# Graph Report - heterodyne  (2026-05-29)

## Corpus Check
- 349 files · ~495,209 words
- Verdict: corpus is large enough that graph structure adds value.

## Summary
- 14676 nodes · 21754 edges · 1969 communities (624 shown, 1345 thin omitted)
- Extraction: 77% EXTRACTED · 23% INFERRED · 0% AMBIGUOUS · INFERRED: 4982 edges (avg confidence: 0.7)
- Token cost: 0 input · 0 output

## Graph Freshness
- Built from commit: `7c329a4f`
- Run `git rev-parse HEAD` and compare to check if the graph is stale.
- Run `graphify update .` after code changes (no API cost).

## Community Hubs (Navigation)
- [[_COMMUNITY_HeterodyneModel Physics Core|HeterodyneModel Physics Core]]
- [[_COMMUNITY_CLI Shell Completion Parity|CLI Shell Completion Parity]]
- [[_COMMUNITY_MCMC ArviZ Visualization|MCMC ArviZ Visualization]]
- [[_COMMUNITY_NLSQ Memory Strategy|NLSQ Memory Strategy]]
- [[_COMMUNITY_NLSQ Result Validation|NLSQ Result Validation]]
- [[_COMMUNITY_JAX Backend Physics|JAX Backend Physics]]
- [[_COMMUNITY_NLSQ Hierarchical Pipeline|NLSQ Hierarchical Pipeline]]
- [[_COMMUNITY_NLSQ Results & Data|NLSQ Results & Data]]
- [[_COMMUNITY_Theory Engine Data Loading|Theory Engine Data Loading]]
- [[_COMMUNITY_CMC Sharding Tests|CMC Sharding Tests]]
- [[_COMMUNITY_Model Mixins Fraction|Model Mixins Fraction]]
- [[_COMMUNITY_CMC Diagnostics MCMC|CMC Diagnostics MCMC]]
- [[_COMMUNITY_CMC IO Shard Loading|CMC I/O Shard Loading]]
- [[_COMMUNITY_CMC Reparameterization|CMC Reparameterization]]
- [[_COMMUNITY_Async IO Utilities|Async I/O Utilities]]
- [[_COMMUNITY_NLSQ Strategy Tests|NLSQ Strategy Tests]]
- [[_COMMUNITY_NLSQ Adapter Wrapper|NLSQ Adapter Wrapper]]
- [[_COMMUNITY_HDF5 Data Pipeline|HDF5 Data Pipeline]]
- [[_COMMUNITY_Core Model Init|Core Model Init]]
- [[_COMMUNITY_Community 19|Community 19]]
- [[_COMMUNITY_Community 20|Community 20]]
- [[_COMMUNITY_Community 21|Community 21]]
- [[_COMMUNITY_Community 22|Community 22]]
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- [[_COMMUNITY_Community 25|Community 25]]
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## God Nodes (most connected - your core abstractions)
1. `NLSQResult` - 265 edges
2. `Structured Logging` - 215 edges
3. `NLSQConfig` - 206 edges
4. `CMCResult` - 134 edges
5. `CMCConfig` - 104 edges
6. `NLSQAdapter` - 81 edges
7. `compute_c2_heterodyne()` - 81 edges
8. `ReparamConfig` - 77 edges
9. `NLSQWrapper` - 75 edges
10. `CPUInfo` - 66 edges

## Surprising Connections (you probably didn't know these)
- `TimedContext context manager` --used_by--> `OutOfCoreStrategy`  [INFERRED]
  docs/architecture/nlsq-fitting-architecture.md → optimization/nlsq/strategies/out_of_core.py
- `CMCConfig` --configures--> `ShardingStrategy`  [INFERRED]
  optimization/cmc/config.py → docs/architecture/cmc-fitting-architecture.md
- `CMCResult` --uses--> `ParameterStats`  [INFERRED]
  optimization/cmc/results.py → docs/architecture/cmc-fitting-architecture.md
- `accumulate_chunks_parallel function` --uses--> `HybridStreamingStrategy`  [INFERRED]
  docs/architecture/nlsq-fitting-architecture.md → optimization/nlsq/strategies/hybrid_streaming.py
- `NLSQ Fitting Architecture` --references--> `Post-Fit ResultValidator`  [EXTRACTED]
  docs/architecture/nlsq-fitting-architecture.md → optimization/nlsq/validation/result_validator.py

## Hyperedges (group relationships)
- **Two-Path Integral Evaluation** — architecture_two_path_integral, architecture_meshgrid_path, architecture_element_wise_path, architecture_physics_utils [EXTRACTED 1.00]
- **Analysis Pipeline Data Flow** — architecture_data_flow, architecture_nlsq_optimizer, architecture_cmc_sampler, architecture_arviz_diagnostics [EXTRACTED 0.85]
- **Numerically Safe Primitive Family** — computational_methods_safe_exp, computational_methods_safe_log, computational_methods_safe_power, computational_methods_safe_divide, computational_methods_smooth_abs [EXTRACTED 1.00]

## Communities (1969 total, 1345 thin omitted)

### Community 0 - "HeterodyneModel Physics Core"
Cohesion: 0.02
Nodes (96): NLSQWrapper returns NLSQResult with success=False when all tiers fail., TestNLSQWrapperRecovery, NLSQAdapter, Adapter for the nlsq library's CurveFit optimizer.      Uses JAX-accelerated non, Adapter for the nlsq library's CurveFit optimizer.      Uses JAX-accelerated non, Adapter for the nlsq library's CurveFit optimizer.      Uses JAX-accelerated non, Check if the NLSQ CurveFit backend is available., NLSQConfig (+88 more)

### Community 1 - "CLI Shell Completion Parity"
Cohesion: 0.03
Nodes (90): all_results(), detect_degeneracy(), from_dict(), from_nlsq_config(), generate_random_starts(), get_n_workers(), include_custom_starts(), _multistart_worker_sequential() (+82 more)

### Community 2 - "MCMC ArviZ Visualization"
Cohesion: 0.02
Nodes (97): compute_c2_heterodyne(), compute_fraction_jit(), compute_transport_jit(), compute_velocity_integral_matrix(), JIT-compiled sample fraction computation.      f_s(t) = f0 * exp(f1 * (t - f2)), JIT-compiled sample fraction computation.      f_s(t) = f0 * exp(f1 * (t - f2)), JIT-compiled sample fraction computation.      f_s(t) = f0 * exp(f1 * (t - f2)), JIT-compiled velocity integral matrix (NLSQ meshgrid path).      Computes M[i,j] (+89 more)

### Community 3 - "NLSQ Memory Strategy"
Cohesion: 0.03
Nodes (68): NLSQWrapper, Stable fallback adapter with memory-aware strategy routing.      Selects between, Stable fallback adapter with memory-aware strategy routing.      Selects between, Stable fallback adapter with memory-aware strategy routing.      Selects between, Initialise the wrapper.          Args:             parameter_names: Names of par, Initialise the wrapper.          Args:             parameter_names: Names of par, Initialise the wrapper.          Args:             parameter_names: Names of par, Stable fallback adapter with memory-aware strategy routing.      Selects between (+60 more)

### Community 4 - "NLSQ Result Validation"
Cohesion: 0.03
Nodes (48): compute_relative_difference(), compute_transport_rate(), compute_velocity_rate(), Numerically safe mathematical primitives for heterodyne physics.  All functions, Square root with protection against negative arguments.      Args:         x: In, Compute element-wise relative difference ``|a - b|`` / max(``|a|``, ``|b|``, 1e-, Force a matrix to be exactly symmetric: (M + M^T) / 2.      Args:         matrix, Transport rate function J(t) = D0·t^α + offset.      Shared by both NLSQ and CMC (+40 more)

### Community 5 - "JAX Backend Physics"
Cohesion: 0.02
Nodes (46): HeterodyneModel, Get current full parameter array.          Returns:             Array of shape (, Get current full parameter array.          Returns:             Array of shape (, Get current parameters as dictionary., Get current parameters as dictionary., Set parameter values.          Args:             params: Either array of shape (, Set parameter values.          Args:             params: Either array of shape (, Compute two-time correlation matrix.          Args:             phi_angle: Detec (+38 more)

### Community 6 - "NLSQ Hierarchical Pipeline"
Cohesion: 0.03
Nodes (64): NLSQResult, Compute correlation matrix from covariance.          Returns:             Correl, Validate result quality.          Returns:             List of warning/error mes, Validate result quality.          Returns:             List of warning/error mes, Generate summary string.          Returns:             Multi-line summary, Result of NLSQ optimization.      Contains fitted parameters, uncertainties, and, Generate summary string.          Returns:             Multi-line summary, Result of NLSQ optimization.      Contains fitted parameters, uncertainties, and (+56 more)

### Community 7 - "NLSQ Results & Data"
Cohesion: 0.03
Nodes (81): HeterodyneModel, dt(), from_config(), n_params(), n_times(), n_varying(), param_names(), q() (+73 more)

### Community 8 - "Theory Engine Data Loading"
Cohesion: 0.04
Nodes (61): detect_total_system_memory(), estimate_peak_memory_gb(), get_adaptive_memory_threshold(), _get_memory_threshold(), NLSQStrategy, _psutil_available(), Memory-aware strategy selection for NLSQ optimization.  Estimates peak memory us, Estimate peak memory for full-Jacobian NLSQ optimization.      The dominant cost (+53 more)

### Community 9 - "CMC Sharding Tests"
Cohesion: 0.03
Nodes (60): _assess_convergence(), CachedModel, clear_model_cache(), get_adapter(), get_cache_stats(), get_or_create_fitter(), get_or_create_model(), is_adapter_available() (+52 more)

### Community 10 - "Model Mixins Fraction"
Cohesion: 0.04
Nodes (81): fit_cmc_jax(), Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl, Fit heterodyne model using Consensus Monte Carlo.      Uses NumPyro's NUTS sampl (+73 more)

### Community 11 - "CMC Diagnostics MCMC"
Cohesion: 0.04
Nodes (65): compute_bfmi(), compute_ess(), compute_posterior_contraction(), compute_r_hat(), Compute Posterior Contraction Ratio for each parameter.      PCR = 1 - posterior, Compute Posterior Contraction Ratio for each parameter.      PCR = 1 - posterior, Compute Posterior Contraction Ratio for each parameter.      PCR = 1 - posterior, Compute rank-normalized R-hat from samples.      Delegates to ``arviz.rhat()`` w (+57 more)

### Community 12 - "CMC I/O Shard Loading"
Cohesion: 0.03
Nodes (64): _build_multi_phi_c2_data(), _build_multi_phi_model(), _CaptureDone, Tests for CMC (Consensus Monte Carlo) core functionality.  Bug Prevented: CMC Mu, Regression tests for het_c7548ee8 / het_e34fa942: fit_cmc_sharded must abort, Regression tests for het_c7548ee8 / het_e34fa942: fit_cmc_sharded must abort, Regression tests for het_c7548ee8 / het_e34fa942: fit_cmc_sharded must abort, Tests for fit_cmc_jax function with various chain configurations. (+56 more)

### Community 13 - "CMC Reparameterization"
Cohesion: 0.05
Nodes (40): Tests for HierarchicalConfig creation and validation., HierarchicalConfig can be created with default stages., Default stages include 'transport', 'velocity', 'fraction', 'all'., Stage with unknown group name raises ValueError., Stage without 'name' key raises ValueError., TestHierarchicalResultCreation, convergence_trajectory(), HierarchicalConfig (+32 more)

### Community 14 - "Async I/O Utilities"
Cohesion: 0.04
Nodes (69): DifferentiationConfig, _backward_difference(), _complex_step_derivative(), compute_adaptive_gradient(), compute_gradient(), compute_gradient_finite_diff(), compute_gradient_parallel(), compute_hessian_finite_diff() (+61 more)

### Community 15 - "NLSQ Strategy Tests"
Cohesion: 0.03
Nodes (73): _available_memory_bytes(), _estimate_n_workers(), _estimate_shard_peak_bytes(), _fit_cmc_pooled(), _fmt_time(), _grid_indices(), _log_runtime_estimate(), _memory_aware_worker_cap() (+65 more)

### Community 16 - "NLSQ Adapter Wrapper"
Cohesion: 0.05
Nodes (48): _ess_bulk_dict(), _ess_tail_dict(), list_shards(), load_inference_data(), load_samples_npz(), load_shard_results(), _r_hat_dict(), Shard I/O for CMC (Consensus Monte Carlo) results.  Provides functions to persis (+40 more)

### Community 17 - "HDF5 Data Pipeline"
Cohesion: 0.05
Nodes (63): from_dict(), from_json(), _apply_initial_parameters(), beta_scaled(), _build_prior(), clamp_to_open_interval(), _compute_beta_concentrations(), _default_prior() (+55 more)

### Community 18 - "Core Model Init"
Cohesion: 0.03
Nodes (54): _compute_c2_elementwise(), _compute_c2_pooled(), _fraction(), _half_transport_elementwise(), _half_transport_pooled(), Per-pair signed velocity integral ``(n_pairs,)``., Per-pair signed velocity integral ``(n_pairs,)``., Sample-fraction f_s(t), smoothly bounded to [0, 1].      Mirrors the implementat (+46 more)

### Community 19 - "Community 19"
Cohesion: 0.03
Nodes (62): MultiprocessingBackend, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, Initialise the multiprocessing backend.          Args:             n_workers: Nu, Initialise the multiprocessing backend.          Args:             n_workers: Nu, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, Initialise the multiprocessing backend.          Args:             n_workers: Nu, Check that CPU resources and multiprocessing are available.          Raises: (+54 more)

### Community 20 - "Community 20"
Cohesion: 0.06
Nodes (39): _assert_nlsq_import(), _assert_no_scipy_import(), _fake_c2(), _fake_config(), _fake_model(), _fake_nlsq_result(), _fake_param_manager(), Smoke tests verifying that the 6 strategy files use nlsq, not scipy.  Each test (+31 more)

### Community 21 - "Community 21"
Cohesion: 0.05
Nodes (45): compute_c2_elementwise(), precompute_shard_grid_from_matrix(), Create ShardGrid for a diagonal block c2[start:end, start:end].      Generates (, Create ShardGrid for a diagonal block c2[start:end, start:end].      Generates (, Element-wise c2 evaluation for CMC (no N×N matrix allocation).      Thin shim ar, Element-wise c2 computation for CMC (no N×N matrix allocation).      This is the, Element-wise c2 computation for CMC (no N×N matrix allocation).      This is the, compute_c2_unified() (+37 more)

### Community 22 - "Community 22"
Cohesion: 0.06
Nodes (31): _fake_nlsq_result(), TestAngleSubset, TestFixedParameterHelpers, TestMultiAngleResult, TestSequentialStrategy, TestStrategyResult, TestThresholds, Result from a fitting strategy execution.      Wraps the NLSQResult with strateg (+23 more)

### Community 23 - "Community 23"
Cohesion: 0.05
Nodes (38): Tests for optimization checkpoint save/load., Save and load a checkpoint; values must survive the trip., Tests for optimization checkpoint save/load., Checksum validates untampered checkpoint., Save and load a checkpoint; values must survive the trip., Tampered JSON file fails integrity check., Checksum validates untampered checkpoint., find_latest_valid returns the most recent uncorrupted checkpoint. (+30 more)

### Community 24 - "Community 24"
Cohesion: 0.05
Nodes (36): Configuration for reference-time reparameterization.      Attributes:         en, Check if a parameter participates in reparameterization., ReparamConfig, Tests for heterodyne/optimization/cmc/reparameterization.py.  Covers: - compute_, Only D0_ref/alpha_ref pair when others disabled., Only D0_sample/alpha_sample pair when others disabled., Only v0/beta pair when others disabled., Can selectively disable pairs. (+28 more)

### Community 25 - "Community 25"
Cohesion: 0.05
Nodes (43): load_nlsq_npz_file(), Load NLSQResult from an NPZ file saved by ``save_nlsq_npz_file``.      Args:, Load NLSQResult from an NPZ file saved by ``save_nlsq_npz_file``.      Args:, Load NLSQResult from an NPZ file saved by ``save_nlsq_npz_file``.      Args:, Load NLSQResult from an NPZ file saved by ``save_nlsq_npz_file``.      Args:, Save NLSQ results to compressed NPZ file.      NPZ format is efficient for large, Save NLSQ results to compressed NPZ file.      NPZ format is efficient for large, save_nlsq_npz_file() (+35 more)

### Community 26 - "Community 26"
Cohesion: 0.04
Nodes (47): Tests for AnalysisSummaryLogger phase tracking., AnalysisSummaryLogger records phase start/end with duration., AnalysisSummaryLogger tracks multiple phases independently., Tests for AnalysisSummaryLogger phase tracking., AnalysisSummaryLogger records phase start/end with duration., AnalysisSummaryLogger stores convergence status., AnalysisSummaryLogger stores named metrics., AnalysisSummaryLogger tracks multiple phases independently. (+39 more)

### Community 27 - "Community 27"
Cohesion: 0.05
Nodes (40): _ast_imports(), _make_config(), _make_model(), _make_streaming_dict_result(), Unit tests for HybridStreamingStrategy.  Verifies: - No scipy.optimize imports i, Verify that scipy.optimize is not imported by the strategy module., AST-level check: scipy.optimize must not appear in any import., Textual guard: the string 'scipy.optimize' must not appear at all. (+32 more)

### Community 28 - "Community 28"
Cohesion: 0.04
Nodes (60): _fit_cmaes(), _fit_local(), _fit_multistart(), fit_nlsq_multistart(), _log_result(), _make_numpy_residual_fn(), Core NLSQ fitting for heterodyne analysis.  Unified entry point for NLSQ optimiz, Attempt CMA-ES or multi-start if configured.      Returns the result if a global (+52 more)

### Community 29 - "Community 29"
Cohesion: 0.04
Nodes (59): _block_until_ready_pytree(), _create_failed_result(), _create_shards_random(), _make_shard_config(), Core CMC fitting functions for heterodyne Bayesian analysis.  Includes the origi, Scale measurement uncertainty for CMC prior tempering.      In Consensus Monte C, Return a copy of ``config`` with a new seed.      All other fields are preserved, Block every JAX array leaf in a pytree and return the original object. (+51 more)

### Community 30 - "Community 30"
Cohesion: 0.06
Nodes (53): apply_baseline_correction(), apply_noise_reduction(), _baseline_polynomial(), _compute_array_hash(), _compute_config_hash(), _estimate_baseline(), from_dict(), _generate_pipeline_id() (+45 more)

### Community 31 - "Community 31"
Cohesion: 0.05
Nodes (55): build_log_space_priors(), build_nlsq_informed_priors(), Build log-normal priors for parameters marked ``log_space=True``.      For param, Build log-normal priors for parameters marked ``log_space=True``.      For param, Build log-normal priors for parameters marked ``log_space=True``.      For param, Build log-normal priors for parameters marked ``log_space=True``.      For param, Build priors centered on NLSQ point estimates.      For each varying parameter,, Build priors centered on NLSQ point estimates.      For each varying parameter, (+47 more)

### Community 32 - "Community 32"
Cohesion: 0.04
Nodes (50): fit_cmc_sharded(), Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ, Fit heterodyne model using sharded Consensus Monte Carlo.      Splits the observ (+42 more)

### Community 33 - "Community 33"
Cohesion: 0.07
Nodes (36): ClusterType, CMCBackend, detect_hardware(), get_available_memory(), get_backend_name(), get_device_status(), HardwareConfig, Hardware configuration and CMC backend selection.  This module provides hardware (+28 more)

### Community 34 - "Community 34"
Cohesion: 0.04
Nodes (33): ConvergenceLogger, Structured logger for optimization convergence diagnostics., Log optimization iteration metrics., Log convergence result., Structured logger for optimization convergence diagnostics., Structured logger for optimization convergence diagnostics., Log diagnostic metric with pass/fail status.          Args:             metric_n, Log optimization iteration metrics. (+25 more)

### Community 35 - "Community 35"
Cohesion: 0.06
Nodes (30): Backend, BackendConfig, _check_jax_available(), ensure_array(), get_array_module(), get_current_backend(), Backend selection and abstraction for heterodyne computations.  The heterodyne p, Return the appropriate array module for the given backend.      Args:         ba (+22 more)

### Community 36 - "Community 36"
Cohesion: 0.06
Nodes (25): json_safe(), Convert object to JSON-serializable form.      Handles:     - JAX arrays -> list, Unit tests for heterodyne.io.json_utils., Tests for json_safe on Python complex numbers., Tests for json_safe on Path and datetime objects., Tests for json_safe on nested dicts and lists., Tests for json_safe fallback behavior., Regression: NaN/Inf must be caught inside numpy arrays/scalars, not just     raw (+17 more)

### Community 37 - "Community 37"
Cohesion: 0.06
Nodes (44): d_offset_to_ratio(), enabled_pairs(), heterodyne_offset_ratios_from_physics(), heterodyne_physics_offsets_from_ratios(), ratio_to_d_offset(), Reference-time reparameterization for heterodyne CMC.  Breaks banana-shaped post, Transform NLSQ point estimates to reparameterized space.      For each enabled p, Transform physics-space parameters to sampling (reparam) space.      Used for in (+36 more)

### Community 38 - "Community 38"
Cohesion: 0.04
Nodes (43): _make_synthetic_model(), Homodyne parity tests for heterodyne NLSQ per-angle-mode dispatch.  Reference: h, Mock HeterodyneModel exposing the minimal API needed by joint fits., `constant` mode optimizes physics params only; β,o are frozen per-angle., Optimizer receives x0 of length 14 (n_varying), not 16, not 14+2·n_phi., Each per-angle NLSQResult records its frozen β,o for downstream viz., Each per-angle NLSQResult from fixed-constant has fitted_correlation,         re, Verify `fit_nlsq_multi_phi` routes each mode to the correct joint fit. (+35 more)

### Community 39 - "Community 39"
Cohesion: 0.05
Nodes (34): _compute_c2_meshgrid(), _half_transport_meshgrid(), Full ``(N, N)`` signed velocity integral., Full ``(N, N)`` signed velocity integral., Meshgrid evaluation — produces ``(N, N)`` matrix., Meshgrid evaluation — produces ``(N, N)`` matrix., Meshgrid evaluation — produces ``(N, N)`` matrix., Full ``(N, N)`` half-transport matrix: exp(-½ q² |∫J dt|).      The ``jnp.exp(jn (+26 more)

### Community 40 - "Community 40"
Cohesion: 0.04
Nodes (51): batch_chi_squared(), compute_c2_heterodyne_multiphi(), compute_chi_squared(), compute_multi_angle_residuals(), compute_residuals(), compute_residuals_jacobian(), _compute_residuals_jit(), compute_transport_integral_matrix() (+43 more)

### Community 41 - "Community 41"
Cohesion: 0.06
Nodes (47): ConfigManager, Manager for heterodyne analysis configuration.      Handles loading, validation,, Update a single optimization config key in-place.          Args:             sec, Update a single optimization config key in-place.          Args:             sec, config_yaml_file(), full_config(), minimal_config(), Tests for configuration manager module.  Tests ConfigManager class for loading a (+39 more)

### Community 42 - "Community 42"
Cohesion: 0.07
Nodes (24): build_init_values_dict(), Check that each initial value lies within the parameter's bounds.      Args:, Check that each initial value lies within the parameter's bounds.      Args:, Check that each initial value lies within the parameter's bounds.      Args:, Build an initial-values dict for NUTS warm-starting.      For each varying param, Build an initial-values dict for NUTS warm-starting.      For each varying param, Build an initial-values dict for NUTS warm-starting.      For each varying param, Check that each initial value lies within the parameter's bounds.      Args: (+16 more)

### Community 43 - "Community 43"
Cohesion: 0.05
Nodes (40): main(), System validation utilities for heterodyne installation.  This module provides c, Test environment detection capabilities., Test that heterodyne package is properly installed., Test Python version compatibility., Test JAX installation and version., Severity level for validation results., Test JAX CPU backend configuration. (+32 more)

### Community 44 - "Community 44"
Cohesion: 0.05
Nodes (29): get_param_names_in_order(), Return the ordered list of parameter names that are set to vary.      Iteration, Return the ordered list of parameter names that are set to vary.      Iteration, Return the ordered list of parameter names that are set to vary.      Iteration, Return the ordered list of parameter names that are set to vary.      Iteration, get_param_names_in_order returns correctly ordered, filtered name lists., With no arguments all registry parameters with vary_default=True are returned., Every entry in the returned list is a non-empty string. (+21 more)

### Community 45 - "Community 45"
Cohesion: 0.05
Nodes (37): accumulate_chunks_parallel(), accumulate_chunks_sequential(), create_ooc_kernels(), GaussNewtonAccumulation, _ooc_compute_chi2_chunk(), _ooc_compute_chunk(), _ooc_worker_cleanup(), _ooc_worker_init() (+29 more)

### Community 46 - "Community 46"
Cohesion: 0.06
Nodes (48): _compute_lpt_schedule(), _compute_threads_per_worker(), _estimate_shard_time(), from_shard_data(), _generate_shard_keys(), _get_physical_cores(), _init_worker_jax(), _load_shared_array() (+40 more)

### Community 47 - "Community 47"
Cohesion: 0.06
Nodes (42): _perturb_init_params(), Add small per-chain perturbations to initial parameters.      Ensures each chain, Hyperparameters for NUTS sampling.      Immutable configuration that fully speci, Validate hyperparameters., Hyperparameters for NUTS sampling.      Immutable configuration that fully speci, Validate hyperparameters., Validate hyperparameters., Add small per-chain perturbations to initial parameters.      Ensures each chain (+34 more)

### Community 48 - "Community 48"
Cohesion: 0.05
Nodes (36): _estimate_physical_workers(), n_workers(), _persistent_worker_event_loop(), Worker pool backend for multi-shard CMC execution.  Spawns persistent workers th, Persistent worker pool for multi-shard CMC execution.      Distributes MCMC shar, Persistent worker pool for multi-shard CMC execution.      Distributes MCMC shar, Initialize with optional worker count.          Args:             n_workers: Num, Initialize with optional worker count.          Args:             n_workers: Num (+28 more)

### Community 49 - "Community 49"
Cohesion: 0.07
Nodes (44): compute_scaling_factors(), log_scaling_factors(), ParameterScaling, Smooth bounded parameter scaling for heterodyne CMC.  Replaces jnp.clip() (zero, Inverse of smooth_bound for initialization.      Recovers the raw (unbounded) va, Build ParameterScaling for each varying parameter.      Uses NLSQ values as cent, Log all scaling factors for debugging.      Emits a header at INFO level, then p, Transform initial values from physics space to z-space.      Only transforms par (+36 more)

### Community 50 - "Community 50"
Cohesion: 0.07
Nodes (37): _combine_shard_posteriors(), Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple, Combine per-shard posteriors via inverse-variance weighted consensus.      Imple (+29 more)

### Community 51 - "Community 51"
Cohesion: 0.07
Nodes (40): apply_auto_corrections(), assess_stage(), _compute_adaptive_thresholds(), export_report(), _level_marker(), QualityControlConfig, QualityController, QualityControlResult (+32 more)

### Community 52 - "Community 52"
Cohesion: 0.05
Nodes (40): Save MCMC convergence diagnostics.      Args:         result: CMC result object, Save MCMC convergence diagnostics.      Args:         result: CMC result object, Save MCMC convergence diagnostics.      Args:         result: CMC result object, save_mcmc_diagnostics(), cmc_result_failed(), cmc_result_full(), cmc_result_minimal(), _degenerate_result() (+32 more)

### Community 53 - "Community 53"
Cohesion: 0.05
Nodes (48): _anti_degen_dict_from_config(), _build_anti_degen_controller(), _fit_joint_averaged_multi_phi(), _fit_joint_fixed_constant_multi_phi(), _fit_joint_multi_phi(), fit_nlsq_cmaes(), _hierarchical_marker_from_controller(), _log_anti_degeneracy_diagnostics() (+40 more)

### Community 54 - "Community 54"
Cohesion: 0.07
Nodes (32): CMCBackend, Abstract base class for CMC execution backends.      Concrete subclasses impleme, Abstract base class for CMC execution backends.      Concrete subclasses impleme, ArraySpec, ArraySpec, _load_shared_shard_data(), Store a numpy array in a shared memory segment.          Args:             name:, Manages shared memory blocks for data common to all CMC shards.      Uses ``mult (+24 more)

### Community 55 - "Community 55"
Cohesion: 0.07
Nodes (32): load_xpcs_data(), Convenience function to load XPCS data.      Args:         file_path: Path to da, Convenience function to load XPCS data.      Args:         file_path: Path to da, _make_symmetric_c2(), Integration tests for HDF5 data I/O and the XPCS loading pipeline.  Bug Prevente, Tests for XPCS HDF5 data loading., Load a flat-layout HDF5 file and verify data fidelity., Load an APS-style /exchange/ HDF5 file. (+24 more)

### Community 56 - "Community 56"
Cohesion: 0.05
Nodes (32): Tests for validate_time_arrays., Matching, strictly increasing arrays return no errors., Non-monotonic t1 returns an error., Different-length arrays return an error., Tests for validate_q_range., q values within range return no errors., q below q_min returns an error., q above q_max returns an error. (+24 more)

### Community 57 - "Community 57"
Cohesion: 0.07
Nodes (30): cluster_shard_modes(), Aggregate per-shard bimodal detections into a cross-shard summary.      Groups d, Jointly cluster shards into two mode populations.      Uses the parameters that, Jointly cluster shards into two mode populations.      Uses the parameters that, Aggregate per-shard bimodal detections into a cross-shard summary.      Groups d, Aggregate per-shard bimodal detections into a cross-shard summary.      Groups d, Aggregate per-shard bimodal detections into a cross-shard summary.      Groups d, Aggregate per-shard bimodal detections into a cross-shard summary.      Groups d (+22 more)

### Community 58 - "Community 58"
Cohesion: 0.07
Nodes (20): AdaptiveRegularizer, current_lambda(), Adaptive Tikhonov regularization for ill-conditioned NLSQ problems.  The 14-para, Adapt the regularization parameter based on cost change.          - If cost_new, Regularize a near-singular covariance matrix.          Adds lambda * I to the co, Reset lambda to initial value., Configuration for adaptive Tikhonov regularization.      Attributes:         lam, Validate configuration. (+12 more)

### Community 59 - "Community 59"
Cohesion: 0.05
Nodes (45): _compute_threads_per_worker(), _estimate_shard_time(), from_shard_data(), _get_physical_cores(), _init_worker_jax(), _joint_payload_param_names(), _load_shared_array(), _load_shared_bytes() (+37 more)

### Community 60 - "Community 60"
Cohesion: 0.05
Nodes (43): compute_g1_transport(), JIT-compiled pointwise g1 correlation from transport coefficient.      g1(t) = e, JIT-compiled pointwise g1 correlation from transport coefficient.      g1(t) = e, JIT-compiled pointwise g1 correlation from transport coefficient.      g1(t) = e, Test g1 correlation computation., Test g1 correlation computation., Tests for JAX backend functions., Tests for JAX backend functions. (+35 more)

### Community 61 - "Community 61"
Cohesion: 0.06
Nodes (30): Run :class:`InputValidator` against the fit inputs (non-strict).      Bounds, fi, Run :class:`InputValidator` against the fit inputs (non-strict).      Bounds, fi, Run :class:`InputValidator` against the fit inputs (non-strict).      Bounds, fi, Run :class:`InputValidator` against the fit inputs (non-strict).      Bounds, fi, _run_input_validation(), Tests for NLSQ input validation., Tests for InputValidator., Well-formed inputs pass validation. (+22 more)

### Community 62 - "Community 62"
Cohesion: 0.06
Nodes (28): get_group_indices(), get_param_index(), Parameter name constants for 14-parameter heterodyne model.  The heterodyne mode, Get index of parameter in flattened array.      Args:         name: Parameter na, Get indices for all parameters in a group.      Args:         group: Group name, Tests for config/parameter_names.py module.  Covers get_param_index and get_grou, get_param_index is case-sensitive., Tests for get_group_indices function. (+20 more)

### Community 63 - "Community 63"
Cohesion: 0.05
Nodes (27): Scientific tests for theory module computations.  This module provides rigorous, Scientific tests for compute_g1_decay., Scientific tests for compute_cross_term_phase., test_ballistic_motion_alpha_2(), test_brownian_diffusion_alpha_1(), test_exponential_formula(), test_g1_decays_with_J(), test_g1_normalized_at_origin() (+19 more)

### Community 64 - "Community 64"
Cohesion: 0.07
Nodes (32): _make_default_params(), _make_time_grid(), Tests for CMC sharding: ShardGrid, precompute_shard_grid, compute_c2_elementwise, ShardGrid stores the original time_grid., Indices match expected searchsorted+clip results., Tests for precompute_shard_grid_from_matrix., From-matrix creates upper-triangle pairs for a shard block., Using entire time grid as one shard. (+24 more)

### Community 65 - "Community 65"
Cohesion: 0.05
Nodes (37): ParameterSpace, Complete parameter space for heterodyne model optimization.      Manages paramet, Complete parameter space for heterodyne model optimization.      Manages paramet, Initialize with defaults from registry., Initialize with defaults from registry., Get initial values as numpy array in canonical order.          Returns:, Get initial values as numpy array in canonical order.          Returns:, Serialize this space to a dict compatible with :meth:`from_config`.          Pro (+29 more)

### Community 66 - "Community 66"
Cohesion: 0.05
Nodes (34): FourierReparameterizer, Handles conversion between Fourier coefficients and per-angle values.      Core, Handles conversion between Fourier coefficients and per-angle values.      Core, Determine whether to use Fourier mode., Determine whether to use Fourier mode., Determine whether to use Fourier mode., Compute Fourier basis matrix B where values = B @ coeffs.          Returns:, Get the Fourier basis matrix.          Returns:             Basis matrix of shap (+26 more)

### Community 67 - "Community 67"
Cohesion: 0.07
Nodes (42): _apply_diagonal_correction(), _cache_is_valid(), _cache_path_for(), DataValidationError, _diag_correct_2d(), has_multi_phi(), has_multi_q(), load_xpcs_batch() (+34 more)

### Community 68 - "Community 68"
Cohesion: 0.06
Nodes (42): analyze_divergences(), _classify_severity(), _compute_hdi_95(), compute_pair_correlations(), compute_trace_diagnostics(), ConvergenceReport, DivergenceReport, log_precision_analysis() (+34 more)

### Community 69 - "Community 69"
Cohesion: 0.07
Nodes (42): _empty_figure(), plot_autocorrelation(), plot_corner(), plot_divergence_scatter(), plot_energy(), plot_forest(), plot_posterior(), plot_posterior_predictive() (+34 more)

### Community 70 - "Community 70"
Cohesion: 0.07
Nodes (42): _apply_angle_filtering_for_plot(), _dispatch_cmc_plots(), _dispatch_experimental_plots(), dispatch_plots(), _dispatch_simulated_plots(), _filter_by_phi(), generate_nlsq_plots(), handle_plotting() (+34 more)

### Community 71 - "Community 71"
Cohesion: 0.06
Nodes (40): _closest_phi_index(), _combine_nlsq_results(), _exclude_first_time_point_for_nlsq(), Optimization execution for heterodyne CLI.  Manages NLSQ and CMC fitting runs, i, Build a single aggregate result for disk output., Build a single aggregate result for disk output., Run NLSQ analysis for all phi angles.      Args:         model: Configured Heter, Run NLSQ analysis for all phi angles.      Args:         model: Configured Heter (+32 more)

### Community 72 - "Community 72"
Cohesion: 0.07
Nodes (36): _is_degenerate_cmc_result(), Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur, Run CMC Bayesian analysis for all phi angles.      Args:         model: Configur (+28 more)

### Community 73 - "Community 73"
Cohesion: 0.06
Nodes (41): _detect_linux_cpu(), _detect_linux_physical_cores_from_sysfs(), Detect physical cores by deduplicating Linux topology package/core IDs., Detect physical cores by deduplicating Linux topology package/core IDs., Detect CPU info on Linux using lscpu and /proc/cpuinfo., Detect CPU info on Linux using lscpu and /proc/cpuinfo., basic_cpu(), _clean_env() (+33 more)

### Community 74 - "Community 74"
Cohesion: 0.06
Nodes (29): Tests for XPCSData dataclass computed properties., shape property returns the c2 array shape., n_times equals number of time points for 2D c2., 2D c2 does not have multiple phi angles., has_multi_q is False when q_values is not set., TestXPCSDataProperties, Container for loaded XPCS data., XPCSData (+21 more)

### Community 75 - "Community 75"
Cohesion: 0.06
Nodes (28): Tests for quantile-based scaling estimation and parameter validation.  Covers: -, Tests for vectorized per-angle estimation., Tests for averaged scaling computation., Tests for auto and constant_averaged scaling modes., Tests for quantile-based contrast/offset estimation., Tests for physics parameter validation., test_all_nan_below_threshold(), test_auto_mode_all_vary() (+20 more)

### Community 76 - "Community 76"
Cohesion: 0.08
Nodes (28): Protocol, FittingStrategy, Protocol for NLSQ fitting strategies., Execute the fitting strategy.          Args:             model: Configured Heter, ExecutionResult, get_executor(), LargeDatasetExecutor, name() (+20 more)

### Community 77 - "Community 77"
Cohesion: 0.07
Nodes (25): Tests for ValidationSeverity enum., Tests for ValidationIssue dataclass., Tests for ValidationReport dataclass., TestValidationIssue, TestValidationReport, TestValidationSeverity, FitQualityConfig, FitQualityReport (+17 more)

### Community 78 - "Community 78"
Cohesion: 0.06
Nodes (29): Detect the HDF5 layout convention used in an open file.          Checks for well, Detect the HDF5 layout convention used in an open file.          Checks for well, Load from APS-U twotime HDF5 format.          Layout expectations:          - ``, Load from APS-U twotime HDF5 format.          Layout expectations:          - ``, Load from APS legacy twotime HDF5 format.          Layout expectations:, Load from APS legacy twotime HDF5 format.          Layout expectations:, Load from HDF5 file.          Supports four layout conventions detected automati, Load from HDF5 file.          Supports four layout conventions detected automati (+21 more)

### Community 79 - "Community 79"
Cohesion: 0.07
Nodes (24): CacheEntry, PerformanceEngine, Caching and lazy loading for XPCS datasets.  Provides an LRU-eviction cache back, Retrieve a cached array.          Returns ``None`` on a cache miss.  On a hit th, Remove a single entry from the cache.          Args:             key: Dataset id, Remove all entries from the cache., Return cache statistics.          Returns:             Dict with keys: ``total_s, Total bytes currently cached (caller must hold lock). (+16 more)

### Community 80 - "Community 80"
Cohesion: 0.06
Nodes (33): format_mcmc_summary(), Format MCMC result as human-readable summary.      Args:         result: CMC res, Format MCMC result as human-readable summary.      Args:         result: CMC res, Format MCMC result as human-readable summary.      Args:         result: CMC res, Format MCMC result as human-readable summary.      Args:         result: CMC res, Format MCMC result as human-readable summary.      Args:         result: CMC res, Tests for format_mcmc_summary., When credible_intervals dict lacks expected keys, NaN used. (+25 more)

### Community 81 - "Community 81"
Cohesion: 0.06
Nodes (40): ConfigurationError, Raised when configuration is invalid., Get a specific parameter value.          Args:             group: Parameter grou, Get a specific parameter value.          Args:             group: Parameter grou, Tests for ConfigManager initialization., Tests for factory methods., Tests for experimental data properties., Tests for temporal settings properties. (+32 more)

### Community 82 - "Community 82"
Cohesion: 0.07
Nodes (20): build_result_from_nlsq(), Normalize any NLSQ package return format to NLSQResult.      Handles 4 return fo, Normalize any NLSQ package return format to NLSQResult.      Handles 4 return fo, Tests for build_result_from_nlsq in result_builder., object with .x, .pcov attrs -> valid NLSQResult., pcov=None -> uncertainties=None., metadata dict propagated., Reduced chi-squared computed correctly. (+12 more)

### Community 83 - "Community 83"
Cohesion: 0.05
Nodes (34): MultiprocessingBackend, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, CMC backend that parallelises NUTS across shards via spawned processes.      Eac, Return multiprocessing backend capabilities.          Returns:             :clas, Check that CPU resources and multiprocessing are available.          Raises:, Return multiprocessing backend capabilities.          Returns:             :clas, Check that CPU resources and multiprocessing are available.          Raises: (+26 more)

### Community 84 - "Community 84"
Cohesion: 0.07
Nodes (39): _compute_theoretical_g1_from_mcmc(), _create_mcmc_analysis_dict(), _create_mcmc_diagnostics_dict(), _create_mcmc_parameters_dict(), _extract_nlsq_metadata(), _prepare_parameter_data(), Result persistence utilities for heterodyne CLI., Write a JSON manifest summarizing all saved result files.      Args:         nls (+31 more)

### Community 85 - "Community 85"
Cohesion: 0.09
Nodes (21): _close_figures(), _make_quality_metric(), _make_quality_report(), _make_validation_issue(), _make_validation_report(), Unit tests for heterodyne.viz.validation module., Severity values not in _SEVERITY_COLORS should get #999999., Close all matplotlib figures after each test. (+13 more)

### Community 86 - "Community 86"
Cohesion: 0.07
Nodes (29): benchmark_cpu_performance(), detect_cpu_info(), _detect_fallback_cpu(), _detect_macos_cpu(), get_jax_cpu_flags(), CPU detection and HPC optimization utilities.  This module provides hardware-awa, Detect CPU info on macOS using sysctl., Detect CPU info on macOS using sysctl. (+21 more)

### Community 87 - "Community 87"
Cohesion: 0.09
Nodes (22): _make_result(), Tests for heterodyne.optimization.nlsq.validation.convergence., Uniform residuals should not trigger outlier warning., A Jacobian with condition number > 1e12 should produce a WARNING., Condition number between 1e8 and 1e12 should produce INFO., A well-conditioned Jacobian should not trigger issues., When residuals are None, no residual checks are done., When jacobian is None, no condition number checks are done. (+14 more)

### Community 88 - "Community 88"
Cohesion: 0.07
Nodes (26): FourierReparamConfig, Configuration for Fourier reparameterization.      Attributes:         mode: Per, Tests for homodyne-parity FourierReparameterizer., Fourier coefficients -> per-angle -> coefficients roundtrip., Independent mode is identity transform., Tests for homodyne-parity FourierReparameterizer., Auto mode uses Fourier only above threshold., Fourier coefficients -> per-angle -> coefficients roundtrip. (+18 more)

### Community 89 - "Community 89"
Cohesion: 0.05
Nodes (39): _adaptive_shard_iters(), fit_cmc_multi_phi(), Joint multi-phi CMC entry point (homodyne parity).      Runs ONE NUTS pass on po, Joint multi-phi CMC entry point (homodyne parity).      Runs ONE NUTS pass on po, Joint multi-phi CMC entry point (homodyne parity).      Runs ONE NUTS pass on po, Joint multi-phi CMC entry point (homodyne parity).      Runs ONE NUTS pass on po, Joint multi-phi CMC entry point (homodyne parity).      Fits the pooled multi-ph, Per-shard ``(warmup, samples)`` with homodyne-style adaptive scaling.      When (+31 more)

### Community 90 - "Community 90"
Cohesion: 0.09
Nodes (19): json_serializer(), load_json(), JSON serialization utilities for JAX arrays and numpy types., Serialize object to JSON string with pretty formatting.      Args:         obj:, Serialize object to JSON string with pretty formatting.      Args:         obj:, Load JSON file.      Args:         path: Path to JSON file      Returns:, Load JSON file.      Args:         path: Path to JSON file      Returns:, Save data to JSON file with pretty formatting.      Uses atomic write (write-to- (+11 more)

### Community 91 - "Community 91"
Cohesion: 0.07
Nodes (30): _build_formatter(), _ContextAdapter, duration(), from_cli_args(), from_dict(), get_logger(), _get_memory_gb(), log_operation() (+22 more)

### Community 92 - "Community 92"
Cohesion: 0.08
Nodes (28): apply_diagonal_correction(), Correct diagonal artifacts in a two-time correlation matrix.      The diagonal o, _make_c2(), Unit tests for diagonal_correction module.  Covers compute_diagonal_mask, apply_, Heterodyne's legacy 'interpolate' spelling remains a basic alias., Heterodyne's legacy 'interpolate' spelling remains a basic alias., Homodyne 'interpolation' is distinct from basic side-band averaging., Homodyne 'interpolation' is distinct from basic side-band averaging. (+20 more)

### Community 93 - "Community 93"
Cohesion: 0.05
Nodes (38): _build_joint_init_values(), _create_joint_init_strategy(), _joint_pooled_nuts_run(), _mcmc_safe_d0_component(), Build the pooled joint model, run one NUTS pass, assemble a CMCResult.      Shar, Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Build the pooled joint model, run one NUTS pass, assemble a CMCResult.      Shar, Build the pooled joint model, run one NUTS pass, assemble a CMCResult.      Shar (+30 more)

### Community 94 - "Community 94"
Cohesion: 0.08
Nodes (36): categorize_dataset(), compute_dataset_statistics(), create_loading_plan(), DatasetSizeCategory, estimate_optimal_time_range(), process_chunks_parallel(), Dataset optimization strategies for XPCS correlation data.  Provides subsampling, Estimate the time range where signal-to-noise exceeds a threshold.      Uses the (+28 more)

### Community 95 - "Community 95"
Cohesion: 0.07
Nodes (20): LogConfiguration, PhaseContext, Context object returned by :func:`log_phase` with timing and memory info., Programmatic logging configuration.      Alternative to ``configure_logging()``, Programmatic logging configuration.      Alternative to ``configure_logging()``, Context object returned by :func:`log_phase` with timing and memory info., Context object returned by :func:`log_phase` with timing and memory info., Context object returned by :func:`log_phase` with timing and memory info. (+12 more)

### Community 96 - "Community 96"
Cohesion: 0.07
Nodes (27): BimodalResult, detect_bimodal(), Result of a bimodality test for a single parameter's samples.      Attributes:, Fit 1- and 2-component Gaussian mixtures and compare BIC.      Uses scikit-learn, Fit 1- and 2-component Gaussian mixtures and compare BIC.      Uses scikit-learn, Fit 1- and 2-component Gaussian mixtures and compare BIC.      Uses scikit-learn, Result of a bimodality test for a single parameter's samples.      Attributes:, Result of a bimodality test for a single parameter's samples.      Attributes: (+19 more)

### Community 97 - "Community 97"
Cohesion: 0.05
Nodes (37): fit_mcmc_jax(), Run ``CMCConfig.validate()`` and raise ``ValueError`` on any error.      Central, Run ``CMCConfig.validate()`` and raise ``ValueError`` on any error.      Central, Run ``CMCConfig.validate()`` and raise ``ValueError`` on any error.      Central, Run ``CMCConfig.validate()`` and raise ``ValueError`` on any error.      Central, Homodyne-parity entry point for heterodyne CMC.      Mirrors ``homodyne.optimiza, Homodyne-parity entry point for heterodyne CMC.      Mirrors ``homodyne.optimiza, Homodyne-parity entry point for heterodyne CMC.      Mirrors ``homodyne.optimiza (+29 more)

### Community 98 - "Community 98"
Cohesion: 0.06
Nodes (29): _compute_lpt_schedule(), _generate_shard_keys(), Release shared memory and any other resources.          Idempotent — safe to cal, Release shared memory and any other resources.          Idempotent — safe to cal, Run NUTS in parallel across all CMC shards.          Orchestrates the full paral, Run NUTS in parallel across all CMC shards.          Orchestrates the full paral, Release shared memory and any other resources.          Idempotent — safe to cal, Run NUTS in parallel across all CMC shards.          Orchestrates the full paral (+21 more)

### Community 99 - "Community 99"
Cohesion: 0.06
Nodes (35): 14 Physics Parameters + 2 Scaling Parameters, Analysis Pipeline, Checkpoint and Recovery, CLI Entry Points, CMA-ES Global Optimization, CMC (Consensus Monte Carlo), CMCConfig Attribute Names, code:block1 (heterodyne/) (+27 more)

### Community 100 - "Community 100"
Cohesion: 0.09
Nodes (33): _compute_mcmc_safe_d0_component(), compute_mcmc_safe_initial_values(), effective_seed(), _extract_adapt_states(), _extract_step_sizes(), from_config(), from_plan(), is_healthy() (+25 more)

### Community 101 - "Community 101"
Cohesion: 0.07
Nodes (30): CMCResult, as_array(), cmc_result_summary_table(), cmc_result_to_arviz(), compare_cmc_nlsq(), from_mcmc_samples(), merge_shard_cmc_results(), n_params() (+22 more)

### Community 102 - "Community 102"
Cohesion: 0.06
Nodes (36): _compute_bfmi(), Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Convert a _run_shard_worker result dict to a CMCResult.      Workers return raw, Compute BFMI from ArviZ InferenceData, returning (bfmi, failed).      Args:, Convert a _run_shard_worker result dict to a CMCResult.      Workers return raw (+28 more)

### Community 103 - "Community 103"
Cohesion: 0.07
Nodes (26): combine_shard_samples(), combine_shard_samples_bimodal(), Combine raw posterior samples from multiple CMC shards.      Homodyne CMC parity, Combine raw posterior samples from multiple CMC shards.      Homodyne CMC parity, Mode-aware combination — cluster shards by posterior mode then combine within cl, Mode-aware combination — cluster shards by posterior mode then combine within cl, filter_by_phi(), PhiAngleFilter (+18 more)

### Community 104 - "Community 104"
Cohesion: 0.1
Nodes (30): _make_args(), _make_nlsq_result(), Unit tests for heterodyne.cli.optimization_runner module., run_nlsq forwards full N×N 2-D data to the fitter — no trim, no sync., run_nlsq excludes the leading time point before fitting 2D data., run_nlsq matches normalized target angles to raw detector angles., run_nlsq matches normalized target angles to raw detector angles., Build a minimal NLSQResult for testing. (+22 more)

### Community 105 - "Community 105"
Cohesion: 0.08
Nodes (20): generate_lhs_starts(), Generate Latin Hypercube starting points, excluding fixed dimensions.      Fixed, Generate Latin Hypercube starting points, excluding fixed dimensions.      Fixed, Tests for the standalone generate_lhs_starts utility., Output shape is exactly (n_starts, n_params)., All generated points satisfy lower <= x <= upper., Zero-volume dimensions (lower == upper) are constant across all starts., Different seeds produce different starting points. (+12 more)

### Community 106 - "Community 106"
Cohesion: 0.08
Nodes (21): Tests for NLSQ fit quality validation., Tests for FitQualityValidator., Normal chi-squared passes., Very high chi-squared triggers warning., Extreme chi-squared triggers error., Parameter at bound edge triggers warning., TestFitQualityValidator, FitQualityValidator (+13 more)

### Community 107 - "Community 107"
Cohesion: 0.07
Nodes (33): _check_registry_spec_sync(), estimate_per_angle_scaling(), extract_nlsq_values_for_cmc(), NLSQ-informed prior construction for heterodyne CMC analysis.  Builds NumPyro di, Validate that init-values key order matches the expected parameter order.      H, Walk registry vs ``_DEFAULT_PRIOR_SPECS``; raise on drift.      Inlined sync che, Validate that init-values key order matches the expected parameter order.      H, Run the construction-time dual-prior sync gate (CLAUDE.md Rule 9).      Built as (+25 more)

### Community 108 - "Community 108"
Cohesion: 0.06
Nodes (9): ParameterIndexMapper, Convert a full-array index to a varying-array index.          Args:, Convert a varying-array index to a full-array index.          Args:, Get the parameter name for a varying-array index.          Args:             var, Look up the varying-array index for a parameter name.          Args:, Check whether a varying parameter uses log-transform.          Args:, Map parameter indices between full, varying, and optimizer spaces.      Paramete, Tests for ParameterIndexMapper. (+1 more)

### Community 109 - "Community 109"
Cohesion: 0.07
Nodes (20): Extract parameter uncertainties from a covariance matrix safely.      Handles si, safe_uncertainties_from_pcov(), Tests for safe_uncertainties_from_pcov()., TestSafeUncertaintiesFromPcov, _extract_n_points(), _extract_nlsq_settings(), NLSQWrapper, NLSQWrapper — stable fallback adapter for heterodyne XPCS optimization.  Role an (+12 more)

### Community 110 - "Community 110"
Cohesion: 0.06
Nodes (30): CMCConfig, Comprehensive configuration for Consensus Monte Carlo (CMC) analysis.      CMC s, Comprehensive configuration for Consensus Monte Carlo (CMC) analysis.      CMC s, Normalise string-valued enable flag and log construction., Normalise string-valued enable flag and log construction., Normalise string-valued enable flag and log construction., Run comprehensive field validation and return a list of error strings., Run comprehensive field validation and return a list of error strings. (+22 more)

### Community 111 - "Community 111"
Cohesion: 0.06
Nodes (18): Tests for ParameterRegistry class., len(registry) returns 16 (14 physics + 2 scaling)., __getitem__ returns ParameterInfo for valid name., __getitem__ raises KeyError for invalid name., __iter__ yields names in canonical order (including scaling)., get_defaults returns dict of default values., get_bounds returns lower and upper bounds lists., get_group returns ParameterInfo list for reference group. (+10 more)

### Community 112 - "Community 112"
Cohesion: 0.1
Nodes (15): GradientMonitor, GradientSnapshot, history(), n_records(), Gradient quality monitoring for NLSQ optimization.  Tracks gradient statistics a, Check whether recent gradients have exploded.          Exploding gradients can c, Summarize gradient history.          Returns:             Dictionary with keys:, Single-iteration gradient statistics.      Attributes:         iteration: Optimi (+7 more)

### Community 113 - "Community 113"
Cohesion: 0.07
Nodes (30): _create_shards(), _create_shards_contiguous(), Partition correlation data into shards for Consensus Monte Carlo.      Two strat, Partition correlation data into shards for Consensus Monte Carlo.      Two strat, Partition correlation data into shards for Consensus Monte Carlo.      Two strat, Partition correlation data into shards for Consensus Monte Carlo.      Two strat, Partition correlation data into shards for Consensus Monte Carlo.      Two strat, Partition correlation data into shards for Consensus Monte Carlo.      Two strat (+22 more)

### Community 114 - "Community 114"
Cohesion: 0.06
Nodes (34): Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t, Convenience wrapper around :func:`fit_cmc_jax` (homodyne parity).      Accepts t (+26 more)

### Community 115 - "Community 115"
Cohesion: 0.06
Nodes (34): _extract_credible_intervals(), _extract_posterior_stats(), Extract mean, std, R-hat, ESS-bulk, ESS-tail from an ArviZ summary.      Falls b, Extract 95 % credible intervals from ArviZ summary or raw samples.      Args:, Extract mean, std, R-hat, ESS-bulk, ESS-tail from an ArviZ summary.      Falls b, Extract mean, std, R-hat, ESS-bulk, ESS-tail from an ArviZ summary.      Falls b, Extract mean, std, R-hat, ESS-bulk, ESS-tail from an ArviZ summary.      Falls b, Extract 95 % credible intervals from ArviZ summary or raw samples.      Args: (+26 more)

### Community 117 - "Community 117"
Cohesion: 0.09
Nodes (12): MinimalLogger, Configurable logger manager for the heterodyne package.      Thread-safe singlet, Configurable logger manager for the heterodyne package.      Thread-safe singlet, Configurable logger manager for the heterodyne package.      Thread-safe singlet, Configurable logger manager for the heterodyne package.      Thread-safe singlet, Tests for MinimalLogger singleton., max_size_mb=0 should use plain FileHandler., When file directory can't be created, file logging is skipped. (+4 more)

### Community 118 - "Community 118"
Cohesion: 0.13
Nodes (34): CV-Based Adaptive Regularization, AntiDegeneracyController, 4-Layer Anti-Degeneracy Defense, NLSQ API Reference (RST), ChunkedStrategy, CMAESWrapper / fit_with_cmaes, OptimizationStrategy fallback chain, fit_nlsq_jax / fit_nlsq_multi_phi (+26 more)

### Community 119 - "Community 119"
Cohesion: 0.06
Nodes (13): Tests for JAX Float64 precision configuration.  Bug Prevented: JAX Float64 Preci, Tests for heterodyne import behavior., Tests for computation output dtypes., Tests for numeric precision requirements., Regression tests for JAX Float64 Precision bug.      BUG DESCRIPTION:     JAX de, Tests for JAX x64 configuration state., Tests for default array dtypes., TestArrayDtypes (+5 more)

### Community 120 - "Community 120"
Cohesion: 0.1
Nodes (19): _make_result(), Tests for heterodyne.optimization.nlsq.validation.bounds., A larger edge fraction should flag more values., Value exactly at lower bound should not be an ERROR (just possibly edge)., Create a minimal NLSQResult for validation testing., Tests for BoundsValidator., Parameters well within bounds should produce no errors or warnings., Parameter outside bounds should produce an ERROR. (+11 more)

### Community 121 - "Community 121"
Cohesion: 0.1
Nodes (14): n_records(), ProgressRecord, ProgressTracker, Optimization progress tracking for NLSQ fitting.  Provides callback-compatible p, Check whether optimization progress has stalled.          Stall is declared when, Return a copy of the full progress history.          Returns:             List o, Generate a human-readable progress summary.          Returns:             Multi-, Single iteration progress snapshot.      Attributes:         iteration: Iteratio (+6 more)

### Community 122 - "Community 122"
Cohesion: 0.09
Nodes (22): apply_recovery(), diagnose_error(), diagnose_failure(), ErrorDiagnosis, Recovery mechanisms for failed NLSQ optimization.  Provides retry logic with pro, Diagnosis of an optimization error.      Attributes:         category: Error cat, Possible corrective actions after an optimization failure., Recommended corrective action with an explanation.      Attributes:         acti (+14 more)

### Community 123 - "Community 123"
Cohesion: 0.15
Nodes (13): NLSQValidationConfig, Thresholds used when validating post-fit quality metrics.      Attributes:, Thresholds used when validating post-fit quality metrics.      Attributes:, Thresholds used when validating post-fit quality metrics.      Attributes:, _make_result(), Tests for heterodyne.optimization.nlsq.validation.result., Tests for ResultValidator., Failed result should not check chi2 or uncertainties. (+5 more)

### Community 124 - "Community 124"
Cohesion: 0.11
Nodes (29): ensure_directory(), Path validation and filesystem utilities., Resolve path to absolute, expanding user and symlinks.      Args:         path:, Validate that a file exists and is readable.      Args:         path: Path to va, Validate and prepare output path.      Args:         path: Output path to valida, Ensure directory exists, creating if necessary.      Args:         path: Directo, resolve_path(), validate_file_exists() (+21 more)

### Community 125 - "Community 125"
Cohesion: 0.07
Nodes (19): PriorDistribution, Prior distribution specification for a parameter., Prior distribution specification for a parameter., Tests for config/parameter_space.py module.  Covers validate, from_config, Prior, to_numpyro uses default rate for exponential., Tests for PriorType enum., PriorType has expected values., Tests for PriorDistribution class. (+11 more)

### Community 126 - "Community 126"
Cohesion: 0.07
Nodes (29): Unit tests for the XPCS data loading and validation API.  Tests are self-contain, The heterodyne.data package imports without error., Tests for validate_weights., Non-negative weights with correct shape return no errors., Weights with wrong shape return an error., XPCSDataLoader and load_xpcs_data are importable from the package., Loader-side correction uses the same symmetric side-band average as homodyne., Loader helper accepts homodyne 'basic'/'interpolation' method names. (+21 more)

### Community 127 - "Community 127"
Cohesion: 0.12
Nodes (28): _compute_data_statistics(), _compute_quality_score(), DataQualityReport, Data validation and quality checks for XPCS data., Validate time array consistency with correlation data.      Args:         t: Tim, Report of data quality validation results., Level of validation to perform., A single validation finding with structured metadata. (+20 more)

### Community 128 - "Community 128"
Cohesion: 0.14
Nodes (17): plot_arviz_posterior(), Plot posterior distributions using ArviZ.      Args:         result: CMC result, _close_figures(), _make_cmc_result(), _make_mock_axes_array(), _make_mock_idata(), Unit tests for heterodyne.viz.mcmc_arviz module., Verify to_inference_data delegates to cmc_result_to_arviz. (+9 more)

### Community 129 - "Community 129"
Cohesion: 0.11
Nodes (30): generate_diagnostic_plots(), _physical_var_names(), plot_autocorr(), plot_diagnostics_summary(), plot_energy(), plot_ess(), plot_forest(), plot_pair_plot() (+22 more)

### Community 130 - "Community 130"
Cohesion: 0.06
Nodes (30): code:block1 (c2(t1, t2) = offset + contrast * [ref_term + sample_term + c), code:block10 (HeterodyneModelBase (ABC)), code:python (log_half_tr = -0.5 * q**2 * J_integral), code:block2 (J_rate(t) = D0 * t^alpha + D_offset     (clipped to >= 0)), code:block3 (J_integral[i, j] = | ∫_{t_i}^{t_j} J_rate(t') dt' |), code:python (midpoints = (J_rate[:-1] + J_rate[1:]) / 2.0), code:block5 (f_s(t) = clip(f0 * exp(f1 * (t - f2)) + f3, 0, 1)), code:python (exponent = clip(f1 * (t - f2), -100, 100)) (+22 more)

### Community 131 - "Community 131"
Cohesion: 0.1
Nodes (32): AdaptiveChunker, filter_by_angle_range / select_single_angle, I/O Utilities API Reference (RST), AsyncWriter, dispatch_command (CLI orchestrator), main / main_hexp / main_hsim (CLI entry), run_nlsq / run_cmc (optimization_runner), build_default_priors / build_log_space_priors (+24 more)

### Community 132 - "Community 132"
Cohesion: 0.15
Nodes (29): configure_xla_mode(), detect_shell_type(), get_venv_path(), install_completion_activation(), _install_completion_bash_activation(), _install_completion_fish_activation(), install_fish_completion(), install_shell_completion() (+21 more)

### Community 133 - "Community 133"
Cohesion: 0.09
Nodes (28): cleanup(), consensus_mc(), estimate_memory(), get_capabilities(), MCMCBackend, Abstract base and factory for MCMC execution backends.  Includes Consensus Monte, Select the appropriate MCMC backend.      Selection order (mirrors homodyne ``se, Select the appropriate MCMC backend.      Selection order (mirrors homodyne ``se (+20 more)

### Community 134 - "Community 134"
Cohesion: 0.07
Nodes (25): NUTSSampler, High-level NUTS sampler wrapping NumPyro's MCMC.      Manages kernel constructio, High-level NUTS sampler wrapping NumPyro's MCMC.      Manages kernel constructio, Run MCMC sampling.          If ``init_params`` are provided, small random pertur, Run MCMC sampling.          If ``init_params`` are provided, small random pertur, Run MCMC seeded from NLSQ warm-start values.          Validates that the initial, Run MCMC seeded from NLSQ warm-start values.          Validates that the initial, Run MCMC seeded from NLSQ warm-start values.          Validates that the initial (+17 more)

### Community 135 - "Community 135"
Cohesion: 0.09
Nodes (30): BimodalConsensusResult type, Bimodal detection min_weight/min_separation postconditions, check_convergence() high-level helper, CMC Fitting Architecture, CMC io.py full save pipeline, CMCResult.chi_squared field, CMCResult per-angle contrast/offset fields, CMCResult.convergence_status field (+22 more)

### Community 136 - "Community 136"
Cohesion: 0.07
Nodes (12): Documentation content validation tests.  Ensures that documentation files exist,, Verify master template contains required sections., CLAUDE.md documents analyzer_parameters config section., Verify master template contains required sections., Verify master template contains required sections., Verify essential documentation files are present., Verify CLAUDE.md references key project concepts., Verify CLAUDE.md references key project concepts. (+4 more)

### Community 137 - "Community 137"
Cohesion: 0.12
Nodes (28): _ap(), cache_compression(), cache_file_path(), cache_filename_template(), cmc_config(), data_file_path(), data_folder_path(), dt() (+20 more)

### Community 138 - "Community 138"
Cohesion: 0.1
Nodes (15): compute_parameter_sensitivity(), format_parameter_table(), perturb_parameters(), Parameter manipulation utilities for NLSQ optimization.  Provides helper functio, Pretty-print a parameter table.      Produces a human-readable multi-line table, Add random perturbation to parameters, staying within bounds.      Each paramete, Compute parameter sensitivity via finite-difference perturbation.      For each, mapper() (+7 more)

### Community 139 - "Community 139"
Cohesion: 0.07
Nodes (22): BackendCapabilities, Static description of what an MCMC backend can do.      Used by the backend sele, Static description of what an MCMC backend can do.      Used by the backend sele, Return CPU backend capabilities.          The CPU backend runs chains sequential, Return CPU backend capabilities.          The CPU backend runs chains sequential, Return CPU backend capabilities.          The CPU backend runs chains sequential, Return multiprocessing backend capabilities.          Returns:             :clas, Return multiprocessing backend capabilities.          Returns:             :clas (+14 more)

### Community 140 - "Community 140"
Cohesion: 0.09
Nodes (27): diffusion_coefficient(), get_default_bounds_array(), interpret_alpha(), PhysicsConstants, Physical constants, parameter bounds, and validation for heterodyne model., Get default bounds as arrays in canonical parameter order.      Returns:, Physical interpretation of transport parameters.      Transport coefficient: J(t, Result of parameter validation with detailed error reporting.      Attributes: (+19 more)

### Community 141 - "Community 141"
Cohesion: 0.07
Nodes (19): AntiDegeneracyController, Orchestrator for the 4-Layer Anti-Degeneracy Defense System.      This controlle, Detect and report parameter degeneracies.      Performs three classes of checks, Transform per-angle parameters to Fourier coefficients.          Parameters, Create callbacks for NLSQ's CurveFit integration.          Returns a dict of cal, Create kwargs for NLSQ's HybridStreamingConfig.          Returns kwargs that can, Create kwargs for NLSQ's HybridStreamingConfig.          Returns kwargs that can, Get parameter group indices for variance regularization.          Returns the st (+11 more)

### Community 142 - "Community 142"
Cohesion: 0.09
Nodes (19): GradientCollapseDetector, Detect Jacobian collapse during iterative optimization.      Tracks the Frobeniu, Record the Frobenius norm of *jacobian* and check for collapse.          Args:, Clear accumulated norm history., Detect Jacobian collapse during iterative optimization.      Tracks the Frobeniu, Detect Jacobian collapse during iterative optimization.      Tracks the Frobeniu, Record the Frobenius norm of *jacobian* and check for collapse.          Args:, Record the Frobenius norm of *jacobian* and check for collapse.          Args: (+11 more)

### Community 143 - "Community 143"
Cohesion: 0.09
Nodes (22): compute_precision_analysis(), Compute precision metrics for each parameter's posterior.      For each paramete, Compute precision metrics for each parameter's posterior.      For each paramete, Compute precision metrics for each parameter's posterior.      For each paramete, Compute precision metrics for each parameter's posterior.      For each paramete, Compute precision metrics for each parameter's posterior.      For each paramete, Compute precision metrics for each parameter's posterior.      For each paramete, compute_precision_analysis returns the four expected keys per parameter. (+14 more)

### Community 144 - "Community 144"
Cohesion: 0.09
Nodes (22): compute_nlsq_comparison_metrics(), Compare posterior statistics against NLSQ point estimates.      For each paramet, Compare posterior statistics against NLSQ point estimates.      For each paramet, Compare posterior statistics against NLSQ point estimates.      For each paramet, Compare posterior statistics against NLSQ point estimates.      For each paramet, Compare posterior statistics against NLSQ point estimates.      For each paramet, Result of a bimodality test for a single parameter's samples.      Attributes:, compute_nlsq_comparison_metrics produces the expected keys and values. (+14 more)

### Community 145 - "Community 145"
Cohesion: 0.07
Nodes (20): ParameterManager, Get initial parameter values for optimization.          Returns the config-speci, Get initial parameter values for optimization.          Returns the config-speci, Get bounds for varying physics parameters.          Returns:             (lower,, Get bounds for varying physics parameters.          Returns:             (lower,, Extract varying parameters from full array.          Args:             full_para, Extract varying parameters from full array.          Args:             full_para, Update stored parameter values.          Args:             params: Either array (+12 more)

### Community 146 - "Community 146"
Cohesion: 0.1
Nodes (27): fit_nlsq_multi_phi(), Fit model to correlation data at multiple phi angles.      Two modes of operatio, Fit model to correlation data at multiple phi angles.      Two modes of operatio, multistart_config(), Additional tests for nlsq/core.py to improve coverage.  Covers: - fit_nlsq_jax w, Tests for nlsq import error fallback to scipy., Tests for fit_nlsq_multi_phi function (lines 223-251)., Tests for fit_nlsq_jax when config is None. (+19 more)

### Community 147 - "Community 147"
Cohesion: 0.07
Nodes (25): LPTScheduler, Longest Processing Time scheduler for load balancing across cores.      Assigns, Longest Processing Time scheduler for load balancing across cores.      Assigns, Initialise the LPT scheduler.          Args:             shard_costs: Estimated, Initialise the LPT scheduler.          Args:             shard_costs: Estimated, Longest Processing Time scheduler for load balancing across cores.      Assigns, Pop and return the next shard index to dispatch.          Returns:             N, Return the number of shards not yet dispatched. (+17 more)

### Community 148 - "Community 148"
Cohesion: 0.07
Nodes (25): compute_log_likelihood_elementwise(), compute_sharded_log_likelihood_elementwise(), prepare_shards_elementwise(), Compute Gaussian log-likelihood via element-wise path (CMC primary).      Uses p, Compute Gaussian log-likelihood via element-wise path (CMC primary).      Uses p, Compute Gaussian log-likelihood via element-wise path (CMC primary).      Uses p, Compute Gaussian log-likelihood via element-wise path (CMC primary).      Uses p, Sum log-likelihoods across shards via element-wise path (production).      Each (+17 more)

### Community 149 - "Community 149"
Cohesion: 0.08
Nodes (19): _make_inputs(), _make_params(), compute_residuals second call is faster than first., trapezoid_cumsum JIT compiles and caches., Verify core functions can be traced by jax.jit without errors., jax.jit(compute_c2_heterodyne) executes without error., jax.jit(smooth_abs) executes without error on typical inputs., jax.jit(create_time_integral_matrix) executes without error. (+11 more)

### Community 150 - "Community 150"
Cohesion: 0.12
Nodes (17): CPUInfo, _parse_lscpu(), Parse lscpu output to extract CPU information., Parse lscpu output to extract CPU information., Parse lscpu output to extract CPU information., CPU hardware information.      Attributes:         physical_cores: Number of phy, CPU hardware information.      Attributes:         physical_cores: Number of phy, amd_cpu() (+9 more)

### Community 151 - "Community 151"
Cohesion: 0.1
Nodes (19): DegeneracyCheck, detect_hierarchical_trigger(), Run all degeneracy checks on a fit result.          Args:             result: Co, Decide whether to invoke the hierarchical fitting strategy.      Returns ``True`, Decide whether to invoke the hierarchical fitting strategy.      Returns ``True`, Check for highly correlated parameter pairs., Check for parameters sitting at their bounds., Check for cost plateau (many iterations, negligible improvement). (+11 more)

### Community 152 - "Community 152"
Cohesion: 0.11
Nodes (26): apply_config_defaults(), ConfigValidationResult, create_example_yaml_config(), load_json_config(), load_yaml_config(), migrate_json_to_yaml_config(), Data configuration for XPCS loading and preprocessing., Result of validating an XPCS configuration dictionary.      Attributes: (+18 more)

### Community 153 - "Community 153"
Cohesion: 0.07
Nodes (18): Tests for DEFAULT_REGISTRY module constant., DEFAULT_REGISTRY is a ParameterRegistry instance., DEFAULT_REGISTRY contains all 16 parameters., DEFAULT_REGISTRY has correct D0_ref bounds., DEFAULT_REGISTRY has correct alpha bounds (widened to [-5, 5] to support sub-dif, DEFAULT_REGISTRY has correct fraction parameter bounds., DEFAULT_REGISTRY has correct fraction parameter bounds., DEFAULT_REGISTRY has sensible vary_default flags. (+10 more)

### Community 154 - "Community 154"
Cohesion: 0.11
Nodes (12): flatten_upper_triangle(), Data preparation for NLSQ fitting.  Converts correlation matrices and weights in, Flatten the upper triangle of a symmetric matrix.      For a two-time correlatio, Flatten the upper triangle of a symmetric matrix.      For a two-time correlatio, Reconstruct symmetric matrix from upper-triangle values.      Args:         flat, Reconstruct symmetric matrix from upper-triangle values.      Args:         flat, unflatten_upper_triangle(), Tests for heterodyne.optimization.nlsq.data_prep. (+4 more)

### Community 155 - "Community 155"
Cohesion: 0.07
Nodes (23): LPTScheduler, Longest Processing Time scheduler for load balancing across cores.      Assigns, Longest Processing Time scheduler for load balancing across cores.      Assigns, Initialise the LPT scheduler.          Args:             shard_costs: Estimated, Initialise the LPT scheduler.          Args:             shard_costs: Estimated, Pop and return the next shard index to dispatch.          Returns:             N, Longest Processing Time scheduler for load balancing across cores.      Assigns, Pop and return the next shard index to dispatch.          Returns:             N (+15 more)

### Community 156 - "Community 156"
Cohesion: 0.08
Nodes (15): AdaptiveSamplingPlan, Sampling plan that adjusts warmup/sample counts based on shard size.      Wraps, Sampling plan that adjusts warmup/sample counts based on shard size.      Wraps, Sampling plan that adjusts warmup/sample counts based on shard size.      Wraps, Sampling plan that adjusts warmup/sample counts based on shard size.      Wraps, Return a :class:`SamplingPlan` adjusted for this shard.          Scaling is sub-, Return a :class:`SamplingPlan` adjusted for this shard.          Scaling is sub-, Return a :class:`SamplingPlan` adjusted for this shard.          Scaling is sub- (+7 more)

### Community 157 - "Community 157"
Cohesion: 0.1
Nodes (28): ArviZ Diagnostics (R-hat, ESS, BFMI), CMC / NUTS Sampler, create_time_integral_matrix, Analysis Data Flow Pipeline, Element-wise Path (CMC), core/jax_backend.py, Meshgrid Path (NLSQ), NLSQ Trust-Region Levenberg-Marquardt (+20 more)

### Community 158 - "Community 158"
Cohesion: 0.13
Nodes (25): _apply_basic_correction_numpy(), _apply_homodyne_statistical_correction_numpy(), _apply_interpolation(), _apply_linear_interpolation_correction_numpy(), _apply_standard_correction_numpy(), _apply_statistical_correction(), _apply_statistical_correction_jax(), _apply_statistical_correction_numpy() (+17 more)

### Community 159 - "Community 159"
Cohesion: 0.09
Nodes (20): _float_or_none(), Writers for MCMC/CMC analysis results., Return a JSON-serializable copy of metadata for tombstone failure records., Return a JSON-serializable copy of metadata for tombstone failure records., Save MCMC/CMC results to files.      Creates:     - {prefix}_summary.json: Param, Return float(x), or None if non-finite (NaN/Inf cannot serialize to JSON)., Save MCMC/CMC results to files.      Creates:     - {prefix}_summary.json: Param, Save MCMC/CMC results to files.      Creates:     - {prefix}_summary.json: Param (+12 more)

### Community 160 - "Community 160"
Cohesion: 0.09
Nodes (22): Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c, Check whether an NLSQ result is suitable for warm-starting CMC.      Validates c (+14 more)

### Community 161 - "Community 161"
Cohesion: 0.09
Nodes (18): ParameterSpace, UnifiedHeterodyneEngine, JAX-accelerated batch least squares solver.          Solves the 2x2 normal equat, NumPy fallback for batch least squares when JAX unavailable., Estimate contrast and offset via batch least squares.          Uses ``solve_leas, solve_least_squares_jax(), Tests for solve_least_squares_jax (batch 2x2 normal equations)., theory=data -> contrast~1, offset~0. (+10 more)

### Community 162 - "Community 162"
Cohesion: 0.11
Nodes (18): from_dict(), Configuration for CMC (Consensus Monte Carlo) analysis.  This module defines CMC, Asynchronous I/O, Structured Logging, Runtime utilities for heterodyne package., Tests for heterodyne.utils.async_io — PrefetchLoader and AsyncWriter.  Covers: -, _format_cmc_table(), _format_diagnostics() (+10 more)

### Community 163 - "Community 163"
Cohesion: 0.11
Nodes (26): get_heterodyne_pooled_model_for_mode(), _heterodyne_pooled_likelihood(), _heterodyne_sample_shared_physics(), Joint multi-phi heterodyne CMC model (homodyne parity).      Mirrors ``homodyne., Joint multi-phi heterodyne CMC model (homodyne parity).      Mirrors ``homodyne., Joint multi-phi CMC model with FIXED per-angle scaling.      Mirrors ``homodyne., Joint multi-phi CMC model with FIXED per-angle scaling.      Mirrors ``homodyne., # NOTE: jnp.clip has discontinuous gradient at bounds. (+18 more)

### Community 164 - "Community 164"
Cohesion: 0.14
Nodes (18): compute_c2_heterodyne_pooled(), Pooled-data c2 evaluator for joint multi-phi CMC (homodyne parity).      Thin sh, _build_pooled_indices(), _gather_vmap_reference(), _random_params(), Numerical parity between vmap+gather and pooled c2 kernels (Phase 4).  Phase 4 o, Vmap+gather reference: builds (n_phi, N, N) stack then gathers., The pooled kernel must agree with the vmap+gather reference path to     within f (+10 more)

### Community 165 - "Community 165"
Cohesion: 0.08
Nodes (10): API compatibility tests for heterodyne public interface.  Ensures the public API, Verify optimization entry points have stable signatures., Verify all __all__ exports are importable., Verify HAS_* flags are booleans., Verify HAS_* flags are booleans., Verify core classes have expected methods and attributes., TestCoreClassSignatures, TestModuleAvailability (+2 more)

### Community 166 - "Community 166"
Cohesion: 0.12
Nodes (7): ParameterStats, Hybrid mapping/sequence for posterior summaries.      Supports dict-style access, _make_cmc_result(), Tests for CMC diagnostics additions in diagnostics.py.  Covers: - :class:`Bimoda, TestGetPosteriorStats, TestGetSamplesArray, TestParameterStats

### Community 167 - "Community 167"
Cohesion: 0.08
Nodes (19): Tests for ParameterSpace.from_config class method., from_config works with empty config., from_config works without 'parameters' key., from_config reads parameter values., from_config reads parameter bounds., Tests for ParameterSpace.from_config class method., from_config works with empty config., from_config works without 'parameters' key. (+11 more)

### Community 168 - "Community 168"
Cohesion: 0.13
Nodes (16): BackendError, ConvergenceError, NLSQConvergenceError, OptimizationError, Exception hierarchy for optimization errors.  Provides structured error types fo, Generic convergence failure (not NLSQ-specific).      Attributes:         iterat, Result validation failure.      Attributes:         validation_type: Category of, Streaming or chunked optimization failure.      Attributes:         chunk_index: (+8 more)

### Community 169 - "Community 169"
Cohesion: 0.12
Nodes (14): Return per-device init slice for the chain block ``[start, start+count)``., _slice_init_params(), combine_shard_samples(), Multi-device parallel MCMC backend using JAX sharding.  Distributes NUTS chains, Combine posterior samples from multiple device shards.      Concatenates sample, Return per-device init slice for the chain block ``[start, start+count)``., Run NUTS sampling distributed across multiple devices.          Splits chains ac, _slice_init_params() (+6 more)

### Community 170 - "Community 170"
Cohesion: 0.1
Nodes (22): dispatch_command(), Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op, Dispatch to appropriate analysis command.      Supports ``--plot-only`` (skip op (+14 more)

### Community 171 - "Community 171"
Cohesion: 0.1
Nodes (24): _generate_cmc_diagnostic_plots(), _load_data(), Command dispatch for heterodyne CLI., Unified optimization dispatcher.      Runs NLSQ and/or CMC based on *method* and, Unified optimization dispatcher.      Runs NLSQ and/or CMC based on *method* and, Unified optimization dispatcher.      Runs NLSQ and/or CMC based on *method* and, Generate CMC-specific diagnostic plots for each result.      Imports ``plot_conv, Generate CMC-specific diagnostic plots for each result.      Imports ``plot_conv (+16 more)

### Community 172 - "Community 172"
Cohesion: 0.13
Nodes (5): AsyncWriter, Asynchronous file writer for NumPy arrays and JSON data.      All writes are dis, Asynchronous file writer for NumPy arrays and JSON data.      All writes are dis, Tests for asynchronous file writer., TestAsyncWriter

### Community 173 - "Community 173"
Cohesion: 0.1
Nodes (19): CMAESWrapper, CMAESWrapperConfig, fit_with_cmaes(), _format_bounds_summary(), CMA-ES optimization wrapper for heterodyne parameter fitting.  Provides a deriva, Convenience function to run CMA-ES from a scalar objective.      Applies adaptiv, Run CMA-ES optimization.          Args:             objective_fn: Scalar objecti, Run CMA-ES optimization.          Args:             objective_fn: Scalar objecti (+11 more)

### Community 174 - "Community 174"
Cohesion: 0.17
Nodes (23): cleanup_completion_files(), cleanup_xla_activation_scripts(), cleanup_xla_config(), CleanupTarget, find_cleanup_targets(), get_venv_path(), interactive_cleanup(), main() (+15 more)

### Community 175 - "Community 175"
Cohesion: 0.1
Nodes (24): _gradient_bearing_source_files(), _iter_clip_lines(), _iter_op_lines(), _physics_source_files(), Lint test: no gradient-killing ops on gradient-bearing physics tensors.  CLAUDE., Find gradient-bearing files in heterodyne/core/.      Includes the original phys, Yield ``(lineno, line)`` for every line in ``path`` containing     ``op_token``, Yield ``(lineno, line)`` for every line in ``path`` containing     ``op_token`` (+16 more)

### Community 176 - "Community 176"
Cohesion: 0.11
Nodes (16): compute_t_ref(), Compute reference time as geometric mean of dt and t_max.      t_ref = sqrt(dt *, Tests for compute_t_ref()., t_ref = sqrt(dt * t_max)., Verify geometric mean property., Negative dt without fallback raises., Negative dt with fallback returns fallback., Zero t_max without fallback raises. (+8 more)

### Community 177 - "Community 177"
Cohesion: 0.11
Nodes (13): Tests for compute_numerical_jacobian., Jacobian of a linear residual has shape (n_residuals, n_params)., Jacobian of r(x) = x - c is the identity matrix., Jacobian of quadratic residual has shape (n_data, n_params)., Jacobian values are all finite for a well-behaved function., Custom step sizes produce a valid (finite) Jacobian., Mismatched step_sizes shape raises ValueError., TestComputeNumericalJacobian (+5 more)

### Community 178 - "Community 178"
Cohesion: 0.13
Nodes (15): build_result_from_scipy(), Construct NLSQResult from scipy.optimize.least_squares output.      Args:, Map scipy least_squares status codes to human-readable reasons., Construct NLSQResult from scipy.optimize.least_squares output.      Args:, Map scipy least_squares status codes to human-readable reasons., _status_to_reason(), _make_scipy_result(), _MockOptimizeResult (+7 more)

### Community 179 - "Community 179"
Cohesion: 0.13
Nodes (16): preprocess_correlation(), preprocess_xpcs_data(), PreprocessingPipeline, Convenience function for comprehensive XPCS preprocessing.      Builds a :class:, Convenience function for comprehensive XPCS preprocessing.      Builds a :class:, Add baseline subtraction step.          Args:             baseline: Baseline val, Add value clipping step.          Args:             min_val: Minimum value, Add outlier removal step.          Args:             n_sigma: Number of standard (+8 more)

### Community 180 - "Community 180"
Cohesion: 0.12
Nodes (17): compute_averaged_scaling(), estimate_per_angle_scaling(), from_config(), n_scaling_params(), n_varying_scaling(), PerAngleScaling, Per-angle scaling utilities for heterodyne XPCS analysis.  Provides functions fo, Get full scaling parameter array.          Returns:             Array of shape ( (+9 more)

### Community 181 - "Community 181"
Cohesion: 0.12
Nodes (23): _plot_1d_experimental_data(), _plot_2d_experimental_data(), _plot_3d_experimental_data(), plot_correlation(), plot_diagonal_decay(), plot_experimental_data(), plot_fit_comparison(), plot_g1_components() (+15 more)

### Community 182 - "Community 182"
Cohesion: 0.12
Nodes (14): create_parser(), Argument parser for heterodyne CLI., Create argument parser for heterodyne CLI.      Returns:         Configured Argu, Validate parsed arguments.      Args:         args: Parsed arguments      Return, Validate parsed arguments.      Args:         args: Parsed arguments      Return, Validate parsed arguments.      Args:         args: Parsed arguments      Return, Validate parsed arguments.      Args:         args: Parsed arguments      Return, validate_args() (+6 more)

### Community 183 - "Community 183"
Cohesion: 0.1
Nodes (14): Unified heterodyne fitting engine with JAX acceleration.      Provides scaling e, Compute negative log-likelihood for heterodyne model.          Uses ``compute_c2, Validate fitting inputs.          Args:             data: Experimental data., Get parameter space information.          Returns         -------         dict, UnifiedHeterodyneEngine, Tests for UnifiedHeterodyneEngine., Engine constructs with default parameter space., ScaledFittingEngine is an alias for UnifiedHeterodyneEngine. (+6 more)

### Community 184 - "Community 184"
Cohesion: 0.09
Nodes (24): _build_reparam_model(), get_heterodyne_model_individual(), get_heterodyne_model_reparam(), NumPyro model definition for heterodyne Bayesian inference., Create NumPyro model with reparameterization for better sampling.      When NLSQ, Create NumPyro model with reparameterization for better sampling.      When NLSQ, Create NumPyro model with reparameterization for better sampling.      When NLSQ, # NOTE: jnp.clip has discontinuous gradient at bounds. (+16 more)

### Community 185 - "Community 185"
Cohesion: 0.14
Nodes (5): PrefetchLoader, Prefetches the next item from an iterable in a background thread.      The backg, Prefetches the next item from an iterable in a background thread.      The backg, Tests for the prefetch iterator wrapper., TestPrefetchLoader

### Community 186 - "Community 186"
Cohesion: 0.08
Nodes (14): Tests for AntiDegeneracyController creation and check methods., Default construction uses sensible threshold values., Tests for the active AntiDegeneracyController orchestrator., from_config() with minimal dict returns a valid controller., Custom thresholds are accepted without error., correlation_threshold <= 0 raises ValueError., enable=False produces a disabled controller., Negative bound_tolerance raises ValueError. (+6 more)

### Community 187 - "Community 187"
Cohesion: 0.08
Nodes (16): base_config_dict(), Characterization test for the active 4-layer anti-degeneracy controller.  Tests, Tests for create_nlsq_callbacks() active-loop integration., create_nlsq_callbacks() returns a dict (possibly empty if not enabled)., create_nlsq_callbacks() returns {} when controller is disabled., Minimal valid config dict for AntiDegeneracyConfig.from_dict()., All values in the callbacks dict are callable., Four equally-spaced phi angles in radians. (+8 more)

### Community 188 - "Community 188"
Cohesion: 0.15
Nodes (22): _check_chi_squared(), _check_condition_number(), _check_convergence_status(), _check_parameter_significance(), _check_physical_bounds(), _check_restart_metadata(), _classify_parameter_status(), _coerce_bool() (+14 more)

### Community 189 - "Community 189"
Cohesion: 0.11
Nodes (16): compress_to_varying(), expand_to_full(), log_mask(), n_varying(), ParameterTransform, Parameter transforms between model space and optimizer space.  Handles: - Expand, Transform optimizer parameters back to full model space.          Args:, Get bounds in optimizer space.          Returns:             (lower, upper) each (+8 more)

### Community 190 - "Community 190"
Cohesion: 0.12
Nodes (13): create_model(), Factory function that returns a model for the requested analysis mode.      Args, Factory function that returns a model for the requested analysis mode.      Args, Tests for create_model() factory and ReducedModel analysis modes., create_model('two_component') returns the full 14-param model., create_model('static_ref') returns a 3-param reference-only model., create_model('static_both') returns a 6-param model., Integration test: compute_correlation runs without error. (+5 more)

### Community 191 - "Community 191"
Cohesion: 0.09
Nodes (15): _make_fake_posterior(), Light integration tests for the CMC analysis pipeline.  These tests exercise the, compute_precision_analysis + compute_nlsq_comparison_metrics pipeline., Fake posterior samples flow through both diagnostic functions without error., NLSQ values for a subset of parameters produce a partial comparison., All HDI widths are positive for random Gaussian samples., Generate dict of fake posterior draws drawn from a Normal distribution.      Mea, CMCConfig can be instantiated and exposes the expected attributes. (+7 more)

### Community 192 - "Community 192"
Cohesion: 0.09
Nodes (17): Basic tests for heterodyne core functionality., Test model can be created from config., Tests for parameter management., Tests for parameter management., Test parameter name constants., Test ParameterSpace defaults., Test ParameterSpace defaults., Tests for NLSQ configuration. (+9 more)

### Community 193 - "Community 193"
Cohesion: 0.08
Nodes (15): Tests for NLSQ core functionality and JAX tracing.  Bug Prevented: JAX Tracing E, Tests to detect numpy operations in JAX code paths., Tests for the main fit_nlsq_jax function., Tests for JAX traceability of residual functions., Tests for residual output dtypes., Regression tests for JAX Tracing Error bug.      BUG DESCRIPTION:     Using nump, test_fit_nlsq_jax_returns_result(), test_fit_nlsq_jax_scipy_fallback() (+7 more)

### Community 194 - "Community 194"
Cohesion: 0.11
Nodes (14): configure_logging(), Configure logging for the heterodyne package.      Simple interface for configur, Configure logging for the heterodyne package.      Simple interface for configur, Configure logging for the heterodyne package.      Simple interface for configur, Tests for configure_logging function., TestConfigureLogging, configure_logging disables propagation to root logger., Tests for configure_logging function. (+6 more)

### Community 195 - "Community 195"
Cohesion: 0.1
Nodes (17): Tests for log_phase context manager., log_phase populates duration after context exit., log_phase populates memory_peak_gb when track_memory=True., log_phase does not swallow exceptions from the context body., Tests for log_phase context manager., log_phase populates duration after context exit., log_phase populates memory_peak_gb when track_memory=True., log_phase does not swallow exceptions from the context body. (+9 more)

### Community 196 - "Community 196"
Cohesion: 0.09
Nodes (16): compute_c2_theory(), High-level validated API for heterodyne correlation computation.      Wraps comp, High-level validated API for heterodyne correlation computation.      Wraps comp, Compute c2 with validation., Compute c2 with validation., Compute weighted residuals with validation., Compute weighted residuals with validation., Compute chi-squared goodness-of-fit statistic.          chi² = sum(residuals²) w (+8 more)

### Community 197 - "Community 197"
Cohesion: 0.1
Nodes (17): check_zero_volume_bounds(), Identify parameter dimensions with zero sampling volume.      A dimension has ze, Identify parameter dimensions with zero sampling volume.      A dimension has ze, Unit tests for AntiDegeneracyController and multi-start LHS utilities.  Tests th, Mismatched array lengths raise ValueError., Single element array with lower == upper → [0]., Tests for the standalone check_zero_volume_bounds utility., Dimensions where lower == upper are returned as fixed indices. (+9 more)

### Community 198 - "Community 198"
Cohesion: 0.09
Nodes (9): _materialise_extracts(), Tests for the diff/categorizer module., Write each ``filename -> payload`` pair as JSON under ``directory``., Identical extracts on both sides → empty gap list, no exceptions., Silent-skip regression guard: missing extracts must raise (not return [])., render_report must surface severity headers and stop hardcoding ``KEEP``., test_render_report_emits_severity_buckets_and_no_keep_hardcoding(), test_run_full_diff_raises_on_missing_extract() (+1 more)

### Community 199 - "Community 199"
Cohesion: 0.13
Nodes (12): build_default_priors_via_builder(), build_log_space_priors_via_builder(), PriorBuilder, Construct NumPyro priors from a parameter registry.      Args:         registry:, Build priors for the varying parameters in *param_space*.          Args:, Walk registry vs ``_DEFAULT_PRIOR_SPECS``; raise on drift.          Delegates to, Functional shim around :class:`PriorBuilder` for callers that     want a one-sho, Functional shim for the legacy log-space-only helper.      The construction-time (+4 more)

### Community 200 - "Community 200"
Cohesion: 0.11
Nodes (18): BoundsError, DegeneracyError, NumericalError, Generic numerical instability (NaN/Inf) detected.      Attributes:         detec, A parameter has hit its optimization bounds.      Attributes:         parameter_, Parameter degeneracy detected during optimization.      Attributes:         affe, Tests for optimization exception hierarchy., Verify inheritance and basic behavior of the exception classes. (+10 more)

### Community 201 - "Community 201"
Cohesion: 0.1
Nodes (18): PBSBackend, PBS/Torque backend for distributed CMC sampling.      Each data shard is submitt, PBS/Torque backend for distributed CMC sampling.      Each data shard is submitt, Serialize shard payload, write PBS script, and submit via qsub.          Args:, PBS/Torque backend for distributed CMC sampling.      Each data shard is submitt, Poll ``qstat`` until all jobs reach a terminal state.          Jobs absent from, Poll ``qstat`` until all jobs reach a terminal state.          Jobs absent from, Load the ``.npz`` result file written by the PBS worker. (+10 more)

### Community 202 - "Community 202"
Cohesion: 0.09
Nodes (17): CPUBackend, CPU-optimized MCMC execution backend.  Runs NUTS chains sequentially (one at a t, Verify that CPU resources are available for sampling.          Checks that at le, Verify that CPU resources are available for sampling.          Checks that at le, Verify that CPU resources are available for sampling.          Checks that at le, Estimate peak CPU memory for a single sequential chain.          Because chains, Estimate peak CPU memory for a single sequential chain.          Because chains, Estimate peak CPU memory for a single sequential chain.          Because chains (+9 more)

### Community 203 - "Community 203"
Cohesion: 0.09
Nodes (17): Run NUTS sampling with sequential chain execution.          Args:             mo, Run NUTS sampling with sequential chain execution.          Args:             mo, Run NUTS sampling with sequential chain execution.          Args:             mo, Run NUTS sampling for a single shard (standard CMCBackend contract).          Fo, Run NUTS sampling for a single shard (standard CMCBackend contract).          Fo, Run NUTS sampling for a single shard (standard CMCBackend contract).          Fo, Run NUTS sampling for a single shard (standard CMCBackend contract).          Fo, Get current parameter values as dictionary. (+9 more)

### Community 204 - "Community 204"
Cohesion: 0.13
Nodes (11): Validate that theoretical C2 values are physically reasonable.      Checks for N, Validate that theoretical C2 values are physically reasonable.      Checks for N, Validate that theoretical C2 values are physically reasonable.      Checks for N, Validate that theoretical C2 values are physically reasonable.      Checks for N, Validate that theoretical C2 values are physically reasonable.      Checks for N, validate_model_output(), Tests for validate_model_output()., Heterodyne C2 can be negative (velocity phase), down to -1.0. (+3 more)

### Community 205 - "Community 205"
Cohesion: 0.14
Nodes (23): ArviZ/NumPyro Import Patch, optimization/cmc/core.py, optimization/cmc/model.py, optimization/cmc/reparameterization.py, compute_t_ref(), Element-Wise Path for CMC, estimate_sigma(), fit_cmc_jax (+15 more)

### Community 206 - "Community 206"
Cohesion: 0.09
Nodes (12): Tests for CMCConfig sharding-related fields., Default num_shards is 'auto'., Can set num_shards to an explicit integer., num_shards=0 is caught by validate()., Default sharding_strategy is 'random'., All valid sharding strategies are accepted., Invalid sharding_strategy is caught by validate()., Default min_points_per_shard is 10_000. (+4 more)

### Community 207 - "Community 207"
Cohesion: 0.09
Nodes (16): Regression tests pinning the CMC NUTS-default contract.  Background — deep-RCA f, ``CMCConfig`` defaults must reach NUTS through ``SamplingPlan.from_config``., Pin the CMC default sampling configuration against the geometric     requirement, Pin the CMC default sampling configuration against the geometric     requirement, ``dense_mass=True`` on a 14-parameter model needs >= 100         warmup steps pe, ``dense_mass=True`` on a 14-parameter model needs >= 100         warmup steps pe, Default ``target_accept_prob`` must be >= 0.90 to keep step         size small e, Default ``target_accept_prob`` must be >= 0.90 to keep step         size small e (+8 more)

### Community 208 - "Community 208"
Cohesion: 0.15
Nodes (12): denormalize_from_unit_cube(), normalize_to_unit_cube(), Map parameter vector from physical bounds to the unit hypercube [0, 1].      Arg, Map parameter vector from physical bounds to the unit hypercube [0, 1].      Arg, Map parameter vector from the unit hypercube [0, 1] to physical bounds.      Thi, Map parameter vector from physical bounds to the unit hypercube [0, 1].      Arg, Map parameter vector from the unit hypercube [0, 1] to physical bounds.      Thi, x == denormalize(normalize(x)) for arbitrary bounded x. (+4 more)

### Community 209 - "Community 209"
Cohesion: 0.11
Nodes (17): adjust_covariance_for_bounds(), Scale a covariance matrix to account for parameter bounds ranges.      When para, Scale a covariance matrix to account for parameter bounds ranges.      When para, Scale a covariance matrix to account for parameter bounds ranges.      When para, Tests for adjust_covariance_for_bounds., Tests for adjust_covariance_for_bounds., Identity covariance with unit-range bounds → identity output., Identity covariance with unit-range bounds → identity output. (+9 more)

### Community 210 - "Community 210"
Cohesion: 0.15
Nodes (20): _apply_mode_filter(), generate_config(), get_template_path(), interactive_builder(), main(), _prompt(), Configuration file generator for heterodyne analysis., Filter config dict sections based on the requested mode.      Args:         conf (+12 more)

### Community 211 - "Community 211"
Cohesion: 0.09
Nodes (12): Tests for ParameterInfo dataclass., validate_value returns True for value within bounds., validate_value returns True at lower bound., validate_value returns True at upper bound., validate_value returns False below lower bound., validate_value returns False above upper bound., clip_value returns same value if within bounds., clip_value clips to lower bound. (+4 more)

### Community 212 - "Community 212"
Cohesion: 0.13
Nodes (15): Call *fn* and validate the result for NaN/Inf.      Args:         fn: Callable r, Validate an array for NaN/Inf values.      Args:         data: Array-like input., safe_compute(), validate_array(), Tests for optimization numerical validation utilities., test_clean_array_passes(), test_clean_result_returned(), test_empty_array_passes() (+7 more)

### Community 213 - "Community 213"
Cohesion: 0.12
Nodes (18): Return whether joint multi-angle scaling should be constant averaged., True when per-angle β,o must be FROZEN (homodyne `constant` parity)., True when β,o are averaged across angles and OPTIMIZED (homodyne `auto`)., Legacy union predicate; retained for backward compatibility.      True if EITHER, True when per-angle β,o must be FROZEN (homodyne `constant` parity)., True when per-angle β,o must be FROZEN (homodyne `constant` parity)., True when β,o are averaged across angles and OPTIMIZED (homodyne `auto`)., True when β,o are averaged across angles and OPTIMIZED (homodyne `auto`). (+10 more)

### Community 214 - "Community 214"
Cohesion: 0.12
Nodes (14): format_nlsq_summary(), Writers for NLSQ optimization results., Format NLSQ result as human-readable summary.      Args:         result: NLSQ fi, Format NLSQ result as human-readable summary.      Args:         result: NLSQ fi, Format NLSQ result as human-readable summary.      Args:         result: NLSQ fi, Format NLSQ result as human-readable summary.      Args:         result: NLSQ fi, Tests for format_nlsq_summary., Tests for format_nlsq_summary. (+6 more)

### Community 215 - "Community 215"
Cohesion: 0.12
Nodes (14): get_model_param_count(), Return total number of sampled parameters for the model.      Accounts for per-a, Return total number of sampled parameters for the model.      Accounts for per-a, Return total number of sampled parameters for the model.      Accounts for per-a, Return total number of sampled parameters for the model.      Accounts for per-a, Return total number of sampled parameters for the model.      Accounts for per-a, Return total number of sampled parameters for the model.      Accounts for per-a, Constant mode: same as auto (no additional per-angle params). (+6 more)

### Community 216 - "Community 216"
Cohesion: 0.11
Nodes (20): _default_params(), _nondegenerate_params(), Regression tests for parameter sensitivity.  Ensures that small perturbations to, +delta and -delta produce similar magnitude c2 changes., +delta and -delta produce similar magnitude c2 changes., Build the 14-element default parameter vector from the registry., Return (t, dt) for the small test grid., Flatten c2 output into a 1-D residual vector (model - 1). (+12 more)

### Community 217 - "Community 217"
Cohesion: 0.14
Nodes (13): _estimate_covariance_from_jac(), JITStrategy, _make_cache_key(), n_cached(), name(), JIT-compiled fitting strategy for medium datasets.  Uses JAX's ``jax.jit`` to pr, Build a hashable cache key for JIT compilation.      The key captures the array, JAX JIT-compiled residual and Jacobian for medium datasets.      Pre-compiles th (+5 more)

### Community 218 - "Community 218"
Cohesion: 0.16
Nodes (15): _build_chunk_slices(), ChunkedStrategy, _compute_chunk_size(), _estimate_available_memory_gb(), _estimate_covariance(), _evaluate_chunks(), from_config(), name() (+7 more)

### Community 219 - "Community 219"
Cohesion: 0.1
Nodes (17): CMAESResult, Detailed result container for a CMA-ES optimization run.      Attributes:, Detailed result container for a CMA-ES optimization run.      Attributes:, Result from CMA-ES optimization.      Matches homodyne's ``CMAESResult`` for str, Unit tests for CMA-ES wrapper utilities.  Focuses on CMAESResult, coordinate tra, Tests for the denormalize_from_unit_cube transform., Tests for the denormalize_from_unit_cube transform., 0 maps back to lower bound. (+9 more)

### Community 220 - "Community 220"
Cohesion: 0.1
Nodes (11): ParameterRegistry, Get default values for all parameters., Get (lower_bounds, upper_bounds) as lists., Get all parameters in a group., Get indices of parameters that vary in optimization., Get names of parameters that should be sampled in log-space., Get names of per-angle scaling parameters., Registry of all heterodyne model parameters with metadata. (+3 more)

### Community 221 - "Community 221"
Cohesion: 0.1
Nodes (14): AdapterConfig, NLSQAdapterBase, Validate input arrays for consistency.          Parameters         ----------, Abstract base class for NLSQ optimization adapters.      Adapters wrap different, Build standardized result dictionary.          Parameters         ----------, Handle optimization errors gracefully.          Parameters         ----------, Abstract base class for NLSQ optimization adapters.      Provides shared methods, Setup parameter bounds arrays.          Parameters         ----------         pa (+6 more)

### Community 222 - "Community 222"
Cohesion: 0.15
Nodes (14): Shard pooled data into ~equal random subsets (homodyne parity).      Used when t, Shard pooled data with proportional per-angle coverage (homodyne parity).      P, shard_pooled_angle_balanced(), shard_pooled_random(), _make_imbalanced_pooled(), _make_pooled(), Build a PooledCMCData from a synthetic (n_phi, n, n) stack., Build a PooledCMCData with a different point count per angle.      Points are of (+6 more)

### Community 223 - "Community 223"
Cohesion: 0.11
Nodes (15): combine_shard_samples(), PjitBackend, Multi-device parallel MCMC backend using JAX sharding.  Distributes NUTS chains, Check that multiple devices are available for sharding.          Logs a warning, Estimate peak memory per device in GB.          Each device holds a fraction of, Check that multiple devices are available for sharding.          Logs a warning, Release resources. No-op for JAX-managed devices., Combine posterior samples from multiple device shards.      Concatenates sample (+7 more)

### Community 224 - "Community 224"
Cohesion: 0.15
Nodes (19): ConstraintRule, ConstraintSeverity, PhysicsViolation, Physics constraint validators for heterodyne parameters., Validate a single parameter against physics constraints.      Args:         para, Severity level for physics constraint violations., Validate constraints that span multiple parameters.      Cross-parameter checks:, Validate a single parameter against physics constraints.      Args:         para (+11 more)

### Community 225 - "Community 225"
Cohesion: 0.1
Nodes (16): Apply this configuration to the logging system.          Returns:             Pa, Apply this configuration to the logging system.          Returns:             Pa, Apply this configuration to the logging system.          Returns:             Pa, Apply this configuration to the logging system.          Returns:             Pa, Configure heterodyne logging.          Thread-safe configuration of the logging, Configure heterodyne logging.          Thread-safe configuration of the logging, Configure heterodyne logging.          Thread-safe configuration of the logging, Configure heterodyne logging.          Thread-safe configuration of the logging (+8 more)

### Community 226 - "Community 226"
Cohesion: 0.11
Nodes (14): effective_warmup_floor(), Return the safe warmup count, applying the Rule 12 floor when needed.      When, Scale warmup and sample counts for a given shard size.          When ``adaptive_, Scale warmup and sample counts for a given shard size.          When ``adaptive_, Scale warmup and sample counts for a given shard size.          When ``adaptive_, Scale warmup and sample counts for a given shard size.          When ``adaptive_, Scale warmup and sample counts for a given shard size.          When ``adaptive_, Scale warmup and sample counts for a given shard size.          When ``adaptive_ (+6 more)

### Community 227 - "Community 227"
Cohesion: 0.12
Nodes (18): AdaptiveSamplingPlan, CMCConfig, optimization/cmc/config.py, optimization/cmc/data_prep.py, CMC Fitting Architecture, optimization/cmc/io.py, optimization/cmc/sampler.py, optimization/cmc/scaling.py (+10 more)

### Community 228 - "Community 228"
Cohesion: 0.14
Nodes (12): make_model_mock(), Return a :class:`~unittest.mock.MagicMock` mimicking :class:`HeterodyneModel`., Validate :func:`make_model_mock` factory., Mock has a param_manager attribute., param_manager.varying_names returns a list of strings., varying_names follow canonical parameter order., get_initial_values returns array of correct length., get_bounds returns (lower, upper) tuple of correct shape. (+4 more)

### Community 229 - "Community 229"
Cohesion: 0.14
Nodes (12): make_nlsq_result(), Validate :func:`make_nlsq_result` factory., Default result reports success=True., Result contains the requested number of parameters., success=False produces a valid (non-converged) result., parameter_names is populated with canonical physics names., Uncertainties array matches parameter count., Covariance matrix is square with correct dimensions. (+4 more)

### Community 230 - "Community 230"
Cohesion: 0.12
Nodes (14): _make_model(), Scientific validation tests for heterodyne physics model.  Validates numerical c, Verify the 14-parameter model structure., Verify the 14-parameter model structure., Verify model produces physically correct results at known limits., Verify model is numerically stable under edge conditions., Verify model is numerically stable under edge conditions., test_c2_values_bounded() (+6 more)

### Community 231 - "Community 231"
Cohesion: 0.16
Nodes (10): Tests for the CMAESResult dataclass (homodyne-parity fields)., CMAESResult can be created with required fields., CMAESResult can be created with required fields., parameters array is accessible and has correct content., diagnostics dict stores generations and evaluations., covariance can be set to an ndarray., CMAESResult is frozen — attribute mutation raises AttributeError., nlsq_refined flag is stored correctly. (+2 more)

### Community 232 - "Community 232"
Cohesion: 0.12
Nodes (16): _apply_mirror(), _apply_nan_mask(), compute_diagonal_mask(), Set diagonal band to NaN., Compute a boolean mask for the diagonal band of a two-time matrix.      Returns, Replace diagonal band using matrix symmetry c2[i,j] = c2[j,i].      For the exac, Tests for compute_diagonal_mask., width=1 masks only the main diagonal. (+8 more)

### Community 233 - "Community 233"
Cohesion: 0.1
Nodes (12): Compute two-time heterodyne correlation.          Args:             params: Para, Get default parameter values as array., Convert parameter array to dictionary.          Args:             params: Parame, Convert parameter dictionary to array.          Args:             param_dict: Di, Compute reference g1 correlation only (1D visualization helper).          .. not, Compute sample g1 correlation only (1D visualization helper).          .. note::, Compute sample g1 correlation only (1D visualization helper).          .. note::, Compute sample fraction only.          Args:             params: Full parameter (+4 more)

### Community 234 - "Community 234"
Cohesion: 0.12
Nodes (13): Reduced heterodyne model with a subset of active parameters.      Inactive param, Reduced heterodyne model with a subset of active parameters.      Inactive param, Validate active params and precompute expansion constants., Validate active params and precompute expansion constants., Get default values for active parameters only., Expand active-parameter array to full 14-element array.          Uses precompute, Get default values for active parameters only., Expand active-parameter array to full 14-element array.          Uses precompute (+5 more)

### Community 235 - "Community 235"
Cohesion: 0.11
Nodes (16): Run NLSQ optimisation with automatic memory-based strategy routing.          Arg, Run NLSQ optimisation with automatic memory-based strategy routing.          Arg, Run NLSQ optimisation with automatic memory-based strategy routing.          Arg, Return ordered list of tiers to attempt, starting from initial_strategy., Return ordered list of tiers to attempt, starting from initial_strategy., Return ordered list of tiers to attempt, starting from initial_strategy., Attempt a single tier up to max_retries times.          Returns:             NLS, Attempt a single tier up to max_retries times.          Returns:             NLS (+8 more)

### Community 236 - "Community 236"
Cohesion: 0.14
Nodes (10): Returns a finite float for a generic well-conditioned Jacobian., Ill-conditioned Jacobian gives a large condition number., Tests for compute_jacobian_condition_number., Condition number of the identity Jacobian is 1., TestComputeJacobianConditionNumber, compute_jacobian_condition_number(), Compute the condition number of J^T @ J.      A large condition number indicates, Compute the condition number of J^T @ J.      A large condition number indicates (+2 more)

### Community 237 - "Community 237"
Cohesion: 0.1
Nodes (11): Builder for constructing result dictionaries.      Provides a fluent interface f, Set optimized parameters., Set parameter covariance matrix., Set number of data points., Set optimization start time., Set recovery actions taken., Set optimization info dict., Set stratification diagnostics. (+3 more)

### Community 238 - "Community 238"
Cohesion: 0.12
Nodes (16): Homodyne-parity validator for NLSQ optimization results.      Validates optimize, Homodyne-parity validator for NLSQ optimization results.      Validates optimize, Initialise ResultValidator.          Parameters         ----------         stric, Initialise ResultValidator.          Parameters         ----------         stric, Validate all result components.          Parameters         ----------         p, Validate all result components.          Parameters         ----------         p, Validate that optimized parameters are finite and within bounds.      Parameters, Validate that optimized parameters are finite and within bounds.      Parameters (+8 more)

### Community 239 - "Community 239"
Cohesion: 0.17
Nodes (5): _build_with(), Shell-injection hardening for the PBS backend (codex W5).  PBSConfig fields are, TestExtraDirectivesValidation, TestPBSConfigValidation, TestScriptGeneration

### Community 240 - "Community 240"
Cohesion: 0.11
Nodes (17): _cancel_job(), _query_job_state(), Return the PBS job-state letter for *job_id*, or ``None`` if purged.      Parses, Return the PBS job-state letter for *job_id*, or ``None`` if purged.      Parses, Send ``qdel`` to *job_id* (best-effort; errors are suppressed)., Send ``qdel`` to *job_id* (best-effort; errors are suppressed)., Submit per-shard PBS jobs, wait for completion, return combined samples., Submit per-shard PBS jobs, wait for completion, return combined samples. (+9 more)

### Community 241 - "Community 241"
Cohesion: 0.1
Nodes (14): Store raw bytes in a shared memory segment.          Args:             name: Log, Release shared memory and any other resources.          Idempotent — safe to cal, Release shared memory and any other resources.          Idempotent — safe to cal, Release shared memory and any other resources.          Idempotent — safe to cal, Serialise a trusted internal dict into shared memory.          Only used for ``C, Release shared memory and any other resources.          Idempotent — safe to cal, Place per-shard numpy arrays into packed shared memory.          Instead of crea, Create all shared memory allocations for worker data.          Called by :meth:` (+6 more)

### Community 242 - "Community 242"
Cohesion: 0.14
Nodes (12): MemoryMapManager, Manage memory-mapped access to large HDF5 datasets.      For datasets that excee, Return a cached read-only file handle, opening if necessary., Open an HDF5 dataset for memory-mapped-like access.          Returns the raw ``h, Read a specific slice from an HDF5 dataset without loading the full array., Eagerly load an HDF5 dataset into memory as an ``ndarray``.          Raises ``Me, Estimate the in-memory size of an HDF5 dataset without loading it.          Args, Read a specific slice from an HDF5 dataset without loading the full array. (+4 more)

### Community 244 - "Community 244"
Cohesion: 0.13
Nodes (18): _apply_parameter_overrides(), _build_mcmc_runtime_kwargs(), _configure_device(), _get_default_config(), _get_package_version(), load_and_merge_config(), Configuration loading and CLI override merging for heterodyne CLI., Apply CLI initial-parameter overrides into the config dict.      Implements homo (+10 more)

### Community 245 - "Community 245"
Cohesion: 0.1
Nodes (15): Set final convergence status.          Args:             status: Convergence sta, Increment warning counter., Set final convergence status (failure is sticky).          Once a failure status, Set final convergence status (failure is sticky).          Once a failure status, Set final convergence status (failure is sticky).          Once a failure status, Return True when the recorded status indicates a failed run., Return True when the recorded status indicates a failed run., Increment warning counter. (+7 more)

### Community 246 - "Community 246"
Cohesion: 0.13
Nodes (11): CMAESConfig, Configuration for CMA-ES optimization via the ``cma`` library.      Attributes:, Validate configuration values., Configuration for CMA-ES optimization.      Attributes:         sigma0: Initial, Validate configuration values., Validate configuration values., Tests for CMA-ES homodyne parity fixes.  Covers: - Fix #0: CMAES_AVAILABLE flag, Tests for CMAESConfig.diagonal_filtering. (+3 more)

### Community 247 - "Community 247"
Cohesion: 0.15
Nodes (15): BimodalConsensusResult, ModeCluster, Result of mode-aware consensus combination.      Attributes:         modes: Mode, A single mode from bimodal consensus combination.      Attributes:         mean:, A single mode from bimodal consensus combination.      Attributes:         mean:, Result of mode-aware consensus combination.      Attributes:         modes: Mode, A single mode from bimodal consensus combination.      Attributes:         mean:, A single mode from bimodal consensus combination.      Attributes:         mean: (+7 more)

### Community 248 - "Community 248"
Cohesion: 0.13
Nodes (14): apply_diagonal_correction_batch(), Apply diagonal correction to a batch of correlation matrices.      Args:, Tests for apply_diagonal_correction_batch., Batch input (k, N, N) returns same shape., Batch input (k, N, N) returns same shape., 2D input is treated as a single matrix., 2D input is treated as a single matrix., 1D input raises ValueError. (+6 more)

### Community 249 - "Community 249"
Cohesion: 0.14
Nodes (13): build_default_priors(), Build default priors from the parameter registry.      Uses ``prior_mean`` and `, Build default priors from the parameter registry.      Uses ``prior_mean`` and `, Build default priors from the parameter registry.      Uses ``prior_mean`` and `, Build default priors from the parameter registry.      Uses ``prior_mean`` and `, _make_space(), Regression tests for log-space prior integration (codex S1).  Two layers of prot, Confirm that switching to log-space priors doesn't move the posterior     mean b (+5 more)

### Community 250 - "Community 250"
Cohesion: 0.16
Nodes (10): clamp_params_to_interior(), clamp_to_interior(), Shift parameter values inward from hard bounds (raw-array path).      Lower-leve, Return a copy of *result* with parameters shifted inward from hard bounds., _make_result(), Regression tests for the public warm-start clamp API (P2-a).  Originally tested, The CLI's private ``_clamp_warmstart_to_interior`` must now forward     to the p, TestClampNLSQResult (+2 more)

### Community 251 - "Community 251"
Cohesion: 0.15
Nodes (13): _make_config(), Integration tests for error recovery and graceful degradation.  Tests that the N, Bounds where lower == upper for a parameter are handled gracefully., When all tiers fail, wrapper returns NLSQResult(success=False)., With enable_recovery=False, only the first tier is attempted., Return a minimal NLSQConfig for testing., Residual function: r = params - target., NLSQAdapter.fit returns failure results instead of raising. (+5 more)

### Community 252 - "Community 252"
Cohesion: 0.16
Nodes (12): _make_failed_result(), _make_mock_model(), _make_success_result(), Tests for core.py dual-adapter routing.  Verifies: 1. _fit_local uses NLSQAdapte, Return a minimal successful NLSQResult for mocking., Return a minimal failed NLSQResult for mocking., Build a minimal mock HeterodyneModel for _fit_local tests., test_fit_joint_multi_phi_fallback_to_wrapper() (+4 more)

### Community 253 - "Community 253"
Cohesion: 0.12
Nodes (13): FallbackInfo, FunctionEvaluationCounter, n_params(), OptimizationResult, params_dict(), Result container for NLSQ optimization.  Provides: - ``NLSQResult`` — primary he, Wraps a callable and counts invocations.      Useful for tracking the number of, Call the wrapped function and increment count. (+5 more)

### Community 254 - "Community 254"
Cohesion: 0.14
Nodes (11): build_result_from_arrays(), _compute_covariance(), Build NLSQResult from raw optimizer output.  Centralizes result construction so, Construct NLSQResult from raw arrays (for non-scipy backends).      Args:, Compute parameter covariance from Jacobian.      Uses the Gauss-Newton approxima, Construct NLSQResult from raw arrays (for non-scipy backends).      Args:, Compute parameter covariance from Jacobian.      Uses the Gauss-Newton approxima, Tests for build_result_from_arrays. (+3 more)

### Community 255 - "Community 255"
Cohesion: 0.16
Nodes (8): chi2_red near 1 should produce no messages., chi2_red between 2 and max_threshold triggers mediocre warning., Boundary: chi2 > 2.0 triggers mediocre., chi2_red between min_threshold and 0.5 triggers possible over-fit., TestCheckChiSquared, check_chi_squared(), Check reduced chi-squared is in a physically reasonable range.      Values well, Check reduced chi-squared is in a physically reasonable range.      Values well

### Community 256 - "Community 256"
Cohesion: 0.11
Nodes (8): checkpoint_dir(), Tests for checkpoint manager integrity enhancements., Create a sample checkpoint for testing., Provide a temporary checkpoint directory., Tests for CheckpointData integrity features., Legacy checkpoints without checksum should get one computed., sample_data(), TestCheckpointData

### Community 257 - "Community 257"
Cohesion: 0.13
Nodes (13): Tests for _clamp_warmstart_to_interior (5% boundary margin)., Tests for _clamp_warmstart_to_interior (5% boundary margin)., alpha_sample=-5 (lower hard bound) must be shifted to -4.5 (5% of range 10)., alpha_sample=-5 (lower hard bound) must be shifted to -4.5 (5% of range 10)., alpha_ref=5 (upper hard bound) must be shifted to 4.5 (5% of range 10)., alpha_ref=5 (upper hard bound) must be shifted to 4.5 (5% of range 10)., alpha_sample in the interior must not be modified., alpha_sample in the interior must not be modified. (+5 more)

### Community 258 - "Community 258"
Cohesion: 0.12
Nodes (16): _clamp_warmstart_to_interior(), CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, CLI wrapper for ``heterodyne.optimization.cmc.priors.clamp_to_interior``.      P, Regression tests for het_c7fb5859: _clamp_warmstart_to_interior must apply     f (+8 more)

### Community 259 - "Community 259"
Cohesion: 0.15
Nodes (11): make_synthetic_c2(), Return a synthetic two-time correlation matrix.      The matrix is symmetric pos, Validate :func:`make_synthetic_c2` factory., Output shape is (n_times, n_times)., Same seed produces identical data., Different seeds produce different data., No NaN or inf values in the output., Diagonal elements are strictly positive. (+3 more)

### Community 260 - "Community 260"
Cohesion: 0.16
Nodes (9): configure_jax_cpu(), Configure JAX for optimal CPU execution.      This should be called before impor, Warn when env-based JAX configuration is likely too late to take effect., Warn when env-based JAX configuration is likely too late to take effect., Configure JAX for optimal CPU execution.      This should be called before impor, Configure JAX for optimal CPU execution.      This should be called before impor, _warn_if_jax_already_imported(), TestConfigureJaxCpu (+1 more)

### Community 261 - "Community 261"
Cohesion: 0.16
Nodes (9): configure_cpu_hpc(), Configure environment variables for HPC CPU optimization.      This function set, Configure environment variables for HPC CPU optimization.      This function set, Configure environment variables for HPC CPU optimization.      This function set, With only one NUMA node, no NUMA-aware settings should be applied., With only one NUMA node, no NUMA-aware settings should be applied., AMD CPUs should get NUMA binding but not Intel KMP_ flags., AMD CPUs should get NUMA binding but not Intel KMP_ flags. (+1 more)

### Community 262 - "Community 262"
Cohesion: 0.16
Nodes (15): from_dict(), from_yaml(), HybridRecoveryConfig, Configuration for NLSQ optimization in the heterodyne analysis pipeline.  This m, Return scaled optimiser settings for a given retry attempt.          Args:, Return scaled optimiser settings for a given retry attempt.          Args:, Return scaled optimiser settings for a given retry attempt.          Args:, Convert *value* to float, returning *default* on failure.      Args:         val (+7 more)

### Community 263 - "Community 263"
Cohesion: 0.11
Nodes (13): Upper bound maps to 1., Fixed dimensions (lower == upper) map to 0., Fixed dimensions (lower == upper) map to 0., Mismatched array shapes raise ValueError., Mismatched array shapes raise ValueError., Tests for the normalize_to_unit_cube transform., Tests for the normalize_to_unit_cube transform., Midpoint of each dimension maps to 0.5. (+5 more)

### Community 264 - "Community 264"
Cohesion: 0.12
Nodes (15): check_shard_bimodality(), Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, Detect bimodality for each parameter across all CMC shards.      Runs :func:`det, check_shard_bimodality processes multi-shard sample dicts correctly. (+7 more)

### Community 265 - "Community 265"
Cohesion: 0.18
Nodes (10): apply_angle_filtering_for_plot(), find_nearest_angle(), normalize_angle_to_symmetric_range(), Angle-specific filtering utilities for multi-phi XPCS data., Find the index of the angle nearest to a target value.      Args:         phi_an, Normalize angle(s) to [-180, 180] range.      Args:         angle: Angle(s) in d, Apply angle filtering for plotting, extracting config from data dict.      This, Select a subset of phi angles by index.      Args:         phi_angles: 1D array (+2 more)

### Community 266 - "Community 266"
Cohesion: 0.12
Nodes (18): _build_fourier_reparameterizer(), _fit_joint_cmaes_multi_phi(), _fit_joint_constant_multi_phi(), Joint multi-angle CMA-ES with NLSQ warm-start and auto-skip.      This mirrors h, Joint multi-angle CMA-ES with NLSQ warm-start and auto-skip.      This mirrors h, Joint multi-angle CMA-ES with NLSQ warm-start and auto-skip.      This mirrors h, Build the Fourier/independent reparameterizer for fallback paths., Build the Fourier/independent reparameterizer for fallback paths. (+10 more)

### Community 267 - "Community 267"
Cohesion: 0.15
Nodes (12): _compute_per_angle_chi2(), Compute per-angle cost and noise-normalised reduced chi-squared.      Joint fits, Compute per-angle cost and noise-normalised reduced chi-squared.      Joint fits, Compute per-angle cost and noise-normalised reduced chi-squared.      Joint fits, Unit tests for the _compute_per_angle_chi2 helper.      Prevention: locks down t, Cost and chi2 are strictly positive for non-zero residuals., cost == 0.5 * sum(residuals²) by definition., chi2 is SSR/(σ²_noise * DOF), not raw MSE, when noise is detectable. (+4 more)

### Community 268 - "Community 268"
Cohesion: 0.18
Nodes (18): handle_nlsq_result(), Normalize a raw NLSQ return value to ``(popt, pcov, info)``.      Handles four r, _make_pcov(), _make_popt(), Dict with 'x' key (StreamingOptimizer output) is normalized., Dict with 'popt' key (alternative naming) is normalized., Object with .x and .pcov attributes is normalized., Object with .popt attribute (no .x) is normalized. (+10 more)

### Community 269 - "Community 269"
Cohesion: 0.14
Nodes (12): MemoryPressureMonitor, Monitor system memory pressure and trigger adaptive responses.      Polls system, Poll system memory; returns (level, available_bytes).          Must be called wi, Monitor system memory pressure and trigger adaptive responses.      Polls system, Poll system memory; returns (level, available_bytes).          Must be called wi, Return the current memory pressure level.          Uses cached value if polled r, Return available system memory in bytes.          Returns:             Available, Return True if memory pressure suggests reducing allocations.          Returns T (+4 more)

### Community 270 - "Community 270"
Cohesion: 0.12
Nodes (15): Save posterior samples to NPZ file.      Args:         result: CMC result object, Save posterior samples to NPZ file.      Args:         result: CMC result object, Save posterior samples to NPZ file.      Args:         result: CMC result object, Save posterior samples to NPZ file.      Args:         result: CMC result object, Save posterior samples to NPZ file.      Args:         result: CMC result object, _save_posterior_samples(), Tests for _save_posterior_samples., Tests for _save_posterior_samples. (+7 more)

### Community 271 - "Community 271"
Cohesion: 0.2
Nodes (3): Tests for AnalysisSummaryLogger., When io.json_utils is unavailable, fallback handles NaN/Inf., TestAnalysisSummaryLogger

### Community 272 - "Community 272"
Cohesion: 0.21
Nodes (15): compute_c2_batch(), compute_c2_batch_with_per_angle_scaling(), compute_theoretical_fits(), extract_parameters_from_result(), get_physical_param_count(), normalize_analysis_mode(), Fit Computation Utilities for Heterodyne NLSQ Results.  Provides functions for c, Get number of physical parameters for an analysis mode.      Args:         analy (+7 more)

### Community 273 - "Community 273"
Cohesion: 0.15
Nodes (11): Payloads carrying realistic per-shard device arrays for sizing., ``_memory_aware_worker_cap`` bounds concurrency by available RAM., End-to-end: under memory pressure the parallel branch is skipped., Payloads carrying realistic per-shard device arrays for sizing., Payloads carrying realistic per-shard device arrays for sizing., ``_memory_aware_worker_cap`` bounds concurrency by available RAM., ``_memory_aware_worker_cap`` bounds concurrency by available RAM., End-to-end: under memory pressure the parallel branch is skipped. (+3 more)

### Community 274 - "Community 274"
Cohesion: 0.21
Nodes (9): _config(), Unit tests for strategies/base.py and strategies/sequential.py., TestSelectStrategy, _estimate_available_memory(), name(), Base strategy interface and strategy selection logic., Estimate available system memory in GB., Select optimal fitting strategy based on data size and resources.      Strategy (+1 more)

### Community 275 - "Community 275"
Cohesion: 0.14
Nodes (10): FractionMixin, Reusable model behavior mixins for heterodyne correlation analysis.  Provides co, Mixin for sample fraction computations.      Requires the consuming class to hav, Compute sample fraction f_s(t) = f0 * exp(f1 * (t - f2)) + f3.          Result i, Compute fraction outer-product matrices for correlation terms.          Construc, Mixin for transport coefficient and integral computations.      Requires the con, Compute pointwise transport rate J(t) = D0 * t^alpha + offset.          Args:, Compute transport integral matrix |integral from t_i to t_j of J(t') dt'|. (+2 more)

### Community 276 - "Community 276"
Cohesion: 0.18
Nodes (6): Tests for velocity computation mixin., For constant velocity, integral from t_i to t_j should be v*(t_j - t_i)., Minimal class satisfying VelocityMixin interface., TestVelocityMixin, VelocityStub, VelocityMixin

### Community 277 - "Community 277"
Cohesion: 0.12
Nodes (9): Tests for ParameterSpace basic functionality., __post_init__ populates values for all parameters (14 physics + 2 scaling)., __post_init__ populates vary flags for all parameters., __post_init__ populates bounds for all parameters., __post_init__ populates priors for all parameters., n_varying returns count of varying parameters., varying_names returns list of varying parameter names., fixed_names returns list of fixed parameter names. (+1 more)

### Community 278 - "Community 278"
Cohesion: 0.12
Nodes (11): Jacobian at default parameters is well-structured., Jacobian has rank >= 10 (some params are insensitive at defaults).          At t, J^T J condition number is finite (not inf/nan).          At default parameters t, D0_ref and D0_sample have non-zero Jacobian column norms.          At default pa, Jacobian at a non-degenerate operating point has full rank.      The registry de, Physics parameters that are active at defaults have non-zero sensitivity., All 14 parameters identifiable off the symmetric singularity., J^T J condition number is finite at the non-degenerate point. (+3 more)

### Community 279 - "Community 279"
Cohesion: 0.15
Nodes (11): Tests for estimate_gradient_noise., Output dict contains the three documented keys., All returned values are finite floats., max_noise_ratio is always >= mean_noise_ratio., noisy_params_fraction is in [0, 1]., Mismatched residual length raises ValueError., Zero residuals do not cause NaN or division errors., TestEstimateGradientNoise (+3 more)

### Community 280 - "Community 280"
Cohesion: 0.12
Nodes (16): build_parameter_labels(), classify_parameter_status(), convert_bounds_to_nlsq_format(), expand_per_angle_parameters(), ExpandedParameters, PreparedData, Validate parameter bounds.      Args:         bounds: Bounds tuple (lower, upper, Validate and clip initial parameters to bounds.      Args:         params: Initi (+8 more)

### Community 281 - "Community 281"
Cohesion: 0.25
Nodes (7): _make_result(), Build a minimal NLSQResult-like object via SimpleNamespace., TestValidateResult, Run all validation checks on an NLSQ result.      Checks are executed unconditio, Run all validation checks on an NLSQ result.      Checks are executed unconditio, Run all validation checks on an NLSQ result.      Checks are executed unconditio, validate_result()

### Community 282 - "Community 282"
Cohesion: 0.12
Nodes (17): Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1., Validate inputs before starting any CMC analysis.      Checks performed:      1. (+9 more)

### Community 283 - "Community 283"
Cohesion: 0.15
Nodes (13): Regression tests: when nlsq_result=None, initial values from     model.get_param, Regression tests: when nlsq_result=None, initial values from     model.get_param, alpha_ref at exact lower bound (-5.0) must be clamped to interior., Regression tests: when nlsq_result=None, initial values from     model.get_param, alpha_ref=0.0 (well inside bounds) must pass through unchanged., alpha_ref at exact lower bound (-5.0) must be clamped to interior., Regression tests: when nlsq_result=None, initial values from     model.get_param, alpha_ref=0.0 (well inside bounds) must pass through unchanged. (+5 more)

### Community 284 - "Community 284"
Cohesion: 0.13
Nodes (16): _build_shard(), _estimate_noise_scale(), prepare_data(), PreparedData, Robust MAD-based noise scale estimate (sigma_MAD = 1.4826 * MAD)., Validate, normalise, and package raw XPCS data for CMC sampling.      This is th, Robust MAD-based noise scale estimate (sigma_MAD = 1.4826 * MAD)., Validate, normalise, and package raw XPCS data for CMC sampling.      This is th (+8 more)

### Community 285 - "Community 285"
Cohesion: 0.15
Nodes (15): _apply_phi_filtering(), load_and_validate_data(), prepare_cmc_data(), Data loading and validation pipeline for heterodyne CLI., Apply phi_filtering config to select angles from data.      Returns matched data, Apply phi_filtering config to select angles from data.      Returns matched data, Apply phi_filtering config to select angles from data.      Returns matched data, Determine phi angles from CLI args or configuration.      Priority: CLI --phi > (+7 more)

### Community 286 - "Community 286"
Cohesion: 0.17
Nodes (14): apply_cli_overrides(), Apply CLI argument overrides to the configuration.      Modifies the ConfigManag, parser(), Unit tests for heterodyne.cli.args_parser module., Tests that CLI overrides are correctly applied to ConfigManager., Build a minimal Namespace with sensible defaults., Tests that CLI overrides are correctly applied to ConfigManager., Build a minimal Namespace with sensible defaults. (+6 more)

### Community 287 - "Community 287"
Cohesion: 0.18
Nodes (15): main(), main_hexp(), main_hsim(), Main entry point for heterodyne CLI., Entry point for ``hexp`` — plot experimental data., Entry point for ``hexp`` — plot experimental data., Entry point for ``hsim`` — plot simulated data., Entry point for ``hsim`` — plot simulated data. (+7 more)

### Community 288 - "Community 288"
Cohesion: 0.12
Nodes (17): _log_warmstart_physical_params(), Log key physical parameter values from an NLSQ warm-start result.      Logs at I, Log key physical parameter values from an NLSQ warm-start result.      Logs at I, Warn when the NLSQ solution is in a degenerate sample-transport regime.      Two, Warn when the NLSQ solution is in a degenerate sample-transport regime.      Two, Warn when the NLSQ solution is in a degenerate sample-transport regime.      Two, Warn when the NLSQ solution is in a degenerate sample-transport regime.      Two, Warn when the NLSQ solution is in a degenerate sample-transport regime.      Two (+9 more)

### Community 289 - "Community 289"
Cohesion: 0.12
Nodes (15): Architectural Invariants & Historical Fixes, CMC Fitting Architecture, code:block1 (optimization/cmc/), Component Map, Critical Features & Fixes, Data Preparation, Design Invariants, I/O Serialization Pipeline (+7 more)

### Community 290 - "Community 290"
Cohesion: 0.12
Nodes (15): 4-Layer Anti-Degeneracy Defense, Backend Adapters, code:block1 (fit_nlsq_jax() / fit_nlsq_multi_phi()), code:block3 (optimization/nlsq/), Component Map, High-Level Architecture, Key Files Reference, Multi-Start Optimization (+7 more)

### Community 291 - "Community 291"
Cohesion: 0.18
Nodes (13): CachedMatrices, create_cached_matrices(), create_physics_factors(), create_physics_factors_from_config(), PhysicsFactors, Pre-computed physics factors for efficient correlation computation., Cached matrices that depend only on time grid.      These are expensive to recom, Create cached matrices from physics factors.      Args:         factors: Physics (+5 more)

### Community 292 - "Community 292"
Cohesion: 0.15
Nodes (15): plot_adaptation_summary(), plot_convergence_diagnostics(), plot_divergence_scatter(), plot_ess_evolution(), plot_kl_divergence_matrix(), MCMC convergence diagnostic plots for heterodyne analysis.  Provides visualizati, Plot divergence analysis scatter plot.      If divergence information is availab, Plot pairwise KL divergence heatmap between parameter posteriors.      Computes (+7 more)

### Community 293 - "Community 293"
Cohesion: 0.17
Nodes (10): make_cmc_config(), Validate :func:`make_cmc_config` factory., Factory output passes CMCConfig validation (no errors on construction)., Keyword overrides are applied correctly., Default warmup/samples are small enough for CI., Checkpoints are disabled by default for test determinism., Adaptive sampling is disabled by default for test determinism., Default seed is set for reproducibility. (+2 more)

### Community 294 - "Community 294"
Cohesion: 0.17
Nodes (10): make_reparam_config(), Tests for CMC test factory fixtures.  Provides reusable factory functions that c, Validate :func:`make_reparam_config` factory., Factory produces a valid ReparamConfig with all pairs enabled., Can override individual reparameterization flags., All three power-law pairs are reported when fully enabled., Disabling a flag removes that pair from enabled_pairs., ReparamConfig is frozen (immutable). (+2 more)

### Community 295 - "Community 295"
Cohesion: 0.15
Nodes (11): Suggest a Tikhonov regularization strength based on detected degeneracies., Suggest a Tikhonov regularization strength based on detected degeneracies., Suggest a Tikhonov regularization strength based on detected degeneracies., suggest_regularization(), Unit tests for NLSQ anti-degeneracy utilities.  Covers GradientCollapseDetector,, Tests for suggest_regularization., Empty checks list → base_lambda returned unchanged., All non-degenerate checks → base_lambda unchanged. (+3 more)

### Community 296 - "Community 296"
Cohesion: 0.12
Nodes (9): Tests for the from_config() classmethod (active orchestrator API)., from_config() returns an AntiDegeneracyController instance., controller.is_enabled is True when config.enable=True and per_angle_scaling=True, controller.is_enabled is False when config.enable=False., controller.is_enabled is False when per_angle_scaling=False., n_physical=14 (heterodyne) is stored on the controller., n_phi is stored on the controller., controller.config is an AntiDegeneracyConfig instance. (+1 more)

### Community 297 - "Community 297"
Cohesion: 0.16
Nodes (11): compute_effective_lambda(), Compute decaying regularization strength.      Applies an exponential schedule s, Compute decaying regularization strength.      Applies an exponential schedule s, Compute decaying regularization strength.      Applies an exponential schedule s, Tests for compute_effective_lambda., At iteration 0 the effective lambda equals base_lambda., Effective lambda follows base * decay_rate^iteration., decay_rate=1 gives constant lambda regardless of iteration. (+3 more)

### Community 298 - "Community 298"
Cohesion: 0.16
Nodes (11): compute_adaptive_cmaes_params(), Compute adaptive population size and max generations from bound ranges.      Sca, Map parameter vector from the unit hypercube [0, 1] to physical bounds.      Thi, Compute adaptive population size and max generations from bound ranges.      Sca, Tests for compute_adaptive_cmaes_params., When all parameter ranges are equal, scale ratio ~ 1 → min values., When scale ratio is very large → max values., Intermediate scale ratio → intermediate values. (+3 more)

### Community 299 - "Community 299"
Cohesion: 0.12
Nodes (13): Homodyne-parity alias for :attr:`posterior_std`., Get posterior samples for a parameter.          Args:             name: Paramete, Get posterior samples for a parameter.          Args:             name: Paramete, Get posterior means as dictionary., Get posterior means as dictionary., Get posterior samples for a parameter.          Args:             name: Paramete, Get posterior means as dictionary., Generate summary string. (+5 more)

### Community 300 - "Community 300"
Cohesion: 0.16
Nodes (10): apply_time_window(), Mask correlation data outside a time window.      Retains only rows and columns, Tests for heterodyne.data.filtering_utils.  Covers apply_time_window (2-D and 3-, Test time-window filtering for 2-D and 3-D correlation matrices., 2-D path returns correct subgrid., 3-D path preserves the phi-angle axis and returns correct subgrid., 3-D indexing selects the correct subgrid elements., Window outside data range raises ValueError. (+2 more)

### Community 301 - "Community 301"
Cohesion: 0.12
Nodes (10): Validate configuration structure., Validate configuration structure., Warn if config_version doesn't match package version., Warn if config_version doesn't match package version., Initialize with configuration dictionary.          Args:             config: Con, Normalize deprecated configuration keys to canonical names., Validate CMC config values.          Args:             cmc_config: CMC configura, Validate CMC config values.          Args:             cmc_config: CMC configura (+2 more)

### Community 302 - "Community 302"
Cohesion: 0.2
Nodes (5): Minimal class satisfying TransportMixin interface., Tests for transport computation mixin., TestTransportMixin, TransportStub, TransportMixin

### Community 303 - "Community 303"
Cohesion: 0.16
Nodes (12): compute_weights_excluding_diagonal(), Compute a weight array with zeros on the diagonal band.      Returns an array of, Tests for compute_weights_excluding_diagonal., Diagonal elements are zero in the weight array., Diagonal elements are zero in the weight array., Off-diagonal elements are 1.0., Off-diagonal elements are 1.0., Output shape matches requested shape. (+4 more)

### Community 304 - "Community 304"
Cohesion: 0.16
Nodes (12): estimate_diagonal_excess(), Estimate the statistical excess of diagonal vs off-diagonal elements.      Compu, Tests for estimate_diagonal_excess., Output dictionary has all expected keys., Output dictionary has all expected keys., mean_excess > 0 when diagonal is inflated above off-diagonal., mean_excess > 0 when diagonal is inflated above off-diagonal., Constant matrix has zero excess. (+4 more)

### Community 305 - "Community 305"
Cohesion: 0.12
Nodes (9): Tests for ParameterSpace.validate method., validate returns empty list for default space., validate detects values outside bounds., validate detects missing values., validate detects missing bounds., validate reports all errors., Fixed parameters outside bounds must still be flagged by validate()., v0=0.0 with vary=False is the documented zero-velocity sentinel — must pass. (+1 more)

### Community 306 - "Community 306"
Cohesion: 0.16
Nodes (9): estimate_per_angle_scaling extracts plausible contrast/offset estimates., Single-exponential g2 on a 64-point log-spaced grid., Contrast and offset estimates are in a physically plausible range., Data passed as a dict with a 'g2' sub-key is also handled., All supplied angle keys produce an entry in the result., Passing angle_keys restricts which keys are processed., An empty array for a key is silently omitted from the result., Offset estimate is always in [0, 1] regardless of input magnitude. (+1 more)

### Community 307 - "Community 307"
Cohesion: 0.17
Nodes (12): _extract_scale(), _make_nlsq_result(), _make_param_space(), Statistical validation tests for the MCMC (CMC) subsystem.  Tests cover prior co, Log-space priors for D0 parameters produce strictly positive samples., Extract the scale parameter from common distribution types., Create a default ParameterSpace with all registry defaults., Build a synthetic NLSQResult matching the varying parameters.      Values are se (+4 more)

### Community 308 - "Community 308"
Cohesion: 0.15
Nodes (9): NLSQNumericalError, Raised when NaN/Inf values are detected during optimization.      Attributes:, NumericalValidator, Runtime numerical validation for optimization tensors.      Checks arrays for Na, Check that all gradient values are finite.          Args:             gradients:, Check parameters for finite values and optional bound violations.          Args:, Check that the loss value is a finite scalar.          Args:             loss_va, Disable all validation checks (zero overhead). (+1 more)

### Community 309 - "Community 309"
Cohesion: 0.14
Nodes (16): execute_optimization_with_fallback(), Execute optimization with automatic fallback on failure.      Tries strategies i, Execute optimization with automatic fallback on failure.      Tries strategies i, _make_mock_nlsq_result(), Return a minimal mock NLSQResult., execute_optimization_with_fallback uses select_nlsq_strategy for auto-selection., Providing start_strategy skips memory-based auto-selection., Providing start_strategy skips memory-based auto-selection. (+8 more)

### Community 311 - "Community 311"
Cohesion: 0.13
Nodes (16): CMC API Reference (RST), Visualization API Reference (RST), CMC I/O (save_shard_results, InferenceData, NPZ), CMC Plotting (plot_trace_summary, etc.), CMC Reparameterization, CMC Sampler (NUTS/NumPyro), ParameterScaling (CMC), DiagonalOverlayResult / compute_diagonal_overlay_stats (+8 more)

### Community 312 - "Community 312"
Cohesion: 0.14
Nodes (15): CMCBackend ABC, optimization/cmc/backends/base.py, optimization/cmc/backends/cpu_backend.py, optimization/cmc/backends/multiprocessing_backend.py, optimization/cmc/backends/pbs.py, optimization/cmc/backends/pjit_backend.py, CMC Subsystem, optimization/cmc/backends/worker_pool.py (+7 more)

### Community 313 - "Community 313"
Cohesion: 0.18
Nodes (8): Unnormalized sinc function sin(x)/x, safe at x=0.      Returns 1.0 at x=0 (the m, Unnormalized sinc function sin(x)/x, safe at x=0.      Returns 1.0 at x=0 (the m, Unnormalized sinc function sin(x)/x, safe at x=0.      Returns 1.0 at x=0 (the m, safe_sinc(), safe_sinc(0) = 1 (mathematical limit)., safe_sinc(0) = 1 (mathematical limit)., Tests for unnormalized sinc: sin(x)/x., TestSafeSinc

### Community 314 - "Community 314"
Cohesion: 0.16
Nodes (11): get_convergence_recommendations(), log_analysis_summary(), Create human-readable diagnostics summary (homodyne-parity).      Mirrors homody, Create human-readable diagnostics summary (homodyne-parity).      Mirrors homody, Generate actionable recommendations for convergence issues., Generate actionable recommendations for convergence issues., Log a formatted CMC analysis summary at INFO/ERROR level., Log a formatted CMC analysis summary at INFO/ERROR level. (+3 more)

### Community 315 - "Community 315"
Cohesion: 0.13
Nodes (10): param_manager(), Tests for config/parameter_manager.py module.  Covers set_vary, set_bounds, vali, Tests for expand_varying_to_full and extract_varying methods., extract_varying -> expand_varying_to_full is identity for varying params., expand_varying_to_full preserves fixed parameter values., Tests for update_values method., update_values accepts dict input., update_values accepts array input. (+2 more)

### Community 316 - "Community 316"
Cohesion: 0.2
Nodes (11): BoundDict, fixed_indices(), from_config(), n_params(), n_varying(), Parameter manager for heterodyne model optimization., Merge config-overridden bounds from ParameterSpace into _default_bounds., Bound specification for a single parameter. (+3 more)

### Community 317 - "Community 317"
Cohesion: 0.16
Nodes (10): compute_per_angle_quantile_scaling(), PerAngleScaling, Per-angle quantile-based β,o estimator for homodyne `constant`-mode parity.  Thi, Per-angle contrast/offset estimates for the FROZEN constant mode., Estimate per-angle β(φ), o(φ) from g2 quantiles.      For each angle i, the offs, Tests for the per-angle quantile β,o estimator used by constant mode., Output vectors have shape (n_phi,), not scalars., Angles with no data fall back to the midpoint of the bounds. (+2 more)

### Community 318 - "Community 318"
Cohesion: 0.13
Nodes (15): get_fallback_strategy(), Determine the next fallback strategy after a failure.      For memory errors the, Determine the next fallback strategy after a failure.      For memory errors the, STREAMING falls back to LARGE., LARGE falls back to STANDARD., STANDARD has no fallback (end of chain)., Memory error from LARGE skips directly to STREAMING., Memory error from STANDARD (already last) → None. (+7 more)

### Community 319 - "Community 319"
Cohesion: 0.17
Nodes (10): Tests for analyze_parameter_sensitivity., Output dict has one key per parameter name., Sensitivity equals the L2 norm of each Jacobian column., An all-zero Jacobian column gives sensitivity 0., Wrong number of names raises ValueError., All sensitivity values are non-negative (they are norms)., TestAnalyzeParameterSensitivity, analyze_parameter_sensitivity() (+2 more)

### Community 320 - "Community 320"
Cohesion: 0.21
Nodes (6): compute_weights(), Compute weight array for NLSQ fitting.      Args:         c2_data: Correlation d, Compute weight array for NLSQ fitting.      Args:         c2_data: Correlation d, Tests for compute_weights., Sigma near zero should not produce inf weights., TestComputeWeights

### Community 321 - "Community 321"
Cohesion: 0.13
Nodes (15): _contiguous_split(), create_shards(), Stratified split by time range.      The full time axis is divided into ``n_shar, Split data into contiguous blocks by flat index order., Stratified split by time range.      The full time axis is divided into ``n_shar, Split a :class:`PreparedData` instance into ``n_shards`` sub-datasets.      Each, Split data into contiguous blocks by flat index order., Stratified split by time range.      The full time axis is divided into ``n_shar (+7 more)

### Community 322 - "Community 322"
Cohesion: 0.19
Nodes (13): _build_pbs_script(), PBS/Torque job submission backend for Consensus Monte Carlo.  Submits per-shard, Raise :class:`ValueError` when *value* does not match *pattern*., Raise :class:`ValueError` if any directive contains shell metacharacters.      `, Reject working_dir values that contain shell metacharacters or .. escapes., Codex W5: validate every shell-bound field at construction time.          Miscon, Return a complete PBS job script as a string., Return a complete PBS job script as a string. (+5 more)

### Community 323 - "Community 323"
Cohesion: 0.19
Nodes (8): SamplingStats can be constructed and exposes expected fields., SamplingStats stores all provided fields without mutation., is_healthy is True when divergence rate and accept prob are within limits., is_healthy is False when divergence_rate >= DIVERGENCE_RATE_HIGH., is_healthy is False when mean_accept_prob <= 0.6., SamplingStats is immutable (frozen dataclass)., A run with zero divergences is healthy provided accept prob is adequate., TestSamplingStatsCreation

### Community 324 - "Community 324"
Cohesion: 0.22
Nodes (11): _has_arviz(), plot_arviz_pair(), plot_arviz_trace(), ArviZ-based MCMC visualization for heterodyne analysis.  Provides publication-qu, Plot pairwise posterior relationships using ArviZ.      Args:         result: CM, Plot pairwise posterior relationships using ArviZ.      Args:         result: CM, Check if ArviZ is available., Convert a CMCResult to an ArviZ InferenceData object.      Delegates to ``cmc_re (+3 more)

### Community 325 - "Community 325"
Cohesion: 0.13
Nodes (15): 10. Timeout, 11. Reparameterization, 12. Bimodal detection, 13. Seed and run identity, 14. Checkpointing, 1. Enable gating, 2. Per-angle mode, 3. Sharding (+7 more)

### Community 326 - "Community 326"
Cohesion: 0.19
Nodes (8): log_calls(), Decorator to log function calls.      Args:         logger: Logger to use. If ``, Decorator to log function calls.      Args:         logger: Logger to use. If ``, Decorator to log function calls.      Args:         logger: Logger to use. If ``, Decorator to log function calls.      Args:         logger: Logger to use. If ``, Tests for log_calls decorator., When logger=None, one is created from func.__module__., TestLogCalls

### Community 327 - "Community 327"
Cohesion: 0.27
Nodes (13): _placeholder(), plot_cmc_summary_dashboard(), _plot_ess_panel(), _plot_posterior_panel(), _plot_rhat_panel(), _plot_trace_panel(), MCMC Summary Dashboard Visualization.  Provides a comprehensive multi-panel CMC, Plot R-hat bar chart with threshold line. (+5 more)

### Community 328 - "Community 328"
Cohesion: 0.18
Nodes (11): _make_pooled_arrays(), Pin the 100,000-point single-shard threshold (n_total > limit shards).      n_to, Return flat (data, t1, t2, phi) pooled arrays for an (n_phi, n, n) stack., fit_mcmc_jax feeds flat pooled arrays straight into ``_fit_cmc_pooled``     inst, fit_mcmc_jax feeds flat pooled arrays straight into ``_fit_cmc_pooled``     inst, fit_mcmc_jax feeds flat pooled arrays straight into ``_fit_cmc_pooled``     inst, 3 angles + forced small shard size → K>1 shards + consensus combine., _run_capture() (+3 more)

### Community 329 - "Community 329"
Cohesion: 0.19
Nodes (8): Gradient health analysis for NLSQ optimization.  Provides diagnostic utilities t, Suggest adaptive finite-difference step sizes for each parameter.      The heuri, suggest_step_sizes(), Parameters with larger column norms should get smaller steps., Huge column norm should clip step to floor., Very small column norm should clip step to ceiling., Zero Jacobian column should produce the max step (ceiling)., TestSuggestStepSizes

### Community 330 - "Community 330"
Cohesion: 0.22
Nodes (6): compute_optimal_x_scale(), Compute x_scale values inversely proportional to gradient norms.      Parameters, When all gradient norms are equal, scale ~ 1.0., Larger gradient norm -> smaller x_scale., Baseline params not in gradient_norms -> falls back to median., TestComputeOptimalXScale

### Community 331 - "Community 331"
Cohesion: 0.15
Nodes (3): from_config(), from_dict(), Anti-Degeneracy Controller — Orchestrator for 4-Layer Defense System.  This modu

### Community 332 - "Community 332"
Cohesion: 0.18
Nodes (10): build_anti_degeneracy_objective(), Wrap an objective with penalty terms for known degenerate parameter pairs., Wrap an objective with penalty terms for known degenerate parameter pairs., Wrap an objective with penalty terms for known degenerate parameter pairs., Tests for build_anti_degeneracy_objective., When no known pairs are present, returns the base objective unchanged., When degenerate pairs are present, wrapped cost >= base cost., Well-separated degenerate pair parameters have lower penalty. (+2 more)

### Community 333 - "Community 333"
Cohesion: 0.14
Nodes (8): Tests for get_group_values method., get_group_values returns reference group parameters., get_group_values returns sample group parameters., get_group_values returns velocity group parameters., get_group_values returns fraction group parameters., get_group_values returns angle group parameters., get_group_values raises ValueError for invalid group., TestGetGroupValues

### Community 334 - "Community 334"
Cohesion: 0.16
Nodes (13): _extract_completion_opts(), _extract_help_flags(), Tests for shell completion system parity and correctness., Run ``command --help`` and extract all ``--long-option`` flags., Run ``command --help`` and extract all ``--long-option`` flags., Extract all ``--flags`` from a completion function in completion.sh., Extract all ``--flags`` from a completion function in completion.sh., Completion script must offer every flag the CLI accepts. (+5 more)

### Community 335 - "Community 335"
Cohesion: 0.14
Nodes (8): Tests for ParameterSpace array operations., get_initial_array returns array of shape (14,)., get_bounds_arrays returns (lower, upper) arrays., get_vary_mask returns boolean array for 14 physics params., array_to_dict converts array to dict., update_from_dict updates values., update_from_dict raises ValueError for unknown keys., TestParameterSpaceArrays

### Community 336 - "Community 336"
Cohesion: 0.14
Nodes (8): Tests for priors.py data-preparation helpers.  Covers: - :func:`get_param_names_, build_init_values_dict builds consistent initial-value dicts., With no NLSQ values the result falls back to prior_mean or default., NLSQ values override the fallback for the supplied parameters., All returned values lie within their registry bounds., An NLSQ value outside bounds is clamped rather than raising., fallback='default' uses the registry default value instead of prior_mean., TestBuildInitValuesDict

### Community 337 - "Community 337"
Cohesion: 0.14
Nodes (13): Unit tests for fallback_chain.py — NLSQ-native routing.  Tests cover: - Descendi, Dict with neither 'x' nor 'popt' raises TypeError., Unrecognized result type raises TypeError., Tuple with length != 2 or 3 raises TypeError., CHUNKED must not appear in OptimizationStrategy enum., String values match NLSQStrategy enum values., _FALLBACK_ORDER must be STREAMING → LARGE → STANDARD (descending)., test_enum_values_match_nlsq_strategy() (+5 more)

### Community 338 - "Community 338"
Cohesion: 0.26
Nodes (7): _make_registry(), Unit tests for heterodyne.optimization.nlsq.validation.result_validator., Parameters with span=0 (fixed) should be silently skipped., Build a minimal ParameterRegistry-like mapping.      ``entries`` maps parameter, TestCheckBoundSaturation, check_bound_saturation(), Check if any parameters are stuck at their bounds.      A parameter is considere

### Community 339 - "Community 339"
Cohesion: 0.14
Nodes (13): prepare_cmc_data(), Data preparation utilities for CMC analysis.  Handles validation, JAX conversion, Validate and convert correlation data to JAX arrays.      Performs shape, dtype,, Split a two-time correlation matrix into shards along both axes.      Each shard, Validate and convert correlation data to JAX arrays.      Performs shape, dtype,, Strategy for partitioning prepared data into shards.      Attributes:         RA, Split a two-time correlation matrix into shards along both axes.      Each shard, Validate and convert correlation data to JAX arrays.      Performs shape, dtype, (+5 more)

### Community 340 - "Community 340"
Cohesion: 0.2
Nodes (11): ChunkInfo, _detect_system_memory(), estimate_array_size(), MemoryBudget, MemoryPressureLevel, Memory budget tracking for large XPCS datasets.  Provides allocation tracking, b, Snapshot of memory budget state.      Attributes:         total_bytes: Total bud, Metadata for a single processing chunk.      Attributes:         start: Start in (+3 more)

### Community 341 - "Community 341"
Cohesion: 0.14
Nodes (7): Tests for invalid arguments and mutual exclusivity., Tests for invalid arguments and mutual exclusivity., An unrecognised --method value must be rejected by argparse., An unrecognised --method value must be rejected by argparse., Passing both --plot and --no-plot must fail., Passing both --plot and --no-plot must fail., TestArgumentValidation

### Community 342 - "Community 342"
Cohesion: 0.15
Nodes (11): _PhaseRecord, Internal record for phase timing., Internal record for phase timing., Internal record for phase timing., Internal record for phase timing., Mark phase start for timing.          Args:             name: Phase name (e.g.,, Mark phase start for timing.          Args:             name: Phase name (e.g.,, Mark phase start for timing.          Args:             name: Phase name (e.g., (+3 more)

### Community 343 - "Community 343"
Cohesion: 0.22
Nodes (7): _ColorFormatter, Optional ANSI color formatter for console logging., Optional ANSI color formatter for console logging., Optional ANSI color formatter for console logging., Optional ANSI color formatter for console logging., Tests for _ColorFormatter., TestColorFormatter

### Community 344 - "Community 344"
Cohesion: 0.19
Nodes (5): PersistentWorkerPool, Persistent process pool for CMC shard dispatch (homodyne parity).      Workers a, Block until a result is available; raises ``queue.Empty`` on timeout., True when the shared result queue has at least one entry., Send ``None`` sentinels to all workers and join them.

### Community 345 - "Community 345"
Cohesion: 0.26
Nodes (4): Recommend CMC backend and chain configuration.      Args:         cpu_info: CPU, _recommend_backend(), With very little memory, chains should be capped., TestRecommendBackend

### Community 346 - "Community 346"
Cohesion: 0.31
Nodes (6): _make_strategy_result(), When covariance is None, identity should be used as fallback., When residuals is None, n_points weight should fall back to 1.0., TestCombineAngleResults, combine_angle_results(), Combine per-angle optimisation results into a single parameter estimate.      St

### Community 347 - "Community 347"
Cohesion: 0.15
Nodes (11): _adjust_covariance_for_normalization(), _compute_normalization_factors(), _denormalize_params(), from_nlsq_config(), _normalize_bounds(), _normalize_params(), Compute normalization factors for bounds-based normalization.      Normalization, Normalize parameters from physical space to [0, 1] space.      Parameters     -- (+3 more)

### Community 348 - "Community 348"
Cohesion: 0.35
Nodes (5): filter_by_angle_range(), Filter 3D correlation data to angles within a range.      Args:         c2_3d: C, TestFilterByAngleRange, AngleRange, Azimuthal angle range for data selection.      Attributes:         phi_min: Mini

### Community 349 - "Community 349"
Cohesion: 0.19
Nodes (8): _create_default_registry(), ParameterInfo, Parameter registry with metadata and bounds for heterodyne model.  All length un, Create default parameter registry for heterodyne model.      Physical bounds are, Metadata for a single model parameter.      Attributes:         name: Parameter, Check if value is within bounds., Clip value to bounds., ParameterInfo supports log_space, prior_mean/std, is_scaling.

### Community 350 - "Community 350"
Cohesion: 0.23
Nodes (5): FractionStub, Tests for fraction computation mixin., Minimal class satisfying FractionMixin interface., TestFractionMixin, FractionMixin

### Community 351 - "Community 351"
Cohesion: 0.24
Nodes (11): apply_recovery(), diagnose_failure(), Deprecated location for NLSQ recovery strategies.  The implementation now lives, Return a new :class:`NLSQConfig` with the plan's overrides applied.      If the, Identify parameters that should be fixed (held constant).      A parameter is fl, Possible corrective actions after an optimization failure., Recommended corrective action with an explanation.      Attributes:         acti, Inspect a failed (or suspect) NLSQ result and propose a recovery plan.      Deci (+3 more)

### Community 352 - "Community 352"
Cohesion: 0.19
Nodes (11): _is_memory_error(), OptimizationStrategy, Fallback chain for NLSQ optimization strategies.  Provides automatic strategy de, Return ``True`` if *error* looks memory-related., Return ``True`` if *error* looks memory-related., Dispatch a single strategy attempt and return ``(popt, pcov, info)``.      Route, Dispatch a single strategy attempt and return ``(popt, pcov, info)``.      Route, Available optimization strategies in descending fallback order.      Values matc (+3 more)

### Community 353 - "Community 353"
Cohesion: 0.21
Nodes (11): compute_quality_metrics(), compute_uncertainties(), determine_convergence_status(), normalize_nlsq_result(), QualityMetrics, Extract parameter uncertainties from covariance matrix.      Args:         covar, Normalize various NLSQ result formats to standard format.      NLSQ can return r, Determine convergence status from optimization info.      Args:         info: Op (+3 more)

### Community 354 - "Community 354"
Cohesion: 0.21
Nodes (7): PBSConfig, Configuration for PBS/Torque job submission.      Attributes:         queue: Tar, Configuration for PBS/Torque job submission.      Attributes:         queue: Tar, Regression for Codex finding C5: PBS worker template must satisfy Rule 8.  Rule, The PBS shell script must export JAX_ENABLE_X64=1 in the prelude., _template(), TestPBSWorkerEnvOrder

### Community 355 - "Community 355"
Cohesion: 0.15
Nodes (7): IncrementalValidationCache, Hash-based cache for validation results to avoid redundant checks., Compute lightweight fingerprint from corner samples, shape, and dtype., Look up a cached validation result by hash., Store a validation result, evicting oldest entry if at capacity., Clear all cached validation results and reset counters., Return cache hit/miss/size statistics.

### Community 356 - "Community 356"
Cohesion: 0.15
Nodes (12): Result of parameter validation., ValidationResult, Tests for validate_time_integral_safety function., Tests for validate_correlation_inputs function., Tests for ValidationResult dataclass., Integration tests combining multiple validators., Tests for validate_parameters function., TestPhysicsValidatorsIntegration (+4 more)

### Community 357 - "Community 357"
Cohesion: 0.19
Nodes (9): Return True when an optimizer result represents a converged fit.      NLSQResult, Return True when an optimizer result represents a converged fit.      NLSQResult, Return True when an optimizer result represents a converged fit.      NLSQResult, _result_converged(), ``_result_converged`` must read ``convergence_passed`` on CMCResult., het_a10cf27e: CMC result with all-shards-failed must NOT report converged., NLSQResult exposes ``success``, not ``convergence_passed``., Conservative default: missing both attrs returns False (not True). (+1 more)

### Community 358 - "Community 358"
Cohesion: 0.24
Nodes (11): BatchResult, compute_batch_statistics(), FitStatistics, format_batch_report(), identify_outlier_fits(), Statistics aggregation across multiple NLSQ fits.  Provides batch-level summarie, Identify fits that are statistical outliers.      A fit is considered an outlier, Format a :class:`BatchResult` as a human-readable summary table.      Args: (+3 more)

### Community 359 - "Community 359"
Cohesion: 0.15
Nodes (6): Tests for heterodyne.core.fitting — UnifiedHeterodyneEngine + JAX solvers., Tests for solve_least_squares_chunked_jax (scan-based accumulation)., Chunked result matches non-chunked for same data., Tests for DatasetSize classification., TestDatasetSize, TestSolveLeastSquaresChunkedJAX

### Community 360 - "Community 360"
Cohesion: 0.15
Nodes (6): _close_figures(), Unit tests for heterodyne.viz.diagnostics module., Close all matplotlib figures after each test., Multi-chain samples: shape (n_chains, n_draws)., samples_2d(), TestPlotResidualMap

### Community 361 - "Community 361"
Cohesion: 0.21
Nodes (8): log_exception(), Log an exception with full context for debugging.      Extracts module, function, Log an exception with full context for debugging.      Extracts module, function, Log an exception with full context for debugging.      Extracts module, function, Log an exception with full context for debugging.      Extracts module, function, Tests for log_exception function., Exception created without raise has no __traceback__., TestLogException

### Community 362 - "Community 362"
Cohesion: 0.15
Nodes (11): Compute the number of shards K for a given dataset.          When ``num_shards``, Compute the number of shards K for a given dataset.          When ``num_shards``, Compute the number of shards K for a given dataset.          When ``num_shards``, Compute the number of shards K for a given dataset.          When ``num_shards``, Resolve the effective per-angle mode for a concrete dataset.          Resolution, Compute the number of shards K for a given dataset.          When ``num_shards``, Compute the number of shards K for a given dataset.          When ``num_shards``, Resolve the effective per-angle mode for a concrete dataset.          Resolution (+3 more)

### Community 363 - "Community 363"
Cohesion: 0.27
Nodes (11): _ds_heatmap(), _mpl_heatmap(), Datashader-based visualization backend for large XPCS datasets.  Provides fast r, Render a grid of correlation heatmaps, one per azimuthal angle.      Uses datash, Render via datashader (requires datashader + pandas)., Fallback rendering via matplotlib., Render a two-time correlation heatmap.      Uses datashader for fast rasterizati, Render a residual heatmap with a symmetric colormap centered at 0.      Uses dat (+3 more)

### Community 364 - "Community 364"
Cohesion: 0.17
Nodes (6): ``_grid_indices`` bounds searchsorted and rejects off-grid time values.      Pin, ``_grid_indices`` bounds searchsorted and rejects off-grid time values.      Pin, ``_grid_indices`` bounds searchsorted and rejects off-grid time values.      Pin, ``_grid_indices`` bounds searchsorted and rejects off-grid time values.      Pin, ``_grid_indices`` bounds searchsorted and rejects off-grid time values.      Pin, TestGridIndicesGuard

### Community 365 - "Community 365"
Cohesion: 0.21
Nodes (9): Regression tests for deprecated import shims.  The two modules below were moved/, Second access of the same symbol must not re-warn (one-shot guard)., Clear the one-shot ``_warned_names`` so a test can re-observe the warning., PEP 562 lazy contract: a bare import must NOT emit DeprecationWarning.      The, Accessing a public symbol externally fires DeprecationWarning once., _reset_numpy_gradients_warned_set(), test_numpy_gradients_attribute_access_warns_once_per_symbol(), test_numpy_gradients_bare_import_is_silent() (+1 more)

### Community 366 - "Community 366"
Cohesion: 0.27
Nodes (4): detect_cluster_type(), Detect the HPC cluster scheduler type from environment.      Returns:         Cl, PBS is checked first, so if both are set PBS wins., TestDetectClusterType

### Community 367 - "Community 367"
Cohesion: 0.17
Nodes (6): Tests for the file-inventory extractor., test_write_json_round_trips(), Write *arrays* to *path* as a compressed ``.npz`` file.          Parameters, Serialise *data* to *path* as a UTF-8 JSON file.          Parameters         ---, Write *arrays* to *path* as a compressed ``.npz`` file.          Parameters, Serialise *data* to *path* as a UTF-8 JSON file.          Parameters         ---

### Community 368 - "Community 368"
Cohesion: 0.17
Nodes (7): Tests for the per-layer boolean properties., With n_phi=4 and per_angle_mode='auto', Fourier is not active., With per_angle_mode='fourier' and n_phi >= 3, Fourier is active., use_shear_weighting must always be False (Layer 5 is D3-dropped)., Layer 5 methods (get_shear_weights, update_shear_phi0) must either         be ab, use_hierarchical is False when hierarchical.enable=False., TestAntiDegeneracyControllerProperties

### Community 369 - "Community 369"
Cohesion: 0.29
Nodes (5): check_convergence(), Check convergence criteria and return (status, warnings).      Returns     -----, Check convergence criteria and return (status, warnings).      Returns     -----, test_mean_shard_bfmi_in_metadata(), TestCheckConvergence

### Community 370 - "Community 370"
Cohesion: 0.15
Nodes (10): Get summary statistics for a parameter.          Args:             name: Paramet, Number of parameters., Validate convergence diagnostics.          Args:             r_hat_threshold: Ma, Get summary statistics for a parameter.          Args:             name: Paramet, Validate convergence diagnostics.          Args:             r_hat_threshold: Ma, Validate convergence diagnostics.          Args:             r_hat_threshold: Ma, Validate convergence diagnostics.          Args:             r_hat_threshold: Ma, Validate convergence diagnostics.          Args:             r_hat_threshold: Ma (+2 more)

### Community 371 - "Community 371"
Cohesion: 0.17
Nodes (4): Tests for angle-specific filtering utilities.  Covers filter_by_angle_range, sel, 3D correlation array: 4 angles, 5x5 time matrices., small_c2_3d(), TestSelectAngles

### Community 372 - "Community 372"
Cohesion: 0.27
Nodes (4): compute_angle_quality(), Compute per-angle quality metrics for multi-phi data.      For each angle slice,, Compute per-angle quality metrics for multi-phi data.      For each angle slice,, TestComputeAngleQuality

### Community 374 - "Community 374"
Cohesion: 0.17
Nodes (9): Tests for SCALING_PARAMS module constant., Tests for SCALING_PARAMS module constant., SCALING_PARAMS contains contrast and offset., SCALING_PARAMS contains contrast and offset., Contrast parameter has [0, 1] bounds., Contrast parameter has [0, 1] bounds., Offset parameter has [0.5, 1.5] bounds., Offset parameter has [0.5, 1.5] bounds. (+1 more)

### Community 375 - "Community 375"
Cohesion: 0.17
Nodes (8): Get all 14 parameter values.          Returns a read-only cached array (``writea, Get all 14 parameter values.          Returns a read-only cached array (``writea, Expand varying parameters to full 14-parameter array.          Fixed parameters, Expand varying parameters to full 14-parameter array.          Fixed parameters, Validate parameters against physics constraints.          Args:             para, Validate parameters against physics constraints.          Args:             para, Validate physics-based constraints beyond simple bound checking.          Checks, Validate physics-based constraints beyond simple bound checking.          Checks

### Community 376 - "Community 376"
Cohesion: 0.17
Nodes (7): Tests for validate_physics method., validate_physics returns empty list for default params., validate_physics catches negative diffusion coefficients., validate_physics catches fraction params outside [0, 1]., validate_physics warns about extreme alpha values., validate_physics uses stored values when params is None., TestValidatePhysics

### Community 377 - "Community 377"
Cohesion: 0.32
Nodes (5): estimate_contrast_offset_from_data(), Estimate contrast and offset from C2 data via physics-informed quantile analysis, Estimate contrast and offset from C2 data via physics-informed quantile analysis, Estimate contrast and offset from C2 data via physics-informed quantile analysis, TestEstimateContrastOffsetFromData

### Community 378 - "Community 378"
Cohesion: 0.36
Nodes (6): execute_with_recovery(), Execute optimization with progressive recovery on failure.      Recovery sequenc, Execute optimization with progressive recovery on failure.      Recovery sequenc, Tests for execute_with_recovery()., TestExecuteWithRecovery, SimpleNamespace

### Community 379 - "Community 379"
Cohesion: 0.17
Nodes (5): TestValidationReport, Post-fit result validation for NLSQ optimization results.  Provides functional-s, Summary of result validation checks.      Attributes:         passed: True when, Return a human-readable multi-line summary of the report., ValidationReport

### Community 380 - "Community 380"
Cohesion: 0.24
Nodes (11): _build_pooled_shard(), extract_phi_info(), PooledCMCData, prepare_mcmc_data(), Validate pooled arrays have matching length, finite values, sane shapes., Return ``(phi_unique, phi_indices)`` with tolerance-aware matching.      Mirrors, Validate + filter pooled XPCS data for joint multi-phi CMC.      Mirrors ``homod, Slice ``prepared`` at ``shard_indices`` into a fresh ``PooledCMCData``.      Re- (+3 more)

### Community 381 - "Community 381"
Cohesion: 0.17
Nodes (12): Validate correlation matrix inputs.      Args:         t1: Time axis 1         t, Validate correlation matrix inputs.      Args:         t1: Time axis 1         t, validate_correlation_inputs(), test_equal_consecutive_times_error(), test_inf_values_error(), test_nan_values_error(), test_negative_values_warning(), test_non_monotonic_t1_error() (+4 more)

### Community 382 - "Community 382"
Cohesion: 0.17
Nodes (5): _parser(), Tests for CLI components (lightweight, no subprocess invocation).  Verifies that, Verify that CLI modules can be imported without error., TestCliImports, TestXlaConfig

### Community 383 - "Community 383"
Cohesion: 0.17
Nodes (7): Tests for ParameterSpace dataclass., Bounds and priors are populated from registry., Returns correct count (14 physics params) with sensible values., Scaling bounds use task-specified defaults., Scaling priors use task-specified defaults., config_manager can be set for bound override., TestParameterSpace

### Community 384 - "Community 384"
Cohesion: 0.23
Nodes (9): categorize(), DatasetSize, jit(), Unified Heterodyne Engine with JAX-Accelerated Least Squares ===================, Dataset size categories for optimization., Memory-efficient chunked solver using ``jax.lax.scan``.          Accumulates nor, NumPy fallback for chunked least squares., Detect and categorize dataset size.          Args:             data: Data array (+1 more)

### Community 385 - "Community 385"
Cohesion: 0.21
Nodes (10): generate_and_plot_fitted_simulations(), Visualization for NLSQ fitting results., Generate forward simulations from fitted parameters and plot.      Uses the fitt, Generate forward simulations from fitted parameters and plot.      Uses the fitt, Generate forward simulations from fitted parameters and plot.      Uses the fitt, Generate forward simulations from fitted parameters and plot.      Uses the fitt, Generate forward simulations from fitted parameters and plot.      Uses the fitt, Percentile-based colour limits with fallback for empty/flat data. (+2 more)

### Community 386 - "Community 386"
Cohesion: 0.23
Nodes (7): Convert string/int log level to logging level constant., Convert string/int log level to logging level constant., Convert string/int log level to logging level constant., Convert string/int log level to logging level constant., _resolve_level(), Tests for _resolve_level helper., TestResolveLevel

### Community 387 - "Community 387"
Cohesion: 0.17
Nodes (8): Regression pins for known-but-previously-untested production bugs.  Each test in, Pin the ``[-5, 5]`` widening of ``alpha_ref`` and ``alpha_sample``.      Tighten, Pin the contract that ``_SHARD_ARRAY_KEYS`` carries the element-wise     time fi, Pin the contract that init_params has shape ``(num_chains,)``.      NumPyro 0.21, test_init_params_have_chain_shape(), TestAlphaBoundsAtLeastFiveWide, TestNoWarmstartShardArraySchema, TestNumpyroInitBroadcast

### Community 388 - "Community 388"
Cohesion: 0.17
Nodes (10): get_model_for_mode(), Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Select and build the appropriate NumPyro model based on per-angle mode.      Fac, Tests for model output validation and parameter counting in cmc/model.py. (+2 more)

### Community 389 - "Community 389"
Cohesion: 0.27
Nodes (12): accumulate_chunks_parallel function, accumulate_chunks_sequential function, classify_fit_quality n_at_bounds parameter, create_ooc_kernels JIT kernel factory, classify_fit_quality / FitQualityValidator, GaussNewtonAccumulation dataclass, NLSQ Fitting Architecture, parallel_accumulator.py module (+4 more)

### Community 390 - "Community 390"
Cohesion: 0.27
Nodes (9): compute_flat_residuals(), compute_nlsq_jacobian(), make_residual_fn(), make_varying_residual_fn(), NLSQ-optimized correlation computation for heterodyne model.  Provides functions, Create residual function that accepts only varying parameters.      Combines Par, Compute Jacobian of residual function via JAX forward-mode autodiff.      Uses `, Compute flat residuals using only upper-triangle elements.      Instead of compu (+1 more)

### Community 391 - "Community 391"
Cohesion: 0.25
Nodes (10): _payloads(), Regression: the joint multi-phi CMC path shards large data (homodyne parity).  P, Workers may finish out of order; results must come back in input order.      Pin, Replace the per-shard NUTS runner with a fast, consistent fake.      Records eve, stub_nuts(), test_dispatch_falls_back_to_sequential_on_parallel_error(), test_dispatch_sequential_for_cpu_backend(), test_dispatch_uses_parallel_when_workers_available() (+2 more)

### Community 392 - "Community 392"
Cohesion: 0.27
Nodes (5): get_optimal_batch_size(), Calculate optimal batch size based on CPU cache hierarchy.      This heuristic a, Calculate optimal batch size based on CPU cache hierarchy.      This heuristic a, Calculate optimal batch size based on CPU cache hierarchy.      This heuristic a, TestGetOptimalBatchSize

### Community 393 - "Community 393"
Cohesion: 0.29
Nodes (4): configure_optimal_device(), Configure device settings for optimal CMC execution.      This function should b, Configure device settings for optimal CMC execution.      This function should b, TestConfigureOptimalDevice

### Community 394 - "Community 394"
Cohesion: 0.29
Nodes (4): diagnose_gradients(), Run a battery of gradient-health checks on a Jacobian.      Args:         jacobi, Large sensitivity ratio should be flagged., TestDiagnoseGradients

### Community 395 - "Community 395"
Cohesion: 0.25
Nodes (6): Tests for classify_fit_quality., TestClassifyFitQuality, classify_fit_quality(), Classify fit quality into a 3-level flag.      Thresholds:      - ``"good"``, Classify fit quality into a 3-level flag.      Thresholds match the homodyne NLS, Classify fit quality into a 3-level flag.      Thresholds:      - ``"good"``

### Community 396 - "Community 396"
Cohesion: 0.25
Nodes (9): from_dict(), DataSlice, FilterResult, QRange, Core type definitions for XPCS data handling., A single slice of XPCS correlation data at a specific angle.      Attributes:, Wavevector range for data selection.      Attributes:         q_min: Minimum wav, Result of a data filtering operation.      Attributes:         data: Filtered da (+1 more)

### Community 398 - "Community 398"
Cohesion: 0.18
Nodes (6): Tests for ParameterManager properties., n_varying returns count of varying parameters., varying_names returns list of strings., varying_indices corresponds to varying_names., fixed_indices and varying_indices are disjoint and complete., TestParameterManagerProperties

### Community 399 - "Community 399"
Cohesion: 0.2
Nodes (10): Zsh completion wrapper must use env vars, not hardcoded paths., The generated zsh wrapper must reference the bash completion         via an envi, The generated zsh wrapper must reference the bash completion         via an envi, TestZshWrapper, get_completion_source_path(), install_bash_completion(), install_zsh_completion(), Get the path to the completion script in the package.      Returns:         Path (+2 more)

### Community 400 - "Community 400"
Cohesion: 0.22
Nodes (9): compare_jacobians(), compute_jacobian_stats(), Jacobian computation and validation utilities.  Provides central finite-differen, Validate a Jacobian matrix for structural issues.      Checks for:     - NaN or, Compare analytic and numerical Jacobians element-wise.      Useful for verifying, Compare analytic and numerical Jacobians element-wise.      Useful for verifying, Compute Jacobian statistics for convergence diagnostics.      Computes the Jacob, Validate a Jacobian matrix for structural issues.      Checks for:     - NaN or (+1 more)

### Community 401 - "Community 401"
Cohesion: 0.18
Nodes (10): Regression tests for het_dd0f825b: BFMI must not be a hard convergence gate., Regression tests for het_dd0f825b: BFMI must not be a hard convergence gate., Build a minimal worker result dict with healthy R-hat but no energy field., Regression tests for het_dd0f825b: BFMI must not be a hard convergence gate., Build a minimal worker result dict with healthy R-hat but no energy field., Regression tests for het_dd0f825b: BFMI must not be a hard convergence gate., Build a minimal worker result dict with healthy R-hat but no energy field., Build a minimal worker result dict with healthy R-hat but no energy field. (+2 more)

### Community 402 - "Community 402"
Cohesion: 0.33
Nodes (9): auto_configure(), configure_xla(), get_cpu_info(), main(), XLA configuration for JAX on CPU., Configure XLA/JAX environment variables for CPU execution.      MUST be called b, Get CPU information for configuration.      Returns:         Dict with cpu_count, Automatically configure XLA based on system resources.      Returns:         Dic (+1 more)

### Community 403 - "Community 403"
Cohesion: 0.24
Nodes (10): plot_nlsq_fit(), Plot NLSQ fit comparison.      Creates three-panel figure:     1. Experimental d, Plot NLSQ fit comparison.      Creates three-panel figure:     1. Experimental d, Tests for NLSQ plotting helpers., plot_nlsq_fit must not crash when c2_data and fitted_correlation are both N×N., plot_nlsq_fit reshape must still work when residuals are a perfect square., plot_nlsq_fit reshape must still work when residuals are a perfect square., test_plot_nlsq_fit_handles_diagonal_masked_residuals() (+2 more)

### Community 404 - "Community 404"
Cohesion: 0.2
Nodes (11): `accumulate_chunks_parallel(chunks, n_workers) → GaussNewtonAccumulation`, `accumulate_chunks_sequential(chunks) → GaussNewtonAccumulation`, code:python (class TimedContext:), Covariance computation, `create_ooc_kernels(physics_config, ...) → tuple[Callable, Callable]`, `GaussNewtonAccumulation`, Parallel Chunk Accumulation, Quality Flag (+3 more)

### Community 405 - "Community 405"
Cohesion: 0.24
Nodes (7): log_performance(), Decorator to log function performance.      Only emits a log record when the fun, Decorator to log function performance.      Only emits a log record when the fun, Decorator to log function performance.      Only emits a log record when the fun, Decorator to log function performance.      Only emits a log record when the fun, Tests for log_performance decorator., TestLogPerformance

### Community 406 - "Community 406"
Cohesion: 0.24
Nodes (7): Create a contextual logger with key-value prefixes.      Context is formatted as, Create a contextual logger with key-value prefixes.      Context is formatted as, Create a contextual logger with key-value prefixes.      Context is formatted as, Create a contextual logger with key-value prefixes.      Context is formatted as, with_context(), Tests for with_context function., TestWithContext

### Community 407 - "Community 407"
Cohesion: 0.22
Nodes (6): BimodalConsensusResult, Bimodal Detection, check_shard_bimodality(), cluster_shard_modes(), optimization/cmc/diagnostics.py, ModeCluster

### Community 408 - "Community 408"
Cohesion: 0.24
Nodes (9): make_correlation_data(), make_g2_synthetic(), make_param_dict(), make_tau_array(), Factory functions that generate synthetic test data for heterodyne tests.  All f, Return a dictionary of all 16 model parameters with registry defaults.      Read, Return a log-spaced array of delay times.      Args:         n: Number of delay, Compute a simple single-exponential g2 correlation function.      Uses the model (+1 more)

### Community 409 - "Community 409"
Cohesion: 0.31
Nodes (4): diagnose_gradient_imbalance(), Diagnose gradient imbalance across parameters.      Args:         gradient_norms, Fewer than 2 nonzero norms -> no imbalance., TestDiagnoseGradientImbalance

### Community 410 - "Community 410"
Cohesion: 0.2
Nodes (9): Characterization tests for the NLSQWrapper port from homodyne.  Verifies NLSQWra, NLSQWrapper can be constructed without arguments (defaults applied)., NLSQWrapper.fit is callable., fit() accepts the same core kwargs homodyne does: data, config,     initial_para, NLSQWrapper is re-exported from the optimization.nlsq package., test_nlsq_wrapper_exposes_fit_method(), test_nlsq_wrapper_fit_signature_matches_homodyne(), test_nlsq_wrapper_is_exported_from_init() (+1 more)

### Community 411 - "Community 411"
Cohesion: 0.2
Nodes (6): Tests for per_angle_mode_actual auto-selection logic., auto mode with n_phi >= constant_scaling_threshold → 'auto_averaged'., auto mode with n_phi < constant_scaling_threshold → 'individual'., Explicit fourier mode → per_angle_mode_actual='fourier'., Disabled controller has per_angle_mode_actual='disabled'., TestPerAngleMode

### Community 412 - "Community 412"
Cohesion: 0.2
Nodes (5): Guard test: ensure no scipy.optimize.least_squares in the NLSQ pipeline.  This t, Verify that scipy.optimize.least_squares is absent from the NLSQ path., ScipyNLSQAdapter class must not exist in adapter.py., adapter.py must have zero scipy.optimize imports., TestNoScipyLeastSquares

### Community 413 - "Community 413"
Cohesion: 0.2
Nodes (6): Tests for set_vary method., set_vary can disable a parameter from varying., set_vary can enable a fixed parameter to vary., set_vary raises ValueError for invalid parameter names., set_vary updates n_varying count., TestSetVary

### Community 414 - "Community 414"
Cohesion: 0.2
Nodes (7): Total parameter count including both scaling and physics parameters.          Re, Total parameter count including both scaling and physics parameters.          Re, Return physics parameters that are held fixed during optimization.          A pa, Return physics parameters that are held fixed during optimization.          A pa, Concise string representation of manager state., Concise string representation of manager state., Concise string representation of manager state.

### Community 415 - "Community 415"
Cohesion: 0.36
Nodes (8): ABC, compute_correlation(), get_default_params(), HeterodyneModelBase, n_params(), param_names(), Model class hierarchy for heterodyne correlation analysis., Abstract base class for heterodyne models.

### Community 416 - "Community 416"
Cohesion: 0.2
Nodes (8): Check if the configuration is valid.          Returns:             ``True`` if `, Check if the configuration is valid.          Returns:             ``True`` if `, Check if the configuration is valid.          Returns:             ``True`` if `, Return a list of configuration error strings.          An empty list means the c, Return a list of configuration error strings.          An empty list means the c, Return a list of configuration error strings.          An empty list means the c, Return a list of configuration error strings.          An empty list means the c, Return a list of configuration error strings.          An empty list means the c

### Community 417 - "Community 417"
Cohesion: 0.2
Nodes (6): Tests for get_fallback_strategy and execute_optimization_with_fallback., MemoryError from LARGE strategy triggers fallback to STREAMING., RuntimeError from STREAMING triggers step to LARGE., When all strategies fail, RuntimeError is raised with informative msg., get_fallback_strategy returns None when STANDARD (last tier) fails., TestFallbackChainRecovery

### Community 418 - "Community 418"
Cohesion: 0.29
Nodes (5): prepare_fit_data(), Prepare correlation data and weights for least-squares fitting.      Flattens da, Prepare correlation data and weights for least-squares fitting.      Flattens da, Tests for prepare_fit_data., TestPrepareFitData

### Community 419 - "Community 419"
Cohesion: 0.24
Nodes (5): Context manager for timing optimizer calls.      Usage::          timer = TimedC, Context manager for timing optimizer calls.      Usage::          timer = TimedC, TimedContext, Tests for TimedContext., TestTimedContext

### Community 420 - "Community 420"
Cohesion: 0.33
Nodes (3): TestCheckCovarianceHealth, check_covariance_health(), Check covariance matrix for ill-conditioning and negative variances.      Checks

### Community 421 - "Community 421"
Cohesion: 0.31
Nodes (4): TestCheckUncertaintyRatios, check_uncertainty_ratios(), Check that parameter uncertainties are not unreasonably large.      A relative u, Check that parameter uncertainties are not unreasonably large.      A relative u

### Community 422 - "Community 422"
Cohesion: 0.2
Nodes (10): _angle_balanced_split(), _random_split(), Split with balanced representation of every phi angle per shard.      Each uniqu, Split with balanced representation of every phi angle per shard.      Each uniqu, Randomly assign data points to shards with a fixed seed.      Args:         data, Randomly assign data points to shards with a fixed seed.      Args:         data, Split with balanced representation of every phi angle per shard.      Each uniqu, Randomly assign data points to shards with a fixed seed.      Args:         data (+2 more)

### Community 423 - "Community 423"
Cohesion: 0.2
Nodes (4): TARGET should be at most 1 % — a commonly recommended threshold., HIGH should be no more than 10 % — warns before CRITICAL., Module-level divergence rate thresholds obey the expected ordering., TestDivergenceRateConstants

### Community 424 - "Community 424"
Cohesion: 0.29
Nodes (9): _make_loader_cfg(), _patch_loader(), Unit tests for CLI data loading pipeline parity., An ordinary in-range request is forwarded verbatim (no sentinel)., CLI loading passes wavevector_q into the loader like homodyne., A legacy ``end_frame=100000`` load-all config must not request an     out-of-ran, test_explicit_frame_range_passes_through(), test_large_end_frame_maps_to_load_all_sentinel() (+1 more)

### Community 425 - "Community 425"
Cohesion: 0.2
Nodes (10): Validate that time integral won't have numerical issues.      For J(t) = D0 * t^, Validate that time integral won't have numerical issues.      For J(t) = D0 * t^, validate_time_integral_safety(), test_full_valid_scenario(), test_large_alpha_overflow_warning(), test_moderate_alpha_no_overflow(), test_negative_alpha_with_positive_t_min_valid(), test_negative_alpha_with_t_min_zero_error() (+2 more)

### Community 426 - "Community 426"
Cohesion: 0.31
Nodes (4): Check a float for NaN/Inf and raise ValueError.      Args:         value: Float, _sanitize_float(), Tests for _sanitize_float., TestSanitizeFloat

### Community 427 - "Community 427"
Cohesion: 0.24
Nodes (9): _bootstrap_xla_env(), Inject ``XLA_FLAGS`` from ``--threads``/``--no-jit`` *before* any     ``heterody, Unit tests for the heterodyne CLI XLA bootstrap., The ``--threads=N`` form is parsed and overrides inherited counts too., Without ``--threads`` the bootstrap must not touch OMP/MKL settings., An explicit ``--threads`` must win over inherited OMP/MKL counts.      Regressio, test_no_threads_leaves_inherited_omp_untouched(), test_threads_equals_form_overrides_inherited() (+1 more)

### Community 428 - "Community 428"
Cohesion: 0.24
Nodes (7): FitResult, Results from unified heterodyne model fitting.      Contains both physical and s, Get comprehensive fit summary.          Returns         -------         dict, Tests for FitResult dataclass., Dict structure has all expected keys., Default optional fields are sensible., TestFitResult

### Community 429 - "Community 429"
Cohesion: 0.24
Nodes (6): ParameterSpace, Get parameter bounds for the 14 physics parameters.          Returns         ---, Get parameter priors for the 14 physics parameters.          Returns         ---, Initialize unified heterodyne engine.          Args:             parameter_space, Parameter space definition with bounds and priors.      Physical parameter bound, Populate physics bounds/priors from parameter registry.

### Community 430 - "Community 430"
Cohesion: 0.29
Nodes (5): compute_diagonal_overlay_stats(), Compute diagonal overlay statistics for visual validation.      Extracts the dia, Compute diagonal overlay statistics for visual validation.      Extracts the dia, Post-hoc correction should yield a smaller RMSE (by construction)., TestComputeDiagonalOverlayStats

### Community 431 - "Community 431"
Cohesion: 0.27
Nodes (6): plot_residual_map(), plot_weight_map(), Diagnostic overlay plots for XPCS analysis.  Provides visualisations that aid in, Visualise the fitting weight matrix.      Args:         weights: Weight matrix,, 2-D heatmap of fit residuals.      Args:         residuals: Residual matrix, sha, TestPlotWeightMap

### Community 432 - "Community 432"
Cohesion: 0.22
Nodes (10): Backend Selection, code:block10 (jax.devices()), code:block11 (Λ_combined = Σ_k Λ_k                    (sum of precision ma), code:block12 (# Effective implementation:), code:python (if not hasattr(numpyro.infer, "initialization"):), Combination methods, Consensus Monte Carlo Combination, merge_shard_cmc_results() (+2 more)

### Community 433 - "Community 433"
Cohesion: 0.22
Nodes (9): AdaptiveSamplingPlan, code:block6 (log_D_at_tref = log(D0) + alpha * log(t_ref)), code:block7 (smooth_bound(raw, low, high) = mid + half * tanh((raw - mid)), code:block8 (scale = sqrt(shard_size / 10_000)), NUTSSampler, Sampler Infrastructure, SamplingPlan, SamplingStats (+1 more)

### Community 434 - "Community 434"
Cohesion: 0.2
Nodes (10): `build_default_priors()` (priors.py), `build_log_space_priors()`, `build_nlsq_informed_priors()`, code:python (contrast, offset = estimate_contrast_offset_from_data(c2_dat), `estimate_contrast_offset_from_data()`, Prior Construction, Prior tempering: `temper_priors()`, Prior validation: `validate_priors()` (+2 more)

### Community 435 - "Community 435"
Cohesion: 0.2
Nodes (8): code:block1 (┌───────────────────────────────────────────────────────────), code:block3 (data/), Component Map, Data Handler Architecture, High-Level Architecture, Key Files Reference, Overview, Table of Contents

### Community 436 - "Community 436"
Cohesion: 0.36
Nodes (8): build_from_manager(), fixed_full_indices(), log_mask(), n_full(), n_varying(), Bidirectional index mapper between parameter spaces.  Maps indices among three r, varying_full_indices(), varying_names()

### Community 437 - "Community 437"
Cohesion: 0.24
Nodes (10): NLSQAdapterBase, NLSQAdapter, NLSQWrapper, fit_with_cmaes, fit_nlsq_jax, execute_optimization_with_fallback, HierarchicalFitter, select_nlsq_strategy (+2 more)

### Community 438 - "Community 438"
Cohesion: 0.31
Nodes (5): Parse an integer from lscpu value, handling formats like '4 (2 online)'., Parse an integer from lscpu value, handling formats like '4 (2 online)'., Parse an integer from lscpu value, handling formats like '4 (2 online)'., _safe_int(), TestSafeInt

### Community 439 - "Community 439"
Cohesion: 0.22
Nodes (3): Signal the producer to stop and release resources.          Safe to call multipl, Shut down the background executor.          Parameters         ----------, Shut down the background executor.          Parameters         ----------

### Community 440 - "Community 440"
Cohesion: 0.31
Nodes (5): compute_gradient_norms(), Compute per-parameter gradient norms using JAX autodiff.      This is model-agno, For r(p) = p, L = sum(p^2), grad_i = 2*p_i., Constant-zero residual -> zero gradients., TestComputeGradientNorms

### Community 441 - "Community 441"
Cohesion: 0.33
Nodes (4): create_diagnostics_dict(), Build a diagnostics dictionary suitable for JSON serialization., Build a diagnostics dictionary suitable for JSON serialization., TestCreateDiagnosticsDict

### Community 442 - "Community 442"
Cohesion: 0.22
Nodes (7): Return samples as a 3-D array of shape (num_chains, num_samples, n_params)., Return samples as a 3-D array of shape (num_chains, num_samples, n_params)., Return samples as a 3-D array of shape (num_chains, num_samples, n_params)., Return per-parameter posterior statistics.          Returns a dict keyed by para, Return samples as a 3-D array of shape (num_chains, num_samples, n_params)., Return per-parameter posterior statistics.          Returns a dict keyed by para, Return per-parameter posterior statistics.          Returns a dict keyed by para

### Community 443 - "Community 443"
Cohesion: 0.31
Nodes (7): apply_q_range_filter(), apply_sigma_clip(), compute_data_mask(), General-purpose data filtering utilities for XPCS correlation data., Remove outliers from correlation data by sigma clipping.      Elements more than, Combine multiple boolean filter conditions into a single mask.      All conditio, Mask data outside a wavevector range.      Assumes the first axis of ``data`` co

### Community 445 - "Community 445"
Cohesion: 0.25
Nodes (5): DataCls, PlainClass, _PrivateClass, Synthetic input for class extractor tests., Subclass

### Community 446 - "Community 446"
Cohesion: 0.22
Nodes (6): param_info(), Tests for config/parameter_registry.py module.  Covers ParameterInfo, ParameterR, Contract tests that pin the registry priors against the geometric     requiremen, CLAUDE.md rule #9 — registry prior_mean/prior_std MUST equal         the (loc, s, registry(), TestPriorSanity

### Community 447 - "Community 447"
Cohesion: 0.22
Nodes (6): Get parameter bounds configuration with caching.          Args:             para, Get parameter bounds configuration with caching.          Args:             para, Get parameter bounds as a list of (min, max) tuples.          Convenience method, Get parameter bounds as a list of (min, max) tuples.          Convenience method, Get parameter bounds as separate lower and upper numpy arrays.          Convenie, Get parameter bounds as separate lower and upper numpy arrays.          Convenie

### Community 448 - "Community 448"
Cohesion: 0.22
Nodes (6): Get physics parameter names that are marked as varying.          Returns the 14-, Get physics parameter names that are marked as varying.          Returns the 14-, Number of active (varying) physics parameters, excluding scaling.          Retur, Number of active (varying) physics parameters, excluding scaling.          Retur, Return physics parameters that should be optimized.          Equivalent to activ, Return physics parameters that should be optimized.          Equivalent to activ

### Community 449 - "Community 449"
Cohesion: 0.33
Nodes (6): fit(), name(), Abstract base class for NLSQ adapters (FR-012).  Provides shared methods for NLS, Run optimization with typed JAX residual-function signature.          Convenienc, supports_bounds(), supports_jacobian()

### Community 450 - "Community 450"
Cohesion: 0.31
Nodes (5): Optimization Exception Hierarchy, Optimization modules for heterodyne analysis., Numerical validation utilities for NLSQ optimization.  Provides runtime checks f, Validate parameter values for NaN/Inf and optional bounds.      Args:         va, validate_parameters()

### Community 451 - "Community 451"
Cohesion: 0.22
Nodes (7): Verify ScipyNLSQAdapter no longer exists in the adapter module., ScipyNLSQAdapter must NOT be importable from adapter module., Verify ScipyNLSQAdapter no longer exists in the adapter module., ScipyNLSQAdapter must NOT be importable from adapter module., adapter.py must not import scipy.optimize at module level., adapter.py must not import scipy.optimize at module level., TestNoScipyAdapter

### Community 452 - "Community 452"
Cohesion: 0.22
Nodes (4): Verify from_dict handles the new keys., nlsq_x_scale should pass through numpy arrays., Homodyne-style nested anti_degeneracy/cmaes blocks should parse., TestNLSQConfigFromDict

### Community 453 - "Community 453"
Cohesion: 0.31
Nodes (5): build_failed_result(), Construct a failed NLSQResult.      Args:         parameter_names: Names for par, Construct a failed NLSQResult.      Args:         parameter_names: Names for par, Tests for build_failed_result., TestBuildFailedResult

### Community 454 - "Community 454"
Cohesion: 0.31
Nodes (5): compute_degrees_of_freedom(), Compute degrees of freedom for chi-squared calculation.      Args:         n_dat, Compute degrees of freedom for chi-squared calculation.      Args:         n_dat, Tests for compute_degrees_of_freedom., TestComputeDegreesOfFreedom

### Community 455 - "Community 455"
Cohesion: 0.22
Nodes (6): AdaptiveChunker, Return a snapshot of the current budget state.          Returns:             Mem, Compute chunk sizes that adapt to available memory and data characteristics., Compute adaptive chunk boundaries.          Args:             total_elements: To, Compute chunk sizes that adapt to available memory and data characteristics., Compute adaptive chunk boundaries.          Args:             total_elements: To

### Community 456 - "Community 456"
Cohesion: 0.22
Nodes (9): test_normalization_always_positive(), test_normalization_at_equal_fractions(), test_normalization_formula(), test_normalization_shape(), compute_normalization_factor(), Compute normalization factor f² for correlation.      f² = (f_s(t₁)² + f_r(t₁)²), Compute normalization factor f² for correlation.      f² = (f_s(t₁)² + f_r(t₁)²), test_normalization_always_positive() (+1 more)

### Community 457 - "Community 457"
Cohesion: 0.22
Nodes (9): Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args:, Attempt to load previously saved NLSQ results for warm-starting CMC.      Args: (+1 more)

### Community 458 - "Community 458"
Cohesion: 0.22
Nodes (9): _get_warmstart_reduced_chi2(), Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq, Extract reduced chi-squared from NLSQ result.      Tries ``result.reduced_chi_sq (+1 more)

### Community 459 - "Community 459"
Cohesion: 0.25
Nodes (7): General N-parameter least squares solver via normal equations.          Solves `, NumPy fallback for general least squares., solve_least_squares_general_jax(), Tests for solve_least_squares_general_jax (N-param linear regression)., 2-param linear fit recovers known coefficients., More data points than parameters., TestSolveLeastSquaresGeneralJAX

### Community 460 - "Community 460"
Cohesion: 0.22
Nodes (9): plot_multistart_summary(), Save and close a figure when a path is provided., Save and close a figure when a path is provided., Loss distribution and convergence summary across multistart attempts.      Three, Loss distribution and convergence summary across multistart attempts.      Three, Loss distribution and convergence summary across multistart attempts.      Three, Loss distribution and convergence summary across multistart attempts.      Three, Loss distribution and convergence summary across multistart attempts.      Three (+1 more)

### Community 461 - "Community 461"
Cohesion: 0.22
Nodes (9): Batch Loading, code:python (from heterodyne.data.xpcs_loader import load_xpcs_data), Convenience Function, Data Loading, HDF5 Format Detection, Multi-Q Support, Structure Probe, Supported Formats (+1 more)

### Community 462 - "Community 462"
Cohesion: 0.22
Nodes (9): code:python (from heterodyne.data.preprocessing import PreprocessingPipel), Core Pipeline Steps, Diagonal Handling, Noise Reduction (`apply_noise_reduction()`), Normalization Utilities, Outlier Removal Detail, Preprocessing Pipeline, PreprocessingProvenance (+1 more)

### Community 463 - "Community 463"
Cohesion: 0.28
Nodes (7): FitResult, plot_multi_angle_comparison(), plot_nlsq_vs_cmc(), NLSQ vs CMC comparison plots for heterodyne analysis.  Provides side-by-side vis, Plot parameter posteriors across multiple phi angles.      Creates a grid showin, Plot parameter posteriors across multiple phi angles.      Creates a grid showin, Plot NLSQ point estimates against CMC posterior distributions.      For each sha

### Community 464 - "Community 464"
Cohesion: 0.32
Nodes (4): compute_per_parameter_sensitivity(), Column-wise L2 norms of the Jacobian.      Each column norm quantifies how sensi, Tests for heterodyne.optimization.gradient_diagnostics., TestComputePerParameterSensitivity

### Community 465 - "Community 465"
Cohesion: 0.25
Nodes (5): Tests for get_diagnostics() method., get_diagnostics() returns a dict with at least 'enabled' key., diag['enabled'] matches controller.is_enabled., reset_monitor() can be called without error., TestAntiDegeneracyControllerDiagnostics

### Community 466 - "Community 466"
Cohesion: 0.25
Nodes (5): Tests for set_bounds method., set_bounds updates the bounds for a parameter., set_bounds raises ValueError for invalid parameter names., set_bounds stores bounds in parameter space., TestSetBounds

### Community 467 - "Community 467"
Cohesion: 0.25
Nodes (5): Tests for from_config class method., from_config works with empty config dict., from_config accepts parameter configurations., from_config uses defaults for unspecified parameters., TestFromConfig

### Community 468 - "Community 468"
Cohesion: 0.29
Nodes (5): Mixin for velocity field and flow computations.      Requires the consuming clas, Compute velocity field v(t) = v0 * t^beta + v_offset.          Args:, Compute velocity integral matrix integral from t_i to t_j of v(t') dt'., Compute cross-term phase factor cos(q * cos(phi) * integral of v dt).          A, VelocityMixin

### Community 469 - "Community 469"
Cohesion: 0.25
Nodes (5): Validate CMCConfig defaults and constraints., CMCConfig() creates a valid config with sensible defaults., Default target_accept_prob is between 0.5 and 0.99., Default num_chains >= 1., TestCMCConfigValidation

### Community 470 - "Community 470"
Cohesion: 0.25
Nodes (5): The three-step prior→names→init pipeline produces a consistent result., init_values only contains names returned by get_param_names_in_order., NLSQ values for a subset of params are reflected in the init dict., build_default_priors → get_param_names_in_order → build_init_values_dict., TestPriorToInitPipeline

### Community 471 - "Community 471"
Cohesion: 0.25
Nodes (7): make_cmc_config(), make_multistart_config(), make_nlsq_config(), Factory functions for configuration objects used in heterodyne tests.  All facto, Return a :class:`~heterodyne.optimization.cmc.config.CMCConfig` tuned for fast t, Return a dict of NLSQ configuration parameters suitable for fast tests.      The, Return a :class:`~heterodyne.optimization.nlsq.multistart.MultiStartConfig` for

### Community 472 - "Community 472"
Cohesion: 0.36
Nodes (4): clip_to_bounds(), Clip parameter array to specified bounds.      Args:         params: Parameter v, Tests for clip_to_bounds()., TestClipToBounds

### Community 473 - "Community 473"
Cohesion: 0.25
Nodes (6): Convert per-angle values to Fourier coefficients.          Uses least squares fi, Convert per-angle values to Fourier coefficients.          Uses least squares fi, Convert per-angle values to Fourier coefficients.          Uses least squares fi, Get initial Fourier coefficients from initial values.          Args:, Get initial Fourier coefficients from initial values.          Args:, Get initial Fourier coefficients from initial values.          Args:

### Community 474 - "Community 474"
Cohesion: 0.25
Nodes (7): Result from a single shard MCMC job.      Attributes:         shard_id: Zero-bas, Call ``qsub`` on *script_path* and return the job ID string.      Raises:, Call ``qsub`` on *script_path* and return the job ID string.      Raises:, Result from a single shard MCMC job.      Attributes:         shard_id: Zero-bas, Call ``qsub`` on *script_path* and return the job ID string.      Raises:, ShardResult, _submit_job()

### Community 475 - "Community 475"
Cohesion: 0.25
Nodes (7): _check_pbs_available(), Return True if ``qsub`` is present on PATH., Return True if ``qsub`` is present on PATH., Return True if ``qsub`` is present on PATH., Check that ``qsub`` is on PATH.          Raises:             RuntimeError: If ``, Check that ``qsub`` is on PATH.          Raises:             RuntimeError: If ``, Check that ``qsub`` is on PATH.          Raises:             RuntimeError: If ``

### Community 476 - "Community 476"
Cohesion: 0.25
Nodes (5): MemoryManager, Release a tracked allocation.          No-op if the label is not currently track, Suggest an optimal chunk size that fits within available budget.          The re, Track memory allocations against a configurable budget.      When *budget_bytes*, Request an allocation of *n_bytes* tracked under *label*.          If the alloca

### Community 477 - "Community 477"
Cohesion: 0.32
Nodes (6): get_completion_script(), get_xla_config_script(), Shell completion and activation scripts for heterodyne.  This subpackage contain, Get the path to the bash completion script.      Returns:         Absolute path, Get the path to the XLA configuration script.      Args:         shell: Shell ty, Get the path to the XLA configuration script.      Args:         shell: Shell ty

### Community 478 - "Community 478"
Cohesion: 0.25
Nodes (7): CMCBackendConfig, TypedDict definitions for configuration structures., Backend configuration for CMC sampling., Backend configuration for CMC sampling., Scattering geometry configuration., Scattering geometry configuration., ScatteringConfig

### Community 479 - "Community 479"
Cohesion: 0.25
Nodes (8): MetadataConfig, ParameterConfig, ParameterGroupConfig, Configuration for a parameter group.      Keys use full parameter names matching, Experiment metadata configuration., Experiment metadata configuration., Configuration for a single parameter., TypedDict

### Community 480 - "Community 480"
Cohesion: 0.25
Nodes (8): Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, Regression for het_676ccc47: save_mcmc_results must write a tombstone     JSON r, TestSaveMCMCResultsAllShardsFailed

### Community 481 - "Community 481"
Cohesion: 0.36
Nodes (4): _create_empty_figure(), Create a minimal placeholder figure with a centered message.      Used as a safe, Create a minimal placeholder figure with a centered message.      Used as a safe, TestCreateEmptyFigure

### Community 482 - "Community 482"
Cohesion: 0.25
Nodes (5): Tests that required arguments are enforced., Omitting --config must cause SystemExit (argparse error)., The -c shorthand must set the config path., The --config flag must set the config path as a Path object., TestRequiredArguments

### Community 483 - "Community 483"
Cohesion: 0.25
Nodes (5): JAX/NumPy solvers in core.fitting handle degenerate inputs gracefully., When the design matrix produces a singular Gram matrix, the solver         retur, Fitting constant (zero-variance) data returns gracefully.          When theory =, All-zero theory data does not crash the batch solver., TestFittingNumericalRecovery

### Community 484 - "Community 484"
Cohesion: 0.25
Nodes (8): plot_simulated_data(), Generate heatmap plots of theoretical/simulated C2 data.      Constructs the het, Generate heatmap plots of theoretical/simulated C2 data.      Constructs the het, Generate heatmap plots of theoretical/simulated C2 data.      Constructs the het, Generate heatmap plots of theoretical/simulated C2 data.      Constructs the het, Generate heatmap plots of theoretical/simulated C2 data.      Constructs the het, Display-only elapsed axes must not alter the model evaluation grid., test_plot_simulated_data_does_not_replace_model_time_grid()

### Community 485 - "Community 485"
Cohesion: 0.36
Nodes (4): plot_pair_correlation(), Parameter correlation matrix heatmap.      Args:         samples: Dict mapping p, The diagonal of the correlation image should be 1.0., TestPlotPairCorrelation

### Community 486 - "Community 486"
Cohesion: 0.25
Nodes (8): Bimodal consensus types, CMCResult, CMCResult methods, code:python (DEFAULT_MIN_ESS = 400.0          # minimum acceptable bulk E), code:python (ps = ParameterStats(["D0_ref", "alpha_ref"], [1e4, 0.5])), ParameterStats, SamplingStats, Standalone functions

### Community 487 - "Community 487"
Cohesion: 0.25
Nodes (8): Adaptive Chunking (`AdaptiveChunker`, `MemoryPressureMonitor`), Background I/O (`PrefetchLoader`, `AsyncWriter`), code:python (from heterodyne.utils.async_io import PrefetchLoader, AsyncW), code:block11 (YAML config on disk), code:python (from heterodyne.data.memory_manager import MemoryManager), code:python (from heterodyne.data.memory_manager import AdaptiveChunker, ), Data Flow Summary, Memory Manager

### Community 488 - "Community 488"
Cohesion: 0.25
Nodes (8): code:block10 (peak_memory_gib = n_points × n_params × bytes_per_element × ), code:block11 (peak ≈ 5e6 × 24 × 8 × 6.5 / 1024³  ≈  5.81 GiB), code:block9 (Decision tree:), Detection priority chain, Environment override, Peak memory formula, Strategy Selection (Memory-Aware), Worked example

### Community 489 - "Community 489"
Cohesion: 0.25
Nodes (7): Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct, Serialise the configuration to a nested dictionary.          The returned struct

### Community 490 - "Community 490"
Cohesion: 0.29
Nodes (6): build_default_priors(), build_nlsq_informed_priors(), optimization/cmc/priors.py, estimate_contrast_offset_from_data(), Prior Tempering vs Sigma Scaling, temper_priors()

### Community 491 - "Community 491"
Cohesion: 0.29
Nodes (7): heterodyne_model(), Create a standard HeterodyneModel for testing.      Uses default parameter value, Create a standard HeterodyneModel for testing.      Uses default parameter value, Create a standard HeterodyneModel for testing.      Uses default parameter value, Configuration for a minimal model (fast tests).      Returns:         Configurat, Configuration for a minimal model (fast tests).      Returns:         Configurat, small_model_config()

### Community 492 - "Community 492"
Cohesion: 0.29
Nodes (7): Real spawn-pool run of the pooled model across worker processes.      Slow (spaw, ``imap_unordered`` progress reporting relies on index-tagged results., Real spawn-pool run of the pooled model across worker processes.      Slow (spaw, Real spawn-pool run of the pooled model across worker processes.      Slow (spaw, Real spawn-pool run of the pooled model across worker processes.      Slow (spaw, test_indexed_wrapper_tags_result_with_shard_index(), test_parallel_pooled_shards_end_to_end()

### Community 493 - "Community 493"
Cohesion: 0.43
Nodes (3): compute_gradient_norm(), Frobenius norm of the Jacobian.      Args:         jacobian: Jacobian matrix of, TestComputeGradientNorm

### Community 496 - "Community 496"
Cohesion: 0.29
Nodes (5): _CaptureDone, Sentinel raised by patched call boundaries after capturing args.      Tests belo, Exception, NLSQOptimizationError, Base exception for all NLSQ optimization errors.      Attributes:         messag

### Community 497 - "Community 497"
Cohesion: 0.29
Nodes (7): Tests for forcing asynchronous JAX sampling results before diagnostics., Regression: shards with all-NaN r_hat (ArviZ failure) but valid std must, Tests for forcing asynchronous JAX sampling results before diagnostics., Tests for forcing asynchronous JAX sampling results before diagnostics., Tests for forcing asynchronous JAX sampling results before diagnostics., Tests for forcing asynchronous JAX sampling results before diagnostics., TestSamplingSynchronization

### Community 498 - "Community 498"
Cohesion: 0.29
Nodes (7): combination_method from CMCConfig is respected., combination_method from CMCConfig is respected., combination_method from CMCConfig is respected., combination_method from CMCConfig is respected., combination_method from CMCConfig is respected., combination_method from CMCConfig is respected., TestCombinationMethodDispatch

### Community 499 - "Community 499"
Cohesion: 0.29
Nodes (5): Regression tests: CMC degenerate warm-start thresholds must be identical     in, Regression tests: CMC degenerate warm-start thresholds must be identical     in, Regression tests: CMC degenerate warm-start thresholds must be identical     in, Regression tests: CMC degenerate warm-start thresholds must be identical     in, TestBugPrevention_ConstantSync

### Community 500 - "Community 500"
Cohesion: 0.43
Nodes (3): plot_convergence_trace(), Plot optimization convergence trace.      Args:         losses: Loss values per, TestPlotConvergenceTrace

### Community 501 - "Community 501"
Cohesion: 0.43
Nodes (3): plot_trace_posterior(), Trace + posterior density plots for MCMC samples.      Creates a two-column layo, TestPlotTracePosterior

### Community 502 - "Community 502"
Cohesion: 0.29
Nodes (7): code:python (c2_model = compute_c2_heterodyne(params, t, q, dt, phi_angle), Likelihood, Model constructors, NumPyro Model, Per-angle scaling modes, Physics dispatch, Sigma estimation

### Community 503 - "Community 503"
Cohesion: 0.29
Nodes (7): Additional diagnostics, code:block13 (IQR-CV = (Q75 - Q25) / max(|median|, 1e-3)   # per parameter), Convergence Diagnostics, High-level convergence helpers (homodyne parity), Per-shard diagnostics, Posterior quality functions (homodyne parity), Sharded convergence

### Community 504 - "Community 504"
Cohesion: 0.29
Nodes (7): 14 Physics Parameters + 2 Scaling, code:yaml (experimental_data:), ConfigManager, Configuration System, Parameter Registry, Parameter Space and Dual Prior System, YAML Schema

### Community 505 - "Community 505"
Cohesion: 0.57
Nodes (7): Analysis Modes, Configuration, Configuration, Configuration, HybridRecoveryConfig, NLSQConfig (Master), NLSQValidationConfig

### Community 506 - "Community 506"
Cohesion: 0.29
Nodes (7): code:block8 ([ varying physics params... ]    # length = pm.n_varying (≤ ), Computation flow (both strategies), Parameter vector layout (multi-angle joint), Parameter vector layout (single-angle), Residual Function Setup, `ResidualJITStrategy` (`strategies/residual_jit.py`), `ResidualStrategy` (`strategies/residual.py`)

### Community 507 - "Community 507"
Cohesion: 0.29
Nodes (7): code:python (fixed_values = jnp.asarray(pm.get_full_values())), code:python (chunk_size = self._chunk_size or config.chunk_size or self._), Fitting Strategies, Hybrid Streaming, JIT Strategy, Out-of-Core, Stratified LS

### Community 508 - "Community 508"
Cohesion: 0.29
Nodes (7): get_heterodyne_model_constant(), Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast, Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast, Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast, Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast, Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast, Create NumPyro model with FIXED (pre-computed) per-angle scaling.      Contrast

### Community 509 - "Community 509"
Cohesion: 0.29
Nodes (7): get_heterodyne_model_constant_averaged(), Create NumPyro model with a single averaged scaling broadcast to all angles., Create NumPyro model with a single averaged scaling broadcast to all angles., Create NumPyro model with a single averaged scaling broadcast to all angles., Create NumPyro model with a single averaged scaling broadcast to all angles., Create NumPyro model with a single averaged scaling broadcast to all angles., Create NumPyro model with a single averaged scaling broadcast to all angles.

### Community 510 - "Community 510"
Cohesion: 0.29
Nodes (7): estimate_sigma(), Estimate measurement uncertainty from data.      Supported methods:      - ``"di, Estimate measurement uncertainty from data.      Supported methods:      - ``"di, Estimate measurement uncertainty from data.      Supported methods:      - ``"di, Estimate measurement uncertainty from data.      Supported methods:      - ``"di, Estimate measurement uncertainty from data.      Supported methods:      - ``"di, Estimate measurement uncertainty from data.      Supported methods:      - ``"di

### Community 511 - "Community 511"
Cohesion: 0.29
Nodes (7): get_heterodyne_model(), Create NumPyro model for heterodyne correlation fitting.      Args:         t: T, Create NumPyro model for heterodyne correlation fitting.      Args:         t: T, Create NumPyro model for heterodyne correlation fitting.      Sigma is sampled a, Create NumPyro model for heterodyne correlation fitting.      Sigma is sampled a, Create NumPyro model for heterodyne correlation fitting.      Sigma is sampled a, Create NumPyro model for heterodyne correlation fitting.      Sigma is sampled a

### Community 512 - "Community 512"
Cohesion: 0.33
Nodes (6): Build a per-shard CMCResult shaped like _joint_pooled_nuts_run output., Build a per-shard CMCResult shaped like _joint_pooled_nuts_run output., A shard with a few divergences (rate <= max_divergence_rate) must NOT be     dro, A shard with a few divergences (rate <= max_divergence_rate) must NOT be     dro, _shard_result(), test_divergent_but_acceptable_shards_are_kept_in_consensus()

### Community 513 - "Community 513"
Cohesion: 0.33
Nodes (5): Pinned-constant parity guard for per_angle_mode taxonomy.  Source of truth: http, Every homodyne mode must be present in heterodyne's public Literal., The controller's use_shear_weighting property must always be False., test_heterodyne_publishes_all_homodyne_modes(), test_l5_shear_weighting_remains_disabled()

### Community 514 - "Community 514"
Cohesion: 0.33
Nodes (5): DataConfig, Serialize this configuration to a plain dictionary.          Returns:, Serialize this configuration to a plain dictionary.          Returns:, Configuration for XPCS data loading and preprocessing.      Attributes:, Configuration for XPCS data loading and preprocessing.      Attributes:

### Community 517 - "Community 517"
Cohesion: 0.33
Nodes (4): Merge CMC config with sensible defaults.          Config values override default, Merge CMC config with sensible defaults.          Config values override default, Return merged CMC config with defaults applied.          Returns:             CM, Return merged CMC config with defaults applied.          Returns:             CM

### Community 518 - "Community 518"
Cohesion: 0.33
Nodes (6): get_xla_config_source_path(), _install_xla_bash_activation(), _install_xla_fish_activation(), Get the path to the XLA config script.      Args:         shell: Shell type ("ba, Install XLA config to bash/zsh activate script., Install XLA config to fish activate script.

### Community 519 - "Community 519"
Cohesion: 0.33
Nodes (5): Test that each correction method produces valid finite output., Test that each correction method produces valid finite output., Mirror method applied to a symmetric matrix is a no-op off-diagonal., Mirror method applied to a symmetric matrix is a no-op off-diagonal., TestCorrectionMethods

### Community 521 - "Community 521"
Cohesion: 0.33
Nodes (3): Verify visualization modules use heterodyne parameter names., Ensure no homodyne parameter names leak into viz code., TestVizParameterNames

### Community 522 - "Community 522"
Cohesion: 0.4
Nodes (4): get_device_config(), __getattr__(), Get the device configuration module.      Returns:         The heterodyne.device, Lazy import hook for deferred module loading.

### Community 523 - "Community 523"
Cohesion: 0.33
Nodes (4): Document the structural degeneracies at registry default parameters.      These, At symmetric defaults, rank is 9/14 (ref/sample collinear; v0/v_offset         c, When ref and sample physics are identical, the mixing fraction         f0*exp(f1, TestJacobianAtSymmetricDefaults

### Community 524 - "Community 524"
Cohesion: 0.33
Nodes (5): _linear_residual(), _quadratic_residual(), Integration tests for the NLSQ analysis pipeline.  Tests Jacobian computation, c, Simple linear residual: r_i = x_i - target_i., Quadratic residual over 10 data points: r_i = (x[0] - i)^2 + x[1]*i.

### Community 525 - "Community 525"
Cohesion: 0.33
Nodes (6): Tests for CMCResult structure and methods., Tests for CMCResult structure and methods., Tests for CMCResult structure and methods., Tests for CMCResult structure and methods., Tests for CMCResult structure and methods., TestCMCResult

### Community 526 - "Community 526"
Cohesion: 0.33
Nodes (6): Tests for graceful degradation when MCMC fails., Tests for graceful degradation when MCMC fails., Tests for graceful degradation when MCMC fails., Tests for graceful degradation when MCMC fails., Tests for graceful degradation when MCMC fails., TestMCMCFailurePath

### Community 527 - "Community 527"
Cohesion: 0.33
Nodes (6): Tests that reparameterized CMC stores expected metadata., Tests that reparameterized CMC stores expected metadata., Tests that reparameterized CMC stores expected metadata., Tests that reparameterized CMC stores expected metadata., Tests that reparameterized CMC stores expected metadata., TestReparamMetadata

### Community 528 - "Community 528"
Cohesion: 0.33
Nodes (5): NLSQOptimizationConfig, OutputConfig, Output configuration., Output configuration., NLSQ optimization configuration.

### Community 529 - "Community 529"
Cohesion: 0.33
Nodes (6): plot_chi_squared_landscape(), 1-D chi-squared profile plot for a single parameter.      Displays how the reduc, 1-D chi-squared profile plot for a single parameter.      Displays how the reduc, 1-D chi-squared profile plot for a single parameter.      Displays how the reduc, 1-D chi-squared profile plot for a single parameter.      Displays how the reduc, 1-D chi-squared profile plot for a single parameter.      Displays how the reduc

### Community 530 - "Community 530"
Cohesion: 0.33
Nodes (6): plot_parameter_uncertainties(), Plot parameter values with uncertainties.      Args:         result: NLSQ result, Plot parameter values with uncertainties.      Args:         result: NLSQ result, Plot parameter values with uncertainties.      Args:         result: NLSQ result, Plot parameter values with uncertainties.      Args:         result: NLSQ result, Plot parameter values with uncertainties.      Args:         result: NLSQ result

### Community 531 - "Community 531"
Cohesion: 0.33
Nodes (6): plot_parameter_evolution(), Parameter values across multistart optimisation attempts.      Displays the traj, Parameter values across multistart optimisation attempts.      Displays the traj, Parameter values across multistart optimisation attempts.      Displays the traj, Parameter values across multistart optimisation attempts.      Displays the traj, Parameter values across multistart optimisation attempts.      Displays the traj

### Community 532 - "Community 532"
Cohesion: 0.33
Nodes (6): plot_fit_surface(), Side-by-side 2D heatmaps: experimental data, fit, and residuals.      Three pane, Side-by-side 2D heatmaps: experimental data, fit, and residuals.      Three pane, Side-by-side 2D heatmaps: experimental data, fit, and residuals.      Three pane, Side-by-side 2D heatmaps: experimental data, fit, and residuals.      Three pane, Side-by-side 2D heatmaps: experimental data, fit, and residuals.      Three pane

### Community 533 - "Community 533"
Cohesion: 0.33
Nodes (6): generate_nlsq_plots(), Generate 3-panel heatmaps (experimental | fit | residuals) per angle.      For e, Generate 3-panel heatmaps (experimental | fit | residuals) per angle.      For e, Generate 3-panel heatmaps (experimental | fit | residuals) per angle.      For e, Generate 3-panel heatmaps (experimental | fit | residuals) per angle.      For e, Generate 3-panel heatmaps (experimental | fit | residuals) per angle.      For e

### Community 534 - "Community 534"
Cohesion: 0.33
Nodes (6): plot_per_angle_residuals(), Per-angle 2D residual heatmap.      Renders one heatmap panel per phi angle, sho, Per-angle 2D residual heatmap.      Renders one heatmap panel per phi angle, sho, Per-angle 2D residual heatmap.      Renders one heatmap panel per phi angle, sho, Per-angle 2D residual heatmap.      Renders one heatmap panel per phi angle, sho, Per-angle 2D residual heatmap.      Renders one heatmap panel per phi angle, sho

### Community 535 - "Community 535"
Cohesion: 0.33
Nodes (6): plot_scaling_comparison(), Contrast and offset comparison: solver vs least-squares post-hoc.      Side-by-s, Contrast and offset comparison: solver vs least-squares post-hoc.      Side-by-s, Contrast and offset comparison: solver vs least-squares post-hoc.      Side-by-s, Contrast and offset comparison: solver vs least-squares post-hoc.      Side-by-s, Contrast and offset comparison: solver vs least-squares post-hoc.      Side-by-s

### Community 536 - "Community 536"
Cohesion: 0.47
Nodes (3): plot_residual_histogram(), Histogram of residuals with Gaussian overlay.      Args:         residuals: Resi, TestPlotResidualHistogram

### Community 537 - "Community 537"
Cohesion: 0.4
Nodes (4): plot_parameter_sensitivity(), Bar chart of per-parameter sensitivity values.      Args:         sensitivity_di, Bar chart of per-parameter sensitivity values.      Args:         sensitivity_di, TestPlotParameterSensitivity

### Community 538 - "Community 538"
Cohesion: 0.47
Nodes (3): plot_diagonal_overlay(), Show before/after diagonal correction on c2.      Overlays the diagonal of the o, TestPlotDiagonalOverlay

### Community 539 - "Community 539"
Cohesion: 0.33
Nodes (6): 4-Stage Pipeline, QC Downstream Policy, Quality Control, QualityController, Relationship to validation.py and validators.py, Result Types

### Community 540 - "Community 540"
Cohesion: 0.33
Nodes (6): CLI Entry Points, CLI Orchestration, Dispatch Flow, --method Behaviour, Phase-Level Logging, t=0 Exclusion for NLSQ

### Community 541 - "Community 541"
Cohesion: 0.33
Nodes (6): Benefits, code:python (from heterodyne.optimization.nlsq import fit_nlsq_jax), `--method` switch (CLI), NLSQ as CMC Warm-Start Provider, Prior recentering, Programmatic API

### Community 542 - "Community 542"
Cohesion: 0.33
Nodes (6): Device & HPC Optimization, Checkpoint Manager, Fit Computation Utilities, Failure Recovery Strategies, heterodyne, JAX Initialization Requirement

### Community 543 - "Community 543"
Cohesion: 0.4
Nodes (6): select_strategy, ChunkedStrategy, OptimizationExecutor, JITStrategy, ResidualStrategy, SequentialStrategy

### Community 544 - "Community 544"
Cohesion: 0.4
Nodes (5): cmc_config_4chains(), CMC configuration with 4 chains (standard).      Returns:         CMCConfig with, CMC configuration with 4 chains (standard).      Returns:         CMCConfig with, CMC configuration with 4 chains (standard).      Returns:         CMCConfig with, CMC configuration with 4 chains (standard).      Returns:         CMCConfig with

### Community 545 - "Community 545"
Cohesion: 0.4
Nodes (4): pytest_configure(), Shared fixtures for heterodyne test suite.  This module provides reusable pytest, Register custom markers., Register custom markers.

### Community 546 - "Community 546"
Cohesion: 0.4
Nodes (5): cmc_config_2chains(), CMC configuration with 2 chains.      Returns:         CMCConfig with 2 chains f, CMC configuration with 2 chains.      Returns:         CMCConfig with 2 chains f, CMC configuration with 2 chains.      Returns:         CMCConfig with 2 chains f, CMC configuration with 2 chains.      Returns:         CMCConfig with 2 chains f

### Community 547 - "Community 547"
Cohesion: 0.6
Nodes (3): GradientHealth, Summary of gradient health for an optimization snapshot.      Attributes:, TestGradientHealth

### Community 549 - "Community 549"
Cohesion: 0.6
Nodes (4): _make_pkg(), End-to-end CLI smoke tests for `python -m tools.parity_audit`., test_diff_subcommand_writes_report(), test_extract_subcommand_writes_json()

### Community 554 - "Community 554"
Cohesion: 0.4
Nodes (5): get_diagonal_correction_methods(), Return the list of supported diagonal correction methods., Reported correction method strings match homodyne exactly., Reported correction method strings match homodyne exactly., test_get_diagonal_correction_methods()

### Community 555 - "Community 555"
Cohesion: 0.4
Nodes (5): get_available_backends(), Return the list of available array backends.      Always includes ``"numpy"``. I, numpy is always in the available backends list., numpy is always in the available backends list., test_get_available_backends()

### Community 556 - "Community 556"
Cohesion: 0.4
Nodes (4): Validate invariants that must hold immediately after construction., Validate invariants that must hold immediately after construction., Validate invariants that must hold immediately after construction., Validate invariants that must hold immediately after construction.

### Community 557 - "Community 557"
Cohesion: 0.5
Nodes (3): Parameter Transforms, Non-linear least squares optimization for heterodyne fitting., Log-Space Conditioning

### Community 558 - "Community 558"
Cohesion: 0.6
Nodes (3): from_dict(), order(), Fourier Reparameterization for Per-Angle Scaling Parameters.  This module replac

### Community 559 - "Community 559"
Cohesion: 0.4
Nodes (5): create_shard_grid(), Create time-index partitions for sharding a correlation matrix.      Divides the, Create time-index partitions for sharding a correlation matrix.      Divides the, Create time-index partitions for sharding a correlation matrix.      Divides the, Create time-index partitions for sharding a correlation matrix.      Divides the

### Community 560 - "Community 560"
Cohesion: 0.4
Nodes (5): merge_shard_results(), Combine per-shard posterior samples via simple concatenation.      For consensus, Combine per-shard posterior samples via simple concatenation.      For consensus, Combine per-shard posterior samples via simple concatenation.      For consensus, Combine per-shard posterior samples via simple concatenation.      For consensus

### Community 561 - "Community 561"
Cohesion: 0.4
Nodes (5): Validate a single shard for common data quality issues.      Checks performed:, Validate a single shard for common data quality issues.      Checks performed:, Validate a single shard for common data quality issues.      Checks performed:, Validate a single shard for common data quality issues.      Checks performed:, validate_shard_data()

### Community 562 - "Community 562"
Cohesion: 0.4
Nodes (5): estimate_shard_memory(), Estimate the device memory footprint of a shard in bytes.      Counts all NumPy, Estimate the device memory footprint of a shard in bytes.      Counts all NumPy, Estimate the device memory footprint of a shard in bytes.      Counts all NumPy, Estimate the device memory footprint of a shard in bytes.      Counts all NumPy

### Community 563 - "Community 563"
Cohesion: 0.5
Nodes (3): __getattr__(), Command-line interface for heterodyne analysis., Lazy imports to avoid eagerly loading heavy dependencies (JAX, etc.).

### Community 564 - "Community 564"
Cohesion: 0.4
Nodes (5): plot_residual_map(), Plot detailed residual analysis.      Args:         result: NLSQ result, Plot detailed residual analysis.      Args:         result: NLSQ result, Plot detailed residual analysis.      Args:         result: NLSQ result, Plot detailed residual analysis.      Args:         result: NLSQ result

### Community 565 - "Community 565"
Cohesion: 0.5
Nodes (4): DiagonalOverlayResult, Statistics from comparing diagonals of experimental vs fitted C2 surfaces., Statistics from comparing diagonals of experimental vs fitted C2 surfaces., TestDiagonalOverlayResult

### Community 566 - "Community 566"
Cohesion: 0.4
Nodes (5): code:block2 (fit_cmc_jax(model, c2_data, phi_angle, config, nlsq_result,), code:block3 (fit_cmc_sharded(model, c2_data, config, nlsq_result)), Execution Flow, Sharded path: `fit_cmc_sharded()`, Single-run path: `fit_cmc_jax()`

### Community 567 - "Community 567"
Cohesion: 0.4
Nodes (5): Caching & Performance, code:python (from heterodyne.data.performance_engine import PerformanceEn), In-Memory LRU Cache (`PerformanceEngine`), Memory-Mapped Access, NPZ Disk Cache

### Community 568 - "Community 568"
Cohesion: 0.4
Nodes (5): 1. Setup Phase, Analysis Mode Selection, code:python (t1_mesh, t2_mesh = np.meshgrid(np.asarray(t), np.asarray(t),), Parameter Vector Layout, Time Axis Handling

### Community 569 - "Community 569"
Cohesion: 0.4
Nodes (5): code:block7 (contrast(phi) = c0 + sum_k [ck * cos(k * phi) + sk * sin(k *), Configuration, Fourier Reparameterization, Mathematical Formulation, Parameter Count Reduction (order = 2)

### Community 570 - "Community 570"
Cohesion: 0.4
Nodes (5): code:block4 (fit_nlsq_jax(model, c2_data, phi_angle, config)), code:block5 (fit_nlsq_multi_phi(model, c2_data, phi_angles, config)), Execution Flow, Multi-Angle: `fit_nlsq_multi_phi()`, Single-Angle: `fit_nlsq_jax()`

### Community 571 - "Community 571"
Cohesion: 0.4
Nodes (5): CMCConfig, fit_cmc_jax, fit_cmc_sharded, build_nlsq_informed_priors, CMCResult

### Community 572 - "Community 572"
Cohesion: 0.4
Nodes (5): CMCBackend, CPUBackend, MultiprocessingBackend, PBSBackend, PjitBackend

### Community 573 - "Community 573"
Cohesion: 0.4
Nodes (5): CLI Data Pipeline, Data Quality Validation, Array Shape/Type Validators, Physics Parameter Validators, XPCS Data Loader

### Community 574 - "Community 574"
Cohesion: 0.5
Nodes (4): cmc_config_1chain(), CMC configuration with single chain (fastest).      Returns:         CMCConfig w, CMC configuration with single chain (fastest).      Returns:         CMCConfig w, CMC configuration with single chain (fastest).      Returns:         CMCConfig w

### Community 575 - "Community 575"
Cohesion: 0.5
Nodes (4): Generate small synthetic C2 data for fast tests.      Returns:         20x20 noi, Generate small synthetic C2 data for fast tests.      Returns:         20x20 noi, Generate small synthetic C2 data for fast tests.      Returns:         20x20 noi, small_c2_data()

### Community 576 - "Community 576"
Cohesion: 0.5
Nodes (4): Generate synthetic C2 data with realistic noise.      Adds Gaussian noise scaled, Generate synthetic C2 data with realistic noise.      Adds Gaussian noise scaled, Generate synthetic C2 data with realistic noise.      Adds Gaussian noise scaled, synthetic_c2_data()

### Community 577 - "Community 577"
Cohesion: 0.5
Nodes (4): jax_rng_key(), Provide a reproducible JAX random key.      Returns:         JAX PRNGKey with se, Provide a reproducible JAX random key.      Returns:         JAX PRNGKey with se, Provide a reproducible JAX random key.      Returns:         JAX PRNGKey with se

### Community 578 - "Community 578"
Cohesion: 0.5
Nodes (4): base_model_config(), Base configuration dictionary for HeterodyneModel.      Returns:         Configu, Base configuration dictionary for HeterodyneModel.      Returns:         Configu, Base configuration dictionary for HeterodyneModel.      Returns:         Configu

### Community 579 - "Community 579"
Cohesion: 0.5
Nodes (4): nlsq_config(), Standard NLSQ configuration.      Returns:         Default NLSQConfig suitable f, Standard NLSQ configuration.      Returns:         Default NLSQConfig suitable f, Standard NLSQ configuration.      Returns:         Default NLSQConfig suitable f

### Community 580 - "Community 580"
Cohesion: 0.5
Nodes (4): ensure_jax_float64(), Session-scoped fixture that verifies JAX x64 mode is enabled.      Returns:, Session-scoped tripwire that verifies JAX x64 mode is enabled.      Autouse ensu, Session-scoped fixture that verifies JAX x64 mode is enabled.      Returns:

### Community 581 - "Community 581"
Cohesion: 0.5
Nodes (4): Create a minimal HeterodyneModel for fast tests.      Returns:         Small Het, Create a minimal HeterodyneModel for fast tests.      Returns:         Small Het, Create a minimal HeterodyneModel for fast tests.      Returns:         Small Het, small_heterodyne_model()

### Community 582 - "Community 582"
Cohesion: 0.5
Nodes (4): fast_nlsq_config(), Fast NLSQ configuration for quick tests.      Returns:         NLSQConfig with m, Fast NLSQ configuration for quick tests.      Returns:         NLSQConfig with m, Fast NLSQ configuration for quick tests.      Returns:         NLSQConfig with m

### Community 583 - "Community 583"
Cohesion: 0.5
Nodes (4): Generate clean synthetic C2 correlation data.      Computes correlation using th, Generate clean synthetic C2 correlation data.      Computes correlation using th, Generate clean synthetic C2 correlation data.      Computes correlation using th, synthetic_c2_clean()

### Community 587 - "Community 587"
Cohesion: 0.5
Nodes (3): Estimate peak memory per PBS node (in GB) for a single shard.          Because e, Estimate peak memory per PBS node (in GB) for a single shard.          Because e, Estimate peak memory per PBS node (in GB) for a single shard.          Because e

### Community 588 - "Community 588"
Cohesion: 0.5
Nodes (4): create_loading_plan, Dataset Optimization, DatasetSizeCategory, Other Utilities

### Community 589 - "Community 589"
Cohesion: 0.5
Nodes (4): `angle_filtering.py` — range-based selection, code:python (from heterodyne.data.angle_filtering import filter_by_angle_), Phi Angle Filtering, `phi_filtering.py` — class-based with averaging

### Community 590 - "Community 590"
Cohesion: 0.5
Nodes (4): CMC Results, JSON Serialization, NLSQ Results, Result Writing

### Community 591 - "Community 591"
Cohesion: 0.5
Nodes (4): Data Shapes at Each Stage, Error Types, Key Config Defaults, Quick Reference Tables

### Community 592 - "Community 592"
Cohesion: 0.5
Nodes (4): Decision conditions, Stratification Decision, What happens during the fit, When stratification activates

### Community 593 - "Community 593"
Cohesion: 0.5
Nodes (4): Analysis mode parameter counts, Key config fields, Quick Reference Tables, Strategy selection

### Community 595 - "Community 595"
Cohesion: 0.5
Nodes (4): _likelihood_boundary_mask(), Boolean mask: True where (t1, t2) is NOT on the t=0 row or column.      Mirrors, Boolean mask: True where (t1, t2) is NOT on the t=0 row or column.      Mirrors, Boolean mask: True where (t1, t2) is NOT on the t=0 row or column.      Mirrors

### Community 596 - "Community 596"
Cohesion: 0.67
Nodes (3): Below the single-shard limit and unforced → exactly one NUTS pass., Below the single-shard limit and unforced → exactly one NUTS pass., test_small_data_runs_single_pass()

### Community 609 - "Community 609"
Cohesion: 0.67
Nodes (3): HeterodyneConfig, Complete heterodyne analysis configuration., Complete heterodyne analysis configuration.

### Community 610 - "Community 610"
Cohesion: 0.67
Nodes (3): Streaming data ingestion configuration., Streaming data ingestion configuration., StreamingConfig

### Community 611 - "Community 611"
Cohesion: 0.67
Nodes (3): LoggingConfig, Logging configuration., Logging configuration.

### Community 612 - "Community 612"
Cohesion: 0.67
Nodes (3): Data stratification configuration., Data stratification configuration., StratificationConfig

### Community 613 - "Community 613"
Cohesion: 0.67
Nodes (3): Temporal/timing configuration., Temporal/timing configuration., TemporalConfig

### Community 614 - "Community 614"
Cohesion: 0.67
Nodes (3): CMCPerShardMCMCConfig, Per-shard MCMC sampler settings., Per-shard MCMC sampler settings.

### Community 615 - "Community 615"
Cohesion: 0.67
Nodes (3): AnalyzerParametersConfig, Grouped parameter configuration for the analyzer., Grouped parameter configuration for the analyzer.

### Community 616 - "Community 616"
Cohesion: 0.67
Nodes (3): CMCCombinationConfig, Shard combination strategy for CMC., Shard combination strategy for CMC.

### Community 617 - "Community 617"
Cohesion: 0.67
Nodes (3): AnalysisConfig, Top-level analysis configuration., Top-level analysis configuration.

### Community 618 - "Community 618"
Cohesion: 0.67
Nodes (3): HmcConfig, HMC-specific sampler configuration., HMC-specific sampler configuration.

### Community 619 - "Community 619"
Cohesion: 0.67
Nodes (3): CMCValidationConfig, Convergence validation criteria for CMC., Convergence validation criteria for CMC.

### Community 620 - "Community 620"
Cohesion: 0.67
Nodes (3): OptimizationConfig, Full optimization configuration., Full optimization configuration.

### Community 621 - "Community 621"
Cohesion: 0.67
Nodes (3): Sequential optimization configuration., Sequential optimization configuration., SequentialConfig

### Community 622 - "Community 622"
Cohesion: 0.67
Nodes (3): CMCInitializationConfig, Initialization strategy for CMC chains., Initialization strategy for CMC chains.

### Community 623 - "Community 623"
Cohesion: 0.67
Nodes (3): CMCOptimizationConfig, CMC (Consensus Monte Carlo) configuration., CMC (Consensus Monte Carlo) configuration.

### Community 624 - "Community 624"
Cohesion: 0.67
Nodes (3): PhiFilteringConfig, Phi-angle filtering configuration., Phi-angle filtering configuration.

### Community 625 - "Community 625"
Cohesion: 0.67
Nodes (3): CMCShardingConfig, Sharding configuration for Consensus Monte Carlo., Sharding configuration for Consensus Monte Carlo.

### Community 626 - "Community 626"
Cohesion: 0.67
Nodes (3): ExperimentalDataConfig, Experimental data file configuration., Experimental data file configuration.

### Community 627 - "Community 627"
Cohesion: 0.67
Nodes (3): HardwareConfig, Hardware and resource configuration., Hardware and resource configuration.

### Community 632 - "Community 632"
Cohesion: 0.67
Nodes (3): Post-Fit (`result_validator.py`, `fit_quality.py`, `convergence.py`), Pre-Fit (`input_validator.py`), Validation

### Community 633 - "Community 633"
Cohesion: 0.67
Nodes (3): CMA-ES Configuration, CMA-ES Global Optimization, code:block6 (Phase 1: NLSQ warm-start)

### Community 634 - "Community 634"
Cohesion: 1.0
Nodes (3): Parameter Manager, Global Parameter Registry, Parameter Space Definition

## Knowledge Gaps
- **7596 isolated node(s):** `Tests for heterodyne package.`, `Shared fixtures for heterodyne test suite.  This module provides reusable pytest`, `Session-scoped tripwire that verifies JAX x64 mode is enabled.      Autouse ensu`, `Provide a reproducible JAX random key.      Returns:         JAX PRNGKey with se`, `Base configuration dictionary for HeterodyneModel.      Returns:         Configu` (+7591 more)
  These have ≤1 connection - possible missing edges or undocumented components.
- **1345 thin communities (<3 nodes) omitted from report** — run `graphify query` to explore isolated nodes.

## Suggested Questions
_Questions this graph is uniquely positioned to answer:_

- **Why does `Structured Logging` connect `Community 162` to `CLI Shell Completion Parity`, `NLSQ Results & Data`, `Theory Engine Data Loading`, `CMC Sharding Tests`, `CMC Reparameterization`, `Async I/O Utilities`, `NLSQ Strategy Tests`, `NLSQ Adapter Wrapper`, `HDF5 Data Pipeline`, `Community 20`, `Community 22`, `Community 23`, `Community 27`, `Community 28`, `Community 29`, `Community 30`, `Community 34`, `Community 35`, `Community 37`, `Community 45`, `Community 558`, `Community 46`, `Community 48`, `Community 49`, `Community 51`, `Community 53`, `Community 56`, `Community 58`, `Community 59`, `Community 61`, `Community 67`, `Community 68`, `Community 69`, `Community 70`, `Community 71`, `Community 584`, `Community 585`, `Community 76`, `Community 77`, `Community 79`, `Community 84`, `Community 597`, `Community 85`, `Community 87`, `Community 94`, `Community 95`, `Community 100`, `Community 103`, `Community 106`, `Community 107`, `Community 109`, `Community 112`, `Community 120`, `Community 121`, `Community 122`, `Community 127`, `Community 129`, `Community 133`, `Community 138`, `Community 152`, `Community 154`, `Community 158`, `Community 163`, `Community 169`, `Community 171`, `Community 173`, `Community 180`, `Community 181`, `Community 184`, `Community 188`, `Community 189`, `Community 202`, `Community 210`, `Community 217`, `Community 218`, `Community 223`, `Community 238`, `Community 244`, `Community 254`, `Community 262`, `Community 265`, `Community 272`, `Community 274`, `Community 275`, `Community 280`, `Community 285`, `Community 291`, `Community 292`, `Community 316`, `Community 322`, `Community 324`, `Community 327`, `Community 329`, `Community 331`, `Community 339`, `Community 340`, `Community 347`, `Community 351`, `Community 352`, `Community 353`, `Community 358`, `Community 363`, `Community 379`, `Community 380`, `Community 384`, `Community 385`, `Community 390`, `Community 400`, `Community 431`, `Community 436`, `Community 443`, `Community 449`, `Community 450`, `Community 463`, `Community 474`?**
  _High betweenness centrality (0.278) - this node is a cross-community bridge._
- **Why does `NLSQResult` connect `NLSQ Hierarchical Pipeline` to `HeterodyneModel Physics Core`, `CLI Shell Completion Parity`, `NLSQ Memory Strategy`, `CMC Sharding Tests`, `Model Mixins Fraction`, `CMC Diagnostics MCMC`, `CMC I/O Shard Loading`, `CMC Reparameterization`, `Community 525`, `Community 527`, `Community 526`, `Community 20`, `Community 22`, `Community 25`, `Community 28`, `Community 31`, `Community 32`, `Community 37`, `Community 38`, `Community 45`, `Community 52`, `Community 53`, `Community 65`, `Community 71`, `Community 76`, `Community 77`, `Community 80`, `Community 82`, `Community 87`, `Community 90`, `Community 104`, `Community 106`, `Community 109`, `Community 120`, `Community 122`, `Community 123`, `Community 141`, `Community 142`, `Community 151`, `Community 159`, `Community 160`, `Community 162`, `Community 173`, `Community 178`, `Community 199`, `Community 213`, `Community 214`, `Community 217`, `Community 218`, `Community 219`, `Community 221`, `Community 228`, `Community 229`, `Community 235`, `Community 237`, `Community 238`, `Community 246`, `Community 250`, `Community 251`, `Community 252`, `Community 253`, `Community 254`, `Community 257`, `Community 258`, `Community 259`, `Community 266`, `Community 270`, `Community 283`, `Community 293`, `Community 294`, `Community 307`, `Community 309`, `Community 351`, `Community 352`, `Community 353`, `Community 358`, `Community 379`, `Community 401`, `Community 403`, `Community 417`, `Community 419`, `Community 451`, `Community 453`, `Community 469`, `Community 480`, `Community 483`, `Community 497`, `Community 498`, `Community 499`?**
  _High betweenness centrality (0.126) - this node is a cross-community bridge._
- **Why does `NLSQConfig` connect `HeterodyneModel Physics Core` to `CLI Shell Completion Parity`, `NLSQ Memory Strategy`, `Community 262`, `NLSQ Hierarchical Pipeline`, `CMC Sharding Tests`, `Model Mixins Fraction`, `Community 267`, `CMC I/O Shard Loading`, `CMC Reparameterization`, `Community 266`, `Community 146`, `Community 20`, `Community 22`, `Community 27`, `Community 28`, `Community 416`, `Community 417`, `Community 38`, `Community 556`, `Community 173`, `Community 53`, `Community 60`, `Community 192`, `Community 451`, `Community 452`, `Community 579`, `Community 582`, `Community 203`, `Community 76`, `Community 213`, `Community 87`, `Community 88`, `Community 217`, `Community 218`, `Community 219`, `Community 221`, `Community 351`, `Community 352`, `Community 483`, `Community 109`, `Community 246`, `Community 122`, `Community 251`, `Community 252`?**
  _High betweenness centrality (0.065) - this node is a cross-community bridge._
- **Are the 256 inferred relationships involving `NLSQResult` (e.g. with `TestClampNLSQResult` and `TestClampToInterior`) actually correct?**
  _`NLSQResult` has 256 INFERRED edges - model-reasoned connections that need verification._
- **Are the 210 inferred relationships involving `ValueError` (e.g. with `.test_basic_exception()` and `.test_custom_level()`) actually correct?**
  _`ValueError` has 210 INFERRED edges - model-reasoned connections that need verification._
- **Are the 196 inferred relationships involving `NLSQConfig` (e.g. with `TestModeTaxonomy` and `TestFixedConstantSemantics`) actually correct?**
  _`NLSQConfig` has 196 INFERRED edges - model-reasoned connections that need verification._
- **Are the 121 inferred relationships involving `CMCResult` (e.g. with `TestGridIndicesGuard` and `TestMemoryAwareWorkerCap`) actually correct?**
  _`CMCResult` has 121 INFERRED edges - model-reasoned connections that need verification._