.gitignore
CHANGELOG.md
CONTEXT.md
Cargo.lock
Cargo.toml
LICENSE
LIMITATIONS.md
README.md
pixi.lock
pixi.toml
pyproject.toml
.github/workflows/publish.yml
benchmarks/.gitignore
benchmarks/README.md
benchmarks/_harness.py
benchmarks/bench_effective_size.md
benchmarks/bench_effective_size.py
benchmarks/bench_estimate_counts.py
benchmarks/bench_inbreeding.md
benchmarks/bench_inbreeding.py
benchmarks/bench_pair_kinship.md
benchmarks/bench_pair_kinship.py
benchmarks/bench_release_300k.py
benchmarks/matrix_exactification.md
benchmarks/matrix_exactification.py
benchmarks/profile_pedigree_graph.py
benchmarks/relationship_counts_rust.md
benchmarks/threshold_structure/benchmark_threshold_structure.py
benchmarks/threshold_structure/compare_threshold_downstream.py
benchmarks/threshold_structure/exactify_threshold_structure.py
benchmarks/threshold_structure/threshold-current-vs-exact-n10k.json
benchmarks/threshold_structure/threshold-current-vs-exact-n1k.json
benchmarks/threshold_structure/threshold-downstream-both-n1k.json
benchmarks/threshold_structure/threshold-downstream-n10k.json
benchmarks/threshold_structure/threshold-downstream-n1k.json
benchmarks/threshold_structure/threshold-exact-n10k.json
benchmarks/threshold_structure/threshold-exact-n1k.json
benchmarks/threshold_structure/threshold-n10k.json
benchmarks/threshold_structure/threshold-n1k.json
crates/core/Cargo.toml
crates/core/src/lib.rs
crates/core/src/bin/pgr_count.rs
crates/core/src/relationships/category.rs
crates/core/src/relationships/csr.rs
crates/core/src/relationships/engine.rs
crates/core/src/relationships/mod.rs
crates/core/src/relationships/multiplicity.rs
crates/core/src/relationships/sets.rs
crates/core/src/relationships/sibling_index.rs
crates/core/tests/parity.rs
crates/core/tests/fixtures/avuncular_and_cousins.counts.json
crates/core/tests/fixtures/avuncular_and_cousins.tsv
crates/core/tests/fixtures/backcross_and_selfing_like.counts.json
crates/core/tests/fixtures/backcross_and_selfing_like.tsv
crates/core/tests/fixtures/deep_inbred_60g.counts.json
crates/core/tests/fixtures/deep_inbred_60g.tsv
crates/core/tests/fixtures/disconnected_components.counts.json
crates/core/tests/fixtures/disconnected_components.tsv
crates/core/tests/fixtures/double_first_cousins.counts.json
crates/core/tests/fixtures/double_first_cousins.tsv
crates/core/tests/fixtures/external_parents.counts.json
crates/core/tests/fixtures/external_parents.tsv
crates/core/tests/fixtures/founder_mz_twins.counts.json
crates/core/tests/fixtures/founder_mz_twins.tsv
crates/core/tests/fixtures/half_cousins.counts.json
crates/core/tests/fixtures/half_cousins.tsv
crates/core/tests/fixtures/half_sibs_both_kinds.counts.json
crates/core/tests/fixtures/half_sibs_both_kinds.tsv
crates/core/tests/fixtures/inbred0.counts.json
crates/core/tests/fixtures/inbred0.tsv
crates/core/tests/fixtures/inbred1.counts.json
crates/core/tests/fixtures/inbred1.tsv
crates/core/tests/fixtures/inbred2.counts.json
crates/core/tests/fixtures/inbred2.tsv
crates/core/tests/fixtures/inbred3.counts.json
crates/core/tests/fixtures/inbred3.tsv
crates/core/tests/fixtures/inbred4.counts.json
crates/core/tests/fixtures/inbred4.tsv
crates/core/tests/fixtures/lineal_five_generations.counts.json
crates/core/tests/fixtures/lineal_five_generations.tsv
crates/core/tests/fixtures/mz_twins_with_children.counts.json
crates/core/tests/fixtures/mz_twins_with_children.tsv
crates/core/tests/fixtures/nuclear_full_sibs.counts.json
crates/core/tests/fixtures/nuclear_full_sibs.tsv
crates/core/tests/fixtures/one_parent_known.counts.json
crates/core/tests/fixtures/one_parent_known.tsv
crates/core/tests/fixtures/random_1k.counts.json
crates/core/tests/fixtures/random_1k.tsv
crates/core/tests/fixtures/random_30k.counts.json
crates/core/tests/fixtures/random_30k.tsv
crates/core/tests/fixtures/sim_d2_n3000.counts.json
crates/core/tests/fixtures/sim_d2_n3000.tsv
crates/core/tests/fixtures/sim_d3_n3000.counts.json
crates/core/tests/fixtures/sim_d3_n3000.tsv
crates/core/tests/fixtures/sim_d6_n3000.counts.json
crates/core/tests/fixtures/sim_d6_n3000.tsv
crates/core/tests/fixtures/single_individual.counts.json
crates/core/tests/fixtures/single_individual.tsv
crates/core/tests/fixtures/small_pedigree.counts.json
crates/core/tests/fixtures/small_pedigree.tsv
crates/core/tests/fixtures/twins_mating_loop.counts.json
crates/core/tests/fixtures/twins_mating_loop.tsv
docs/architecture.md
docs/code-quality-review.md
docs/tskit-performance-opportunities.md
docs/adr/0001-dp-kinship-bench-split-rejected.md
docs/adr/0002-pair-engines-read-only-collaborators.md
docs/adr/0003-relationship-plan-documents-not-drives-engines.md
docs/adr/0004-registry-aligned-max-degree-semantics.md
docs/adr/0005-exact-on-demand-pairwise-kinship.md
docs/adr/0006-public-api-and-coordinate-semantics.md
docs/adr/0007-rust-core-host-boundary-and-release.md
docs/adr/0008-inbreeding-via-genome-node-meuwissen-luo-walk.md
docs/adr/0009-kinship-is-a-pinned-float32-recurrence.md
docs/adr/0010-row-streaming-relationship-engine.md
docs/adr/0011-scalar-estimate-exact-set-excludes-lineal-codes.md
docs/code-quality-review/README.md
docs/code-quality-review/pgq-001-fix-pair-coordinate-space-mismatch-after-from-subsample.md
docs/code-quality-review/pgq-002-replace-loose-constructor-inputs-and-dense-id-remapping-with-a-validated-input-model.md
docs/code-quality-review/pgq-003-decompose-pedigreegraph-move-relationship-engines-out-of-core-py.md
docs/code-quality-review/pgq-004-make-relationship-extraction-semantics-a-single-explicit-plan-instead-of-duplicated-degree-branches.md
docs/code-quality-review/pgq-005-replace-stringly-typed-effective-size-payload-dicts-with-explicit-typed-models.md
docs/code-quality-review/pgq-006-split-effective-size-py-into-focused-estimator-modules.md
docs/code-quality-review/pgq-007-simplify-or-fully-support-assemble-csc-s-extra-contract.md
docs/code-quality-review/pgq-008-decompose-kinship-kernel-py-and-shrink-dp-kinship-s-state-machine.md
docs/code-quality-review/pgq-009-reassess-the-experimental-bfs-engine-after-core-relationship-semantics-are-centralized.md
docs/code-quality-review/pgq-010-add-architecture-guardrails-for-large-files-and-hidden-coordinate-type-contracts.md
pedigree_graph/__init__.py
pedigree_graph/_bfs_engine.py
pedigree_graph/_bfs_kernel.py
pedigree_graph/_cohort_utils.py
pedigree_graph/_cohorts.py
pedigree_graph/_core.py
pedigree_graph/_errors.py
pedigree_graph/_frames.py
pedigree_graph/_inbreeding_kernel.py
pedigree_graph/_input.py
pedigree_graph/_kinship_allocator.py
pedigree_graph/_kinship_csc.py
pedigree_graph/_kinship_depth.py
pedigree_graph/_kinship_dp.py
pedigree_graph/_kinship_dp_depth.py
pedigree_graph/_kinship_kernel.py
pedigree_graph/_kinship_matrix.py
pedigree_graph/_kinship_pairwise.py
pedigree_graph/_lineage.py
pedigree_graph/_lineage_kernel.py
pedigree_graph/_ne_caballero_toro.py
pedigree_graph/_ne_common.py
pedigree_graph/_ne_estimate.py
pedigree_graph/_ne_family_size.py
pedigree_graph/_ne_founders.py
pedigree_graph/_ne_hill.py
pedigree_graph/_ne_metadata.py
pedigree_graph/_ne_rates.py
pedigree_graph/_ne_results.py
pedigree_graph/_pair_extractor.py
pedigree_graph/_pair_utils.py
pedigree_graph/_properties.py
pedigree_graph/_registry.py
pedigree_graph/_streaming_counter.py
pedigree_graph/_threads.py
pedigree_graph/_topology.py
pedigree_graph/_view.py
pedigree_graph/effective_size.py
pedigree_graph/experimental.py
pedigree_graph/py.typed
pedigree_graph/relationships.py
pedigree_graph/summaries.py
pedigree_graph/typing.py
pedigree_graph.egg-info/PKG-INFO
pedigree_graph.egg-info/SOURCES.txt
pedigree_graph.egg-info/dependency_links.txt
pedigree_graph.egg-info/requires.txt
pedigree_graph.egg-info/scm_file_list.json
pedigree_graph.egg-info/scm_version.json
pedigree_graph.egg-info/top_level.txt
tests/conftest.py
tests/relationship_predicates.py
tests/test_architecture_guardrails.py
tests/test_benchmark_contract.py
tests/test_bfs_kernel.py
tests/test_cohort_utils.py
tests/test_cohorts.py
tests/test_construction.py
tests/test_effective_size.py
tests/test_effective_size_api.py
tests/test_effective_size_metadata.py
tests/test_effective_size_scaling.py
tests/test_errors.py
tests/test_estimate_effective_sizes.py
tests/test_estimate_relationship_counts.py
tests/test_experimental.py
tests/test_frame_inputs.py
tests/test_from_arrays_sex.py
tests/test_generation_kinship_summary.py
tests/test_inbreeding.py
tests/test_inbreeding_kernel.py
tests/test_inbreeding_properties.py
tests/test_input.py
tests/test_kinship_kernel.py
tests/test_kinship_matrices.py
tests/test_kinship_properties.py
tests/test_lineage.py
tests/test_n_ancestors.py
tests/test_n_descendants.py
tests/test_ne_common_properties.py
tests/test_ne_h1_parity.py
tests/test_ne_properties.py
tests/test_pair_engines.py
tests/test_pair_engines_properties.py
tests/test_pair_extraction_properties.py
tests/test_pair_kinship.py
tests/test_pair_kinship_registry_properties.py
tests/test_pair_utils_properties.py
tests/test_parity_v071.py
tests/test_partial_generation_labels.py
tests/test_pedigree_graph.py
tests/test_properties.py
tests/test_relationship_pairs.py
tests/test_relationship_pairs_golden.py
tests/test_relationship_plan.py
tests/test_relationships_registry.py
tests/test_review_6c_fixes.py
tests/test_row_order.py
tests/test_threads.py
tests/test_topology.py
tests/test_view.py
tests/test_view_relationship_pairs.py
tests/data/small_pedigree.parquet
tests/data/ne_baseline_6b/closed_line_5.json
tests/data/ne_baseline_6b/manifest.json
tests/data/ne_baseline_6b/skip_gen.json
tests/data/ne_baseline_6b/small_pedigree.json
tests/data/ne_baseline_6b/wf_n20_g4.json
tests/data/ne_baseline_6b/wf_n40_g5_birth_years.json
tests/data/ne_baseline_6b/wf_n60_g6.json
tests/data/parity_v0.7.1/avuncular_and_cousins.npz
tests/data/parity_v0.7.1/backcross_and_selfing_like.npz
tests/data/parity_v0.7.1/deep_inbred_60g.npz
tests/data/parity_v0.7.1/disconnected_components.npz
tests/data/parity_v0.7.1/double_first_cousins.npz
tests/data/parity_v0.7.1/external_parents.npz
tests/data/parity_v0.7.1/founder_mz_twins.npz
tests/data/parity_v0.7.1/half_cousins.npz
tests/data/parity_v0.7.1/half_sibs_both_kinds.npz
tests/data/parity_v0.7.1/lineal_five_generations.npz
tests/data/parity_v0.7.1/manifest.json
tests/data/parity_v0.7.1/mz_twins_with_children.npz
tests/data/parity_v0.7.1/nuclear_full_sibs.npz
tests/data/parity_v0.7.1/one_parent_known.npz
tests/data/parity_v0.7.1/random_1k.npz
tests/data/parity_v0.7.1/single_individual.npz
tests/data/parity_v0.7.1/small_pedigree.npz
tests/data/parity_v0.7.1/twins_mating_loop.npz
tests/data/relationship_pairs_v0.8/avuncular_and_cousins.npz
tests/data/relationship_pairs_v0.8/backcross_and_selfing_like.npz
tests/data/relationship_pairs_v0.8/deep_inbred_60g.npz
tests/data/relationship_pairs_v0.8/disconnected_components.npz
tests/data/relationship_pairs_v0.8/double_first_cousins.npz
tests/data/relationship_pairs_v0.8/external_parents.npz
tests/data/relationship_pairs_v0.8/founder_mz_twins.npz
tests/data/relationship_pairs_v0.8/half_cousins.npz
tests/data/relationship_pairs_v0.8/half_sibs_both_kinds.npz
tests/data/relationship_pairs_v0.8/lineal_five_generations.npz
tests/data/relationship_pairs_v0.8/manifest.json
tests/data/relationship_pairs_v0.8/mz_twins_with_children.npz
tests/data/relationship_pairs_v0.8/nuclear_full_sibs.npz
tests/data/relationship_pairs_v0.8/one_parent_known.npz
tests/data/relationship_pairs_v0.8/random_1k.npz
tests/data/relationship_pairs_v0.8/single_individual.npz
tests/data/relationship_pairs_v0.8/small_pedigree.npz
tests/data/relationship_pairs_v0.8/twins_mating_loop.npz
tests/parity/README.md
tests/parity/__init__.py
tests/parity/capture_v08.py
tests/parity/dump_relationship_inputs.py
tests/parity/generate_baseline.py
tests/parity/generate_ne_baseline.py
tests/parity/generate_relationship_pairs.py
tests/parity/pedigrees.py