pen-stack 7.2.3__tar.gz → 8.0.0__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 (601) hide show
  1. {pen_stack-7.2.3 → pen_stack-8.0.0}/CHANGELOG.md +2468 -2048
  2. {pen_stack-7.2.3 → pen_stack-8.0.0}/CITATION.cff +24 -19
  3. {pen_stack-7.2.3 → pen_stack-8.0.0}/PKG-INFO +350 -309
  4. {pen_stack-7.2.3 → pen_stack-8.0.0}/README.md +49 -10
  5. pen_stack-8.0.0/benchmarks/agentic_baseline/README.md +47 -0
  6. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/chat_grounding/SHA256SUMS +1 -1
  7. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/chat_routing/SHA256SUMS +1 -1
  8. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/chat_safety/SHA256SUMS +1 -1
  9. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/genome_writing_bench/README.md +87 -87
  10. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/genome_writing_bench/SHA256SUMS +7 -7
  11. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/genome_writing_bench/SUBMISSIONS.md +53 -53
  12. pen_stack-8.0.0/benchmarks/genotox_panel/README.md +107 -0
  13. pen_stack-8.0.0/benchmarks/grounding_llm_on/README.md +58 -0
  14. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/loop/SHA256SUMS +2 -2
  15. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/offtarget/integrase/README.md +23 -23
  16. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/offtarget/integrase/SHA256SUMS +4 -4
  17. pen_stack-8.0.0/benchmarks/offtarget/integrase_chalberg/README.md +61 -0
  18. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/oracle/SHA256SUMS +5 -5
  19. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/position_effect/README.md +68 -60
  20. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/position_effect/SHA256SUMS +1 -1
  21. pen_stack-8.0.0/benchmarks/position_effect_human/README.md +119 -0
  22. pen_stack-8.0.0/benchmarks/position_effect_human/SHA256SUMS +2 -0
  23. pen_stack-8.0.0/benchmarks/priorart/epridict/README.md +62 -0
  24. pen_stack-8.0.0/benchmarks/priorart/epridict/SHA256SUMS +5 -0
  25. pen_stack-8.0.0/benchmarks/priorart/gsh_recovery/README.md +66 -0
  26. pen_stack-8.0.0/benchmarks/priorart/gsh_recovery/SHA256SUMS +4 -0
  27. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/writer_efficiency/SHA256SUMS +2 -2
  28. {pen_stack-7.2.3 → pen_stack-8.0.0}/benchmarks/writespec/SHA256SUMS +4 -4
  29. {pen_stack-7.2.3 → pen_stack-8.0.0}/configs/intent_weights.yaml +57 -42
  30. {pen_stack-7.2.3 → pen_stack-8.0.0}/configs/llm.yaml +13 -0
  31. {pen_stack-7.2.3 → pen_stack-8.0.0}/configs/monitor_queries.yaml +33 -33
  32. {pen_stack-7.2.3 → pen_stack-8.0.0}/configs/rules/delivery.yaml +49 -49
  33. {pen_stack-7.2.3 → pen_stack-8.0.0}/data/curated/bridge_offtarget_energetics.json +201 -201
  34. {pen_stack-7.2.3 → pen_stack-8.0.0}/data/curated/cast_systems.yaml +59 -59
  35. {pen_stack-7.2.3 → pen_stack-8.0.0}/data/curated/integrase_att.yaml +66 -66
  36. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/DEPLOY.md +39 -39
  37. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/INFRA.md +64 -64
  38. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/MCP.md +24 -24
  39. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/REPRO.md +46 -46
  40. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/biosecurity.md +82 -64
  41. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/cards/atlas.md +41 -41
  42. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/cards/durability.md +43 -43
  43. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/cards/offtarget_data.md +117 -117
  44. pen_stack-8.0.0/docs/cards/priorart.md +66 -0
  45. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/cards/safety.md +39 -39
  46. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/dissemination.md +34 -34
  47. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/index.md +48 -48
  48. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/position_effect.md +57 -57
  49. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/positioning.md +55 -55
  50. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/private_data_formats.md +61 -61
  51. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/quickstart.md +64 -64
  52. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/responsible_use.md +96 -84
  53. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/scope.md +50 -50
  54. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/scorecard.md +54 -54
  55. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/tpe_bench.md +48 -48
  56. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/tutorials/score-deliverability.md +36 -36
  57. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/tutorials/where-can-i-write.md +45 -45
  58. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/tutorials/which-writer-reaches-locus.md +41 -41
  59. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/writer_verification.md +46 -46
  60. {pen_stack-7.2.3 → pen_stack-8.0.0}/docs/wtkb.md +25 -25
  61. pen_stack-8.0.0/pen_stack/__init__.py +2 -0
  62. pen_stack-8.0.0/pen_stack/active/acquire.py +165 -0
  63. pen_stack-8.0.0/pen_stack/active/design.py +66 -0
  64. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/adapt/__init__.py +14 -14
  65. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/adapt/finetune.py +33 -33
  66. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/agent/__init__.py +1 -1
  67. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/agent/orchestrator.py +7 -1
  68. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/agent/tools.py +130 -130
  69. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/api/manifest.py +2 -1
  70. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/atlas/__init__.py +1 -1
  71. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/atlas/crosslink.py +175 -141
  72. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/atlas/guide_design.py +178 -174
  73. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/atlas/universe.py +75 -75
  74. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/atlas/writer_recommend.py +165 -103
  75. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/bridge/__init__.py +1 -1
  76. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/bridge/activity.py +52 -52
  77. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/data/__init__.py +1 -1
  78. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/design/generate.py +12 -1
  79. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/design/space.py +1 -0
  80. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/design/writer_variants.py +122 -121
  81. pen_stack-8.0.0/pen_stack/graph/query.py +148 -0
  82. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/mech/__init__.py +1 -1
  83. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/monitor/__init__.py +1 -1
  84. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/__init__.py +1 -1
  85. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/delivery_immune.py +2 -1
  86. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/delivery_predict.py +196 -136
  87. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/immune_profile.py +292 -271
  88. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/optimize.py +278 -251
  89. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/planner/pipeline.py +87 -86
  90. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/rag/__init__.py +1 -1
  91. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/rag/llm.py +37 -0
  92. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/rules/evaluators.py +330 -312
  93. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/safety/gate.py +58 -37
  94. pen_stack-8.0.0/pen_stack/safety/pfam_scan.py +157 -0
  95. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/safety/registry.py +17 -0
  96. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/safety/screen.py +5 -2
  97. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/score/__init__.py +1 -1
  98. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/score/recalibrate.py +77 -77
  99. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/server/__init__.py +1 -1
  100. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/server/api.py +647 -566
  101. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/spec/extract.py +26 -4
  102. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/twin/data/position_effect.py +251 -224
  103. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/twin/mechanistic.py +136 -119
  104. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/twin/outcome.py +132 -102
  105. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/twin/position_effect.py +443 -369
  106. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/ui/__init__.py +1 -1
  107. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/validate/__init__.py +1 -1
  108. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/validate/known_biology_expr.py +38 -38
  109. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/validate/paper3_benchmark.py +2 -2
  110. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/verify/proof.py +206 -176
  111. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/__init__.py +1 -1
  112. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_assay.py +80 -78
  113. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_bridge.py +47 -47
  114. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_cast.py +97 -97
  115. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_enumerate.py +271 -271
  116. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_integrase.py +155 -129
  117. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_nuclease.py +98 -66
  118. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_paste.py +41 -41
  119. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/offtarget_predict.py +6 -3
  120. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack.egg-info/PKG-INFO +350 -309
  121. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack.egg-info/SOURCES.txt +16 -0
  122. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack.egg-info/requires.txt +2 -0
  123. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_phase0.json +8 -8
  124. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_phase1_5.json +10 -10
  125. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_phase2.json +11 -11
  126. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_phase3.json +10 -10
  127. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_a.json +11 -11
  128. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_acq.json +8 -8
  129. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_aldesign.json +8 -8
  130. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_alvalidate.json +8 -8
  131. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_atlas.json +8 -8
  132. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_b.json +11 -11
  133. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ba.json +9 -9
  134. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ba_v33.json +9 -9
  135. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ba_v45.json +8 -8
  136. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_bench.json +8 -8
  137. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_c.json +9 -9
  138. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_cal.json +8 -8
  139. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_calib.json +8 -8
  140. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_challenge.json +8 -8
  141. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_chat.json +8 -8
  142. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_cite.json +8 -8
  143. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_closedloop.json +8 -8
  144. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_continual.json +8 -8
  145. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_cosci2.json +8 -8
  146. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_crit.json +8 -8
  147. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ct.json +8 -8
  148. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_d.json +10 -10
  149. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_delivery.json +8 -8
  150. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_drift.json +8 -8
  151. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_e.json +9 -9
  152. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_env.json +8 -8
  153. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ep.json +9 -9
  154. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_epitope.json +8 -8
  155. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_expr2.json +7 -7
  156. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_f.json +8 -8
  157. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_frontend.json +8 -8
  158. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_g.json +8 -8
  159. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_gen.json +8 -8
  160. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_genotox.json +8 -8
  161. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_graph.json +8 -8
  162. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_h.json +8 -8
  163. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_hybrid.json +8 -8
  164. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_immune.json +8 -8
  165. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_immune2.json +8 -8
  166. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_ingest.json +8 -8
  167. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_innate.json +8 -8
  168. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_loop.json +8 -8
  169. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_manifest.json +8 -8
  170. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_mc.json +10 -10
  171. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_mcp.json +8 -8
  172. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_mech.json +8 -8
  173. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_mon.json +8 -8
  174. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_o.json +8 -8
  175. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_offtarget.json +8 -8
  176. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_offtarget2.json +9 -9
  177. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_openapi.json +8 -8
  178. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_oracle.json +8 -8
  179. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_orch.json +8 -8
  180. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_outcome.json +8 -8
  181. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_pareto.json +8 -8
  182. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_peg.json +8 -8
  183. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_penchat.json +9 -9
  184. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_plan.json +8 -8
  185. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_policy.json +9 -9
  186. pen_stack-8.0.0/prereg/SHA256_LOCK_ws_priorart.json +10 -0
  187. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_profile.json +8 -8
  188. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_proto.json +8 -8
  189. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_r.json +14 -14
  190. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_redteam.json +9 -9
  191. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_route.json +9 -9
  192. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_screen.json +10 -10
  193. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_seroprev.json +8 -8
  194. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_simlab.json +8 -8
  195. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_twincal.json +8 -8
  196. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_uq.json +9 -9
  197. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_v.json +8 -8
  198. {pen_stack-7.2.3 → pen_stack-8.0.0}/prereg/SHA256_LOCK_ws_vcell.json +8 -8
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  510. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/web/server.py +0 -0
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  513. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/durability.py +0 -0
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  519. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/ood.py +0 -0
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  522. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/structure3d.py +0 -0
  523. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/uncertainty.py +0 -0
  524. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack/wgenome/writability.py +0 -0
  525. {pen_stack-7.2.3 → pen_stack-8.0.0}/pen_stack.egg-info/dependency_links.txt +0 -0
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  581. {pen_stack-7.2.3 → pen_stack-8.0.0}/scripts/build_rag_corpus.py +0 -0
  582. {pen_stack-7.2.3 → pen_stack-8.0.0}/scripts/calibrate_immune_axes.py +0 -0
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  587. {pen_stack-7.2.3 → pen_stack-8.0.0}/scripts/p1_build_atlas.py +0 -0
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