LICENSE
README.md
pyproject.toml
src/factorforge/__init__.py
src/factorforge/__main__.py
src/factorforge/database.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/engines/__init__.py
src/factorforge/engines/registry.py
src/factorforge/engines/ml/__init__.py
src/factorforge/engines/ml/plant_optimizer.py
src/factorforge/engines/v1_archived/__init__.py
src/factorforge/engines/v2/__init__.py
src/factorforge/engines/v2/codon_table_builder.py
src/factorforge/engines/v2/construct_builder.py
src/factorforge/engines/v2/exporter.py
src/factorforge/engines/v2/optimizer.py
src/factorforge/engines/v2/pipeline.py
src/factorforge/engines/v2/scoring.py
src/factorforge/engines/v2/utils.py
src/factorforge/engines/v2/validator.py
src/factorforge/engines/v2/rules/__init__.py
src/factorforge/engines/v2/rules/domesticator.py
src/factorforge/engines/v2/rules/reverse_translator.py
src/factorforge/engines/v2/rules/rule_engine.py
src/factorforge/engines/v3/__init__.py
src/factorforge/engines/v3/explain.py
src/factorforge/engines/v3/metrics.py
src/factorforge/engines/v3/modeling_bart_decoder.py
src/factorforge/engines/v3/pipeline.py
src/factorforge/engines/v3/synonym_mask.py
src/factorforge/engines/v3/tokenizer.py
src/factorforge/engines/v3/inference/__init__.py
src/factorforge/engines/v3/inference/constrained_decoder.py
src/factorforge/engines/v3/inference/v2_adapter.py
src/factorforge/ml/__init__.py
src/factorforge/ml/feasibility.py
src/factorforge/ml/metrics.py
src/factorforge/schemas/__init__.py
src/factorforge/schemas/design_package.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_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_compare_v1_v2.py
tests/test_database.py
tests/test_restriction_sites.py
tests/test_sequence_validator.py