codontrace 0.3.0b2__tar.gz → 0.3.0b4__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 (875) hide show
  1. codontrace-0.3.0b4/.github/workflows/ci.yml +136 -0
  2. codontrace-0.3.0b4/CHANGELOG.md +711 -0
  3. codontrace-0.3.0b4/CITATION.cff +20 -0
  4. codontrace-0.3.0b4/CONTRIBUTING.md +30 -0
  5. codontrace-0.3.0b4/MANIFEST.in +36 -0
  6. codontrace-0.3.0b4/PKG-INFO +406 -0
  7. codontrace-0.3.0b4/README.md +352 -0
  8. codontrace-0.3.0b4/RELEASE_EVIDENCE.md +64 -0
  9. codontrace-0.3.0b4/docs/ADF_MACRO_LIFECYCLE.md +28 -0
  10. codontrace-0.3.0b4/docs/API_STABILITY_POLICY.md +18 -0
  11. codontrace-0.3.0b4/docs/BENCHMARK_SCENARIO_SUITE.md +30 -0
  12. codontrace-0.3.0b4/docs/CAPSULE_TRANSFER_VALIDATION.md +7 -0
  13. codontrace-0.3.0b4/docs/CAUSAL_INTERVENTION_PROTOCOL.md +29 -0
  14. codontrace-0.3.0b4/docs/CAUSAL_VALIDATION_PROTOCOL.md +7 -0
  15. codontrace-0.3.0b4/docs/CLAIMGATE_STANDALONE.md +59 -0
  16. codontrace-0.3.0b4/docs/CLAIM_CONTROL.md +3 -0
  17. codontrace-0.3.0b4/docs/CLAIM_GATE_POLICY.md +7 -0
  18. codontrace-0.3.0b4/docs/CLAIM_LADDER.md +30 -0
  19. codontrace-0.3.0b4/docs/CLAIM_LADDER_MAP.md +41 -0
  20. codontrace-0.3.0b4/docs/CONTRIBUTION_LEDGER.md +28 -0
  21. codontrace-0.3.0b4/docs/DISCOVERY_EXPERIMENT_PROTOCOL.md +7 -0
  22. codontrace-0.3.0b4/docs/DISCOVERY_GATE_PROTOCOL.md +30 -0
  23. codontrace-0.3.0b4/docs/ENGINE_REPLAY_CONTRACT.md +47 -0
  24. codontrace-0.3.0b4/docs/EVENT_GRAPH_AND_CAUSAL_PROTOCOL.md +28 -0
  25. codontrace-0.3.0b4/docs/FEATURE_WIRING_MATRIX.md +31 -0
  26. codontrace-0.3.0b4/docs/GENESIS_COMPATIBILITY_MATRIX.md +28 -0
  27. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01.md +563 -0
  28. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_ODD.md +333 -0
  29. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG.md +294 -0
  30. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_01.md +152 -0
  31. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_02.md +192 -0
  32. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_03.md +148 -0
  33. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_04.md +144 -0
  34. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_05.md +136 -0
  35. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_01_PREREG_AMENDMENT_LOCK.md +133 -0
  36. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_02.md +44 -0
  37. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_02_PREREG.md +42 -0
  38. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_03.md +46 -0
  39. codontrace-0.3.0b4/docs/HARD_EXPERIMENT_03_PREREG.md +72 -0
  40. codontrace-0.3.0b4/docs/ILW5_CAMPAIGN.md +59 -0
  41. codontrace-0.3.0b4/docs/ILW5_PARTIAL_RESULTS.md +103 -0
  42. codontrace-0.3.0b4/docs/ILW6_EXPLORATORY.md +54 -0
  43. codontrace-0.3.0b4/docs/ILW_PILOT_S2_RESULTS.md +82 -0
  44. codontrace-0.3.0b4/docs/ILW_PREREG_V1.md +226 -0
  45. codontrace-0.3.0b4/docs/INNOVATION_PROTECTION.md +28 -0
  46. codontrace-0.3.0b4/docs/LLM_REVIEW_AND_RULE_API.md +15 -0
  47. codontrace-0.3.0b4/docs/ODD_REPORTING.md +32 -0
  48. codontrace-0.3.0b4/docs/OEE_LONG_HORIZON_PROTOCOL.md +31 -0
  49. codontrace-0.3.0b4/docs/PERFORMANCE_PHASE1.md +43 -0
  50. codontrace-0.3.0b4/docs/PHASE2_CLAIM_GATE_POLICY.md +28 -0
  51. codontrace-0.3.0b4/docs/PHASE2_SCIENTIFIC_EVIDENCE_LADDER.md +9 -0
  52. codontrace-0.3.0b4/docs/PHASE_D_LITERATURE.md +65 -0
  53. codontrace-0.3.0b4/docs/PHASE_E_LITERATURE.md +72 -0
  54. codontrace-0.3.0b4/docs/PHASE_G_MATERIALS_LITERATURE.md +59 -0
  55. codontrace-0.3.0b4/docs/PHASE_H_CI_AI_PATH.md +163 -0
  56. codontrace-0.3.0b4/docs/PHASE_INDEX.md +39 -0
  57. codontrace-0.3.0b4/docs/PHASE_I_CI_EVIDENCE.md +156 -0
  58. codontrace-0.3.0b4/docs/PHASE_J_REPLAY_CI.md +154 -0
  59. codontrace-0.3.0b4/docs/PHASE_K_CI_DEPTH.md +183 -0
  60. codontrace-0.3.0b4/docs/PHASE_L_AVIDA_FIDELITY.md +212 -0
  61. codontrace-0.3.0b4/docs/QD_DESCRIPTOR_GUIDE.md +19 -0
  62. codontrace-0.3.0b4/docs/QD_SEARCH_LOOP.md +7 -0
  63. codontrace-0.3.0b4/docs/SCIENTIFIC_AUTHORITIES_2026.md +315 -0
  64. codontrace-0.3.0b4/docs/SCIENTIFIC_CLAIM_LADDER.md +18 -0
  65. codontrace-0.3.0b4/docs/SCIENTIFIC_EXPERIMENT_PROTOCOL.md +5 -0
  66. codontrace-0.3.0b4/docs/SCIENTIFIC_LIMITS.md +28 -0
  67. codontrace-0.3.0b4/docs/SCIENTIFIC_METHOD_NOTES.md +27 -0
  68. codontrace-0.3.0b4/docs/SOCIAL_COLLECTIVE_INTELLIGENCE_PROTOCOL.md +39 -0
  69. codontrace-0.3.0b4/docs/STUDIO_BOUNDARY.md +67 -0
  70. codontrace-0.3.0b4/docs/STUDIO_PHASE1_EXECUTION_SPEC.md +96 -0
  71. codontrace-0.3.0b4/docs/TRANSLATION_PROFILE_SEMANTIC_PROXY.md +28 -0
  72. codontrace-0.3.0b4/docs/VARIABLE_GENOME_AND_STRUCTURAL_MUTATION.md +28 -0
  73. codontrace-0.3.0b4/docs/WHY_NOT_INTELLIGENCE_YET.md +460 -0
  74. codontrace-0.3.0b4/docs/api.md +333 -0
  75. codontrace-0.3.0b4/docs/colab/README.md +6 -0
  76. codontrace-0.3.0b4/docs/concepts.md +120 -0
  77. codontrace-0.3.0b4/docs/design/ASME_VV40_CONTEXT_OF_USE.md +20 -0
  78. codontrace-0.3.0b4/docs/design/AVIDA_DAT.md +32 -0
  79. codontrace-0.3.0b4/docs/design/ESP32_BRIDGE_v0.1.md +72 -0
  80. codontrace-0.3.0b4/docs/design/HARD_EXPERIMENT_01_V2_ASSAY_INVALID.md +24 -0
  81. codontrace-0.3.0b4/docs/design/MABE2_DATAFILE.md +21 -0
  82. codontrace-0.3.0b4/docs/design/MODES_CHANNON_MEASUREMENT_NEIGHBORS.md +27 -0
  83. codontrace-0.3.0b4/docs/design/OPEN_ENDED_DISCOVERY_CLAIMGATE_PIPELINE_v2.md +177 -0
  84. codontrace-0.3.0b4/docs/design_notes/a25_final_scientific_library_hardening.md +70 -0
  85. codontrace-0.3.0b4/docs/design_notes/a25_metadata_evidence_validation_context.md +16 -0
  86. codontrace-0.3.0b4/docs/design_notes/a25_strengthened_final_acceptance_patch.md +25 -0
  87. codontrace-0.3.0b4/docs/design_notes/a35_developer_evidence_chain_hardening.md +47 -0
  88. codontrace-0.3.0b4/docs/design_notes/phase2_strong_scientific_layer.md +65 -0
  89. codontrace-0.3.0b4/docs/design_notes/strong_library_phase1.md +71 -0
  90. codontrace-0.3.0b4/docs/extensibility.md +83 -0
  91. codontrace-0.3.0b4/docs/genesis_causal_capsule_runtime.md +39 -0
  92. codontrace-0.3.0b4/docs/hard_experiment_01/AMD03_CODE_DEVIATIONS.md +35 -0
  93. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1D_DOUBLE_PRIME_HONESTY.md +167 -0
  94. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1D_PILOT_DIAGNOSIS.md +155 -0
  95. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1D_PILOT_REPORT.md +53 -0
  96. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1E_PILOT_REPORT.md +105 -0
  97. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1E_SCIENCE_BRIEF.md +317 -0
  98. codontrace-0.3.0b4/docs/hard_experiment_01/WAVE_1_LOCK_V7_PILOT_REPORT.md +29 -0
  99. codontrace-0.3.0b4/docs/hard_experiment_01/morris_e6_design.md +141 -0
  100. codontrace-0.3.0b4/docs/hard_experiment_01/morris_e6_smoke.json +124 -0
  101. codontrace-0.3.0b4/docs/hard_experiment_01/pilot_v5.json +2239 -0
  102. codontrace-0.3.0b4/docs/hard_experiment_01/pilot_v6.json +3393 -0
  103. codontrace-0.3.0b4/docs/hard_experiment_01/pilot_v7.json +3966 -0
  104. codontrace-0.3.0b4/docs/hard_experiment_01/results_v1.json +4030 -0
  105. codontrace-0.3.0b4/docs/hard_experiment_01/results_v2.json +4044 -0
  106. codontrace-0.3.0b4/docs/hard_experiment_01/results_v3.json +5467 -0
  107. codontrace-0.3.0b4/docs/hard_experiment_01/results_v5.json +5538 -0
  108. codontrace-0.3.0b4/docs/hard_experiment_01/results_v6.json +10191 -0
  109. codontrace-0.3.0b4/docs/hard_experiment_01/results_v7.json +10201 -0
  110. codontrace-0.3.0b4/docs/hard_experiment_02/HE02_SCIENCE_BRIEF.md +14 -0
  111. codontrace-0.3.0b4/docs/hard_experiment_02/PILOT_REPORT.md +17 -0
  112. codontrace-0.3.0b4/docs/hard_experiment_02/pilot_v1.json +953 -0
  113. codontrace-0.3.0b4/docs/hard_experiment_02/smoke_v1.json +363 -0
  114. codontrace-0.3.0b4/docs/hard_experiment_03/HE03_SCIENCE_BRIEF.md +16 -0
  115. codontrace-0.3.0b4/docs/initialization.md +101 -0
  116. codontrace-0.3.0b4/docs/non_goals.md +64 -0
  117. codontrace-0.3.0b4/docs/open_ended_discovery/SCIENCE_BRIEF.md +22 -0
  118. codontrace-0.3.0b4/docs/open_ended_discovery/campaign_v1.md +33 -0
  119. codontrace-0.3.0b4/docs/protocol/CLAIM_LADDER_PROTOCOL_v0.1.md +361 -0
  120. codontrace-0.3.0b4/docs/rag/README.md +65 -0
  121. codontrace-0.3.0b4/docs/rag/corpus/avida_cfg_deme_group.md +36 -0
  122. codontrace-0.3.0b4/docs/rag/corpus/avida_cfg_organism_messaging.md +36 -0
  123. codontrace-0.3.0b4/docs/rag/corpus/cao_yang_2026_vocabulary_verifier_gaps.md +35 -0
  124. codontrace-0.3.0b4/docs/rag/corpus/channon_2024_tokyo_type1.md +35 -0
  125. codontrace-0.3.0b4/docs/rag/corpus/chaturvedi_2026_role_mls.md +35 -0
  126. codontrace-0.3.0b4/docs/rag/corpus/conlin_2023_dol_multicellularity_avida.md +35 -0
  127. codontrace-0.3.0b4/docs/rag/corpus/goldsby_2012_pnas_task_switching.md +36 -0
  128. codontrace-0.3.0b4/docs/rag/corpus/goldsby_ofria_avida_messaging_germline.md +36 -0
  129. codontrace-0.3.0b4/docs/rag/corpus/gorelick_2004_normalized_mutual_entropy_dol.md +35 -0
  130. codontrace-0.3.0b4/docs/rag/corpus/jaxlife_2024.md +35 -0
  131. codontrace-0.3.0b4/docs/rag/corpus/michod_2007_pnas_export_of_fitness.md +35 -0
  132. codontrace-0.3.0b4/docs/rag/corpus/miikkulainen_forrest_2021_nature_mi.md +36 -0
  133. codontrace-0.3.0b4/docs/rag/corpus/okasha_2006_levels_of_selection.md +35 -0
  134. codontrace-0.3.0b4/docs/rag/corpus/price_1970_selection_and_covariance.md +35 -0
  135. codontrace-0.3.0b4/docs/rag/corpus/price_1972_extension_covariance_selection.md +35 -0
  136. codontrace-0.3.0b4/docs/rag/corpus/soros_stanley_2014_chromaria.md +36 -0
  137. codontrace-0.3.0b4/docs/rag/corpus/stanley_2017_open_endedness_creative_intelligence.md +35 -0
  138. codontrace-0.3.0b4/docs/rag/corpus/szathmary_maynard_smith_michod_transitions.md +35 -0
  139. codontrace-0.3.0b4/docs/scientific_freshness_matrix_integration.md +9 -0
  140. codontrace-0.3.0b4/examples/claimgate_audit_hard_experiment_01.py +62 -0
  141. codontrace-0.3.0b4/examples/collective_joss_drive_resume.py +270 -0
  142. codontrace-0.3.0b4/examples/collective_joss_evidence_benchmark.py +1032 -0
  143. codontrace-0.3.0b4/examples/genesis_hard_experiment_01.py +52 -0
  144. codontrace-0.3.0b4/examples/genesis_materials_world.py +98 -0
  145. codontrace-0.3.0b4/examples/genesis_phase_i_ci_evidence.py +84 -0
  146. codontrace-0.3.0b4/examples/genesis_phase_j_replay_ci.py +70 -0
  147. codontrace-0.3.0b4/examples/genesis_phase_k_ci_depth.py +79 -0
  148. codontrace-0.3.0b4/examples/genesis_phase_l_avida_fidelity.py +78 -0
  149. codontrace-0.3.0b4/examples/genesis_rag_query.py +65 -0
  150. codontrace-0.3.0b4/examples/genesis_scientific_gaps_2026.py +92 -0
  151. codontrace-0.3.0b4/examples/genesis_tokyo_type1_measurement.py +63 -0
  152. codontrace-0.3.0b4/firmware/esp32/README.md +23 -0
  153. codontrace-0.3.0b4/firmware/esp32/main.py +110 -0
  154. codontrace-0.3.0b4/firmware/esp32/sketch_arduino.ino +30 -0
  155. codontrace-0.3.0b4/pyproject.toml +145 -0
  156. codontrace-0.3.0b4/src/codontrace/__init__.py +768 -0
  157. codontrace-0.3.0b4/src/codontrace/actions.py +1330 -0
  158. codontrace-0.3.0b4/src/codontrace/claimgate/__init__.py +47 -0
  159. codontrace-0.3.0b4/src/codontrace/claimgate/__main__.py +48 -0
  160. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/__init__.py +55 -0
  161. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/avida.py +166 -0
  162. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/codontrace.py +333 -0
  163. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/codontrace_he02.py +334 -0
  164. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/codontrace_he03.py +179 -0
  165. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/esp32_bridge.py +422 -0
  166. codontrace-0.3.0b4/src/codontrace/claimgate/adapters/mabe2.py +137 -0
  167. codontrace-0.3.0b4/src/codontrace/claimgate/auditor.py +410 -0
  168. codontrace-0.3.0b4/src/codontrace/claimgate/ladder.py +64 -0
  169. codontrace-0.3.0b4/src/codontrace/claimgate/schema.py +378 -0
  170. codontrace-0.3.0b4/src/codontrace/engine.py +3291 -0
  171. codontrace-0.3.0b4/src/codontrace/engine_digest.py +213 -0
  172. codontrace-0.3.0b4/src/codontrace/engine_results.py +107 -0
  173. codontrace-0.3.0b4/src/codontrace/genesis/__init__.py +2763 -0
  174. codontrace-0.3.0b4/src/codontrace/genesis/artifacts.py +1036 -0
  175. codontrace-0.3.0b4/src/codontrace/genesis/benchmark_suite.py +798 -0
  176. codontrace-0.3.0b4/src/codontrace/genesis/birth.py +1795 -0
  177. codontrace-0.3.0b4/src/codontrace/genesis/campaign.py +677 -0
  178. codontrace-0.3.0b4/src/codontrace/genesis/capsule.py +1818 -0
  179. codontrace-0.3.0b4/src/codontrace/genesis/claim_gate.py +815 -0
  180. codontrace-0.3.0b4/src/codontrace/genesis/collective_deme.py +726 -0
  181. codontrace-0.3.0b4/src/codontrace/genesis/deme_selection.py +202 -0
  182. codontrace-0.3.0b4/src/codontrace/genesis/discovery_campaign.py +254 -0
  183. codontrace-0.3.0b4/src/codontrace/genesis/discovery_runner.py +380 -0
  184. codontrace-0.3.0b4/src/codontrace/genesis/discovery_witness.py +1183 -0
  185. codontrace-0.3.0b4/src/codontrace/genesis/empirical_systematics.py +410 -0
  186. codontrace-0.3.0b4/src/codontrace/genesis/environment.py +1462 -0
  187. codontrace-0.3.0b4/src/codontrace/genesis/food_patch_signal.py +264 -0
  188. codontrace-0.3.0b4/src/codontrace/genesis/hard_experiment_01.py +3186 -0
  189. codontrace-0.3.0b4/src/codontrace/genesis/hard_experiment_01_morris.py +623 -0
  190. codontrace-0.3.0b4/src/codontrace/genesis/hard_experiment_02.py +993 -0
  191. codontrace-0.3.0b4/src/codontrace/genesis/hard_experiment_03.py +810 -0
  192. codontrace-0.3.0b4/src/codontrace/genesis/ilw/INTEGRATION_DAG.json +535 -0
  193. codontrace-0.3.0b4/src/codontrace/genesis/ilw/__init__.py +264 -0
  194. codontrace-0.3.0b4/src/codontrace/genesis/ilw/adapter_honesty.py +46 -0
  195. codontrace-0.3.0b4/src/codontrace/genesis/ilw/campaign.py +722 -0
  196. codontrace-0.3.0b4/src/codontrace/genesis/ilw/chain_runtime.py +1287 -0
  197. codontrace-0.3.0b4/src/codontrace/genesis/ilw/conservation.py +154 -0
  198. codontrace-0.3.0b4/src/codontrace/genesis/ilw/dag.py +223 -0
  199. codontrace-0.3.0b4/src/codontrace/genesis/ilw/dual_resource_world.py +138 -0
  200. codontrace-0.3.0b4/src/codontrace/genesis/ilw/event_consumer.py +86 -0
  201. codontrace-0.3.0b4/src/codontrace/genesis/ilw/event_ledger.py +236 -0
  202. codontrace-0.3.0b4/src/codontrace/genesis/ilw/exploratory.py +705 -0
  203. codontrace-0.3.0b4/src/codontrace/genesis/ilw/integrated_smoke.py +261 -0
  204. codontrace-0.3.0b4/src/codontrace/genesis/ilw/knockouts.py +81 -0
  205. codontrace-0.3.0b4/src/codontrace/genesis/ilw/orphan.py +62 -0
  206. codontrace-0.3.0b4/src/codontrace/genesis/ilw/pilot.py +692 -0
  207. codontrace-0.3.0b4/src/codontrace/genesis/ilw/prereg.py +553 -0
  208. codontrace-0.3.0b4/src/codontrace/genesis/ilw/scheduler.py +81 -0
  209. codontrace-0.3.0b4/src/codontrace/genesis/ilw/seed_namespace.py +90 -0
  210. codontrace-0.3.0b4/src/codontrace/genesis/ilw/world_spec.py +197 -0
  211. codontrace-0.3.0b4/src/codontrace/genesis/isolation_assay.py +190 -0
  212. codontrace-0.3.0b4/src/codontrace/genesis/learning_payoff.py +320 -0
  213. codontrace-0.3.0b4/src/codontrace/genesis/logic9.py +447 -0
  214. codontrace-0.3.0b4/src/codontrace/genesis/materials.py +1967 -0
  215. codontrace-0.3.0b4/src/codontrace/genesis/metrics/__init__.py +11 -0
  216. codontrace-0.3.0b4/src/codontrace/genesis/metrics/division_of_labor.py +150 -0
  217. codontrace-0.3.0b4/src/codontrace/genesis/multi_generation.py +1661 -0
  218. codontrace-0.3.0b4/src/codontrace/genesis/novelty_proposer.py +264 -0
  219. codontrace-0.3.0b4/src/codontrace/genesis/organism.py +1266 -0
  220. codontrace-0.3.0b4/src/codontrace/genesis/phase_e.py +1993 -0
  221. codontrace-0.3.0b4/src/codontrace/genesis/phase_h.py +829 -0
  222. codontrace-0.3.0b4/src/codontrace/genesis/phase_i.py +1620 -0
  223. codontrace-0.3.0b4/src/codontrace/genesis/phase_j.py +898 -0
  224. codontrace-0.3.0b4/src/codontrace/genesis/phase_k.py +1764 -0
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  780. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_element_registry.py +0 -0
  781. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_elements.py +0 -0
  782. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_extensibility_backcompat.py +0 -0
  783. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_extensibility_no_app_drift.py +0 -0
  784. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_fitness.py +0 -0
  785. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_fitness_signal_registry.py +0 -0
  786. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_generalization_snapshots.py +0 -0
  787. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_genome_spec.py +0 -0
  788. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_adf_runtime_unification.py +0 -0
  789. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_end_to_end_validation.py +0 -0
  790. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_evidence_consistency.py +0 -0
  791. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_examples_compatibility.py +0 -0
  792. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_public_api_manifest.py +0 -0
  793. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_public_api_unification.py +0 -0
  794. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_reference_integrity.py +0 -0
  795. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_release_zip_integrity.py +0 -0
  796. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_runtime_wiring.py +0 -0
  797. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_integration_scientific_freshness_matrix.py +0 -0
  798. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_learning.py +0 -0
  799. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_lineage.py +0 -0
  800. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_liveness.py +0 -0
  801. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_memory.py +0 -0
  802. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_mutation.py +0 -0
  803. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_mutation_genome_spec.py +0 -0
  804. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_mutation_operator_maturity.py +0 -0
  805. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_organism.py +0 -0
  806. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_package_hygiene.py +0 -0
  807. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_adf_runtime_execution.py +0 -0
  808. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_capsule_ttl_locality.py +0 -0
  809. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_energy_effect_organism.py +0 -0
  810. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_from_bits_spec.py +0 -0
  811. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_population_stigmergy_integration.py +0 -0
  812. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase1_runtime_contract.py +0 -0
  813. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_adf_usefulness_claim_thresholds.py +0 -0
  814. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_claim_digest_consistency.py +0 -0
  815. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_finite_guards.py +0 -0
  816. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_gap_public_apis.py +0 -0
  817. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_manifest_validation_strict.py +0 -0
  818. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase2_semantic_proxy_engine_wiring.py +0 -0
  819. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase_b_no_collapsed_alias_schemas.py +0 -0
  820. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase_b_public_api_bindings.py +0 -0
  821. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase_b_scientific_maturity_report.py +0 -0
  822. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_phase_c_dynamic_environment.py +0 -0
  823. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_plugin_api_safety.py +0 -0
  824. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_population.py +0 -0
  825. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_population_capsule_audit.py +0 -0
  826. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_population_memory_audit.py +0 -0
  827. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_reproduction.py +0 -0
  828. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_result_consistency_validator.py +0 -0
  829. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_ribosome.py +0 -0
  830. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_role_detection_runtime.py +0 -0
  831. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_scale_ladder_benchmark.py +0 -0
  832. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_scheduler_protocol.py +0 -0
  833. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_social_behavior_descriptor_counts.py +0 -0
  834. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_social_heldout_distinctness.py +0 -0
  835. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_stigmergy_layer.py +0 -0
  836. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_substrate.py +0 -0
  837. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_substrate_physics_config.py +0 -0
  838. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_substrate_rule_config.py +0 -0
  839. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_swarm_metrics_controls.py +0 -0
  840. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_topology_protocol.py +0 -0
  841. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_trace_memory_audit.py +0 -0
  842. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_v3_core_regression_patch.py +0 -0
  843. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_v3_rereview_integrity.py +0 -0
  844. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genesis_world_mapping.py +0 -0
  845. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_genome.py +0 -0
  846. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_initialization.py +0 -0
  847. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_ledger_refs.py +0 -0
  848. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_memory_delayed_evidence_science.py +0 -0
  849. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_mutation.py +0 -0
  850. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_mutation_fuzz.py +0 -0
  851. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_no_side_effects.py +0 -0
  852. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_object_serialization.py +0 -0
  853. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_plugins.py +0 -0
  854. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_publish_readiness_a7.py +0 -0
  855. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_replay.py +0 -0
  856. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_replay_hash.py +0 -0
  857. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_replay_snapshot_continuity.py +0 -0
  858. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_rng.py +0 -0
  859. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_scenario_diversity.py +0 -0
  860. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_scenario_runtime_logic_a10.py +0 -0
  861. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_scenario_runtime_logic_a11.py +0 -0
  862. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_simulation.py +0 -0
  863. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_timeline_replay.py +0 -0
  864. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_trace.py +0 -0
  865. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_types.py +0 -0
  866. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_world.py +0 -0
  867. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_world_events.py +0 -0
  868. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tests/test_world_objects.py +0 -0
  869. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_evidence_consistency.py +0 -0
  870. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_examples_integration.py +0 -0
  871. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_genesis_references.py +0 -0
  872. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_package_hygiene.py +0 -0
  873. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_release_zip.py +0 -0
  874. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/audit_runtime_wiring.py +0 -0
  875. {codontrace-0.3.0b2 → codontrace-0.3.0b4}/tools/build_clean_release_zip.py +0 -0
@@ -0,0 +1,136 @@
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+ name: CI
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+
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+ "on":
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+ push:
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+ pull_request:
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+
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+ permissions:
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+ contents: read
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+
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+ env:
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+ FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
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+ PIP_DISABLE_PIP_VERSION_CHECK: "1"
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+
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+ jobs:
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+ ubuntu-full-tests:
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+ name: Full pytest (${{ matrix.os }}, Python ${{ matrix.python-version }})
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+ runs-on: ${{ matrix.os }}
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+ timeout-minutes: 60
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+ strategy:
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+ fail-fast: false
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+ matrix:
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+ os: [ubuntu-latest]
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+ python-version: ["3.11", "3.12", "3.13", "3.14"]
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+ steps:
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+ - name: Checkout
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+ uses: actions/checkout@v6
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v6
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+ cache: pip
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+
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+ - name: Install test dependencies
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+ run: |
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+ python -m pip install --upgrade pip setuptools wheel
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+ python -m pip install -e . pytest
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+
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+ - name: Compile package, tests, examples, and tools
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+ run: python -m compileall -q src tests examples tools
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+
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+ - name: Enforce core boundary with AST import guard
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+ run: python tools/check_core_boundary.py
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+
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+ - name: Reject probe leftovers in the checkout
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+ run: |
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+ python - <<'PY'
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+ import fnmatch
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+ from pathlib import Path
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+
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+ skip_parts = {".git", ".venv", "venv", "__pycache__"}
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+
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+ def is_leftover(path: Path) -> bool:
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+ name = path.name
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+ if name.startswith(".grok_write_probe"):
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+ return True
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+ if name.startswith(".size_test_") and path.suffix == ".txt":
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+ return True
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+ return any(
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+ fnmatch.fnmatch(name, pattern)
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+ for pattern in ("*_FULL_RESTORE*", "*_backup*", "*.orig")
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+ )
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+
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+ junk = sorted(
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+ p
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+ for p in Path(".").rglob("*")
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+ if p.is_file()
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+ and skip_parts.isdisjoint(p.parts)
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+ and is_leftover(p)
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+ )
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+ if junk:
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+ raise SystemExit("probe leftovers must not ship: " + ", ".join(map(str, junk)))
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+ print("no probe leftovers")
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+ PY
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+
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+ - name: Run full test suite
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+ run: python -m pytest tests --disable-plugin-autoload
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+
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+ core-smoke-cross-os:
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+ name: Core smoke (${{ matrix.os }}, Python ${{ matrix.python-version }})
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+ runs-on: ${{ matrix.os }}
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+ timeout-minutes: 30
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+ strategy:
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+ fail-fast: false
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+ matrix:
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+ os: [windows-latest, macos-latest]
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+ python-version: ["3.11", "3.12", "3.13", "3.14"]
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+ steps:
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+ - name: Checkout
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+ uses: actions/checkout@v6
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v6
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+ cache: pip
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+
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+ - name: Install test dependencies
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+ run: |
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+ python -m pip install --upgrade pip setuptools wheel
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+ python -m pip install -e . pytest
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+
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+ - name: Compile package, tests, examples, and tools
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+ run: python -m compileall -q src tests examples tools
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+
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+ - name: Enforce core boundary with AST import guard
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+ run: python tools/check_core_boundary.py
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+
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+ - name: Run release-critical tests
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+ run: python -m pytest tests/test_export_import.py tests/test_api_signature.py tests/test_genesis_causal_mechanism_hardening.py tests/test_genesis_causal_mechanism_runtime_wiring_integrity.py tests/test_genesis_integration_public_api_unification.py tests/test_genesis_integration_runtime_wiring.py tests/test_genesis_eval_bugfixes.py tests/release tests/genesis_gates --disable-plugin-autoload
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+
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+ lint-type:
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+ name: Lint and typecheck (Ubuntu, Python 3.12)
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+ runs-on: ubuntu-latest
115
+ timeout-minutes: 20
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+ continue-on-error: true
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+ steps:
118
+ - name: Checkout
119
+ uses: actions/checkout@v6
120
+
121
+ - name: Set up Python
122
+ uses: actions/setup-python@v6
123
+ with:
124
+ python-version: "3.12"
125
+ cache: pip
126
+
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+ - name: Install lint and typecheck dependencies
128
+ run: |
129
+ python -m pip install --upgrade pip setuptools wheel
130
+ python -m pip install -e ".[dev]"
131
+
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+ - name: Ruff
133
+ run: python -m ruff check src tests
134
+
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+ - name: Mypy
136
+ run: python -m mypy --strict src