LICENSE
MANIFEST.in
README.md
pyproject.toml
cherimoya/__init__.py
cherimoya/cheri.py
cherimoya/cherimoya.py
cherimoya/deep_lift_shap.py
cherimoya/io.py
cherimoya/losses.py
cherimoya/performance.py
cherimoya/training.py
cherimoya/wrappers.py
cherimoya.egg-info/PKG-INFO
cherimoya.egg-info/SOURCES.txt
cherimoya.egg-info/dependency_links.txt
cherimoya.egg-info/entry_points.txt
cherimoya.egg-info/requires.txt
cherimoya.egg-info/top_level.txt
cherimoya_cli/__init__.py
cherimoya_cli/__main__.py
cherimoya_cli/defaults.py
cherimoya_cli/utils.py
cherimoya_cli/commands/__init__.py
cherimoya_cli/commands/attribute.py
cherimoya_cli/commands/evaluate.py
cherimoya_cli/commands/fit.py
cherimoya_cli/commands/install_skill.py
cherimoya_cli/commands/marginalize.py
cherimoya_cli/commands/negatives.py
cherimoya_cli/commands/pipeline.py
cherimoya_cli/commands/pipeline_json.py
cherimoya_cli/commands/seqlets.py
cherimoya_cli/skills/cherimoya/SKILL.md
cherimoya_cli/skills/cherimoya/references/assay-defaults.md
cherimoya_cli/skills/cherimoya/references/cli-training-pipeline.md
cherimoya_cli/skills/cherimoya/references/cli.md
cherimoya_cli/skills/cherimoya/references/concepts.md
cherimoya_cli/skills/cherimoya/references/input-files.md
cherimoya_cli/skills/cherimoya/references/interpreting-outputs.md
cherimoya_cli/skills/cherimoya/references/troubleshooting.md
cherimoya_cli/skills/cherimoya/references/using-in-python.md
cherimoya_cli/skills/cherimoya/references/using-tangermeme.md
tests/__init__.py
tests/conftest.py
tests/test_cheri.py
tests/test_cheri_autotune.py
tests/test_compile.py
tests/test_deep_lift_shap.py
tests/test_ema.py
tests/test_io.py
tests/test_losses.py
tests/test_model.py
tests/test_performance.py
tests/test_training.py
tests/test_utils.py
tests/test_wrappers.py
tests/commands/__init__.py
tests/commands/conftest.py
tests/commands/test_attribute.py
tests/commands/test_attribute_to_seqlets.py
tests/commands/test_compile_knob.py
tests/commands/test_config_keys.py
tests/commands/test_evaluate.py
tests/commands/test_fit.py
tests/commands/test_install_skill.py
tests/commands/test_marginalize.py
tests/commands/test_negatives.py
tests/commands/test_pipeline.py
tests/commands/test_pipeline_dry_run.py
tests/commands/test_seqlets.py
tests/commands/test_step_skipping.py