LICENSE
README.md
pyproject.toml
src/factorforge/__init__.py
src/factorforge/__main__.py
src/factorforge/database.py
src/factorforge/design_review.py
src/factorforge/validation_registry.py
src/factorforge/validation_report.py
src/factorforge/analysis/__init__.py
src/factorforge/analysis/feasibility.py
src/factorforge/analysis/metrics.py
src/factorforge/analysis/sequence_risks.py
src/factorforge/benchmark/models.py
src/factorforge/benchmark/runner.py
src/factorforge/cli/__init__.py
src/factorforge/cli/benchmark_cli.py
src/factorforge/cli/legacy_cli.py
src/factorforge/cli/main.py
src/factorforge/constraints/__init__.py
src/factorforge/constraints/type_iis.py
src/factorforge/core/host_model.py
src/factorforge/core/reranker.py
src/factorforge/core/slate_engine.py
src/factorforge/core/slate_generator.py
src/factorforge/core/interfaces/__init__.py
src/factorforge/core/interfaces/exporter.py
src/factorforge/core/interfaces/optimizer.py
src/factorforge/core/interfaces/validator.py
src/factorforge/data/nbenthamiana_codons.json
src/factorforge/data/nbenthamiana_golden_set.json
src/factorforge/data/ntabacum_codons.json
src/factorforge/data/wolffia_globosa_codons.json
src/factorforge/data/profiles/nbev11_cds_all_derived_codons.json
src/factorforge/data/profiles/nbev11_cds_all_derived_filtered_stats.json
src/factorforge/data/profiles/nbev11_cds_all_derived_manifest.json
src/factorforge/data/profiles/nbev11_cds_hc_derived_codons.json
src/factorforge/data/profiles/nbev11_cds_hc_derived_filtered_stats.json
src/factorforge/data/profiles/nbev11_cds_hc_derived_manifest.json
src/factorforge/data/profiles/qld183_v103_derived_codons.json
src/factorforge/data/profiles/qld183_v103_derived_manifest.json
src/factorforge/data/profiles/qld183_v103_filtered_stats.json
src/factorforge/data/reference/reference_policy_manifest.json
src/factorforge/data/templates/high_expression.json
src/factorforge/data/templates/standard_expression.json
src/factorforge/db/__init__.py
src/factorforge/db/connector.py
src/factorforge/discovery/__init__.py
src/factorforge/discovery/acquisition.py
src/factorforge/discovery/acquisition_logger.py
src/factorforge/discovery/filter.py
src/factorforge/discovery/generator.py
src/factorforge/discovery/panel_builder.py
src/factorforge/discovery/schemas.py
src/factorforge/discovery/slate.py
src/factorforge/discovery/traits.py
src/factorforge/engines/__init__.py
src/factorforge/engines/balanced_optimizer.py
src/factorforge/engines/dp_adapter.py
src/factorforge/engines/dp_v2.py
src/factorforge/engines/dp_v2_1.py
src/factorforge/engines/dp_v2_1_1.py
src/factorforge/engines/registry.py
src/factorforge/engines/targeted_remediator.py
src/factorforge/engines/lm/__init__.py
src/factorforge/engines/lm/adapter.py
src/factorforge/engines/lm/diagnostics.py
src/factorforge/engines/lm/inference.py
src/factorforge/engines/lm/models/__init__.py
src/factorforge/engines/lm/models/mbart_codon.py
src/factorforge/engines/lm/tokenizer/control_tokenizer.py
src/factorforge/engines/profile/__init__.py
src/factorforge/engines/profile/codon_table_builder.py
src/factorforge/engines/profile/construct_builder.py
src/factorforge/engines/profile/exporter.py
src/factorforge/engines/profile/optimizer.py
src/factorforge/engines/profile/pipeline.py
src/factorforge/engines/profile/scoring.py
src/factorforge/engines/profile/scoring_ml.py
src/factorforge/engines/profile/utils.py
src/factorforge/engines/profile/validator.py
src/factorforge/engines/profile/rules/__init__.py
src/factorforge/engines/profile/rules/domesticator.py
src/factorforge/engines/profile/rules/reverse_translator.py
src/factorforge/engines/profile/rules/rule_engine.py
src/factorforge/engines/sllm/adapters.py
src/factorforge/engines/sllm/automaton.py
src/factorforge/engines/sllm/compiler.py
src/factorforge/engines/sllm/decoder.py
src/factorforge/engines/sllm/interfaces.py
src/factorforge/engines/sllm/data/__init__.py
src/factorforge/engines/sllm/data/corpus_builder.py
src/factorforge/engines/sllm/data/tokenizer.py
src/factorforge/engines/sllm/model/__init__.py
src/factorforge/engines/sllm/model/arch.py
src/factorforge/engines/sllm/model/baselines.py
src/factorforge/engines/sllm/model/export_onnx.py
src/factorforge/evaluation/evaluator.py
src/factorforge/evaluation/evidence_logger.py
src/factorforge/evaluation/metrics.py
src/factorforge/evaluation/models.py
src/factorforge/io/__init__.py
src/factorforge/io/fasta.py
src/factorforge/io/validation.py
src/factorforge/learning/__init__.py
src/factorforge/learning/ranker.py
src/factorforge/profiles/profile_snapshot.py
src/factorforge/protein_risk/__init__.py
src/factorforge/protein_risk/annotate.py
src/factorforge/protein_risk/kd_scale.py
src/factorforge/protein_risk/risk_classifier.py
src/factorforge/protein_risk/sp_predict.py
src/factorforge/protein_risk/tm_predict.py
src/factorforge/registry/__init__.py
src/factorforge/registry/method_registry.py
src/factorforge/registry/model_registry.py
src/factorforge/registry/registry_loader.py
src/factorforge/registry/version_manifest.json
src/factorforge/registry/versioning.py
src/factorforge/review/__init__.py
src/factorforge/review/evaluation_integrity.py
src/factorforge/rules/models.py
src/factorforge/rules/registry.py
src/factorforge/schemas/__init__.py
src/factorforge/schemas/design_package.py
src/factorforge/schemas/design_package.schema.json
src/factorforge/schemas/evidence.py
src/factorforge/schemas/run_config.schema.json
src/factorforge/scoring/quantization.py
src/factorforge/sops/config.py
src/factorforge/utils/__init__.py
src/factorforge/utils/construct_id.py
src/factorforge/utils/exceptions.py
src/factorforge/utils/restriction_sites.py
src/factorforge/utils/sequence_identity.py
src/factorforge/utils/sequence_validator.py
src/factorforge/utils/validation.py
src/factorforge/validation/__init__.py
src/factorforge/validation/cli.py
src/factorforge/validation/hub.py
src/factorforge/validation/package_generator.py
src/factorforge_cds.egg-info/PKG-INFO
src/factorforge_cds.egg-info/SOURCES.txt
src/factorforge_cds.egg-info/dependency_links.txt
src/factorforge_cds.egg-info/entry_points.txt
src/factorforge_cds.egg-info/requires.txt
src/factorforge_cds.egg-info/top_level.txt
src/scratch/integrity_test.py
src/scripts/seed_fixtures.py
tests/test_baselines.py
tests/test_benchmark_cli_output_guard.py
tests/test_benchmark_codon_table_metadata.py
tests/test_benchmark_harness.py
tests/test_benchmark_regression.py
tests/test_benchmark_scoring.py
tests/test_benchmark_smoke.py
tests/test_cai.py
tests/test_codon_table_manifest.py
tests/test_cross_engine_evaluation.py
tests/test_database.py
tests/test_db_connector.py
tests/test_design_package_schema.py
tests/test_design_package_semantics.py
tests/test_design_package_serialization.py
tests/test_design_review.py
tests/test_docs_consistency.py
tests/test_dp_v2_1_1.py
tests/test_dp_v2_1_initiation.py
tests/test_fasta_io.py
tests/test_gc_content.py
tests/test_host_profile_metadata.py
tests/test_iupac_validation.py
tests/test_legacy_cli.py
tests/test_lm_alpha_contract.py
tests/test_math_v2_dp_optimality.py
tests/test_multi_engine_governance.py
tests/test_no_raw_sequence_logging.py
tests/test_openbio_missing_metric_contract.py
tests/test_optional_postgres.py
tests/test_parameter_registry.py
tests/test_partial_dp_rescue.py
tests/test_prepare_lm_dataset.py
tests/test_protein_risk.py
tests/test_quantized_scoring.py
tests/test_registry_production_sync.py
tests/test_restriction_sites.py
tests/test_rule_registry.py
tests/test_sequence_validator.py
tests/test_sllm_biological_pipeline.py
tests/test_slm_decoder.py
tests/test_slm_interface.py
tests/test_sop_profile.py
tests/test_suite_capability_compat.py
tests/test_translation_integrity.py
tests/test_validation_contract_compat.py
tests/test_validation_registry.py
tests/test_validation_report.py
tests/test_version_manifest.py
tests/test_worked_example.py