.gitattributes
.gitignore
.gitmodules
CHANGELOG.md
CLAUDE.md
LICENSE
README.md
build_singer.md
gwf.md
other-lai-tools.md
paral-assess.md
pixi.lock
pyproject.toml
workflow.py
.claude/agents/code-api-consistency-reviewer.md
.claude/agents/code-frontend-reviewer.md
.claude/agents/code-python-reviewer.md
.claude/agents/code-theming-reviewer.md
.claude/agents/code-ui-heuristics-reviewer.md
.claude/commands/review-apply.md
.claude/commands/review-init.md
.claude/commands/review.md
.devcontainer/Dockerfile
.devcontainer/README.md
.devcontainer/devcontainer.json
.devcontainer/init-firewall.sh
.devcontainer/mcp-setup/generate-config.sh
.devcontainer/mcp-setup/install.sh
.devcontainer/mcp-setup/pixi.toml
.devcontainer/mcp-setup/servers.txt
.devcontainer/mcp-setup/test-servers.sh
.github/workflows/conda-release.yml
.github/workflows/pypi-release.yml
.github/workflows/quarto-publish.yml
.vscode/vscode.css
conda-build/README.md
conda-build/build_env.yaml
conda-build/meta.yaml
data/data_table.csv
docs/.gitignore
docs/README.md
docs/_quarto.yml
docs/autodoc.mustache
docs/custom.scss
docs/objects.txt
docs/styles.css
docs/_extensions/machow/interlinks/.gitignore
docs/_extensions/machow/interlinks/_extension.yml
docs/_extensions/machow/interlinks/interlinks.lua
docs/_inv/griffe_objects.txt
docs/_inv/numpy_objects.txt
docs/_inv/python_objects.txt
docs/api/FitResult.qmd
docs/api/Painting.qmd
docs/api/RateThroughTime.qmd
docs/api/_sidebar.yml
docs/api/_styles-quartodoc.css
docs/api/accumulate.accumulate_sufficient_statistics.qmd
docs/api/archaic.ArchaicResult.qmd
docs/api/bp.bp_paint.qmd
docs/api/bp.bp_smooth.qmd
docs/api/bp.bp_smooth_track.qmd
docs/api/bp.bp_vs_deadband_experiment.qmd
docs/api/branch_stats.branch_expected_stats.qmd
docs/api/compare.head_to_head.qmd
docs/api/compare.nearest_reference_paint.qmd
docs/api/compare.rfmix_paint.qmd
docs/api/compare.score_painter.qmd
docs/api/compare.tspaint_paint.qmd
docs/api/dating.branch_cell_stats.qmd
docs/api/dating.composite_transition.qmd
docs/api/dating.directional_rate_splines.qmd
docs/api/dating.fit_poisson_spline.qmd
docs/api/dating.log_time_grid.qmd
docs/api/dating.make_Q_of_cell.qmd
docs/api/dating.paint_qt.qmd
docs/api/dating.rate_through_time_binned.qmd
docs/api/dating.select_lambda_gcv.qmd
docs/api/dating.split_branch.qmd
docs/api/detect_archaic.qmd
docs/api/detect_ghost.qmd
docs/api/diagnostics.edge_span_summary.qmd
docs/api/diagnostics.node_persistence.qmd
docs/api/diagnostics.persistence_summary.qmd
docs/api/em.build_emissions.qmd
docs/api/em.m_step_Q.qmd
docs/api/em.m_step_pi.qmd
docs/api/em.m_step_w.qmd
docs/api/ensemble.MergedSegment.qmd
docs/api/ensemble.merge_posterior_tables.qmd
docs/api/experiments.admixture_experiment.qmd
docs/api/experiments.age_sweep.qmd
docs/api/experiments.arg_ensemble_experiment.qmd
docs/api/experiments.flicker_vs_true_boundaries.qmd
docs/api/experiments.fragmentation_experiment.qmd
docs/api/experiments.impure_reference_experiment.qmd
docs/api/experiments.impure_reference_sweep.qmd
docs/api/experiments.scaling_sweep.qmd
docs/api/experiments.singer_ensemble_experiment.qmd
docs/api/fit.qmd
docs/api/fit_rate_through_time.qmd
docs/api/foreign_tracts.qmd
docs/api/index.qmd
docs/api/introgression.GhostResult.qmd
docs/api/introgression.ReferenceQC.qmd
docs/api/introgression.foreignness_track.qmd
docs/api/io.add_mutations.qmd
docs/api/io.check_persistence.qmd
docs/api/io.relate.qmd
docs/api/io.singer.qmd
docs/api/io.tsinfer.qmd
docs/api/io.write_haploid_vcf.qmd
docs/api/io_genotypes.Variants.qmd
docs/api/local_ancestry_truth.qmd
docs/api/make_generator_2state.qmd
docs/api/model.query_emission.qmd
docs/api/model.stationary_distribution.qmd
docs/api/model.tip_emission.qmd
docs/api/model.transition_matrix.qmd
docs/api/model.validate_generator.qmd
docs/api/output.Segment.qmd
docs/api/output.hard_segments.qmd
docs/api/output.loo_posterior_table.qmd
docs/api/output.missing_info_mask.qmd
docs/api/output.posterior_at.qmd
docs/api/output.posterior_table.qmd
docs/api/paint.qmd
docs/api/pruning.prune_root.qmd
docs/api/pruning.prune_tree.qmd
docs/api/ranked.ranked_tree_sequence.qmd
docs/api/reference_qc.qmd
docs/api/sim.admixture_demography.qmd
docs/api/sim.admixture_demography_with_ghost.qmd
docs/api/sim.simulate_admixture_impure_refs.qmd
docs/api/sim.simulate_admixture_with_ghost.qmd
docs/api/simulate_admixture.qmd
docs/api/validate.balanced_accuracy.qmd
docs/api/validate.breakpoint_flicker.qmd
docs/api/validate.breakpoint_precision_recall.qmd
docs/api/validate.map_truth.qmd
docs/api/validate.mean_confidence.qmd
docs/api/validate.per_base_accuracy.qmd
docs/api/validate.reliability_curve.qmd
docs/api/validate.switch_density.qmd
docs/api/validate.tract_boundary_error.qmd
docs/notebooks/bp_smoother.ipynb
docs/notebooks/calibration.ipynb
docs/notebooks/dating.ipynb
docs/notebooks/fragmentation.ipynb
docs/notebooks/introgression_qc.ipynb
docs/notebooks/neanderthal_power.ipynb
docs/notebooks/painting.ipynb
docs/notebooks/showcase.ipynb
docs/pages/assumptions.qmd
docs/pages/code_paths.qmd
docs/pages/dating.qmd
docs/pages/inference.qmd
docs/pages/model.qmd
docs/pages/overview.qmd
docs/pages/results.qmd
examples/workflow.py
explore/rung2_profile.png
explore/rung2_profile.py
explore/rung4_profile.png
explore/rung4_profile.py
explore/rung5_scenarios.png
explore/rung5_scenarios.py
explore/rung6_calibration.png
explore/rung6_calibration.py
explore/rung6_singer_diag.py
explore/rung_paint_qt.py
explore/spline_resolution.png
explore/spline_resolution.py
external/README.md
external/tools.ini
external/envs/Recomb-Mix/pixi.toml
external/envs/SALAI-Net/pixi.toml
external/envs/SINGER/pixi.toml
external/envs/gnomix/pixi.toml
notebooks/00_persistence_check.ipynb
notebooks/01_sim_admixture_truth.ipynb
notebooks/02_calibration_flicker.ipynb
notebooks/03_regimes_and_scaling.ipynb
notes/admix_dating_design.md
plans/PLAN_A_workflows.md
plans/PLAN_B_archaic_detector.md
review-kit/README.md
review-kit/TEMPLATE_AUTHORS.md
review-kit/USAGE.md
scripts/bump_changelog.py
scripts/bump_version.py
scripts/docs-build-render.sh
scripts/docs-run-notebooks.sh
scripts/gen_docs_notebooks.py
scripts/git-commit.sh
scripts/github-release.sh
scripts/rename.py
scripts/tmux-project.sh
src/tspaint/__init__.py
src/tspaint/accumulate.py
src/tspaint/api.py
src/tspaint/archaic.py
src/tspaint/branch_stats.py
src/tspaint/cli.py
src/tspaint/compare.py
src/tspaint/diagnostics.py
src/tspaint/em.py
src/tspaint/ensemble.py
src/tspaint/experiments.py
src/tspaint/ids.py
src/tspaint/install.py
src/tspaint/introgression.py
src/tspaint/io.py
src/tspaint/io_genotypes.py
src/tspaint/io_relate.py
src/tspaint/io_rfmix.py
src/tspaint/io_singer.py
src/tspaint/io_tsinfer.py
src/tspaint/metrics.py
src/tspaint/model.py
src/tspaint/output.py
src/tspaint/parallel.py
src/tspaint/pruning.py
src/tspaint/ranked.py
src/tspaint/serialize.py
src/tspaint/sim.py
src/tspaint/track.py
src/tspaint/validate.py
src/tspaint.egg-info/PKG-INFO
src/tspaint.egg-info/SOURCES.txt
src/tspaint.egg-info/dependency_links.txt
src/tspaint.egg-info/entry_points.txt
src/tspaint.egg-info/requires.txt
src/tspaint.egg-info/top_level.txt
src/tspaint/benchmark/__init__.py
src/tspaint/benchmark/_common.py
src/tspaint/benchmark/_msp.py
src/tspaint/benchmark/_provision.py
src/tspaint/benchmark/_tspaint.py
src/tspaint/benchmark/cli.py
src/tspaint/benchmark/export.py
src/tspaint/benchmark/gnomix.py
src/tspaint/benchmark/recombmix.py
src/tspaint/benchmark/rfmix.py
src/tspaint/benchmark/salai.py
src/tspaint/benchmark/score.py
src/tspaint/bp/__init__.py
src/tspaint/bp/experiments.py
src/tspaint/bp/horizontal.py
src/tspaint/dating/__init__.py
src/tspaint/dating/em.py
src/tspaint/dating/estep.py
src/tspaint/dating/grid.py
src/tspaint/dating/mstep.py
tests/test_accumulate.py
tests/test_api.py
tests/test_archaic.py
tests/test_benchmark_cli.py
tests/test_benchmark_common.py
tests/test_benchmark_export_score.py
tests/test_benchmark_gnomix.py
tests/test_benchmark_integration.py
tests/test_benchmark_parsers.py
tests/test_benchmark_setup.py
tests/test_benchmark_singer.py
tests/test_benchmark_tspaint.py
tests/test_bp.py
tests/test_branch_stats.py
tests/test_cli.py
tests/test_cli_singer.py
tests/test_compare.py
tests/test_credibility.py
tests/test_dating.py
tests/test_em.py
tests/test_ensemble.py
tests/test_experiment.py
tests/test_ids.py
tests/test_inferred.py
tests/test_install.py
tests/test_install_paths.py
tests/test_introgression.py
tests/test_io_frontends.py
tests/test_m_step.py
tests/test_output.py
tests/test_parallel.py
tests/test_pruning.py
tests/test_ranked.py
tests/test_rfmix.py
tests/test_segmentation.py
tests/test_serialize.py
tests/test_sim.py
tests/test_singer.py
tests/test_subset_data.py
tests/test_validate.py
tests/test_workflow_support.py