CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
ENGINEERING_PLAN.md
LICENSE
MANIFEST.in
README.md
ROADMAP.md
SECURITY.md
mkdocs.yml
pyproject.toml
benchmarks/README.md
benchmarks/profile_core.py
docs/api.md
docs/architecture.md
docs/cli.md
docs/correlation.md
docs/datasets.md
docs/getting_started.md
docs/hmm.md
docs/index.md
docs/inference.md
docs/inference_matching.md
docs/information.md
docs/instantaneous_edges.md
docs/leida.md
docs/lowrank.md
docs/method_inventory.md
docs/model_artifacts.md
docs/nbs.md
docs/partition_graphs.md
docs/reference.md
docs/release.md
docs/state_alignment.md
docs/state_scoring.md
docs/state_selection.md
docs/state_stability.md
docs/states.md
docs/storage.md
docs/tutorial_xcpd_to_states.md
docs/xcpd_input.md
src/dfc_kit.egg-info/PKG-INFO
src/dfc_kit.egg-info/SOURCES.txt
src/dfc_kit.egg-info/dependency_links.txt
src/dfc_kit.egg-info/entry_points.txt
src/dfc_kit.egg-info/requires.txt
src/dfc_kit.egg-info/top_level.txt
src/dfckit/__init__.py
src/dfckit/_arrays.py
src/dfckit/_preprocessing.py
src/dfckit/_validation.py
src/dfckit/cli.py
src/dfckit/data.py
src/dfckit/reference.py
src/dfckit/segments.py
src/dfckit/artifacts/__init__.py
src/dfckit/artifacts/_fields.py
src/dfckit/artifacts/_json.py
src/dfckit/artifacts/_numpy.py
src/dfckit/artifacts/models.py
src/dfckit/artifacts/state_alignment.py
src/dfckit/artifacts/state_results.py
src/dfckit/artifacts/state_scoring.py
src/dfckit/artifacts/state_stability.py
src/dfckit/commands/__init__.py
src/dfckit/commands/parser.py
src/dfckit/commands/reporting.py
src/dfckit/commands/source.py
src/dfckit/commands/stability.py
src/dfckit/commands/states.py
src/dfckit/connectivity/__init__.py
src/dfckit/connectivity/_edge_products.py
src/dfckit/connectivity/correlation.py
src/dfckit/connectivity/instantaneous.py
src/dfckit/connectivity/leida.py
src/dfckit/connectivity/lowrank.py
src/dfckit/connectivity/partition.py
src/dfckit/connectivity/windows.py
src/dfckit/inference/__init__.py
src/dfckit/inference/endpoints.py
src/dfckit/inference/hc3.py
src/dfckit/inference/matching.py
src/dfckit/inference/multiple_testing.py
src/dfckit/inference/nbs.py
src/dfckit/inference/paired.py
src/dfckit/inference/state_metrics.py
src/dfckit/information/__init__.py
src/dfckit/information/_artifact.py
src/dfckit/information/estimators.py
src/dfckit/information/fixed.py
src/dfckit/information/summary.py
src/dfckit/io/__init__.py
src/dfckit/io/xcpd.py
src/dfckit/states/__init__.py
src/dfckit/states/alignment.py
src/dfckit/states/cap.py
src/dfckit/states/cross_validation.py
src/dfckit/states/data.py
src/dfckit/states/hmm.py
src/dfckit/states/interpretation.py
src/dfckit/states/kmeans.py
src/dfckit/states/metrics.py
src/dfckit/states/scoring.py
src/dfckit/states/selection.py
src/dfckit/states/stability.py
src/dfckit/states/streaming.py
src/dfckit/states/streaming_hmm.py
src/dfckit/storage/__init__.py
src/dfckit/storage/_statistics.py
src/dfckit/storage/builders.py
src/dfckit/storage/store.py
src/dfckit/storage/summary.py
tests/__init__.py
tests/fixtures/audited_kernels.json
tests/integration/__init__.py
tests/integration/test_leida_state_pipeline.py
tests/integration/test_model_artifact_pipeline.py
tests/integration/test_xcpd_information.py
tests/integration/test_xcpd_sliding_window.py
tests/integration/test_xcpd_state_pipeline.py
tests/regression/__init__.py
tests/regression/test_audited_kernels.py
tests/regression/test_information_reference.py
tests/regression/test_nbs_independent_reference.py
tests/regression/test_nbs_reference.py
tests/unit/__init__.py
tests/unit/test_artifact_helpers.py
tests/unit/test_cli.py
tests/unit/test_correlation.py
tests/unit/test_cross_validation.py
tests/unit/test_data.py
tests/unit/test_endpoint_inference.py
tests/unit/test_ets.py
tests/unit/test_hmm.py
tests/unit/test_inference.py
tests/unit/test_inference_matching.py
tests/unit/test_information.py
tests/unit/test_information_io.py
tests/unit/test_information_summary.py
tests/unit/test_internal_helpers.py
tests/unit/test_leida.py
tests/unit/test_lowrank.py
tests/unit/test_model_io.py
tests/unit/test_mtd.py
tests/unit/test_nbs.py
tests/unit/test_outofcore.py
tests/unit/test_outofcore_hmm.py
tests/unit/test_partition_graph.py
tests/unit/test_preprocessing.py
tests/unit/test_public_api.py
tests/unit/test_reference.py
tests/unit/test_sliding_window.py
tests/unit/test_stability.py
tests/unit/test_state_alignment_io.py
tests/unit/test_state_interpretation.py
tests/unit/test_state_metric_inference.py
tests/unit/test_state_results.py
tests/unit/test_state_scoring_io.py
tests/unit/test_state_selection.py
tests/unit/test_state_selection_io.py
tests/unit/test_state_stability_io.py
tests/unit/test_states.py
tests/unit/test_storage.py
tests/unit/test_store_summary.py
tests/unit/test_xcpd.py