.zenodo.json
CITATION.cff
LICENSE
Licence.txt
MANIFEST.in
NOVELTY_EVIDENCE.md
README.md
pyproject.toml
examples/klebsiella/expected/cluster_result.json
examples/klebsiella/expected/summary.json
examples/synthetic/clonal.yaml
examples/synthetic/make_data.py
examples/synthetic/null.yaml
examples/synthetic/planted.yaml
examples/synthetic/planted_confirmation.yaml
src/amr_clonalshare/__init__.py
src/amr_clonalshare/archephy.py
src/amr_clonalshare/attribution.py
src/amr_clonalshare/baselines.py
src/amr_clonalshare/censored.py
src/amr_clonalshare/cli.py
src/amr_clonalshare/clonality.py
src/amr_clonalshare/config.py
src/amr_clonalshare/core.py
src/amr_clonalshare/evalues.py
src/amr_clonalshare/fusion.py
src/amr_clonalshare/inference.py
src/amr_clonalshare/influence.py
src/amr_clonalshare/io.py
src/amr_clonalshare/jsonio.py
src/amr_clonalshare/lineage.py
src/amr_clonalshare/phenotype.py
src/amr_clonalshare/qc.py
src/amr_clonalshare/realised.py
src/amr_clonalshare/report.py
src/amr_clonalshare/report_html.py
src/amr_clonalshare/schemas.py
src/amr_clonalshare/small_n.py
src/amr_clonalshare/stats.py
src/amr_clonalshare/synthetic.py
src/amr_clonalshare/tva.py
src/amr_clonalshare.egg-info/PKG-INFO
src/amr_clonalshare.egg-info/SOURCES.txt
src/amr_clonalshare.egg-info/dependency_links.txt
src/amr_clonalshare.egg-info/entry_points.txt
src/amr_clonalshare.egg-info/requires.txt
src/amr_clonalshare.egg-info/top_level.txt
tests/conftest.py
tests/test_agent_screen.py
tests/test_archephy.py
tests/test_attribution.py
tests/test_censored.py
tests/test_clonality.py
tests/test_concentration.py
tests/test_config_strictness.py
tests/test_diagnostics.py
tests/test_evalues.py
tests/test_fusion.py
tests/test_inference.py
tests/test_manuscript_claims.py
tests/test_null_uniformity.py
tests/test_phenotype.py
tests/test_pipeline.py
tests/test_properties.py
tests/test_public_release_contract.py
tests/test_qc.py
tests/test_realised.py
tests/test_release_gates.py
tests/test_report.py
tests/test_report_html.py
tests/test_small_n.py
tests/test_ssuis_provenance.py
tests/test_stats.py
tests/test_surveillance_integration.py
tests/test_tva_dispersion_misspecification.py
tests/test_tva_fail_closed.py