LICENSE
README.md
pyproject.toml
src/factorforge/__init__.py
src/factorforge/__main__.py
src/factorforge/database.py
src/factorforge/analysis/__init__.py
src/factorforge/analysis/feasibility.py
src/factorforge/analysis/metrics.py
src/factorforge/cli/__init__.py
src/factorforge/cli/legacy_cli.py
src/factorforge/cli/main.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/templates/high_expression.json
src/factorforge/data/templates/standard_expression.json
src/factorforge/engines/__init__.py
src/factorforge/engines/registry.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/io/__init__.py
src/factorforge/io/fasta.py
src/factorforge/io/validation.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/registry_loader.py
src/factorforge/schemas/__init__.py
src/factorforge/schemas/design_package.py
src/factorforge/schemas/design_package.schema.json
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_validator.py
src/factorforge/utils/validation.py
src/factorforge/validation/__init__.py
src/factorforge/validation/cli.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
tests/test_baselines.py
tests/test_benchmark_codon_table_metadata.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_database.py
tests/test_design_package_schema.py
tests/test_design_package_semantics.py
tests/test_design_package_serialization.py
tests/test_docs_consistency.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_no_raw_sequence_logging.py
tests/test_openbio_missing_metric_contract.py
tests/test_parameter_registry.py
tests/test_protein_risk.py
tests/test_registry_production_sync.py
tests/test_restriction_sites.py
tests/test_sequence_validator.py
tests/test_translation_integrity.py
tests/test_worked_example.py