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.
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/PKG-INFO +3 -3
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/README.md +2 -2
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/pyproject.toml +1 -1
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/__init__.py +13 -0
- factorforge_cds-3.5.11/src/factorforge/engines/dp_v2_4.py +870 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/version_manifest.json +12 -3
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/PKG-INFO +3 -3
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/SOURCES.txt +4 -0
- factorforge_cds-3.5.11/tests/test_dp_v2_4_0.py +249 -0
- factorforge_cds-3.5.11/tests/test_dp_v2_4_review.py +108 -0
- factorforge_cds-3.5.11/tests/test_hpx_viewer_review.py +59 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_multi_engine_governance.py +2 -2
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_version_manifest.py +2 -2
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/LICENSE +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/setup.cfg +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/__main__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/feasibility.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/metrics.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/analysis/sequence_risks.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/benchmark/models.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/benchmark/runner.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/benchmark_cli.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/legacy_cli.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/cli/main.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/contracts.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/ledger.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/closed_loop/readiness.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/allocator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/policy.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/qa.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/codon/twin_generator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/constraints/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/constraints/type_iis.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/experiment.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/host_model.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/exporter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/optimizer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/interfaces/validator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/policy.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/reranker.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/slate_engine.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/core/slate_generator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/human_stemcell_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/nbenthamiana_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/nbenthamiana_golden_set.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/ntabacum_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/human_stemcell_derived_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/human_stemcell_policy.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_filtered_stats.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_all_derived_manifest.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_filtered_stats.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/nbev11_cds_hc_derived_manifest.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_derived_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_derived_manifest.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/profiles/qld183_v103_filtered_stats.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/reference/reference_policy_manifest.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/templates/high_expression.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/templates/standard_expression.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/data/wolffia_globosa_codons.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/database.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/db/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/db/connector.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/design_review.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/acquisition.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/acquisition_logger.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/filter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/generator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/panel_builder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/schemas.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/slate.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/discovery/traits.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/balanced_optimizer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_adapter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_1.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_1_1.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_2.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/dp_v2_3.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/adapter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/diagnostics.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/inference.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/models/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/models/mbart_codon.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/lm/tokenizer/control_tokenizer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/local_rewriter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/codon_table_builder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/construct_builder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/exporter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/optimizer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/pipeline.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/domesticator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/reverse_translator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/rules/rule_engine.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/scoring.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/scoring_ml.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/utils.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/profile/validator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/adapters.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/automaton.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/compiler.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/corpus_builder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/data/tokenizer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/decoder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/interfaces.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/arch.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/baselines.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/sllm/model/export_onnx.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/stemcell_3dp.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/structural_pause.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/structure_web.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/engines/targeted_remediator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/evaluator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/evidence_logger.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/metrics.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/evaluation/models.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/initiation_mfe.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/guards/plant_rna_guards.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/fasta.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/package_compiler.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/io/validation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/learning/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/learning/ranker.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/annotations.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/bridge.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/cli.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/contracts.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/nbfold/pipeline.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/pipeline/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/pipeline/design_pipeline.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/profiles/profile_snapshot.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/annotate.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/kd_scale.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/risk_classifier.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/sp_predict.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/protein_risk/tm_predict.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/method_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/model_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/registry_loader.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/registry/versioning.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/review/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/review/evaluation_integrity.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/rules/models.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/rules/registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/design_package.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/design_package.schema.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/evidence.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/schemas/run_config.schema.json +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/scoring/quantization.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/sops/config.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/structure/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/structure/auto_annotator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/structure/auto_resolver.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/telemetry/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/telemetry/gcs_reconciliation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/telemetry/training_logger.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/construct_id.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/exceptions.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/restriction_sites.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/sequence_identity.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/sequence_validator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/utils/validation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation/__init__.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation/cli.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation/hub.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation/package_generator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation/tradeoff_suite.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge/validation_report.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/dependency_links.txt +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/entry_points.txt +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/requires.txt +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/src/factorforge_cds.egg-info/top_level.txt +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_3dp_review_regressions.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_3dp_validation_suite.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_auto_annotator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_baselines.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_cli_output_guard.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_codon_table_metadata.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_harness.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_regression.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_scoring.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_benchmark_smoke.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_cai.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_candidate_review_safety.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_codon_table_manifest.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_cross_engine_evaluation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_database.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_database_configuration.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_db_connector.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_schema.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_semantics.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_package_serialization.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_design_review.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_docs_consistency.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_1_1.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_1_initiation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_2_0.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_dp_v2_3_0.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_durable_reconciliation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_enterprise_integration_396.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_fasta_io.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_gc_content.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_host_profile_metadata.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_hpx_viewer.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_initiation_mfe.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_iupac_validation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_job350_codon_twins.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_job351_closed_loop_foundation.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_job355_design_experiment.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_learning_workflow_boundary.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_legacy_cli.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_lm_alpha_contract.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_local_rewriter.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_math_v2_dp_optimality.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_nbfold_phase_c.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_nbfold_phase_c_benchmark.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_nbfold_pipeline.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_no_raw_sequence_logging.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_oct23_review.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_onnx_adapter_contract.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_openbio_missing_metric_contract.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_optional_postgres.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_parameter_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_partial_dp_rescue.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_plant_rna_guards.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_policy_type_iis_targets.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_prepare_lm_dataset.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_protein_risk.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_public_surface_scanner.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_quantized_scoring.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_registry_production_sync.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_restriction_sites.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_rule_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_scientific_web_397.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_sequence_validator.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_sllm_biological_pipeline.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_slm_decoder.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_slm_interface.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_sop_profile.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_stemcell_3dp.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_structural_pause.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_suite_capability_compat.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_training_logger.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_translation_integrity.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_validation_contract_compat.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_validation_registry.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_validation_report.py +0 -0
- {factorforge_cds-3.5.10 → factorforge_cds-3.5.11}/tests/test_worked_example.py +0 -0
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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`).
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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`).
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