pen-stack 8.0.1__tar.gz → 8.0.3__tar.gz

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 (602) hide show
  1. {pen_stack-8.0.1 → pen_stack-8.0.3}/CHANGELOG.md +2529 -2495
  2. {pen_stack-8.0.1 → pen_stack-8.0.3}/CITATION.cff +1 -1
  3. {pen_stack-8.0.1 → pen_stack-8.0.3}/PKG-INFO +382 -381
  4. {pen_stack-8.0.1 → pen_stack-8.0.3}/README.md +5 -4
  5. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_grounding/SHA256SUMS +1 -1
  6. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_routing/SHA256SUMS +1 -1
  7. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_safety/SHA256SUMS +1 -1
  8. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_bench/LEADERBOARD.md +66 -66
  9. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_bench/README.md +87 -87
  10. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_bench/SUBMISSIONS.md +53 -53
  11. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genotox_panel/README.md +24 -1
  12. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/loop/SHA256SUMS +2 -2
  13. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/offtarget/integrase/README.md +23 -23
  14. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/offtarget/integrase/SHA256SUMS +4 -4
  15. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/oracle/SHA256SUMS +5 -5
  16. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/position_effect/README.md +68 -68
  17. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/position_effect/SHA256SUMS +1 -1
  18. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/priorart/epridict/README.md +62 -62
  19. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/priorart/epridict/SHA256SUMS +5 -5
  20. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/priorart/gsh_recovery/README.md +66 -66
  21. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/priorart/gsh_recovery/SHA256SUMS +4 -4
  22. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/writer_efficiency/SHA256SUMS +2 -2
  23. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/writespec/SHA256SUMS +4 -4
  24. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/intent_weights.yaml +57 -57
  25. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/monitor_queries.yaml +33 -33
  26. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/delivery.yaml +49 -49
  27. pen_stack-8.0.3/configs/safety/genotoxic_loci.yaml +57 -0
  28. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/bridge_offtarget_energetics.json +201 -201
  29. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/cast_systems.yaml +59 -59
  30. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/integrase_att.yaml +66 -66
  31. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/DEPLOY.md +39 -39
  32. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/INFRA.md +64 -64
  33. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/MCP.md +24 -24
  34. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/REPRO.md +46 -46
  35. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/biosecurity.md +102 -102
  36. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/atlas.md +41 -41
  37. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/durability.md +43 -43
  38. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/offtarget_data.md +117 -117
  39. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/priorart.md +66 -66
  40. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/safety.md +39 -39
  41. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/dissemination.md +34 -34
  42. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/index.md +48 -48
  43. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/position_effect.md +57 -57
  44. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/positioning.md +55 -55
  45. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/private_data_formats.md +61 -61
  46. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/quickstart.md +64 -64
  47. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/responsible_use.md +96 -96
  48. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/scope.md +50 -50
  49. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/scorecard.md +54 -54
  50. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/tpe_bench.md +48 -48
  51. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/tutorials/score-deliverability.md +36 -36
  52. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/tutorials/where-can-i-write.md +45 -45
  53. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/tutorials/which-writer-reaches-locus.md +41 -41
  54. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/writer_verification.md +46 -46
  55. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/wtkb.md +25 -25
  56. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/__init__.py +1 -1
  57. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/acquire.py +165 -165
  58. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/design.py +66 -66
  59. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/__init__.py +14 -14
  60. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/finetune.py +33 -33
  61. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/__init__.py +1 -1
  62. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/tools.py +130 -130
  63. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/__init__.py +1 -1
  64. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/crosslink.py +179 -175
  65. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/guide_design.py +178 -178
  66. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/universe.py +75 -75
  67. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/writer_recommend.py +165 -165
  68. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/__init__.py +1 -1
  69. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/activity.py +52 -52
  70. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/__init__.py +1 -1
  71. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/writer_variants.py +122 -122
  72. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/query.py +148 -148
  73. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/mech/__init__.py +1 -1
  74. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/monitor/__init__.py +1 -1
  75. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/__init__.py +1 -1
  76. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery_predict.py +196 -196
  77. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/immune_profile.py +292 -292
  78. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/optimize.py +278 -278
  79. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/pipeline.py +87 -87
  80. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/__init__.py +1 -1
  81. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/evaluators.py +330 -330
  82. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/gate.py +58 -58
  83. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/score/__init__.py +1 -1
  84. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/score/recalibrate.py +77 -77
  85. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/server/__init__.py +1 -1
  86. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/server/api.py +647 -647
  87. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/data/position_effect.py +251 -251
  88. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/mechanistic.py +136 -136
  89. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/outcome.py +132 -132
  90. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/position_effect.py +454 -443
  91. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/ui/__init__.py +1 -1
  92. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/__init__.py +1 -1
  93. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/known_biology_expr.py +38 -38
  94. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/verify/proof.py +206 -206
  95. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/__init__.py +1 -1
  96. pen_stack-8.0.3/pen_stack/wgenome/genotoxic_blocklist.py +88 -0
  97. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_assay.py +80 -80
  98. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_bridge.py +47 -47
  99. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_cast.py +97 -97
  100. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_enumerate.py +271 -271
  101. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_integrase.py +155 -155
  102. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_nuclease.py +98 -98
  103. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_paste.py +41 -41
  104. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/PKG-INFO +382 -381
  105. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/SOURCES.txt +2 -0
  106. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_phase0.json +8 -8
  107. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_phase1_5.json +10 -10
  108. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_phase2.json +11 -11
  109. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_phase3.json +10 -10
  110. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_a.json +11 -11
  111. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_acq.json +8 -8
  112. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_aldesign.json +8 -8
  113. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_alvalidate.json +8 -8
  114. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_atlas.json +8 -8
  115. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_b.json +11 -11
  116. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ba.json +9 -9
  117. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ba_v33.json +9 -9
  118. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ba_v45.json +8 -8
  119. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_bench.json +8 -8
  120. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_c.json +9 -9
  121. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_cal.json +8 -8
  122. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_calib.json +8 -8
  123. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_challenge.json +8 -8
  124. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_chat.json +8 -8
  125. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_cite.json +8 -8
  126. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_closedloop.json +8 -8
  127. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_continual.json +8 -8
  128. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_cosci2.json +8 -8
  129. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_crit.json +8 -8
  130. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ct.json +8 -8
  131. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_d.json +10 -10
  132. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_delivery.json +8 -8
  133. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_drift.json +8 -8
  134. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_e.json +9 -9
  135. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_env.json +8 -8
  136. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ep.json +9 -9
  137. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_epitope.json +8 -8
  138. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_expr2.json +7 -7
  139. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_f.json +8 -8
  140. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_frontend.json +8 -8
  141. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_g.json +8 -8
  142. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_gen.json +8 -8
  143. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_genotox.json +8 -8
  144. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_graph.json +8 -8
  145. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_h.json +8 -8
  146. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_hybrid.json +8 -8
  147. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_immune.json +8 -8
  148. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_immune2.json +8 -8
  149. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_ingest.json +8 -8
  150. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_innate.json +8 -8
  151. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_loop.json +8 -8
  152. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_manifest.json +8 -8
  153. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_mc.json +10 -10
  154. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_mcp.json +8 -8
  155. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_mech.json +8 -8
  156. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_mon.json +8 -8
  157. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_o.json +8 -8
  158. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_offtarget.json +8 -8
  159. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_offtarget2.json +9 -9
  160. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_openapi.json +8 -8
  161. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_oracle.json +8 -8
  162. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_orch.json +8 -8
  163. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_outcome.json +8 -8
  164. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_pareto.json +8 -8
  165. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_peg.json +8 -8
  166. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_penchat.json +9 -9
  167. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_plan.json +8 -8
  168. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_policy.json +9 -9
  169. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_priorart.json +10 -10
  170. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_profile.json +8 -8
  171. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_proto.json +8 -8
  172. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_r.json +14 -14
  173. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_redteam.json +9 -9
  174. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_route.json +9 -9
  175. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_screen.json +10 -10
  176. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_seroprev.json +8 -8
  177. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_simlab.json +8 -8
  178. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_twincal.json +8 -8
  179. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_uq.json +9 -9
  180. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_v.json +8 -8
  181. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_vcell.json +8 -8
  182. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_verify.json +8 -8
  183. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_writer.json +8 -8
  184. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_writespec.json +8 -8
  185. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/SHA256_LOCK_ws_wv.json +8 -8
  186. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/paper1.yaml +60 -60
  187. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/paper2.yaml +74 -74
  188. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/paper3.yaml +64 -64
  189. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/paper4.yaml +71 -71
  190. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/phase0.yaml +28 -28
  191. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_a.yaml +57 -57
  192. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_atlas.yaml +18 -18
  193. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_b.yaml +50 -50
  194. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ba.yaml +45 -45
  195. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ba_v33.yaml +12 -12
  196. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_bench.yaml +25 -25
  197. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_chat.yaml +20 -20
  198. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_crit.yaml +16 -16
  199. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_d.yaml +11 -11
  200. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ep.yaml +40 -40
  201. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_expr2.yaml +39 -39
  202. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_f.yaml +38 -38
  203. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_frontend.yaml +21 -21
  204. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_g.yaml +37 -37
  205. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_h.yaml +32 -32
  206. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_mc.yaml +51 -51
  207. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_mon.yaml +21 -21
  208. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_offtarget2.yaml +106 -106
  209. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_priorart.yaml +169 -169
  210. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_route.yaml +9 -9
  211. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_seroprev.yaml +40 -40
  212. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_uq.yaml +62 -62
  213. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_wv.yaml +20 -20
  214. {pen_stack-8.0.1 → pen_stack-8.0.3}/pyproject.toml +1 -1
  215. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/build_capsid_fitness.py +98 -98
  216. {pen_stack-8.0.1 → pen_stack-8.0.3}/setup.cfg +4 -4
  217. {pen_stack-8.0.1 → pen_stack-8.0.3}/LICENSE +0 -0
  218. {pen_stack-8.0.1 → pen_stack-8.0.3}/MANIFEST.in +0 -0
  219. {pen_stack-8.0.1 → pen_stack-8.0.3}/bench/run.py +0 -0
  220. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/agentic_baseline/README.md +0 -0
  221. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_grounding/README.md +0 -0
  222. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_headtohead/README.md +0 -0
  223. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_routing/README.md +0 -0
  224. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/chat_safety/README.md +0 -0
  225. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/delivery/SHA256SUMS +0 -0
  226. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_bench/SHA256SUMS +0 -0
  227. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_bench/tasks.yaml +0 -0
  228. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_challenge/README.md +0 -0
  229. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/genome_writing_challenge/SUBMISSIONS.md +0 -0
  230. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/grounding_llm_on/README.md +0 -0
  231. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/offtarget/SHA256SUMS +0 -0
  232. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/offtarget/integrase_chalberg/README.md +0 -0
  233. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/position_effect_human/README.md +0 -0
  234. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/position_effect_human/SHA256SUMS +0 -0
  235. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/verify/SHA256SUMS +0 -0
  236. {pen_stack-8.0.1 → pen_stack-8.0.3}/benchmarks/writer_efficiency/README.md +0 -0
  237. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/aav_serotype_tropism.yaml +0 -0
  238. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/antipeg.yaml +0 -0
  239. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/atlas_families.yaml +0 -0
  240. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/bridge_offtarget_profile.yaml +0 -0
  241. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/calibration/preexisting_nab_independent.yaml +0 -0
  242. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/capsid_epitope_oracle.yaml +0 -0
  243. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/capsid_sequences.fasta +0 -0
  244. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/cargo_polish.yaml +0 -0
  245. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/cell_types.yaml +0 -0
  246. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/datasets.yaml +0 -0
  247. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/delivery_constraints.yaml +0 -0
  248. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/delivery_rules.yaml +0 -0
  249. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/delivery_vehicles.yaml +0 -0
  250. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/expression/modifiers.yaml +0 -0
  251. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/expression/promoters.yaml +0 -0
  252. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/gates_v3.yaml +0 -0
  253. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/genotoxicity_oracle.yaml +0 -0
  254. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/gsh_validated_heldout.yaml +0 -0
  255. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/known_unknowns.yaml +0 -0
  256. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/llm.yaml +0 -0
  257. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/metric_guide.yaml +0 -0
  258. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/mhc_epitope_oracle.yaml +0 -0
  259. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/oracles/execution.yaml +0 -0
  260. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/oracles/reliability.yaml +0 -0
  261. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/oracles/scope_cards.yaml +0 -0
  262. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/compliance.yaml +0 -0
  263. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/fold.yaml +0 -0
  264. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/multiplex.yaml +0 -0
  265. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/payload.yaml +0 -0
  266. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/rules/reachability.yaml +0 -0
  267. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/safety/hazard_registry.yaml +0 -0
  268. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/safety/policy.yaml +0 -0
  269. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/safety/probes.yaml +0 -0
  270. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/score_axes.yaml +0 -0
  271. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/seroprevalence.yaml +0 -0
  272. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/target_sites.yaml +0 -0
  273. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/universe_crosswalk.yaml +0 -0
  274. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/write_types.yaml +0 -0
  275. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/writer_sequences.fasta +0 -0
  276. {pen_stack-8.0.1 → pen_stack-8.0.3}/configs/wtkb_curated.yaml +0 -0
  277. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/bridge_offtarget_profile_measured.parquet +0 -0
  278. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/gene_coords.parquet +0 -0
  279. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/curated/unified_editor_universe.parquet +0 -0
  280. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/offtarget/enumerated_cache.parquet +0 -0
  281. {pen_stack-8.0.1 → pen_stack-8.0.3}/data/offtarget/motif_cache.parquet +0 -0
  282. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/BACKLOG.md +0 -0
  283. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/RELEASING.md +0 -0
  284. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/STABILITY.md +0 -0
  285. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/agent.md +0 -0
  286. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/alphagenome_feasibility.md +0 -0
  287. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/autonomy.md +0 -0
  288. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/benchmark_circularity.md +0 -0
  289. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/build_interface.md +0 -0
  290. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/position_effect_data.md +0 -0
  291. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/cards/writer_efficiency_data.md +0 -0
  292. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/challenge.md +0 -0
  293. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/closed_loop.md +0 -0
  294. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/co_scientist.md +0 -0
  295. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/co_scientist_loop.md +0 -0
  296. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/delivery.md +0 -0
  297. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/delivery_immunology.md +0 -0
  298. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/delivery_recommender.md +0 -0
  299. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/digital_twin.md +0 -0
  300. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/environment.md +0 -0
  301. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/experiment_design.md +0 -0
  302. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/generative_design.md +0 -0
  303. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/immune_profiler.md +0 -0
  304. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/integrations.md +0 -0
  305. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/live_oracles.md +0 -0
  306. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/mechanistic_constraints.md +0 -0
  307. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/offtarget.md +0 -0
  308. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/oracle_mesh.md +0 -0
  309. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/oracles.md +0 -0
  310. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/rule_spec.md +0 -0
  311. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/rules.md +0 -0
  312. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/tutorials/compare-families.md +0 -0
  313. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/uncertainty.md +0 -0
  314. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/verify.md +0 -0
  315. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/verify_service.md +0 -0
  316. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/world_model.md +0 -0
  317. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/writer_efficiency.md +0 -0
  318. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/writespec_bench.md +0 -0
  319. {pen_stack-8.0.1 → pen_stack-8.0.3}/docs/writespec_profile.md +0 -0
  320. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/_resources.py +0 -0
  321. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/__init__.py +0 -0
  322. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/brains.py +0 -0
  323. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/campaign.py +0 -0
  324. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/active/validate.py +0 -0
  325. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/ingest.py +0 -0
  326. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/pipeline.py +0 -0
  327. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/recalibrate.py +0 -0
  328. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/adapt/report.py +0 -0
  329. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/cite.py +0 -0
  330. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/co_scientist.py +0 -0
  331. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/epistemic.py +0 -0
  332. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/guardrails.py +0 -0
  333. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/mcp_server.py +0 -0
  334. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/orchestrator.py +0 -0
  335. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/orchestrator_live.py +0 -0
  336. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/pen_agent.py +0 -0
  337. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/agent/scope.py +0 -0
  338. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/api/__init__.py +0 -0
  339. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/api/manifest.py +0 -0
  340. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/build_wtkb.py +0 -0
  341. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/expand.py +0 -0
  342. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/schema.py +0 -0
  343. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/scorecard.py +0 -0
  344. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/variant_propose.py +0 -0
  345. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/writer_efficiency.py +0 -0
  346. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/writer_predict.py +0 -0
  347. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/atlas/writer_verify.py +0 -0
  348. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/cli.py +0 -0
  349. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/fold_qc.py +0 -0
  350. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/guide_qc.py +0 -0
  351. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/ingest.py +0 -0
  352. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/offtarget.py +0 -0
  353. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/offtarget_energetics.py +0 -0
  354. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/ortholog_screen.py +0 -0
  355. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/bridge/pipeline.py +0 -0
  356. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/build/__init__.py +0 -0
  357. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/build/cloudlab.py +0 -0
  358. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/build/ingest.py +0 -0
  359. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/build/protocol.py +0 -0
  360. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/build/simlab.py +0 -0
  361. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/cli.py +0 -0
  362. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/encode.py +0 -0
  363. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/genome.py +0 -0
  364. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/ingest_chromatin.py +0 -0
  365. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/ingest_integration.py +0 -0
  366. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/ingest_safety_annot.py +0 -0
  367. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/data/ingest_trip.py +0 -0
  368. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/__init__.py +0 -0
  369. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/capsid_generate.py +0 -0
  370. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/generate.py +0 -0
  371. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/pareto.py +0 -0
  372. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/design/space.py +0 -0
  373. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/env/__init__.py +0 -0
  374. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/env/genome_writing_env.py +0 -0
  375. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/env/policies.py +0 -0
  376. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/__init__.py +0 -0
  377. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/build.py +0 -0
  378. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/cell_types.py +0 -0
  379. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/ingest.py +0 -0
  380. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/graph/schema.py +0 -0
  381. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/loop/__init__.py +0 -0
  382. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/loop/continual.py +0 -0
  383. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/loop/cycle.py +0 -0
  384. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/loop/drift.py +0 -0
  385. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/mech/classify_atlas.py +0 -0
  386. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/mech/whitelist.py +0 -0
  387. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/monitor/europepmc.py +0 -0
  388. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/monitor/run.py +0 -0
  389. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/monitor/triage.py +0 -0
  390. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/__init__.py +0 -0
  391. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/affinity.py +0 -0
  392. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/cache.py +0 -0
  393. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/energetics.py +0 -0
  394. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/genome.py +0 -0
  395. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/protein_design.py +0 -0
  396. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/reliability.py +0 -0
  397. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/rna.py +0 -0
  398. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/schema.py +0 -0
  399. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/status.py +0 -0
  400. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/structure.py +0 -0
  401. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/structure_run.py +0 -0
  402. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/oracles/vcell.py +0 -0
  403. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/ada_risk.py +0 -0
  404. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/antipeg_oracle.py +0 -0
  405. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/capsid_epitope_oracle.py +0 -0
  406. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/cargo.py +0 -0
  407. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/cargo_polish.py +0 -0
  408. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/chromosome.py +0 -0
  409. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery.py +0 -0
  410. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery_constraints.py +0 -0
  411. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery_immune.py +0 -0
  412. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery_immunology.py +0 -0
  413. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/delivery_vehicles.py +0 -0
  414. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/genotoxicity_oracle.py +0 -0
  415. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/immune_mhc2.py +0 -0
  416. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/innate_sensing.py +0 -0
  417. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/multiplex.py +0 -0
  418. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/report.py +0 -0
  419. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/router.py +0 -0
  420. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/seroprevalence_oracle.py +0 -0
  421. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/planner/target_site.py +0 -0
  422. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/corpus.py +0 -0
  423. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/embed.py +0 -0
  424. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/ground.py +0 -0
  425. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/index.py +0 -0
  426. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/llm.py +0 -0
  427. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/qa.py +0 -0
  428. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rag/retrieve.py +0 -0
  429. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/__init__.py +0 -0
  430. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/loader.py +0 -0
  431. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/schema.py +0 -0
  432. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/solver.py +0 -0
  433. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/rules/spec.py +0 -0
  434. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/__init__.py +0 -0
  435. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/audit.py +0 -0
  436. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/pfam_scan.py +0 -0
  437. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/policy.py +0 -0
  438. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/redteam.py +0 -0
  439. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/registry.py +0 -0
  440. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/screen.py +0 -0
  441. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/safety/standards.py +0 -0
  442. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/score/therapeutic.py +0 -0
  443. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/__init__.py +0 -0
  444. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/clarify.py +0 -0
  445. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/extract.py +0 -0
  446. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/__init__.py +0 -0
  447. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/cell.py +0 -0
  448. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/chem.py +0 -0
  449. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/feature.py +0 -0
  450. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/gene.py +0 -0
  451. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/locus.py +0 -0
  452. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/resolvers/phenotype.py +0 -0
  453. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/satisfy.py +0 -0
  454. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/service.py +0 -0
  455. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/spec/writespec.py +0 -0
  456. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/__init__.py +0 -0
  457. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/calibrate.py +0 -0
  458. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/twin/data/__init__.py +0 -0
  459. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/ui/app.py +0 -0
  460. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/adapt_demo.py +0 -0
  461. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/agent_eval.py +0 -0
  462. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_adversarial_tasks.py +0 -0
  463. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_coscientist_tasks.py +0 -0
  464. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_graph_tasks.py +0 -0
  465. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_rule_tasks.py +0 -0
  466. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_trust_tasks.py +0 -0
  467. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/bench_writetype_tasks.py +0 -0
  468. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/blind_gsh_discovery.py +0 -0
  469. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/cargo_directionality.py +0 -0
  470. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/closed_loop.py +0 -0
  471. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/durability_baselines.py +0 -0
  472. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/experiment_design.py +0 -0
  473. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/expr_controls.py +0 -0
  474. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/forward_hypotheses.py +0 -0
  475. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/generative_design.py +0 -0
  476. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/guide_qc_demo.py +0 -0
  477. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/heldout_celltype_expr.py +0 -0
  478. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/immune_calibration.py +0 -0
  479. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/intent_specification.py +0 -0
  480. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/offtarget_energetics_eval.py +0 -0
  481. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/out_of_scope_refusal.py +0 -0
  482. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/outcome_calibration.py +0 -0
  483. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/outcome_prediction.py +0 -0
  484. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/paper3_benchmark.py +0 -0
  485. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/paper4_real_validation.py +0 -0
  486. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/paper4_validation.py +0 -0
  487. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/protocol_safety.py +0 -0
  488. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/safety_screening.py +0 -0
  489. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/selective_prediction.py +0 -0
  490. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/seq_vs_measured.py +0 -0
  491. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/target_site_controls.py +0 -0
  492. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/uncertainty_eval.py +0 -0
  493. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/ungrounded_baseline.py +0 -0
  494. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/within_locus_ranking.py +0 -0
  495. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/validate/writer_recovery.py +0 -0
  496. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/verify/__init__.py +0 -0
  497. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/verify/schema.py +0 -0
  498. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/verify/service.py +0 -0
  499. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/__init__.py +0 -0
  500. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/guide.py +0 -0
  501. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/llm.py +0 -0
  502. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/llm_provider.py +0 -0
  503. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/router.py +0 -0
  504. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/server.py +0 -0
  505. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/web/tools.py +0 -0
  506. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/chromatin_seq.py +0 -0
  507. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/durability.py +0 -0
  508. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/export_tracks.py +0 -0
  509. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/features.py +0 -0
  510. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/gsh_baseline.py +0 -0
  511. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/mesh_features.py +0 -0
  512. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_data.py +0 -0
  513. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/offtarget_predict.py +0 -0
  514. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/ood.py +0 -0
  515. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/providers.py +0 -0
  516. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/safety.py +0 -0
  517. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/structure3d.py +0 -0
  518. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/uncertainty.py +0 -0
  519. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack/wgenome/writability.py +0 -0
  520. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/dependency_links.txt +0 -0
  521. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/entry_points.txt +0 -0
  522. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/requires.txt +0 -0
  523. {pen_stack-8.0.1 → pen_stack-8.0.3}/pen_stack.egg-info/top_level.txt +0 -0
  524. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_acq.yaml +0 -0
  525. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_aldesign.yaml +0 -0
  526. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_alvalidate.yaml +0 -0
  527. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ba_v45.yaml +0 -0
  528. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_c.yaml +0 -0
  529. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_cal.yaml +0 -0
  530. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_calib.yaml +0 -0
  531. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_challenge.yaml +0 -0
  532. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_cite.yaml +0 -0
  533. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_closedloop.yaml +0 -0
  534. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_continual.yaml +0 -0
  535. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_cosci2.yaml +0 -0
  536. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ct.yaml +0 -0
  537. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_delivery.yaml +0 -0
  538. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_drift.yaml +0 -0
  539. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_e.yaml +0 -0
  540. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_env.yaml +0 -0
  541. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_epitope.yaml +0 -0
  542. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_gen.yaml +0 -0
  543. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_genotox.yaml +0 -0
  544. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_graph.yaml +0 -0
  545. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_hybrid.yaml +0 -0
  546. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_immune.yaml +0 -0
  547. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_immune2.yaml +0 -0
  548. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_ingest.yaml +0 -0
  549. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_innate.yaml +0 -0
  550. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_loop.yaml +0 -0
  551. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_manifest.yaml +0 -0
  552. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_mcp.yaml +0 -0
  553. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_mech.yaml +0 -0
  554. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_o.yaml +0 -0
  555. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_offtarget.yaml +0 -0
  556. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_openapi.yaml +0 -0
  557. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_oracle.yaml +0 -0
  558. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_orch.yaml +0 -0
  559. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_outcome.yaml +0 -0
  560. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_pareto.yaml +0 -0
  561. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_peg.yaml +0 -0
  562. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_penchat.yaml +0 -0
  563. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_plan.yaml +0 -0
  564. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_policy.yaml +0 -0
  565. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_profile.yaml +0 -0
  566. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_proto.yaml +0 -0
  567. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_r.yaml +0 -0
  568. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_redteam.yaml +0 -0
  569. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_screen.yaml +0 -0
  570. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_simlab.yaml +0 -0
  571. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_twincal.yaml +0 -0
  572. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_v.yaml +0 -0
  573. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_vcell.yaml +0 -0
  574. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_verify.yaml +0 -0
  575. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_writer.yaml +0 -0
  576. {pen_stack-8.0.1 → pen_stack-8.0.3}/prereg/ws_writespec.yaml +0 -0
  577. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/build_rag_corpus.py +0 -0
  578. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/calibrate_immune_axes.py +0 -0
  579. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/fetch_artifacts.sh +0 -0
  580. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/fetch_licensed_sources.py +0 -0
  581. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/offtarget_chromatin_incremental.py +0 -0
  582. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/offtarget_chromatin_matched.py +0 -0
  583. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/offtarget_chromatin_validation.py +0 -0
  584. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_build_atlas.py +0 -0
  585. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_build_durability.py +0 -0
  586. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_build_position_effect.py +0 -0
  587. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_build_writer_eff.py +0 -0
  588. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_export_tracks.py +0 -0
  589. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_safety_concordance.py +0 -0
  590. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_train_safety.py +0 -0
  591. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p1_validation_report.py +0 -0
  592. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p2_build_atlas.py +0 -0
  593. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p2_build_human_head.py +0 -0
  594. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p3_benchmark_report.py +0 -0
  595. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p4_genome_scan.py +0 -0
  596. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p52_build_genotox_oracle.py +0 -0
  597. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/p53_build_epitope_oracle.py +0 -0
  598. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/pa_epridict_distinctness.py +0 -0
  599. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/reproduce.py +0 -0
  600. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/validate_components.py +0 -0
  601. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/ws_b_report.py +0 -0
  602. {pen_stack-8.0.1 → pen_stack-8.0.3}/scripts/ws_c_report.py +0 -0

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the package file manually.