factorforge-cds 3.5.10__tar.gz → 3.5.11__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 (271) hide show
  1. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/PKG-INFO +3 -3
  2. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/README.md +2 -2
  3. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/pyproject.toml +1 -1
  4. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/__init__.py +13 -0
  5. factorforge_cds-3.5.11/src/factorforge/engines/dp_v2_4.py +870 -0
  6. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/version_manifest.json +12 -3
  7. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/PKG-INFO +3 -3
  8. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/SOURCES.txt +4 -0
  9. factorforge_cds-3.5.11/tests/test_dp_v2_4_0.py +249 -0
  10. factorforge_cds-3.5.11/tests/test_dp_v2_4_review.py +108 -0
  11. factorforge_cds-3.5.11/tests/test_hpx_viewer_review.py +59 -0
  12. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_multi_engine_governance.py +2 -2
  13. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_version_manifest.py +2 -2
  14. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/LICENSE +0 -0
  15. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/setup.cfg +0 -0
  16. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/__init__.py +0 -0
  17. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/__main__.py +0 -0
  18. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/__init__.py +0 -0
  19. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/feasibility.py +0 -0
  20. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/metrics.py +0 -0
  21. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/sequence_risks.py +0 -0
  22. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/benchmark/models.py +0 -0
  23. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/benchmark/runner.py +0 -0
  24. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/__init__.py +0 -0
  25. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/benchmark_cli.py +0 -0
  26. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/legacy_cli.py +0 -0
  27. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/main.py +0 -0
  28. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/__init__.py +0 -0
  29. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/contracts.py +0 -0
  30. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/ledger.py +0 -0
  31. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/readiness.py +0 -0
  32. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/__init__.py +0 -0
  33. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/allocator.py +0 -0
  34. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/policy.py +0 -0
  35. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/qa.py +0 -0
  36. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/twin_generator.py +0 -0
  37. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/constraints/__init__.py +0 -0
  38. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/constraints/type_iis.py +0 -0
  39. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/__init__.py +0 -0
  40. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/experiment.py +0 -0
  41. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/host_model.py +0 -0
  42. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/__init__.py +0 -0
  43. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/exporter.py +0 -0
  44. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/optimizer.py +0 -0
  45. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/validator.py +0 -0
  46. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/policy.py +0 -0
  47. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/reranker.py +0 -0
  48. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/slate_engine.py +0 -0
  49. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/slate_generator.py +0 -0
  50. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/human_stemcell_codons.json +0 -0
  51. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/nbenthamiana_codons.json +0 -0
  52. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/nbenthamiana_golden_set.json +0 -0
  53. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/ntabacum_codons.json +0 -0
  54. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/human_stemcell_derived_codons.json +0 -0
  55. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/human_stemcell_policy.json +0 -0
  56. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_codons.json +0 -0
  57. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_filtered_stats.json +0 -0
  58. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_manifest.json +0 -0
  59. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_codons.json +0 -0
  60. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_filtered_stats.json +0 -0
  61. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_manifest.json +0 -0
  62. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_derived_codons.json +0 -0
  63. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_derived_manifest.json +0 -0
  64. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_filtered_stats.json +0 -0
  65. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/reference/reference_policy_manifest.json +0 -0
  66. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/templates/high_expression.json +0 -0
  67. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/templates/standard_expression.json +0 -0
  68. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/wolffia_globosa_codons.json +0 -0
  69. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/database.py +0 -0
  70. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/db/__init__.py +0 -0
  71. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/db/connector.py +0 -0
  72. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/design_review.py +0 -0
  73. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/__init__.py +0 -0
  74. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/acquisition.py +0 -0
  75. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/acquisition_logger.py +0 -0
  76. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/filter.py +0 -0
  77. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/generator.py +0 -0
  78. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/panel_builder.py +0 -0
  79. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/schemas.py +0 -0
  80. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/slate.py +0 -0
  81. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/traits.py +0 -0
  82. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/balanced_optimizer.py +0 -0
  83. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_adapter.py +0 -0
  84. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2.py +0 -0
  85. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_1.py +0 -0
  86. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_1_1.py +0 -0
  87. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_2.py +0 -0
  88. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_3.py +0 -0
  89. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/__init__.py +0 -0
  90. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/adapter.py +0 -0
  91. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/diagnostics.py +0 -0
  92. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/inference.py +0 -0
  93. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/models/__init__.py +0 -0
  94. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/models/mbart_codon.py +0 -0
  95. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/tokenizer/control_tokenizer.py +0 -0
  96. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/local_rewriter.py +0 -0
  97. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/__init__.py +0 -0
  98. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/codon_table_builder.py +0 -0
  99. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/construct_builder.py +0 -0
  100. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/exporter.py +0 -0
  101. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/optimizer.py +0 -0
  102. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/pipeline.py +0 -0
  103. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/__init__.py +0 -0
  104. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/domesticator.py +0 -0
  105. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/reverse_translator.py +0 -0
  106. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/rule_engine.py +0 -0
  107. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/scoring.py +0 -0
  108. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/scoring_ml.py +0 -0
  109. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/utils.py +0 -0
  110. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/validator.py +0 -0
  111. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/registry.py +0 -0
  112. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/adapters.py +0 -0
  113. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/automaton.py +0 -0
  114. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/compiler.py +0 -0
  115. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/__init__.py +0 -0
  116. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/corpus_builder.py +0 -0
  117. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/tokenizer.py +0 -0
  118. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/decoder.py +0 -0
  119. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/interfaces.py +0 -0
  120. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/__init__.py +0 -0
  121. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/arch.py +0 -0
  122. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/baselines.py +0 -0
  123. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/export_onnx.py +0 -0
  124. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/stemcell_3dp.py +0 -0
  125. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/structural_pause.py +0 -0
  126. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/structure_web.py +0 -0
  127. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/targeted_remediator.py +0 -0
  128. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/evaluator.py +0 -0
  129. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/evidence_logger.py +0 -0
  130. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/metrics.py +0 -0
  131. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/models.py +0 -0
  132. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/__init__.py +0 -0
  133. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/initiation_mfe.py +0 -0
  134. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/plant_rna_guards.py +0 -0
  135. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/__init__.py +0 -0
  136. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/fasta.py +0 -0
  137. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/package_compiler.py +0 -0
  138. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/validation.py +0 -0
  139. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/learning/__init__.py +0 -0
  140. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/learning/ranker.py +0 -0
  141. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/__init__.py +0 -0
  142. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/annotations.py +0 -0
  143. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/bridge.py +0 -0
  144. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/cli.py +0 -0
  145. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/contracts.py +0 -0
  146. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/pipeline.py +0 -0
  147. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/pipeline/__init__.py +0 -0
  148. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/pipeline/design_pipeline.py +0 -0
  149. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/profiles/profile_snapshot.py +0 -0
  150. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/__init__.py +0 -0
  151. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/annotate.py +0 -0
  152. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/kd_scale.py +0 -0
  153. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/risk_classifier.py +0 -0
  154. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/sp_predict.py +0 -0
  155. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/tm_predict.py +0 -0
  156. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/__init__.py +0 -0
  157. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/method_registry.py +0 -0
  158. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/model_registry.py +0 -0
  159. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/registry_loader.py +0 -0
  160. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/versioning.py +0 -0
  161. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/review/__init__.py +0 -0
  162. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/review/evaluation_integrity.py +0 -0
  163. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/rules/models.py +0 -0
  164. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/rules/registry.py +0 -0
  165. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/__init__.py +0 -0
  166. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/design_package.py +0 -0
  167. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/design_package.schema.json +0 -0
  168. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/evidence.py +0 -0
  169. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/run_config.schema.json +0 -0
  170. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/scoring/quantization.py +0 -0
  171. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/sops/config.py +0 -0
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  181. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/restriction_sites.py +0 -0
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  183. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/sequence_validator.py +0 -0
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  190. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation_registry.py +0 -0
  191. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation_report.py +0 -0
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  194. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/requires.txt +0 -0
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  196. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_3dp_review_regressions.py +0 -0
  197. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_3dp_validation_suite.py +0 -0
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  200. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_cli_output_guard.py +0 -0
  201. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_codon_table_metadata.py +0 -0
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  205. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_smoke.py +0 -0
  206. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_cai.py +0 -0
  207. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_candidate_review_safety.py +0 -0
  208. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_codon_table_manifest.py +0 -0
  209. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_cross_engine_evaluation.py +0 -0
  210. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_database.py +0 -0
  211. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_database_configuration.py +0 -0
  212. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_db_connector.py +0 -0
  213. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_schema.py +0 -0
  214. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_semantics.py +0 -0
  215. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_serialization.py +0 -0
  216. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_review.py +0 -0
  217. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_docs_consistency.py +0 -0
  218. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_1_1.py +0 -0
  219. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_1_initiation.py +0 -0
  220. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_2_0.py +0 -0
  221. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_3_0.py +0 -0
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  224. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_fasta_io.py +0 -0
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  226. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_host_profile_metadata.py +0 -0
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  232. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_job355_design_experiment.py +0 -0
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  237. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_math_v2_dp_optimality.py +0 -0
  238. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_nbfold_phase_c.py +0 -0
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  240. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_nbfold_pipeline.py +0 -0
  241. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_no_raw_sequence_logging.py +0 -0
  242. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_oct23_review.py +0 -0
  243. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_onnx_adapter_contract.py +0 -0
  244. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_openbio_missing_metric_contract.py +0 -0
  245. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_optional_postgres.py +0 -0
  246. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_parameter_registry.py +0 -0
  247. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_partial_dp_rescue.py +0 -0
  248. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_plant_rna_guards.py +0 -0
  249. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_policy_type_iis_targets.py +0 -0
  250. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_prepare_lm_dataset.py +0 -0
  251. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_protein_risk.py +0 -0
  252. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_public_surface_scanner.py +0 -0
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  254. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_registry_production_sync.py +0 -0
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  256. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_rule_registry.py +0 -0
  257. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_scientific_web_397.py +0 -0
  258. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_sequence_validator.py +0 -0
  259. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_sllm_biological_pipeline.py +0 -0
  260. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_slm_decoder.py +0 -0
  261. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_slm_interface.py +0 -0
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  267. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_translation_integrity.py +0 -0
  268. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_validation_contract_compat.py +0 -0
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  270. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_validation_report.py +0 -0
  271. {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_worked_example.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: factorforge-cds
3
- Version: 3.5.10
3
+ Version: 3.5.11
4
4
  Summary: FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex.
5
5
  Author-email: Eijex <eijex.lab@gmail.com>
6
6
  License-Expression: AGPL-3.0-only
@@ -52,7 +52,7 @@ Dynamic: license-file
52
52
 
53
53
  FactorForge performs deterministic CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
54
54
 
55
- FactorForge v3.5.10 uses independently versioned engines:
55
+ FactorForge v3.5.11 uses independently versioned engines:
56
56
 
57
57
  | Generation | Engine | Version | Availability |
58
58
  |---|---|---:|---|
@@ -134,7 +134,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
134
134
  ## Citing
135
135
 
136
136
  ```
137
- FactorForge v3.5.10 (2026). Open-source constraint-based CDS design and sequence review.
137
+ FactorForge v3.5.11 (2026). Open-source constraint-based CDS design and sequence review.
138
138
  Eijex. https://github.com/eijex/factorforge-cds
139
139
  ```
140
140
 
@@ -14,7 +14,7 @@
14
14
 
15
15
  FactorForge performs deterministic CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
16
16
 
17
- FactorForge v3.5.10 uses independently versioned engines:
17
+ FactorForge v3.5.11 uses independently versioned engines:
18
18
 
19
19
  | Generation | Engine | Version | Availability |
20
20
  |---|---|---:|---|
@@ -96,7 +96,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
96
96
  ## Citing
97
97
 
98
98
  ```
99
- FactorForge v3.5.10 (2026). Open-source constraint-based CDS design and sequence review.
99
+ FactorForge v3.5.11 (2026). Open-source constraint-based CDS design and sequence review.
100
100
  Eijex. https://github.com/eijex/factorforge-cds
101
101
  ```
102
102
 
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "factorforge-cds"
7
- version = "3.5.10"
7
+ version = "3.5.11"
8
8
  description = "FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex."
9
9
  readme = "README.md"
10
10
  license = "AGPL-3.0-only"
@@ -20,6 +20,13 @@ def _load_dp_v2_3():
20
20
  return DPV230EngineAdapter
21
21
 
22
22
 
23
+ def _load_dp_v2_4():
24
+ """Load DP v2.4.0 engine when requested."""
25
+ from .dp_v2_4 import DPV240EngineAdapter
26
+
27
+ return DPV240EngineAdapter
28
+
29
+
23
30
  def register_builtin_engines() -> None:
24
31
  """Register bundled engines."""
25
32
  from .profile.optimizer import RuleBasedOptimizer
@@ -37,6 +44,12 @@ def register_builtin_engines() -> None:
37
44
  metadata={**engine_metadata("dp_v2_3"), "stable": False},
38
45
  )
39
46
 
47
+ EngineRegistry.register_lazy(
48
+ "dp_v2_4",
49
+ _load_dp_v2_4,
50
+ metadata={**engine_metadata("dp_v2_4"), "stable": False},
51
+ )
52
+
40
53
  EngineRegistry.register(
41
54
  "profile",
42
55
  RuleBasedOptimizer,