LICENSE
README.md
pyproject.toml
src/genome_entropy/__init__.py
src/genome_entropy/config.py
src/genome_entropy/errors.py
src/genome_entropy/logging_config.py
src/genome_entropy.egg-info/PKG-INFO
src/genome_entropy.egg-info/SOURCES.txt
src/genome_entropy.egg-info/dependency_links.txt
src/genome_entropy.egg-info/entry_points.txt
src/genome_entropy.egg-info/requires.txt
src/genome_entropy.egg-info/top_level.txt
src/genome_entropy/cli/__init__.py
src/genome_entropy/cli/main.py
src/genome_entropy/cli/commands/__init__.py
src/genome_entropy/cli/commands/download.py
src/genome_entropy/cli/commands/encode3di.py
src/genome_entropy/cli/commands/entropy.py
src/genome_entropy/cli/commands/estimate_tokens.py
src/genome_entropy/cli/commands/orf.py
src/genome_entropy/cli/commands/run.py
src/genome_entropy/cli/commands/translate.py
src/genome_entropy/encode3di/__init__.py
src/genome_entropy/encode3di/encoder.py
src/genome_entropy/encode3di/encoding.py
src/genome_entropy/encode3di/gpu_utils.py
src/genome_entropy/encode3di/multi_gpu.py
src/genome_entropy/encode3di/prostt5.py
src/genome_entropy/encode3di/token_estimator.py
src/genome_entropy/encode3di/types.py
src/genome_entropy/entropy/__init__.py
src/genome_entropy/entropy/shannon.py
src/genome_entropy/io/__init__.py
src/genome_entropy/io/fasta.py
src/genome_entropy/io/genbank.py
src/genome_entropy/io/jsonio.py
src/genome_entropy/orf/__init__.py
src/genome_entropy/orf/finder.py
src/genome_entropy/orf/types.py
src/genome_entropy/pipeline/__init__.py
src/genome_entropy/pipeline/runner.py
src/genome_entropy/translate/__init__.py
src/genome_entropy/translate/translator.py
tests/test_basic.py
tests/test_cli_smoke.py
tests/test_encoder_methods.py
tests/test_entropy.py
tests/test_genbank.py
tests/test_gpu_discovery.py
tests/test_logging_config.py
tests/test_multi_gpu_encoding.py
tests/test_orf_finder.py
tests/test_prostt5_integration.py
tests/test_token_budget_batches.py
tests/test_token_estimator.py
tests/test_translation.py