factorforge-cds 3.5.2__tar.gz → 3.5.3__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 (201) hide show
  1. {factorforge_cds-3.5.2/src/factorforge_cds.egg-info → factorforge_cds-3.5.3}/PKG-INFO +2 -2
  2. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/README.md +1 -1
  3. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/pyproject.toml +1 -1
  4. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/version_manifest.json +1 -1
  5. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3/src/factorforge_cds.egg-info}/PKG-INFO +2 -2
  6. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_multi_engine_governance.py +2 -2
  7. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_version_manifest.py +1 -1
  8. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/LICENSE +0 -0
  9. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/setup.cfg +0 -0
  10. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/__init__.py +0 -0
  11. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/__main__.py +0 -0
  12. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/analysis/__init__.py +0 -0
  13. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/analysis/feasibility.py +0 -0
  14. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/analysis/metrics.py +0 -0
  15. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/analysis/sequence_risks.py +0 -0
  16. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/benchmark/models.py +0 -0
  17. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/benchmark/runner.py +0 -0
  18. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/cli/__init__.py +0 -0
  19. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/cli/benchmark_cli.py +0 -0
  20. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/cli/legacy_cli.py +0 -0
  21. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/cli/main.py +0 -0
  22. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/constraints/__init__.py +0 -0
  23. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/constraints/type_iis.py +0 -0
  24. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/host_model.py +0 -0
  25. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/interfaces/__init__.py +0 -0
  26. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/interfaces/exporter.py +0 -0
  27. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/interfaces/optimizer.py +0 -0
  28. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/interfaces/validator.py +0 -0
  29. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/reranker.py +0 -0
  30. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/slate_engine.py +0 -0
  31. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/core/slate_generator.py +0 -0
  32. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/nbenthamiana_codons.json +0 -0
  33. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/nbenthamiana_golden_set.json +0 -0
  34. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/ntabacum_codons.json +0 -0
  35. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_all_derived_codons.json +0 -0
  36. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_all_derived_filtered_stats.json +0 -0
  37. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_all_derived_manifest.json +0 -0
  38. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_hc_derived_codons.json +0 -0
  39. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_hc_derived_filtered_stats.json +0 -0
  40. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/nbev11_cds_hc_derived_manifest.json +0 -0
  41. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/qld183_v103_derived_codons.json +0 -0
  42. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/qld183_v103_derived_manifest.json +0 -0
  43. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/profiles/qld183_v103_filtered_stats.json +0 -0
  44. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/reference/reference_policy_manifest.json +0 -0
  45. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/templates/high_expression.json +0 -0
  46. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/templates/standard_expression.json +0 -0
  47. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/data/wolffia_globosa_codons.json +0 -0
  48. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/database.py +0 -0
  49. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/db/__init__.py +0 -0
  50. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/db/connector.py +0 -0
  51. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/design_review.py +0 -0
  52. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/__init__.py +0 -0
  53. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/acquisition.py +0 -0
  54. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/acquisition_logger.py +0 -0
  55. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/filter.py +0 -0
  56. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/generator.py +0 -0
  57. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/panel_builder.py +0 -0
  58. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/schemas.py +0 -0
  59. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/slate.py +0 -0
  60. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/discovery/traits.py +0 -0
  61. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/__init__.py +0 -0
  62. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/balanced_optimizer.py +0 -0
  63. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/dp_adapter.py +0 -0
  64. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/dp_v2.py +0 -0
  65. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/dp_v2_1.py +0 -0
  66. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/dp_v2_1_1.py +0 -0
  67. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/__init__.py +0 -0
  68. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/adapter.py +0 -0
  69. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/diagnostics.py +0 -0
  70. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/inference.py +0 -0
  71. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/models/__init__.py +0 -0
  72. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/models/mbart_codon.py +0 -0
  73. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/lm/tokenizer/control_tokenizer.py +0 -0
  74. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/__init__.py +0 -0
  75. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/codon_table_builder.py +0 -0
  76. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/construct_builder.py +0 -0
  77. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/exporter.py +0 -0
  78. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/optimizer.py +0 -0
  79. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/pipeline.py +0 -0
  80. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/rules/__init__.py +0 -0
  81. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/rules/domesticator.py +0 -0
  82. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/rules/reverse_translator.py +0 -0
  83. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/rules/rule_engine.py +0 -0
  84. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/scoring.py +0 -0
  85. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/scoring_ml.py +0 -0
  86. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/utils.py +0 -0
  87. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/profile/validator.py +0 -0
  88. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/registry.py +0 -0
  89. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/adapters.py +0 -0
  90. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/automaton.py +0 -0
  91. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/compiler.py +0 -0
  92. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/data/__init__.py +0 -0
  93. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/data/corpus_builder.py +0 -0
  94. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/data/tokenizer.py +0 -0
  95. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/decoder.py +0 -0
  96. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/interfaces.py +0 -0
  97. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/model/__init__.py +0 -0
  98. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/model/arch.py +0 -0
  99. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/model/baselines.py +0 -0
  100. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/sllm/model/export_onnx.py +0 -0
  101. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/engines/targeted_remediator.py +0 -0
  102. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/evaluation/evaluator.py +0 -0
  103. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/evaluation/evidence_logger.py +0 -0
  104. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/evaluation/metrics.py +0 -0
  105. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/evaluation/models.py +0 -0
  106. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/io/__init__.py +0 -0
  107. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/io/fasta.py +0 -0
  108. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/io/validation.py +0 -0
  109. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/learning/__init__.py +0 -0
  110. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/learning/ranker.py +0 -0
  111. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/profiles/profile_snapshot.py +0 -0
  112. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/__init__.py +0 -0
  113. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/annotate.py +0 -0
  114. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/kd_scale.py +0 -0
  115. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/risk_classifier.py +0 -0
  116. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/sp_predict.py +0 -0
  117. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/protein_risk/tm_predict.py +0 -0
  118. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/__init__.py +0 -0
  119. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/method_registry.py +0 -0
  120. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/model_registry.py +0 -0
  121. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/registry_loader.py +0 -0
  122. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/versioning.py +0 -0
  123. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/review/__init__.py +0 -0
  124. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/review/evaluation_integrity.py +0 -0
  125. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/rules/models.py +0 -0
  126. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/rules/registry.py +0 -0
  127. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/schemas/__init__.py +0 -0
  128. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/schemas/design_package.py +0 -0
  129. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/schemas/design_package.schema.json +0 -0
  130. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/schemas/evidence.py +0 -0
  131. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/schemas/run_config.schema.json +0 -0
  132. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/scoring/quantization.py +0 -0
  133. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/sops/config.py +0 -0
  134. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/__init__.py +0 -0
  135. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/construct_id.py +0 -0
  136. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/exceptions.py +0 -0
  137. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/restriction_sites.py +0 -0
  138. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/sequence_identity.py +0 -0
  139. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/sequence_validator.py +0 -0
  140. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/utils/validation.py +0 -0
  141. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation/__init__.py +0 -0
  142. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation/cli.py +0 -0
  143. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation/hub.py +0 -0
  144. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation/package_generator.py +0 -0
  145. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation_registry.py +0 -0
  146. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/validation_report.py +0 -0
  147. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge_cds.egg-info/SOURCES.txt +0 -0
  148. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge_cds.egg-info/dependency_links.txt +0 -0
  149. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge_cds.egg-info/entry_points.txt +0 -0
  150. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge_cds.egg-info/requires.txt +0 -0
  151. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge_cds.egg-info/top_level.txt +0 -0
  152. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/scratch/integrity_test.py +0 -0
  153. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/scripts/seed_fixtures.py +0 -0
  154. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_baselines.py +0 -0
  155. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_cli_output_guard.py +0 -0
  156. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_codon_table_metadata.py +0 -0
  157. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_harness.py +0 -0
  158. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_regression.py +0 -0
  159. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_scoring.py +0 -0
  160. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_benchmark_smoke.py +0 -0
  161. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_cai.py +0 -0
  162. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_codon_table_manifest.py +0 -0
  163. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_cross_engine_evaluation.py +0 -0
  164. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_database.py +0 -0
  165. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_db_connector.py +0 -0
  166. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_design_package_schema.py +0 -0
  167. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_design_package_semantics.py +0 -0
  168. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_design_package_serialization.py +0 -0
  169. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_design_review.py +0 -0
  170. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_docs_consistency.py +0 -0
  171. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_dp_v2_1_1.py +0 -0
  172. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_dp_v2_1_initiation.py +0 -0
  173. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_fasta_io.py +0 -0
  174. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_gc_content.py +0 -0
  175. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_host_profile_metadata.py +0 -0
  176. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_iupac_validation.py +0 -0
  177. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_legacy_cli.py +0 -0
  178. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_lm_alpha_contract.py +0 -0
  179. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_math_v2_dp_optimality.py +0 -0
  180. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_no_raw_sequence_logging.py +0 -0
  181. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_openbio_missing_metric_contract.py +0 -0
  182. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_optional_postgres.py +0 -0
  183. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_parameter_registry.py +0 -0
  184. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_partial_dp_rescue.py +0 -0
  185. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_prepare_lm_dataset.py +0 -0
  186. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_protein_risk.py +0 -0
  187. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_quantized_scoring.py +0 -0
  188. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_registry_production_sync.py +0 -0
  189. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_restriction_sites.py +0 -0
  190. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_rule_registry.py +0 -0
  191. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_sequence_validator.py +0 -0
  192. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_sllm_biological_pipeline.py +0 -0
  193. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_slm_decoder.py +0 -0
  194. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_slm_interface.py +0 -0
  195. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_sop_profile.py +0 -0
  196. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_suite_capability_compat.py +0 -0
  197. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_translation_integrity.py +0 -0
  198. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_validation_contract_compat.py +0 -0
  199. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_validation_registry.py +0 -0
  200. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_validation_report.py +0 -0
  201. {factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_worked_example.py +0 -0
{factorforge_cds-3.5.2/src/factorforge_cds.egg-info → factorforge_cds-3.5.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: factorforge-cds
3
- Version: 3.5.2
3
+ Version: 3.5.3
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
@@ -127,7 +127,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
127
127
  ## Citing
128
128
 
129
129
  ```
130
- FactorForge v3.5.2 (2026). Open-source constraint-based CDS design and sequence review.
130
+ FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
131
131
  Eijex. https://github.com/eijex/factorforge-cds
132
132
  ```
133
133
 
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/README.md RENAMED
@@ -90,7 +90,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
90
90
  ## Citing
91
91
 
92
92
  ```
93
- FactorForge v3.5.2 (2026). Open-source constraint-based CDS design and sequence review.
93
+ FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
94
94
  Eijex. https://github.com/eijex/factorforge-cds
95
95
  ```
96
96
 
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "factorforge-cds"
7
- version = "3.5.2"
7
+ version = "3.5.3"
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"
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/src/factorforge/registry/version_manifest.json RENAMED
@@ -2,7 +2,7 @@
2
2
  "schema_version": "1.0",
3
3
  "product": {
4
4
  "name": "FactorForge",
5
- "version": "3.5.2",
5
+ "version": "3.5.3",
6
6
  "release_status": "web_api_deployed_tag_pending",
7
7
  "previous_stable_version": "3.4.5"
8
8
  },
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3/src/factorforge_cds.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: factorforge-cds
3
- Version: 3.5.2
3
+ Version: 3.5.3
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
@@ -127,7 +127,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
127
127
  ## Citing
128
128
 
129
129
  ```
130
- FactorForge v3.5.2 (2026). Open-source constraint-based CDS design and sequence review.
130
+ FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
131
131
  Eijex. https://github.com/eijex/factorforge-cds
132
132
  ```
133
133
 
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_multi_engine_governance.py RENAMED
@@ -13,7 +13,7 @@ from factorforge.analysis.metrics import load_codon_usage_table
13
13
 
14
14
  def test_version_manifest_governance():
15
15
  """Verify product and multi-generation engine SemVer decoupling."""
16
- assert product_version() == "3.5.1"
16
+ assert product_version() == "3.5.2"
17
17
 
18
18
  # Gen 1 (Rule)
19
19
  assert engine_generation("profile") == 1
@@ -76,7 +76,7 @@ def test_api_provenance_envelope():
76
76
  assert response["success"] is True
77
77
  assert "provenance" in response
78
78
  prov = response["provenance"]
79
- assert prov["product_version"] == "3.5.1"
79
+ assert prov["product_version"] == "3.5.2"
80
80
  assert prov["engine_id"] == "dp"
81
81
  assert prov["engine_generation"] == 2
82
82
  assert prov["engine_version"] == "2.0.1"
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/tests/test_version_manifest.py RENAMED
@@ -6,7 +6,7 @@ from factorforge.registry.versioning import engine_version, public_version_metad
6
6
  def test_product_and_engine_versions_are_independently_declared() -> None:
7
7
  metadata = public_version_metadata()
8
8
 
9
- assert __version__ == "3.5.1"
9
+ assert __version__ == "3.5.2"
10
10
  assert metadata["product"]["release_status"] == "web_api_deployed_tag_pending"
11
11
  assert metadata["engines"]["profile"]["generation"] == 1
12
12
  assert metadata["engines"]["dp"]["version"] == engine_version("dp")
{factorforge_cds-3.5.2 → factorforge_cds-3.5.3}/LICENSE RENAMED
File without changes