AUTHORS.md
CHANGELOG.md
CITATION.cff
IMPORT_PROVENANCE.json
LICENSE
MANIFEST.in
README.md
README.pypi.md
pyproject.toml
configs/biology.yaml
configs/nested.yaml
docs/CONFIGURATION.md
docs/METHODS.md
docs/RELEASE.md
docs/VALIDATION.md
docs/assets/README.md
docs/assets/girafi-overview.png
examples/expression.csv
examples/generate.py
examples/ppi.tsv
scripts/check_wheel.py
scripts/generate_reference.py
src/girafi/__init__.py
src/girafi/__main__.py
src/girafi/cli.py
src/girafi/config.py
src/girafi/core.py
src/girafi/data.py
src/girafi/pipeline.py
src/girafi/provenance.json
src/girafi/result.py
src/girafi/validation.py
src/girafi.egg-info/PKG-INFO
src/girafi.egg-info/SOURCES.txt
src/girafi.egg-info/dependency_links.txt
src/girafi.egg-info/entry_points.txt
src/girafi.egg-info/requires.txt
src/girafi.egg-info/top_level.txt
tests/conftest.py
tests/test_cli.py
tests/test_contracts.py
tests/test_reference.py
tests/test_workflows.py
tests/data/ppi_reference.json
tests/data/ppi_reference.npz
tests/reference/README.md
tests/reference/ppi_engine.py