LICENSE
MANIFEST.in
MANIFEST.md
README.md
THESIS_CLAIMS.md
USER_MANUAL.md
pyproject.toml
configs/chua_arctan_wu2023_caputo.json
configs/chua_classical_lure_default.yaml
configs/chua_fractional_nonsmooth.yaml
configs/lure_biased_multiparam_q09998.yaml
configs/lure_candidate_route.yaml
configs/machado_candidate_route.yaml
configs/report_heatmap_inputs.json
configs/unified_caputo_protocol.json
configs/user_chua_fractional_h001_exploratory.yaml
configs/validation_chua_integer_q1.json
configs/validation_contract.json
configs/validation_efork3_ghoreishi_ghaffari.json
configs/examples/chua_arctan_attractor_only_fractional.yaml
configs/examples/chua_arctan_attractor_only_integer.yaml
configs/examples/chua_arctan_fractional_centered_lure_df.yaml
configs/examples/chua_continuation_fractional_abm.yaml
configs/examples/chua_continuation_fractional_efork3.yaml
configs/examples/chua_continuation_integer.yaml
configs/examples/chua_continuation_multiparameter_fractional.yaml
configs/examples/chua_fractional_basin.yaml
configs/examples/chua_fractional_bifurcation.yaml
configs/examples/chua_fractional_centered_lure_df.yaml
configs/examples/chua_fractional_hiddenness_strict.yaml
configs/examples/chua_fractional_lyapunov.yaml
configs/examples/chua_fractional_validation_architecture.yaml
configs/examples/chua_fractional_zero_one.yaml
configs/examples/chua_full_protocol.yaml
configs/examples/chua_integer_centered_lure_df.yaml
configs/examples/chua_nonsmooth_biased_df_search.yaml
configs/examples/chua_nonsmooth_exact_danca_non_reproducible.yaml
configs/examples/chua_seed_lure_biased_fractional.yaml
configs/examples/chua_seed_lure_biased_integer.yaml
configs/examples/chua_seed_lure_centered_fractional.yaml
configs/examples/chua_seed_lure_centered_integer.yaml
docs/adapting_new_systems.md
docs/api_reference.md
docs/api_stability.md
docs/archive_policy.md
docs/chua_arctan_wu2023_methodology.md
docs/citation.md
docs/cli_migration_legacy_entrypoints.md
docs/code_reference_map.md
docs/contributing.md
docs/dependency_policy.md
docs/development_hygiene.md
docs/dynamical_analysis.md
docs/efork3_validation.md
docs/examples.md
docs/examples_index.md
docs/external_tools.md
docs/f4_internal_lyapunov_validation.md
docs/f5_dynamics_diagnostics.md
docs/f6_integrated_chaos_validator.md
docs/f7_method_comparison.md
docs/figure_export_policy.md
docs/figure_gallery.md
docs/figure_scripts_inventory.md
docs/figure_scripts_policy.md
docs/final_freeze_checklist.md
docs/fractional_chua_algebra_validation.md
docs/freeze_status.md
docs/getting_started.md
docs/hiddenness_verification.md
docs/index.md
docs/installation.md
docs/integer_chua_reference.md
docs/library_structure.md
docs/lure_candidate_route.md
docs/lyapunov_cloned_dynamics.md
docs/lyapunov_methods.md
docs/manual_manifest.md
docs/manual_manifest.yaml
docs/migration_unified_methodology.md
docs/notebooks.md
docs/phase_f_closure.md
docs/physical_separation.md
docs/poincare_diagnostics.md
docs/published_validation_coverage.md
docs/published_validation_data_extraction_v1.json
docs/published_validation_data_extraction_v1.md
docs/quick_start.md
docs/references.bib
docs/repository_layout.md
docs/scientific_scope.md
docs/software_scientific_validation.md
docs/systems.md
docs/testing.md
docs/testing_policy.md
docs/tests_inventory.md
docs/tests_refactor_report.md
docs/unified_report.md
docs/validation_evidence.md
docs/validation_methodology.md
docs/versioning.md
docs/workflows.md
docs/research/GUIA_CODIGOS_PIPELINE.md
docs/research/analysis.md
examples/README.md
examples/aggregate_existing_robustness_overlay.py
examples/create_robustness_overlay_config.py
examples/custom_system_definition.py
examples/dynamical_analysis_gallery.py
examples/integer_lure_chua_protocol.py
examples/list_final_candidates.py
examples/minimal_chua_protocol.py
examples/new_system_workflow_spec.py
examples/quickstart_equilibria.py
examples/chua_arctan_wu2023/01_search.py
examples/chua_arctan_wu2023/02_continue.py
examples/chua_arctan_wu2023/03_verify.py
examples/chua_arctan_wu2023/04_plot.py
examples/chua_arctan_wu2023/README.md
examples/chua_arctan_wu2023/reproducibility.yaml
examples/chua_arctan_wu2023/run_example.py
examples/chua_arctan_wu2023/run_seed_generation.py
examples/chua_arctan_wu2023/run_validation.py
examples/chua_integer_lure_reference/01_search.py
examples/chua_integer_lure_reference/02_continue.py
examples/chua_integer_lure_reference/03_verify.py
examples/chua_integer_lure_reference/04_plot.py
examples/chua_integer_lure_reference/README.md
examples/chua_integer_lure_reference/reproducibility.yaml
examples/chua_integer_lure_reference/run_example.py
examples/chua_nonsmooth_biased_hidden_attractor/01_search.py
examples/chua_nonsmooth_biased_hidden_attractor/02_continue.py
examples/chua_nonsmooth_biased_hidden_attractor/03_verify.py
examples/chua_nonsmooth_biased_hidden_attractor/04_plot.py
examples/chua_nonsmooth_biased_hidden_attractor/README.md
examples/chua_nonsmooth_biased_hidden_attractor/__init__.py
examples/chua_nonsmooth_biased_hidden_attractor/reproducibility.yaml
examples/chua_nonsmooth_biased_hidden_attractor/run_example.py
examples/notebooks/README.md
hidden_attractors/__init__.py
hidden_attractors/_stability.py
hidden_attractors/candidates.py
hidden_attractors/cli.py
hidden_attractors/contracts.py
hidden_attractors/io.py
hidden_attractors/parallel.py
hidden_attractors/paths.py
hidden_attractors/protocol_cli.py
hidden_attractors/reproducibility.py
hidden_attractors/validation_contract.py
hidden_attractors/analysis/__init__.py
hidden_attractors/analysis/bifurcation.py
hidden_attractors/analysis/boundedness.py
hidden_attractors/analysis/integrated_chaos_validator.py
hidden_attractors/analysis/lyapunov.py
hidden_attractors/analysis/lyapunov_api.py
hidden_attractors/analysis/lyapunov_cloned.py
hidden_attractors/analysis/lyapunov_fractional.py
hidden_attractors/analysis/lyapunov_methods.py
hidden_attractors/analysis/method_comparison.py
hidden_attractors/analysis/phase_f_closure.py
hidden_attractors/analysis/poincare.py
hidden_attractors/analysis/spectral.py
hidden_attractors/analysis/trajectory.py
hidden_attractors/analysis/zero_one.py
hidden_attractors/basins/__init__.py
hidden_attractors/basins/classification.py
hidden_attractors/cli/__init__.py
hidden_attractors/cli/basin.py
hidden_attractors/cli/bifurcation.py
hidden_attractors/cli/chaos_test.py
hidden_attractors/cli/continuation.py
hidden_attractors/cli/hiddenness.py
hidden_attractors/cli/inspect.py
hidden_attractors/cli/lyapunov.py
hidden_attractors/cli/main.py
hidden_attractors/cli/protocol.py
hidden_attractors/cli/published.py
hidden_attractors/cli/report.py
hidden_attractors/cli/robustness.py
hidden_attractors/cli/run.py
hidden_attractors/cli/seed.py
hidden_attractors/cli/validate.py
hidden_attractors/configs/__init__.py
hidden_attractors/configs/examples/__init__.py
hidden_attractors/configs/examples/chua_arctan_attractor_only_fractional.yaml
hidden_attractors/configs/examples/chua_arctan_attractor_only_integer.yaml
hidden_attractors/configs/examples/chua_arctan_fractional_centered_lure_df.yaml
hidden_attractors/configs/examples/chua_fractional_basin.yaml
hidden_attractors/configs/examples/chua_fractional_bifurcation.yaml
hidden_attractors/configs/examples/chua_fractional_centered_lure_df.yaml
hidden_attractors/configs/examples/chua_full_protocol.yaml
hidden_attractors/configs/examples/chua_integer_centered_lure_df.yaml
hidden_attractors/continuation/__init__.py
hidden_attractors/continuation/continuation_fractional.py
hidden_attractors/continuation/continuation_integer.py
hidden_attractors/continuation/memory.py
hidden_attractors/diagnostics/__init__.py
hidden_attractors/diagnostics/periodicity.py
hidden_attractors/diagnostics/zero_one.py
hidden_attractors/integrations/__init__.py
hidden_attractors/integrations/_q1_coefficients.py
hidden_attractors/integrations/abm.py
hidden_attractors/integrations/abm_fractional.py
hidden_attractors/integrations/adm_wu2023.py
hidden_attractors/integrations/efork.py
hidden_attractors/integrations/external_tools.py
hidden_attractors/integrations/fractional_c.py
hidden_attractors/integrations/general.py
hidden_attractors/integrations/numba_kernels.py
hidden_attractors/integrations/rk4.py
hidden_attractors/integrations/selector.py
hidden_attractors/lure/__init__.py
hidden_attractors/lure/compatibility.py
hidden_attractors/lure/decomposition.py
hidden_attractors/lure/describing_function.py
hidden_attractors/lure/nyquist.py
hidden_attractors/lure/seeds.py
hidden_attractors/lure/transfer.py
hidden_attractors/models/__init__.py
hidden_attractors/models/chua.py
hidden_attractors/native/__init__.py
hidden_attractors/native/backends.py
hidden_attractors/native/contracts.py
hidden_attractors/native/rhs_registry.py
hidden_attractors/native/csrc/chua_abm_full_history_lib.c
hidden_attractors/native/csrc/chua_basin_lib.c
hidden_attractors/native/csrc/chua_frac_backend_lib.c
hidden_attractors/native/csrc/chua_frac_lyapunov_efork_benettin.c
hidden_attractors/native/csrc/chua_hidden_backend.c
hidden_attractors/native/csrc/fractional_integrators.c
hidden_attractors/native/csrc/fractional_integrators.h
hidden_attractors/native/csrc/fractional_variational_lyapunov_lib.c
hidden_attractors/native/csrc/general_fde_solver.c
hidden_attractors/plotting/__init__.py
hidden_attractors/plotting/basin.py
hidden_attractors/plotting/biased_chua.py
hidden_attractors/plotting/bifurcation.py
hidden_attractors/plotting/dynamics.py
hidden_attractors/plotting/export.py
hidden_attractors/plotting/generate_publication_figures.py
hidden_attractors/plotting/generate_unified_report_figures.py
hidden_attractors/plotting/lyapunov.py
hidden_attractors/plotting/manifest.py
hidden_attractors/plotting/matignon.py
hidden_attractors/plotting/overlays.py
hidden_attractors/plotting/plot_basins.py
hidden_attractors/plotting/plot_continuation.py
hidden_attractors/plotting/plot_df.py
hidden_attractors/plotting/plot_matignon.py
hidden_attractors/plotting/plot_sphere_tests.py
hidden_attractors/plotting/plot_trajectories.py
hidden_attractors/plotting/plot_transfer.py
hidden_attractors/plotting/registry.py
hidden_attractors/plotting/render_all.py
hidden_attractors/plotting/renderers.py
hidden_attractors/plotting/style.py
hidden_attractors/plotting/zero_one.py
hidden_attractors/references/__init__.py
hidden_attractors/references/claims.py
hidden_attractors/references/registry.py
hidden_attractors/references/validator.py
hidden_attractors/seed_generation/__init__.py
hidden_attractors/seed_generation/chua.py
hidden_attractors/seed_generation/chua_arctan_wu2023.py
hidden_attractors/seed_generation/core.py
hidden_attractors/seed_generation/lure.py
hidden_attractors/solvers/__init__.py
hidden_attractors/solvers/efork_published.py
hidden_attractors/solvers/history.py
hidden_attractors/solvers/integer.py
hidden_attractors/systems/__init__.py
hidden_attractors/systems/base.py
hidden_attractors/systems/builtins.py
hidden_attractors/systems/fischer_benchmarks.py
hidden_attractors/systems/lure.py
hidden_attractors/systems/requirements.py
hidden_attractors/validation/__init__.py
hidden_attractors/validation/chua_arctan_wu2023.py
hidden_attractors/validation/manifest.py
hidden_attractors/validation/nonsmooth.py
hidden_attractors/validation/states.py
hidden_attractors/validation/symmetry.py
hidden_attractors/validation/wolfram_artifacts.py
hidden_attractors/verification/__init__.py
hidden_attractors/verification/basins.py
hidden_attractors/verification/candidate_gate.py
hidden_attractors/verification/classifiers.py
hidden_attractors/verification/equilibria.py
hidden_attractors/verification/hiddenness.py
hidden_attractors/verification/hiddenness_contract.py
hidden_attractors/verification/jacobian.py
hidden_attractors/verification/sphere_tests.py
hidden_attractors/verification/stability.py
hidden_attractors/verification/status_labels.py
hidden_attractors/workflows/__init__.py
hidden_attractors/workflows/attractor_only.py
hidden_attractors/workflows/basin_runner.py
hidden_attractors/workflows/biased_chua.py
hidden_attractors/workflows/bifurcation.py
hidden_attractors/workflows/centered_lure_df.py
hidden_attractors/workflows/config_loader.py
hidden_attractors/workflows/contracts.py
hidden_attractors/workflows/danca_abm_sphere_controls.py
hidden_attractors/workflows/fractional_report_run.py
hidden_attractors/workflows/integer_lure.py
hidden_attractors/workflows/lyapunov.py
hidden_attractors/workflows/protocol.py
hidden_attractors/workflows/refined_basin.py
hidden_attractors/workflows/robustness_overlay.py
hidden_attractors/workflows/simple_runner.py
hidden_attractors/workflows/specs.py
hidden_attractors/workflows/sphere_controls.py
hidden_attractors/workflows/strict_target_refinement.py
release_package/ARCTAN_C590_PROMOTION_BOUNDARY.md
release_package/DOCS_COMMAND_SYNC_REPORT.md
release_package/FINAL_PYPI_TRACEABILITY_REPORT.md
release_package/PROGRAM_SUMMARY.md
release_package/PUBLISHING_POLICY.md
release_package/PYPI_BLOCKING_ITEMS.md
release_package/PYPI_RELEASE_CHECKLIST.md
release_package/PYPI_RELEASE_REPORT.md
release_package/README_RELEASE.md
release_package/REMAINING_WORK.md
release_package/SAMPLE_RUN.md
release_package/archive_manifest.json
release_package/reproducibility_checklist.md
release_package/sample_input/README.md
release_package/sample_input/chua_fractional_minimal.yaml
release_package/sample_input/chua_integer_reference_minimal.yaml
release_package/sample_output/README.md
release_package/sample_output/expected_cli_help_summary.json
release_package/sample_output/expected_release_readiness_summary.json
release_package/sample_output/expected_validation_contract_status.json
release_package/sample_output/sample_output_manifest.json
tests/conftest.py
tests/test_abm_fractional_diagnostics.py
tests/test_adm_wu2023.py
tests/test_archive_independence.py
tests/test_attractor_only.py
tests/test_attractor_status_labels.py
tests/test_basin_smoke.py
tests/test_biased_chua_example_single_entrypoint.py
tests/test_biased_figure_manifest.py
tests/test_bibliographic_validation.py
tests/test_bifurcation_cli.py
tests/test_bifurcation_smoke.py
tests/test_boundedness_diagnostics.py
tests/test_candidate_gate.py
tests/test_centered_lure_workflow.py
tests/test_chua_arctan_wu2023_algebra.py
tests/test_chua_arctan_wu2023_seed_generation.py
tests/test_chua_arctan_wu2023_validation_contract.py
tests/test_chua_candidate_extended_hiddenness.py
tests/test_ci_dependency_policy_consistency.py
tests/test_classical_route_scope.py
tests/test_cli_overrides.py
tests/test_cli_smoke.py
tests/test_cloned_dynamics_discrepancy_diagnostics.py
tests/test_cloned_dynamics_fischer_published_all_rows.py
tests/test_cloned_dynamics_published_structure.py
tests/test_cloned_dynamics_reproduction_limitations.py
tests/test_cloned_dynamics_synthetic.py
tests/test_config_loader.py
tests/test_continuation_cli.py
tests/test_continuation_memory_policy.py
tests/test_continuation_memory_validation.py
tests/test_current_candidate_selection.py
tests/test_current_protocol_evidence_scope.py
tests/test_danca_candidate_traceability.py
tests/test_deferred_robustness_scope.py
tests/test_diagnostics_partial_scope.py
tests/test_documentation_references.py
tests/test_dynamical_analysis.py
tests/test_efork_published_validation.py
tests/test_f4_internal_lyapunov_validation.py
tests/test_f4_no_false_method_validation.py
tests/test_f5_diagnostics_contract.py
tests/test_f5_global_runner.py
tests/test_f6_integrated_chaos_validator.py
tests/test_f7_method_comparison.py
tests/test_figure_export_contract.py
tests/test_figure_manifest.py
tests/test_figure_tests_do_not_write_real_library_figures.py
tests/test_final_freeze_audit_artifact.py
tests/test_fractional_memory_validation.py
tests/test_fractional_nonsmooth_algebra.py
tests/test_fractional_variational_benchmarks.py
tests/test_freeze_audit_json_outputs.py
tests/test_general_solver.py
tests/test_hiddenness_contract.py
tests/test_homogenization_rules.py
tests/test_integer_lure_workflow.py
tests/test_integrator_crosscheck.py
tests/test_integrator_method_validation.py
tests/test_integrator_selector.py
tests/test_integrator_workflow_compatibility.py
tests/test_latex_report_user_manual_sync.py
tests/test_library_seed_and_workflow_api.py
tests/test_lure_compatibility.py
tests/test_lure_seed_families.py
tests/test_lure_seed_filtering.py
tests/test_lure_seeds_modal.py
tests/test_lyapunov_api.py
tests/test_lyapunov_cli.py
tests/test_lyapunov_fractional_variational.py
tests/test_lyapunov_integer_audit.py
tests/test_lyapunov_promotion.py
tests/test_lyapunov_registry_f3.py
tests/test_manual_claims_consistency.py
tests/test_manual_cli_consistency.py
tests/test_manual_freeze_audit_reference.py
tests/test_manual_manifest.py
tests/test_manual_manifest_consistency.py
tests/test_markdown_docs_claim_status.py
tests/test_markdown_docs_cli_consistency.py
tests/test_memory_normalization.py
tests/test_native_fractional_variational_backend.py
tests/test_no_absolute_local_paths.py
tests/test_no_absolute_paths_in_promoted_evidence.py
tests/test_no_direct_savefig_outside_export.py
tests/test_no_external_figure_paths_in_promoted_validation.py
tests/test_no_external_paths_in_promoted_artifacts.py
tests/test_no_false_certification.py
tests/test_no_false_chaos_certification_f3.py
tests/test_no_legacy_cli_in_manuals.py
tests/test_no_legacy_entrypoints_in_ci_or_docs.py
tests/test_no_loose_active_scripts.py
tests/test_no_loose_figure_scripts.py
tests/test_no_plot_titles.py
tests/test_nonsmooth_nonlinearities.py
tests/test_official_protocol.py
tests/test_official_wolfram_artifacts.py
tests/test_package_smoke.py
tests/test_packaged_yaml_examples.py
tests/test_phase_F_closure.py
tests/test_plotting_style_contract.py
tests/test_poincare_diagnostics.py
tests/test_poincare_method_validation.py
tests/test_promoted_figures_export_policy.py
tests/test_public_entry_points_are_unified.py
tests/test_published_case_reproduction.py
tests/test_published_continuation_comparison.py
tests/test_published_reference_claims_are_conservative.py
tests/test_published_validation_coverage.py
tests/test_pypi_packaging.py
tests/test_python_version_metadata.py
tests/test_quick_start_cli_consistency.py
tests/test_quick_start_commands.py
tests/test_reference_data.py
tests/test_regression_reference_values.py
tests/test_release_docs_no_mojibake.py
tests/test_release_package_samples.py
tests/test_release_readiness_metadata.py
tests/test_report_figure_paths.py
tests/test_reproducibility.py
tests/test_reproducibility_metadata.py
tests/test_root_repository_hygiene.py
tests/test_scientific_scope_docs.py
tests/test_scientific_software_algebra.py
tests/test_scientific_software_hiddenness.py
tests/test_scientific_software_integrators.py
tests/test_seed_cli.py
tests/test_spectral_diagnostics.py
tests/test_stage_flags.py
tests/test_symmetry_validator.py
tests/test_systems_and_legacy_facade.py
tests/test_test_suite_classification.py
tests/test_thesis_claims.py
tests/test_user_manual.py
tests/test_user_manual_claims_consistency.py
tests/test_user_manual_exists.py
tests/test_validation_contract.py
tests/test_validation_manifest.py
tests/test_validation_states.py
tests/test_weyl_caputo_justification.py
tests/test_wolfram_python_consistency.py
tests/test_wolfram_validations.py
tests/test_workflow_smoke.py
tests/test_yaml_loading.py
tests/test_zero_one_diagnostics.py
tests/test_zero_one_test.py
tests/cli/test_continuation_order_cli.py
tests/cli/test_seed_order_cli.py
tests/helpers/test_documentation_text.py
tests/hygiene/test_tests_do_not_write_real_artifacts.py
tests/scientific_contract/test_continuation_order_contract.py
tests/scientific_contract/test_seed_transfer_contract.py
tools/release/validate_wheel_install.py