1 -1
  851. package/src/ui/dist/assets/index-CHzJ2xtB.js +3530 -0
  852. package/src/ui/dist/assets/index-DH-zxoZ3.css +33 -0
  853. package/src/ui/dist/assets/{plugin-notebook-HbW2K-1c.js → plugin-notebook-JRhysCqj.js} +2 -2
  854. package/src/ui/dist/assets/{project-sync-C9IdzdZW.js → project-sync-DPmWKmKD.js} +1 -1
  855. package/src/ui/dist/assets/{zoom-out-E_gaeAxL.js → zoom-out-DAukFWen.js} +3 -3
  856. package/src/ui/dist/index.html +3 -3
  857. package/src/skills/analysis-campaign/references/artifact-orchestration.md +0 -58
  858. package/src/skills/baseline/references/memory-playbook.md +0 -40
  859. package/src/skills/baseline/references/publishable-baseline-package.md +0 -30
  860. package/src/skills/write/references/outline-evidence-contract-example.md +0 -107
  861. package/src/skills/write/references/paper-experiment-matrix-template.md +0 -131
  862. package/src/skills/write/references/paper-section-playbook.md +0 -64
  863. package/src/skills/write/references/reviewer-first-writing.md +0 -64
  864. package/src/skills/write/references/revision-checklist.md +0 -70
  865. package/src/skills/write/references/section-contracts.md +0 -82
  866. package/src/skills/write/references/sentence-level-proofing.md +0 -49
  867. package/src/ui/dist/assets/AiManusChatView-Bv-Z8YpU.js +0 -204
  868. package/src/ui/dist/assets/CliPlugin-BCKcpc35.js +0 -109
  869. package/src/ui/dist/assets/CodeEditorPlugin-DbOfSJ8K.js +0 -2
  870. package/src/ui/dist/assets/GitCommitViewerPlugin-CIUqbUDO.js +0 -1
  871. package/src/ui/dist/assets/LabCopilotPanel-BHxOxF4z.js +0 -14
  872. package/src/ui/dist/assets/LabPlugin-BKoZGs95.js +0 -22
  873. package/src/ui/dist/assets/NotebookEditor-BEQhaQbt.js +0 -81
  874. package/src/ui/dist/assets/PdfViewerPlugin-c-RK9DLM.js +0 -17
  875. package/src/ui/dist/assets/SearchPlugin-CxF9ytAx.js +0 -16
  876. package/src/ui/dist/assets/VNCViewer-BoLGLnHz.js +0 -11
  877. package/src/ui/dist/assets/bot-DREQOxzP.js +0 -6
  878. package/src/ui/dist/assets/chevron-up-C9Qpx4DE.js +0 -6
  879. package/src/ui/dist/assets/file-content-BZMz3RYp.js +0 -1
  880. package/src/ui/dist/assets/file-diff-panel-CQhw0jS2.js +0 -1
  881. package/src/ui/dist/assets/file-jump-queue-DA-SdG__.js +0 -1
  882. package/src/ui/dist/assets/git-commit-horizontal-DxZ8DCZh.js +0 -6
  883. package/src/ui/dist/assets/image-Bgl4VIyx.js +0 -6
  884. package/src/ui/dist/assets/index-BpV6lusQ.css +0 -33
  885. package/src/ui/dist/assets/index-CBNVuWcP.js +0 -2496
  886. package/src/ui/dist/assets/index-DrUnlf6K.js +0 -1
  887. package/src/ui/dist/assets/index-NW-h8VzN.js +0 -1
  888. package/src/ui/dist/assets/pdf-effect-queue-J8OnM0jE.js +0 -6
  889. package/src/ui/dist/assets/popover-CLc0pPP8.js +0 -1
  890. package/src/ui/dist/assets/select-Cs2PmzwL.js +0 -11
  891. package/src/ui/dist/assets/sigma-ClKcHAXm.js +0 -6
  892. package/src/ui/dist/assets/trash-DwpbFr3w.js +0 -11
  893. package/src/ui/dist/assets/useCliAccess-NQ8m0Let.js +0 -1
  894. package/src/ui/dist/assets/useFileDiffOverlay-FuhcnKiw.js +0 -1
@@ -2,6 +2,13 @@
2
2
 
3
3
  This manual documents the current DeepScientist `Settings` surface and the YAML files it actually edits. The structure intentionally follows a PyTorch-style reference pattern: short summary, schema, parameters, defaults, allowed values, runtime effect, and practical notes.
4
4
 
5
+ If DeepScientist is already running, this should be your first stop. The intended path is:
6
+
7
+ 1. start DeepScientist
8
+ 2. open the web `Settings` page
9
+ 3. use the structured UI first
10
+ 4. edit raw YAML only when you are headless, automating setup, or doing bulk changes
11
+
5
12
  Implementation sources:
6
13
 
7
14
  - `src/ui/src/components/settings/settingsFormCatalog.ts`
@@ -12,12 +19,19 @@ Implementation sources:
12
19
 
13
20
  ## Overview
14
21
 
22
+ This guide works best if you use it in two passes:
23
+
24
+ 1. first read the page-level sections in this document to find the right `Settings` page
25
+ 2. then read the field reference only for the page you are actually using
26
+
27
+ If you try to read the entire file from top to bottom as one long schema, it will feel heavier than it needs to.
28
+
15
29
  The `Settings` page writes directly to the following files:
16
30
 
17
31
  | File | UI category | Purpose |
18
32
  | --- | --- | --- |
19
33
  | `~/DeepScientist/config/config.yaml` | Runtime | Main runtime config: home path, daemon, UI, logging, Git, skill sync, cloud, ACP |
20
- | `~/DeepScientist/config/runners.yaml` | Models | Runner config: `codex` / `claude` binary path, model defaults, approval policy, sandbox, retries |
34
+ | `~/DeepScientist/config/runners.yaml` | Models | Runner config for `codex` / `claude` / `kimi` / `opencode`: binary path, model defaults, permissions, sandbox, retries, env |
21
35
  | `~/DeepScientist/config/connectors.yaml` | Connectors | QQ, Telegram, Discord, Slack, Feishu, WhatsApp, Lingzhu connector config |
22
36
  | `~/DeepScientist/config/plugins.yaml` | Extensions | Plugin discovery, enable/disable overrides, trust policy |
23
37
  | `~/DeepScientist/config/mcp_servers.yaml` | MCP | External MCP servers only; not built-in `memory`, `artifact`, or `bash_exec` |
@@ -28,10 +42,246 @@ Button semantics:
28
42
  - `Check` / `Validate`: local schema validation only.
29
43
  - `Test`: run a lightweight readiness probe. The exact behavior depends on the file type and is described later in this document.
30
44
 
45
+ ## Most Common Jobs After First Launch
46
+
47
+ If you are new to the `Settings` page, start from the task you actually want to complete:
48
+
49
+ | What you want to do | Open this page first |
50
+ | --- | --- |
51
+ | Change the default language, home path, daemon defaults, web port, or Git policy | `Runtime` |
52
+ | Switch the default runner or configure Claude / Kimi / OpenCode after launch | `Models` |
53
+ | Bind a chat platform or inspect connector state | `Connectors` |
54
+ | Reuse or publish baselines | `Baselines` |
55
+ | Enable and test DeepXiv | `DeepXiv` |
56
+ | Add plugins or plugin load paths | `Extensions` |
57
+ | Register external MCP servers | `MCP` |
58
+
31
59
  Connector-specific setup guides:
32
60
 
33
61
  - `docs/en/03_QQ_CONNECTOR_GUIDE.md`
34
62
  - `docs/en/04_LINGZHU_CONNECTOR_GUIDE.md`
63
+ - `docs/en/10_WEIXIN_CONNECTOR_GUIDE.md`
64
+ - `docs/en/16_TELEGRAM_CONNECTOR_GUIDE.md`
65
+ - `docs/en/17_WHATSAPP_CONNECTOR_GUIDE.md`
66
+ - `docs/en/18_FEISHU_CONNECTOR_GUIDE.md`
67
+ - `docs/en/28_DISCORD_CONNECTOR_GUIDE.md`
68
+ - `docs/en/29_SLACK_CONNECTOR_GUIDE.md`
69
+
70
+ ## Visual Tour Of The Core Settings Pages
71
+
72
+ The pages below cover the main configuration surfaces you should use after launch.
73
+
74
+ ### Runtime
75
+
76
+ Route:
77
+
78
+ - `/settings/config`
79
+
80
+ This page edits:
81
+
82
+ - `~/DeepScientist/config/config.yaml`
83
+
84
+ Use this page when you need to change:
85
+
86
+ - home path, default locale, and default runner
87
+ - daemon policy, web binding, logging, Git, and skill sync defaults
88
+ - hardware prompt policy and cloud / ACP compatibility knobs
89
+
90
+ How to use it:
91
+
92
+ 1. open the page
93
+ 2. change only the fields related to the task you are doing right now
94
+ 3. click `Save`
95
+ 4. use `Check` or `Test` if you want confirmation before leaving
96
+
97
+ Good first tasks here:
98
+
99
+ - switch `default_locale`
100
+ - change the web port
101
+ - adjust `default_runner`
102
+ - review Git and logging defaults
103
+
104
+ Do not start here when:
105
+
106
+ - you are trying to bind one specific connector
107
+ - you are trying to configure one specific runner in detail
108
+ - you need runtime diagnostics rather than configuration
109
+
110
+ ![Runtime settings page](../images/settings/settings-config-en.png)
111
+
112
+ ### Models
113
+
114
+ Route:
115
+
116
+ - `/settings/runners`
117
+
118
+ This page edits:
119
+
120
+ - `~/DeepScientist/config/runners.yaml`
121
+
122
+ Use this page when you need to:
123
+
124
+ - switch the global default runner
125
+ - confirm which runner is currently active
126
+ - configure Codex / Claude Code / Kimi Code / OpenCode without editing `runners.yaml` by hand
127
+
128
+ How to use it:
129
+
130
+ 1. decide which runner you want to use by default
131
+ 2. enable only the runner you actually want active
132
+ 3. fill the runner-specific path, config dir, model, and runtime knobs
133
+ 4. click `Save`
134
+ 5. click `Check` and then `Test`
135
+
136
+ Good first tasks here:
137
+
138
+ - enable Claude after `claude` already works in the terminal
139
+ - enable Kimi after `kimi` already works in the terminal
140
+ - reuse an existing OpenCode install
141
+
142
+ Do not start here when:
143
+
144
+ - the real problem is a connector delivery issue
145
+ - the real problem is that DeepScientist is unhealthy before any runner even starts
146
+
147
+ ![Models settings page](../images/settings/settings-runners-en.png)
148
+
149
+ ### Connectors
150
+
151
+ Route:
152
+
153
+ - `/settings/connector`
154
+
155
+ This page edits:
156
+
157
+ - `~/DeepScientist/config/connectors.yaml`
158
+
159
+ Use this page when you need to:
160
+
161
+ - choose which connector to configure next
162
+ - jump from the connector catalog into a specific platform page
163
+ - keep connector setup visual-first instead of opening `connectors.yaml` immediately
164
+
165
+ How to use it:
166
+
167
+ 1. start from the catalog page
168
+ 2. open one connector at a time
169
+ 3. save that connector before sending real test traffic
170
+ 4. only after the first real inbound message, expect discovered targets and runtime state to become useful
171
+
172
+ Do not start here when:
173
+
174
+ - you need system-wide diagnosis before touching any connector
175
+ - the runtime itself is not healthy enough to host connectors at all
176
+
177
+ ![Connectors overview page](../images/settings/settings-connectors-overview-en.png)
178
+
179
+ ### Baselines
180
+
181
+ Route:
182
+
183
+ - `/settings/baselines`
184
+
185
+ This page edits:
186
+
187
+ - the baseline registry under the DeepScientist home rather than one raw config file
188
+
189
+ Use this page when you need to:
190
+
191
+ - inspect reusable published baselines
192
+ - attach an existing baseline before launch
193
+ - publish a confirmed quest baseline into the shared registry
194
+
195
+ How to use it:
196
+
197
+ 1. open this page before launch if you already have a reusable baseline
198
+ 2. open it after a quest succeeds if you want to publish that baseline for future reuse
199
+ 3. stay here for registry-level baseline work; go back to quest pages for quest-specific work
200
+
201
+ ![Baselines settings page](../images/settings/settings-baselines-en.png)
202
+
203
+ ### DeepXiv
204
+
205
+ Route:
206
+
207
+ - `/settings/deepxiv`
208
+
209
+ This page edits:
210
+
211
+ - the `literature.deepxiv` block in `~/DeepScientist/config/config.yaml`
212
+
213
+ Use this page when you need to:
214
+
215
+ - enable or disable DeepXiv
216
+ - configure the literature token and timeout defaults
217
+ - use the guided setup flow instead of editing `config.yaml` manually
218
+
219
+ How to use it:
220
+
221
+ 1. open the page
222
+ 2. start the guided setup flow if you do not already know the exact fields
223
+ 3. save the token and defaults
224
+ 4. test the route from the same page before relying on it in real work
225
+
226
+ ![DeepXiv settings page](../images/settings/settings-deepxiv-en.png)
227
+
228
+ ### Extensions
229
+
230
+ Route:
231
+
232
+ - `/settings/plugins`
233
+
234
+ This page edits:
235
+
236
+ - `~/DeepScientist/config/plugins.yaml`
237
+
238
+ Use this page when you need to:
239
+
240
+ - configure plugin discovery paths
241
+ - enable or disable optional local extensions
242
+ - adjust plugin trust policy
243
+
244
+ How to use it:
245
+
246
+ 1. keep the default path if you are not actively using local plugins
247
+ 2. add plugin paths only when you actually have plugins to load
248
+ 3. treat this page as a plugin registry page, not a general runtime diagnosis page
249
+
250
+ ![Extensions settings page](../images/settings/settings-plugins-en.png)
251
+
252
+ ### MCP
253
+
254
+ Route:
255
+
256
+ - `/settings/mcp_servers`
257
+
258
+ This page edits:
259
+
260
+ - `~/DeepScientist/config/mcp_servers.yaml`
261
+
262
+ Use this page when you need to:
263
+
264
+ - register or edit external MCP servers
265
+ - review MCP connection settings without touching the built-in MCP namespaces
266
+ - validate external MCP integration before using it in quests
267
+
268
+ How to use it:
269
+
270
+ 1. add one external MCP server at a time
271
+ 2. keep built-in MCP expectations separate from external MCP setup
272
+ 3. validate the external MCP server before using it in a real quest
273
+
274
+ ![MCP settings page](../images/settings/settings-mcp-servers-en.png)
275
+
276
+ ## How To Read The Rest Of This Document
277
+
278
+ From this point onward, the file switches into field-level reference mode.
279
+
280
+ The fastest way to use the remaining sections is:
281
+
282
+ 1. find the page you actually need
283
+ 2. skim its screenshot and operational notes above
284
+ 3. jump to the field reference below only for the fields you are about to change
35
285
 
36
286
  ## `config.yaml`
37
287
 
@@ -109,10 +359,10 @@ acp:
109
359
 
110
360
  - Type: `string`
111
361
  - Default: `codex`
112
- - Allowed values: currently `codex`, `claude`
362
+ - Allowed values: `codex`, `claude`, `kimi`, `opencode`
113
363
  - UI label: `Default runner`
114
364
  - Meaning: runner used when a project does not override it.
115
- - Notes: in the current branch, `codex` is the primary path and `claude` remains a reserved slot.
365
+ - Notes: new quests inherit this default; existing quests may override it in project settings. Switch only to a runner that is enabled and already passes `ds doctor`.
116
366
 
117
367
  **`default_locale`**
118
368
 
@@ -192,6 +442,37 @@ acp:
192
442
  - UI label: `Default start mode`
193
443
  - Meaning: preferred startup surface when launching DeepScientist.
194
444
 
445
+ ### TUI debug launch switches
446
+
447
+ TUI debug is not a persistent config field. It is a per-launch diagnostic switch for inspecting the current TUI surface, input route, Web analog, and render summary.
448
+
449
+ Start with:
450
+
451
+ ```bash
452
+ ds --tui --debug
453
+ ds --tui --debug --debug-log /tmp/deepscientist_tui_debug.jsonl
454
+ ```
455
+
456
+ Environment variables:
457
+
458
+ - `TUI_DEBUG=1`
459
+ - `DEEPSCIENTIST_TUI_DEBUG=1`
460
+ - `TUI_DEBUG_LOG=/tmp/deepscientist_tui_debug.jsonl`
461
+ - `DEEPSCIENTIST_TUI_DEBUG_LOG=/tmp/deepscientist_tui_debug.jsonl`
462
+
463
+ Default log path:
464
+
465
+ ```text
466
+ /tmp/deepscientist_tui_debug.jsonl
467
+ ```
468
+
469
+ Safety requirements:
470
+
471
+ - Config editor buffers and password/secret/token fields are redacted in debug JSONL.
472
+ - Debug JSONL can be attached to issue reports or regression notes, but search it for real tokens first.
473
+ - Terminal recordings, tmux logs, and `script` transcripts capture the real screen; they are outside the JSONL redaction boundary.
474
+ - Web does not yet have an equivalent `?debug=1` inspector; TUI currently provides only the `web_analog` mapping.
475
+
195
476
  ### Logging
196
477
 
197
478
  **`logging.level`**
@@ -413,10 +694,32 @@ These settings are compatibility knobs for ACP-style external consumers.
413
694
 
414
695
  ### Summary
415
696
 
416
- `runners.yaml` defines which runner executes projects and what its default model, approval policy, sandbox, and retry behavior should be. In the current open-source release:
697
+ `runners.yaml` defines which CLI runner DeepScientist can launch, which model defaults it should use, how retries behave, and which runner-specific flags should be passed through.
698
+
699
+ Current built-in runners:
700
+
701
+ - `codex`
702
+ - OpenAI Codex CLI path, including Codex-compatible provider profiles
703
+ - `claude`
704
+ - Claude Code CLI path, including Anthropic or compatible gateway setups that already work in Claude Code
705
+ - `kimi`
706
+ - Official Kimi Code CLI path, including login state and config already working in `~/.kimi`
707
+ - `opencode`
708
+ - OpenCode CLI path, including provider/model configurations managed directly by OpenCode
417
709
 
418
- - `codex`: primary path, enabled by default
419
- - `claude`: TODO / reserved slot, disabled by default, not runnable yet
710
+ The Settings page maps DeepScientist to an already-working CLI runner. Gemini, Ollama, MiniMax, GLM, Bailian, and other providers still need to be configured in the corresponding CLI first:
711
+
712
+ - Codex provider / profile: see [15 Codex Provider Setup](./15_CODEX_PROVIDER_SETUP.md)
713
+ - Claude Code / Anthropic-compatible / Ollama: see [24 Claude Code Setup](./24_CLAUDE_CODE_PROVIDER_SETUP.md)
714
+ - OpenCode / Gemini / Ollama: see [25 OpenCode Setup](./25_OPENCODE_PROVIDER_SETUP.md)
715
+ - vLLM, Ollama, SGLang, and local backend overview: see [21 Local Model Backends Guide](./21_LOCAL_MODEL_BACKENDS_GUIDE.md)
716
+
717
+ Recommended validation order:
718
+
719
+ 1. make the underlying CLI work first, such as `codex exec ...`, `claude -p ...`, or `opencode run ...`
720
+ 2. fill `binary`, `config_dir`, `profile` / `model`, and `env` in Settings
721
+ 3. click `Test` or run `ds doctor --runner <name>`
722
+ 4. only then start a real quest
420
723
 
421
724
  ### Schema
422
725
 
@@ -426,25 +729,63 @@ codex:
426
729
  binary: codex
427
730
  config_dir: ~/.codex
428
731
  profile: ""
429
- model: gpt-5.4
732
+ model: inherit
430
733
  model_reasoning_effort: xhigh
431
734
  approval_policy: never
432
735
  sandbox_mode: danger-full-access
433
736
  retry_on_failure: true
434
- retry_max_attempts: 5
435
- retry_initial_backoff_sec: 1.0
436
- retry_backoff_multiplier: 2.0
437
- retry_max_backoff_sec: 8.0
438
- mcp_tool_timeout_sec: 180000
737
+ retry_max_attempts: 7
738
+ retry_initial_backoff_sec: 10.0
739
+ retry_backoff_multiplier: 6.0
740
+ retry_max_backoff_sec: 1800.0
741
+ mcp_tool_timeout_sec: 172800
439
742
  env: {}
440
743
  claude:
441
744
  enabled: false
442
745
  binary: claude
443
746
  config_dir: ~/.claude
444
747
  model: inherit
445
- model_reasoning_effort: ""
748
+ permission_mode: bypassPermissions
749
+ mcp_timeout_ms: 172800000
750
+ mcp_tool_timeout_ms: 172800000
751
+ retry_on_failure: true
752
+ retry_max_attempts: 4
753
+ retry_initial_backoff_sec: 10.0
754
+ retry_backoff_multiplier: 4.0
755
+ retry_max_backoff_sec: 600.0
756
+ env: {}
757
+ status: supported
758
+ kimi:
759
+ enabled: false
760
+ binary: kimi
761
+ config_dir: ~/.kimi
762
+ model: inherit
763
+ agent: ""
764
+ thinking: false
765
+ yolo: true
766
+ mcp_tool_timeout_ms: 172800000
767
+ retry_on_failure: true
768
+ retry_max_attempts: 4
769
+ retry_initial_backoff_sec: 10.0
770
+ retry_backoff_multiplier: 4.0
771
+ retry_max_backoff_sec: 600.0
446
772
  env: {}
447
- status: reserved_todo
773
+ status: supported
774
+ opencode:
775
+ enabled: false
776
+ binary: opencode
777
+ config_dir: ~/.config/opencode
778
+ model: inherit
779
+ default_agent: ""
780
+ variant: ""
781
+ mcp_timeout_ms: 172800000
782
+ retry_on_failure: true
783
+ retry_max_attempts: 4
784
+ retry_initial_backoff_sec: 10.0
785
+ retry_backoff_multiplier: 4.0
786
+ retry_max_backoff_sec: 600.0
787
+ env: {}
788
+ status: supported
448
789
  ```
449
790
 
450
791
  ### Editable fields
@@ -452,153 +793,184 @@ claude:
452
793
  **`enabled`**
453
794
 
454
795
  - Type: `boolean`
455
- - Default: `codex=true`, `claude=false`
456
796
  - UI label: `Enabled`
457
- - Meaning: whether this runner can be selected and used.
797
+ - Meaning: whether the runner can be selected and executed.
798
+ - Practical rule: enable only the runners whose CLI binary and auth path already work on this machine.
458
799
 
459
800
  **`binary`**
460
801
 
461
802
  - Type: `string`
462
- - Default: `codex` or `claude`
463
803
  - UI label: `Binary`
464
804
  - Meaning: command name or absolute path used to launch the runner.
465
- - `Test` behavior: checks whether the binary is on `PATH`.
466
- - Resolution order for `codex`: env override, explicit path, local `PATH`, then bundled fallback.
467
- - One-off note: you can temporarily override this with `ds --codex /absolute/path/to/codex`.
468
- - First-run note: DeepScientist does not finish Codex authentication for you. Before the first `ds`, make sure `codex login` (or just `codex`) has completed successfully.
469
- - Repair note: if the bundled dependency is missing after `npm install -g @researai/deepscientist`, install Codex explicitly with `npm install -g @openai/codex`.
805
+ - Defaults:
806
+ - `codex -> codex`
807
+ - `claude -> claude`
808
+ - `opencode -> opencode`
809
+ - `Test` behavior: checks whether the binary is available on `PATH` or at the configured path.
470
810
 
471
811
  **`config_dir`**
472
812
 
473
813
  - Type: `string`
474
- - Default: `~/.codex` or `~/.claude`
475
814
  - UI label: `Config directory`
476
- - Meaning: global runner home for auth and global config.
815
+ - Meaning: global runner home used for auth and global settings.
816
+ - Defaults:
817
+ - `codex -> ~/.codex`
818
+ - `claude -> ~/.claude`
819
+ - `opencode -> ~/.config/opencode`
477
820
 
478
821
  **`profile`**
479
822
 
480
823
  - Type: `string`
481
- - Default: `""`
482
824
  - UI label: `Codex profile`
483
- - Meaning: optional Codex profile name passed through as `codex --profile <name>`.
484
- - Use this when your Codex CLI is already configured for a provider-backed setup such as MiniMax, GLM, Volcengine Ark, or Alibaba Bailian.
485
- - One-off note: you can also leave this field empty and launch with `ds --codex-profile <name>`.
486
- - Combined note: one-off profile and binary overrides can be combined as `ds --codex /absolute/path/to/codex --codex-profile <name>`.
825
+ - Runners: `codex`
826
+ - Meaning: optional Codex profile passed as `codex --profile <name>`.
827
+ - Use this when Codex itself is already configured for a provider-backed profile.
487
828
 
488
829
  **`model`**
489
830
 
490
831
  - Type: `string`
491
- - Default: `codex=gpt-5.4`, `claude=inherit`
492
832
  - UI label: `Default model`
493
- - Meaning: default model used when a project does not override it.
494
- - Startup note: DeepScientist's Codex readiness probe uses this configured model first. If your Codex account cannot access it, DeepScientist falls back to the current Codex default model and persists `model: inherit`.
495
- - Provider-profile note: when `profile` is set, `model: inherit` is usually the right choice so the Codex profile itself controls the provider model.
833
+ - Meaning: default runner model when a quest or request does not override it.
834
+ - Default: `inherit` for all four runners.
835
+ - Recommended rule:
836
+ - keep `inherit` when the CLI should decide the provider/model itself
837
+ - set a fixed model only when you want DeepScientist to override every turn
496
838
 
497
839
  **`model_reasoning_effort`**
498
840
 
499
841
  - Type: `string`
500
- - Default: `codex=xhigh`
501
842
  - UI label: `Reasoning effort`
843
+ - Runners: `codex`
844
+ - Meaning: default Codex reasoning effort.
502
845
  - Allowed values: `""`, `minimal`, `low`, `medium`, `high`, `xhigh`
503
- - Meaning: default reasoning intensity.
504
- - Compatibility note: when DeepScientist detects a Codex CLI older than `0.63.0`, it automatically downgrades `xhigh` to `high` for the startup probe and runner command. This covers MiniMax's currently recommended `@openai/codex@0.57.0` path.
505
846
 
506
847
  **`approval_policy`**
507
848
 
508
849
  - Type: `string`
509
- - Default: `never`
510
850
  - UI label: `Approval policy`
851
+ - Runners: `codex`
852
+ - Meaning: Codex approval behavior for privileged actions.
511
853
  - Allowed values: `never`, `on-failure`, `on-request`, `untrusted`
512
- - Meaning: how the runner should ask for permission on privileged actions.
513
- - Runtime note: the launcher now starts Codex in YOLO mode by default. Passing `ds --yolo false` temporarily restores the non-YOLO pair `approval_policy=on-request` and `sandbox_mode=workspace-write`.
514
854
 
515
855
  **`sandbox_mode`**
516
856
 
517
857
  - Type: `string`
518
- - Default: `danger-full-access`
519
858
  - UI label: `Sandbox mode`
859
+ - Runners: `codex`
860
+ - Meaning: Codex filesystem / process sandbox mode.
520
861
  - Allowed values: `read-only`, `workspace-write`, `danger-full-access`
521
- - Meaning: filesystem / process access mode for the runner.
522
862
 
523
- **`env`**
863
+ **`permission_mode`**
524
864
 
525
- - Type: `mapping<string, string>`
526
- - Default: `{}`
527
- - UI availability:
528
- - global settings: editable in the `runners` structured form as `env`
529
- - project settings: `Project settings -> Codex environment`
530
- - Project-settings behavior:
531
- - click `Add` to create a new variable row
532
- - `OPENAI_BASE_URL` and `OPENAI_API_KEY` are shown by default
533
- - changes are not auto-saved; click `Save env vars`
534
- - empty values are ignored and are not injected into the Codex process
535
- - Meaning: extra environment variables passed to Codex when DeepScientist starts a Codex run.
536
- - Common use: provider-backed Codex setups that need API keys or custom base URLs.
537
-
538
- **`retry_on_failure`**
539
-
540
- - Type: `boolean`
541
- - Default: `true`
542
- - UI label: `Retry on failure`
543
- - Meaning: retry a failed turn automatically.
865
+ - Type: `string`
866
+ - UI label: `Permission mode`
867
+ - Runners: `claude`
868
+ - Meaning: Claude Code permission mode passed through as `--permission-mode`.
869
+ - Common values: `default`, `bypassPermissions`, `dontAsk`, `acceptEdits`, `delegate`, `plan`
870
+ - Recommended local automation default: `bypassPermissions`
544
871
 
545
- **`retry_max_attempts`**
872
+ **`mcp_timeout_ms`**
546
873
 
547
874
  - Type: `number`
548
- - Default: `5`
549
- - UI label: `Max attempts`
550
- - Meaning: total allowed attempts for one turn.
551
- - Notes: runtime hard-caps this at `5`.
875
+ - Runners: `claude`, `opencode`
876
+ - Meaning:
877
+ - `claude`: MCP server startup timeout forwarded as `MCP_TIMEOUT`
878
+ - `opencode`: timeout for fetching tools from each MCP server during startup
879
+ - Note: OpenCode's `mcp_timeout_ms` is not tool execution timeout.
552
880
 
553
- **`retry_initial_backoff_sec`**
881
+ **`mcp_tool_timeout_ms`**
554
882
 
555
883
  - Type: `number`
556
- - Default: `1.0`
557
- - UI label: `Initial backoff (s)`
558
- - Meaning: delay before the first retry.
884
+ - Runners: `claude`, `kimi`
885
+ - Meaning:
886
+ - `claude`: per-tool MCP timeout forwarded as `MCP_TOOL_TIMEOUT`
887
+ - `kimi`: MCP tool execution timeout written to `.kimi/config.toml` as `mcp.client.tool_call_timeout_ms`
559
888
 
560
- **`retry_backoff_multiplier`**
889
+ **`agent`**
561
890
 
562
- - Type: `number`
563
- - Default: `2.0`
564
- - UI label: `Backoff multiplier`
565
- - Meaning: exponential backoff multiplier.
891
+ - Type: `string`
892
+ - UI label: `Kimi agent`
893
+ - Runners: `kimi`
894
+ - Meaning: optional Kimi agent name passed through as `kimi --agent <name>`.
895
+ - Leave empty unless the same agent profile already works in direct Kimi CLI usage.
566
896
 
567
- **`retry_max_backoff_sec`**
897
+ **`thinking`**
568
898
 
569
- - Type: `number`
570
- - Default: `8.0`
571
- - UI label: `Max backoff (s)`
572
- - Meaning: upper bound on retry delay after exponential growth.
899
+ - Type: `boolean`
900
+ - UI label: `Thinking mode`
901
+ - Runners: `kimi`
902
+ - Meaning: whether DeepScientist should pass `--thinking` to Kimi by default.
573
903
 
574
- **`status`**
904
+ **`yolo`**
905
+
906
+ - Type: `boolean`
907
+ - UI label: `Yolo mode`
908
+ - Runners: `kimi`
909
+ - Meaning: whether DeepScientist should pass `--yolo` so Kimi does not stop for interactive approval prompts.
910
+ - Recommended unattended local automation default: `true`
911
+
912
+ **`default_agent`**
913
+
914
+ - Type: `string`
915
+ - UI label: `Default agent`
916
+ - Runners: `opencode`
917
+ - Meaning: optional OpenCode agent name passed through as `opencode run --agent <name>`.
918
+ - Leave empty unless the same agent name already works in direct OpenCode CLI usage.
919
+
920
+ **`variant`**
575
921
 
576
922
  - Type: `string`
577
- - Default: `claude=reserved_todo`
578
- - UI label: `Status note`
579
- - Meaning: operator-facing note such as `reserved_todo` or `experimental`.
923
+ - UI label: `Variant`
924
+ - Runners: `opencode`
925
+ - Meaning: optional OpenCode provider-specific variant passed through as `--variant`.
926
+ - Use only when your OpenCode provider documents that flag.
580
927
 
581
- ### File-level companion fields
928
+ **`env`**
929
+
930
+ - Type: `mapping<string, string>`
931
+ - UI label: `Environment variables`
932
+ - Meaning: extra environment variables injected only for this runner.
933
+ - Common examples:
934
+ - Codex: `OPENAI_API_KEY`, `OPENAI_BASE_URL`
935
+ - Claude: `ANTHROPIC_API_KEY`, `ANTHROPIC_BASE_URL`, `CLAUDE_CODE_MAX_OUTPUT_TOKENS`
936
+ - Kimi: usually empty unless your local Kimi CLI path requires extra environment variables
937
+ - OpenCode: provider-specific environment variables only if your OpenCode provider setup requires them
938
+
939
+ **`retry_on_failure` / `retry_max_attempts` / `retry_initial_backoff_sec` / `retry_backoff_multiplier` / `retry_max_backoff_sec`**
940
+
941
+ - Type: `boolean` / `number`
942
+ - Meaning: automatic turn retry policy for the runner.
943
+ - Defaults:
944
+ - `codex`: more aggressive retry ladder
945
+ - `claude` / `kimi` / `opencode`: shorter ladder
582
946
 
583
947
  **`mcp_tool_timeout_sec`**
584
948
 
585
949
  - Type: `number`
586
- - Default: `180000`
587
- - Meaning: allow long-running MCP tool calls, especially durable `bash_exec` flows.
950
+ - Runners: `codex`
951
+ - Meaning: maximum MCP tool wait time, mainly for long `bash_exec` flows.
588
952
 
589
- **`env`**
953
+ **`status`**
590
954
 
591
- - Type: `mapping[string, string]`
592
- - Default: `{}`
593
- - UI location: environment editor at the bottom of each runner card
594
- - Meaning: per-runner environment overrides.
955
+ - Type: `string`
956
+ - Meaning: operator-facing note.
957
+ - Current practical meaning:
958
+ - `codex`, `claude`, `kimi`, `opencode`: available built-in paths
595
959
 
596
960
  ### Practical guidance
597
961
 
598
- - For most installs, keep `codex.enabled: true` and `claude.enabled: false`.
599
- - Do not switch `default_runner` away from `codex` in the current release.
600
- - Do not lower `mcp_tool_timeout_sec` casually if your workflow uses long-running tools.
601
- - Keep retry timing close to `1s / 2x / 8s max` unless you have a specific reason to slow recovery down.
962
+ - Use the runner that already works on your machine and matches the provider path you want.
963
+ - Use `claude` when Claude Code already works directly on the machine and you want Anthropic / Claude-native execution.
964
+ - Use `kimi` when the official Kimi Code CLI already works directly on the machine and you want a separate Moonshot-native runner path.
965
+ - Use `opencode` when your model/provider setup already works best through OpenCode.
966
+ - `default_runner` can now be switched away from `codex` safely if the target runner is enabled and passes `ds doctor`.
967
+ - New quests follow `config.default_runner`.
968
+ - Existing quests can override the runner in project settings.
969
+ - Do not lower `mcp_tool_timeout_sec` casually if your workflow uses long-running `bash_exec` sessions.
970
+ - For Kimi, the important timeout is `mcp_tool_timeout_ms`, because the upstream default is much shorter than the long-running `bash_exec` waits DeepScientist often needs.
971
+ - For Claude, the practical execution cap is already large by default; the more common issue is MCP startup timeout, handled by `mcp_timeout_ms`.
972
+ - For OpenCode, `mcp_timeout_ms` only affects MCP tool discovery / startup, not the execution time of one MCP call.
973
+
602
974
 
603
975
  ## `connectors.yaml`
604
976