pen-stack 6.2.2__tar.gz → 6.2.3__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 (444) hide show
  1. {pen_stack-6.2.2 → pen_stack-6.2.3}/CHANGELOG.md +23 -0
  2. {pen_stack-6.2.2 → pen_stack-6.2.3}/CITATION.cff +1 -1
  3. {pen_stack-6.2.2 → pen_stack-6.2.3}/PKG-INFO +3 -3
  4. {pen_stack-6.2.2 → pen_stack-6.2.3}/README.md +2 -2
  5. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/known_unknowns.yaml +18 -2
  6. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/__init__.py +1 -1
  7. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack.egg-info/PKG-INFO +3 -3
  8. {pen_stack-6.2.2 → pen_stack-6.2.3}/pyproject.toml +1 -1
  9. {pen_stack-6.2.2 → pen_stack-6.2.3}/LICENSE +0 -0
  10. {pen_stack-6.2.2 → pen_stack-6.2.3}/MANIFEST.in +0 -0
  11. {pen_stack-6.2.2 → pen_stack-6.2.3}/bench/run.py +0 -0
  12. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_bench/LEADERBOARD.md +0 -0
  13. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_bench/README.md +0 -0
  14. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_bench/SHA256SUMS +0 -0
  15. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_bench/SUBMISSIONS.md +0 -0
  16. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_bench/tasks.yaml +0 -0
  17. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_challenge/README.md +0 -0
  18. {pen_stack-6.2.2 → pen_stack-6.2.3}/benchmarks/genome_writing_challenge/SUBMISSIONS.md +0 -0
  19. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/antipeg.yaml +0 -0
  20. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/atlas_families.yaml +0 -0
  21. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/bridge_offtarget_profile.yaml +0 -0
  22. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/capsid_epitope_oracle.yaml +0 -0
  23. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/capsid_sequences.fasta +0 -0
  24. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/cargo_polish.yaml +0 -0
  25. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/cell_types.yaml +0 -0
  26. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/datasets.yaml +0 -0
  27. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/delivery_constraints.yaml +0 -0
  28. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/delivery_rules.yaml +0 -0
  29. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/delivery_vehicles.yaml +0 -0
  30. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/gates_v3.yaml +0 -0
  31. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/genotoxicity_oracle.yaml +0 -0
  32. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/gsh_validated_heldout.yaml +0 -0
  33. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/intent_weights.yaml +0 -0
  34. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/llm.yaml +0 -0
  35. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/monitor_queries.yaml +0 -0
  36. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/oracles/scope_cards.yaml +0 -0
  37. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/rules/delivery.yaml +0 -0
  38. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/rules/fold.yaml +0 -0
  39. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/rules/multiplex.yaml +0 -0
  40. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/rules/payload.yaml +0 -0
  41. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/rules/reachability.yaml +0 -0
  42. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/safety/hazard_registry.yaml +0 -0
  43. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/safety/policy.yaml +0 -0
  44. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/safety/probes.yaml +0 -0
  45. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/score_axes.yaml +0 -0
  46. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/seroprevalence.yaml +0 -0
  47. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/target_sites.yaml +0 -0
  48. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/universe_crosswalk.yaml +0 -0
  49. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/write_types.yaml +0 -0
  50. {pen_stack-6.2.2 → pen_stack-6.2.3}/configs/wtkb_curated.yaml +0 -0
  51. {pen_stack-6.2.2 → pen_stack-6.2.3}/data/curated/bridge_offtarget_energetics.json +0 -0
  52. {pen_stack-6.2.2 → pen_stack-6.2.3}/data/curated/bridge_offtarget_profile_measured.parquet +0 -0
  53. {pen_stack-6.2.2 → pen_stack-6.2.3}/data/curated/gene_coords.parquet +0 -0
  54. {pen_stack-6.2.2 → pen_stack-6.2.3}/data/curated/unified_editor_universe.parquet +0 -0
  55. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/BACKLOG.md +0 -0
  56. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/DEPLOY.md +0 -0
  57. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/INFRA.md +0 -0
  58. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/MCP.md +0 -0
  59. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/RELEASING.md +0 -0
  60. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/REPRO.md +0 -0
  61. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/STABILITY.md +0 -0
  62. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/agent.md +0 -0
  63. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/alphagenome_feasibility.md +0 -0
  64. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/autonomy.md +0 -0
  65. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/benchmark_circularity.md +0 -0
  66. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/biosecurity.md +0 -0
  67. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/build_interface.md +0 -0
  68. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/cards/atlas.md +0 -0
  69. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/cards/durability.md +0 -0
  70. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/cards/safety.md +0 -0
  71. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/challenge.md +0 -0
  72. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/closed_loop.md +0 -0
  73. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/co_scientist.md +0 -0
  74. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/co_scientist_loop.md +0 -0
  75. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/delivery.md +0 -0
  76. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/delivery_immunology.md +0 -0
  77. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/digital_twin.md +0 -0
  78. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/dissemination.md +0 -0
  79. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/environment.md +0 -0
  80. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/experiment_design.md +0 -0
  81. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/generative_design.md +0 -0
  82. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/index.md +0 -0
  83. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/integrations.md +0 -0
  84. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/mechanistic_constraints.md +0 -0
  85. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/oracles.md +0 -0
  86. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/positioning.md +0 -0
  87. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/private_data_formats.md +0 -0
  88. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/quickstart.md +0 -0
  89. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/responsible_use.md +0 -0
  90. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/rules.md +0 -0
  91. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/scope.md +0 -0
  92. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/scorecard.md +0 -0
  93. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/tutorials/compare-families.md +0 -0
  94. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/tutorials/score-deliverability.md +0 -0
  95. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/tutorials/where-can-i-write.md +0 -0
  96. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/tutorials/which-writer-reaches-locus.md +0 -0
  97. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/uncertainty.md +0 -0
  98. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/verify.md +0 -0
  99. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/world_model.md +0 -0
  100. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/writer_verification.md +0 -0
  101. {pen_stack-6.2.2 → pen_stack-6.2.3}/docs/wtkb.md +0 -0
  102. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/_resources.py +0 -0
  103. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/active/__init__.py +0 -0
  104. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/active/acquire.py +0 -0
  105. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/active/design.py +0 -0
  106. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/active/validate.py +0 -0
  107. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/__init__.py +0 -0
  108. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/finetune.py +0 -0
  109. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/ingest.py +0 -0
  110. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/pipeline.py +0 -0
  111. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/recalibrate.py +0 -0
  112. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/adapt/report.py +0 -0
  113. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/__init__.py +0 -0
  114. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/cite.py +0 -0
  115. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/co_scientist.py +0 -0
  116. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/epistemic.py +0 -0
  117. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/guardrails.py +0 -0
  118. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/mcp_server.py +0 -0
  119. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/orchestrator.py +0 -0
  120. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/orchestrator_live.py +0 -0
  121. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/pen_agent.py +0 -0
  122. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/scope.py +0 -0
  123. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/agent/tools.py +0 -0
  124. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/api/__init__.py +0 -0
  125. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/api/manifest.py +0 -0
  126. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/__init__.py +0 -0
  127. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/build_wtkb.py +0 -0
  128. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/crosslink.py +0 -0
  129. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/expand.py +0 -0
  130. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/schema.py +0 -0
  131. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/scorecard.py +0 -0
  132. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/universe.py +0 -0
  133. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/variant_propose.py +0 -0
  134. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/atlas/writer_verify.py +0 -0
  135. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/__init__.py +0 -0
  136. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/activity.py +0 -0
  137. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/cli.py +0 -0
  138. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/fold_qc.py +0 -0
  139. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/guide_qc.py +0 -0
  140. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/ingest.py +0 -0
  141. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/offtarget.py +0 -0
  142. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/offtarget_energetics.py +0 -0
  143. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/ortholog_screen.py +0 -0
  144. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/bridge/pipeline.py +0 -0
  145. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/build/__init__.py +0 -0
  146. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/build/ingest.py +0 -0
  147. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/build/protocol.py +0 -0
  148. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/build/simlab.py +0 -0
  149. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/cli.py +0 -0
  150. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/__init__.py +0 -0
  151. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/encode.py +0 -0
  152. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/genome.py +0 -0
  153. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/ingest_chromatin.py +0 -0
  154. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/ingest_integration.py +0 -0
  155. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/ingest_safety_annot.py +0 -0
  156. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/data/ingest_trip.py +0 -0
  157. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/design/__init__.py +0 -0
  158. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/design/generate.py +0 -0
  159. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/design/pareto.py +0 -0
  160. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/design/space.py +0 -0
  161. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/env/__init__.py +0 -0
  162. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/env/genome_writing_env.py +0 -0
  163. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/env/policies.py +0 -0
  164. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/__init__.py +0 -0
  165. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/build.py +0 -0
  166. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/cell_types.py +0 -0
  167. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/ingest.py +0 -0
  168. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/query.py +0 -0
  169. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/graph/schema.py +0 -0
  170. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/loop/__init__.py +0 -0
  171. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/loop/continual.py +0 -0
  172. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/loop/cycle.py +0 -0
  173. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/loop/drift.py +0 -0
  174. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/mech/__init__.py +0 -0
  175. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/mech/classify_atlas.py +0 -0
  176. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/mech/whitelist.py +0 -0
  177. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/monitor/__init__.py +0 -0
  178. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/monitor/europepmc.py +0 -0
  179. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/monitor/run.py +0 -0
  180. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/monitor/triage.py +0 -0
  181. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/__init__.py +0 -0
  182. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/cache.py +0 -0
  183. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/energetics.py +0 -0
  184. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/genome.py +0 -0
  185. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/protein_design.py +0 -0
  186. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/rna.py +0 -0
  187. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/schema.py +0 -0
  188. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/structure.py +0 -0
  189. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/oracles/vcell.py +0 -0
  190. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/__init__.py +0 -0
  191. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/antipeg_oracle.py +0 -0
  192. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/capsid_epitope_oracle.py +0 -0
  193. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/cargo.py +0 -0
  194. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/cargo_polish.py +0 -0
  195. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/delivery.py +0 -0
  196. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/delivery_constraints.py +0 -0
  197. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/delivery_immunology.py +0 -0
  198. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/delivery_vehicles.py +0 -0
  199. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/genotoxicity_oracle.py +0 -0
  200. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/immune_profile.py +0 -0
  201. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/innate_sensing.py +0 -0
  202. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/multiplex.py +0 -0
  203. {pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/planner/optimize.py +0 -0
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  397. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_gen.yaml +0 -0
  398. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_genotox.yaml +0 -0
  399. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_graph.yaml +0 -0
  400. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_h.yaml +0 -0
  401. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_immune.yaml +0 -0
  402. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_ingest.yaml +0 -0
  403. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_innate.yaml +0 -0
  404. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_loop.yaml +0 -0
  405. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_manifest.yaml +0 -0
  406. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_mc.yaml +0 -0
  407. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_mcp.yaml +0 -0
  408. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_mech.yaml +0 -0
  409. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_mon.yaml +0 -0
  410. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_o.yaml +0 -0
  411. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_openapi.yaml +0 -0
  412. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_orch.yaml +0 -0
  413. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_outcome.yaml +0 -0
  414. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_pareto.yaml +0 -0
  415. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_peg.yaml +0 -0
  416. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_plan.yaml +0 -0
  417. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_policy.yaml +0 -0
  418. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_profile.yaml +0 -0
  419. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_proto.yaml +0 -0
  420. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_r.yaml +0 -0
  421. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_redteam.yaml +0 -0
  422. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_route.yaml +0 -0
  423. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_screen.yaml +0 -0
  424. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_seroprev.yaml +0 -0
  425. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_simlab.yaml +0 -0
  426. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_twincal.yaml +0 -0
  427. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_uq.yaml +0 -0
  428. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_v.yaml +0 -0
  429. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_vcell.yaml +0 -0
  430. {pen_stack-6.2.2 → pen_stack-6.2.3}/prereg/ws_wv.yaml +0 -0
  431. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_build_atlas.py +0 -0
  432. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_build_durability.py +0 -0
  433. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_export_tracks.py +0 -0
  434. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_safety_concordance.py +0 -0
  435. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_train_safety.py +0 -0
  436. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p1_validation_report.py +0 -0
  437. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p2_build_atlas.py +0 -0
  438. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p3_benchmark_report.py +0 -0
  439. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p4_genome_scan.py +0 -0
  440. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p52_build_genotox_oracle.py +0 -0
  441. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/p53_build_epitope_oracle.py +0 -0
  442. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/ws_b_report.py +0 -0
  443. {pen_stack-6.2.2 → pen_stack-6.2.3}/scripts/ws_c_report.py +0 -0
  444. {pen_stack-6.2.2 → pen_stack-6.2.3}/setup.cfg +0 -0
{pen_stack-6.2.2 → pen_stack-6.2.3}/CHANGELOG.md RENAMED
@@ -3,6 +3,29 @@
3
3
  All notable changes to PEN-STACK are documented here. This file follows
4
4
  [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
5
5
 
6
+ ## [6.2.3] - 2026-06-12 - v6.2.3: scope matcher covers functional titer + durability (patch)
7
+
8
+ **Honesty-coverage fix (from the 20-query acceptance suite, `phase_6.2/PEN-STACK_ACCEPTANCE_TESTS.md`).** The
9
+ known-unknowns matcher (`configs/known_unknowns.yaml`) had no entry for *functional titer / absolute in-vivo
10
+ expression magnitude* and its *durability* terms were too narrow ("how long will it last **in a patient**"), so
11
+ common measured-endpoint questions ("what functional titer (% of normal)?", "how long will episomal AAV
12
+ expression last?") were not explicitly deferred. The no-fabrication spine already held (no titer/half-life was
13
+ ever emitted, and the immune profile lists `patient_specific_titer`), but the matcher should flag these
14
+ proactively.
15
+
16
+ ### Added / Fixed
17
+ - `configs/known_unknowns.yaml`: new known-unknown `in_vivo_expression_magnitude` (functional titer / % of normal
18
+ / absolute expression — a measured clinical endpoint, never predicted; PEN-STACK gives the relative mechanistic
19
+ proxy + immune context); broadened `long_term_clinical_durability` match-terms/patterns to catch "how long will
20
+ … last/persist", "durability", "half-life". Regression test
21
+ `tests/unit/test_ws_api.py::test_scope_defers_titer_and_durability_questions`.
22
+
23
+ ### Acceptance suite result
24
+ - 20/20 behave as specified at the engine level: grounded where earned, refusing where unsafe (ricin/botulinum),
25
+ abstaining/deferring where honest (titer, durability, phenotype), no fabricated number. T10 (RNP↔AAV) and T12
26
+ (multiplex translocation) are enforced via `delivery.cargo_form_compatible` and `multiplex.translocation_risk`
27
+ on the structured design fields (`writer_output_form`, `edits`).
28
+
6
29
  ## [6.2.2] - 2026-06-12 - v6.2.2: safe-harbour locus-nickname resolution (patch)
7
30
 
8
31
  **Usability fix.** Site Finder / `/plan` / `/writable` returned 0 plans for `AAVS1` because it is a genomic
{pen_stack-6.2.2 → pen_stack-6.2.3}/CITATION.cff RENAMED
@@ -1,7 +1,7 @@
1
1
  cff-version: 1.2.0
2
2
  message: "If you use PEN-STACK, please cite it as below."
3
3
  title: "PEN-STACK: open infrastructure for genome writing"
4
- version: 6.2.2
4
+ version: 6.2.3
5
5
  date-released: 2026-06-11
6
6
  authors:
7
7
  - family-names: "Mahaboob Ali"
{pen_stack-6.2.2 → pen_stack-6.2.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pen-stack
3
- Version: 6.2.2
3
+ Version: 6.2.3
4
4
  Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
5
5
  Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
6
6
  License: MIT
@@ -90,9 +90,9 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
90
90
  [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
91
91
  [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
92
92
  [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
93
- [![Version](https://img.shields.io/badge/version-6.2.2-blue.svg)](CHANGELOG.md)
93
+ [![Version](https://img.shields.io/badge/version-6.2.3-blue.svg)](CHANGELOG.md)
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  [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
95
- [![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
95
+ [![Tests](https://img.shields.io/badge/tests-371%20passing-success.svg)](tests/)
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  [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
97
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  [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
98
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  [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
{pen_stack-6.2.2 → pen_stack-6.2.3}/README.md RENAMED
@@ -15,9 +15,9 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
15
15
  [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
16
16
  [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
17
17
  [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
18
- [![Version](https://img.shields.io/badge/version-6.2.2-blue.svg)](CHANGELOG.md)
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+ [![Version](https://img.shields.io/badge/version-6.2.3-blue.svg)](CHANGELOG.md)
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  [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
20
- [![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
20
+ [![Tests](https://img.shields.io/badge/tests-371%20passing-success.svg)](tests/)
21
21
  [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
22
22
  [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
23
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{pen_stack-6.2.2 → pen_stack-6.2.3}/configs/known_unknowns.yaml RENAMED
@@ -36,8 +36,24 @@ known_unknowns:
36
36
  cassette in a given epigenome) — it does NOT predict multi-year in-vivo persistence, immune clearance,
37
37
  or clonal dynamics in a patient"
38
38
  match_terms: ["long-term in-vivo", "long term in vivo", "years of expression", "clinical durability",
39
- "persist in the patient", "how long will it last in", "in-vivo persistence", "clonal"]
40
- patterns: ["\\bhow long (will|would) (it|the cassette|expression) (last|persist) (in|in a)\\b"]
39
+ "persist in the patient", "how long will it last in", "in-vivo persistence", "clonal",
40
+ "how long will expression last", "how long will it last", "how long will the cassette",
41
+ "expression duration", "half-life", "half life", "will it persist", "how durable",
42
+ "durability magnitude", "how long does"]
43
+ patterns: ["\\bhow long\\b[^?]{0,60}\\b(last|persist|express|stay expressed|remain)\\b",
44
+ "\\bduration of (expression|the cassette|the transgene)\\b"]
45
+
46
+ - id: in_vivo_expression_magnitude
47
+ title: "absolute in-vivo expression magnitude / functional titer"
48
+ requires: "an in-vivo expression / pharmacokinetic measurement (functional titer, % of normal, ng/mL) in a
49
+ living organism"
50
+ why: "PEN-STACK computes a RELATIVE, dimensionless mechanistic expression proxy (promoter × copy ×
51
+ accessibility) and the immune context — it does NOT predict an absolute in-vivo functional titer, a
52
+ percent-of-normal level, or a protein concentration; that is a measured clinical endpoint, never predicted"
53
+ match_terms: ["titer", "titre", "percent of normal", "% of normal", "percent normal", "iu/ml", "ng/ml",
54
+ "absolute expression", "expression level in vivo", "how much protein", "how much will it express",
55
+ "what level of expression", "protein concentration", "serum level", "plasma level"]
56
+ patterns: ["\\bwhat (functional )?titer\\b", "\\b\\d+\\s*% of normal\\b"]
41
57
 
42
58
  - id: higher_order_epistasis
43
59
  title: "higher-order epistasis / multi-edit interaction beyond the translocation screen"
{pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack/__init__.py RENAMED
@@ -1,2 +1,2 @@
1
1
  """PEN-STACK v3.0 - open infrastructure for genome writing."""
2
- __version__ = "6.2.2"
2
+ __version__ = "6.2.3"
{pen_stack-6.2.2 → pen_stack-6.2.3}/pen_stack.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pen-stack
3
- Version: 6.2.2
3
+ Version: 6.2.3
4
4
  Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
5
5
  Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
6
6
  License: MIT
@@ -90,9 +90,9 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
90
90
  [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
91
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  [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
92
92
  [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
93
- [![Version](https://img.shields.io/badge/version-6.2.2-blue.svg)](CHANGELOG.md)
93
+ [![Version](https://img.shields.io/badge/version-6.2.3-blue.svg)](CHANGELOG.md)
94
94
  [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
95
- [![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
95
+ [![Tests](https://img.shields.io/badge/tests-371%20passing-success.svg)](tests/)
96
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  [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
97
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  [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
98
98
  [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
{pen_stack-6.2.2 → pen_stack-6.2.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "pen-stack"
7
- version = "6.2.2"
7
+ version = "6.2.3"
8
8
  description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
9
9
  readme = "README.md"
10
10
  requires-python = ">=3.11"
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