AGENTS.md
LICENSE
README.md
pyproject.toml
src/homoeogwas_launcher.py
src/homoeogwas/__init__.py
src/homoeogwas/__main__.py
src/homoeogwas/audit.py
src/homoeogwas/calibration.py
src/homoeogwas/cli.py
src/homoeogwas/demo_data.py
src/homoeogwas/design_depth.py
src/homoeogwas/diagnostics.py
src/homoeogwas/evidence.py
src/homoeogwas/followup.py
src/homoeogwas/formal_provenance.py
src/homoeogwas/gp.py
src/homoeogwas/grm.py
src/homoeogwas/grm_cache.py
src/homoeogwas/group_family.py
src/homoeogwas/input_qc.py
src/homoeogwas/interact.py
src/homoeogwas/interact_batch.py
src/homoeogwas/interaction_config.py
src/homoeogwas/io.py
src/homoeogwas/jsonutil.py
src/homoeogwas/kernel.py
src/homoeogwas/khom_tier1.py
src/homoeogwas/lmm.py
src/homoeogwas/markers.py
src/homoeogwas/mcp_server.py
src/homoeogwas/omnib_family.py
src/homoeogwas/parallel.py
src/homoeogwas/plots.py
src/homoeogwas/prep.py
src/homoeogwas/report_card.py
src/homoeogwas/resampling_checkpoint.py
src/homoeogwas/run_registry.py
src/homoeogwas/scan.py
src/homoeogwas/sim.py
src/homoeogwas/species_config.py
src/homoeogwas/species_split.py
src/homoeogwas/triad3.py
src/homoeogwas/workflow.py
src/homoeogwas.egg-info/PKG-INFO
src/homoeogwas.egg-info/SOURCES.txt
src/homoeogwas.egg-info/dependency_links.txt
src/homoeogwas.egg-info/entry_points.txt
src/homoeogwas.egg-info/requires.txt
src/homoeogwas.egg-info/top_level.txt
src/homoeogwas/r/gwas_plots.R
tests/test_audit.py
tests/test_benchmark_omnib_parallel.py
tests/test_benchmark_v201_aggregate_audit.py
tests/test_benchmark_v201_cli.py
tests/test_benchmark_v201_comparators.py
tests/test_benchmark_v201_contracts.py
tests/test_benchmark_v201_shards.py
tests/test_benchmark_v201_simulation.py
tests/test_benchmark_v201_track_application.py
tests/test_benchmark_v201_track_fit.py
tests/test_benchmark_v201_track_omnib.py
tests/test_benchmark_v201_track_scaling.py
tests/test_benchmark_v5_failure_accounting.py
tests/test_benchmark_v5_marker_masks.py
tests/test_benchmark_v5_plink_reference.py
tests/test_benchmark_v5_prepared_identity.py
tests/test_benchmark_v5_resource_gate.py
tests/test_benchmark_v5_resource_probe_producer.py
tests/test_benchmark_v5_snpxsnp_streaming.py
tests/test_calibration.py
tests/test_cli.py
tests/test_design_depth.py
tests/test_evidence.py
tests/test_followup_regression_contract.py
tests/test_gp.py
tests/test_grm.py
tests/test_grm_cache.py
tests/test_group_family.py
tests/test_input_qc.py
tests/test_interact.py
tests/test_interact_batch.py
tests/test_interaction_config.py
tests/test_j3_hardening.py
tests/test_kernel.py
tests/test_kernel_fallback.py
tests/test_khom_tier1.py
tests/test_launcher.py
tests/test_lmm.py
tests/test_lmm_diagnostics.py
tests/test_lmm_multi.py
tests/test_loco.py
tests/test_manifest_hash_streaming.py
tests/test_markers.py
tests/test_omnib_family.py
tests/test_omnib_family_calibration.py
tests/test_omnib_followup.py
tests/test_omnib_panel_context.py
tests/test_omnib_pool_reuse.py
tests/test_parallel.py
tests/test_plots.py
tests/test_prep.py
tests/test_prepare_wheat_f2143_matched_edges.py
tests/test_report_card.py
tests/test_resampling_checkpoint.py
tests/test_rplot.py
tests/test_run_registry.py
tests/test_scan.py
tests/test_scan_parallel.py
tests/test_sim.py
tests/test_smooth_null_variance.py
tests/test_species_config.py
tests/test_species_split.py
tests/test_task5_review_fixes.py
tests/test_task9_contract_fix.py
tests/test_workflow.py