CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
mkdocs.yml
pyproject.toml
setup.py
analysis/__init__.py
analysis/benchmark_allocation_throughput.py
analysis/benchmark_backend_phases.py
analysis/benchmark_capacity_prefix.py
analysis/benchmark_dense_sufficient_statistics.py
analysis/benchmark_genomics_storage.py
analysis/compare_backend_revisions.py
analysis/review_backend_costs.py
analysis/stability_analysis.py
analysis/cluster/prepare_backend_comparison.py
analysis/proof_checks/backend_symbolic.py
analysis/trade_study/__init__.py
analysis/trade_study/_common.py
analysis/trade_study/_convergence_detector_design.py
analysis/trade_study/_convergence_margin_design.py
analysis/trade_study/_convergence_policy_safety_design.py
analysis/trade_study/_modern_defaults_data.py
analysis/trade_study/_modern_defaults_design.py
analysis/trade_study/_modern_defaults_io.py
analysis/trade_study/_modern_defaults_metrics.py
analysis/trade_study/_modern_defaults_reduction.py
analysis/trade_study/_modern_defaults_results.py
analysis/trade_study/_modern_defaults_spec.py
analysis/trade_study/_modern_defaults_trial.py
analysis/trade_study/_residual_convergence_design.py
analysis/trade_study/_surrogate.py
analysis/trade_study/_vbpca_kwargs.py
analysis/trade_study/_world.py
analysis/trade_study/convergence_detector.py
analysis/trade_study/convergence_detector_summary.py
analysis/trade_study/convergence_policy_safety.py
analysis/trade_study/convergence_replay.py
analysis/trade_study/convergence_stability_study.py
analysis/trade_study/modern_defaults_study.py
analysis/trade_study/option_a_aspect_ratio.py
analysis/trade_study/option_a_figures.py
analysis/trade_study/option_a_pipeline.py
analysis/trade_study/residual_convergence_followup.py
analysis/trade_study/sensitivity_report.py
analysis/trade_study/v3_compare.py
analysis/trade_study/v4_phase2_sequential.py
analysis/trade_study/validate_convergence_margins.py
analysis/trade_study/validate_shipped_defaults.py
analysis/trade_study/manifests/convergence_policy_safety_v1.json
analysis/trade_study/manifests/modern_defaults_screen_v1.json
analysis/trade_study/manifests/residual_convergence_v1.json
docs/IMPLEMENTATION_PLAN.md
docs/changelog.md
docs/citation.md
docs/index.md
docs/limitations.md
docs/api/migration-05.md
docs/api/model-selection.md
docs/api/options.md
docs/api/plotting.md
docs/api/preprocessing.md
docs/api/results.md
docs/api/utilities.md
docs/api/vbpca.md
docs/concepts/algorithm.md
docs/concepts/convergence.md
docs/concepts/data-convention.md
docs/concepts/model-selection.md
docs/gallery/index.md
docs/getting-started/installation.md
docs/getting-started/quickstart.md
docs/howto/compatibility-modes.md
docs/howto/convergence.md
docs/howto/numerical-validation.md
docs/howto/plotting.md
docs/howto/runtime-tuning.md
docs/javascripts/mathjax.js
docs/releases/0.4.11.md
docs/releases/0.4.12.md
docs/releases/0.4.6.md
docs/releases/0.4.7.md
docs/releases/0.5.0.md
docs/tutorials/basic-dense-pca.md
docs/tutorials/cv-diagnostics.md
docs/tutorials/genomics-dosage.md
docs/tutorials/missing-aware-pipeline.md
docs/tutorials/missing-data-model-selection.md
docs/tutorials/preprocessing-mixed-data.md
docs/tutorials/sparse-data.md
examples/mixed-missing-table.ipynb
scripts/_convergence_analysis.py
scripts/_convergence_diagnostic.py
scripts/_rms_original_vs_internal.py
scripts/_rms_oscillation_trace.py
scripts/benchmark_dense_masked_kernels.py
scripts/benchmark_dense_runtime.py
scripts/benchmark_posterior_variance.py
scripts/benchmark_regression_check.py
scripts/benchmark_selection_cost.py
scripts/benchmark_sparse_mask_explicit.py
scripts/benchmark_study.md
scripts/build_gallery.py
scripts/build_runtime_profile.py
scripts/check_fitting_identity.py
scripts/check_gallery_site.py
scripts/check_numerical_reference.py
scripts/check_public_examples.py
scripts/check_release_artifacts.py
scripts/check_release_metadata.py
scripts/check_sdist_tests.py
scripts/check_sparse_allocations.py
scripts/docs_gallery_hook.py
scripts/example_compatibility_modes.py
scripts/example_component_selection.py
scripts/example_feature_output.py
scripts/example_masked_pipeline.py
scripts/example_missing_pca.py
scripts/example_raw_cell_cv.py
scripts/example_sparse_pca.py
scripts/gallery_dense.py
scripts/gallery_plots.py
scripts/gallery_raw_cv.py
scripts/gallery_selection.py
scripts/gallery_sparse.py
scripts/profile_core_vbpca.py
scripts/run_performance_comparison.py
scripts/validate_benchmark_reproducibility.py
scripts/snippets/stored_observations.py
src/vbpca_py/__init__.py
src/vbpca_py/_categorical_scores.py
src/vbpca_py/_converge.py
src/vbpca_py/_cost.py
src/vbpca_py/_cpu_limits.py
src/vbpca_py/_encoding_checks.py
src/vbpca_py/_expand.py
src/vbpca_py/_feature_names.py
src/vbpca_py/_full_update.py
src/vbpca_py/_mean.py
src/vbpca_py/_memory.py
src/vbpca_py/_missing.py
src/vbpca_py/_missingness_checks.py
src/vbpca_py/_monitoring.py
src/vbpca_py/_native.py
src/vbpca_py/_noise_statistics.py
src/vbpca_py/_options.py
src/vbpca_py/_pca_full.py
src/vbpca_py/_posterior_variance.py
src/vbpca_py/_preprocessing_state.py
src/vbpca_py/_projection.py
src/vbpca_py/_remove_empty.py
src/vbpca_py/_rms.py
src/vbpca_py/_rotate.py
src/vbpca_py/_runtime_execution.py
src/vbpca_py/_runtime_fingerprint.py
src/vbpca_py/_runtime_policy.py
src/vbpca_py/_runtime_profiles.py
src/vbpca_py/_selection_core.py
src/vbpca_py/_solver_options.py
src/vbpca_py/_sparse_error.py
src/vbpca_py/_sparsity.py
src/vbpca_py/_types.py
src/vbpca_py/_validation.py
src/vbpca_py/configuration.py
src/vbpca_py/defaults.py
src/vbpca_py/dense_update_kernels.cpp
src/vbpca_py/dense_update_kernels.pyi
src/vbpca_py/encoding.py
src/vbpca_py/errpca_pt.cpp
src/vbpca_py/errpca_pt.pyi
src/vbpca_py/estimators.py
src/vbpca_py/legacy.py
src/vbpca_py/masking.py
src/vbpca_py/model_selection.py
src/vbpca_py/noise_update_kernels.cpp
src/vbpca_py/noise_update_kernels.pyi
src/vbpca_py/options.py
src/vbpca_py/plotting.py
src/vbpca_py/preprocessing.py
src/vbpca_py/py.typed
src/vbpca_py/raw_model_selection.py
src/vbpca_py/results.py
src/vbpca_py/rotate_update_kernels.cpp
src/vbpca_py/rotate_update_kernels.pyi
src/vbpca_py/sparse_update_kernels.cpp
src/vbpca_py/sparse_update_kernels.pyi
src/vbpca_py/subtract_mu_from_sparse.cpp
src/vbpca_py/subtract_mu_from_sparse.pyi
src/vbpca_py/thread_limits.h
src/vbpca_py/thread_workers.h
src/vbpca_py.egg-info/PKG-INFO
src/vbpca_py.egg-info/SOURCES.txt
src/vbpca_py.egg-info/dependency_links.txt
src/vbpca_py.egg-info/requires.txt
src/vbpca_py.egg-info/top_level.txt
tests/test_backend_comparison_receipts.py
tests/test_backend_rearrangements.py
tests/test_bias_update_order.py
tests/test_categorical_scores.py
tests/test_check_data_missingness.py
tests/test_cluster_backend_snapshots.py
tests/test_configuration.py
tests/test_converge.py
tests/test_convergence_detector.py
tests/test_convergence_margin_design.py
tests/test_convergence_margin_selection.py
tests/test_convergence_policy_safety.py
tests/test_convergence_replay.py
tests/test_convergence_stability_study.py
tests/test_cost.py
tests/test_cov_writeback_autotune.py
tests/test_cov_writeback_correctness.py
tests/test_coverage_small_utils.py
tests/test_defaults.py
tests/test_dense_input_views.py
tests/test_dense_mask_storage.py
tests/test_dense_masked_parallelism.py
tests/test_dense_sufficient_statistics.py
tests/test_diagnostic_memory.py
tests/test_documentation_examples.py
tests/test_documented_sparse_example.py
tests/test_encoder_drop_weighting.py
tests/test_encoder_groups.py
tests/test_encoding_aware_scores.py
tests/test_encoding_checks.py
tests/test_endpoint_cost.py
tests/test_estimators.py
tests/test_estimators_and_model_selection.py
tests/test_estimators_coverage.py
tests/test_expand.py
tests/test_explained_variance_factors.py
tests/test_feature_output.py
tests/test_fitting_identity_gate.py
tests/test_full_update.py
tests/test_full_update_coverage.py
tests/test_integration.py
tests/test_markdown_examples.py
tests/test_mean.py
tests/test_missing.py
tests/test_missing_edge_cases.py
tests/test_model_selection.py
tests/test_model_selection_rank_zero.py
tests/test_modern_defaults_checkpoints.py
tests/test_modern_defaults_design.py
tests/test_modern_defaults_reduction.py
tests/test_modern_defaults_runner.py
tests/test_modern_small_values.py
tests/test_monitoring.py
tests/test_native_estimator.py
tests/test_native_failures.py
tests/test_native_selection.py
tests/test_native_sparse_validation.py
tests/test_noise_statistics.py
tests/test_noise_trajectories.py
tests/test_notebook_examples.py
tests/test_numeric_encoding_schema.py
tests/test_numerical_contracts.py
tests/test_observation_masker.py
tests/test_observed_empty_axes.py
tests/test_octave_execution.py
tests/test_octave_parity_smoke.py
tests/test_octave_reference_algorithms.py
tests/test_option_values.py
tests/test_options.py
tests/test_ordinal_encoder.py
tests/test_pca_full.py
tests/test_pca_full_utils.py
tests/test_perf_benchmarks.py
tests/test_pipeline_example.py
tests/test_posterior_variance.py
tests/test_preprocessing.py
tests/test_preprocessing_gap.py
tests/test_preprocessing_sparse.py
tests/test_preprocessing_transforms.py
tests/test_preprocessor_state.py
tests/test_preprocessor_validation.py
tests/test_probe_coverage.py
tests/test_properties.py
tests/test_pruning_state.py
tests/test_public_api.py
tests/test_rank_zero_rotation.py
tests/test_rank_zero_updates.py
tests/test_raw_model_selection.py
tests/test_recommended_stopping.py
tests/test_release_artifacts.py
tests/test_release_metadata.py
tests/test_remove_empty.py
tests/test_residual_convergence_design.py
tests/test_residual_convergence_followup.py
tests/test_result_contracts.py
tests/test_rms.py
tests/test_rms_regression.py
tests/test_rotate.py
tests/test_runtime_evidence.py
tests/test_runtime_policy.py
tests/test_runtime_policy_dense.py
tests/test_runtime_robustness.py
tests/test_scaler_units.py
tests/test_sdist_qualification.py
tests/test_sklearn_compat.py
tests/test_sparse_error.py
tests/test_sparse_explicit_mask.py
tests/test_sparse_observed_zero_indices.py
tests/test_sparse_pattern_groups.py
tests/test_sparse_probe_partition.py
tests/test_sparse_views.py
tests/test_trade_study_config.py
tests/test_unavailable_slowing_down.py
tests/test_update_equations.py
tests/test_update_trajectory.py
tests/test_variable_cell_cv.py
tests/test_variance_update_order.py
tests/test_warm_start_layouts.py
tests/test_warm_start_ownership.py
tests/typing_results.py
tests/data/legacy_pca_full_dense.mat
tests/data/legacy_pca_full_missing.mat
tests/data/legacy_rotate_to_pca.mat
tools/allocation_counter.c