.gitignore
.readthedocs.yaml
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
python-publish.yml
doc/Makefile
doc/make.bat
doc/requirements.in
doc/requirements.txt
doc/changelog/CHANGELOG_0.1.0-beta.md
doc/changelog/CHANGELOG_0.1.1.md
doc/changelog/CHANGELOG_0.2.0.md
doc/changelog/CHANGELOG_0.3.0.md
doc/changelog/CHANGELOG_0.4.0.md
doc/source/conf.py
doc/source/index.rst
doc/source/api/index.rst
doc/source/user_guide/cleaners.md
doc/source/user_guide/index.rst
tests/test_dataset.py
tests/test_mutation.py
tests/test_pipeline.py
tests/test_sequence.py
tidymut/__init__.py
tidymut.egg-info/PKG-INFO
tidymut.egg-info/SOURCES.txt
tidymut.egg-info/dependency_links.txt
tidymut.egg-info/requires.txt
tidymut.egg-info/top_level.txt
tidymut/cleaners/__init__.py
tidymut/cleaners/base_config.py
tidymut/cleaners/basic_cleaners.py
tidymut/cleaners/cdna_proteolysis_cleaner.py
tidymut/cleaners/cdna_proteolysis_custom_cleaners.py
tidymut/cleaners/ddg_dtm_cleaners.py
tidymut/cleaners/human_domainome_custom_cleaners.py
tidymut/cleaners/human_domainome_sup2_cleaner.py
tidymut/cleaners/human_domainome_sup4_cleaner.py
tidymut/cleaners/protein_gym_cleaner.py
tidymut/cleaners/protein_gym_custom_cleaners.py
tidymut/core/__init__.py
tidymut/core/alphabet.py
tidymut/core/codon.py
tidymut/core/constants.py
tidymut/core/dataset.py
tidymut/core/mutation.py
tidymut/core/pipeline.py
tidymut/core/sequence.py
tidymut/core/types.py
tidymut/utils/__init__.py
tidymut/utils/cleaner_workers.py
tidymut/utils/data_source.py
tidymut/utils/dataset_builders.py
tidymut/utils/label_resolvers.py
tidymut/utils/mutation_converter.py
tidymut/utils/raw_data_downloader.py
tidymut/utils/sequence_io.py
tidymut/utils/type_converter.py
tools/changelog.py
tools/generate_changelog.sh